Biology Topic 7 Save My Exams

Head to savemyexams.co.
uk for more awesome resources
YOUR NOTES
DP Biology DP 
7. Nucleic Acids (HL Only)
CONTENTS
7.1 DNA Structure & Replication
7.1.1 DNA Structure
7.1.2 Mechanism of DNA Replication
7.1.3 Non-coding DNA
7.1.4 DNA Sequencing
7.1.5 Skills: The Hershey & Chase Experiment
7.1.6 Skills: Nucleosomes & Molecular Visualisation Software
7.2 Transcription & Gene Expression
7.2.1 Regulation of Gene Expression by Proteins
7.2.2 Environment & Gene Expression
7.2.3 Transcription
7.2.4 Post-transcriptional Modification
7.2.5 Skills: Analysing DNA Methylation Patterns
7.3 Translation
7.3.1 Translation
7.3.2 Ribosomes
7.3.3 Translation in Prokaryotes
7.3.4 Bioinformatics
7.3.5 Levels of Protein Structure
7.3.6 Skills: Polysomes & Ribosomes
Page 1 of 58
© 2015-2023 Save My Exams, Ltd. · Revision Notes, Topic Questions, Past Papers
Head to savemyexams.co.uk for more awesome resources
7.1 DNA Structure & Replication YOUR NOTES


7.1.1 DNA Structure
Nucleosomes
Unlike most prokaryotic DNA which is referred to as ‘naked’, eukaryotic nuclear DNA is
associated with proteins called histones (to form chromatin)
Histones package the DNA into structures called nucleosomes
The nucleosome consists of a strand of DNA coiled around a core of eight histone
proteins (octamer) to form a bead-like structure
DNA takes two turns around the histone core and is held in place by an additional
histone protein
The DNA molecule continues to be wound around a series of nucleosomes to form
what looks like a ‘string of beads’
Nucleosomes help to supercoil the DNA, resulting in a compact structure which saves
space within the nucleus
Nucleosomes also help to protect DNA and facilitate movement of chromosomes
during cell division
An analogy for supercoiling is twisting an elastic band repeatedly until it forms
additional coils
Nucleosomes can be tagged with proteins to promote or suppress transcription
Structure of a nucleosome
Page 2 of 58
YOUR NOTES

DNA is wrapped around a series of nucleosomes.

Nucleosomes coil tightly around each other to form the chromosome structure.
Page 3 of 58
Franklin's Investigations YOUR NOTES

NOS Making careful observations—Rosalind Franklin’s X-ray diffraction 
provided crucial evidence that DNA is a double helix.
In the 1950s Rosalind Franklin and Maurice Wilkins used a technique called X-ray
diffraction to study the structure of DNA
Franklin’s work was instrumental to Crick and Watson's model as the diffraction
patterns indicated that DNA had a double-helical structure
X-ray diffraction involves directing a beam of X-rays onto the molecule being studied
X-rays have a shorter wavelength and higher energy than visible light
The short wavelength allows X-rays to pass through the molecule, interacting with any
electrons within the atoms
The interaction causes X-rays to scatter (diffraction) at angles that indicate the
arrangement of atoms
The scattering pattern can be recorded on a film (similar to having an X-ray of a bone),
with dark marks appearing where the X-rays strike the film
Rotating the sample allows for the three-dimensional molecular structure to be
studied
Franklin was able to refine her methods and produce a clear diffraction pattern of DNA
Using mathematical techniques and available knowledge about DNA, Franklin deduced
that
DNA strands were helices - as represented by the X-shape
The pitch of the helix - as represented by the angle of the X-shape
The distance between nucleotides
Phosphates are located on the outside of the molecule
DNA was double stranded
Summary of Rosalind Franklin’s X-ray diffraction investigation, the diffraction pattern

represents the position of atoms in the sample of DNA
Page 4 of 58
DNA Structure Suggests Semi-conservative Replication YOUR NOTES

The discovery of the structure of DNA was due to experimental evidence and inputs from a 
range of independent researchers
Franklin’s X-ray diffraction patterns identified a compact double helix
Erwin Chargaff showed that DNA was composed of an equal number of purine and
pyrimidine bases which suggested base pairing
Crick and Watson used this evidence to build various physical models of DNA
One model had the bases facing outwards but Franklin argued they should face
inwards due to their hydrophobic nature
It was determined that if adenine paired with thymine and cytosine paired with guanine
in an antiparallel orientation a highly compact structure would result
When Crick and Watson proposed their model for the structure of DNA, they realised that
the double stranded structure suggested a mechanism for its replication during the cell
cycle
This was a key question that any model would have to address
Crick and Watson stated that as one chain of the double helix was the complement of the
other, either chain could act as a template during replication
They postulated that hydrogen bonds break, allowing separation of the chains
Each separate chain then acts as a template for the formation of a new
complementary chain on itself
This theory was called semi-conservative DNA replication as half of the original DNA
molecule is kept (conserved) in each of the two new DNA molecules
An opposing theory suggested DNA replicated ‘conservatively’
The entire original DNA double helix would stay together and serve as a template for a
new DNA molecule
Crick and Watsons' theory of semi-conservative DNA replication was later proven by
Meselson and Stahl
Page 5 of 58
YOUR NOTES

Semi-conservative replication of DNA
 Exam Tip
You don't need to memorise the nature of purine and pyrimidine bases in DNA; C and
T are pyrimidines; A and G are purines. A purine always bonds to a pyrimidine in the A-
T and C-G rules of base-pairing.
Page 6 of 58
7.1.2 Mechanism of DNA Replication YOUR NOTES


