How do cells

maintain life?
In this unit students investigate the workings of the biochemical pathways could lead to improvements in
cell from several perspectives. They explore the agricultural practices.
relationship between nucleic acids and proteins
Students apply their knowledge of cellular processes
as key molecules in cellular processes. Students
through investigation of a selected case study,
analyse the structure and function of nucleic acids
data analysis, and/or a bioethical issue. Examples
as information molecules, gene structure and
of investigation topics include, but are not limited
expression in prokaryotic and eukaryotic cells, and
to: discovery and development of the model of the
proteins as a diverse group of functional molecules.
structure of DNA, proteomic research applications,
They examine the biological consequences of
transgenic organism use in agriculture, use,
manipulating the DNA molecule and applying
research, and regulation of gene technologies,
biotechnologies.
including CRISPR-Cas9, outcomes and unexpected
Students explore the structure, regulation, and consequences of the use of enzyme inhibitors such
rate of biochemical pathways, with reference to as pesticides and drugs, research into increasing
photosynthesis and cellular respiration. They efficiency of photosynthesis or cellular respiration, or
explore how the application of biotechnologies to impact of poisons on the cellular respiration pathway.

Reproduced from VCAA VCE Biology Study Design 2022-2026

54

UNIT 3

AOS1
What is the role of
nucleic acids and proteins
in maintaining life?
In this area of study students explore the expression
of the information encoded in a sequence of DNA to
form a protein and outline the nature of the genetic
code and the proteome. They apply their knowledge
to the structure and function of the DNA molecule
to examine how molecular tools and techniques can
be used to manipulate the molecule for a particular
purpose. Students compare gene technologies used to
address human and agricultural issues and consider
the ethical implications of their use.

Outcome 1
On completion of this unit the student should be able
to analyse the relationship between nucleic acids and
proteins, and evaluate how tools and techniques can be
used and applied in the manipulation of DNA.

Reproduced from VCAA VCE Biology Study Design 2022-2026

 55

CHAPTER

2
Nucleic acids and proteins
2A Protein structure and function 2D Gene expression

2B Nucleic acids 2E Gene regulation

2C Genes 2F The protein secretory pathway

Key knowledge
• nucleic acids as information molecules that encode instructions for the synthesis of proteins: the
structure of DNA, the three main forms of RNA (mRNA, rRNA, and tRNA), and a comparison of
their respective nucleotides
• the genetic code as a universal triplet code that is degenerate and the steps in gene expression,
including transcription, RNA processing in eukaryotic cells, and translation by ribosomes
• the structure of genes: exons, introns, and promoter and operator regions
• the basic elements of gene regulation: prokaryotic trp operon as a simplified example of a
regulatory process
• amino acids as the monomers of a polypeptide chain and the resultant hierarchical levels of
structure that give rise to a functional protein
• proteins as a diverse group of molecules that collectively make an organism’s proteome, including
enzymes as catalysts in biochemical pathways
• the role of rough endoplasmic reticulum, Golgi apparatus, and associated vesicles in the export of
proteins from a cell via the protein secretory pathway

Image: UGREEN 3S/[Link]

56 Chapter 2: Nucleic acids and proteins

2A P ROTEIN STRUCTURE
AND FUNCTION
Have you been thinking of going to the gym? Want to start working out? Well, if you have, you’ve
probably realised that in order to maximise your gains, you need to start loading up on protein
powder – after all, that’s what all the professionals do. But how does protein powder actually
help gain muscle? Does it have any other functions?

Image: Evgeniy Losev/[Link]

Lesson 2A
In this lesson you will learn about the functional diversity of proteins, including
how their function is determined, and the molecular structure of proteins.

Prerequisite knowledge Future applications

Year 11 Lesson 2D
Ribosomes, which can either be free-floating Gene expression involves the production
within a cell’s cytosol or attached to the rough of proteins via the processes of transcription
endoplasmic reticulum, are organelles present and translation.
in nearly all living cells, serving as the site of
protein synthesis. Chapter 3
Enzymes are proteins that serve as biological
Year 11 catalysts that increase the rate of chemical
Many of the channels and carriers embedded reactions within the body. Their structure and
within the plasma membrane are composed folding can be influenced by many factors, such
of proteins. as temperature and pH.

Study design dot points

• amino acids as the monomers of a polypeptide chain and the resultant hierarchical levels of structure that
give rise to a functional protein
• proteins as a diverse group of molecules that collectively make an organism’s proteome, including enzymes
as catalysts in biochemical pathways

Key knowledge units

The functional diversity of proteins [Link]

Amino acid structure [Link]

Protein structure [Link]

The functional diversity of proteins [Link]

O verview
Proteins are a diverse group of molecules that perform many different functions in cells,
ranging from structural support in skin and hair to catalysing chemical reactions.

T heory details
Proteins, also known as polypeptides, are one of the four types of biomacromolecules. protein a biomacromolecule
They are large complex structures which are crucial to the functioning and development made of amino acid chains folded
of all living organisms, serving a variety of different functions. While not an exhaustive list, into a 3D shape
some of the functions of proteins are outlined in Figure 1. polypeptide a long chain of amino
acids. Proteins can be made of one
or many polypeptides
 2A THEORY 57

Due to the functional diversity of proteins, they are of particular interest to researchers. proteome all the proteins that are
This is especially so because proteins rarely act in isolation, but rather, they often act expressed by a cell or organism at
together to form complex structures and processes. Therefore, the proteome, which a given time
refers to the entire set of proteins expressed by an organism at a given time, is a topic of
significant interest.

(a) (b) (c)

Function: Function: Function:
Enzymes Transport Structural

Explanation: Explanation: Explanation:

Enzymes are Typically embedded Support cell
organic catalysts in membranes, controlling and tissue shape
that speed up the entry and exit of The fibrous,
chemical reactions RNA polymerase substances from a cell Chloride channels elongated structure
embedded within of keratin
Examples: Examples: Examples:
the plasma
• Catalase: breaks down hydrogen peroxide • Chloride channels • Keratin: a tough protein
membrane
into water and oxygen • Glucose channels found in skin, hair, and nails
• Amylase: a digestive enzyme that breaks • Sodium-potassium pumps • Elastin: found in elastic connective tissues
down starch into maltose such as the skin
• RNA polymerase: catalyses the formation • Collagen: found in connective tissues such
of mRNA from DNA as tendons and ligaments

(d)
Function: Function:
Hormones Receptors

Explanation: Explanation:
Many peptide Receive signal
hormones are chemical from the environment
messengers used to An insulin receptor
communicate and induce Examples: protein (blue)
changes in cells • Acetylcholine embedded in the
receptors plasma membrane
Examples: • Hormone receptors and bound to
• Insulin: regulates blood
the hormone
sugar levels
insulin (orange)
• Amylase: a digestive enzyme that breaks down
starch into maltose
• Adrenaline: increases heart rate and expands airways
(e) (f) (g)
Function: Function:
Defence Motor/contractile Function:
Explanation: Storage
Involved in the
Explanation: contraction and
Involved in the immune movement of muscles, Explanation:
system by recognising The motor
the movement of internal Act as reserves
and destroying pathogens The structure protein kinesin
cell contents around the for metal ions
of an antibody transporting Ferritin storing iron
cytoplasm, and the and other molecules
a large vesicle
movement of cilia throughout organisms
along a
Examples: and flagella
microtubule
• Antibodies (immunoglobulins) Examples: Examples:
• Complement proteins • Myosin and actin: work together to enable • Ferritin: storage of iron
muscle contraction • Casein: storage of amino acids,
• Kinesin: moves along microtubules, carbohydrates, and minerals
enabling mitosis and vesicular transport

Images: (a, b, d) Juan Gaertner, (c, g) StudioMolekuul, (f) SciePro/[Link]

Figure 1 The functional diversity of proteins enzyme an organic molecule,

typically a protein, that catalyses
(speeds up) specific reactions
peptide hormone a protein
signalling molecule that regulates
The VCAA has not expected students to memorise specific examples of proteins (e.g. keratin, collagen). physiology or behaviour
However, students should appreciate the functional diversity of proteins and the fact that they are crucial
antibody a protein produced by
to the functioning and development of all living organisms.
plasma cells during the adaptive
immune response that is specific
to an antigen and combats
pathogens in a variety of ways.
Also known as immunoglobulin
58 Chapter 2: Nucleic acids and proteins

Amino acid structure [Link]

O verview
Amino acids serve as the building blocks of proteins. Their chemical structure is
composed of a central carbon atom, a carboxyl group, an amino group, an R-group,
and a hydrogen atom.

T heory details
In terms of the molecular structure of amino acids, each amino acid consists of a central carboxyl group the functional
carbon atom that is bonded to a hydrogen atom, a carboxyl group (COOH), an amino group on amino acid molecules
that contains a hydroxyl group
group (NH2), and an R-group (Figure 2). Of the 20 different types of amino acids in
(OH) and an oxygen double-
existence, each has its own specific R-group. Therefore, the R-group uniquely determines
bonded to a carbon atom
the identity of a particular amino acid. This also explains why proteins are not only made
amino group the functional group
up of carbon (C), hydrogen (H), oxygen (O), and nitrogen (N) atoms, but they can also be
on amino acid molecules that is
made up of other elements such as sulphur (S) depending on the R-group present.
made up of one nitrogen and two
central carbon hydrogens (NH2)
amino group H carboxyl group R-group the variable portion of
an amino acid molecule. It can
be one of twenty variations and
H O determines the identity of the
N C C amino acid
H O H

R-group

Figure 2 The basic structure of an amino acid

Additionally, each R-group has its own chemical properties, which can affect how hydrophobic having a tendency
different amino acids within a protein interact with each other. For example, an amino to repel and be insoluble in water
acid with a hydrophobic R-group is more likely to form bonds with other hydrophobic hydrophilic having a tendency
R-group amino acids than it would with an amino acid containing a hydrophilic R-group. to be attracted to and dissolve
in water
(a) alanine (b) tryptophan

HN

CH3 hydrophobic R-group CH2

HN CH COOH HN CH COOH
2 2
hydrophobic R-group

(c) tyrosine
hydrophilic R-group

CH2 OH
monomer a molecule that
is the smallest building block
HN CH COOH
2 of a polymer

Figure 3 The structure of the amino acids (a) alanine, (b) tryptophan, and (c) tyrosine polymer a large molecule that
is made up of small, repeated
When amino acids are joined together, they form a long chain known as a polypeptide monomer subunits
chain, or protein. Because different amino acids have similar basic structures and can act condensation reaction a reaction
as repeating subunits, they are known as monomers. When monomers are joined together, where two monomers join to form
they form polymers. Therefore, polypeptides or proteins are the polymers of amino a larger molecule, producing water
acids. The joining of amino acids together occurs at a cell’s ribosomes via a condensation as a by-product
reaction, which results in the formation of peptide bonds between adjacent amino acids. peptide bond the chemical bond
linking two amino acids
 2A THEORY 59

peptide
condensation reaction bond

amino acids polypeptide

(monomer) (polymer)
Figure 4 The formation of polypeptide polymers from amino acid monomers

While the VCAA does not expect students to memorise the 20 different amino acids and their R-groups,
it is expected that students will be able to draw a generalised diagram of an amino acid, which is depicted
in Figure 2.

Protein structure [Link]

O verview
There are four levels of protein structure: the sequence of amino acids (primary), their
arrangement into alpha-helices, beta-pleated sheets, or random coils (secondary), the
functional 3D shape of the protein (tertiary), and the bonding of multiple polypeptide
chains together (quaternary).

T heory details
In order for a protein to function correctly, the polypeptide chain(s) produced must primary structure the first level
carefully fold into the correct shape. The four levels of protein structure describe how of protein structure, which refers
polypeptide chains fold to form this functional structure, beginning from the primary to the sequence of amino acids
structure and becoming increasingly more complex to form secondary and tertiary in a polypeptide chain
structures. Some proteins can also have a quaternary structure. secondary structure the level
of protein structure where the
Table 1 The different levels of protein structure amino acid chain forms either
alpha-helices, beta-pleated
Structure level Diagram
sheets, or random coils
Primary Arg tertiary structure the functional
Met Asp Val Gly
Ile Lys
Val Asp Leu
The primary structure of a protein refers to 3D shape of a polypeptide chain
the sequence (or order) of amino acids in a quaternary structure the level
polypeptide chain. Ala Leu Gln Ser Leu Ala of protein structure where
Phe Lys Leu
multiple polypeptide chains bond
Secondary together, or other non-protein
groups are added to form a fully
The secondary structure of a protein is formed
functional protein
when a polypeptide chain folds and coils by
forming hydrogen bonds between amino acids alpha helix an organised coiled
of its different sections. When this occurs, secondary structure of proteins
structures such as alpha (α α) helices and beta- α-helix β-pleated sheets random coil beta-pleated sheet an organised
pleated (β β) sheets are formed. Random coils are folded secondary structure
irregular portions of secondary structure that join
of proteins
alpha-helices and beta-pleated sheets.
random coil an irregular
Tertiary secondary structure of proteins
The tertiary structure refers to the overall that is neither an alpha helix nor
functional 3D shape of a protein. For a protein a beta-pleated sheet
to be functional, it must at a minimum have a disulphide bond a strong covalent
tertiary structure. The tertiary structure of a bond occurring between two
protein is formed when the secondary structures sulphur atoms
further fold by forming interactions and bonds
between amino acids and R-groups of its different
sections. Disulphide bonds can also often
form between cysteine amino acids due to the
presence of sulphur atoms in their R-groups to
further stabilise the protein’s 3D structure.
cont'd
60 Chapter 2: Nucleic acids and proteins

Table 1 Continued

Structure level Chain

Quaternary
The quaternary structure is formed when
prosthetic group a non-protein
two or more polypeptide chains with tertiary
structures join together. Polypeptide chains group bound to a protein. For
with tertiary or quaternary structure can have example, a vitamin or ion
a prosthetic group attached. However, it is
important to remember that not all proteins
will have a quaternary structure.

A key protein with

quaternary structure,
Rubisco, will be explored in
detail in lesson 5B.

HAEMOGLOBIN Haem group

Haemoglobin, which is a protein responsible for
carrying oxygen in red blood cells, is one example of
a protein that has a quaternary structure.
It is composed of four polypeptide chains bonded
together, and within each of these chains, there is also
an iron ion embedded within a haem prosthetic group.

Image: Raimundo79/[Link]

Figure 5 The molecular structure of haemoglobin

Ultimately, the folding of a protein into its functional tertiary or quaternary structure
relies on its primary structure. Depending on the sequence of amino acids, the R-groups
will interact with each other differently, forming different bonds that favour folding into
specific 3D structures. Therefore, the functional diversity of proteins arises due to the
ability to create an unlimited number of complex combinations of amino acids that fold
into polypeptides of varying shapes and sizes.
Additionally, since protein folding depends on the primary structure of a protein, if there
are any changes to the original sequence of amino acids, a protein may no longer be able
to fold correctly, preventing it from functioning normally.

Theory summary
Proteins demonstrate functional diversity through the various roles that they serve in
living organisms. Amino acids are the monomers of proteins, and they join together via
condensation reactions to form polypeptide chains. The primary level of protein structure
refers to the sequence of amino acids, the secondary level of protein structure involves
alpha helices, beta-pleated sheets, and random coils, the tertiary level is the functional 3D
structure of a protein, and when there are two or more polypeptides in a protein it is said
to have a quaternary structure.

Protein serves as a core component of muscle. Therefore, by increasing your protein intake, you can
increase your muscle mass. But apart from contributing to muscle mass, protein also has a variety
of other functions, such as its involvement in signalling and reception, transport, muscle contraction,
storage, immunity, and structure.
 2A QUESTIONS 61

2A QUESTIONS
Theory review questions

Question 1

Proteins have a
A large range of different functions.
B limited number of functions.

Question 2

Label the parts of the amino acid.

L H M

H O
N C C
H O H

O N

Question 3

Which one of the following statements about amino acids is incorrect?

A The R-group is specific for each type of amino acid.
B The joining of amino acids occurs at the ribosomes.
C Amino acids are only composed of carbon, hydrogen, nitrogen, and oxygen atoms.
D Amino acids are monomers, which join together to form polymers known as polypeptides.

Question 4

Match the level of protein structure to its description.

Protein structure Description

• tertiary I _ sequence of amino acids
• primary II _ functional 3D structure of the protein
• secondary III _ composed of two or more polypeptide chains
• quaternary IV _ formation of alpha helices and beta-pleated sheets

SAC skills questions

Data analysis

Use the following information to answer Questions 5–9.

In the human body, proteins rarely act in isolation, but rather, they come together to form large complex processes.
For example, the ability of the body to form blood clots to prevent blood loss when blood vessels are damaged involves over
21 different proteins. These proteins are known as coagulation factors and are activated through a complex set of pathways
known as the coagulation cascade, which helps form a blood clot.
There are two pathways involved in initiating coagulation: the intrinsic and extrinsic pathways. After either of these pathways
is activated, they both converge into the common pathway to form a stable blood clot.
62 Chapter 2: Nucleic acids and proteins

The coagulation cascade

Activation of intrinsic pathway

XII XIIa
Activation of extrinsic pathway
XI XIa

IX IXa VIIa VII

VIIIa

X Xa X Coagulation factors

Va

Prothrombin (II) Thrombin (IIa)

Fibrinogen (I) Fibrin (Ia)

XIIIa
Formation of blood clot

Key
Intrinsic pathway Extrinsic pathway Common pathway

When doctors conduct coagulation tests, they measure how long each pathway takes to form a clot, allowing them to detect
abnormalities in the coagulation cascade. For example, the activated partial thromboplastin time (APTT) measures the
speed of the intrinsic and common pathways and the prothrombin time (PT) measures the speed of the extrinsic and
common pathways.
Individuals diagnosed with haemophilia, a blood clotting disorder, have difficulty in forming blood clots, often due to
an abnormal version of coagulation factor VIII. Therefore, they often suffer from spontaneous bleeding and bruising.
Their coagulation test is characterised by a prolonged activated partial thromboplastin time.

Blood test results involving two different individuals

Test Individual A (male) Individual B (female) Normal reference values

Prothrombin time (seconds) 12.8 11.5 10–13

Activated partial thromboplastin 44.9 30.9 25–36

time (seconds)

Red blood cell count (million/ 4.7 2.9 Male: 4.3–5.9

mm3)
Female: 3.5–5.5

Haemoglobin level (g/dL) 14.5 12.5 Male: 13.5–17.5

Female: 12.0–16.0

Question 5

To gain an understanding of how coagulation factors interact with each other, researchers would be most interested
in studying
A individual coagulation factors.
B multiple coagulation factors.

