D1.

2 Protein Synthesis
SL/HL Terms Tick HL Terms Tick
Transcription 5’ to 3’
RNA Promoter
RNA Polymerase Initiation of Transcription
Hydrogen Bonding Transcription Factors
Complementary Base Pairing Gene Expression
Uracil Non-Coding DNA
Somatic Cells Telomeres
Gene Expression Introns
Genes Exons
Translation Post-Transcriptional
Modification of mRNA
Ribosome 5’ Cap
Small Subunit (of Ribosomes) 3’ Poly A Tail
Large Subunit (of Ribosomes) Spliceosome
Messenger RNA (mRNA) A Site (Aminoacyl Site)
Transfer RNA (tRNA) P Site (Peptidyl Site)
Genetic Code E Site (Exit Site)
Codon Pre-Proinsulin
Anticodon Proinsulin
Degeneracy of the Genetic Code Proteome
Universality of the Genetic Code Proteasomes
Stop Codon
Start Codon
Mutation
Base Substitution Mutation

IB Guiding Questions
How does a cell produce a sequence of amino acids from a sequence of DNA bases?
How is the reliability of protein synthesis ensured?

Linking Questions:
How does the diversity of proteins produced contribute to the functioning of a cell?
What biological processes depend on hydrogen bonding?

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DNA and RNA
Question: Distinguish between the
structures of RNA and DNA.

Transcription http://www.youtube.com/watch?v=ubdoUqmNF98
Transcription is the synthesis of RNA, using DNA as a template. The enzyme RNA
polymerase transcribes DNA to RNA.

Question: Explain transcription.

RNA polymerase attaches to the

beginning of a gene on DNA.

RNA polymerase separates the DNA

strands.

An mRNA molecule is produced on the

template DNA strand, using the enzyme
RNA polymerase to link RNA nucleotides
into a single polynucleotide (by
condensation reactions).

RNA polymerase uses complementary base pairing to pair DNA and RNA nucleotides. RNA
polymerase reaches the end of the gene, and the mRNA molecule is released.

DNA and RNA Complementary Base Pairs

During transcription, RNA nucleotides form complementary base pairs with DNA nucleotides of
the gene being transcribed. The DNA and RNA bases are held together by hydrogen bonds.
The DNA - RNA base pairs are:

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Stability of DNA
DNA is a stable molecule, due to the strong
covalent bonds between the nucleotides.

Single DNA strands can be used as a

template for transcribing a base sequence,
without the DNA base sequence changing.

In somatic cells that do not divide, such

sequences must be conserved throughout
the life of a cell.

Somatic cells are non-reproductive cells in

an organism.

Protein Synthesis
Protein synthesis consists of two
stages:

- Transcription is the synthesis of

RNA, using DNA as a template.

- Translation is the synthesis of

polypeptides (proteins) by
ribosomes, using the genetic code
of mRNA.

Transcription is Expression of Genes

Gene expression is the process by which genetic information in a gene is used to synthesise a
functional polypeptide. A gene must be transcribed to mRNA before the mRNA can be translated
by a ribosome. Not all genes in a cell are expressed at any given time. Gene expression can be
switched on and off by regulating transcription of genes. If transcription does not occur, then
translation cannot occur.

Translation is Polypeptide Synthesis

Translation is the synthesis of polypeptides by ribosomes. Ribosomes require messenger RNA
(mRNA) and transfer RNA (tRNA) to synthesise polypeptides. mRNA brings the genetic code to
the ribosome, and tRNA brings amino acids to the ribosome.

Ribosomes
Ribosomes are organelles found in cells which translate the genetic code of mRNA to a
polypeptide.
Ribosomes are composed of two subunits:
- Small subunit
- Large subunit
Two tRNA molecules can bind simultaneously to the large subunit of a ribosome.

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Messenger RNA
Messenger RNA (mRNA) contains the
genetic code in the form of codons.

mRNA binds to the small subunit of a

ribosome to initiate translation.
Codons are a sequence of three nucleotides
that code for an amino acid.
Ribosomes use the sequence of codons on
mRNA to determine the sequence of amino
acids in a polypeptide.

Transfer RNA
Transfer RNA (tRNA) transfers amino acids
from the cytoplasm to the ribosome.

tRNA molecules have an anticodon, which

binds to mRNA codons.

The binding of codons of mRNA and

anticodons of tRNA in the ribosome by
complementary base pairing ensures that the
correct sequence of amino acids is
synthesized by the ribosome.

Codons and Anticodons

During translation, codons of mRNA bind to

anticodons of tRNA, within ribosomes, by
complementary base pairing.

Codons and anticodons form hydrogen bonds between complementary nucleotides.

