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WEEK 5: PROTEINS
POLAR NEUTRAL AMINO ACIDS
PROTEINS AA
- Naturally occurring, unbranched polymer
- Most abundant substance in nearly all cells, Serine Ser S -Posttranslational
next to water modification of proteins
- Contains: C, H, O, N, & S (most)
- Monomer: AMINO ACIDS Cysteine Cys C - Active part of many
enzymes
- COA synthesis

Threonine Thr T -Posttranslational

modification of proteins

Asparagine Asn N -Posttranslational

AMINO ACIDS modification of proteins
- Building blocks for proteins
- Organic compound that contains both –NH2 Glutamine Gln Q - Nitrogen Carrier
and –COOH
- AAs found in proteins are always Tyrosine Tyr Y - Precursor of Thyroid
alpha-amino acids Hormones, Melanin
- 20 standard amino acids normally present in
proteins
• classified according to side chain polarity

NON-POLAR AMINO ACIDS

AA
POLAR ACIDIC AMINO ACIDS
Glycine Gly G - 1st step of heme synthesis.
- Inhibitory NTA in the SC AA
- Collagen
Aspartic Asp D - Participates in many
Alanine Ala A - Carrier of ammonia Acid metabolic pathways
Valine Val V Glutamic Glu E - ionic form is an excitatory
Accumulation in Maple Syrup Acid NTS
Leucine Lei L Urine Disease. - Precursor of GABA
Isoleucine Ile I

Proline Pro P Collagen

POLAR BASIC AMINO ACIDS
Phenylalan Phe F - Precursor of Tyrosine
ine -Accumulates in AA
Phenylketonuria
Histidine His H - precursor of histamine
Methionine Met M - Methyl group transfer
Lysine Lys K - Precursor of carnitine
Tryptophan Trp W - Precursor of Melatonin,
Arginine Arg R - precursor of creatinine and
Serotonin, Niacin
urea

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ESSENTIAL AMINO ACIDS Fischer Projection

- must be obtained from the diet because the Top: -COOH
body cannot synthesize them in adequate Bottom: R group
amounts Horizontal: -NH2 (denotes handedness)

MNEMONICS:

PVT TIM HALL always Argues, never Tyres.

PVT TIM HALL

Phenylalanine Threonine Histidine ACID-BASE PROPERTIES

- AMINO ACIDS
Valine Isoleucine Arginine • White, crystalline solids in pure form
• Not very soluble in water
Tryptophan Methionine Leucine - AAs are charged species both in solid state
and in solution
Lysine - Both acidic (COOH) and basic (NH2)
groups are present
Always argues: the A is for Arg, not Asp. - In neutral solution:
-COOH LOSE protons -> NEGATIVE
Never tyres': T is not Tyr, but both Thr and Trp. -NH2 ACCEPT protons -> POSITIVE

COMPLETE DIETARY PROTEIN

- contains ALL of the essential amino acids in
the same relative amounts that the body In AAs, an INTERNAL acid-base reaction occurs.
needs them
- Animal sources - Casein from milk, meat ZWITTERION
dish and eggs - 1 atom has + charge
- 1 atom has - charges
- ZERO net charge
INCOMPLETE DIETARY PROTEIN - Structure changes when the pH of a
- does not contain adequate amounts OR solution changes
does not contain all of the essential amino
acids ISOELECTRIC POINT
Limiting amino acid - essential amino acid - pH at which the AA exists primarily in
that is missing or present in inadequate zwitterion form (>99%)
amounts In an incomplete dietary protein - AAs in their zwitterion form are not attracted
- Plan sources towards an applied electric field because
Lys is absent in wheat, rice, oats and corn there is NO NET CHARGE
Met is absent in beans and peas - no migration of molecules towards a
Trp is absent in corn and beans cathode or anode
- Animal source- Trp is absent in gelatin - Isoelectric focusing is used in
electrophoresis to separate proteins using a
!! not all animal source are complete dietary pH gradient
protein, but mostly
PEPTIDES
CHIRALITY - Unbranched chain of covalently-linked AAs
- 19 out of 20 AA are chiral->enantiomeric - Classified by the number of AA residues
paris Dipeptide – 2 AAs, Tripeptide – 3 AAs, and
- Glycine in the only achiral standard AA so on..
- AAs found in nature are generally L Oligopeptide – 10 to 20 AAs
isomers, except some bacterias Polypeptide – >20 Aas

