AS BIOLOGY Chapter 6 topic 3

Protein synthesis
6.2 Protein synthesis

6.2.1 state that a polypeptide is coded for by a gene and that a

gene is a sequence of nucleotides that forms part of a DNA
molecule

6.2.2 describe the principle of the universal genetic code in

which different triplets of DNA bases either code for specific
amino acids or for start and stop signals
The genetic code: timeline
 The central dogma of genetics

• Genes are simply codes for making polypeptides.

• DNA is stored in the nucleus, yet the polypeptide is
produced in the cytoplasm by ribosomes.
• mRNA (messenger RNA) is a message from the
nucleus to the ribosome – instructions for how to put
the polypeptide together.
• The genetic code is the sequence of bases on mRNA –
this tells the ribosome which amino acids to use.
 Example: skin color

Polypeptide are
The molecule shown below is
proteins or subunit
melanin and determines skin
of proteins
color. The more you have the
darker your skin color is.
 Example: cell function

Proteins determine the structure

and function of cells. What are
the functions of these proteins?
What is the genetic code?
• All three-letter words
• Start with the same word
• Finish with ‘end’ – not in the sentence
• Many words and phrases repeated or reused
• All three-letter words = DNA is transcribed in triplets, this gives
mRNA codons (genetic code) – sequences of three RNA
bases
• Start with the same word = each gene starts with a ‘start’
codon
• Finish with ‘end’ – not in the sentence = ‘stop’ codon at end of
gene
• Many words and phrases repeated or reused = there are 64
different combinations but infinite polypeptides. Many are
reused.
 What is the genetic code?
• The genetic code of an organism is the sequence of bases
along its DNA.
• It contains thousands of sections called genes.
• Each gene codes for a specific polypeptide.
one gene

thousands more bases

in gene (not shown)
• All polypeptides are made from amino acids, so the
sequence of bases in a gene must code for amino acids.
• The genetic code is almost universal – the same
sequence of bases codes for the same amino acids in all
organisms.
 The triplet code
Given that there are four bases in DNA, and these code for
20 amino acids, what is the basis for the genetic code?

 If one base = one amino acid,

possible amino acids = 4
 If two bases = one amino acid,
possible amino acids = 16 (4×4)

 If three bases = one amino acid,

possible amino acids = 64 (4×4×4)

The existence of a three-base (triplet) code was confirmed

by experiments by Francis Crick and his colleagues in 1961.
The triplet code is degenerate, which means that each
amino acid is coded for by more than one triplet.
 What is mRNA?
When a polypeptide is required, the triplet code of its gene is
converted into a molecule of messenger RNA (mRNA).
This process is called transcription and is the first stage of
protein synthesis.

Like DNA, mRNA is a nucleic

acid, but it differs in that:

 it is single stranded,
not double stranded

 it contains ribose instead of mRNA strand

deoxyribose during
transcription
 it contains uracil instead of thymine.
 Transcription and codons
During transcription, the mRNA is built up by complementary
base pairing, using the DNA as a template. The DNA’s base
triplets are converted into mRNA codons.

What are the codons in the mRNA transcribed from this

sequence of DNA base triplets?

DNA triplets TAC GCA GAT TAC

mRNA codons AUG CGU CUA AUG

The genetic code is non-overlapping: each base is only

part of one triplet/codon, and each triplet/codon codes just
one amino acid.
 Cracking the Code
• The first codon was deciphered in 1961 by Marshall Nirenberg, of the
National Institutes of Health, along with his colleagues.
• Nirenberg synthesized an artificial mRNA by linking together many identical
RNA nucleotides containing uracil as their base. No matter where the
genetic message started or stopped, it could contain only one codon (UUU)
over and over.
• Nirenberg added this ‘poly-U’ polynucleotide to a test-tube mixture
containing amino acids, ribosomes, and the other components required for
protein synthesis. His artificial system translated the poly-U mRNA into a
polypeptide containing many units of the amino acid phenylalanine (Phe, or
F), strung together as a long polyphenylalanine chain. Thus, Nirenberg
determined that the mRNA codon UUU specifies the amino acid
phenylalanine. Soon, the amino acids specified by the codons AAA, GGG,
and CCC were also identified.
• Although more elaborate techniques were required to decode mixed triplets
such as AUA and CGA, all 64 codons were deciphered by the mid-1960s.
The genetic code
 The genetic code
Is universal
- All living things use the same code
- All living things have the same bases
- Codons code for the same amino acids no matter what
the organism