Both mRNA and tRNA contain uracil, so the complementary base pairs are:
- Cytosine - Guanine
- Adenine – Uracil

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Features of the Genetic Code
Twenty amino acids are found in the
proteins of living organisms.
The genetic code must be able to code
for all 20 amino acids.
Combining nucleotides into sequences
of three nucleotides produces 64
different codons, which can code for 20
different amino acids.

The genetic code is universal, as the

same code is used in all life forms.
The genetic code is degenerate, as
more than one codon may code for the
same amino acid.
There are three stop codons, which do
not code for an amino acid, and
terminate translation.
The anticodon of the first tRNA in
translation binds to a start codon.

The Genetic Code http://www.youtube.com/watch?v=LsEYgwuP6ko

The sequence of amino acids in a polypeptide can be
determined using the codon sequences in mRNA,
combined with a table of mRNA codons.

Question: Determine the sequence of amino acids for

mRNA with the following sequence of codons:
CUA GAU CGA AUC

Movement of Ribosomes
- The ribosome moves along mRNA from
codon to codon.
- At each codon, a tRNA enters the
ribosome.
- When two tRNAs are present in the
ribosome, a peptide bond forms between
their amino acids.
- One tRNA loses its amino acid and
leaves the ribosome.
- The polypeptide chain grows as the
ribosome moves from codon to codon.
- The polypeptide, small and large
ribosomal subunits and tRNA are
released when a stop codon enters the
ribosome.

5
Translation http://www.youtube.com/watch?v=BcOZ-_f5e0c
Question: Describe translation.
- Translation is the synthesis of polypeptides
using the genetic code of mRNA by
ribosomes.
- There are specific codons for each amino
acid on the mRNA.
- The small ribosomal subunit binds to mRNA
at the start codon.
- A tRNA with a complementary anticodon
binds to the mRNA codon by hydrogen
bonding.
- The large ribosomal subunit attaches to form
a ribosome.
- A second tRNA molecule enters the
ribosome, as there are two tRNA binding
sites in the large ribosomal subunit.
- A peptide bond forms between the two amino
acids by a condensation reaction, releasing
one tRNA from the ribosome.
- The ribosome moves from codon to codon
along the mRNA, adding amino acids to a
growing polypeptide.
- When the ribosome reaches a stop codon,
the large and small subunits separate.
- The tRNA and polypeptide are released.

Mutations http://www.youtube.com/watch?v=hRnrIpUMyZQ
A mutation is a change to the DNA sequence of an organism. A mutation to a single nucleotide
in the gene for haemoglobin can cause the disease sickle cell anaemia.
Sickle Cell Anaemia
- A single base substitution mutation for
the alpha globin molecule of
haemoglobin causes sickle cell anaemia.
- A base substitution mutation involves the
swapping of one nucleotide for another.
- In the case of sickle cell anaemia, the
base substitution mutation of DNA
changes one codon, which changes one
amino acid in the alpha-globin molecule.
- If a person has two copies of the sickle
cell allele, they suffer from sickle cell
anaemia.
- The red blood cells of a person with
sickle cell disease form a sickle shape,
and they may block small blood vessels.

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Directionality of RNA
The enzyme RNA polymerase can only
add nucleotides in the 5’ to 3’ direction
during transcription.

The C-5 of a nucleotide is added to the C-

3 end of the preceding nucleotide,
producing a sugar-phosphate backbone
for RNA.

Ribosomes Move from 5’ to 3’ During Translation

Translation is the production of
polypeptides by ribosomes using mRNA
genetic code.

The 5’ end of mRNA enters the

ribosome.
The ribosome moves along the mRNA
molecule in a 5’ to 3’ direction

Stages of Transcription

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Initiation of Transcription and the Promoter Region

Promoters are non-coding sections of DNA. Promoters for different genes have different base
sequences. The promoter is a section of DNA where RNA polymerase binds to initiate
transcription of a gene. Genes can be turned on (producing mRNA which is expressed as a
polypeptide) or off at different stages of an organism's/cell’s life cycle.

Transcription Factors Control Gene Expression

Regulation of genes is important in responding to changes in the environment and for cell
differentiation. Transcription factors are regulator proteins which attach to the promoter region.
Transcription factors control whether RNA polymerase can attach to the promoter region, thus
controlling gene expression.

Non-Coding Sequences of DNA

Coding DNA are gene sequences that code for mRNA and are expressed as functional
polypeptides. Non-coding DNA are sections of DNA that do not code for functional
polypeptides. Some sections of non-coding DNA have functions such as:
Controlling gene expression: Some base sequences, such as promoter regions, are sites
where regulatory proteins bind. These proteins may promote or inhibit the transcription of
genes.
Genes for tRNA and rRNA: Transcription of these genes produces tRNA and rRNA (ribosomal
RNA).
Telomeres: are repetitive base sequences at the ends of the chromosomes.
When eukaryotic DNA is replicated, the ends of the molecule cannot be copied, so a short
section of the base sequence is lost. The presence of telomeres at either end of the DNA
molecule prevents important genes from being lost. The length of the telomeres limit the number
of possible cell cycles.

