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UNIT 3: AREA OF STUDY 1 – MOLECULES OF LIFE.........................................................................................2

CHAPTER 1 – THE CHEMICAL NATURE OF CELLS..........................................................................................2
LIFE AT THE MOLECULAR LEVEL..........................................................................................................................2
The composition of living organisms..............................................................................................................3
BIOLOGICALLY IMPORTANT INORGANIC MOLECULES..............................................................................................4
ORGANIC MOLECULES........................................................................................................................................5
BIOLOGICAL MEMBRANES................................................................................................................................... 6
CHAPTER 2 – ENZYMES AND OTHER BIOMOLECULES..................................................................................8
ENZYMES AND CELLULAR PROCESSES.................................................................................................................8
Metabolism.....................................................................................................................................................8
Enzymes are biological catalysts...................................................................................................................8
Activation energy and enzymes.....................................................................................................................9
Factors affecting enzyme activity...................................................................................................................9
Regulating enzyme affinity...........................................................................................................................10
Enzymes and disease..................................................................................................................................10
Anabolic and catabolic reactions.................................................................................................................10
BIOMOLECULES – SYNTHESIS AND TRANSPORT...................................................................................................11
Controlling cell functions – nucleus..............................................................................................................11
Assembling proteins - ribosomes.................................................................................................................11
Transporting and processing – endoplasmic reticulum...............................................................................11
Packaging for export – Golgi apparatus.......................................................................................................11
Storage of biomolecules..............................................................................................................................12
Removing wastes and debris.......................................................................................................................12
CHAPTER 3 – ENERGY TRANSFORMATIONS.................................................................................................12
LIFE NEEDS ENERGY.........................................................................................................................................12
What is energy?...........................................................................................................................................12
Exergonic and endergonic reactions...........................................................................................................13
ATP – ENERGY FROM GLUCOSE........................................................................................................................13
ADP/ATP cycle.............................................................................................................................................13
Harvesting the energy from glucose............................................................................................................13
Glycolysis: anaerobic, occurs in the cytosol................................................................................................14
Krebs cycle: anaerobic, occurs in the mitochondrion..................................................................................14
Electron transport: aerobic, occurs in the mitochondrion............................................................................14
Fermentation: anaerobic, occurs in the cytosol...........................................................................................14
GETTING GLUCOSE...........................................................................................................................................14
Photosynthesis – converting solar energy...................................................................................................14
Factors affecting the rate of photosynthesis................................................................................................15
Chemosynthesis...........................................................................................................................................15
STORING ENERGY.............................................................................................................................................15
Energy reserves in flowering plants.............................................................................................................15
Energy storage in mammals........................................................................................................................16
Energy balance in animals...........................................................................................................................16
CHAPTER 4 – DNA, PROTEINS AND PROTEOMES.........................................................................................16
LIFE HAS A COMMON ORIGIN..............................................................................................................................16
DNA – THE MATTER OF INHERITANCE.................................................................................................................16
DEOXYRIBONUCLEIC ACID (DNA)......................................................................................................................16
Nucleotides – building blocks of DNA..........................................................................................................17
DNA is a double-stranded helix...................................................................................................................17
RIBONUCLEIC ACID (RNA)................................................................................................................................ 18
SYNTHESIS OF POLYPEPTIDES...........................................................................................................................18
PROTEIN FORMATION........................................................................................................................................19
PROTEIN STRUCTURE....................................................................................................................................... 19
THE ROLE OF PROTEINS IN CELLS......................................................................................................................19
Proteomics........................................................................................................................................................20

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UNIT 3: AREA OF STUDY 1 – MOLECULES OF LIFE

CHAPTER 1 – THE CHEMICAL NATURE OF CELLS

Life at the Molecular Level

 All organisms are composed of cells, the basic functional unit of all organisms
 The Cell Theory is one of the fundamental principles of biology
 Cells share many similarities but their differences are related to their particular
roles in organisms

Cells are the functional units of life

 Cells perform similar basic processes and many also carry out highly specialised
functions
 Activities of cells require considerable energy
 Processes are catalyzed by enzymes and are precisely regulated

