6 Nucleic Acids and Protein Synthesis

AS Level
Chapter 6
Nucleic Acids and

Protein Synthesis
Chapter Outline
Part 1 : Nucleic Acids
• Structure of Nucleotides
• RNA and DNA
• Semi-Conservative DNA Replication
Part 2 : Protein Synthesis

• Triplet Code → Codon → Anticodon
• Transcription
• RNA processing
• Translation
• Gene mutation
→ Sickle cell anaemia
Updated on 13/7/21 by Beh SJ @behlogy
Part 1:
Nucleic Acids
Introduction to Genetic Materials
Characteristics:
1) Ability to carry instructions/information
• Blueprint for the construction and behaviour of cells
2) Ability to be copied
• Pass on exact copy of information to
daughter cells
DNA structure discovered by

James Watson and Francis Crick, 1953
(but is quite contraversial...) Rosalind
Franklin

Nucleic Acids
• Monomer = Nucleotides
• Polymer = Polynucleotides
• 2 types:
1. DNA
2. RNA
• Bond between adjacent monomers after condensation

= phosphodiester bond
• Bond between complementary base pairs
= hydrogen bond

Nucleotides
A nucleotide consists of:
1) Nitrogenous base : Purine or pyrimidine base
2) Pentose sugar : 5 carbon sugar, either deoxyribose or ribose
3) Phosphate group: Negatively charged, making DNA a negatively
charged molecule

Nitrogenous Bases
2 major types of nitrogenous bases:
Purine bases – has 2 rings:

1) Adenine
2) Guanine
(Pure As Gold)
Pyrimidine bases – has 1 ring only:

1) Cytosine
2) Uracil (RNA only)
3) Thymine (DNA only)

Complementary Base Pairs
• Pairing of bases is precise
• Purine always binds with pyrimidine
• So DNA molecule has same width throughout

RNA
• RNA = Ribonucleic acid
• Single-stranded
• Forms a single helix
3 components in ribonucleotides:
1) Nitrogenous base
2) Ribose sugar
• Contains 1 oxygen atom more
than deoxyribose
3) Phosphate group
• Bases: A, U, C, G

P/S: Adenosine Triphosphate (ATP) is a RNA nucleotide

DNA
• DNA = Deoxyribonucleic acid
• Double-stranded
• Forms a double helix
• Have complementary base pairs
• Longer than RNA
3 components in deoxyribonucleotides:
1) Nitrogenous base
2) Deoxyribose sugar
• Contains 1 oxygen atom less than ribose
3) Phosphate group
• Bases: A, T, C, G
What are the
structural
differences btwn
RNA and DNA?

Structure of DNA
• Linking of nucleotides occurs in nucleus during S phase of cell cycle
• DNA replication occurs
• Bond between adjacent monomers after condensation =
phosphodiester bond
Structure of DNA:
1) DNA has a sugar-phosphate
backbone
• Formed by alternating sugar
and phosphate groups
→ Linked by phosphodiester bonds
• Strong covalent bonds

Phosphodiester
bond

Structure of DNA
2) Complementary base pairing occurs
between opposite strands
• 2 H bonds between A = T
• 3 H bonds between G ≡ C
→ H bonds hold the 2 strands together
→ Easily broken for transcription to
RNA or replication
• Pairing of bases is precise

• Purine always binds with pyrimidine
→ 2 rings + 1 ring = 3 rings
→ Distance between strands always the same
Hydrogen Bonding
• Between complementary bases of 2 DNA strands
• Important for 3D structure of molecule

• Many H bonds give stability
• But individual H bonds are weak
Important for DNA replication / transcription

• So strands can be separated
• H bonds only form between specific bases
→ Fewer mistakes
• H bonds also can easily reform without chemical reaction

Structural Characteristics of DNA
3) Two strands of polynucleotides are
antiparallel
• Run in opposite directions
• One strand runs from the 5’ to 3’
direction
• The other runs from 3’ to 5’
Deoxyribose sugar Updated on 13/7/21 by Beh SJ @behlogy

Two strands of polynucleotides are antiparallel
It’s called 5’ bcs it is 5’

2’ 3’
nearest to carbon 5 1’
4’ 4’
1’ 5’
3’ 2’
5’ 2’ 3’
1’ 4’
4’
3’ 1’
2’ 5’
It’s called 3’ bcs it is
nearest to carbon 3