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PEPTIDE BONDS BIOLOGICALLY IMPORTANT SMALL PEPTIDES

- amide bond that covalently links the
–COOH group of one AA and –NH2 group 1. OXYTOCIN
of another AA - Nonapeptide with 6 AAs in a loop held by a
disulfide bond
- Ile on C3 ; Leu on C8
- Regulates uterine contractions and milk
letdown

2. VASOPRESSIN (ADH)
- Peptide chains have directionality because - Antidiuretic Hormone
it has 2 different ends - Nonapeptide with 6 AAs in a loop held by a
disulfide bond
- Phe on C3 ; Arg on C8
- Regulates excretion of water in the kidneys
- Sequence may be indicated using the
standard 3-letter abbreviations 3. ENKEPHALINS
- Pentapeptide
- Met: Tyr-Gly-Gly-Phe-Met
- Leu: Tyr-Gly-Gly-Phe-Leu

Neurotransmitter - binds receptors in the

brain to reduce pain (nociception)

4. GLUTATHIONE
- Tripeptide
Backbone- sequence of peptide bonds and - Glu-Cys-Gly
⍺-carbon –CH groups in a peptide - Glu is bonded to Cys via the side chain
Substituents- R groups carboxyl rather than the ⍺-carbon

Antioxidant - Protects cellular contents from

PEPTIDE NOMENCLATURE reactive oxygen species
1. The C-terminal AA residue keeps its full AA
name.
2. All other AAs have their names end in –yl PROTEINS
e.g. tryptophyl, cysteinyl, glutaminyl,
asparaginyl CLASSIFICATION
3. The AA sequence naming begins at the
N-terminal Number of Peptide Chemical
Chains Composition
Glu-Ser-Ala — glutamylserylalanine
Gly-Tyr-Leu-Val — glycyltyrosylleucylvaline Monomeric- one Simple- only AA
peptide chain residues are present
ISOMERIC PEPTIDES
- Peptides containing the same AAs but in
different order Multimeric- more than Conjugated- one or
- Different physical and chemical properties one (subunits) more non-AA entities
- Number of possible isomers increases present (prosthetic
rapidly as chain length increases group)
- Given n AAs in a sequence, the number of
isomers = n!

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• Between different parts of a single chain

that folds back on itself – involves several
U-turns in protein chain arrangement
• Between atoms in different peptide chains
in proteins that contain more than one chain
• Lie in the plane of the shee
- R groups are found alternating above and
below the sheet

GENERAL STRUCTURAL CHARACTERISTICS Unstructured segment – protein secondary

structure that is neither an ⍺ helix nor a β pleated
Protein – polypeptide chain with at least 40 AA sheet
residues
3. Tertiary
4 Levels of Protein Structure - Overall 3D shape of a protein due to the
interactions between amino acid side chains
1. Primary (R groups)
• amino acid sequence
• order of attachment of amino acids to each Interactions:
other through peptide linkages 1. Covalent disulfide bonds – –SH groups of
• each protein has its own unique AA 2 Cys
sequence 2. Electrostatic attractions (salt bridges) –
• each protein has the same specific Acidic and basic R groups
sequence regardless of where it is found 3. Hydrogen bonds – 2 Polar R groups
within an organism 4. Hydrophobic attractions – 2 nonpolar R
groups
2. Secondary
• Arrangement in space adopted by the 4. Quaternary
protein backbone - Highest level of protein organization
• Due to hydrogen bonding between - Found only on multimeric proteins
- Carbonyl oxygen atom on a peptide - 2 or more subunits held together by
linkage noncovalent interactions (same as in tertiary
- Amide hydrogen atom on another structure)
peptide linkage - Noncovalent interactions are weaker and
• Segments involved can be more easily disrupted compared to those
- 2 segments from different found in the tertiary
backbones
- 2 segments from the same
backbone that folded back upon
itself
Alpha helix
- Single protein chain
- Resembles a coiled spring (helix)
- Right-handed (clockwise) spiral
configuration
- Maintained by H bond that are oriented
parallel to the axis of the helix
- All R groups extend outward from the spiral