Is degenerate
- There are 64 codons
- But only 20 amino acids
- The same amino acid may be coded for by more than one
codon
- Reduced impact of base-substitution mutation, as amino
acid produced could still be the same
 Evidence for evolution
• The Genetic Code is Universal:
All living things use the same genetic code whether they are plants,
animals, or bacteria. This is one of the strongest pieces of evidence that
all living things have a common ancestor

• Expression of genes from different species: one species can be

programmed to produce proteins of a second species by introducing
DNA from the second species into the first.
6.2 Protein synthesis

6.2.3 describe how the information in DNA is used during

transcription and translation to construct polypeptides, including
the roles of:
• RNA polymerase
• Messenger RNA (mRNA)
• Codons
• Transfer RNA (tRNA)
• Anticodons
• ribosomes
6.2 Protein synthesis

6.2.4 state that the strand of a DNA molecule that is used in

transcription is called the transcribed or template strand and
that the other strand is called the non-transcribed strand
6.2.5 explain that, in eukaryotes, the RNA molecule formed
following transcription (primary transcript) is modified by the
removal of non-coding sequences (introns) and the joining
together of coding sequences (exons) to form mRNA
 Stage 1: Transcription
RNA polymerase makes an mRNA molecule that is
complementary to the DNA molecule
 Transcription
• In the nucleus, part of a DNA molecule unwinds and unzips as
the hydrogen bonds between the bases break (helicase).
• Free activated RNA nucleotides pair up with the exposed bases
of one strand only (transcribed strand or template strand).
• As the RNA nucleotides pair up with their complementary ones,
their sugar-phosphate groups are bonded together
(phosphodiester bond) by RNA polymerase to form a sugar-
phosphate backbone.
• The new single-stranded molecule which has formed is called
messenger RNA (mRNA).
• It leaves the nucleus via a pore in the nuclear envelope.
 Transcription
DNA Replication Transcription
DNA-DNA DNA-mRNA
A-T A-U Non-transcribed /
RNA Polymerase C-G C-G coding strand
(enzyme) that Same as mRNA except
makes the mRNA T is replaced with a U
(uracil)

Non-transcribed
TAGCAGTACAG
/ Coding strand

ATCGTCATGTC

Transcribed
/Template strand
Template strand
mRNA Base pairing rules used
to make mRNA, except
UAGCAGUACAG
U replaces T.
Transcribed and non-transcribed strand
Template strand
Base pairing rules used
to make mRNA, except
U replaces T.

Non-transcribed strand
Same as mRNA except T is
replaced with a U (uracil)
If the Template strand is AATGCCTA, What would the mRNA
be?..............................._____________

If the Coding/nontranscribed strand is AATGCCTA, What would

the mRNA be?..............................._____________

Coding strand
TAGCAGTACAG
ATCGTCATGT C

Template strand
If the Template strand is AATGCCTA, What would the mRNA be?
If the Template strand is AATGCCTA, What would the mRNA be?
.............................. UUACGGAU

If the Coding strand is AATGCCTA, What would the mRNA

be?...............................___________
be?..............................AAUGCCUA

Coding strand
TAGCAGTACAG
ATCGTCATGT C

Template strand
Transcription
 Transcription
RNA polymerase separates the DNA strands and…

Synthesizes mRNA strands which are…

Complementary to the template strand…

Meaning U is complementary to A, A is complementary

to T, etc.

The mRNA is the same as the non-transcribed strand

except U replaces T.
 The central dogma of genetics

In a bacterial cell, which lacks a nucleus, mRNA produced by

transcription is immediately translated without additional processing.
• In eukaryotic cell,
the nucleus provides
a separate
compartment for
transcription.
• The original RNA
transcript, called
pre-mRNA, is
processed in various
ways before leaving
the nucleus as
mRNA.
Modifying RNA (RNA splicing) in eukaryotes
 RNA splicing

Pre-mRNA

• In eukaryotes, the mRNA is modified (partly changed) before it leaved

the nucleus
• The original molecule is called the primary transcript
• The process of modification is called RNA processing, one step in this
processing is RNA splicing
• Splicing is the removal of sections called introns, the nucleotide
sequences that remain after the introns are removed are called exons.
• Exons are joined together after removal of the introns
 Alternative splicing