5’ 3’
You only need to be given what one end of

the DNA molecule is called to label the rest!
5’ 3’
Example question:
5’ – T A A A G C C C T A – 3’
Given the sequence of DNA above, calculate:
• the total number of bases in the length of DNA
• the number of purines and pyrimidines
• the number of H bonds in the DNA molecule
A:
DNA is double-stranded so…. A = T, whereas G ≡ C so…..
Total no. of bases = 10 * 2 = 20
5’ – T A A A G C C C T A – 3’
3’ – A T T T C G G G A T– 5’
Complementary base pairing occurs so….
5’ – T A A A G C C C T A – 3’ No. of H bonds = (2*6) + (3*4) = 24
3’ – A T T T C G G G A T– 5’
No. of purines = 10
No. of pyrimidines = 10
Semi-Conservative
DNA Replication
Semi-Conservative DNA Replication
• Occurs in the nucleus during
S phase of interphase
• Requires ATP
• Enzymes needed:
1. Helicase
• To break H bonds to separate 2 DNA strands
2. DNA polymerase
• To synthesise a new strand of DNA (in the 5’ to 3’ direction)
• To catalyse the formation of phosphodiester bond
• Proofreads DNA
3. DNA ligase
• To join DNA fragments together
• To catalyse the formation of phosphodiester bonds
1. DNA double helix unwinds
• The whole DNA molecule is unwound eventually
2. Helicase break H bonds

• 2 DNA strands separated
• Both strands are used as templates

3. Free, activated DNA nucleotides are
activated with 2 additional phosphates
• Have 3 phosphate groups in total
• Free in the nucleus for synthesis of new
strands
• The bases of activated nucleotides form

H bonds with bases on each exposed
parent DNA strands
• According to the rules of
complementary base pairing

4. DNA polymerase attach to each of the two separated
parental strands
• Catalysing the formation of a new strand of DNA
• DNA pol links activated nucleotides together

→ By removing 2 phosphate groups (which are then recycled!)
→ Catalysing phosphodiester bond formation
• DNA pol also proofreads DNA!
• This occurs step-by-step
• Process continues along whole

DNA molecule

Slight complication:
• DNA polymerase attach to each of the
two separated parental strands
→ But the two enzymes move in opposite
directions
→ And new DNA strand always formed in DNA pol moving from 3’ to 5’
the 5’ to 3’ direction 3’
5’
3’
New DNA formed from 5’ to 3’
3’
Process able to continue
as DNA unwinds
5’
New DNA formed from 5’ to 3’
5’ 3’
Another DNA pol needed
to start process again
5’
DNA pol moving from 3’ to 5’
• One DNA strand is synthesised continuously
→ Called the leading strand
• The other is synthesised in sections known as Okazaki fragments
→ Called the lagging strand
• The fragments are joined by an enzyme, DNA ligase

→ catalyses the formation of phosphodiester bonds

Result:
• 2 DNA molecules
• Each containing 1 original strand
and 1 newly synthesised strand
→ This is why it’s called
semi-conservative replication

Other models of DNA Replication
DNA molecule has DNA molecule has 1 Each DNA strand

either 2 old strands parental strand and 1 has mixture of old
or 2 new strands new strand and new strands

How did scientists know it was semi-conservative ?
• Meselson & Stahl’s experiment (1958)
• Using bacteria E.coli & different nitrogen sources
1) Grow E.coli with nitrogen-15

→ For many generations
→ So all DNA contains only 15N in their nucleotides
→ Extract & centrifuge samples to separate DNA
→ Result: All DNA is heavy
2) Transferred to a medium with nitrogen-14

→ Allowed E.coli to divide again (1 gen, approx. 20min)
→ Centrifuge & observe
→ Result: All DNA is a hybrid. Has 1 heavy strand + 1 light strand.
→ Repeated for 2 more generations & DNA is observed

15N
1 heavy DNA 14N
2 hybrid DNA
2 light DNA
2 hybrid DNA
6 light DNA
2 hybrid DNA

Other models of DNA Replication
The results prove that DNA replication followed the
semi-conservative model, NOT conservative or disruptive.