Leading Strand & Lagging Strand
Double-stranded DNA consists of two antiparallel strands (oriented in opposite
directions)
During DNA replication, the two strands are ‘unzipped’ and DNA polymerase moves along
each template strand linking nucleotides together to form a new strand
Crucially, DNA polymerase can only add new nucleotides in a 5’ to 3’ direction
As the template strands are antiparallel, replication needs to proceed in opposite
directions
As the replication fork opens up in one direction only, each new strand is synthesised
differently
The leading strand is made continuously, following the fork as it opens
The lagging strand is made discontinuously, in short fragments, away from the fork
As more template strand is exposed, new fragments (called Okazaki fragments) are
created
Okazaki fragments are later joined together by DNA ligase to form a continuous
complementary DNA strand
Page 7 of 58
YOUR NOTES

During DNA replication, synthesis of the leading strand is continuous but synthesis of the
the lagging strand is discontinuous in small fragments (not all the enzymes involved are
shown)
Page 8 of 58
Enzymes Involved in DNA Replication YOUR NOTES

DNA replication is carried out by a complex system of enzymes working as a team 
Helicase unwinds the DNA double helix at the replication fork by flattening out its helical
structure
Analogy - think about untwisting a rope ladder
Helicase then causes the hydrogen bonds between the two strands to break
Analogy - unzipping a zipper
DNA gyrase releases the strain within the supercoiled areas to allow helicase access to the
helix
Single-stranded binding proteins keep the separated strands apart whilst the template
strand is copied
DNA primase generates a short RNA primer on the template strands
Providing an initiation point for DNA polymerase III to add new nucleotides
A number of polymerases are involved in DNA replication, each with different functions
Two of these polymerases are
DNA polymerase III, which starts replication next to the RNA primer linking
nucleotides in a 5’ to 3’ direction to form a new strand
DNA polymerase I, which removes the RNA primers on the leading and lagging strands
and replaces it with DNA
DNA ligase joins up the Okazaki fragments by catalysing the formation of sugar-
phosphate bonds
Page 9 of 58
Direction of Replication YOUR NOTES

Similar to transcription and translation, DNA replication must occur in the 5’ to 3’ direction 
DNA polymerase only works in a 5’ to 3’ direction, adding nucleotides to the 3’ end
DNA polymerases can only add nucleotides to the 3’ end of a primer
DNA nucleotides have a phosphate bonded to the 5’ carbon of the deoxyribose sugar
When DNA polymerase adds a new nucleotide to extend the DNA strand, the 5’ phosphate
group of the incoming DNA nucleotide bonds to the free 3’ -OH group on the growing
strand
DNA nucleotides have a phosphate bonded to the 5’ carbon of the pentose sugar
Page 10 of 58
YOUR NOTES

When DNA polymerase adds a new nucleotide, the 5’ phosphate group of the incoming
nucleotide bonds to the free 3’ -OH group on the growing strand
Page 11 of 58
7.1.3 Non-coding DNA YOUR NOTES


Non-coding Regions of DNA
DNA molecules are very long but only certain regions code for the production of
polypeptides
These are called coding sequences
In humans only 1.5% of the genome contains coding sequences
The majority of a eukaryotic genome contains non-coding regions of DNA that do not code
for polypeptides but have other important functions
Non-coding gene regulatory sequences are involved in the control of gene expression by
enhancing or suppressing transcription
Non-coding sequences can produce functional RNA molecules like transfer RNA (tRNA)
Introns are non-coding sequences of DNA found within genes of eukaryotic organisms
Different proteins can be produced from a gene depending on how introns are
removed
Telomeres are regions of repeated nucleotide sequences at the end of chromosomes
that provide protection during cell division
The repeated sequence facilitates binding of an RNA primer at the end of the
chromosome leading to synthesis of an Okazaki fragment
Without telomeres, DNA replication could not continue to the end of the DNA molecule
and chromosomes would become shorter after every cell division
Nonetheless, telomeres shorten with age due to oxidative damage within cells
Loss of telomeres during ageing can be accelerated by smoking, exposure to
pollution, obesity, stress and poor diet
Antioxidants in the diet are claimed to reduce the rate of telomere shortening
Page 12 of 58
YOUR NOTES

The RNA molecule produced from the transcription of a gene contains introns that must be
removed before translation can occur.
Page 13 of 58
DNA Profiling YOUR NOTES

DNA profiling (sometimes called genetic fingerprinting) enables individuals to be 
identified based on their DNA profiles
It can be used in forensic investigations or paternity testing
Short, non-coding regions of DNA called variable number tandem repeats (VNTRs)
are analysed
The frequency that VNTRs are repeated is unique between different individuals
VNTRs are inherited and are similar in close relatives but different in unrelated
people
Monozygotic (identical) twins inherit identical VNTRs so can’t be differentiated
through profiling
To compare the respective DNA profiles of individuals, different regions of DNA
containing the VNTRs can be excised with restriction enzymes or amplified by PCR
(Polymerase Chain Reaction)
The VNTR region for individuals will be a different size as they have different numbers
of repeats
The resulting restriction fragment or amplified DNA will also be a different size
Different sized fragments will generate a unique DNA profile in gel
electrophoresis
DNA profile of specific VNTRs from three individuals. Different VNTRs could be analysed
simultaneously which would result in more bands in each column
Page 14 of 58
7.1.4 DNA Sequencing YOUR NOTES