Question 6

An abnormal coagulation factor VIII could be caused by

A malfunctions in other coagulation factors which lead to the production of an abnormal coagulation factor VIII.
B an altered primary structure for this protein, which causes different bonds and interactions between nearby R-groups,
leading to a different tertiary structure.
 2A QUESTIONS 63

Question 7

Haemophilia is characterised by a
A decreased extrinsic and common pathway time.
B prolonged extrinsic and common pathway time.
C decreased intrinsic and common pathway time.
D prolonged intrinsic and common pathway time.

Question 8

In the table provided, the individual suffering from haemophilia is most likely
A individual A.
B individual B.
C neither individual A nor B.

Question 9

Based on the blood test results

A individual B suffers from a high haemoglobin level.
B individual A suffers from a high haemoglobin level.
C individual B suffers from a low red blood cell count.

Exam-style questions
Within lesson

Question 10 (1 MARK)

The proteome is
A all the proteins in a cell, tissue, or organism.
B the complete set of chromosomes found inside a gamete.
C the set of genes that code for all the proteins in an organism.
D the entire set of proteins expressed by an organism at a given time.
Adapted from VCAA 2018 Section A Q2

Question 11 (1 MARK)

Consider the structure and functional importance of proteins. Which one of the following statements about proteins is false?
A The tertiary structure of a protein can be stabilised by disulphide bridges.
B Two proteins with different amino acid sequences will likely have different functions.
C A change in the secondary structure of a protein will affect the biological function of the protein.
D Proteins with a quaternary structure are always more active than proteins without a quaternary structure.
Adapted from VCAA 2017 Section A Q1

Question 12 (1 MARK)

For a protein to be functional, it must have a

A tertiary structure.
B primary structure.
C secondary structure.
D quaternary structure.
64 Chapter 2: Nucleic acids and proteins

Use the following diagram to answer Questions 13 and 14.

The following diagram represents the joining of two organic monomers.

OH
NH2 O H C O

R — C — C — OH H—N—C—H
H R
H2O

Question 13 (1 MARK)

The diagram represents monomers of an organic molecule being joined together. The monomers are
A amino acids.
B nucleic acids.
C monopeptides.
D monosaccharides.

Question 14 (1 MARK)

The ‘R’ symbol on the monomer represents

A one of 25 possible amino acids.
B the chemical element rubidium.
C a variable group specific to the amino acid.
D the continuation of the carbon-hydrogen-nitrogen chain.
Adapted from VCAA 2018 Section A Q3

Question 15 (3 MARKS)

The diagrams represent four levels of structure with respect to the folding and assembly of a protein. The diagrams are not
to scale.

W X Y Z

Images (left to right): ibreakstock, magnetix, chromatos, Raimundo79/[Link]

a Identify which diagram represents each structural level of a protein. (1 MARK)

b Describe how the functional 3D structure of a protein is formed. (1 MARK)
c Suggest how the functional diversity of proteins arises. (1 MARK)
Adapted from VCAA 2015 Section B Q1

Question 16 (5 MARKS)

Oxytocin is a peptide hormone that has an important role in social bonding, childbirth, lactation, and sperm movement.
It is produced in an area of the brain known as the hypothalamus and released by a nearby gland called the posterior
pituitary gland.
a Name the bond that joins the monomers of oxytocin. (1 MARK)
b Draw and label the general structure of the oxytocin monomer. (2 MARKS)
c Oxytocin is a relatively simple peptide hormone and is composed from a single chain of nine amino acids joined together.
Identify and describe the level of protein structure that oxytocin folds into. (2 MARKS)
Adapted from VCAA 2017 Section B Q1
 2A QUESTIONS 65

Multiple lessons

Question 17 (1 MARK)

All specialised cells that secrete protein molecules uniquely

A have an extensive endoplasmic reticulum.
B have a flexible plasma membrane.
C have large vacuoles for storage.
D contain numerous chloroplasts.
Adapted from VCAA 2015 Section A Q5

Question 18 (1 MARK)

Consider the diagram of the plasma membrane.

S U
Identify which of the following molecule(s) are made up of many amino acids. R T
A S
B R
C R&T
D S&U
Adapted from VCAA 2017 Section B Q1 Image: sciencepics/[Link]
Image: sciencepics/[Link]

Key science skills and ethical understanding

Question 19 (10 MARKS)

Albumin is a globular protein involved in many different processes within the body, one
of which is the transport of substances around the body. It has many hydrophilic R-groups
on the outside and many hydrophobic R-groups facing the interior of the protein. It is also
highly insoluble in lipids. The given image depicts the structure of albumin.
a Explain why albumin is highly insoluble in lipids. (2 MARKS)
b Albumin normally constitutes 50% of human plasma protein, making it important
for regulating blood pressure. Identify two other functional roles of proteins in living
organisms. (2 MARKS)
c While low albumin levels are often caused by liver diseases, malnutrition, and burns,
high albumin levels are often caused by dehydration. Albumin in the urine can be indicative of kidney disease.
A doctor working for Médecins Sans Frontières at a refugee camp was concerned about the blood albumin levels of her
patients. She took blood samples from each of her patients to run a test for blood albumin, and documented these results.
The normal range of albumin is 3.5 to 5.5 grams per decilitre (g/dL).

8
Number of people

0.5 1.5 2.5 3.5 4.5 5.5 6.5 7.5 8.5

Blood albumin range (g/dL)

i According to these results, how many of her patients have abnormal albumin levels? (1 MARK)
ii 
During the test, someone used an uncalibrated scale to measure the weight of the albumin in each blood sample.
Identify the type of error that has occurred. Justify your response. (2 MARKS)
66 Chapter 2: Nucleic acids and proteins

d In Melbourne, another doctor measured blood albumin levels in one patient from several blood samples taken during
a single visit.

Sample Blood albumin level (g/dL)

1 5.75

2 3.21

3 4.12

4 4.25

i Explain whether these results are precise. (1 MARK)

ii 
Based on the bioethical concept of non-maleficence, suggest whether the doctor should have taken multiple blood
samples from the patient. (2 MARKS)
 2B THEORY 67

2B N
 UCLEIC ACIDS
Shopping at IKEA is always an enjoyable experience, providing an immersive adventure within their
almost endless and sprawling warehouse. But after you’ve laid your eyes on one of their Swedish
furniture masterpieces and bought it, you’re faced with the challenging task of assembling it.
But you, knowing that you’re a genius, realise that assembling IKEA furniture is super easy.
Who needs the instructions right? How hard could it be?

Image: Prachana Thong-on/[Link]

Lesson 2B
In this lesson you will learn about the functional and structural differences
between the two types of nucleic acids – DNA and RNA.

Prerequisite knowledge Future applications

Year 11 Lesson 2D
DNA is tightly packaged around histone Nucleic acids are fundamental to the
proteins to form chromosomes within the production of proteins, serving a role in the
nucleus of a cell. transcription of DNA into mRNA, the formation
of ribosomes, and the assembly of amino acids
Lesson 2A into polypeptides.
DNA is responsible for storing the information
required to make proteins, determining the Chapter 4
sequence of amino acids, and allowing for the Researchers are capable of manipulating
huge functional diversity of proteins. DNA using a variety of different mechanisms,
allowing them to edit an organism’s genome
and produce genetically modified organisms.

Study design dot point

• nucleic acids as information molecules that encode instructions for the synthesis of proteins:
the structure of DNA, the three main forms of RNA (mRNA, rRNA, and tRNA) and a comparison
of their respective nucleotides

Key knowledge units

Introduction to nucleic acids [Link]

DNA [Link]

RNA [Link]

Introduction to nucleic acids [Link]

O verview
Nucleic acids are polymers of nucleotide monomers, which not only store genetic
information, but also form molecules that aid in the production of proteins.

T heory details
Found in every living organism on Earth, nucleic acids are large polymers composed nucleic acid the class of
from nucleotide monomers that store genetic information and help produce the proteins macromolecule that includes DNA
required for survival. There are two types of nucleic acids – deoxyribonucleic acid (DNA) and RNA. All nucleic acids are
and ribonucleic acid (RNA). While there are several distinct differences between DNA polymers made out of nucleotide
monomers
and RNA nucleotides, at a fundamental level, they both follow the same basic structure
(Figure 1). polymer a large molecule that
is made up of small, repeated
monomer subunits
68 Chapter 2: Nucleic acids and proteins

Every nucleotide includes: nucleotide the monomer subunit

of nucleic acids. Made up of a
• a phosphate group nitrogen-containing base, a five-
• a five-carbon (pentose) sugar carbon sugar molecule (ribose in
• a nitrogen-containing base. RNA and deoxyribose in DNA),
and a phosphate group
(a) (b)
nitrogenous base monomer a molecule that
is the smallest building block
phosphate of a polymer
phosphate DNA (deoxyribonucleic acid)
5’ nitrogenous a double-stranded nucleic acid
1’ base chain made up of nucleotides.
5’
DNA carries the instructions for
five-carbon 4’ 1’ proteins which are required for
sugar
cell and organism survival
3’ 2’
3’ RNA (ribonucleic acid) a single-
stranded nucleic acid chain made
five-carbon sugar
up of nucleotides. Includes mRNA,
Figure 1 (a) The basic structure of a nucleotide and (b) the chemical structure of a DNA nucleotide rRNA, and tRNA
Within the five-carbon sugar, each carbon is assigned a number in a clockwise direction,
with the first carbon being labelled 1’ (one prime) and the last carbon being labelled 5’
(five prime). The three carbons of particular interest include:
Check out scientific
• 1’ which attaches to the nitrogenous base investigation 2.1 to put
• 3’ which attaches to the phosphate of the following nucleotide this into action!
• 5’ which attaches the five-carbon sugar to the phosphate group of the nucleotide.
Therefore, the 3’ and 5’ ends of nucleotides are significant in contributing to the
directional nature of nucleic acids (Figure 2).

HN2
nitrogenous base
five-carbon sugar N
5’-pho

phosphate N
sphat

O N N HN2
e-sug

-O O 5’
P
O N
ar-3’-

N
sugar

O- H H
5’-pho

H 3’ H N HN2
-phos

O H N
sphat

-O P O 5’
N
phate

O N
e-sug

O H H
ar-3’-
backb

H 3’ H N
O H N
5’-pho

phosphodiester -O 5’
P O
o

O
ne

bond
sp

O H H
hate-

H 3’ H
OH H
sugar
-3’

Figure 2 A polymer of nucleotides joined together

When many nucleotides bond together, they form a polynucleotide chain. The bonds phosphodiester bond a strong
joining nucleotides are strong covalent bonds known as phosphodiester bonds, which covalent bond linking a five-carbon
form via condensation reactions and exist between the sugar group of one nucleotide and sugar to a phosphate group
the phosphate group of another. The linkage of sugars and phosphate groups is commonly condensation reaction a reaction
referred to as the sugar-phosphate backbone of nucleic acids. where two monomers join to form
a larger molecule, producing water
as a by-product
sugar-phosphate backbone
a strong covalently linked chain of
five-carbon sugar molecules and
phosphate groups in a nucleic
acid chain
 2B THEORY 69

DNA [Link]
O verview
Deoxyribonucleic acid (DNA) consists of two strands of nucleotides bonded together via
complementary base pairing, forming a double-helix which runs in an antiparallel fashion.

T heory details
Inside the nucleus of human eukaryotic cells, DNA is packaged into 46 chromosomes, chromosome a structure made
each of which contains tens of thousands of different genes. Each of these genes carries of protein and nucleic acids that
the instructions required to make a protein. Therefore, as DNA determines the structure carries genetic information
of a protein, and proteins play a vital role in the structure and function of cells and tissues, gene a section of DNA that
DNA is essential for life. carries the code to make a protein

Be aware that DNA is found in places besides the nucleus. For example, the mitochondria and chloroplasts
have their own DNA. Additionally, as prokaryotes don’t have nuclei, their circular chromosome is located
within the nuclear region of the cytoplasm.

The complete set of DNA in an organism is referred to as the genome. In order for life to genome the complete set of DNA
continue, DNA, and by extension the traits it codes for, must be heritable and passed down housed within an organism
from parents to their children. antiparallel a characteristic of
DNA strands describing how
Structure of DNA each strand runs in an opposite
direction to the other. One strand
DNA is composed of two polynucleotide chains which run antiparallel to each
runs in a 3’  5’ direction and the
other, meaning that while one strand runs in a 3’ to 5’ direction, the other runs in a other runs in a 5’  3’ direction
5’ to 3’ direction. The two chains are subsequently joined together via the rules of
complementary base pairing
complementary base pairing, which dictates the pairs of nucleotides that can join describes which nucleotides can
together to form hydrogen bonds with each other. Each DNA nucleotide is composed form hydrogen bonds with each
of a phosphate group, a deoxyribose sugar, and one of four possible nitrogenous other. C pairs with G, A pairs with
bases – adenine, thymine, cytosine, or guanine (Figure 3). The base pairing rules are: T (or U in RNA)
• adenine (A) will always form a pair with thymine (T)
• guanine (G) will always form a pair with cytosine (C).
(a) (c)
3’ A T C G T A G T C T G A T C A G G G T A 5’ 5’ 3’
5’ T A G C A T C A G A C T A G T C C C A T 3’ G C
T A
T T
(b)
A T
5’ 3’
T A
C G
T A
A T
sugar-phosphate
G C
backbones

G C

G C C G
T A
A T
A = Adenine (A)
A G = Guanine (G)
A T C = Cytosine (C)
A T
T = Thymine (T)
5’ 3’
3’ hydrogen bond 5’

Figure 3 (a) DNA can be represented using the letters corresponding to each nitrogenous base and (b)
with complementary base pairing, it forms a double stranded molecule (c) which is wound as a double helix.
70 Chapter 2: Nucleic acids and proteins

By understanding complementary base pairing, it is possible to predict the nucleotide double helix the structure of
sequence of a strand of DNA given the nucleotide sequence of the complementary strand. double-stranded DNA in the
Furthermore, using the same rules, it is also possible to deduce that in a double-stranded nucleus of eukaryotic cells, where
DNA molecule, there will always be equal numbers of A and T nucleotides, and equal each DNA strand wraps around a
central axis
numbers of G and C nucleotides.
nuclear DNA DNA that is located
Given the sheer length of DNA (the human nuclear genome is approximately three billion in the nucleus of a cell
base pairs long or 1.8 m in length), DNA needs to be compressed and stored effectively.
To do this, the two strands of DNA twist around each other, forming a double helix,
which can help compress and store DNA. In nuclear DNA, this helix structure also coils DNA
around proteins known as histones, which then condense further to form tightly packed
chromosomes (Figure 4).

RNA [Link]
O verview
Ribonucleic acid (RNA) is a single strand of nucleotides that comes in a variety of different
forms and is found in many different parts of the cell. histone
proteins chromosome
T heory details image: Designua/[Link]

While RNA serves many different functions within cells, it is primarily involved in the Figure 4 The packaging of nuclear
synthesis of proteins. There are several different types of RNA, including messenger RNA DNA into chromosomes
(mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA) (Table 1). messenger RNA (mRNA)
Table 1 The three types of RNA and their corresponding function and structure RNA molecules that are produced
during transcription and carry
RNA Function Diagram genetic information from the
nucleus to the ribosomes
messenger RNA (mRNA) Carries genetic information bases
from the nucleus to the transfer RNA (tRNA)
ribosomes for protein synthesis RNA that recognises specific
codons on the mRNA strand and
adds the corresponding amino acid
to the polypeptide chain during
protein synthesis
ribosomal RNA (rRNA)
RNA that is a key structural
sugar-phosphate backbone component of ribosomes,
which assemble proteins
transfer RNA (tRNA) Delivers specific amino acids to
the ribosome after recognising
specific nucleotide sequences
on mRNA

anticodon

Hydrogen bonds create some areas of

base pairing, causing folding in the strand

ribosomal RNA (rRNA) Serves as the main structural

component of ribosomes
within cells
The roles of mRNA, tRNA,
and rRNA will be further
explored in lesson 2D, which
delves into the formation
of proteins through the
processes of transcription
and translation.
 2B THEORY 71

Structure of RNA
The structure of RNA is relatively similar to that of DNA. However, instead of a
deoxyribose sugar, RNA contains a ribose sugar, and instead of thymine, RNA contains
another nitrogenous base known as uracil. RNA is also single-stranded instead of
double-stranded. Additionally, while DNA is inherited from generation to generation,
RNA is typically synthesised on demand. These differences are summarised in Table 2.
Table 2 The differences between DNA and RNA

DNA RNA

Structure Double-stranded Single-stranded

Sugar Deoxyribose sugar Ribose sugar

Nucleotides Adenine, thymine, cytosine, guanine Adenine, uracil, cytosine, guanine

Lifetime Inherited, long-term storage Temporary, short-lived molecules

While RNA is single-stranded, the principle of complementary base pairing still exists and
can help RNA fold into many different structures. In RNA, adenine pairs with uracil (A–U)
and guanine pairs with cytosine (G–C).
The main difference between ribose sugar and deoxyribose sugar is the presence
or absence of an oxygen atom at the 2’ position of the five-carbon sugar. This can be easily
remembered through the extended names of DNA and RNA, with deoxy- signifying
the absence of oxygen (Figure 5).

5’ O 5’ O
HOCH OH HOCH OH
2 2
4’ C C 1’ 4’ C C 1’
H H H H
H 3’ 2’ H 3’ 2’ H
H
C C C C

OH H OH OH

Deoxyribose Ribose
Figure 5 The difference between deoxyribose and ribose sugar

DNA tends to be double stranded (dsDNA) and RNA tends to be single stranded (ssRNA). However, like
most things in biology, there are always exceptions to the rule. Some bacterial viruses (such as those in
the Microviridae family) contain single-stranded DNA (ssDNA) and other viruses, including rotaviruses,
contain double-stranded RNA (dsRNA).
When asked to differentiate between DNA and RNA, if possible, you should rely on the nucleotides
present in a strand, as DNA will contain thymine whilst RNA will contain uracil. To double check, you can
also look at the five-carbon sugar found within each nucleotide – DNA contains one less oxygen molecule
than RNA on the 2’ carbon.