Part2:
Protein Synthesis
How does the nucleus control all
activities of the cell?
• Cell’s activities refer to chemical reactions in the cells
• All chemical reactions are controlled by enzymes
• All enzymes are made of proteins
Therefore,
• DNA contains information for the
synthesis of proteins
• Genome = Total set of genes in a cell
• Gene = Region of DNA which
codes for a polypeptide
→ Determines the exact sequence
of amino acids
→ Determine primary structure of proteins
→ As well as secondary, tertiary and quaternary structures
Intro to Protein Synthesis
Process:
1) Transcription
• DNA is copied to mRNA
• Takes place in nucleus
2) RNA processing
• mRNA modification in nucleus
3) Translation
• mRNA is translated into
polypeptide chain
• Takes place at ribosomes at
RER/cytoplasm
How do genes code for proteins?
• Triplet code = sequence of
3 nucleotide bases in DNA
→ Codes for 1 amino acid
But there’s….
4*4*4 = 64 possible different
triplet codes and only 20
amino acids
• More than 1 triplet code can

code for the same amino acid
→The triplet code is degenerate
→ E.g. CAA, CAG, CAT and CAC
code for amino acid, valine

Things needed for Protein Synthesis
Types of RNA involved in protein synthesis:
• Messenger RNA (mRNA)
• Transfer RNA (tRNA)

– 20 types
• Ribosomal RNA (rRNA)

– made in nucleolus
– makes up the ribosome

mRNA
• Single-stranded
• AUCG
• Copy of the gene that codes for a polypeptide
• Made in nucleus and moves to ribosome (small
subunit)
• Codes for sequence of amino acids
• Codon = set of 3 bases on mRNA

• mRNA sequences is a series of codons
• mRNA sequence of codons dictate which amino
acids will be added to polypeptide chain
• Set of 3 bases on mRNA Codon
• Read by tRNA
• Start codon: AUG
→ Starts translation
→ Every 1st amino acid in a polypeptide chain - methionine
• Stop codon: UAA, UAG, UGA (textbook got this wrong!)

→ Stops translation and production of polypeptide chain

tRNA
• Made in nucleus
• Found in cytoplasm and ribosome
• Single stranded – 3 loops
→ Clover-leaf shaped
• 20 diff types of tRNA for 20 diff amino

acids
• Carries a specific amino acid to

ribosomes
• Anticodon = specific exposed 3 bases on

one loop
→ Anticodon forms complementary base
pairs with codon mRNA at ribosome
→ Different tRNA type, different anticodon
tRNA
• tRNA holds amino acids in place, side by side
→ for peptide bond formation
→ at the ribosome
• tRNA molecules can be reused after leaving
ribosome

rRNA
• Single-stranded
• Made in nucleolus
• Make up ribosomes
P/S: no need to
memorise the
numbers

Ribosomes
• rRNA + some proteins = ribosomes
• Site of protein synthesis
aka translation
Two ribosomal subunits:

• Small subunit – binding site for mRNA
• Large subunit
– 3 sites: E, P, A
– P and A are 2 binding sites for tRNA carrying amino acids
to bind to mRNA
– E site = tRNA exit site
– Also contains peptidyl transferase to catalyse the
formation of peptide bond to form polypeptide
Things needed for Protein Synthesis
• Occurs in the nucleus during
G1 or G2 phase of interphase
• Requires ATP
• Enzymes needed:
1. Helicase
• To break H bonds to separate 2 DNA strands
2. RNA polymerase
• To synthesise a new strand of RNA (in the 5’ to 3’ direction)
• To catalyse the formation of phosphodiester bond
3. Peptidyl transferase
• To catalyse the formation of peptide bond
Transcription
Stage One: Transcription
1. DNA double helix unwinds
• Only part of the DNA (gene) unwinds
2. Helicase break H bonds

• 2 DNA strands separated
• Only 1 strand is used as template
non-transcribed strand
transcribed / template strand

3. Free, activated RNA nucleotides
• Form H bonds with bases on
DNA template strand
• According to the rules of
complementary base pairing

4. RNA polymerase attach to template
• To catalyse the formation of mRNA
• RNA pol joins activated RNA nucleotides together

→ Catalysing phosphodiester bond formation
• mRNA forms in the 5’ to 3’ direction

→ This is the primary transcript
or pre-mRNA

Stage Two: RNA processing
• The pre-RNA has exons and introns
• Introns = non-coding sequences
→ Removed via RNA splicing
• Exons = coding sequences
→ Joined together to form mature mRNA
→ Mature mRNA leaves the nucleus via the nuclear pore

Translation
Stage Three: Translation
1. mRNA binds to ribosome
• Translation starts at START codon of mRNA
(Codon: AUG, codes for methionine)
2. tRNA carries specific amino acid to ribosome