Beta pleated sheet

- 2 fully extended protein chain segments in
the same or different molecules are held
together by hydrogen bonds
- Hydrogen bonds

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REACTIONS
called
collagen fibrils
HYDROLYSIS
• Occurs when a protein or small peptide in a
solution of strong acid or
base is heated
• Reverse of the formation reaction of a peptide GLOBULAR PROTEIN
bond →
Amine and Carboxylic acid groups are regenerated MYOGLOBIN HEMOGLOBIN

• Stores O2 in the Transports O2 from the

muscles lungs to
• Monomer that the tissue
• Complete hydrolysis – all peptide bonds are contains a • Tetramer with each
broken, freeing up all AAs heme group subunit
• Partial hydrolysis – some, but not all peptide • Has a higher affinity containing a heme
bonds are broken, for O2 than group
producing a mixture of free Aas and small peptides hemoglobin
• Protein digestion – enzyme-catalyzed hydrolysis
of ingested proteins

DENATURATION CONJUGATED PROTEINS

• Partial or complete disorganization of a protein’s
characteristic 3D shape due to disruption of its IMMUNOGLOBULINS
secondary, tertiary, or quaternary structural • Conjugated protein produced by an
interactions organism as a protective response to
• Does NOT affect the primary structure specific foreign substances
• Leads to loss of biochemical activity • Structure
• Often leads to loss of water solubility → - 4 polypeptide chains
precipitation of denatured protein (COAGULATION) - 2 heavy chains – 400-500 Aas
- 2 light chains
- Carbohydrate content varies between
immunoglobulins

CLASSIFICATION OF PROTEINS BASED ON LIPOPROTEINS

SHAPE • Conjugated protein used to suspend lipids and
transport them through the bloodstream
• Spherical structure of lipid core +
shell of phospholipids, cholesterol, and proteins
FIBROUS PROTEIN
4 Types:
ALPHA KERATIN COLLAGEN 1. Chylomicrons – transport dietary TAG
2. Very-Low-Density Lipoproteins (VLDL) –
• Protective coating for • Most abundant
transport endogenous TAG from liver to adipose
organism protein
tissue
• Found in hair, • Found in skin, bones,
3. Low-Density Lipoproteins (LDL) – transport
fingernails, toenails, tendons,
endogenous cholesterol from liver to tissue
wool, feathers, claws ligaments, blood
4. High-Density Lipoproteins (HDL) – collect
• Individual helical vessels
excess cholesterol from tissues and transport them
molecules usually twine • Triple helix with 3
back to the liver
about one another to chains of AAs
form a coiled coil • Gly-X-Y
• Nonstandard AAs
- 4-hydroxyproline
- 5-hydroxylysine –
attachment of CHO
• Form aggregates

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WEEK 6: ENZYMES
MODELS OF ENZYME ACTION
ENZYMES
Active Site
- Catalyst for biochem reactions (faster rate) - small portion that actually participates in the
- lowers the activation energy of a reaction interaction with a substrate
- Not consumed during the reaction - Usually a crevice-like location in the enzyme
- Usually globular proteins; few are nucleic where the substrate fits
acids
- Enzyme-Substrate complex
TERMS - Intermediate reaction species that is formed
when the substrate binds to the active site
Substrate – the substance on which an enzyme - Allows the substrate to encounter more
acts favorable reaction conditions
Product –substance produced by the action of
enzyme on substrate
Active site – region or domain where the substrate
Lock and Key Model Induced Fit Model
binds
Cofactor – nonprotein component that assists in The active site has a The enzyme has
catalysis fixed, rigid geometrical enough flexibility to
conformation allow for small changes
STRUCTURE in its shape or
geometry
Simple Enzyme Conjugated Enzyme