Theory summary
Nucleic acids are responsible not only for carrying genetic information, but also for
synthesising proteins. There are two types of nucleic acids – deoxyribonucleic acid (DNA)
and ribonucleic acid (RNA), which are each composed of a phosphate group, a five-carbon
sugar, and a nitrogenous base. Differences between DNA and RNA include the sugar
molecule present, the nitrogenous bases present, and whether they form single or double
strands (Table 3).
72 Chapter 2: Nucleic acids and proteins

Table 3 Similarities and differences between DNA and RNA

DNA RNA

Similarities • nucleotides follow the same basic structure (phosphate group, five-carbon sugar, nitrogen-containing bases)
• contain the nucleotides adenine, guanine, and cytosine
• contain a sugar phosphate backbone
• follow the complementary base pairing rule: C pairs with G, A pairs with T (or U)

Differences • nucleotides contain a deoxyribose sugar • nucleotides contain a ribose sugar

• contains the base thymine (T) • contains the base uracil (U)
• double-stranded • single-stranded
• inherited/long-term storage • temporary molecules

There’s a reason for IKEA printing instructions – and wasting paper is certainly not one of them.
Instructions are included so that you can accurately and efficiently assemble your IKEA furniture.
Just like our cells, nucleic acids, and in particular DNA and RNA, form the instructions for the
production of proteins, and without them life would not be able to exist.

Image: Nattapat.J/[Link]

2B QUESTIONS
Theory review questions

Question 1

Fill in the blanks with the following terms. Terms may be used multiple times or not at all.
• uracil • polymers
• ribose • monomers
• thymine • deoxyribose
• guanine • single-stranded
• cytosine • double-stranded

Nucleic acids are _of nucleotide _. While DNA is composed of a _ sugar, RNA is composed of a
_ sugar. Additionally, DNA contains the nitrogenous base _, whereas RNA contains the nitrogenous base
_. DNA is also a _ molecule, allowing it to form a double helix, whereas RNA is a _ molecule.

Question 2

Label the parts of the nucleotide.

X 3’ Y

Z
 2B QUESTIONS 73

Question 3

Which one of the following sequences correctly represents DNA?

3’ A A A T C G T C A T 5’
A
3’ T T T A G C A G T A 5’

3’ G G T A A A T T T T G U A 5’
B
5’ C C A T T T A A A A C A T 3’

3’ A A T G C T A T G C A T C G A T C C 5’
C
5’ T T A C G A T A C G T A G C T A G G 3’

5’ A A T G C G C T G C U T C A T G T T A A G 3’
D
5’ T T A C G C G A C G A A G T A C A A T T C 5’

Question 4

Match each type of RNA to its appropriate description.

RNA Description
• mRNA I _ serves as the main structural component of ribosomes within cells
• rRNA II _ carries genetic information from the nucleus to the ribosomes for protein synthesis
• tRNA III _ delivers specific amino acids to the ribosomes after recognising specific
nucleotide sequences

SAC skills questions

Case study analysis

Use the following information to answer Questions 5–8.

In 1962, James Watson, Francis Crick, and Maurice Wilkins were awarded the Nobel Prize in Physiology or Medicine for the
discovery of the structure of DNA as well as its shape as a double helix. However, the absence of Rosalind Franklin, another
researcher who heavily contributed to the discovery, is certainly notable. Unfortunately, her pivotal role in contributing to the
discovery has been largely forgotten, shrouding the work in controversy.
In fact, the discovery of the structure of DNA would not have been possible if it were not for the work of Rosalind Franklin.
Her work and expertise in the field of X-ray crystallography, which is a technique used to photograph the molecular structure
of compounds, provided the crucial X-ray photographs that were used to interpret and determine the structure of DNA.
While Franklin was not able to fully interpret the photographs herself, Watson and Crick obtained the photographs through
unconventional methods without asking for her permission, effectively stealing her work. Then, through their interpretation
of her work, they were finally able to determine the structure of DNA.
Unfortunately, Franklin passed away in 1958 from ovarian cancer and due to the stringent rules of the Nobel Prize, recipients
must be alive to receive the award. Due to an unfortunate series of events and her premature death, she was not given the
credit that she fully deserved for her contribution to the discovery of the structure of DNA.

Question 5

Rosalind Franklin could not be awarded the Nobel Prize because

A to be awarded the Nobel Prize, the recipient must be alive.
B her contribution to the discovery of the structure of DNA was unrecognised.

Question 6

Reference to the double helix shape of DNA refers to it being a

A double-stranded molecule.
B single-stranded molecule.
74 Chapter 2: Nucleic acids and proteins

Question 7

Without complementary base pairing, DNA would not be able to form a

A chain of nucleotides.
B double helix.

Question 8

The use of Franklin’s X-ray crystallography photographs by Watson and Crick without her permission primarily violates the
bioethical concept of
A non-maleficence.
B beneficence.
C integrity.
D respect.

Exam-style questions
Within lesson

Question 9 (1 MARK)

A particular DNA double helix is 100 nucleotide pairs long and contains 40 cytosine bases. The number of adenine bases in
this DNA double helix would be
A 10.
B 20.
C 40.
D 60.
Adapted from VCAA 2012 Exam 1 Section A Q5

Use the following information to answer Questions 10 and 11.

The following diagram represents a chain of nucleic acids.

W X
5’ Y
3’
Z

3’ 5’

Question 10 (1 MARK)

A nucleic acid is made up of nucleotides which are linked by a sugar-phosphate backbone.

According to the diagram, structure(s)
A Y and Z must make up the sugar-phosphate backbone.
B Y and X must make up the sugar-phosphate backbone.
C Y is a ribose sugar molecule.
D X is a phosphate group.
Adapted from VCAA 2015 Section A Q3
 2B QUESTIONS 75

Question 11 (1 MARK)

If the nucleotide structure W is the base thymine, then

A sub-unit X must be the base uracil.
B sub-unit X must be the base adenine.
C sub-unit Y must be the base cytosine.
D sub-unit X must be the nucleotide adenine.

Question 12 (1 MARK)

Which one of the following rows correctly describes a difference between DNA and RNA?

DNA contains RNA contains

A the same number of guanine and thymine nitrogen bases a different number of guanine and thymine nitrogen bases

B ribose sugar deoxyribose sugar

C the nitrogen base thymine the nitrogen base uracil

D no hydrogen bonding between strands hydrogen bonding between complementary strands

Adapted from VCAA 2017 Sample Exam Section A Q2

Question 13 (1 MARK)

A gene involved in the function of the male reproductive system has been sequenced.
A small section of this gene is shown in the diagram.
The sequence of nucleotides on the complementary sequence of DNA would be
C G T G A G G C C A
A GCACUCCGGU.
B CGTGAGGCCA.
C GCACTCCGGT.
D TCCAGAATTG.

Question 14 (1 MARK)

A particular mRNA strand is 50 nucleotide bases long and contains 10 adenine bases. The number of thymine bases in this
mRNA strand would be
A 0.
B 10.
C 40.
D 50.
Adapted from VCAA 2012 Exam 1 Section A Q5

Question 15 (1 MARK)

A fragment of DNA on chromosome 7 from a person, Doug, is sequenced. The nucleotide sequence is shown.
G A T G G A T C G A G G T C
Doug

For the sequence of nucleotides shown, the total number of cytosine bases on the complementary strand would be
A 0.
B 2.
C 6.
D 8.
Adapted from VCAA 2012 Exam 2 Section A Q15
76 Chapter 2: Nucleic acids and proteins

Multiple lessons

Question 16 (1 MARK)

Genes
A are made up of the five nucleotide bases: adenine, thymine, cytosine, guanine, and uracil.
B contain the genetic information required to make proteins.
C can only be found in the nuclear DNA of a eukaryotic cell.
D are made up of amino acid monomers.

Use the following information to answer Questions 17 and 18.

The diagrams represent two of the four major groups of biomacromolecules.

Group A Group B
Question 17 (1 MARK)

Each monomer of a macromolecule from Group A is made up of a

A carboxyl group, an R group, and an amino group.
B carboxylic acid, an R group, and an amino acid group.
C ribose sugar, a phosphate group, and a nitrogen-containing base.
D deoxyribose sugar, a phosphate group, and a nitrogen-containing base.
Adapted from VCAA 2016 Section A Q3

Question 18 (1 MARK)

A feature that can be seen in the diagram of the macromolecule in Group B is

A its deoxyribose subunits.
B the double-helical structure of DNA.
C the complementary base pairing of C–G and A–U.
D the antiparallel arrangement of two complementary strands of amino acids.
Adapted from VCAA 2015 Section A Q4

Question 19 (1 MARK)

Nitrogen is an essential component of many of the molecules needed for growth and reproduction. Some bacteria live in the
root systems of certain plant species, taking the nitrogen from our atmosphere and producing nitrogen-containing compounds
(such as ammonia). These compounds can then be taken up by the plants and used to produce molecules that are essential for
life. Soils lacking in these bacteria and nitrogen-containing fertilisers may become nitrogen deficient. Plants growing in these
soils may be unable to produce sufficient levels of
A carbohydrates.
B nucleic acids.
C fatty acids.
D cellulose.
Adapted from VCAA 2012 Exam 1 Section A Q6
 2B QUESTIONS 77

Question 20 (4 MARKS)

Researchers studying macromolecules found two tightly packed polymers in the nucleus of an animal cell. A short section of
these macromolecules is shown in the diagram.

Image: StudioMolekuul/[Link]

a Name the two types of macromolecules shown in the diagram. (2 MARKS)

b Identify the monomers of the two types of macromolecules identified in part a. (2 MARKS)
Adapted from VCAA 2014 Section B Q9

Key science skills and ethical understanding

Question 21 (10 MARKS)

Two scientists were busy analysing two biological polymer samples.

a All polymers are made up of repeating sequences of monomers. Scientists can determine the sequence of monomers in
a sample by sequencing the sample.
i What information is obtained from protein sequencing? (1 MARK)
ii What information is obtained from gene sequencing? (1 MARK)
Adapted from VCAA 2017 Northern Hemisphere Exam 1 Section B Q7

b Sample 1 only contained single-stranded sequences of DNA while sample 2 contained double-stranded sequences
of DNA. After sequencing one of the samples, they plotted the number of individual nucleotides on a graph.

140
number of nucleotides

120

100

80

60

40

20

0
Sample 1 Sample 2 adenine guanine X Y
nucleotide
78 Chapter 2: Nucleic acids and proteins

i Identify the nucleotides represented by the bars labelled X and Y on the graph. (1 MARK)
ii 
Scientist A argued that the graph shows data from Sample 1, while Scientist B argued that it is more likely that the
graph shows data from Sample 2. Which scientist is correct? Explain your reasoning. (2 MARKS)
iii What is the length of the DNA strand in the sequenced sample? (1 MARK)
iv Draw a labelled diagram of a single monomer of the macromolecule found in Sample 2. (2 MARKS)
Adapted from VCAA 2014 Section B Q9

c When obtaining DNA samples from other individuals, consent must be given prior to the extraction of DNA. Identify the
bioethical concept which researchers must follow in order to satisfy this requirement. Justify your response. (2 MARKS)
 2C THEORY 79

2C G
 ENES
01000101 01100100 01110010 01101111 01101100 01101111 00100000 00100011 00110001.
Zeros and ones form the foundation of all your electronic devices through what is known as the
binary code. The binary code consists of different sequences and combinations of zeroes and ones
that can be translated into specific functions. Can you decipher the code written above? But more
importantly, is there a similar phenomenon occurring in our own cells? How do our cells store genetic
information? Is there another code that can be used? Image: SVshot/[Link]

Lesson 2C
In this lesson you will learn how the genetic code enables nucleic acids to
encode the information required for protein synthesis as well as the general
structure of genes.

Prerequisite knowledge Future applications

Lesson 2A Lesson 2D
The genetic code provides a series of rules Gene expression involves the production of
followed by living organisms via the production functional proteins through the processes of
of proteins. transcription, RNA processing, and translation.
Lesson 2B Lesson 9A
Genes are sections of DNA that carry the Genes can often be altered through the
instructions required to make a protein. occurrence of mutations, which involves
Important properties of DNA include its permanent changes to the DNA sequence
double-stranded helical structure, as well of genes, potentially leading to abnormally
as its directional nature. functioning proteins.

Study design dot points

• the genetic code as a universal triplet code that is degenerate and the steps in gene expression, including
transcription, RNA processing in eukaryotic cells, and translation by ribosomes
• the structure of genes: exons, introns, and promoter and operator regions

Key knowledge units

DNA to protein [Link]

Gene structure [Link]

DNA to protein [Link]

O verview
Protein synthesis relies on the existence of the genetic code, which is a series of rules that
determine how genetic information is transcribed and translated into functional proteins.

T heory details
Cells produce proteins by reading and interpreting the genetic information stored gene a section of DNA that
within genes through a series of processes known as transcription, RNA processing carries the code to make a protein
(post-transcriptional modifications), and translation. During transcription and RNA transcription the process
processing, the DNA sequence of the gene is copied into RNA nucleotides in the form of whereby a sequence of DNA is
mRNA. The mRNA is then decoded during translation to specify the sequence of amino used as a template to produce a
acids required for the polypeptide chain. These processes are only possible due to the complementary sequence of mRNA
existence of the genetic code (Figure 1). translation the process where an
mRNA sequence is read to produce
a corresponding amino acid
sequence to build a polypeptide
80 Chapter 2: Nucleic acids and proteins

messenger RNA (mRNA)

RNA molecules that are produced
transcription and translation during transcription and carry
RNA processing genetic information from the
nucleus to the ribosomes
DNA messenger
protein genetic code the set of rules by
sequence RNA
which information is encoded in
of a gene (mRNA)
genetic material

Figure 1 Protein synthesis involves the processes of transcription, RNA processing, and translation. The processes of
The genetic code is a series of rules that define how genetic information stored within transcription, RNA
processing, and translation
nucleotides is transcribed and translated into functional proteins. The foundation of the
are explored in further detail
genetic code relies on the grouping of adjacent nucleotides into groups of three. In DNA, in lesson 2D.
a group of three adjacent DNA nucleotides is known as a triplet, and when a DNA triplet
is transcribed into an mRNA molecule, the three nucleotides become known as a codon.
triplet the sequence of three
Codons and triplets are crucial to the production of proteins, as each triplet or codon nucleotides in DNA coding for one
codes for a specific amino acid in the final polypeptide chain. There are also specific amino acid
triplets and codons that instruct the cell to start and stop protein synthesis. In doing so, codon the sequence of three
they determine which nucleotides are transcribed and translated into a functional protein nucleotides in mRNA coding for
and explain why the order of nucleotides or codons essentially determines the order of one amino acid
amino acids in a protein (Figure 2).

DNA triplets 3’ 5’
T A C G A A T T T C T C

transcription and RNA processing

A U G C U U A A A G A G
mRNA codons
5’ 3’

translation

amino acids met leu lys glu

Figure 2 Triplets and codons are groups of three nucleotides, coding for specific amino acids.

To determine the amino acid coded for by a specific codon, a codon table can be used
(Figure 3). When using a codon table, simply begin at the left-hand side, which refers to
the first base of the codon. Next, observe the top of the table, which refers to the second
start codon the sequence of three
base of the codon, and finally, observe the right-hand side, which refers to the third base
nucleotides in mRNA that signals
of the codon.
the start of translation
Also note that while the start codon (AUG) codes for the amino acid methionine, stop codon the sequence of three
signalling the initiation of translation, the stop codons (UAA, UAG, UGA), which signal nucleotides in mRNA that signals
for the termination of translation, do not code for a specific amino acid. the end of translation
 2C THEORY 81

Second Base
First Base U C A G Third Base
UUU UCU UAU UGU U
phe tyr cys The VCAA does not require
UUC UCC UAC UGC C students to memorise the
U ser STOP codon table or remember all
UUA UCA UAA STOP UGA A
CODON of the different amino acids.
leu CODON
UUG UCG UAG UGG trp G However, they do frequently
supply the table on exams
CUU CCU CAU CGU U
his and ask students to extract
CUC CCC CAC CGC C information from it. The
C pro arg
CUA leu CCA CAA CGA A amino acid table can also be
gln
CUG CCG CAG CGG G displayed for DNA triplets
instead of RNA codons,
AUU ACU AAU AGU U
asn ser requiring students to look for
AUC ile ACC AAC AGC C thymine instead of uracil.
A AUA ACA thr AAA AGA A
met (START lys arg
AUG ACG AAG AGG G
CODON)
GUU GCU GAU GGU U
asp
GUC GCC GAC GGC C
G val ala gly
GUA GCA GAA GGA A
glu
GUG GCG GAG GGG G

Figure 3 The codon table provides the amino acid coded for by each specific codon.

Aside from the fact that the genetic code is based on groupings of three adjacent
nucleotides, some other properties of the genetic code are summarised in Table 1.
Table 1 Properties of the genetic code

Property Description Image

Universal Nearly all living organisms use the same codons to code codon amino acid
for specific amino acids.
UUA leucine
Unambiguous Each codon is only capable of coding for one specific
amino acid. For example, the codon UUA only codes for
the amino acid leucine.

Degenerate While each codon only codes for one amino acid codons amino acid
(unambiguous), each amino acid may be coded for by
multiple different codons (degenerate). For example, both
the codons UUA and UUG code for the amino acid leucine.
UUA
This provides a degree of redundancy, where changes to UUG
the original DNA sequence through mutations may not CUU
leucine
necessarily lead to the insertion of a different amino acid. CUC
CUA
CUG

Non-overlapping Each triplet or codon is read independently, without

overlapping from adjacent triplets or codons.
mRNA

1 2 3

Gene structure [Link]

O verview
Genes can be composed of many different components, including a promoter region,
introns, exons, termination sequences, and operator regions.