DNA Sequencing
Application: Use of nucleotides containing dideoxyribonucleic acid to
stop DNA replication in preparation of samples for base sequencing
DNA sequencing allows for the nucleotide base sequence of an organism's genetic
material to be determined
Most methods for sequencing DNA involve the use of chain-terminating
dideoxynucleotides
The dideoxy chain-termination method was developed by Frederick Sanger in 1977
The chain-termination method uses modified nucleotides called dideoxynucleotides
Dideoxynucleotides have a slightly different structure to standard nucleotides
They lack the 3’-hydroxyl group so cannot form a covalent bond with the next
nucleotide to be incorporated by DNA polymerase
Dideoxynucleotides prevent elongation of the nucleotide chain, which therefore
terminates
Advances in technology have enabled the development of rapid high-throughput
sequencing methods which allow scientists to sequence the genomes of organisms
rapidly
Once the dideoxynucleotide is added to the developing strand DNA polymerase stops the
replication of the developing DNA strand to produce a shortened DNA chain
The chain termination method in action
DNA sample of interest is used as a template in chain-termination PCR
Deoxynucleotides and fluorescently-labelled dideoxynucleotides are used
In the extension step of PCR, DNA polymerase will incorporate deoxynucleotides
If a dideoxynucleotide is randomly incorporated, extension stops
Because of the nature of PCR, billions of copies of the DNA sequence of interest will be
produced that will be terminated (by a dideoxynucleotides) at random lengths
The fragments can separated by size in gel electrophoresis
Page 15 of 58
The fluorescent marker corresponds to a particular ‘terminator’ nucleotide and can be YOUR NOTES
visualised 
This allows the base sequence to be built up one base at a time
High-throughput method of carrying out the chain termination method
Page 16 of 58
7.1.5 Skills: The Hershey & Chase Experiment YOUR NOTES


Skills: The Hershey & Chase Experiment
Which Biomolecule is the Heritable Material?
DNA was identified in 1869 but many scientists assumed that protein was the heritable
material
owing to the fact that there are 20 amino acids and only 4 nucleotide bases
In the 1950s, Alfred Hershey and Martha Chase showed that DNA, not protein, is a factor of
heredity responsible for carrying genetic information from one generation to another
Viruses that infect bacteria were used in their experiment as they only consist of DNA
encapsulated by a protein coat
This would allow the biomolecule of heredity (ie. the one that caused bacterial cells to be
used to produce viral progeny) to be easily determined
Analysis of results of the Hershey and Chase experiment provided
evidence that DNA is the genetic material.
Hershey and Chase took advantage of the chemical differences between DNA and
proteins
DNA contains phosphorus but no sulfur
Amino acids (that make up proteins) contain sulfur but no phosphorus
Bacteria grown in separate media containing either radioactive sulfur (35S) or radioactive
phosphorus (32P) were infected with viruses
The progeny viruses contained either 35S labelled proteins or 32P labelled DNA
Unlabelled bacteria were then infected separately with either type of virus
Bacteria would be expected to contain the heritable material following infection
A blender was used to remove attached viruses from the bacterial cells and centrifugation
was used to isolate the bacteria
Viruses are small so remained in the supernatant in the centrifuge tube
Bacteria are larger so formed a pellet
Only the bacteria infected by 32P labelled viruses (DNA) were shown to be radioactive
This suggested that DNA (and not protein) was transferred to bacteria and is the
hereditary (genetic) material
Page 17 of 58
YOUR NOTES

Hershey and Chase's experiment provided unequivocal proof that DNA is the heritable
material
Page 18 of 58
7.1.6 Skills: Nucleosomes & Molecular Visualisation Software YOUR NOTES


Skills: Nucleosomes & Molecular Visualisation Software
Molecular visualisation software can be used to help understand molecular structures
Macromolecules like protein, DNA, RNA and complex carbohydrates can be
visualised as 3-D structures
This allows researchers to analyse macromolecules and/or study interactions between
them
Primary sequence information can be related to structure and function
This helps to relate how structure might relate to chemical or biological behaviour
Macromolecules can be represented in many different ways including ball and stick atom
models or simplified ribbon representations that show the protein backbone
Most molecular visualisation software is freely available on the Internet or can be
accessed through many bioinformatics repositories such as the Protein Data Bank (PDB)
Analysing the association between protein and DNA within a nucleosome
Visit the Protein Data Bank PDB site and search for: 6T79 structure of human nucleosome
(do not put the search term in quotes)
Select the “3D view” to view the protein structure in mol*
The 3-D structure of the nucleosome can be viewed
The DNA double helix can be clearly seen surrounding the histone proteins
Rotate or zoom into the image to visualise the different components
The DNA can be seen to make two loops around the histone octamer core
Look carefully - the tails of each histone protein can be seen projected from the
nucleosome core
These can be chemically modified to help regulate gene expression
Try changing different settings in the viewer or select a different viewer such as JSmol
Page 19 of 58
YOUR NOTES

Structure of human nucleosome yeast tRNA showing the association between DNA (in 2
loops around the edge) and histones (central region)
Page 20 of 58
7.2 Transcription & Gene Expression YOUR NOTES


7.2.1 Regulation of Gene Expression by Proteins
The Promoter Region

The function of the promoter
Only some DNA sequences code for the production of polypeptides, these are called
coding sequences
Non-coding sequences produce functional RNA molecules like transfer RNA (tRNA) or are
involved in the regulation of gene expression such as enhancers, silencers and promoters
The promoter is a non-coding sequence located near to a gene
The promoter is not itself transcribed
The promoter acts as the binding site for RNA Polymerase during the initiation of
transcription
Binding of RNA Polymerase to the promoter is under the control of various regulatory
proteins
Page 21 of 58
Gene Expression Regulated by Proteins YOUR NOTES