• In some cases, a given primary transcript molecule can be spliced in

different ways – alternative splicing
• This results in different mRNAs being made from the original primary
transcript
• These different mRNAs will produce different proteins when translated
• One gene can code for several different proteins or different forms of
the same protein
Transcription
6.2 Protein synthesis

6.2.3 describe how the information in DNA is used during

transcription and translation to construct polypeptides, including
the roles of:
• RNA polymerase
• Messenger RNA (mRNA)
• Codons
• Transfer RNA (tRNA)
• Anticodons
• ribosomes
 Stage 2: Amino acid activation
• In the cytoplasm, there are free
amino acids and transfer RNA
(tRNA) molecules.
• At one end of each tRNA
molecule is a site to which an
amino acid can bind. At the
other end are three unpaired
bases.
• The base triplet is called an
anticodon.
• Each tRNA molecule bonds with
a particular amino acid, under
the control of a specic enzyme
and with energy from ATP.
The structure of tRNA
Each tRNA is
reused after the
ribosome has
removed it’s amino
acid.
 Stage 3: Translation

• The ribosome is the Amino

Polypeptide acids
enzyme that pairs tRNA’s
tRNA with
with the mRNA and makes amino acid
attached
peptide bonds between Ribosome

amino acids.
• The mRNA is read from 5’ tRNA
to 3’. Anticodon

5 Codons 3
mRNA
 Translation uses the genetic code
• mRNA is used as a template, or instructions, to make a
polypeptide, or protein.

• Each three mRNA nucleotides (codon) codes for one

amino acid AUG UAC CUA GUC AUU
• How many amino acids are coded for in the above mRNA
molecule?___
• Which amino acid is coded for is called the genetic code.
Decode this piece of mRNA
AUG UUU ACU AAU UGA
Amino acid sequence:_____ _____ _____ _____ _____

The genetic
code!
Amino Acid 3
There are 20 different kinds Amino acid
attachment site
5

Would the codon in the

mRNA be TTC, AAG, or
UUC?

• Notice that tRNAs are Hydrogen

bonds
made of RNA.
• This RNA sequence is
also the product of
transcription.

Anticodon
 Structure and function of ribosome

• In the cytoplasm, the mRNA molecule attaches to a ribosome.

• Ribosomes are made of ribosomal RNA (rRNA) and protein
and contain a small and a large subunit.
 The initiation of translation

• the mRNA binds to the small subunit. Six bases at a time are exposed to
the large subunit.
• The first three exposed bases, or codon, are always AUG.
• A tRNA molecule with the complementary anticodon, UAC, forms
hydrogen bonds with this codon.
• This tRNA molecule has the amino acid methionine attached to it.
Fig. 17-18-1

Translation
E 3
mRNA
P A
5 site site
Fig. 17-18-2

Translation Ribosome moves

forward one
E
codon at a time.
3
mRNA
P A
5 site site
ATP

ADP
The ribosome catalyzes the
formation of a peptide bond
between neighboring amino E

acids.
P A

There are
two binding
sites for
tRNAs.
Fig. 17-18-3

Translation
E 3
mRNA
P A
5 site site
ATP

ADP

P A

P A
Fig. 17-18-4

Translation
Ribosome ready for E 3
mRNA
next tRNA P A
5 site site
ATP

ADP

E E

P A P A

ADP
ATP

P A
Fig. 17-19-1

Translation
 Amino
Polypeptide acids

tRNA with
amino acid
attached
Ribosome

tRNA

Anticodon

5 Codons 3
mRNA
Stages of protein synthesis
From DNA to amino acids
Review: Which is the ribosome, the Rough
ER, the polypeptide and the mRNA?

A
C

B
RER
Modifies proteins, multiple
polypeptides may come
together here to make
proteins with quaternary
structure, disulfide bonds may
form here.

Golgi body
Sugars added to proteins to
make glycoproteins, first
amino acid methionine
removed to make functioning
proteins, and in plants
enzymes convert sugars into
cell wall components.
Lysosomes also form here.
Disulfide bonds may form
here.
Exocytosis
Also called cell secretion. If the
protein excreted is an enzyme,
it is called an extracellular
enzyme.
6.2 Protein synthesis

6.2.6 state that a gene mutation is a change in the sequence

of base pairs in a DNA molecule that may result in an altered
polypeptide

6.2.7 explain that a gene mutation is a result of substitution or

deletion or insertion of nucleotides in DNA and outline how
each of these types of mutation may affect the polypeptide
produced
 Mutations
• An unpredictable change in the genetic material of an organism
• Generally, amino acid sequence is altered, so primary structure
of protein also altered, possibly tertiary structure and the active
site of the protein if it’s an enzyme.
• When a gene mutation occurs, the DNA is changed within a
gene and a new allele is produced.
• Sometimes the structure of an entire chromosome is affected
and these are called chromosome mutations.
• Mutagen: any substance that increases the chances of a
mutation. Ex: ultraviolet radiation, mustard gas (WWI) and
ionizing radiation.