composed entirely of Protein (Apoenzyme) + Only substrates with The active site of the
protein (AA chains) non protein part complementary enzyme changes its
(Cofactor) = geometry can be shape in order to
Holoenzyme accommodated by the accommodate its
active site substrate
Cofactors – provide additional chemically reactive
functional groups ENZYME SPECIFICITY
• May be permanently or temporarily bonded to the
apoenzyme - extent to which an enzyme’s activity is
restricted to a specific substrates
Coenzymes – small organic molecules ← Vitamins
Metal ions – Zn2+, Mg2+, Fe2+, Fe3+, Cu+, Cu2+ 1. Absolute specificity – enzyme catalyzes only
← Minerals one reaction; e.g. catalase

NOMENCLATURE 2. Group specificity – enzyme acts only on

molecules with a specific functional group
1. Suffix: e.g. carboxypeptidase
–ase - indicates that the substance is an
enzyme 3. Linkage specificity – enzyme acts only on a
–in - still found in the first enzymes specific chemical bond; e.g. phosphatase
discovered
e.g. urease, lactate dehydrogenase, pepsin, 4. Stereochemical specificity – enzyme acts only
trypsin on a particular stereoisomer
2. Prefix
- indicates the type of reaction
e.g. hydrolysis → hydrolase, oxidation → oxidase CLASSES OF ENZYMES

3. In addition to or in lieu of the type of reaction, the OXIDOREDUCTASE

identity of the substrate is often noted
e.g. pyruvate carboxylase, glucose oxidase, urease - Catalyzes an oxidation-reduction (redox)
lactase reaction

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- Requires a coenzyme that is oxidized or

reduced as the substrate is reduced or
oxidized

ISOMERASE

- Catalyzes rearrangement of atoms

TRANSFERASE (isomerization) of a substrate in a reaction,
converting it into a molecule isomeric with
- Catalyzes transfer of a functional group itself
from one molecule to another - Only one product and only one reactant
• Transaminases – catalyzes the transfer of
an amino group
• Kinases – catalyzes the transfer of a
phosphate group

LIGASE

- Catalyzes the bonding together of two

HYDROLASE molecules into one with the use of ATP

- Catalyzes a hydrolysis reaction

- Addition of water molecule causes a bond to
break

FACTORS THAT AFFECT ENZYME ACTIVITY

TEMPERATURE

LYASE - Measure of kinetic energy of molecules

● ↑ temperature → ↑ motion of molecules →
- Catalyzes the addition of a group to a ↑ collisions between substrate & enzyme →
double bond OR removal of a group to faster reaction rate
form a double bond in a manner that Optimum temperature – temperature at
DOES NOT involve hydrolysis or oxidation which an enzyme exhibits maximum activity

DENATURATION - When temperature increases

beyond the optimum temperature

Humans – optimum temperature is 37C

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Fever > 40 – can lead to enzyme denaturation, - Substrate concentration is constant +

dysfunction, and death Enzyme concentration is increased → faster
reaction rate
- Increases the concentration of enzymes
allows more substrate molecules to be
accommodated

pH

- Can lead to changes on the charge of acidic

and basic amino acids located on the active
site
- Can lead to protonation or deprotonation of
groups on the substrate
- Changes in pH can lead to denaturation and
loss of catalytic activity

Optimum pH – pH at which an enzyme exhibits

maximum activity
- Usually pH 7.0 – 7.5
- Pepsin – pH 2.0
- Trypsin – pH 8.0

ENZYME INHIBITION
SUBSTRATE CONCENTRATION
COMPETITIVE INHIBITION
- Enzyme concentration is constant +
Substrate concentration is increased → - Competitive inhibitor – molecule that
faster reaction rate until it reaches the sufficiently resembles the substrate in
maximum reaction rate (velocity) shape and charge distribution that it
competes with the substrate for occupancy
SATURATION - as substrate concentration of the active site
increases and enzymes become fully occupied, - Presence of inhibitor at the active sites
each incoming substrate must wait for an empty prevents normal substrate from binding → ↓
active site enzyme activity
- Can be reduced by increasing the
Turnover number – the number of substrate concentration of the substrate
molecules transformed