• Binds to large subunit of ribosome
• Has specific tRNA / anticodon for
the amino acid
• Anticodon of tRNA complementary base pair
to codon on mRNA by forming H bonds

3. A second tRNA molecule with amino acids
binds with the next codon on mRNA
• Two tRNAs hold amino acids in place, side
by side for peptide bond formation
• 2 tRNAs are bound at the ribosome at a time

4. Peptidyl transferase in the ribosome
→ Catalyses the formation of peptide bond
between the two amino acids

5. Ribosome moves along one codon more
on the mRNA
• In the 5’ to 3’ direction
• Next tRNA arrives and amino acids are
added one at a time
• Previous tRNA detaches, moves away
and is recycled
• Polypeptide is released when STOP

codon (UAA, UAG, UGA) reached

• Polyribosomes are often used
→ One mRNA may have many ribosomes binding to it
→ Many polypeptides of the same type can be made
from 1 mRNA
→ Fast response to the cell’s changing requirements

• mRNA is short-lived / labile.
• Production of protein is only for a short period of time
• But why?
• Gene expression can be controlled

→ Gene expression = process of DNA → protein
→ Prevents too much product forming
→ Efficient for energy use

Protein Synthesis Summary

Q: How do we know which codon codes for what amino acid?
A: Use a codon table!

Example question:
Given the sequence of the DNA template strand below, what is the
sequence of amino acids in the resulting polypeptide chain?
DNA TAC TGA ATA GCC CCG AAA ATT
mRNA
Polypeptide

Mutation
Mutations
• Random change in the
nucleotide sequence of a gene
→ Affects phenotype
(appearance/trait) of organism
https://www.youtube.com/watch?v=oTMpl8_9684
Two types of mutations:

a) Chromosome mutation
• Change in structure/number
of chromosomes
b) Gene mutation

Gene Mutations
• Mutations = change in the
sequence of bases in a gene
→ Causes altered codons in mRNA
seq
→ May alter amino acid seq of
polypeptide chain
• Can result in new alleles

• Alleles = diff forms of one gene

Gene Mutations
Types of gene mutations:
• Substitution
• Insertion/Addition
• Deletion
• The simplest form of mutation

involves only a change of one
nucleotide
→ Point mutations / base mutations

Base substitution
• Only one nucleotide is replaced by another
Can result in one of 3 types of mutations:

1. Silent mutation
= triplet code / codon still codes for the same amino acid
2. Nonsense mutation
= stop codon is introduced
3. Missense mutation
= triplet code / codon codes for a different amino acid

Base substitution
Result in STOP codon

Triplet code Premature chain Only one amino acid
changed but termination of the polypeptide
amino acid seq is Subsequent amino seq is affected
unaffected acids are not
If amino acid has side chain
formed with different property,
tertiary structure is more
affected.
Normal, Incomplete, Faulty protein, may
functional non-functional be still functional
protein polypeptide
Base Insertion + Base Deletion
Results:
1. Frameshift mutations
• Deleting/inserting one nucleotide of DNA will change which
bases are read together
• All subsequent codons are affected, all subsequent amino
acids affected
• Faulty, non-functional protein
2. Nonsense mutation
• Result in STOP codon
• Premature chain termination
• Subsequent amino acids are not formed
• Incomplete, non-functional polypeptide
Base Insertion + Base Deletion
Q: But what if 3 nucleotides are deleted at once?
A:
Can result in the deletion of 1 codon
Deletion of 1 amino acid
Protein may still be functional!

Example: Sickle Cell Anaemia
• Inherited blood disorder
• Affects the structure of the haemoglobin
• Cause: Base substitution in gene coding for β-globin

P/S: the textbook is
wrong and yes, you
need to rmb that T is
replaced by A.
• Base substitution in gene coding for β-globin results in

→different mRNA codon
→different tRNA brings a different amino acid to ribosome
→ leads to a change of 6th amino acid in polypeptide chain

→Altered primary structure
→Glutamic acid is polar whereas valine is non-polar
→Changed secondary, tertiary and quaternary structure
Mutated β-globin causes:
• Hb molecule to become less soluble
• Stick tgr to form fibres
• Less able to bind oxygen
• Cells to become crescent /

sickle-shaped
• Sickled red blood cells are prone to
rupture (haemolysis)
• May block blood vessels