T heory details
Within each gene there are several different regions, each with its own specific function.
The purposes of these regions will become more apparent in lesson 2D, when we consider
the processes of transcription, RNA processing, and translation in more detail (Table 2).
82 Chapter 2: Nucleic acids and proteins

Table 2 The key regions of genes

promoter the sequence of DNA to
Region Description
which RNA polymerase binds
Promoter The promoter region is an upstream binding site for RNA polymerase, which RNA polymerase the enzyme
is an enzyme responsible for transcription. When RNA polymerase binds to responsible for constructing a
the promoter region of a gene, it allows for the transcription of that particular pre-mRNA sequence from a DNA
gene. Therefore, the promoter region effectively denotes the starting position
sequence during transcription
and direction of transcription. In eukaryotes, the promoter region is often the
sequence of bases ‘TATAAA’, commonly known as the TATA box. enzyme an organic molecule,
typically a protein, that catalyses
Introns Introns are regions of non-coding DNA that do not contribute to the final protein (speeds up) specific reactions
as they are removed during RNA processing (post-transcriptional modifications).
TATA box a type of promoter
Importantly, only eukaryotic genes contain introns – prokaryotic genes do not
contain introns. region
introns non-coding regions
Exons Exons are regions of coding DNA, which are transcribed and translated into the of DNA that do not code for
final protein. These can be found in both eukaryotes and prokaryotes. proteins. They are spliced out
Termination sequence The termination sequence represents a sequence of DNA that signals for the end during RNA processing
of transcription. exons regions of DNA that code
for proteins and are not spliced out
Operator The operator region serves as the binding site for repressor proteins, which can
during RNA processing
then inhibit gene expression. This region is typically only found in prokaryotic
genes, as eukaryotes have different regions for regulating gene expression. termination sequence
a sequence of DNA that signals
Leader The leader region is the section of DNA just upstream of the coding region, the end of transcription
and downstream of the promoter and operator. The leader region plays a critical
operator a short region of DNA
role in one mode of regulating gene expression in prokaryotes discussed in
that interacts with repressor
later lessons.
proteins to alter the transcription
of an operon
promoter termination
(TATA box) sequence repressor protein a protein
coded for by a regulatory gene
that prevents gene expression by
binding to its operator
TATAAA exon intron exon intron
gene expression the process of
reading the information stored
Figure 4 Eukaryotic genes often contain a promoter region, introns, exons, and a termination sequence.
within a gene to create a functional
promoter product, typically a protein
termination
sequence leader region the segment of
operator
DNA or mRNA that immediately
precedes the coding region. Also
exon exon exon known as the leader segment or
leader sequence
transcription inhibited

leader trailer

repressor protein In lesson 2E, the significance

Figure 5 Prokaryotic genes often contain a promoter region, an operator region, a leader region, exons, and a of the operator region,
termination sequence. leader region, and repressor
proteins in regulating gene
expression will be explored.
Theory summary
The information required to produce proteins is stored within genes in the form of DNA
triplets. Through the process of transcription, these DNA triplets are used as a template
to produce mRNA codons. Then, through the process of translation, these mRNA codons
are used to code for specific amino acids within a polypeptide chain. Key features of the
genetic code include its universal, unambiguous, degenerate, and non-overlapping nature.

The genetic code is the mechanism through which our cells store genetic information.
Using the different nucleotide bases – adenine, thymine, cytosine, guanine, and uracil – it is
possible to construct varying sequences that come together to form triplets, codons, and
anticodons. Then, through complementary base-pairing, each codon will code for a specific
amino acid to form the final protein.
 2C QUESTIONS 83

2C QUESTIONS
Theory review questions

Question 1

Fill in the blanks with the following terms.

• amino acid
• codon
• triplet

In the genetic code, three bases in a DNA sequence are known as a _, while three bases in mRNA are known as a
_, and three bases in tRNA are known as an anticodon. To determine which triplets or codons correspond to which
_, a triplet or codon table can be used.

Question 2

Match the property of the genetic code to its description.

Property Description
• universal I _ many different codons can code for the same amino acid
• degenerate II _ each codon is only capable of coding for a single amino acid
• unambiguous III _ each triplet or codon is read independently of adjacent triplets
• non-overlapping or codons
IV _ nearly all living organisms use the same set of rules and codons
to code for proteins

Question 3

Match the region of a gene to its description.

Region Description
• exons I _ binding site of RNA polymerase, denoting the starting position
• introns of transcription
• operator II _ a sequence of DNA which signals for the end of transcription
• promoter III _ binding site for repressor proteins
• termination sequence IV _ non-coding regions of DNA
V _ coding regions of DNA

Question 4

Categorise the following regions as prokaryotic, eukaryotic, or both.

I termination sequence _
II promoter _
III operator _
IV introns _
84 Chapter 2: Nucleic acids and proteins

SAC skills questions

Case study analysis

Use the following information to answer Questions 5–8.

Since the beginning of the 21st century and the rise of the internet, the amount of content we consume and produce online is
increasing at an exponential rate. Every minute in 2018, there were over three million Google searches, over four million videos
watched on YouTube, and over 150 million emails sent. Currently, the only way of storing data is on physical hard drives, which
require a significant amount of space and only last for around 100 years. Are there any alternative methods for storing data?
Fortunately for us, the answer to our data problem lies within our very own bodies! DNA, which has been used since the
beginning of time to store the code for the production of proteins, has proven to be an extremely versatile and stable method
of storing information. The significance of DNA as a source of data storage stems from its incredible data density, with
estimates claiming that each gram of DNA could potentially house more than 250 million gigabytes of data. Scientists have
already successfully stored an extract of the music from Super Mario Brothers in synthetic DNA. While the classic theme song
can now be listened to by people living 100 000 years into the future, the cost of this technology is still quite high and it takes
more time to extract the data in DNA compared to existing hard drives.

Converting Converting Synthesis

Digital files Binary code Nucleotide code Artifical DNA

010000100 011100100 CAGTAACA CATTCGGA
001010111 011010111 CATTGACA CAAGCAA
010101010 011101010 CATAAGAA CAGTCTCG
001110011 010110011 CAGGTATA CATCGACC

Reading Decoding Sequencing

Question 5

Which type of data would be best to store on artificial DNA?

A Large media files, so people can watch movies whenever they want.
B Highly sensitive information that needs protection.
C Small files that are regularly accessed.
D Very large files that are rarely needed.

Question 6

The genetic code is grouped into groups of

A two nucleotides.
B five nucleotides.
C four nucleotides.
D three nucleotides.

Question 7

DNA is composed of the bases

A thymine, uracil, cytosine, guanine.
B adenine, thymine, uracil, cytosine.
C adenine, uracil, cytosine, guanine.
D adenine, thymine, cytosine, guanine.

Question 8

Which one of the following statements is incorrect?

A A protein could be used to convert the nucleotide code into artificial DNA.
B A zero or one would directly translate to an adenine, thymine, guanine, or cytosine.
C The artificial DNA would be lighter than the hard drive that the binary code is stored on.
D The artificial DNA that stores digital files would be universal, degenerate, unambiguous, and non-overlapping.
 2C QUESTIONS 85

Exam-style questions
Within lesson

Use the following information to answer Questions 9–11.

Spinocerebellar ataxia type 1 is a condition that causes a loss of muscle coordination. It is caused by a mutation, which involves
permanent changes to a DNA sequence, causing an increase in the number of repeats in the DNA triplet GTC. In the template
strand of DNA, the regular gene sequence has between 25 and 36 GTC repeats, but in the mutant gene there are between 43
and 81 GTC repeats. The following codon table can be used to determine amino acids coded for by a nucleotide sequence.

1st position 2nd position 3rd position

(5’ end) U C A G (3’ end)

U Phe Ser Tyr Cys U

Phe Ser Tyr Cys C

Leu Ser STOP STOP A

Leu Ser STOP Trp G

C Leu Pro His Arg U

Leu Pro His Arg C

Leu Pro Gln Arg A

Leu Pro Gln Arg G

A Ile Thr Asn Ser U

Ile Thr Asn Ser C

Ile Thr Lys Arg A

Met Thr Lys Arg G

G Val Ala Asp Gly U

Val Ala Asp Gly C

Val Ala Glu Gly A

Val Ala Glu Gly G

Question 9 (1 MARK)

The corresponding codon belonging to the repeated DNA sequence is

A GTC.
B GUC.
C CAG.
D CUG.

Question 10 (1 MARK)

The amino acid coded for by the template DNA sequence GTC is
A Asn.
B Gln.
C Val.
D His.
86 Chapter 2: Nucleic acids and proteins

Question 11 (1 MARK)

Thirty GTC repeats would code for

A 30 amino acids.
B 20 amino acids.
C 10 amino acids.
D 90 amino acids.
Adapted from VCAA 1998 CAT3 Article 1

Question 12 (1 MARK)

Bacteria, viruses, humans, and koalas all use the same triplet code to produce proteins. Which property of the genetic code
does this refer to?
A universal
B degenerate
C unambiguous
D non-overlapping

Multiple lessons

Question 13 (7 MARKS)

Myosin is a contractile protein involved in the movement of muscles. It functions via the conversion of chemical energy in the
form of ATP into mechanical energy, thereby causing muscle contraction. Myosin is a protein composed of many different
polypeptide chains. The following codon table can be used to determine amino acids coded for by a nucleotide sequence.

1st position 2nd position 3rd position

(5’ end) U C A G (3’ end)

U Phe Ser Tyr Cys U

Phe Ser Tyr Cys C

Leu Ser STOP STOP A

Leu Ser STOP Trp G

C Leu Pro His Arg U

Leu Pro His Arg C

Leu Pro Gln Arg A

Leu Pro Gln Arg G

A Ile Thr Asn Ser U

Ile Thr Asn Ser C

Ile Thr Lys Arg A

Met Thr Lys Arg G

G Val Ala Asp Gly U

Val Ala Asp Gly C

Val Ala Glu Gly A

Val Ala Glu Gly G

a The following mRNA sequence describes a small segment of one of the polypeptide chains of myosin – AUG CUU AUU
ACU GGG GAG UCU GGU GCC.
i Using the table provided, what is the amino acid sequence that the mRNA sequence codes for? (1 MARK)
ii What is the corresponding DNA template strand to the mRNA sequence? (1 MARK)
b Identify the level of protein structure that myosin folds into. Justify your response. (2 MARKS)
c Identify three key differences in structure between mRNA and DNA. (3 MARKS)
 2C QUESTIONS 87

Question 14 (5 MARKS)

A recent study has suggested that mutations, which are permanent changes to a DNA sequence, occurring within the p53
gene in humans represent a significant risk for the development of certain cancers.
a While mutations can often lead to the production of polypeptides with different amino acid sequences, sometimes
mutations still produce the same amino acid. Explain how this may occur. (2 MARKS)
b There are many different regions within a gene that are crucial to its functioning.
i Describe the difference between introns and exons. (1 MARK)
ii Explain whether an operator region would be found within the p53 gene of humans. (1 MARK)
iii Describe the purpose of the promoter region of a gene. (1 MARK)
Adapted from VCAA 1999 CAT3 Article 4

Key science skills and ethical understanding

Question 15 (8 MARKS)

Mutations, which involve permanent changes to a DNA sequence, are primarily responsible for the development of cancers.
This is because when mutations occur, they affect the DNA sequence of a gene, leading to the production of different amino
acids and potentially causing proteins to malfunction. While mutations often occur spontaneously, there are also many
environmental factors that can cause them, such as UV radiation. For example, UV radiation from the sun has been attributed
to a high rate of skin cancer.
In an effort to investigate the effect of UV radiation on the development of skin cancer, researchers recruited a small group of
mice. The group of mice were divided into two groups, with one group exposed to UV radiation while the other group lived in
the dark. After several weeks, they were assessed for the formation of skin cancer.

a Identify the dependent and independent variables in the researchers’ experiment. (2 MARKS)
b Identify a possible hypothesis for the experiment. (1 MARK)
c Identify two factors that should be controlled within the experiment. (2 MARKS)
d Suggest how the researchers could increase the precision of their experiment. (1 MARK)
e Describe the relevance of the bioethical concept of beneficence to the experiment conducted by the researchers. (2 MARKS)
88 Chapter 2: Nucleic acids and proteins

2D G
 ENE EXPRESSION
Never been to a restaurant before? Well lucky for you, here’s a simple guide on what to do when
you visit a restaurant:
• Decide what to eat by looking at the menu.
• Call the waiter and let them know what you’d like to order.
• The waiter will write down your order and pass it on to the chef.
• The chef will receive your order and begin making your food.
• The waiter will bring the cooked food to your table.
Something similar to this process is happening inside the cells in your body. Who’s the waiter of
the human body? Who’s the chef of the human body? Is there somewhere angry patrons can write
Image: Semen Kuzmin/[Link]
reviews about the service they receive?

Lesson 2D
In this lesson you will learn how genes are expressed to produce proteins
through the processes of transcription, RNA processing, and translation.

Prerequisite knowledge Future applications

Lesson 2A Lesson 2E
Proteins are crucial to the functioning of Regulatory genes are involved in the
the body and have a diverse range of roles. production of repressor molecules that can
They are the product of translation. either inhibit or allow the expression of genes
under certain circumstances.
Lesson 2C
The genetic code represents a series of rules Lesson 2F
used by living organisms to transcribe and Proteins, which are the final products of gene
translate genetic material into proteins. expression, can be exported out of cells via the
protein secretory pathway so that they can be
used elsewhere in the body.

Study design dot point

• the genetic code as a universal triplet code that is degenerate and the steps in gene expression,
including transcription, RNA processing in eukaryotic cells, and translation by ribosomes

Key knowledge units

Gene expression [Link]

Transcription [Link]

RNA processing [Link]

Translation [Link]

Gene expression [Link]

O verview
The production of functional gene products such as proteins or non-coding strands
of RNA is known as gene expression.

T heory details
Gene expression is a complex series of events which results in the formation of gene expression the process of
functional gene products such as proteins or non-coding strands of RNA. It is through reading the information stored
gene expression that it is possible for living organisms to produce the proteins and within a gene to create a functional
products crucial for maintaining life. product, typically a protein
 2D THEORY 89

The stages of gene expression involved in the production of proteins include (Figure 1):
• transcription, which involves the copying of DNA into pre-mRNA transcription the process
whereby a sequence of DNA
• RNA processing, which modifies the pre-mRNA molecule to produce mRNA
is used as a template to produce
• translation, which involves the decoding of the mRNA strand into a polypeptide chain. a complementary sequence
of mRNA
precursor messenger RNA
transcription RNA processing translation (pre-mRNA) the immediate
product of transcription of a DNA
sequence. Requires modifications
DNA pre-messenger messenger before it can undergo translation
sequence RNA RNA protein messenger RNA (mRNA)
of a gene (pre-mRNA) (mRNA) RNA molecules that are produced
during transcription and carry
genetic information from the
nucleus to the ribosomes
translation the process
Figure 1 The processes of gene expression including transcription, RNA processing, and translation where an mRNA sequence is
In the production of other RNA molecules such as tRNA and rRNA, only the transcription read to produce a corresponding
and RNA processing stages occur. This is relatively intuitive, in that RNA is not composed amino acid sequence to build
a polypeptide
of protein, and therefore do not require translation. When producing these strands of
RNA, different enzymes are used, and therefore instead of mRNA, other forms of RNA are transfer RNA (tRNA)
produced. RNA that recognises specific
codons on the mRNA strand and
adds the corresponding amino acid
Transcription [Link] to the polypeptide chain during
O verview protein synthesis
ribosomal RNA (rRNA)
Transcription is the first stage of gene expression and involves the creation of a pre-mRNA
RNA that is a key structural
molecule by converting the genetic information found in DNA into RNA. component of ribosomes,
which assemble proteins
T heory details
enzyme an organic molecule,
In eukaryotes, DNA is large and cannot leave the nucleus. The process of transcription typically a protein, that catalyses
creates an intermediary molecule known as mRNA, which serves as a copy of DNA (speeds up) specific reactions
in RNA that can leave the nucleus and transport the code for protein around the cell.
As DNA is stored within the nucleus of eukaryotes, the process of transcription must
also occur within the nucleus. In prokaryotes, however, because DNA is free-floating
within the cytoplasm due to the absence of a nucleus, DNA is transcribed into
mRNA within the cytoplasm. transcription factor proteins
that bind to the promoter region
It is also important to remember that the primary product of transcription in eukaryotes and control the functioning of
is known as pre-mRNA, which undergoes further modifications during RNA processing RNA polymerase
to become mRNA. The process of transcription can be broken down into three stages – promoter the sequence of DNA to
initiation, elongation, and termination (Table 1). which RNA polymerase binds
Table 1 The general stages of transcription RNA polymerase the enzyme
responsible for constructing a
Stage Description pre-mRNA sequence from a DNA
sequence during transcription
Initiation To begin transcription, specific proteins called transcription factors bind to the promoter
region to initiate transcription. With the help of transcription factors, RNA polymerase template strand the strand
binds to the promoter region. This signals for the weak hydrogen bonds between the two of DNA transcribed by RNA
strands of DNA to break, resulting in the bases of each strand being exposed and the DNA polymerase to produce a
helix being unwound and unzipped. RNA polymerase is then able to start transcription. complementary pre-mRNA strand

Elongation RNA polymerase moves along the template strand of DNA, reading the nucleotide coding strand the strand of
sequence and uses free-floating complementary RNA nucleotides to produce a new single- DNA not transcribed by RNA
stranded RNA molecule known as pre-mRNA. The pre-mRNA molecule is synthesised in a polymerase, contains an identical
5’ to 3’ direction, so new RNA nucleotides are added to the exposed 3’ end. This pre-mRNA sequence to the mRNA strand
strand has a complementary nucleotide sequence to the DNA template strand. The strand produced (except thymine is
of DNA that is not read by RNA polymerase is called the coding strand. As the coding replaced with uracil in mRNA)
strand is also complementary to the template strand, the coding strand is identical to the
termination sequence a sequence
pre-mRNA strand (except the pre-mRNA includes uracil instead of thymine).
of DNA that signals the end
Termination Transcription ends when RNA polymerase reaches the termination sequence of a gene, of transcription
signalling the end of transcription. RNA polymerase then detaches, releasing the pre- ribosome an organelle made of
mRNA molecule and the DNA molecule winds up again into a double helix. The pre-mRNA rRNA and protein that is the site
molecule is then processed to become mRNA, carrying the message for protein synthesis
of protein synthesis. Can be free
from DNA in the nucleus to the ribosomes located in the cytosol or attached to the rough
in the cytosol or attached to the
endoplasmic reticulum of the cell.
rough endoplasmic reticulum
90 Chapter 2: Nucleic acids and proteins

coding strand
RNA polymerase
direction of
movement
5’ 3’

3’ 3’ 5’
termination
template strand sequence
promoter pre-mRNA
region

coding strand

pre-mRNA 3’
5’

template strand

Figure 2 DNA is transcribed by RNA polymerase into a pre-mRNA molecule

The VCAA does not assess transcription in terms of the initiation, elongation, and termination stages.
Instead, those three stages are simply a framework for memorising the process of transcription.
When asked to outline the process of transcription on past VCAA Biology exams (e.g. 2016 Section B Q6b,
2013 Section B Q6ai) the following points were required:
• DNA unwinds/unzips
• RNA polymerase catalyses transcription through the joining of complementary RNA nucleotides
• transcription of the DNA template strand into pre-mRNA occurs
• pre-mRNA is complementary to the DNA template strand
• in the pre-mRNA, adenine (A) pairs with uracil (U), not with thymine (T).

RNA processing [Link]

O verview
RNA processing, also known as post-transcriptional modifications, involves the
modification of the pre-mRNA molecule into an mRNA molecule that can be used
in translation.