Gene expression varies in different cells 
Genes are not expressed equally in every cell
Essential genes needed for the survival of an organism are expressed all the time
eg. Genes for the main enzymes in the respiratory pathways or ATP synthase
Other genes are only expressed when needed and at levels that make specific
amounts of protein
eg. The gene for rhodopsin that is only expressed in light-sensitive receptor cells
of the eye
Regulatory mechanisms exist to ensure the correct genes are expressed at the correct
time
These mechanisms are different between prokaryotes and eukaryotes but both
employ transcription factors and other proteins that bind to specific sequences in
DNA
Regulation of gene expression in eukaryotes
Eukaryotes regulate gene expression in response to variations in their environment
Specific proteins bind to DNA to regulate transcription and ensure that only the genes
required are being expressed in the correct cells, at the correct time and to the right level
This is key to how processes of cellular differentiation and development in multicellular
organisms are controlled
Regulatory transcription factor proteins include activators and repressors, they are unique
to a specific gene
Activator proteins bind to enhancer sequences and increase the rate of transcription
Repressor proteins bind to silencer sequences and decrease or block transcription
General transcription factors are a type of transcription factors that bind directly to the
promoter to help initiate transcription
This helps RNA polymerase to attach to the promoter and start transcribing the gene
In eukaryotes, several general transcription factors are needed for transcription
A transcription factor binding to the promoter region of a gene which allows RNA
polymerase to bind and for transcription to occur.
Regulation of gene expression in prokaryotes
Unlike in eukaryotes, only one general transcription factor and RNA polymerase is needed
to initiate transcription
Page 22 of 58
When prokaryotes need to respond to environmental changes, additional proteins interact YOUR NOTES
directly with target regions of DNA to alter the level of gene expression 
For example, the genes involved in the breakdown and metabolism of lactose by
Escherichia coli are repressed in the absence of lactose
When no lactose is available, a repressor protein binds to DNA near the promoter of
the genes for the proteins that degrade lactose (lacZ, lacY and lacA)
The repressor physically blocks RNA polymerase from accessing that section of
the bacteria's genome
If lactose is present, the repressor protein is released from the DNA allowing RNA
polymerase to begin transcription
The genes are expressed and the lactose-degrading enzymes are produced
Lactose can be broken down and used for energy generation in this way
Once all the available lactose is metabolised, the genes are repressed again
This mechanism of negative feedback ensures that a cell’s resources are not wasted
making proteins that are not needed
In the absence of lactose the repressor protein binds which prevents RNA polymerase from
initiating transcription of genes coding for enzymes used to metabolise lactose.
When lactose is present it binds to the repressor protein allowing RNA polymerase to bind to
the promoter and begin transcription
Page 23 of 58
Exam Tip YOUR NOTES

 In your exam you may be asked to describe how the regulation of gene expression

affects mRNA produced by transcription or the amount of final polypeptide that is
produced. To help answer this, it is important to understand the roles of the various
different sections of a gene (promoter, coding sequence, terminator) and the
processes of transcription and translation.
Page 24 of 58
7.2.2 Environment & Gene Expression YOUR NOTES


Environment & Gene Expression
Environment and Gene Expression
An organism’s internal or external environment can influence gene expression patterns
The levels of regulatory proteins or transcription factors can be affected in response to
environmental stimuli such as light, and chemicals including drugs and hormones
For example, enzymes are activated in response to ultraviolet radiation and increase the
expression and production of melanin, leading to skin pigmentation
Temperature can also influence gene expression as demonstrated by organisms
The Himalayan rabbit (Oryctolagus cuniculus L.) possesses a gene for the
development of pigmentation in its fur
The gene is inactive above 35°C but active between 15°C and 25°C
In the parts of the body that are cooler such as ears, feet and nose the gene
becomes active making these areas black
Temperature also affects the expression of the sex chromosomes in Australia's
bearded dragon lizards (Pogona barbata)
Lizards raised in hot temperatures were female in appearance and were capable
of bearing offspring
Despite having the ZZ chromosomes usually found in male lizards
There is much debate about whether a particular phenotype or behaviour can be attributed
to inheritance or environment
Environmental factors explain the differences observed between identical twins as they
age
Identical twins have the same DNA but their individual genomes can come under
different outside influences
They can change independently, leading to phenotypic differences such as height
Twin studies have shown that environmental factors have a greater influence on
many disease states (e.g. cancer and rheumatoid arthritis) compared to genetic
influence
Page 25 of 58
YOUR NOTES

DNA is wrapped around histone proteins which form a nucleosome. Nucleosomes coil
tightly around each other to form the chromosome structure.
Page 26 of 58
Epigenetics YOUR NOTES

NOS: Looking for patterns, trends and discrepancies; there is mounting 
evidence that the environment can trigger heritable changes in epigenetic
factors
Epigenetics is the genetic control by factors other than an individual’s DNA sequence
Epigenetics is a broad term that encompasses (m)any alterations
That induce switching-on and switching-off of genes, but
Without changing the actual genetic code
Epigenetics involves heritable changes in gene function, without changes to the DNA
sequence
In eukaryotic cells, nuclear DNA is wrapped around proteins called histones to form
chromatin
Chromatin can be chemically modified in different ways to alter gene expression
Methylation of DNA (chemical addition of a -CH3 group)
Histone modification via acetylation, methylation and phosphorylation of amino
acid tails
Such modifications are called epigenetic tags and collectively, all the epigenetic tags in an
organism is called the epigenome
The epigenome can undergo changes due to environmental factors
Smoking, stress, exercise and diet can cause epigenetic changes
Internal signalling from the body's own cells can also cause modifications to occur
Epigenetic modification is independent, histone modification in one area is not linked to
modification in another
Like the genome, the epigenome is heritable
Mounting evidence demonstrates that modifications to the epigenome in one
generation can be passed on to the next generation at cellular or whole organism level
 Exam Tip
Epigenetics can be distinguished from mutations, both of which lead to changes in
the expressed characteristics of genes. Whilst mutations affect the genetic code
itself eg. by altered nucleotide sequences, epigenetics affect the way the code is
read.
Think about an identical passage of text being read by two different people, one with
perfect Queen's English and the other with a very strong regional dialect. Despite
the text being the same (no mutations), the effect of the dialect (epigenetics) might
alter the meaning of the piece drastically to a listener.
Page 27 of 58
7.2.3 Transcription YOUR NOTES