Cell structure
 No such thing as a typical cell as they are specialised for different purposes and
their structures reflect those purposes
 Features shared by all cells – cytoplasm
– plasma membrane
– DNA (deoxyribonucleic acid)
 Fundamentally different types of cells – prokaryotes and eukaryotes
 Prokaryotes are small and lack membrane-bound organelles- they contain a
single circular DNA chromosome and their cell wall is composed of murein
 Eukaryotes have an internal membrane system forming the nuclear membrane
and many other organelles
 Organelles – sub-cellular structures involved in specific functions of the cell

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The composition of living organisms

 Similarities between different organisms increase when you look more closely at
cells and the atoms and molecules they are composed of
 Four elements – C, H, O and N – make up 9% of organisms by weight

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 Similarities of organisms at molecular level points to common origin

 Atom – basic unit of all matter
 Element – substance consisting of only one kind of atom
 Molecule – two or more atoms (same/different) chemically bonded together
 Compound – molecule containing more than one type of atom
 Organic compound – energy-rich compound composed of C and H produced by
living organisms
 Inorganic compound – energy-poor compound found in living/non-living things

Biologically Important Inorganic Molecules

Water – the medium of life

 Living organisms are usually 70-90% water
 Chemical reactions in living organisms take place in a watery medium
 Biologically important properties of water include:
– solvent properties
– high heat of vaporisation
– high heat capacity
– cohesion
– surface tension
 Solvent properties – dissolves large number of compounds and can ionize ionic
compounds and excludes non-polar molecules
 High heat of vaporisation – requires large amounts of heat to evaporate
 High heat capacity – absorbs great deal of heat with little increase in
temperature
 Cohesion – strong tendency of water molecules to stick together
 Surface tension – produced by strength of bonds between water molecules
 pH – concentration of H+ molecules/L of solution and is a measure of the acidity
or alkalinity of a solution

Oxygen and carbon dioxide

 Oxygen – needed to release energy from food molecules, therefore constant
supply necessary to maintain activity of cells
 Oxygen not very soluble in water so organisms that obtain oxygen from water are
often small, flat and relatively inactive
 Gills allow larger aquatic animals to sufficiently extract oxygen from water
 Carbon dioxide – main source of carbon for production of organic molecules
 Recycling of carbon in ecosystems therefore important to survival of organisms

Nitrogen
 Nitrogen – component of all proteins, therefore required by organisms in large
amounts
 Nitrogen fixing – certain bacteria/cyanobacteria convert atmospheric nitrogen
into compounds usable by plants

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Minerals
 Mineral salts – naturally occurring inorganic compounds produced by the
weathering of rocks
 Mineral ions – found in cytosol of cells, structural components and molecules of
many enzymes and vitamins
 May be incorporated into other important organic compounds in cells

Organic Molecules

 Four main types of organic molecules:

– carbohydrates
– lipids
– proteins
– nucleic acids

Carbohydrates
 Most abundant organic compounds in nature
 Carbohydrates:
– energy source/storage
– structural components
– part of both DNA and RNA
– form glycoproteins and glycolipids as in cell membranes
 Composed of C, H and O
 Monosaccharide – basic subunits of carbohydrates, meaning “single sugar”
 Disaccharide – two sugars joined together, meaning “two sugars”
 Polysaccharide – many sugars joined together, meaning “many sugars”

Nucleic acid
 Genetic material of all organisms and determine inherited features of organism
 Nucleotide – basic subunit composed of a sugar, a phosphate and a base
 DNA – carries ‘instructions’ required to assemble proteins from amino acids
 RNA – plays major role in the manufacture of proteins within cells

Lipids
 ‘Fatty’ substances which are non-polar, hydrophobic molecules
 Major components of cell membranes
 Lipids:
– store energy
– structural components (form effective barriers b/n two watery environs.)
– form steroids
 Simple lipids – composed of C, H and O
 Compound lipids – contain fatty acids, glycerols and other elements
 Saturated fat – has maximum number of H atoms with no double bonds
between carbon atoms