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 Genes consist of introns and exons.
Introns are sections of DNA or RNA that do not code for a protein, and interrupt the gene
sequence.
Exons are sections of DNA or RNA that do code for a protein.
Introns are removed from mRNA after transcription.

Introns and Exons http://www.youtube.com/watch?v=O0wouZGmXwI

After transcription mRNA contains exons and introns.
Question: Explain how mRNA is processed to remove the introns.

Post-Transcriptional Modification of mRNA:

When a gene is transcribed in eukaryotes, the pre-mRNA contains introns and exons. The
exons code for a polypeptide, but the introns need to be removed from the RNA molecule. A
cap is added to the 5’ end of the mRNA and a poly-A tail is added to the 3’ end of the mRNA
to stabilize the mRNA. Spliceosomes attach to both ends of an intron. The spliceosomes cut
out the intron. The exons are spliced together to form mature mRNA. The mature mRNA is
translated into a polypeptide by a ribosome.

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Splicing of Exons
Exons from one mRNA can be spliced together in different combinations. One gene may code
for different proteins, based on how the exons are spliced together.

Ribosome Binding Sites

The small ribosomal subunit
has a binding site for mRNA.

The large ribosomal subunit has

three binding sites for tRNAs:

- A Site (Aminoacyl
Site)
- P Site (Peptidyl site)
- E Site (Exit site)

tRNA Binding Sites

The functions of the tRNA binding sites on the large ribosomal subunit are:
A Site (Aminoacyl Site): The tRNA brings a new amino acid into the ribosome to be added to
the elongating polypeptide chain.
P Site (Peptidyl site): Holds tRNA with the growing polypeptide chain.
A peptide bond forms between the amino acid held in the A site and P site. This bonding
releases the tRNA into the E site.
E Site (Exit site): After the tRNA enters the E site, it is released from the ribosome.

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Translation

Translation involves three stages:

- Initiation
- Elongation
- Termination

Translation: Initiation
The small ribosomal subunit binds to the
mRNA at the start codon (AUG).

A tRNA molecule with the anticodon

complementary to the start codon binds to
the mRNA.

The large ribosomal subunit binds to the

small ribosomal subunit.

The tRNA is in the P site. A second codon

enters the A site.

A tRNA with the complementary anticodon

(complementary to the second codon) enters
the A site.

A peptide bond forms between the two amino

acids.

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Translation: Elongation
The elongation of the polypeptide involves
a repeated cycle of events:
- The ribosome moves
(translocates) along the mRNA by
three bases towards the 3’ end of
the mRNA. Moving one tRNA into
the E site, which exits the
ribosome.
- A new tRNA is in the P site. A new
tRNA (with the anticodon
complementary to the codon) with
amino acid enters the A site.
- The two neighbouring amino acids
bond, resulting in a growing
polypeptide chain.
- The two neighbouring amino acids
bond, resulting in a growing
polypeptide chain.

Translation: Termination
A stop codon enters the A site, then:
- No tRNA is available to enter the A site, causing the release of the polypeptide from the
P site.
- The tRNA detaches from the ribosome.
- The mRNA detaches from the ribosome.
- The large subunit and small subunit separate.
The polypeptide may need to be modified after translation to become a functional protein.

Modification of Polypeptides http://www.youtube.com/watch?v=5Px94fV-Po0

Many polypeptides must be modified after translation before they can function.
Question: Explain how pre-proinsulin is modified to form insulin.

Pre-proinsulin is formed by transcription and translation.

Pre-proinsulin is converted to functional insulin in two steps:
Formation of Proinsulin:
A signal peptide is removed from preproinsulin within the rough endoplasmic reticulum to form
proinsulin.
Formation of Insulin:
Proinsulin is sent to the Golgi apparatus and is packaged into a secretory vesicle.
Within the secretory vesicle, a protein chain is removed from proinsulin to form an alpha chain
and a beta chain.
The alpha and beta chains join by disulfide bonds to form functional insulin.
Insulin is secreted into the bloodstream by exocytosis.

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Proteasomes
A proteome is the entire complement of proteins that is expressed by a cell or organism.
The cell synthesizes all of the proteins required by the cell.
Proteins which are no longer required are broken down to amino acids by proteasomes.
Proteasomes are large protein complexes which break down unneeded proteins to amino acids
through hydrolysis reactions.
The amino acids are recycled to synthesize proteins that are required by the cell.

End Topic 9C Notes

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