Nucleosomes Regulate Transcription
Nucleosomes are the structural unit of DNA packaging in eukaryotes that facilitate
supercoiling
Within a nucleosome, DNA is wrapped around proteins called histones
The tails of histones can be chemically modified which can influence whether a gene will
be expressed or not
An acetyl group, methyl group or a phosphate group can be added
Chemical modifications can either activate or deactivate genes by making the gene
more or less accessible to transcription factors
Methyl groups can also be directly added to DNA to change the activity of a gene
Acetylation and methylation of histone tails
Positively charged lysine (an amino acid) in histone tails binds to negatively charged DNA
This helps DNA to coil tightly around the histone protein core
Adding an acetyl group (acetylation) to lysine neutralises the charge, causing the DNA to
be less tightly wrapped
RNA polymerase and transcription factors can more easily access the DNA so gene
expression is stimulated
Adding a methyl group (methylation) to lysine maintains the positive charge causing the
DNA to be more tightly wrapped and therefore inhibits transcription/expression
Acetylation of the Nucleosome

Methylation of DNA
DNA methylation commonly involves the direct addition of a methyl group (-CH3) to
cytosine bases which can influence gene expression
Methylation of DNA suppresses the transcription of the affected gene by inhibiting the
binding of transcription factors
Page 28 of 58
Cells use this mechanism to lock genes in the ‘off’ position YOUR NOTES
DNA methylation can be affected by many environmental, lifestyle or age-related factors 
Direction of Transcription
The synthesis of mRNA occurs in three stages:
Initiation
Elongation
Termination
During initiation, RNA polymerase binds near the promoter, causing the DNA strands to
separate to form an open complex
During elongation, RNA polymerase moves along the antisense strand
RNA polymerase adds the 5‘ end of the free RNA nucleotide to the 3’ end of the
growing mRNA molecule
Elongation occurs in a 5’ to 3’ direction, synthesising a single strand of RNA
Termination occurs when RNA polymerase reaches a terminator sequence
Which triggers the detachment of the polymerase enzyme and mRNA strand
The antisense strand of the DNA molecule is the one that is transcribed
Page 29 of 58
7.2.4 Post-transcriptional Modification YOUR NOTES


Modification of RNA
In all kingdoms of life, gene expression can be regulated after an mRNA transcript has
been produced
Post-transcriptional modification of mRNA
Helps prevent degradation
mRNA is single stranded and therefore, inherently unstable
Increases the efficiency of protein synthesis
In eukaryotes, expands the complexity of the proteome
Prokaryotic mRNA does not require any significant post-transcriptional modification as
translation can occur immediately which prevents degradation of the mRNA
In eukaryotes, transcription and translation occur in separate parts of the cell, allowing for
significant post-transcriptional modification to occur
In eukaryotes, the immediate product of an mRNA transcript is called pre-mRNA which
needs to be modified to form mature mRNA
Three post-transcriptional events must occur
1. A methylated cap is added to the 5' end to protect against degradation by
exonucleases
2. A poly-A tail (long chain of adenine nucleotides) is added to the 3' end for further
protection and to help the transcript exit the nucleus
3. Non-coding sequences are removed through mRNA splicing
Page 30 of 58
mRNA Splicing YOUR NOTES

Eukaryotic genes contain both coding and non-coding sequences of DNA 
Coding sequences are called exons
Non-coding sequences are called introns
During transcription the whole gene is transcribed including all introns and exons
Introns are not translated as they do not code for amino acids and need to be
removed
Before the pre-mRNA exits the nucleus, splicing occurs, during which
Introns (non-coding sections) are removed
Exons (coding sections) are joined together
The resulting mature mRNA molecule contains only exons and exits the nucleus
before joining a ribosome for translation
The RNA molecule (known as pre-mRNA) produced from the transcription of a gene contains
introns that must be removed (to form mature mRNA) before translation can occur
Page 31 of 58
Alternative splicing YOUR NOTES

The exons (coding regions) of genes can be spliced in many different ways to produce 
different mature mRNA molecules through alternative splicing
A particular exon may or may not be incorporated into the final mature mRNA
Polypeptides translated from alternatively spliced mRNAs may differ in their amino acid
sequence, structure and function
This means that a single eukaryotic gene can code for multiple proteins
This is part of the reason why the proteome is much bigger than the genome
Image showing the alternative splicing of a gene to produce two different proteins
 Exam Tip
It is important you learn the terms pre-mRNA and mRNA, their location and whether
they include introns as well as exons. A handy way to distinguish between introns
and exons is to remember that EXons are EXpressed.
Page 32 of 58
7.2.5 Skills: Analysing DNA Methylation Patterns YOUR NOTES


Skills: Analysing DNA Methylation Patterns
Methylation of DNA
Methyl groups (-CH3) can be directly added to DNA to change the activity of a gene
DNA methylation commonly involves the direct addition of a methyl group to cytosine
bases which can influence gene expression
Methylation of DNA suppresses the transcription of the affected gene by inhibiting the
binding of transcription factors
Cells use this mechanism to lock genes in the ‘off’ position
DNA methylation involves the addition of a methyl group to a cytosine nucleotide

Analysing DNA Methylation Patterns
DNA methylation varies throughout a lifetime and can be affected by environmental,
lifestyle or age-related factors
Changes in DNA methylation are observed in genetic diseases like cancer
DNA methylation can be used as a biomarker to identify cancer related genes
This could help develop therapeutics to improve early diagnosis of disease
Numerous methods are available to identify which cytosine bases have been methylated
Page 33 of 58
Analysis of methylation patterns between a disease and non-disease state can help YOUR NOTES
identify disease marker genes 
DNA Methylation analysis showing reduced methylation of tumour-specific genes in

cancerous cells. Reduced methylation results in genes always being ‘switched on’ which
can lead to cancer
Page 34 of 58
7.3 Translation YOUR NOTES