T heory details
Following transcription, the pre-mRNA molecule must undergo RNA processing, also 5’ methyl-G cap a molecule
known as post-transcriptional modifications, before being sent to the ribosomes for added to the 5’ end of pre-mRNA
translation. RNA processing only occurs in eukaryotic cells, taking place in the nucleus. during RNA processing
After RNA processing, the pre-mRNA molecule simply becomes known as an mRNA 3’ poly-A tail a chain of adenine
molecule or a mature mRNA molecule. The processing modifications include: nucleotides added to the 3’ end of
pre-mRNA during RNA processing
• the addition of a 5’ methyl-G cap and a 3’ poly-A tail introns non-coding regions of
• the removal of introns and the splicing of exons together. DNA that do not code for proteins.
They are spliced out during RNA
processing
splicing process where introns are
cut out of a pre-mRNA molecule,
Frequently, you will hear the process of turning DNA into a protein as only transcription and translation.
and exons are joined together
This is because RNA processing, or post-transcriptional modifications, can often be classified as part of
the transcription stage of protein synthesis. exons regions of DNA that code
for proteins and are not spliced out
during RNA processing
Addition of a 5’ methyl-G cap and a 3’ poly-A tail
The addition of a methyl-guanine cap (methyl-G cap) at the 5’ end and a chain of adenine
nucleotides (poly-A tail) to the 3’ end serve to stabilise the mRNA molecule, preventing it
from degrading and allowing it to bind to ribosomes during translation.
 2D THEORY 91

Splicing
From lesson 2C, you should remember that introns are non-coding regions of DNA spliceosome the enzyme that
and exons are coding regions of DNA. The sections of pre-mRNA corresponding to removes introns from the pre-
introns must be removed and the regions corresponding to exons must be joined mRNA molecule and joins exons
together during RNA processing
together. This occurs through the process of splicing via a complex molecule known
as a spliceosome, which removes the introns and splices the exons together (Figure 3).

pre-mRNA
exon intron

5’ 3’

RNA processing
mRNA

5’ methyl-G cap exons only 3’ poly-A tail

Figure 3 Transcribed pre-mRNA must undergo post-transcriptional modifications before it can be translated.

Unlike eukaryotes,
prokaryotic transcription and
translation occur very close
RNA processing only occurs within eukaryotic cells. An easy way to remember this is by recalling that to each other in cytoplam.
while eukaryotic genes are composed of both introns and exons, prokaryotic genes are composed solely This concept will underpin
of exons. Therefore, prokaryotic mRNA can be directly translated without undergoing post-transcriptional one of the major mechanisms
modifications. Notably, transcription and translation take place very close to each other within the of gene regulation within the
cytoplasm in prokaryotes, which is significantly different to gene expression in eukaryotes. trp operon in lesson 2E.

Alternative splicing
Sometimes, exons can also be removed during the splicing process. This means that a alternative splicing the process
single pre-mRNA strand can produce many different mRNA molecules depending on where different exons may be
which exons are spliced out or kept. This process is known as alternative splicing and spliced, resulting in a single gene
allows for a single gene to give rise to many different mRNA strands and code for many producing multiple different
different proteins (Figure 4). mRNA strands

exon 1 exon 2 exon 3 exon 4

pre-mRNA

alternative
splicing

1 2 3 4 1 3 4 1 2 4 1 4
Figure 4 Alternative splicing can create many different strands of mRNA from a single gene.

An easy way to remember the difference between introns and exons is that exons exit the nucleus for
translation, whereas introns stay inside the nucleus.
92 Chapter 2: Nucleic acids and proteins

Translation [Link]
O verview
Translation involves reading and converting the information carried in the mRNA
molecule into a polypeptide chain.

T heory details
After a pre-mRNA molecule is produced from a DNA template strand and undergoes
post-transcriptional modifications, it is ready for translation. To undergo translation,
the mRNA molecule exits the nucleus through a nuclear pore and travels to a ribosome
either in the cytosol or attached to the rough endoplasmic reticulum (Figure 5). During
translation, the mature mRNA molecule is decoded and translated into a sequence of
amino acids, eventually forming a polypeptide chain.

transcription

pre-mRNA
protein

post-transcriptional
modifications
ribosome

mRNA
translation
DNA

nuclear pore
nucleus cytoplasm

Figure 5 The mRNA molecule travels through the nuclear pore to reach the ribosome located in the cytosol or
attached to the rough endoplasmic reticulum.

There are a number of key players involved in translation including mRNA, rRNA, tRNA,
and amino acids. Translation can be broken down into three stages – initiation, elongation,
and termination (Table 2).
codon the sequence of three
Table 2 The general stages of translation nucleotides in mRNA coding for
one amino acid
Stage Description start codon the sequence of three
Initiation The 5’ end of the mRNA molecule binds to the ribosome and is read until the start nucleotides in mRNA that signals
codon (AUG) is recognised. Then, a tRNA molecule with a complementary anticodon the start of translation
(UAC) binds to the ribosome and delivers the amino acid methionine, signifying the anticodon the sequence of three
commencement of translation. nucleotides on a tRNA molecule
that recognises a specific sequence
Elongation After the first amino acid is attached, the mRNA molecule is fed through the ribosome
so that the next codon can be matched to its complementary tRNA anticodon. Then, of three nucleotides (codon) on an
complementary tRNA molecules deliver specific amino acids to the ribosome, which bind mRNA strand
to adjacent amino acids with a peptide bond via a condensation reaction. The first tRNA peptide bond the chemical bond
molecule then leaves the ribosome and is free to pick up another amino acid, and the next linking two amino acids
mRNA codon is exposed for more tRNA-delivered amino acids to add to the growing amino
condensation reaction a reaction
acid chain.
where two monomers join to form
Termination The reading of mRNA, delivery of amino acids by tRNA, and the linking of amino acids in a larger molecule, producing water
the polypeptide chain continues until the ribosome reaches a stop codon on the mRNA as a by-product
molecule. The stop codon signals the end of translation as there are no corresponding stop codon the sequence of three
tRNA molecules. The polypeptide chain is then released by the ribosome into the cytosol or
nucleotides in mRNA that signals
endoplasmic reticulum.
the end of translation
 2D THEORY 93

growing tRNA
polypeptide

polypeptide
Thr anticodon Arg
tRNA
mRNA amino acid Gly
G GC
UG U
5’ CCA 3’

codon
movement of mRNA
through ribosome
ribosome

Figure 6 The translation of mRNA at the ribosome

AUG CUU AAA GAG

mRNA codons
5’ 3’
translation

tRNA anticodons UAC GAA UUU CUC

amino acids met leu lys glu

Figure 7 The tRNA molecules which carry specific amino acids have anticodons complementary to the
mRNA codons.

The VCAA does not assess translation in terms of the initiation, elongation, and termination stages.
Instead, those three stages are simply a framework for memorising the process of translation. When asked
to outline the process of translation on past VCAA Biology exams (e.g. 2018 Section B Q1a, 2014 Section B
Q7a), the following points were required:
• ribosome binds to and reads the mRNA molecule
• tRNA anticodons are complementary to the mRNA codons
• tRNA brings the corresponding amino acids to the ribosome
• adjacent amino acids are joined together into a polypeptide chain via a condensation reaction.

Following translation, the mRNA molecule can be reused to produce more polypeptides. exocytosis a type of bulk
At the endoplasmic reticulum and Golgi apparatus, each polypeptide chain is folded and transport that moves large
modified into a fully functional protein, which can either remain in the cell for use, or it substances out of a cell
can be exported out of the cell via the process of exocytosis.

Theory summary
Gene expression involves the formation of a functional gene product such as proteins or
non-coding strands of RNA. Proteins are produced through the processes of transcription,
which involves copying genetic information into the form of pre-mRNA, RNA processing,
which involves modifications to the pre-mRNA molecule to become mRNA, and
translation, which involves the decoding and interpretation of the mRNA molecule into a
sequence of amino acids to form a polypeptide chain (Table 3).
94 Chapter 2: Nucleic acids and proteins

Table 3 Summary of the three stages of protein synthesis

Transcription RNA processing Translation

Key ideas • RNA polymerase binds to the • Addition of a methyl-G cap to the • mRNA molecule binds
promoter region 5’ end to the ribosome
• DNA unwinds • Addition of a poly-A tail to the 3’ end • tRNA anticodons complementary to
• RNA polymerase reads the • Introns removed and exons spliced mRNA codons deliver corresponding
DNA template strand and uses together amino acids to the ribosome
complementary RNA nucleotides to • Adjacent amino acids are joined with
catalyse the formation of pre-mRNA peptide bonds via a condensation
• Transcription is terminated when the reaction to form a polypeptide
termination sequence is recognised • Translation ends when a STOP codon
is recognised

Location Nucleus Nucleus Ribosomes

Product pre-mRNA from DNA template strand mRNA from pre-mRNA Polypeptide from mRNA

3 translation
mRNA
tRNA
amino acids

2 RNA processing
nucleotides tRNA bringing
amino acid to
RNA ribosome
polymerase

mRNA
being
tRNA translated
leaves

gene
tRNA
n ucleus pre-mRNA leaves

ribosomes adding
1 transcription amino acids
polypeptide to the growing
chain polypeptide chain
cytoplasm

transcription RNA processing translation

DNA pre-mRNA mRNA protein

Image: VectorMine/[Link]

Figure 8 Summary of transcription, RNA processing, and translation

Just like the process of ordering food at a restaurant, your cells are constantly ordering proteins to
be made. First, the order needs to be written down by the waiter in the form of mRNA through the
process of transcription, before being sent off to the chef in the form of a ribosome to produce the
final protein through the process of translation. Now, you’ll not only be an expert at ordering food
at restaurants, but you will also be well versed in the processes of transcription and translation!

Image: HAKINMHAN/[Link]
 2D QUESTIONS 95

2D QUESTIONS
Theory review questions

Question 1

Gene expression involves the

A formation of functional gene products such as proteins or non-coding strands of RNA.
B process of translation, followed by transcription, and then RNA processing.

Question 2

The locations for the processes of transcription and translation occur in the
A nucleus and cytosol, respectively.
B cytosol and nucleus, respectively.

Question 3

Fill in the blanks with the following terms. Terms may be used multiple times or not at all.
• template strand • pre-mRNA
• coding strand • codons
• 3’ poly-A tail • triplets
• anticodons • mRNA

To create protein from genetic information, a cell must undergo a series of steps. The first is transcription, where the DNA
_ is read and transcribed into _. However, it must be processed before translation by splicing introns and
the addition of a 5’ methyl-G cap and a _. The mRNA can now be translated. This is possible due to its sequences of
three nucleotides in the mRNA known as _. At the ribosome, mRNA is used to create a protein.

Question 4

Fill in the blanks with the following terms. Terms may be used multiple times or not at all.
• START codon • nucleus
• STOP codon • codons
• anticodons • triplets
• ribosome

Translation occurs at a _, where the ribosome binds to the mRNA strand and reads it. The process is facilitated by
tRNA molecules and their tri-nucleotide sequences known as _. Amino acids delivered by tRNA molecules are linked
into a polypeptide chain until a _ is reached and translation is terminated.

Question 5

Label the parts of the following diagram from the list of terms.
• transcription • mRNA
• translation • codon
• amino acid • triplet
• anticodon • rRNA
• protein • tRNA

Process W
ribosome

Y Z
96 Chapter 2: Nucleic acids and proteins

SAC skills questions

Case study analysis

Use the following information to answer Questions 6–9.

In eukaryotes, there are many different mechanisms that exist to regulate the process of gene expression. These include the
use of silencer regions within genes, which serve to downregulate gene expression by inhibiting transcription, and enhancer
regions within genes, which serve to upregulate gene expression by activating transcription. The use of these mechanisms only
applies to the production of mRNA – they have no effect on the length of time that an mRNA molecule can remain within the
cytosol and be translated into proteins.
One of the primary methods of determining how long an mRNA molecule can remain within a cell depends on the length of its
poly-A tail. This is because the poly-A tail is responsible for stabilising the mRNA molecule and protecting it against enzymatic
attack and degradation. mRNA molecules with longer poly-A tails can persist for longer due to their increased resistance
against degradation.
Another method of maintaining mRNA levels within a cell involves the use of microRNAs, which are another form of RNA.
MicroRNAs are produced through the process of transcription, using a different type of RNA polymerase. When microRNAs
are loaded into a complex known as an RNA-induced silencing complex (RISC), they are capable of binding to complementary
strands of mRNA molecules within the cytosol and cleaving the mRNA molecule, rendering it obsolete.

Question 6

Enhancers are regions within genes involved in

A upregulating gene expression.
B downregulating gene expression.

Question 7

A shorter poly-A tail will result in

A a decreased rate of degradation of an mRNA molecule.
B an increased rate of degradation of an mRNA molecule.
C no change to the speed of degradation of an mRNA molecule.
D a significantly decreased rate of degradation of an mRNA molecule.

Question 8

The production of microRNAs would involve the process of

A transcription, as microRNAs are forms of rRNA.
B translation, as microRNAs are composed of protein.
C translation, as microRNAs involve the use of tRNA and rRNA molecules.
D transcription, as microRNAs are complementary to genes stored within the nucleus.

Question 9

MicroRNAs would not contain the nucleotide

A uracil.
B thymine.
C adenine.
D cytosine.
 2D QUESTIONS 97

Exam-style questions
Within lesson

Question 10 (1 MARK)

A molecule of messenger RNA could include the nucleotide sequence

A CTGTATUTA
B AGTGUACTT
C GTACGTAGG
D CUACGAGUU
Adapted from VCAA 2011 Exam 1 Section A Q4

Use the following information to answer Questions 11 and 12.

Ricin is a naturally occurring, powerful poison that affects eukaryotic organisms. Studies have concluded that ricin stops the
movement of a ribosome along a specific molecule labelled Molecule X.

ribosome Molecule X

direction of ribosome movement

Question 11 (1 MARK)

Which monomer is Molecule X made of?

A fatty acids
B nucleotides
C amino acids
D carbohydrates

Question 12 (1 MARK)

At the stage shown in the diagram, Molecule X contains regions corresponding to

A exons only.
B introns only.
C both exons and introns.
D neither exons or introns.
Adapted from VCAA 2017 Northern Hemisphere Exam Section B Q23

Multiple lessons

Question 13 (1 MARK)

The genome of the Northern white-cheeked gibbon, Nomascus leucogenys, has been sequenced and compared to other primate
species. The N. leucogenys genome would
A include the base uracil.
B include only the non-coding DNA sequences.
C be identical to the genome of the buffed-cheeked gibbon, Nomascus annamensis.
D contain the same nitrogenous base types to the genome of the black-crested gibbon, Nomascus concolor.
Adapted from VCAA 2015 Section A Q24
98 Chapter 2: Nucleic acids and proteins

Question 14 (5 MARKS)

Consider the template strand of the hypothetical gene shown. The exons are in bold type.

3’ TAC ACC GCT TAT TTT CAT CTT TCT GCA TAG GAT ATC 5’
The DNA triplet TAC indicates START for transcription, and the mRNA codon that it produces will code for the amino acid
methionine, which remains in the resulting polypeptide. The DNA triplets ATC, ATT, and ACT code for a STOP instruction.

a Identify the total number of amino acids present in the polypeptide expressed by this gene. Justify your response. (2 MARKS)
b The template strand is used to produce mRNA.
i What is the pre-mRNA strand that would be produced from this DNA sequence? (1 MARK)
ii What is the corresponding mRNA sequence following RNA processing? (1 MARK)
iii Using the table provided, what is the amino acid sequence produced when the mRNA molecule is translated? (1 MARK)

1st position 2nd position 3rd position

(5’ end) U C A G (3’ end)

U Phe Ser Tyr Cys U

Phe Ser Tyr Cys C

Leu Ser STOP STOP A

Leu Ser STOP Trp G

C Leu Pro His Arg U

Leu Pro His Arg C

Leu Pro Gln Arg A

Leu Pro Gln Arg G

A Ile Thr Asn Ser U

Ile Thr Asn Ser C

Ile Thr Lys Arg A

Met Thr Lys Arg G

G Val Ala Asp Gly U

Val Ala Asp Gly C

Val Ala Glu Gly A

Val Ala Glu Gly G

Question 15 (4 MARKS)

The hormone insulin is a relatively small protein. Researchers studying the production of insulin in the cells of the pancreas
noted that one of the early steps in this process is the formation of a polypeptide called preproinsulin. Researchers noted that
the formation of this polypeptide requires different forms of Molecule Z shown.

Molecule Z

anticodon
 2D QUESTIONS 99

a Molecule Z is crucial to the functioning of cells.

i Identify the process Molecule Z is involved in. (1 MARK)
ii Describe the role of anticodons in this process. (2 MARKS)
b Proteins have four levels of protein structure. If preproinsulin has not been configured into alpha helices or beta-pleated
sheets, what level of structure does it have? (1 MARK)

Question 16 (9 MARKS)

Scientists studying the nucleus of the fruit fly Drosophila melanogaster observed distinct types of nucleic acid chains. One type
of nucleic acid chain was able to pass through the nuclear membrane and move to a ribosome. After the nucleic acid chain
attached to the ribosome, a polymer was produced.
a What type of molecule is this nucleic acid chain? (1 MARK)
b Identify the enzyme responsible for the creation of the nucleic acid chain. (1 MARK)
c Describe the steps that occur within a cell that result in the production of this nucleic acid chain. (3 MARKS)
d What type of molecule is the polymer produced? (1 MARK)
e Describe the steps that occur at the ribosome that convert this nucleic acid chain into the polymer. (3 MARKS)
Adapted from VCAA 2014 Section B Q7

Question 17 (3 MARKS)

The following diagram outlines various events that occur in cells when DNA is activated.
Label the structures and stages shown in the diagram.

Stage Y
B events inside
the nucleus
C

nuclear membrane D

G
E Stage Z
events outside
the nucleus

F
Adapted from VCAA 2013 Section B Q6

Key science skills and ethical understanding

Question 18 (9 MARKS)

Scientists have investigated how the nucleus accumulates the essential proteins that it needs to function. They found a
possible reason while studying a certain normal polypeptide sequence, and an abnormal version. The abnormal polypeptide
produced was not able to cross the nuclear membrane in the same way the normal form did. The amino acids in the normal
(N) and abnormal (A) polypeptides are shown. A sequence of six amino acids from the middle is magnified.
100 Chapter 2: Nucleic acids and proteins

cut cut
normal
(N) D E F

section of polypeptide
magnified

cut cut
abnormal
(A) D* E* F*

same section of polypeptide

magnified

An experiment was carried out where both polypeptides were cut into three smaller chains – D, E, and F (D*, E*, and F*) –
as shown. Each polypeptide was put into a cell and then its accumulation in the nucleus was measured. The table shows
the results of the experiment.