NONCOMPETITIVE INHIBITION
ENZYME CONCENTRATION
- Noncompetitive inhibitor – molecule that
decreases enzyme activity by binding to a
site other than the active site

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- Substrate is still able to bind to the active Positive regulator – ↑ enzyme activity → active
site, but the presence of the inhibitor site changes in a way that it can more readily
changes the enzyme structure in such a accept substrate
way that is sufficient to prevent proper
enzyme catalytic action Negative regulator - ↓ enzyme activity → active
- Increasing substrate concentration DOES site changes in a way that substrate is less readily
NOT reverse the inhibition accepted

IRREVERSIBLE INHIBITION

- Irreversible inhibitor – molecule that

inactivates enzymes by forming strong
covalent bonds to an amino acid side chain
at the active site
- Substrates are permanently prevented from
binding to the active site
- Structure of the inhibitor DOES NOT
resemble that of the substrate
- Excess substrate DOES NOT reverse the
inhibition process
FEEDBACK CONTROL

- Process in which activation or inhibition of

the first reaction in a sequence is controlled
by a product of the reaction sequence
- If ↓ [product] → the reaction sequence
proceeds rapidly
- If ↑ [product] → action of the first enzyme
becomes inhibited

REGULATION OF ENZYME ACTIVITY PROTEOLYTIC ENZYMES AND ZYMOGENS

ALLOSTERIC ENZYME - Enzymes are produced in inactive form and
later activated when appropriate
- Enzyme with 2 or more protein chains and 2 - Usually see in proteolytic enzymes
kinds of binding sites
Zymogen (proenzyme) – inactive precursor of
Characteristics; proteolytic enzymes
1. Composed of 2 or more subunits →
has QUATERNARY structure
2. Has 2 kinds of binding sites → 1 for
substrate, 1 for regulator
3. Active and regulatory binding sites are
distinct from each other, both in location
and in shape
4. Binding of a molecule at the regulatory
site causes changes in the overall 3d
structure of the enzyme

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- Enzyme inhibition is also utilized by certain

prescription drugs
• ACE inhibitors
• Sulfa drugs
• Penicillins
• Statins

COVALENT MODIFICATION OF ENZYMES

- Covalent modification - adding or removing

a group from enzyme by forming or
breaking a covalent bond
- Serves as an on/off switch for the enzyme

Phosphorylation – addition of a phosphate group ←

kinases

Dephosphorylation – removal of a phosphate group

← phosphatases
-

MEDICAL USES OF ENZYMES AND THEIR

INHIBITORS

DIAGNOSIS

- Certain enzymes are not normally found in

the blood and produced only in certain types
of cells
- Increase in the level of these enzymes
indicates a leak of intracellular contents and
thus indicates tissue or organ damage

Examples:
• AST/ALT – liver function tests
• Amylase/lipase – pancreatitis
• CK, AST, LDH – myocardial infarction
• ADA – test for TB pleural effusion

TREATMENT OF CERTAIN DISEASES

- Enzyme replacement therapy for those with

enzyme deficiencies
• Pompe’s Disease
• Lactose intolerance
• Severe combined immunodeficiency

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WEEK 7: NUCLEIC ACIDS

Prefix: Sugar Suffix: N-Base
Central Dogma of Molecular Biology Deoxyribose- Deoxy- Purine- -osine
- Flow of information
Ribose- NONE Pyrimidin- -dine

NUCLEOTIDE FORMATION

- Nucleoside + Phosphate
Phosphate attached to C5’ (phosphoester
linkage)
NUCLEOTIDES Condensation (H2O)

- Pentose sugar Naming:

Nucleoside name + 5’- ()phosphate

NUCLEIC ACIDS: DNA & RNA

- is bonded to both:
Phosphate group - Nucleotides are linked together by
sugar-phosphate bonds
- Base protruding from the chain at regular
intervals
- Sequence of the base side chains
N-containing heterocyclic base distinguishes various DNAs and RNAs from
each other