7.3.1 Translation
Initiation of Translation
Initiation of translation involves assembly of the components that carry out
the process.
During translation, the specific sequence of messenger RNA (mRNA) is translated to
produce a polypeptide chain consisting of amino acids
mRNA is a single stranded, linear, RNA molecule that transfers the information in DNA
from the nucleus into the cytoplasm
Translation is categorised into three stages: initiation, elongation and termination
Translation occurs in the cytoplasm at complex molecules made of protein and RNA called
ribosomes
Ribosomes have a two-subunit (large and small) structure that helps bind mRNA
Ribosomes have three tRNA binding sites termed “E” (exit), “P” (peptidyl) and “A”
(aminoacyl)
At the A site the mRNA codon joins with the tRNA anticodon
At the P site the amino acids attached to the tRNA are joined by peptide bonds
At the E site the tRNA exits the ribosome
Another key molecule in translation is transfer RNA (tRNA) that decodes mRNA
tRNA molecules are single stranded RNA molecules that fold to form a clover-shaped
structure
The folded structure is held together by hydrogen bonds between bases at
different points on the strand
tRNA molecules are the shortest of the RNA molecules, being only around 80
nucleotides in length
There are 20 different types of tRNA molecule, one for each of the amino acids
involved in protein synthesis
tRNA molecules have a region that binds to a specific amino acid as well as a three-
nucleotide region called an anticodon that is complementary to the codon on mRNA
The role of tRNA molecule is to carry a specific amino acid to the ribosome
Page 35 of 58
YOUR NOTES

Structure of tRNA
In eukaryotic cells, the mRNA molecule leaves the nucleus through the nuclear pores
Translation is initiated by the following process
A small ribosomal subunit attaches to the 5’ end of mRNA
An initiator tRNA molecule carrying the amino acid methionine binds to the small
ribosomal subunit
The initiator tRNA occupies the “P” site on the ribosome
The ribosome moves along the mRNA until it locates a start codon (AUG)
The large ribosomal subunit binds to the small subunit
Elongation of the polypeptide can begin
Elongation of the Polypeptide

The initiator tRNA currently occupies the “P” site, the next codon on the mRNA signals for
the corresponding tRNA to bind at the “A” site
The two amino acids (attached to the tRNAs) are linked with a peptide bond, forming
a dipeptide
Synthesis of the peptide chain now involves a repeated cycle of events
In the cytoplasm, free tRNA molecules bind to their corresponding amino acids and
transport them to the ribosome
The ribosome shifts along the mRNA one codon (three bases) at a time
The initiator tRNA in the “P” site moves to the “E” site which releases it
The tRNA carrying the peptide chain moves from the “A” site to the “P” site
The next mRNA codon is exposed and a tRNA with the complementary anticodon
binds to the unoccupied “A” site whilst its amino acid is linked to the polypeptide
chain
The cyclical process is repeated as new amino acids are added to the growing chain
Page 36 of 58
Termination of Translation YOUR NOTES

The process of elongation continues until one of three ‘stop’ codons (UAA, UAG and UGA) 
on the mRNA molecule is reached
Stop codons do not code for a tRNA molecule but act as a signal for translation to
stop
The polypeptide chain and mRNA are released from the ribosome
The ribosome disassembles back into two separate subunits
And can await the arrival of the next mRNA molecule
Page 37 of 58
YOUR NOTES

Page 38 of 58
Following the initiation of protein synthesis, translation involves a repeated cycle of events YOUR NOTES
to build the polypeptide chain, tRNA molecules move into the A, P and E sites as the 
ribosome reads the mRNA
 Exam Tip
You don't need to remember the precise base sequences of start and stop codons
for your examination.
Page 39 of 58
tRNA-activating Enzymes YOUR NOTES

Amino acids are paired to specific tRNA molecules through the action of tRNA-activating 
enzymes
Each tRNA activating enzyme recognises a specific tRNA molecule
tRNA-activating enzymes, in common with most enzymes, are substrate-specific and
recognise the correct tRNA molecules by their shape
Nucleotide sequence variability between tRNA molecules results in variation in their
three-dimensional structure
Active sites of tRNA-activating enzymes are optimised to bind a specific tRNA
Initially, a tRNA-activating enzyme binds to ATP and a specific amino acid
The active site of the enzyme attracts a conformationally-specific tRNA molecule
The tRNA molecule is bound to the amino acid using ATP (phosphorylation) to create a high
energy bond
The stored energy in this bond will be used later in peptide bond formation to link the
amino acid to the growing polypeptide chain
This is an example of how an anabolic reaction like protein synthesis utilises the
energy stored in ATP
A tRNA molecule with an amino acid attached is called a charged tRNA
Specific tRNA-activating enzymes are involved in charging an amino acid to a specific tRNA
molecule
Page 40 of 58
7.3.2 Ribosomes YOUR NOTES


Structure of Ribosomes
Ribosomes are found in cells
Either freely in the cytoplasm (of all cells)
Or bound to the endoplasmic reticulum (ER) to form rough ER (only in eukaryotic cells)
Ribosomes are the site of protein synthesis
They consist of a large and a small subunit composed of protein and ribosomal RNA
(rRNA)
Protein provides structure to the ribosome
rRNA facilitates the binding of mRNA and tRNA and catalyses the formation of
peptide bonds between amino acids
Ribosomes have three tRNA binding sites and one mRNA binding site
mRNA sits in a groove between the two subunits and the ribosome moves along, forming a
polypeptide as it travels
A diagram of a ribosome, showing the small and large subunits
Free Ribosomes
In eukaryotic cells, protein synthesis commonly occurs at free ribosomes in the cytoplasm
Free ribosomes can move within the cytoplasm and synthesise proteins for use primarily
within the cell
As opposed to proteins destined to be secreted extracellularly
Proteins synthesised on free ribosomes are destined for use within the cytosol (the
fluid part of the cytoplasm)
And within large organelles such as mitochondria and chloroplasts
Page 41 of 58
Bound Ribosomes YOUR NOTES