Polypeptide Accumulates in nucleus

N yes

A no

D no

E yes

F no

D* no

E* no

F* no

a Identify the independent and dependent variables of this experiment. (2 MARKS)

b Which polypeptides were easily able to cross the nuclear envelope? Justify your response. (2 MARKS)
c Polypeptide E accumulated in the nucleus whereas polypeptide E* did not. Suggest a reason why polypeptide E* did not
accumulate in the nucleus. (1 MARK)
d How could the scientists improve the precision of their experiment? (2 MARKS)
e Medical research often requires large amounts of funding. However, ethical dilemmas can often arise when deciding
which research projects deserve the most funding. With reference to one bioethical concept, suggest one criterion that
should be considered when determining which research projects deserve the most funding. (2 MARKS)
Adapted from VCAA 2014 Section B Q2
 2E THEORY 101

2E G
 ENE REGULATION
Teachers are a crucial component of every classroom. We all know that when teachers are away and
replaced by substitute teachers, there is no chance of any work getting completed. Or if the teacher
doesn’t show up after 15 minutes, there is almost no chance of finding the students for the rest of the
day as they’ve all disbanded and gone for an early lunch. But just like teachers, is there something
inside our cells that keeps everyone in check? What makes sure that our cells don’t just stop working
after 15 minutes? Image: [Link]/[Link]

Lesson 2E
In this lesson you will learn how regulatory genes initiate or inhibit
transcription, specifically how the trp operon is switched on and off as a
simple model of gene regulation.

Prerequisite knowledge Future applications

Lesson 2C Lesson 2F
Genes are composed of many different regions, The amount of protein exported by a cell is
including a promoter region, coding regions dependent on the amount of protein produced.
known as exons, a termination region, and an Gene regulation is the mechanism which
operator region. ultimately determines the amount of protein
produced within a cell.
Lesson 2D
Gene regulation is the modulation of gene Chapter 3
expression, which primarily involves the The mechanism of how a repressor can be
production of proteins via transcription, RNA deactivated by another molecule through
processing, and translation. a change in its functional 3D shape is also
applicable to enzymes. Enzymes can be
inhibited by other molecules through a 3D
conformational change.

Study design dot point

• the basic elements of gene regulation: prokaryotic trp operon as a simplified example of a regulatory process

Key knowledge units

Gene regulation [Link]

How the trp operon works [Link]

Gene regulation [Link]

O verview
Regulatory genes code for proteins that influence the expression of structural genes, gene regulation the control of
preventing the over or under expression of a particular protein and allowing the cell to gene expression, typically achieved
by switching transcription on or off
adapt to its needs.
gene expression the process of
T heory details reading the information stored
within a gene to create a functional
The human body uses a significant amount of energy each day – with every heartbeat,
product, typically a protein
every breath, and even every thought, energy must be expended. Therefore, in order to
structural gene a segment
maintain adequate energy levels, we need to be smart about how our limited energy supply
of DNA that doesn’t code for
is used and distributed. But apart from staying completely still or clearing our minds of
regulatory proteins, but instead
their thoughts, how can our cells conserve energy? Gene regulation! codes for proteins that play a role
Gene regulation involves the process of either inhibiting or activating gene expression. in the structure or function of a cell
In doing so, organisms can prevent the unnecessary production of gene products such as or organism
proteins when they are not required, thereby conserving energy. There are two types of regulatory gene a segment of
genes involved in gene regulation – structural genes and regulatory genes (Table 1). DNA responsible for producing
The important link between these two types of genes is that regulatory genes are proteins that control the
expression of other genes
responsible for controlling the expression of other genes, such as structural genes.
102 Chapter 2: Nucleic acids and proteins

Table 1 Structural and regulatory genes

repressor protein a protein
Gene Description
coded for by a regulatory gene
Structural Structural genes are responsible for producing proteins that are involved in the structure or that prevents gene expression by
gene function of a cell. For example, they may code for enzymes, transport proteins, receptors, binding to its operator
or peptide hormones. These genes are often found downstream (towards the 3’ end of the activator protein a protein coded
coding strand) of the regulatory gene that controls them.
for by a regulatory gene that
Regulatory Regulatory genes are responsible for the production of regulatory proteins such as repressor increases gene expression
gene proteins, which inhibit or decrease the expression of structural genes. Activator proteins, on promoter the sequence of DNA to
the other hand, can initiate or increase the expression of structural genes. Regulatory proteins which RNA polymerase binds
can turn gene expression off or on, as well as increase or decrease the rate of gene expression
operator a short region of DNA
by promoting or hindering transcription. They can also control the types of post-transcriptional
modifications that occur, such as the way in which a gene’s pre-mRNA is spliced. that interacts with repressor
proteins to alter the transcription
From lesson 2C, you should remember that genes are composed of many different of an operon
components such as a promoter, an operator, initiation and termination sequences, operon a cluster of linked genes
introns and exons, and the influence each of these has on protein production. In certain that all share a common promoter
and operator and are transcribed
organisms, such as prokaryotes, multiple structural genes that share a common purpose
at the same time
can often be arranged into groups so that their expression is efficiently controlled by a
single promoter and operator in what is known as an operon (Figure 1).
regulatory promoter operon
DNA
template 3’ 5’
strand

regulatory gene operator structural genes trailer region

structural promoter leader region
Figure 1 The basic structure of an operon with three structural genes

Because operators are always located downstream of the gene’s promoter region, they can be
used as a binding site for repressor or activator proteins, which are produced by regulatory
genes, and control gene expression. For example, consider the following scenarios:
• operator region is bound with a repressor protein – RNA polymerase cannot move
downstream from the promoter region, inhibiting transcription of the gene.
• operator region is not bound with a repressor protein – RNA polymerase is free to move
downstream from the promoter region, allowing for the transcription of the gene as usual.
Apart from helping organisms conserve energy, gene regulation also ensures that cells
produce the appropriate proteins. For example, even though every somatic cell within the
human body is genetically identical and contains all the same genes, not all cells express the
same genes. For example, skin cells express and produce different proteins to heart cells.

How the trp operon works [Link]

O verview
The trp operon contains a series of genes that are involved in the production of the amino
acid tryptophan, which can subsequently be used in protein production.

T heory details
In certain species of bacteria such as Escherichia coli (E. coli), the trp operon regulates trp operon a series of genes
the expression of structural genes which code for proteins that are involved in the within certain species of bacteria
production of the amino acid tryptophan. The trp operon is composed of a series of that encode for the production of
the amino acid tryptophan
structural genes (trpE, trpD, trpC, trpB, and trpA) which are controlled by a common
promoter and operator. The entire trp operon is controlled by a regulatory gene located
upstream (Figure 2).
regulatory gene trp operon
DNA
template 3’ trpE trpD trpC trpB trpA 5’
strand
promoter promoter operator leader structural genes trailer
Figure 2 The trp operon involves a series of structural genes, a promoter, and an operator.

The amino acid tryptophan can be used as a building block for the formation of large and
complex proteins. However, because energy is a finite resource and should be conserved,
 2E THEORY 103

the expression of the structural genes coding for proteins involved in the production
of the amino acid tryptophan should only be expressed when required. Therefore, the
expression of the trp operon and the trp structural genes it contains depends on the levels
of tryptophan present within the cell:
• high levels of tryptophan – transcription of the trp structural genes is stopped in order
to prevent unnecessary production of tryptophan.
• low levels of tryptophan – transcription of the trp structural genes is started in order to
increase the amount of tryptophan available.
There are two different mechanisms of regulation that control the expression of trp structural
genes within the trp operon when tryptophan levels are high: repression and attenuation.
These two mechanisms have major differences in terms of the process of regulation, however,
they both function to regulate the expression of trp structural genes and therefore the
production of tryptophan.

Repression
In trp operon repression, to regulate the expression of the structural genes, the regulatory trp operon repression mechanism
gene for the trp operon is constantly expressed, producing a repressor protein. When high for gene regulation within the trp
levels of intracellular tryptophan are present, tryptophan binds to the repressor protein operon whereby repressor proteins
which induces a conformational change in the repressor protein, changing it into its active stop the initiation of transcription
when tryptophan levels are high
form. This allows the repressor protein to bind to the operator region (Figure 3). In this way,
the repressor protein can prevent transcription of the structural genes by blocking the path conformational change a change
in the three-dimensional shape of
of RNA polymerase, inhibiting unnecessary production of tryptophan.
macromolecules such as proteins
regulatory gene
promoter promoter operator leader trailer
DNA
template 3’ trpE trpD trpC trpB trpA 5’
strand
3’ transcription inhibited
5’
RNA
polymerase
active
tryptophan repressor

Figure 3 When tryptophan levels are high, the repressor protein binds to the operator and prevents transcription of
the trp operon.

Conversely, when tryptophan levels are low, there is an insufficient quantity of intracellular
tryptophan molecules available to bind consistently to the repressor protein (Figure 4).
This causes the repressor protein to become inactive and detach from the operator
region, allowing RNA polymerase to transcribe the trp structural genes so that the level
of tryptophan can increase. However, as tryptophan accumulates in the cell, it will once
again bind to the repressor protein, activating it and slowly inhibiting transcription of the
trp structural genes. Together, these mechanisms keep the amount of tryptophan available
within the cell at a relatively constant level to ensure that energy and resources are
expended appropriately.
promoter promoter
regulatory gene operator leader trailer trp operon attenuation
DNA mechanism for gene regulation
template 3’ trpE trpD trpC trpB trpA 5’ within the trp operon whereby the
strand premature ceasing of translation
3’ stops transcription when
RNA
5’ polymerase tryptophan levels are high
mRNA
inactive leader region the segment of
repressor 5’ DNA or mRNA that immediately
Figure 4 When tryptophan levels are low, the repressor protein detaches from the operator, allowing transcription of precedes the coding region. Also
the trp operon to occur. known as the leader segment or
leader sequence
Attenuation attenuator sequence part of the
The second mode of trp regulation within the trp operon is trp operon attenuation. leader region within the trp operon
Where the process of repression responds to the concentration of intracellular tryptophan, that allows for attenuation
attenuation occurs in response to the amount of tRNA-bound tryptophan. In attenuation, terminator hairpin a loop
transcription of the trp structural genes begins but is stopped early before any actual formed in mRNA in the presence
of tryptophan that ceases
proteins are made.
transcription of the trp operon
104 Chapter 2: Nucleic acids and proteins

There are two key things to keep in mind to understand how attenuation works. Step 1
First, transcription and translation occur simultaneously and very close to each other operator leader
within the cytoplasm in prokaryotes. This contrasts with eukaryotes, where transcription RNA
polymerase
occurs in the nucleus before the separate process of translation happens in the cytosol.
trpE
Second, the leader region that sits just before the five trp structural genes is pivotal to
attenuation. mRNA attenuator
It includes what is known as an attenuator sequence. The attenuator sequence is found at
ribosome
the end of the leader region and comes after two trp codons in a row. Step 2
When tryptophan levels are high in a cell (i.e. the cell does not want to waste energy trpE
making more tryptophan), the process of attenuation works as follows (Figure 5):
1 The processes of transcription and translation of the trp operon begin and occur
simultaneously.
Step 3
2 The ribosome involved in translation arrives at the two tryptophan codons in a row.
The tRNA-bound tryptophan that is present in the cell travels to the ribosome and is trpE
added to the protein that is being made by the ribosome.
terminator
3 This causes the mRNA molecule being read by the ribosome to fold in a specific way via hairpin
hydrogen bonds and form a terminator hairpin loop.
4 The folding of the terminator hairpin loop causes the mRNA molecule to separate from Step 4
the template DNA at the attenuator sequence. trpE
5 RNA polymerase detaches from the DNA, causing transcription to stop before any
separates
structural genes are transcribed. Without these structural genes, new tryptophan
cannot be synthesised.
Conversely, when tryptophan levels are low in a cell, the cell does not want the process of Step 5
attenuation to occur - it wants more tryptophan to be made. In this situation, the process
occurs differently (Figure 6):
trpE
1 The processes of transcription and translation of the trp operon begin and occur
simultaneously.
2 The ribosome involved in translation arrives at the two tryptophan codons in a row.
Due to there being no tRNA-bound tryptophan in the cell, when the ribosome involved
Figure 5 When tryptophan levels
in translation arrives at the attenuator sequence that codes for two tryptophan amino are high, attenuation causes the
acids it pauses. Meanwhile, the RNA polymerase involved in transcription continues termination of transcription and
along the DNA. translation of the trp operon.

3 This causes the mRNA molecule to fold in a specific way via hydrogen bonds and form
an antiterminator hairpin loop.
antiterminator hairpin a loop
4 The antiterminator hairpin loop does not cause the mRNA to separate from the
formed in mRNA when tryptophan
template strand at the attenuator sequence.
is not present that ensures the
5 RNA polymerase continues to read the DNA template strand, transcribing the transcription of the structural
structural genes for proteins involved in the synthesis of tryptophan and translation genes in the trp operon
can continue.

Step 1 Step 2 Step 3 Step 4 Step 5

operator leader
RNA
polymerase
trpE

trpE

trpE

trpE

trpE

mRNA attenuator remains

attached
antiterminator
ribosome *pause* hairpin

Figure 6 When tryptophan levels are low, the mRNA remains attached to RNA polymerase and transcription and
translation continue.

It is important to note that whilst repression and attenuation regulate the expression of
the trp operon, the processes are not perfect. A low level of transcription and translation
of the trp operon will occur regardless of the regulation. This is important as it ensures
that a cell is never completely without tryptophan. Still, repression and attenuation are
critical for the cell to function efficiently.
 2E QUESTIONS 105

Theory summary
Gene regulation involves the regulation of gene expression in order to prevent the
overproduction or underproduction of proteins. Genes can be classified into two types
- structural and regulatory genes - with regulatory genes controlling the expression of
structural genes. The trp operon provides two models of prokaryotic gene regulation.
Repression involves a repressor molecule binding to the operator region of the trp operon
when tryptophan levels are high, preventing transcription from taking place. Alternatively,
when tryptophan levels are low, the repressor molecule does not bind to the operator region.
Attenuation involves the premature ceasing of transcription of the trp operon when
tryptophan levels are high via the folding of the mRNA molecule into a terminator hairpin
loop. Conversely, when tryptophan levels are low the mRNA folds into an antiterminator
hairpin loop which doesn’t cause transcription to stop, meaning the structural genes of the
operon are transcribed (Table 2).
Table 2 Summary of trp operon

Tryptophan levels

Low High

• Regulatory gene is transcribed • Regulatory gene is transcribed

• Repressor protein is unbound to operator • Repressor protein is bound to operator
Repression
• Structural genes are transcribed • Structural genes are not transcribed
• Tryptophan is produced • No tryptophan is produced

• Regulatory gene is transcribed • Regulatory gene is transcribed

• Ribosome pauses, mRNA folds a specific way • Ribosome does not pause, mRNA folds a different way
Attenuation
• Transcription and translation continue • Transcription stops and translation ends
• Tryptophan is produced • No tryptophan is produced

Just like our structural genes represent students within a classroom, our regulatory genes represent
the teachers that control the classroom. In doing so, regulatory genes are responsible for controlling
the expression of structural genes. Without regulatory genes, our cells would not be able to control
the expression of genes, leading to the production of unnecessary proteins and the inability to
maintain stable energy levels.
Image: jittawit21/[Link]

2E QUESTIONS
Theory review questions

Question 1

Fill in the blanks with the following terms. Terms may be used multiple times or not at all.
• repressor proteins • RNA polymerase • regulatory genes • promoter
• structural proteins • DNA polymerase • structural genes • operator

_ are responsible for the production of proteins that are involved in the structure and functioning of an organism.
Conversely, _ are responsible for producing regulatory proteins such as _ which control the expression of
other genes. These proteins bind to the _ region of operons, preventing _ from transcribing the genes.

Question 2

Which one of the following statements is false?

A Regulatory genes can code for proteins that regulate the expression of structural genes.
B Operons consist of a series of genes controlled by a common promoter and operator.
C Organisms can conserve energy by preventing the transcription of genes.
D Regulatory genes do not contain a promoter region.
106 Chapter 2: Nucleic acids and proteins

Question 3

Label the parts of the following diagram.

DNA template strand 3’ trpE trpD trpC trpB trpA 5’

W X Y Z leader trailer

Question 4

Fill in the blanks with the following terms. Terms may be used multiple times or not at all.

• transcribed • translated • high

• preventing • allowing • low

Under repression, when tryptophan levels are _, the repressor protein detaches from the operator region,
_ trp structural genes to be _. Conversely, when tryptophan levels are _, tryptophan binds to
the repressor protein, allowing it to bind to the operator region, thereby _ transcription of the trp structural genes.
Under attenuation, when tryptophan levels are _ the mRNA molecule will detach from the DNA molecule causing
transcription and translation to stop, whereas when tryptophan levels are _ the mRNA molecule will stay attached.

SAC skills questions

Case study analysis

Use the following information to answer Questions 5–8.

Escherichia coli is a species of bacteria that uses glucose as its primary source of energy. However, when glucose is scarce,
E. coli must use alternate pathways to generate energy. One of these pathways involves the lac operon, which is a series
of genes that share a common promoter and operator involved in the production of enzymes responsible for the digestion
of lactose into glucose and galactose. By digesting lactose into glucose and galactose, glucose can be used in cellular
respiration to produce energy. However, the activation of the lac operon is tightly regulated so that E. coli can conserve energy.
Transcription of lac operon genes is only required when glucose levels are low and lactose levels are high.
When lactose levels are high, some lactose is converted into allolactose, which involves a slight change in its chemical
structure. Allolactose binds to and induces a 3D conformational change in the lac repressor protein, causing it to detach from
the DNA strand. This allows RNA polymerase to bind to the promoter region, initiating transcription of the lac operon and the
three structural proteins encoded by the structural genes are produced.
Conversely, when lactose levels are low, the repressor protein binds to the DNA strand, thereby preventing the transcription
of the lac operon. This allows for bacteria, such as E. coli, which have the lac operon, to conserve energy and only produce the
enzymes required for the digestion of lactose when required. The following diagram depicts the lac operon.

regulatory gene operator

DNA template strand 3’ lacZ lacY lacA 5’

promoter promoter structural genes

Question 5

The lac operon is expressed when

A lactose levels are high and glucose levels are high.
B lactose levels are high and glucose levels are low.
C lactose levels are low and glucose levels are high.
D lactose levels are low and glucose levels are low.

Question 6

Allolactose can
A bind to the repressor protein, causing it to detach from the DNA strand.
B bind to the promoter region, causing transcription of the lac operon.
C inhibit RNA polymerase, causing transcription of the lac operon.
D be directly used as an energy source in E. coli.
 2E QUESTIONS 107

Question 7

The lac repressor protein is produced by a

A regulatory gene and binds to the promoter region of the lac operon.
B structural gene and binds to the promoter region of the lac operon.
C regulatory gene and binds to the operator region of the lac operon.
D structural gene and binds to the operator region of the lac operon.