DEOXYRIBONUCLEIC RIBONUCLEIC ACID

ACID

Deoxyribose Ribose

Purine: Pyrimidine: Purine: Pyrimidine:

Adenine Cytosine Adenine Cytosine
Guanine Thymine Guanine Uracil

Nucleus Cytoplasm

• Storage and transfer of • Synthesis of proteins

genetic information • Synthesized from
• Indirectly controls the DNA during
functions of living cells transcription
• Passed from existing to
new cells during cell
division

NUCLEOSIDE FORMATION PRIMARY STRUCTURE

- Pentose + Nitrogenous base - Sequence in which nucleotides are linked

N-base attached to C1 together in a nucleic acid
Condensation (H2O)
1. DIRECTIONALITY
- 5’ end - free PO4 @ C5’

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- 3’ end - free OH @ C3’ Rosalind Franklin & Maurice Wilkins (1950s)

- Read from 5 – 3 - used x-ray diffraction to photograph and
analyze DNA; revealing that DNA molecules
2. NON-TERMINAL PHOSPHATE GROUPS are helical
- has a 1- charge
- Bonded to 2 sugars via a 3’-5’ James Watsons & Francis Crick (1953)
phosphodiester bond. - Deduced the structure of DNA & postulated
a 3D model that accounted for all available
data
In common with protein primary structure
1. Directionality DNA DOUBLE HELIX
2. Backbones do not vary in structure
3. The sequence of attachments to the - 2 polynucleotide strands coiled around
backbone is the distinguishing feature each other in a manner that is similar to a
spiral staircase
- Sugar-Phosphate backbones form the two
strands with the bases extending inward
between them
- Antiparallel strands are connected by
hydrogen bonds between complementary
bases
Adenine → Thymine
Cytosine → Guanine

BASE PAIRING

- Limited size of the interior of the double

DNA helix → only pairings with 1 small base
DNA STRUCTURE DISCOVERY (pyrimidine) and 1 large base (purine) can
fit
Friedrich Miescher (1868) - Hydrogen-bonding is more favorable for the
- first isolated and characterized “nuclein” AT and GC base-pairings
- Complementary nature of nitrogenous
1940’s bases → prediction opposite strand
Oswald Avery, Colin Macleod, Maclyn McCarty
extracted a virulent strain of S. pneumoniae and Interactions that stabilize the DNA Helix
used it to transform a nonvirulent strain to a virulent
strain 1. Hydrogen Bonding Interactions
- - H bonds by themselves are weak forces
Erwin Chargaff – Chargaff’s Rules - Each DNA has multitudes of base pairs that
1. The base composition varies from one the collective form significant strength
species to another
2. DNA from different tissues have the same 2. Base-Stacking Interactions
base composition - Bases in a DNA double helix are positioned
3. The base composition of DNA in a given with the planes of their rings parallel
species does not change with an organisms - Interactions involving a given base and the
age, nutritional state, or changing parallel bases above and below it
environment - Purine and pyrimidine bases are
4. The number of adenosine residues is equal hydrophobic → hydrophobic interactions
to the number of thymidine residues, and between stacked bases
the number of guanosine residues is equal
to the number of cytidine residues. ( A = T ;
C=G) DNA REPLICATION

DISCOVERY OF THE DNA DOUBLE HELIX - The 2 strands of DNA are separated

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- Each strand acts as a template for the - removes the RNA primers and fills the gaps
synthesis of a complementary strand with deoxyribonucleotides
- Results in 2 DNA molecules with bases
identical to those of the parent double helix 8. DNA Ligase
- Each DNA molecule is made up of one old - seals the nicks between Okazaki fragments
and one new strand → by catalyzing the formation of
SEMICONSERVATIVE phosphodiester bonds

- Helicase - unwinds DNA double helix at the DNA ORGANIZATION

replication fork
- DNA polymerase – elongates the growing CHROMATIN
strand by adding deoxyribonucleotides - condensed form of DNA; allows it to fit
inside the nucleus
STEPS IN REPLICATION - “beads on a string”