Eukaryotic cells make thousands of proteins that need to be delivered to the correct 
location, sometimes in different tissues/organs altogether
When free ribosomes make proteins destined for lysosomes, or secretion from the cell, the
ribosome becomes bound to the endoplasmic reticulum (ER)
Signal sequences in the growing polypeptide chain dictate whether the free ribosome
needs to move to the ER
The signal sequence occurs at the beginning polypeptide
Signal recognition proteins bind to the polypeptide, pausing translation
The free ribosome binds to a receptor on the ER, forming rough ER
Translation is re-initiated and the polypeptide chain moves inside the ER
The synthesised protein can be carried via a vesicle to the Golgi apparatus before being
secreted out of the cell
Proteins destined for lysosomes or secretion out of the cell are synthesised by ribosomes
bound to the endoplasmic reticulum
Page 42 of 58
7.3.3 Translation in Prokaryotes YOUR NOTES


Translation in Prokaryotes
Prokaryotic cells have a less complex ultrastructure than eukaryotic cells
Eukaryote cells are divided up into membrane-bound compartments called organelles
Transcription and translation happen in different compartments because ribosomes
are separated from the nucleus
The lack of a nucleus is a defining cellular feature of prokaryotes, allowing transcription
and translation to take place in the same compartment
Translation can occur immediately after transcription due to the absence of a nuclear
membrane
Both processes proceed simultaneously and likely in a coupled fashion
Translation starts even before the mRNA has finished being transcribed from the
DNA
Transcription and translation occur simultaneously in prokaryotes due to the absence of a

nuclear membrane. Ribosomes start translating the mRNA whilst it is still being synthesised.
Page 43 of 58
7.3.4 Bioinformatics YOUR NOTES


Bioinformatics
The 21st Century has seen a tremendous increase in the amount of biological data
This has been due to rapid advances in DNA sequencing and other technologies
Developments in scientific research have been accompanied by improvements in
computing, enabling scientists to interpret complex biological data using bioinformatics
applications
Bioinformatics is an interdisciplinary field that develops methods and software to help
further our understanding of life by making sense of this data
Although many new bioinformatics applications are at the forefront of applied
computing, most scientific research uses standard tools and databases
Data related to gene sequence, protein structure, gene expression or metabolites is
curated, annotated and stored in databases such as GenBank, NCBI, EBI, PDB
A range of open source software tools is available to query this data
Sequence similarity
If a scientist has an unknown DNA sequence, they can determine if it codes for a gene
BLAST (Basic Local Alignment Search Tool) search can compare the unknown DNA
sequence to all known gene sequences in a particular database
BLAST finds regions of similarity between sequences
The search returns ‘hits’ which are the sequences most related to the search sequence
(depending on the parameters set)
There are many variations of BLAST that can be used for different analyses such as protein
sequences or comparing multiple input sequences at once
Genetic variation and evolutionary relationships
Scientists can compare homologous gene sequences between many organisms
Sequences are compared using an alignment tool such as Clustal W (there are many
alternatives)
This aligns (stacks) the sequences based on similar regions so that variable regions
can be identified
This determines the degree of similarity between organisms which gives an indication of
how closely related the organisms are
There may be a common ancestral origin but in some organisms, the gene might have
accumulated differences over times from random mutations
Tree-like evolutionary diagrams (phylogenetic trees) can be constructed with software
such as PhyloWin to show the degree of relatedness to a recent common ancestor
Phylogenetic analysis is useful for biological classification, conservation studies,
forensics or molecular epidemiology which can help dictate public health policy
Variants of highly infectious pathogens such as SARS-CoV-2 (a well-known
coronavirus) can be identified using these techniques
Sequencing DNA to determine protein sequences
The genetic code can be used to determine the amino acid sequence within a protein
This primary structure information can be used to predict how proteins will fold into
their tertiary structure
Page 44 of 58
This gives a greater level of understanding of how a protein functions or interacts with YOUR NOTES
other proteins or molecules 
Such information can be used for a range of applications, such as drug design or novel
protein engineering in synthetic biology
Bioinformatics allows for large amounts of biological data to be available instantly to

researchers across the globe
Page 45 of 58
7.3.5 Levels of Protein Structure YOUR NOTES


Primary Structure
Levels of Protein Structure
Proteins are relatively large, complex molecules that contain one or more chains of amino
acids known as polypeptides
The three-dimensional arrangement of polypeptide chains dictates a protein's structure
and function
There are four levels of structure in proteins
Three levels are structural aspects of a single polypeptide chain
The fourth level relates to a protein that has more than one polypeptide chain
Primary structure
The sequence of amino acids bonded by covalent peptide bonds is the primary structure
of a protein
The DNA of a cell determines the primary structure of a protein by instructing the cell to add
certain amino acids in specific quantities in a specific, ordered sequence
This affects the shape, and therefore the function, of the protein
The primary structure is specific for each protein
Some mutations can lead to the incorrect amino acid being incorporated into the
polypeptide chain which can affect the function of the protein
Page 46 of 58
YOUR NOTES

The primary structure of a protein. The three-letter abbreviations indicate the specific
amino acid (there are 20 commonly found in cells of living organisms).
Page 47 of 58
Secondary Structure YOUR NOTES

Secondary structure is the formation of complex shapes within the polypeptide chain 
Secondary structure of a protein occurs due to weak hydrogen bonds
Hydrogen bonds form between carboxyl (C=O) groups and amino (H-N-H) groups
The bonds usually form between non-adjacent amino acids resulting in a change in
shape of the linear polypeptide chain
There are two shapes that can form within proteins due to the hydrogen bonds:
Alpha-helix (or α-helix)
Beta-pleated sheet (or β-pleated sheet)
The secondary structure of a protein with the α-helix and β-pleated sheets.
The magnified regions illustrate how the hydrogen bonds form between peptide bonds.
Page 48 of 58
Tertiary Structure YOUR NOTES