• A person that inherited TWO
mutated β-globin alleles (HbS) will
have sickle cell anaemia
→ One from mother, one from father
• A person with ONE HbS and ONE HbA

(normal β-globin allele) is only a
carrier
→ Still have one working copy
→ No disease

Chapter Outline
Part 1 : Nucleic Acids
• Structure of Nucleotides
• RNA and DNA
• Semi-Conservative DNA Replication
Part 2 : Protein Synthesis

• Triplet Code → Codon → Anticodon
• Transcription
• RNA processing
• Translation
• Gene mutation
→ Sickle cell anaemia
Videos!
On the controversy of Watson & Crick’s experiment:
•Rosalind Franklin vs. Watson & Crick - Science History Rap Battle
https://www.youtube.com/watch?v=35FwmiPE9tI
•DNA Replication
(in a bit more detail than you need to know)
https://www.youtube.com/watch?v=5qSrmeiWsuc
https://www.youtube.com/watch?v=TNKWgcFPHqw
•Transcription and Translation: From DNA to Protein

https://www.youtube.com/watch?v=bKIpDtJdK8Q
•Banana DNA Experiment

https://www.youtube.com/watch?v=pdDP9OcqcbA
A little unrelated, but pretty inspiring:

•How simple ideas lead to big discoveries
https://www.youtube.com/watch?v=F8UFGu2M2gM

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AS Level

Nucleic Acids and

Part 2 : Protein Synthesis

DNA structure discovered by

Updated on 13/7/21 by Beh SJ @behlogy

• Bond between adjacent monomers after condensation

Updated on 13/7/21 by Beh SJ @behlogy

Updated on 13/7/21 by Beh SJ @behlogy

Purine bases – has 2 rings:

Pyrimidine bases – has 1 ring only:

Updated on 13/7/21 by Beh SJ @behlogy

Updated on 13/7/21 by Beh SJ @behlogy

Updated on 13/7/21 by Beh SJ @behlogy

Updated on 13/7/21 by Beh SJ @behlogy

Updated on 13/7/21 by Beh SJ @behlogy

Updated on 13/7/21 by Beh SJ @behlogy

Updated on 13/7/21 by Beh SJ @behlogy

• Pairing of bases is precise

• Important for 3D structure of molecule

Important for DNA replication / transcription

Updated on 13/7/21 by Beh SJ @behlogy

Deoxyribose sugar Updated on 13/7/21 by Beh SJ @behlogy

It’s called 5’ bcs it is 5’

Updated on 13/7/21 by Beh SJ @behlogy

You only need to be given what one end of

2. Helicase break H bonds

Updated on 13/7/21 by Beh SJ @behlogy

• The bases of activated nucleotides form

Updated on 13/7/21 by Beh SJ @behlogy

• DNA pol links activated nucleotides together

• This occurs step-by-step

• Process continues along whole

Updated on 13/7/21 by Beh SJ @behlogy

• The fragments are joined by an enzyme, DNA ligase

Updated on 13/7/21 by Beh SJ @behlogy

Updated on 13/7/21 by Beh SJ @behlogy

DNA molecule has DNA molecule has 1 Each DNA strand

Updated on 13/7/21 by Beh SJ @behlogy

• Using bacteria E.coli & different nitrogen sources

1) Grow E.coli with nitrogen-15

2) Transferred to a medium with nitrogen-14

Updated on 13/7/21 by Beh SJ @behlogy

1 heavy DNA 14N

Updated on 13/7/21 by Beh SJ @behlogy

Updated on 13/7/21 by Beh SJ @behlogy

• More than 1 triplet code can

Updated on 13/7/21 by Beh SJ @behlogy

• Messenger RNA (mRNA)

• Transfer RNA (tRNA)

• Ribosomal RNA (rRNA)

Updated on 13/7/21 by Beh SJ @behlogy

• Codon = set of 3 bases on mRNA

• Stop codon: UAA, UAG, UGA (textbook got this wrong!)

Updated on 13/7/21 by Beh SJ @behlogy

• 20 diff types of tRNA for 20 diff amino

• Carries a specific amino acid to

• Anticodon = specific exposed 3 bases on

Updated on 13/7/21 by Beh SJ @behlogy

Updated on 13/7/21 by Beh SJ @behlogy

Two ribosomal subunits:

2. Helicase break H bonds

transcribed / template strand

Updated on 13/7/21 by Beh SJ @behlogy

• RNA pol joins activated RNA nucleotides together