- Usually occurs at multiple sites within a NUCLEOSOME

molecule - DNA is wrapped 2x around an octamer of
- Replication is bidirectional histones

1. Origin of replication H1 histone binds to linker DNA and nucleosome to

- base sequence recognized by proteins that stabilize the chromatin fiber
initiate replication
↓ SOLENOID
helicase is deposited onto the DNA - Supercoils to further compact DNA
molecule

2. Helicase GENE
- breaks the H-bonds that hold base pairs
together → unwinding of the DNA double - Fundamental unit of heredity
helix at the replication fork - Encompasses the DNA sequences that
● encode the structural components of the
3. Single stranded binding protein gene product
- maintains separation of strands ● regulate its expression (adjacent to 5’-end)

4. Topoisomerase Genetic locus

- relaxes DNA and relieves torsional strain - specific position or location on a
chromosome
5. Primase
- inserts short RNA segments to initiate ALLELE
replication - matching alternate versions of each version
of a gene on a chromosome in a diploid cell
6. DNA Polymerase III - found on the same genetic locus on the
- recognizes RNA primers and adds new homologous chromosome.
deoxyribonucleotides at the 3’ end, resulting ● 2 alleles for each gene – 1 from the mother
in elongation of the strand in the 5’ to 3’ & 1 from the father
direction; proofreading (3’,5’-exonuclease ● If identical in base sequence →
activity) homozygous
● If not identical in base sequence →
Leading strand heterozygous
- Continuous synthesis from 5’ to 3’ GENOME
-
Lagging strand - Complete set of genetic instructions found
- Okazaki Fragments in an organism
- Human haploid cell (sperm or egg):
7. DNA Polymerase I distributed in 23 chromosomes
- During fertilization:

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Sperm (haploid) 23 Bases: Thymine → Uracil

+ Egg (haploid) 23 Needs Primer: NO
- = Zygote (diploid) 46 Proofreading: NO

- Diploid cells: 23 pairs (total of 46) DNA → hnRNA → mRNA

- 22 pairs of autosomal chromosomes
- 1 pair of sex chromosomes (X or Y) TRANSCRIPTION STEPS
• Female – XX
• Male – XY 1. DNA unwinds at a location, exposing the
desired sequence of bases

RNA 2. Free ribonucleotides align on one of the

strands (template strand) to form new base
TYPES OF RNA
pairs.
● Uracil rather than Thymine aligns with
rRNA mRNA Adenine bases

Ribosomal RNA Messenger RNA 3. RNA polymerase is involved in linking the

• Most abundant type • Carries the information ribonucleotides to the growing hnRNA
• associates with proteins specifying the amino acid molecule
to form ribosomes sequence of a protein to
the ribosomes 4. RNA polymerase encounters a sequence of
• Molecular mass varies
bases that is read as a stop signal
with the length of the
protein
• Only form of RNA that is
translated POST TRANSCRIPTION
- hnRNA → mRNA

hnRNA / ptRNA / tRNA Gene- base sequence: consists of alternating

pre-mRNA introns and exons
Heterogeneous nuclear Transfer RNA
Exons – code for genetic information
RNA • Second most abundant
Primary transcript RNA • Delivers amino acids to
Introns – do not code for genetic information
the ribosomes for protein
• Found only on the synthesis Splicing
nucleus - deletion of introns & splicing of retained
• RNA formed directly by exons
DNA transcription - Facilitated by snRNA
• Converted to mRNA Ribozymes
during post-transcription ALTERNATIVE SPLICING
processing Ribozymes
• RNA molecules with - In the body, the estimated number of
enzymatic activity proteins vastly exceeds the estimated
snRNA
- Small nuclear
number of genes
RNA - Process by which several different proteins
- Facilitates the that are variations of a basic structural motif
conversion of can be produced from a single gene
hnRNA to mRNA
- Transcriptome - all of the mRNA molecules that
can be generated from a genome
TRANSCRIPTION THE GENETIC CODE

- DNA directs the synthesis of RNA - nucleotide sequence in a given mRNA

- molecules that carry the coded determines the amino acid
- information for protein synthesis - sequence for the protein synthesized under
that mRNA’s direction
Backbone: Deoxyribose → Ribose