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 Unsaturated fat – has at least one double bond between carbon atoms in chain
Proteins
 More complex than carbohydrates and make up over 50% of dry weight of cells
 Proteins:
– structural component
– enzymes, hormones, carrier molecules, etc.
 Composed of C, H, O and N (some contain S, P and more)
 Amino acid – basic subunit of proteins which bond together with peptide bonds
 Polypeptide – proteins, meaning “many peptide bonds”
 20 different amino acids commonly found in proteins, either synthesized or
obtained
 Each kind of organism has its own unique proteins
 Four levels of protein structure – primary, secondary, tertiary and quaternary
 Primary structure – actual sequence of amino acids in polypeptide
 Secondary structure – pleating/coiling of proteins held by hydrogen bonds
 Tertiary structure – distinctive 3-D shape of polypeptide (globular/fibrous)
 Quaternary structure – when two or more polypeptide combine together

Biological Membranes

 Plasma membrane encloses contents of cells and allows cytosol to have

different composition from surrounding external environment by selectively
regulating movement of substances into and out of the cell
 Membranes:
– permit selective control of molecules entering and leaving cells
– are active environments in which many essential chemical reactions of life
occur
– establish compartments within cell
– restrict movement of substances between one part of cell and another,
permitting regulation of many enzymatic processes that occur in cell
– have protein receptors involved in intercellular communication
– are involved in cell-cell recognition

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– produce electrical activity in excitable cells

Membrane composition
 Composed of phospholipid bilayer associated with proteins, carbohydrates and
cholesterol
 Phospholipid – polar molecule with hydrophilic phosphate head and
hydrophobic lipid tail
 Proteins – provide channels through which water-soluble molecules and ions
pass
 Carbohydrates – play role in recognition and adhesion between cells
 Cholesterol – makes membrane more stable and decreases permeability to
small water-soluble molecules

Molecules crossing membranes

 Movement of molecules in and out of cell depends on composition of membrane
and surface area available for exchange
 Lipid-soluble molecules of various sizes pass easily
 Tiny molecules pass between phospholipids molecules
 Small uncharged molecules pass through bilayer
 Larger water-soluble molecules pass through protein channels

Diffusion
 Diffusion – passive movement of molecules along concentration gradient
 Concentration gradient – difference in concentration between two solutions

Osmosis
 Osmosis – passive movement of water molecules through partially permeable
membrane along concentration gradient (“water diffusing along own con. grad.”)
 Hyperosmotic – dilute solution where water molecules are in high concentration

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 Hyposmotic – concentrated solution where water molecules are in low

concentration
Protein-mediated transport
 Membrane proteins form selective channels that permit or enhance passage of
specific ions and molecules
 Facilitated diffusion – passive process that occurs through protein channels
 Active transport – active process that can move molecules against
concentration gradient through protein channels
 In both processes:
– transport is more rapid than simple diffusion
– transport is selective as channels are specific
– channels become saturated as concentration of substances being transported
increases
– transport of one substance can be inhibited by presence of another substance
able to use channels as a result of competition for available channel

CHAPTER 2 – ENZYMES AND OTHER BIOMOLECULES

Enzymes and cellular processes

Certain basic processes must be performed by all cells:

– obtain nutrients
– grow
– maintain and repair themselves
– provide energy for movement and metabolism
– eliminate wastes
Biomolecules – biological molecules that are produced and assembled into new
organelles or used for the repair and maintenance of cells
Enzymes control the synthesis of these various biomolecules and many other
cellular processes that keep the cells alive

Metabolism
 Metabolism – overall chemical activity of cells, including the synthesis of organic
molecules, various energy transforming and recycling processes and the
decomposition of unwanted substances
 Metabolic pathways – chains of reactions catalysed by hundreds of enzymes
working in chains
 Substrates – molecules that bind to the active site of an enzyme on which it acts
 More than 1000 enzymes inside each cell with many different reactions occurring
simultaneously as enzymes located at specific sites within cells

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Enzymes are biological catalysts