Question 8

When lactose levels are low and glucose levels are high
A the repressor protein inhibits the translation of the lac operon.
B RNA polymerase is actively transcribing the lac operon.
C glucose is being used as the primary source of energy.
D the production of the repressor protein is inhibited.

Exam-style questions
Within lesson

Use the following information to answer Questions 9 and 10.

Tryptophan is an amino acid that is produced by many bacteria. Genes that code for enzymes that produce tryptophan are
found on bacterial DNA and together are called the trp operon. When the binding of a trp repressor protein occurs, the process
of tryptophan production is inhibited. This process is illustrated in the following diagram.
trp repressor trp repressor binds to trp operon

production of tryptophan unable to proceed

DNA strand trp operon

Question 9 (1 MARK)

The trp repressor will bind to

A the promoter region.
B the operator region.
C pre-mRNA.
D tRNA.
Adapted from VCAA 2017 Northern Hemisphere Exam Section A Q27

Question 10 (1 MARK)

Which one of the following statements is correct concerning the trp operon?
A The trp repressor molecule is encoded by a structural gene.
B The trp operon is most active when trp concentration is high.
C Low concentrations of tryptophan increase the likelihood of trp repressor releasing from the DNA.
D High concentrations of RNA polymerase increase the likelihood of the regulation of the trp operon occurring via attenuation.
Adapted from VCAA 2017 Northern Hemisphere Exam Section A Q28

Multiple lessons

Question 11 (1 MARK)

Which one of the following statements regarding the structure of a gene in a eukaryotic cell is correct?
A Only prokaryotes exhibit gene regulation.
B An intron is transcribed but not translated.
C Structural genes encode for repressor proteins.
D A regulatory gene is always found downstream of the gene it controls.
108 Chapter 2: Nucleic acids and proteins

Question 12 (9 MARKS)

The following diagram outlines the processes involved in the production of proteins within a cell.

Process X pre-messenger RNA Process Y messenger RNA Process Z

protein
(pre-mRNA) (mRNA)
Structure P

a Identify and describe the purpose of Process X. (2 MARKS)

b Identify and describe the purpose of Process Z. (2 MARKS)
c Outline the key events that occur during Process Y. (3 MARKS)
d Provided that Structure P is composed of two different types of genes, describe the roles of each type of gene. (2 MARKS)

Question 13 (8 MARKS)

In certain species of bacteria such as Escherichia coli (E. coli), the trp operon regulates the expression of a series of structural
genes which code for proteins that are involved in the production of the amino acid tryptophan. These structural genes are all
controlled by a common promoter and operator. The entire trp operon is controlled by a regulatory gene located upstream.
The functioning of the trp operon can be regulated by two major processes - repression and attenuation.
regulatory gene

3’ trpE trpD trpC trpB trpA 5’

promoter promoter operator leader trailer

a Name a structural gene found in the trp operon. (1 MARK)
b Outline the role of the repressor protein in the trp operon. (2 MARKS)
c Describe the process of attenuation in the trp operon when tryptophan levels are high within a cell. (3 MARKS)
d Suggest why the controlled regulation of the trp operon is crucial for the survival of E. coli. (2 MARKS)
Adapted from VCAA 2017 Section A Q2

Key science skills and ethical understanding

Question 14 (9 MARKS)

Sinead and Gillian designed an experiment to test the effect of tryptophan concentration on the production of enzymes
involved in tryptophan synthesis, which are encoded for by trp structural genes found in the trp operon. The experimental
setup is shown in the following diagram. AU represents arbitrary units.

Sample 1 Sample 2 Sample 3 Sample 4

E. coli broth E. coli broth E. coli broth E. coli broth
0 AU 10 AU 20 AU 30 AU
tryptophan added tryptophan added tryptophan added tryptophan added

a Outline what an experimental control is and explain its purpose. Identify the sample which acts as an experimental control
in this experiment. (3 MARKS)
b Suggest one safety consideration that should be applied in this experiment. (1 MARK)
c State a possible hypothesis Sinead and Gillian were testing. (1 MARK)
d Sinead and Gillian forgot to label each test tube in their experiment. 3
Concentration of tryptophan
synthesising enzymes (AU)

i Identify the type of error that has occurred. (1 MARK)

ii 
In order to cover up their error, Sinead and Gillian decided to
2
falsify their results. Identify the bioethical concept which has
been violated by their actions. (1 MARK)
iii 
Considering the following graph, match each test tube to its 1
expected corresponding sample. Using your knowledge of the
trp operon, briefly explain your response. (2 MARKS)
0
Sample K Sample L Sample M Sample N
 2F THEORY 109

2F T HE PROTEIN SECRETORY
PATHWAY
When was the last time you sent a letter? You might find it hard to believe, but just a few decades
ago, before the rise of phones, laptops, and computers, to communicate with other people, you
had to send them a letter. You had to physically write a letter before packaging it into an envelope
and placing it within a post box. Afterwards, it would be whirled away by the post office who would
sort the letters, eventually delivering it to your target letterbox. Just like the post office, within your
cells there is a complex postal network involved in the transportation of substances around cells.
Who’s responsible for sorting and delivering the letters in your cells?

Image: Nils Versemann/[Link]

Lesson 2F
In this lesson you will explore how proteins are exported from cells through
the process of exocytosis and the various organelles involved.

Prerequisite knowledge Future applications

Year 11 Chapter 3
There are many different organelles involved in Enzymes are proteins responsible for increasing
the protein secretory pathway such as the rough the rate of reactions. They can often be exported
endoplasmic reticulum, the Golgi apparatus, out of cells for use elsewhere in the body.
mitochondria, and secretory vesicles.
Lesson 6A
Lesson 2D In order to export proteins from a cell, energy
Proteins are products of gene expression, which is required. Energy, in the form of ATP,
involves the processes of transcription and can be produced in large quantities by the
translation. Following the translation of proteins mitochondria for use within cells through the
at ribosomes, they can then be exported from process of aerobic cellular respiration.
the cell for use elsewhere.

Study design dot point

• the role of rough endoplasmic reticulum, Golgi apparatus, and associated vesicles in the export of proteins
from a cell via the protein secretory pathway

Key knowledge unit

The protein secretory pathway [Link]

The protein secretory pathway [Link]

O verview
The protein secretory pathway involves various different organelles that produce, fold,
modify, and package proteins, eventually exporting them from the cell via the process
of exocytosis.

T heory details
Many of the proteins produced by cells do not actually remain in the cell that produced ribosome an organelle made of
them. Instead, they are often exported out of the cell so that they can be used elsewhere in rRNA and protein that is the site
the body. For example, while peptide hormones such as insulin are produced by cells in the of protein synthesis. Can be free
pancreas, they are released into the bloodstream so that they can travel around the body in the cytosol or attached to the
rough endoplasmic reticulum
and reach target cells found in the liver.
exocytosis a type of bulk
In VCE Biology, you need to understand how a protein made at a ribosome can travel transport that moves large
through various organelles, and how it is eventually secreted via a process known as substances out of a cell
exocytosis into the extracellular environment.
110 Chapter 2: Nucleic acids and proteins

Exocytosis
Exocytosis is the process by which the contents of a vesicle are released from a cell. vesicle a small fluid-filled
It is a form of bulk transport, which allows for the movement of large substances such organelle enclosed in a
as proteins out of cells. Importantly, bulk transport is also a form of active transport, phospholipid membrane that
and therefore, the process of exocytosis requires the input of energy. The stages involved transports substances around
the cell
in exocytosis include:
bulk transport a type of active
1 A vesicle containing secretory products is transported to the plasma membrane. transport that uses vesicles to
2 The membrane of the vesicle fuses with the plasma membrane. move large molecules or groups of
molecules into or out of the cell
3 The secretory products are released from the cell into the extracellular environment.
active transport the movement
of molecules across a
outside the cell semipermeable membrane
secretory products requiring an energy input
3 secretory products
the substances inside a vesicle
2
that are being transported out of
the cell
plasma membrane
the phospholipid bilayer with
embedded proteins which
plasma membrane separates the intracellular
environment from the
vesicle
extracellular environment

1 cytoplasm

Figure 1 The process of exocytosis

The other form of bulk
Exocytosis is possible due to the fluid nature of the plasma membrane, which allows it to transport is called
fuse with the vesicle. The fluid nature of the plasma membrane refers to its ability to be endocytosis, and is simply
the opposite of exocytosis.
mobile and flexible – that is, the plasma membrane is not a static structure incapable of
Instead of exporting large
moving. Additionally, aside from the export of proteins, the process of exocytosis can also molecules, endocytosis
be used in the export of waste products to ensure that toxins do not build up within the involves the engulfment of
intracellular environment. molecules by extensions
of the plasma membrane,
The protein secretory pathway importing them into the cell.

While there are many different organelles involved in the protein secretory pathway, the
primary organelles involved include the ribosomes, the rough endoplasmic reticulum, rough endoplasmic reticulum (RER)
the Golgi apparatus, and transport and secretory vesicles. The roles of these organelles a membranous organelle shaped
are described in Table 1 and the protein secretory pathway is depicted in Figure 2. like a series of connected, flattened
cylinders that folds and transports
proteins via its attached ribosomes
1 ribosome 2 rough endoplasmic recticulum 5 secretory vesicle
Golgi apparatus an organelle
cell membrane made of flattened sacs of
membrane involved in modifying,
sorting, and packaging proteins.
cytoplasm protein Also known as the Golgi body or
Golgi complex

DNA mRNA

3 transport vesicle 4 Golgi apparatus

Figure 2 The protein secretory pathway

 2F THEORY 111

Table 1 The function of key organelles in the protein secretory pathway

Organelle Function Description

1 Ribosome Synthesises proteins The ribosomes are the sites of protein synthesis. They assemble polypeptide
chains from amino acids by translating mRNA.

2 Rough Folds and transports proteins If a protein is destined to be secreted, the ribosome synthesising it is usually
endoplasmic attached to the rough endoplasmic reticulum rather than being free in the
reticulum cytosol. The environment inside the rough endoplasmic reticulum allows for the
correct folding of the newly formed polypeptide chain before being passed to the
Golgi apparatus.

3 Transport vesicle Transports proteins A transport vesicle containing the protein buds off the rough endoplasmic reticulum
and travels to the Golgi apparatus. The vesicle fuses with the Golgi membrane and
releases the protein into its lumen.

4 Golgi apparatus Modifies and packages proteins Proteins can have chemical groups (e.g. sugar molecules) added or removed at the
Golgi apparatus, where they are often packaged into secretory vesicles for export or
released directly into the cytosol for use by the cell.

5 Secretory vesicle Transports proteins Secretory vesicles containing proteins for export bud off the Golgi apparatus and
travel through the cytoplasm, fusing with the plasma membrane. This releases
the proteins contained from within, into the extracellular environment through the
process of exocytosis.

It’s important to note that other organelles can also be involved in the protein secretory mitochondrion (pl. mitochondria)
pathway, but to a lesser extent. For example, mitochondria are the site of ATP synthesis a double-membrane-bound
and provide the energy required to move vesicles around the cell and modify the proteins organelle that is the site of the
produced. The plasma membrane is another organelle involved, fusing with vesicles and second and third stages of aerobic
cellular respiration
facilitating the release of proteins from the cell. Additionally, the nucleus stores DNA,
which contains the instructions for mRNA and therefore downstream protein synthesis.
Golgi apparatus

mitochondrion
RER

nuclear envelope

nucleolus

Figure 3 An electron micrograph depicting the rough endoplasmic reticulum, a mitochondrion, and the nucleus
Figure 4 An electron micrograph
depicting the Golgi apparatus
Theory summary
Proteins are produced at ribosomes, folded in the rough endoplasmic reticulum, transported
via transport vesicles to the Golgi apparatus, where they are modified and packaged
into secretory vesicles, and then subsequently exported from the cell via the process of
exocytosis. Exocytosis is a form of bulk transport, involving the fusion of a secretory vesicle
with the plasma membrane, releasing its contents into the extracellular environment.

The mastermind behind the cellular post office within your cells is the Golgi apparatus. After receiving
proteins synthesised by the ribosomes, which are transported there from the rough endoplasmic
reticulum via transport vesicles, it modifies the proteins and packages them into secretory vesicles for
export. From there, the proteins can then be transported to their final destination. However, the only
difference between the Golgi apparatus and your local post office is that the Golgi apparatus will never
lose a single protein, while you might not be able to say the same for your local post office.

Image: Kateryna Kon/[Link]

112 Chapter 2: Nucleic acids and proteins

2F QUESTIONS
Theory review questions

Question 1

Label the parts of the following diagram.

D E F

DNA mRNA

Question 2

Match the organelle to its description.

Organelle Description
• ribosome I _ can have ribosomes attached to it, facilitating the folding of proteins
• mitochondrion II _ a fluid-filled sac containing substances such as proteins for export
• Golgi apparatus III _ the site of ATP production via aerobic cellular respiration
• secretory vesicle IV _ involved in the modification and packaging of proteins
• endoplasmic reticulum V _ the site of protein synthesis

Question 3

Fill in the blanks with the following terms. Terms may be used multiple times or not at all.
• into • intracellular
• out of • extracellular
• energy • secretory vesicle
• glucose

Exocytosis is a form of bulk transport, involving the movement of large substances such as proteins _ a cell. Because
it is also a form of active transport, the direct input of _ is required. The process of exocytosis involves the fusion of a
_ to the plasma membrane, releasing its contents into the _ environment.

Question 4

Which one of the following processes correctly Process L

Process K
depicts the process of exocytosis?
Process J
A Process J
B Process K
C Process L

Image: Soleil Nordic/[Link]

 2F QUESTIONS 113

SAC skills questions

Case study analysis

Use the following information to answer Questions 5–8.

Endocytosis involves the bulk transport of large molecules or groups of molecules into cells. It is crucial to the functioning of
cells, because many of the molecules that cells need to survive are too large to travel across the plasma membrane through
alternative methods such as protein channels. Once inside the cell, these substances can be used for metabolic processes
or structural elements of the cell. Endocytosis can also be an effective defence mechanism. Certain immune cells can engulf
invading microorganisms or toxins and destroy them through the fusion of the vesicle with a lysosome. The stages involved in
endocytosis include:
1. The folding of the plasma membrane inwards to form a cavity that fills with extracellular fluid and the target molecules.
2. The entrapment of the target molecules through the continued folding of the plasma membrane back on itself until the
two ends of the membrane meet and fuse, trapping the target molecules inside the vesicle.
3. The budding of the vesicle off the plasma membrane and into the cell, where it can be transported to the appropriate
cellular location.

outside the cell

1 2

3
plasma membrane
vesicle

cytoplasm

There are also two subcategories of endocytosis – phagocytosis and pinocytosis. While phagocytosis involves the engulfment
of solid material, pinocytosis involves the process of engulfing molecules that are dissolved in the extracellular fluid.

Question 5

Endocytosis involves the

A movement of substances into a cell.
B movement of substances out of a cell.

Question 6

The molecules entering a cell via endocytosis are

A enclosed within a vesicle.
B not enclosed within a vesicle.

Question 7

Phagocytosis involves the movement of

A solid material out of a cell.
B solid material into a cell.
C liquids out of a cell.
D liquids into a cell.
114 Chapter 2: Nucleic acids and proteins

Question 8

Proteins found in the extracellular environment would have been produced at

A the smooth endoplasmic reticulum.
B the nucleus.
C a ribosome.
D a vesicle.

Exam-style questions
Within lesson

Question 9 (1 MARK)

All specialised cells that secrete protein molecules

A have minimal ribosomes.
B contain numerous vacuoles.
C do not have a plasma membrane.
D have an extensive rough endoplasmic reticulum.

Question 10 (1 MARK)

Which one of the following statements is false?

A Protein export involves vesicular transport of proteins out of the cell.
B Protein export involves the fusion of vesicles with the plasma membrane.
C Protein export involves specialised vesicles transporting specific proteins.
D Protein export involves sorting and modification of proteins at the Golgi apparatus.

Question 11 (1 MARK)

Gastrin is a peptide hormone that is released from cells in the stomach, duodenum, and pancreas. It aids digestion by
stimulating the secretion of gastric acid by cells that line the stomach. One likely pathway for the production of gastrin in
stomach cells could be
A nucleus  ribosome  rough endoplasmic reticulum  vesicle  Golgi apparatus
B nucleus  ribosome  Golgi apparatus  vesicle  rough endoplasmic reticulum
C nucleus  vesicle  rough endoplasmic reticulum  Golgi apparatus  ribosome
D nucleus  Golgi apparatus  rough endoplasmic reticulum  vesicle

Use the following information to answer Questions 12 and 13.

The following diagram shows the structure of certain organelles within a cell.

Image: Tefi/[Link]
 2F QUESTIONS 115

Question 12 (1 MARK)

Organelle Y
A folds and dispatches protein.
B is involved in the production of lipids.
C contains numerous vesicles for protein transport.
D synthesises most of the ATP molecules required for active transport.
Adapted from VCAA 2018 Northern Hemisphere Exam Section A Q1

Question 13 (1 MARK)

Organelle X
A is only made of protein.
B contains many phospholipids.
C is the site of protein modification.
D can also exist in the cytosol, unattached to other organelles.

Question 14 (1 MARK)

B lymphocytes are a type of immune cell that produce large amounts of antibodies. Antibodies are proteins that bind to and
deactivate foreign substances like bacteria or toxins. B lymphocytes
A undertake large amounts of endocytosis.
B have extensive networks of endoplasmic reticulum.
C must use facilitated diffusion to transport antibodies out of the cell.
D do not have a Golgi apparatus, as they are specialised to make one type of protein.
Adapted from VCAA 2015 Section B Q5

Question 15 (6 MARKS)

In animal cells, tight junctions are multi-protein complexes that mediate cell-to-cell adhesion and regulate transport through
the extracellular matrix. Proteins that form these complexes are made within the cell.
a Identify the cellular organelle where the primary structure of these proteins is made. (1 MARK)
b Outline the secretory pathway of these proteins. (3 MARKS)
c Draw a labelled diagram to illustrate the exocytosis of these complex proteins from a cell. (2 MARKS)
Adapted from VCAA 2016 Section A Q7

Multiple lessons

Question 16 (5 MARKS)

Neurotransmitters are signalling molecules used to communicate between neurons and certain tissues of the body.
One type of neurotransmitter is called acetylcholine, which can be released from the ends of neurons via the process of
exocytosis. From there, it can diffuse across the synaptic cleft and bind to receptors on another neuron or tissue type.
The receptors that interact with acetylcholine are proteins embedded within the plasma membrane. The following
diagram shows the release of acetylcholine at the junction between a neuron and a muscle cell.

axon of neuron

vesicle containing acetylcholine

synaptic cleft
membrane of muscle cell

acetylcholine receptor
116 Chapter 2: Nucleic acids and proteins

a Outline the events that would occur at a ribosome in the synthesis of an acetylcholine receptor. (3 MARKS)
b Describe the role of mRNA in the synthesis of the acetylcholine receptor. (1 MARK)
c Identify the organelle where the acetylcholine receptor would be packaged into secretory vesicles. (1 MARK)
Adapted from VCAA 2017 Section A Q21

Key science skills and ethical understanding

Question 17 (8 MARKS)

Alzheimer’s disease is a progressive brain disorder that causes problems with memory, thinking, and behaviour. It is
characterised by the build-up of a protein called beta-amyloid around neurons as individuals grow older. A group of scientists
hypothesised that increased endocytosis, which involves the uptake of substances via a vesicle, by neurons of amyloid
precursor protein (APP) may contribute to the accumulation of beta-amyloid proteins. The following diagram shows the
process of endocytosis.