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Codon - Activated tRNA with complementary

- 3-base sequence used to specify each anticodon (UAC) attaches to the start
amino acid codon via complementary base pairing
• 61/64 possible codons code for specific - Complex interacts with large ribosomal
amino acids subunit to form the initiation complex
• 3/64 code for stop signals for protein
synthesis 2. ELONGATION

assignment of the 64 mRNA codons to specific - The site adjacent to the P site is called the
amino acids or stop signals: A site (aminoacyl)
- A site codon is exposed & bonded to by
AUG – start codon; codes for METHIONINE tRNA with the matching anticodon
- Peptidyl transferase links P site AA with A
UAG - site AA to form a dipeptide on A site tRNA
UAA - stop codon; terminates translation - tRNA at the P site becomes free and is
UGA - released, and the ribosome shifts along the
mRNA (translocation)
PROPERTIES OF THE GENETIC CODE - tRNA with the peptide moves to the P site,
and the next codon is exposed at the A site
1. UNAMBIGUOUS - Codon at A site bonds matching tRNA &
- Each codon specifies no more than 1 AA. peptide at P site is transferred to the A site

2. DEGENERATE OR REDUNDANT Peptidyl transferase – catalyzes the acyl transfer

- More than 1 codon can specify a single AA. reaction during elongation
- For AAs with >1 codon, the first 2 bases are
usually the same. 3. TERMINATION

3. UNIVERSAL - Polypeptide continues to elongate until a

- The code is the same in all organisms (with stop codon is reached
very few exceptions that occur in - Any of the stop codons can terminate the
mitochondria). process
- Polypeptide is cleaved from the tRNA via
4. COMMALESS OR CONTIGUOUS hydrolysis
- There are no spaces or commas between - Ribosome dissociates
codons on an mRNA - mRNA is released

TRANSLATION POST TRANSLATION PROCESS

- tRNA molecules function as intermediaries • Gives the protein its final form before it is
that deliver amino acids to the mRNA and completely functional
ribosome for protein synthesis
- 3’ end –binds to AA 1. Met residue during initiation is removed via
- Anticodon loop – consists of 7 paired bases, hydrolysis
the middle 3 of which constitute the 2. Covalent modification – formation of disulfide
anticodon bridges between 2 Cys
- Anticodon – 3 nucleotide sequence on tRNA 3. Completion of folding of polypeptides into their
molecule that is complementary to a codon active conformations
on an mRNA molecule

1. INITIATION
POLYSOMES/ POLYRIBOSOMES
- mRNA attaches to the surface of the small - Complex of mRNA with several ribosomes
subunit of the ribosome - Identical protein chains can be synthesized
- Start codon (AUG) occupies the P site almost simultaneously from 1 strand of
(peptidyl) mRNA

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- As a ribosome moves along the length of - Small particle that contains DNA or RNA
the mRNA, another ribosome can bind to surrounded by a protein coat that cannot
the place it vacated reproduce without the aid of a host cell
- Invades a host cell and utilizes the host
cell’s machinery in order to reproduce →
disruption of normal cell operation causes
disease

• DNA viruses – replicates uses DNA polymerase

• RNA viruses – can replicate using
- RNA-dependent RNA polymerase
- RNA-dependent DNA synthesis using
reverse transcriptase

VACCINE

• Preparation containing an inactive or weakened

form of a virus or
bacterium
• Triggers antibody production to confer immunity
against a certain
disease

MEDICAL CORRELATIONS

MUTATIONS

1. Silent Mutation
- 1 nucleotide changes; same AA

2. Missense Mutation
- 1 nucleotide changes; different AA

3. Nonsense Mutation
- Stop codon is generated

4. Frameshift Mutation
- Deletion of Codon/AA

Examples:

1. Sickle Cell Disease - Missense Mutation

- GAG → GUG
- @ 6th AA (Glutamic acid → Valine)

2. Cystic Fibrosis - Frameshift Mutation

- Deletion of 3 nucleotides (CTT)

VIRUSES

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