 Enzymes – act as catalysts for chemical reactions in the body and increase the
rate of chemical reactions by millions of times
 Catalyst – speeds up (catalyses) reactions that would otherwise occur too slowly
for survival
 Enzymes:
– are globular proteins
– are substrate specific
– can be reused over and over again
– are needed in small amounts and are neither reactants nor products
– make a reaction take place more easily
– can catalyse a reaction in either direction (synthesis/decomposition)
– do not change the direction of a reaction
– do not change the final amount of product
– can be denatured by extreme increase in heat/pH
 Active site – part of an the enzyme that interacts with the substrate and is
structurally complementary to specific substrate
 Lock-and-key interaction – substrate molecules have right shape to fit an
enzyme
 Induced-fit mechanism – actual interaction between substrate and enzyme
changes shape of enzyme to produce right fit

Activation energy and enzymes

 Activation energy – energy required to start a chemical reaction
 Enzymes act by reducing amount of activation energy required for a particular
reaction to occur, allowing the reaction to take place more easily

Factors affecting enzyme activity

 Enzyme action involves specific binding between enzyme and substrate
molecules
 Any condition that changes the shape of enzyme (denaturation) affects activity of
enzyme and rate of reaction

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 Chemical reactions are affected by amount of substrate/enzyme present or

accumulation of product
 Denaturation – irreversible change in protein structure
 Temperature – warming increases rate of most chemical reactions
 However, extreme increase in heat can denature enzymes
 Optimum temperate range – temperature at which enzyme’s catalytic activity is
greatest (range immediately below critical temperate = denaturation)
 Balance between general increase in reaction rate with increasing temperature
and increasing rate of denaturation of enzyme molecules
 Optimal temperatures for particular enzymes may vary in different species
 pH – many enzymes are neutral or slightly acidic
 Increase in pH affects 3-D shape of enzymes and therefore affects active site

Regulating enzyme affinity

Affinity – the ease with which an enzyme binds with its substrate
Cells regulate affinity by attaching other molecules to enzyme to alter shape of
active site, which allows cell to increase/decrease rate of reaction
Chemical inhibition – other chemical substance that inhibits enzyme function by
binding to active site of enzyme or another part so that shape of active site is
altered (can be reversible, irreversible, competitive or noncompetitive)
If more substrate is present, net reaction will go to the right
If the product accumulates, net reaction will slow and eventually go left
Coenzymes –very small organic molecules that are associated with particular
enzymes and are essential for their activity
Must be obtained from plants or microorganisms as cannot be synthesized
Donate electrons or protons

Enzymes and disease

 Several inherited diseases (‘inborn errors of metabolism) involve inability to
manufacture particular enzyme required to break down substances that are not
normally part of diet
 Galactosaemia – inherited condition due to an error (mutation) in gene
responsible for producing one of the enzymes needed to convert galactose
 Lactose intolerance – lactose is not digested normally in small intestine
 Phenylketonuria – metabolic disorder where ‘missing’ enzyme (phenylalanine
hydroxylase) is unable to catalyse conversion of phenylalanine

Anabolic and catabolic reactions

 Anabolism – building of larger molecules from smaller molecules, which requires
energy to construct new bonds (endergonic)
 Catabolism – breakdown of macromolecules into smaller molecules, releasing
energy when bonds are broken (exergonic)
 Metabolism = anabolism + catabolism
 Most important anabolic reactions of living organisms are those of autotrophic
organisms – photosynthesis

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 Dehydration – where molecule of water is removed with addition of subunit in

synthesis of macromolecules (condensation)
 Hydrolysis – adding molecule of water to break down subunit of polymer

Biomolecules – synthesis and transport

 Synthesis, packaging and transport of organic molecules in eukaryote cells

involves coordinated activity of number of organelles, including nucleus,
ribosomes, ER, Golgi apparatus and vesicles

Controlling cell functions – nucleus

 Nucleus is usually largest organelle in a cell
 Nucleoli – site of synthesis of ribosomal RNA (rRNA)
 Nuclear membrane – double membrane surrounding nucleus containing many
nuclear pores
 DNA – contains instructions for building enzymes needed to manufacture organic
molecules required, therefore maintenance of cell structure and function is under
control of DNA
 mRNA – copy of DNA instructions for a particular protein