Image: Aldona Griskeviciene/[Link]

The scientists cultured neurons from mice and aged them in vitro. Mouse neurons undergo three developmental stages: they
develop axons and dendrites after a week, reach peak maturation at 21 days, and exhibit aging at 28 days. The researchers
compared 21-day-old neurons with 28-day-old ones for differences in APP endocytosis and beta-amyloid levels.
a Identify the independent and dependent variables of this experiment. (2 MARKS)
b The scientists found that aged neurons had 50% more beta-amyloid proteins, double the amount of APP endocytosis, and
larger vesicles.
i Do these results support or disprove the scientist’s hypothesis? Justify your response. (1 MARK)
ii Explain why the size of vesicles may be significant. (1 MARK)
iii Identify and explain one limitation of these results. (2 MARKS)
c Describe the relevance of the bioethical concept of non-maleficence to the experimental scenario. (2 MARKS)
 Nucleic acids Protein synthesis Proteins

functional protein
• DNA stores genetic information • Proteins have a diverse range of functions
• mRNA transports genetic information to the ribosomes 1. transcription (e.g. structural, enzyme, motor, transport, signalling, storage).

page
• tRNA carries specific amino acids to ribosomes for translation

Rotate
amino acid Amino acid structure
• rRNA forms ribosomes that synthesise proteins
pre-mRNA central carbon group
DNA RNA amino group H carboxyl group
deoxyribonucleic acid ribonucleic acid polypeptide
chain H O
double-stranded single-stranded N C C
H O H
mature A A A
A
mRNA G R
G C C
A A A
G A
C G G
R-group
2. post-transcriptional
modification ribosome Protein structure
G C G Primary structure involves the sequence of amino acids.
CHAPTER 2 SUMMARY

3. translation
C G C Arg
Met Asp Val Ile Lys
A T A Gly Val Asp Leu
thymine uracil
T A U Gene regulation – trp operon
G C G When tryptophan levels are high, regulation can occur via repression Ala Leu Ser Leu Ala
Phe Gln
or attenuation. In repression, tryptophan binds to the repressor Lys Leu
which allows the repressor to bind to the operator to inhibit Secondary structure involves folding into alpha-helices,
A T U transcription of trp structural genes, thereby conserving energy. beta-pleated sheets, and random coils.
Conversely, when tryptophan levels are low, the repressor is released
C G G
from the operator, allowing transcription to occur.
G C C regulatory
HOCH HOCH promoter gene promoter operator leader trailer
O OH O OH α-helix β-pleated sheets random coil
2 2
REVIEW

H H H H H H
H H 3’ trpE trpD trpC trpB trpA 5’
OH H OH OH 3’ transcription inhibited Tertiary structure involves
deoxyribose sugar ribose sugar 5’ the functional 3D structure
active
repressor of a protein.
Nucleotide structure
tryptophan RNA
polymerase
In attenuation, high tryptophan
phosphate leader levels cause the mRNA molecule
5’ nitrogenous RNA polymerase being transcribed to fold into a
base terminator loop and detach from the Quaternary structure
1’ trpE
DNA which stops transcription and involves two or more
five-carbon translation. When tryptophan levels polypeptide chains
sugar are low, the mRNA molecule folds joining together.
terminator
hairpin into an antiterminator loop and
3’ ribosome remains attached, ultimately
allowing tryptophan to be produced.
117
118 Chapter 2: Nucleic acids and proteins

CHAPTER 2 SAC PRACTICE

SAC skills covered in this section:
✔ Case study analysis ✔ Data analysis ✔ Bioethical deep dive

INSULIN (24 MARKS)

Hormones
There are many different mechanisms that exist within the body to help maintain a stable internal environment
so that the body functions correctly. Factors which must be kept relatively constant include blood glucose levels,
pH, temperature, the concentration of ions such as sodium and potassium, and many more. One of the mechanisms
that the body can use to maintain this stable internal environment includes the use of hormones, which are cell
signalling molecules.
Hormones are commonly composed of protein and can be used to transmit signals from one part of the body to
another. For example, hormones are often released by cells into the bloodstream, where they travel to distant target
cells. On those distant target cells are receptors, which are also typically composed of protein, with a complementary
shape to the hormone. When the hormone binds to the receptor, specific cellular pathways are activated. The following
diagram illustrates the binding of a hormone to its receptor.

Key

hormone
blood vessel
direction of
movement

source
cell

target cell

receptor

1 Describe the function of a hormone. (1 MARK)

2 Identify two factors that should be kept relatively constant within the body. (2 MARKS)
3 Explain the significance of shape in the role of hormones and their receptors. (1 MARK)

Blood glucose levels

Blood glucose levels are one of the many factors that must be kept at a relatively constant level within the body.
Typically, normal blood glucose levels range from 4.0–7.8 mmol/L, with the average level being around 5.0 mmol/L.
When blood glucose levels deviate from their normal value, the body releases certain hormones in order to reduce or
increase the amount of glucose within the blood. For example, if blood glucose levels rise above the normal value, then
hormones will be released to reduce blood glucose levels. Conversely, if blood glucose levels fall below the normal value,
then hormones will be released to increase blood glucose levels. The two hormones which regulate this process are
known as:
• insulin, which reduces blood glucose levels by increasing the uptake of glucose by cells
• glucagon, which increases blood glucose levels by increasing the breakdown of glycogen into glucose.
 REVIEW 119

increased uptake
release of insulin of glucose
by cells dec
reas
high e
blood glucose blood glucose
levels low se levels
increased breakdown increa
release of glucagon of glycogen
into glucose

Both insulin and glucagon are hormones composed of protein and, when required, are exported from the cell that
produced them. Insulin is produced by beta cells in the pancreas, whereas glucagon is produced by alpha cells in the
pancreas. Both hormones play a crucial role in regulating blood glucose levels, and ensure that they remain relatively
constant within the body.
4 Name the monomer that makes up insulin. (1 MARK)
5 There are many stages involved in the production of insulin. Outline the process that occurs in the cytosol which
directly leads to the production of insulin. (3 MARKS)
6 Outline the pathway insulin would take to be exported out of a cell after its production. (3 MARKS)
7 Describe the post-transcriptional modifications that would occur to a strand of pre-mRNA coding
for insulin. (3 MARKS)
8 Describe the difference between structural and regulatory genes. (1 MARK)

Insulin
When insulin binds to receptors located on the cell surface, a series of events are initiated that lead to the insertion of
glucose channels within the plasma membrane. These glucose channels are capable of transporting glucose from the
extracellular environment into the cell, thereby increasing cellular uptake of glucose and decreasing blood glucose levels.
The following diagram depicts the binding of insulin to its receptor, which increases the number of glucose channels.

glucose
molecules
glucose-specific
carrier molecules
insulin receptor sent to plasma
insulin membrane
molecules
bind initiates a series of reactions

insulin
molecules

extracellular environment intracellular environment

9 Describe the events that would occur if blood glucose levels increased. (2 MARKS)
10 Suggest a reason other than diabetes why blood glucose levels may rise. (1 MARK)
11 Insulin is composed of two polypeptide chains, an alpha chain and a beta chain. Identify the level of protein structure
that insulin displays. Justify your response. (2 MARKS)
12 Bacteria, humans, pigs, and cows all produce insulin through the same pathway of protein synthesis. Explain why
this is possible. (1 MARK)
120 Chapter 2: Nucleic acids and proteins

Diabetes
Malfunctions can arise in the regulation of blood glucose levels. When this occurs, individuals can develop diabetes,
which can be categorised into:
• type 1 diabetes, which occurs when individuals do not produce enough insulin
• type 2 diabetes, which occurs when insulin receptors become resistant to insulin, potentially due to changes in
shape, and can no longer adequately bind to it.

The percentage of individuals between 20–79 who have been diagnosed with either type 1 or type 2 diabetes

No data 0% 2% 4% 6% 8% 10% 12.5% 15% 17.5% 20% >25%

Source: International Diabetes Federation, Diabetes Atlas

Due to their inability to effectively control blood glucose levels, diabetics often require daily injections of insulin to help
manage their blood glucose levels. While insulin used to be harvested from other animals, it is now commonly made
artificially. However, in many countries, there are significant barriers in terms of the availability and accessibility of
insulin. For example, in America, it was reported that in 2018, the average price of insulin per unit was nearly $100.
In Australia, however, the average price per unit of insulin in 2018 was reported to be under $10. This significant
difference in price has largely been attributed to the power that large pharmaceutical companies hold, where they
effectively hold a monopoly over the production and distribution of insulin.
13 Based on the image, what is the percentage of individuals diagnosed with either type 1 or type 2 diabetes
in Australia? (1 MARK)
14 With reference to the bioethical concept of justice, suggest whether pharmaceutical companies should decrease
their pricing of insulin. (2 MARKS)
 REVIEW 121

CHAPTER 2 EXAM PRACTICE 60

min

Section A (16 MARKS)

Question 1 (1 MARK)

The genetic code specifies 20 different amino acids that can form proteins. Which one of the following explains the
functional diversity of proteins?
A 20 amino acids allow for a large number of different combinations within a polypeptide.
B The processes of transcription and translation determine a protein’s function.
C Nucleic acids are synthesised frequently within a cell.
D Proteins cannot be inhibited or broken down.
Adapted from VCAA 2017 Sample Exam Section A Q1

Use the following information to answer Questions 2 and 3.

The following diagram depicts a molecule crucial to the process of protein synthesis.
anticodon

Structure X

Structure Y

Question 2 (1 MARK)

Structure X is known as
A DNA.
B tRNA.
C rRNA.
D mRNA.

Question 3 (1 MARK)

Structure Y is a molecular monomer of

A DNA.
B RNA.
C lipids.
D proteins.
Adapted from VCAA 2012 Exam 1 Section A Q4

Question 4 (1 MARK)

The proteome is
A the set of proteins undergoing the transcription process in an organism.
B all proteins, carbohydrates, lipids, and nucleic acids in an organism.
C the entire set of proteins expressed by an organism.
D the most common protein in an organism.
Adapted from VCAA 2011 Exam 1 Section A Q1
122 Chapter 2: Nucleic acids and proteins

Question 5 (1 MARK)

A particular DNA double helix is 100 nucleotide pairs long and contains 25 adenine bases. The number of uracil bases in
this DNA double helix would be
A 0.
B 25.
C 75.
D 100.
Adapted from VCAA 2012 Exam 1 Section A Q5

Question 6 (1 MARK)

Which one of the following events does not occur during repression when tryptophan levels are high in a cell?
A Tryptophan binds to the trp repressor.
B Enzymes that produce tryptophan are produced.
C The transcription factor is inhibited from binding to the promoter.
D A repressor protein is bound to the operator region of the trp operon.

Question 7 (1 MARK)

Which of the following statements about gene regulation is false?

A Repressor proteins bind to the operator region.
B Structural genes code for proteins that are not involved in gene regulation.
C Regulatory genes control the expression of structural genes using transcription factors.
D Transcription factors are proteins that control gene expression at the transcription and translation stages.
Adapted from VCAA 2016 Section A Q32

Question 8 (1 MARK)

Different cells within an organism have different proteins. In some cases, different proteins can be coded for by the same
gene. One gene can code for several proteins because
A of alternative splicing.
B there are 20 amino acids.
C of the specificity of the genetic code.
D genes can alter their sequence during transcription.
Adapted from VCAA 2017 Section B Q1c

Question 9 (1 MARK)

Proteins are not part of the structure of

A the plasma membrane.
B messenger RNA.
C haemoglobin.
D antibodies.
Adapted from VCAA 2012 Exam 1 Section A Q8

Question 10 (1 MARK)

Which one of the following statements about the structure of a eukaryotic gene is false?
A Introns undergo the transcription process.
B Exons contain the protein-coding sequence.
C A promoter region is found upstream of a gene.
D Alternative splicing results in different sets of introns being translated.
Adapted from VCAA 2017 Sample Exam Section A Q6
 REVIEW 123

Use the following information to answer Questions 11 and 12.

The following diagram shows one of the major biomacromolecules in living things.

Question 11 (1 MARK)

The monomers comprising the macromolecule vary in their

A sugar-phosphate backbones.
B nitrogen-containing bases.
C phosphate groups.
D sugar groups.
Adapted from VCAA 2016 Section A Q3

Question 12 (1 MARK)

A portion of the coding strand of a macromolecule has the sequence -TACGTGCTTGAT-. The mRNA strand produced
from this coding strand during transcription would be
A -TACGTGCTTGAT-
B -ATGCACGAACTA-
C -AUGCACGAACUA-
D -UACGUGCUUGAU-
Adapted from VCAA 2016 Section A Q4

Question 13 (1 MARK)

Bacteria can have a gene from another species inserted (e.g. a human gene), and they can be cultured to produce a given
protein in large quantities. It is possible to introduce a human gene into bacteria because the DNA code is
A universal.
B redundant.
C degenerate.
D non-overlapping.
Adapted from VCAA 2013 Section A Q36
124 Chapter 2: Nucleic acids and proteins

Use the following information to answer Questions 14 and 15.

The following diagram represents part of a DNA molecule.

5’ V W
3’ X
Y

3’
5’

Question 14 (1 MARK)

A hydrogen bond is formed between sub-units

A X and Y.
B Y and Z.
C V and W.
D X and Y and Y and Z.
Adapted from VCAA 2015 Section A Q3

Question 15 (1 MARK)

Which one of the following statements is false?

A Sub-unit V could be adenine.
B Sub-unit Y is a deoxyribose sugar.
C Sub-unit X is the same in every DNA nucleotide.
D This diagram displays the deoxyribose sugar-phosphate backbone.

Question 16 (1 MARK)

The following codon table can be used to determine the sequence of amino acids coded for by a nucleotide sequence.

1st position 2nd position 3rd position

(5’ end) U C A G (3’ end)

U Phe Ser Tyr Cys U

Phe Ser Tyr Cys C

Leu Ser STOP STOP A

Leu Ser STOP Trp G

C Leu Pro His Arg U

Leu Pro His Arg C

Leu Pro Gln Arg A

Leu Pro Gln Arg G

A Ile Thr Asn Ser U

Ile Thr Asn Ser C

Ile Thr Lys Arg A

Met Thr Lys Arg G

B Val Ala Asp Gly U

Val Ala Asp Gly C

Val Ala Glu Gly A

Val Ala Glu Gly G

 REVIEW 125

The following nucleotide sequence is found on the template strand at a particular site in the genome.
GCT TTA CGG TTA TAT ACC
Due to a DNA change, the bolded nucleotide in this sequence was changed from a T to a G. What would be the result of
this DNA change?
A The peptide chain would be shortened.
B The fifth amino acid would change from tyr to cys.
C The sixth amino acid would change from cys to STOP.
D There would be no change in the amino acid sequence.

Section B (25 MARKS)

Question 17 (6 MARKS)

The following diagrams represent examples of the four levels of protein structure. Note that the diagrams are not to scale.

W X

Y Z

a Identify the level of protein structure represented in the diagrams W, X, Y, and Z. (2 MARKS)
b Describe the functional significance of Z. (1 MARK)
c Outline the process that occurs at a ribosome which leads to the production of Y. (3 MARKS)

Question 18 (6 MARKS)

Diphtheria is a serious bacterial infection caused by the bacterium Corynebacterium ribosome

Molecule X
diphtheriae, with symptoms including difficulty breathing, heart failure, paralysis
and in severe cases, death. It achieves this through the production of toxins which
kill healthy tissues within the respiratory tract, causing the buildup of dead cells in
what is known as a pseudomembrane, eventually blocking the airways. One way
direction of ribosome movement
diphtheria toxin works is by stopping the movement of ribosomes along a certain
molecule. This molecule has been labelled as Molecule X in the following diagram.
a Identify Molecule X and describe its function. (2 MARKS)
b Outline the process involved in the production of Molecule X. (3 MARKS)
c State the cellular process which diphtheria toxin is thought to interfere with. (1 MARK)
126 Chapter 2: Nucleic acids and proteins

Question 19 (6 MARKS)

Human insulin is a macromolecule composed of two polypeptide chains. The chains are connected by disulphide bonds.
a Identify the monomers that make up insulin. (1 MARK)
b Describe the structure of the monomers of insulin, and explain how they differ from the monomers of DNA. (2 MARKS)
c Insulin found in other animals differs from human insulin. The following table compares the differences seen in the
primary structure of human, cow, pig, and sheep insulin.

Amino acid position number within

Alpha chain Beta chain

- 8 - 9 - 10 - - 30 -

human - thr - ser- ile - thr

cow - ala - ser - val - ala

pig - thr - ser - ile - ala

sheep - ala - gly - val - ala

i 
Humans with diabetes take insulin injections to help control their blood glucose levels. If no human insulin is
available, it is possible to use similar insulin from another animal. According to the table, explain which animal’s
insulin structure is the least similar to human insulin. (1 MARK)
ii 
Do cows, pigs, and sheep have an identical sequence of nucleotides at amino acid position 30 in the beta
chain? Justify your response. (2 MARKS)
Adapted from VCAA 2012 Exam 1 Section B Q3

Question 20 (7 MARKS)

The trp operon was originally identified in Escherichia coli. The trp operon has five structural genes: trpE, trpD, trpC, trpB,
and trpA. These genes code for proteins which help a cell produce the amino acid tryptophan. The diagram shows the
order of the genes found in the trp operon. The dotted lines represent the DNA nucleotides between the genes.

… … …
X promoter Y leader trpE trpD trpC trpB trpA trailer …
… …

a What is an operon? (1 MARK)

b Identify regions X and Y. (2 MARKS)
c Identify the region to which RNA polymerase binds to. (1 MARK)
d Explain how the trp operon functions when tryptophan levels are low. (3 MARKS)
Adapted from VCAA 2017 Section A Q2