Coding strand DNA: TGTTTCGATATGGGCTCGAGTCACT

mRNA: UGUUUGCAUAUGGGCUCGAGUCACU
• A gene is made up of a sequence of nucleotides, each
with its own base.
• The different alleles of a gene contain slightly different
sequences of bases.
 Types of gene mutation

Substitution Insertion Deletion

Original sequence

Mutated sequence

Which type of mutation will have significant effect

on the structure and function of the polypeptide the
allele codes for, why?

Base insertion or deletions always have large

effects, because they alter every set of three bases
that ‘follows’ them in the DNA molecule -- frame
shifts
 Reading frame

‘The red dog ate the bug’

‘ T Her edd oga tet heb ug’

UGG UUU GGC UCA

 Start Codons in mRNA Stop
codon codon

AUGUUUGCAUAUGGGCUCGAGUGA
AUGUUUGCAUAGGGGCUCGAGUGA Mutation 1
AUGUUCGCAUAUGGGCUCGAGUGA Mutation 2

• Base substitution: one base takes the place of another.

Least significant.
• Sometimes silent mutations in which case no effect.
Sometimes a stop codon (nonsense mutation) is created
though in which case there is a significant effect.
 Start Codons in mRNA Stop
codon codon

AUGUUUGCAUAUGGGCUCGAGUGA
AUGUUUGCAUAGGGGCUCGAGUGA Mutation 1
AUGUUCGCAUAUGGGCUCGAGUGA Mutation 2
AUGUUUAGCAUAUGGGCUCGAGUG Mutation 3

AUGUUGCAUAUGGGCUCGAGUGA Mutation 4

• Base addition: one extra base is added to the sequence.

• Base deletion: one or more bases are lost from the sequence.
• Changes all triplets in the DNA that follow and all codons in the resulting
mRNA that follows.
• This is why they are called frame shift mutations.
• Generally the mutated protein is non-functional, and sometimes a stop
codon is created as a result of the frame shift.
Substitution mutations
 Frame shift mutation
• Addition or deletion of one or more bases to a gene will
result in frame shift mutations
• This disrupts the reading frame, resulting in completely
different translation
• Often, the effects are so large that the protein that is made
is totally useless. Or the addition or deletion may introduce
a ‘stop’ triplet part way through a gene, so that the protein
is incomplete.
 Base substitution: one base takes the place of
another. Least significant.
• Sometimes silent mutations in which case no
effect. Base substitutions are often silent
mutations because many amino acids have more
than one triplet code
• Sometimes a stop codon is created though in
which case there is a significant effect, this is
called nonsense mutation.
• Sometimes one amino acid is changed altering
the primary structure of the protein. The
secondary, tertiary and quaternary structure may
be altered. This is called missense mutation.
Silent mutation
Which type of gene mutation?
Effect on the amino acid sequence?

Wild type

Mutant

Silent mutation, no effect on amino acid sequence

Which type of gene mutation?
Effect on the amino acid sequence?

Wild type

Mutant

Missense mutation
A range of effects depending on the location within the
protein and the identity of the new amino acid
Which type of gene mutation?
Effect on the amino acid sequence?

Wild type

Mutant

Nonsense mutation:
Effect depends on how close the new stop codon is to
the beginning of the coding sequence
Which type of gene mutation?
Effect on the amino acid sequence?

Wild type

Mutant

Insertion (1 nucleotide-pair insertion):

Frameshift causing immediate nonsense
Which type of gene mutation?
Effect on the amino acid sequence?

Wild type

Mutant

Deletion (1 nucleotide-pair deletion):

Frameshift causing extensive missense
Which type of gene mutation?
Effect on the amino acid sequence?

Wild type

Mutant

Deletion (3 nucleotide-pair deletion):

No frameshift, but one amino acid is missing
 Coding strand

Template strand