Assembling proteins - ribosomes

 rRNA passes from nucleus into cytoplasm and becomes part of ribosome
 mRNA also passes into cytoplasm and binds to ribosome, initiating protein
synthesis
 Ribosomes are found either free in cytoplasm or attached to membranes
 Free ribosomes produce protein that generally function as enzymes
 Bound ribosomes produce proteins that are destined for export from cell

Transporting and processing – endoplasmic reticulum

 Endoplasmic reticulum – extensive network of interconnected membranous
sacs and tubules branching throughout cell and can be smooth or rough
 ER is connected to nuclear membrane and is believed to arise from it
 Contains enzymes and protein that are important in many aspects of metabolism,
including processing and sorting of proteins, adding sugar chains to proteins and
ensuring that proteins are correctly folded
 Critical role in regulating concentration of cytoplasmic calcium which, in turn,
regulates many cellular functions
 RER – abundant in cells that actively synthesis and export proteins
 SER – involved in synthesis of other molecules

Packaging for export – Golgi apparatus

 Golgi apparatus – stack of cisternae and matrix that encompasses it
 Major site for the sorting of proteins to different sub-cellular compartments
 Proteins synthesized by RER are further modified in Golgi apparatus and then
packaged in vesicles for export from cell

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 Vesicles – membrane-bound organelles often involved in transport (exocytosis)

Storage of biomolecules
 Organisms maintain stores of chemical energy in form of carbohydrates and
lipids

Removing wastes and debris

 Lysosomes – membrane-bound vesicles that are sites of breakdown of debris
within the cell as it is filled with powerful ‘digestive’ enzymes
 Vacuoles – membrane-bound liquid-filled spaces that provide turgidity and
storage in plant cells and are involved with intracellular digestion in animal cells

CHAPTER 3 – ENERGY TRANSFORMATIONS

Life needs energy

What is energy?
 Energy – the capacity to do work
 Energy exists in many forms (e.g., light, heat, sound, mechanical, electrical,
kinetic and chemical)
 Energy cannot be created or destroyed, but it can be changed from one form to
another

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 Living organisms require energy to grow, move, respond, reproduce and

maintain and repair themselves
 Kinetic energy – the energy of movement
 Potential energy – stored energy
 Chemical energy – energy stored in the bonds of molecules – the energy of life
is largely chemical energy
 Energy efficiency – how much energy is extracted from a reaction
 The Laws of Thermodynamics:
- energy cannot be created or destroyed (but it can be changed from one form to
another)
- the entropy (or randomness) of the universe is increasing
 Energy conversions always result in some energy being ‘lost’ to the surroundings
as heat (it is referred to as ‘lost’ as it is not available for use)
 Homeothermy – continual generation of heat energy as a byproduct of chemical
reactions that allows endotherms to maintain stable body temperatures
 Autotrophs obtain their energy from the sun (photosynthesis) while
heterotrophs obtain their energy from organic compounds in food

Exergonic and endergonic reactions

 Exergonic reactions – reactions that result in a net release of energy
(decomposition)
 Endergonic reactions – reactions that require an input of energy (synthesis)
 Enzymes control all of these chemical reactions in cells
 ∆G – the change in energy from initial state to final state

ATP – energy from glucose

ADP/ATP cycle
 ATP (adenosine triphosphate) – the major source of available energy for
virtually all cellular functions
 ADP + Pi ↔ ATP
 Energy is stored in the bonds formed when ADP combines with P i to form ATP
and is then released when the Pi bond is broken to form ADP

Harvesting the energy from glucose

 Glucose – 6-C energy-rich molecule that is broken apart in a series of chemical
reactions that involve transferring energy in ‘small packets’ used to produce ATP
 Anaerobic pathway – glucose is broken down to form 2 ATP molecules and
lactic acid (in animals) or ethanol and carbon dioxide (in plants) in the absence of
oxygen
 Aerobic pathway – glucose is broken down to form 36-38 ATP molecules and
carbon dioxide and water in the presence of oxygen

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 Cellular respiration – the aerobic breakdown of glucose to drive the production

of ATP
 C6H12O6 + 6O2  6CO2 + 6H2O + 36-38 ATP

Glycolysis: anaerobic, occurs in the cytosol

 Glucose – first stage of respiration which involves the anaerobic breakdown of
glucose into 2 pyruvate molecules in the cytosol of the cell
 C6H12O6 + 2 ADP + 2P + 2NAD+  2 pyruvate + 2ATP + 2NADH

Krebs cycle: anaerobic, occurs in the mitochondrion

 Krebs cycle – anaerobic breakdown of pyruvate molecules into 6 carbon dioxide
molecules and several charged electron carriers in mitochondrial matrix

Electron transport: aerobic, occurs in the mitochondrion

 Electron transport – the successive passage of electrons from one cytochrome
or flavoprotein to another by a series of oxidation-reduction reactions during the
aerobic production of ATP in the cristae of mitochondria

Fermentation: anaerobic, occurs in the cytosol

 Fermentation – pyruvate is converted via an anaerobic pathway to either lactic
acid (in animals) or alcohol and carbon dioxide (in plants)
 Fermentation is necessary as it prevents the accumulation of pyruvate and thus
allows glycolysis to continue
 Animals – C6H12O6  lactic acid + 2 ATP
 Plants – C6H12O6  ethanol + carbon dioxide + 2 ATP

 Oxygen debt – the amount of oxygen required to fuel the recycling of lactic acid

 Lipids and proteins can also enter aerobic pathways at various places and be
broken down to form ATP
 Fats provide more energy/g than either carbohydrates or proteins

Getting glucose

 Autotrophs make glucose during photosynthesis by combining carbon dioxide

and water
 Chemoautotrophs – prokaryotes that get the energy they need by carrying out
energy-releasing reactions between inorganic molecules
 Heterotrophs get the organic compounds they need by eating other organisms
or their products

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Photosynthesis – converting solar energy

 The ultimate source of energy for virtually all living organisms is the radiant
energy of sunlight
 Photosynthesis – the process whereby chlorophyll traps light energy and
manufactures glucose from carbon dioxide and water

Factors affecting the rate of photosynthesis

 Light compensation point – the light intensity at which the rate of carbon
dioxide produced by cellular respiration equals the rate that carbon dioxide is
used in photosynthesis
 Light intensity – increase in light intensity usually results in increase in rate
 Temperature – increase in temperature results in increase in rate before
denaturation
 Presence of oxygen – decrease in oxygen results in increase in rate
 Presence of water – less water results in closed stoma which prevents carbon
dioxide from entering leaves therefore decrease in rate
 Amount of chlorophyll – more chlorophyll results in increase in rate

Chemosynthesis
 Chemosynthesis – process by which autotrophic bacteria use chemical energy
within inorganic molecules to make organic matter

Storing energy

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Energy reserves in flowering plants

 Plants store carbohydrates mainly in the form of starch
 Various parts of a plant may be modified to store energy reserves

Energy storage in mammals

 The ability to store energy reserves is necessary for survival
 Animals store carbohydrates as glycogen with the remainder stored as fats

Energy balance in animals

 Metabolism is the name for the sum of all processes occurring in an organism
and reflects the overall energy requirements of an organism
 In animals, the amount of energy needed each day depends on factors such as
basal metabolic rate, body size, activity level and environmental temperature
 Basal metabolic rate – amount of energy required to maintain basic functions in
a resting unstressed animal per unit time, excluding extra energy required for
activity or maintaining homeothermy

CHAPTER 4 – DNA, PROTEINS AND PROTEOMES

Life has a common origin

All organisms contain DNA as their genetic material and use the same genetic codes
Organisms have very similar amino acid sequences to code for the same
fundamentally important proteins even though the organisms are very different

DNA – the matter of inheritance

 Genome – all the genes of an organism

 Proteome – all the functional proteins produced by an organism (i.e., the products of
the genome)
 Gene – unit of heredity that provides a template for the production of proteins from
amino acids using a specific code for each amino acid
 There are more functional proteins in the proteome than there are genes in the
genome, leading to the conclusion that 1 gene does not code for 1 protein

Deoxyribonucleic acid (DNA)

 In prokaryotes, DNA is located in the cytoplasm (nucleoid) and consists of a

single circular chromosome and polasmids

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 In eukaryotes, DNA is located in the nucleus (chromosomal DNA), mitochondria

(mitochondrial DNA) and in the chloroplasts of photosynthetic eukaryotes

Nucleotides – building blocks of DNA

 DNA – carrier of genetic information in all cellular organisms and most viruses
 DNA is a macromolecule (polynucleotide) made up of monomers of nucleotides
 A nucleotide is composed of:
- a 5-carbon deoxyribose sugar
- a phosphate
- one of four nitrogen-containing bases (either purines or pyrimidines)
 Purines – bases with a double ring structure (A and G)
 Pyrimidines – bases with a single ring structure (T and C)

DNA is a double-stranded helix

 Complementary base pairing – A always pairs with T and G always pairs with
C, resulting in two polynucleotide strands joining together to form the double-
stranded DNA molecule where the concentration of one base is always equal to
that which it pairs with (i.e., con(A)= con(T), con(C) = con(G))
 Antiparallel – polynucleotide strands are parallel but run in different directions
(i.e., one runs 5’ to 3’ and the other 3’ to 5’)

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Ribonucleic acid (RNA)

 RNA – nucleic acid with a vital role in protein synthesis

 RNA is different from DNA in that it is a single chain of nucleotides, the sugar is
ribose and, instead of thymine, uracil is complementary to adenine
 There are three main forms of RNA
- ribosomal RNA (rRNA) which make up ribosomes
- messenger RNA (mRNA) which carries copy of genetic code from DNA to
ribosome for protein synthesis
- transfer RNA (tRNA) which brings amino acids to ribosome to form
polypeptides

Synthesis of polypeptides

 The polypeptide produced when mRNA is translated will probably not be the final
functional protein
 Post-translational modification may involve:
- proteases cleaving part(s) of the polypeptide
- addition of carbohydrates
- addition of lipid, phosphate or methyl groups
- insertion of a cofactor into an enzyme
 Transcription – the copying of the nucleotide sequence of DNA into the
nucleotide sequence of RNA
 Translation – the assembly of a polypeptide according to the nucleotide
sequence of RNA using the ‘genetic code’

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 Codon – a three-nucleotide sequence that codes for a particular amino acid

and are essentially the ‘instructions’ for polypeptide assembly carried in mRNA
 AUG – special ‘start’ codon while UAA, UAG and UGA – special ‘stop’ codons
 The ‘universal’ genetic code gives the codons for the 20 common amino acids
and stop codons for nuclear DNA
 The genetic code is:
- degenerate – some amino acids are coded for by more than on codon
- universal – each codon codes for a particular amino acid in all species
 As a consequence of the genetic code, genes can be taken from one species
and inserted into the genome of another without altering the gene product
 Incorrect protein formation – usually a result in an error in the nucleotide
sequence of a gene

Protein formation

 The general structure of an amino acid is:

- the amino group (NH2)
- a carboxyl group (COOH)
- a side chain (R) - the difference in amino acids is the difference in side
chains
 Peptide bonds – bonds that link amino acids together
 Peptide bond formation – a dehydration (or condensation) reaction that
involves the removal of a water molecule
 Polypeptide – formed by many amino acids linking together

Protein structure

 Primary structure – linear sequence of amino acids

 Secondary structure – hydrogen bonding between amino acids causes the
chain to either pleat or coil
 Tertiary structure – the folding of the polypeptide chain causes it to take on a
complex 3D shape
 Quaternary structure – some functional proteins consist of two or more
polypeptide chains
 Chaperone proteins – proteins that help large polypeptides to fold correctly
(also known as heat shock proteins)

The role of proteins in cells

 Catalytic – enzymes

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 Structural – collagen, plasma membrane

 Contractile elements – actin and myosin fibres
 Transport – haemoglobin, protein channels
 Regulatory – hormones
 Immunologic – antibodies
 Cell recognition and signal transduction – marker proteins, receptor proteins

Proteomics

 Proteomics – the technologies used in the study of the structure, function and
interactions of the proteome
 Proteomics should lead to an understanding of the causes of disease,
contributing to the development of treatments for various diseases
 Physiological genomics – examines how a one-dimensional code is
transformed into the multiple dimensions of living organisms

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