Polar and non-polar amino acids are relevant to the bonds formed 
between R groups
Tertiary structure refers to how the polypeptide chain folds to form a complex, three-
dimensional shape
Tertiary structure gives proteins a very specific shape that is important for function
Such as receptor sites on cell membranes and active sites in enzymes
Folding results from interactions between R groups (side chains) of the amino acids and
the surrounding environment
A number of different interactions between R-groups contribute to the tertiary structure
Hydrogen bonds form between polar R-groups
Hydrophobic interactions form between the R-groups of non-polar amino acids
within the interior of proteins to avoid contact with water
Covalent bonds form between the R-groups of cysteine amino acids to form
disulphide bridges
Ionic bonds form between positively and negatively charged R-groups
Page 49 of 58
YOUR NOTES

The interactions that occur between the R groups of amino acids determine the tertiary
structure and function of a protein
Page 50 of 58
Quaternary Structure YOUR NOTES

Quaternary structure 
Large proteins often consist of multiple polypeptide chains functioning together as a
larger biologically active macromolecule
Each polypeptide chain is referred to as a subunit of the protein
Many proteins also contain non-polypeptide components (prosthetic groups) and are
classed as conjugated proteins
Quaternary structure refers to how polypeptides and other components are arranged
This relates closely to function
Proteins with only one polypeptide chain do not have a quaternary structure
Haemoglobin is a conjugated protein, having quaternary structure, as it consists of
multiple polypeptide chains (making four subunits) each with a prosthetic group
There are two pairs of identical polypeptide chains (α–globins and β–globins)
Each subunit has a prosthetic haem group which contains an iron atom (Fe)
The quaternary structure of haemoglobin

Four subunits (polypeptide chains) and prosthetic haem groups work together to carry
oxygen
Summary of Bonds in Proteins Table
Page 51 of 58
YOUR NOTES

 Exam Tip
Familiarise yourself with the difference between the four structural levels found in
proteins, noting which bonds are found at which level. Remember that the hydrogen
bonds in tertiary structures are between the R groups whereas in secondary
structures the hydrogen bonds form between the amino and carboxyl groups.
Page 52 of 58
7.3.6 Skills: Polysomes & Ribosomes YOUR NOTES


Identifying Polysomes
Translation can occur simultaneously at multiple positions along mRNA
Polysomes (or polyribosomes) are groups of two or more ribosomes translating the same
mRNA transcript
Multiple copies of the same polypeptide chain can be made simultaneously from a single
mRNA transcript
Polysomes effectively increase the amount of polypeptide produced
In electron micrographs, polysomes look like ‘beads on a string’ with each bead
representing a ribosome
There are visible differences between eukaryotes and prokaryotes
In prokaryotes, the lack of a nucleus means transcription and translation are coupled
Translation starts before the mRNA has finished being transcribed from the DNA
On an electron micrograph, multiple polysomes can appear on growing mRNA
strands along the DNA molecule
In eukaryotes, mRNA is transported out of the nucleus prior to translation
On an electron micrograph, polysomes are seen on the mRNA with no involvement of
DNA
As ribosomes move in the same 5’ to 3’ direction along the mRNA, ribosomes towards the
3’ end have longer polypeptide chains being synthesised
Electron micrograph of prokaryotic polysomes, the image shows simultaneous

transcription and translation of a bacterial gene
Page 53 of 58
YOUR NOTES

Electron micrograph of eukaryotic polysomes, polypeptide chains can be seen emerging

from the ribosomes
Page 54 of 58
Visualising the Structure of Ribosomes YOUR NOTES

There are many ‘open source’ databases that contain data relating to the three- 
dimensional structure of proteins
The most commonly used ones are PDB (Protein Data Bank) and Swiss-Prot
Such databases allow researchers to analyse biological molecules and study
interactions between them
This helps relate structure to biological function
Data relating to the three-dimensional structure of biological molecules can be visualised
using molecular visualisation software such as Mol* or Jmol
Molecules can be represented in many different ways including ball and stick atom models
or simplified ribbon representations that show the protein backbone
Most molecular visualisation software is freely available on the Internet or can be
accessed through many bioinformatics repositories
Analysing the structure of the eukaryotic ribosome
Visit the PDB and search for: Yeast 80S ribosome 4V7R (do not put the search term in
quotes)
Eukaryotic ribosome are complex molecules consisting predominantly of ribosomal RNAs
and multiple proteins - these are represented in different colours
The molecule appears to be made of two distinct halves (subunits)
Rotate or zoom into the image to visualise the different components
Try and identify the ribosomal RNA in the two subunits (hover the cursor over)
An opening (groove) between the subunits should be visible - mRNA passes through here
Analysing the structure of a tRNA molecule
Search for: 1YFG in the PDB (1YFG is the database identifier for yeast initiator tRNA)
You should be able to recognise the loop structures
Consider how this structure is specific to the tRNA-activating enzyme
Try and identify the anticodon region and amino acid binding site (acceptor arm)
Try selecting a different viewer such as JSmol
Investigate changing settings in the viewer
Page 55 of 58
YOUR NOTES

Structure of yeast tRNA
Page 56 of 58
Page 57 of 58
Page 58 of 58

Biology Topic 7 Save My Exams

Uploaded by

Copyright:

Available Formats

Biology Topic 7 Save My Exams

Uploaded by

Document Information

Copyright

Available Formats

Share this document

Share or Embed Document

Sharing Options

Did you find this document useful?

Is this content inappropriate?

Copyright:

Available Formats

Biology Topic 7 Save My Exams

Uploaded by

Copyright:

Available Formats

Head to savemyexams.co.

uk for more awesome resources

7. Nucleic Acids (HL Only)

7.1 DNA Structure & Replication YOUR NOTES

DNA is wrapped around a series of nucleosomes.

Franklin's Investigations YOUR NOTES

Summary of Rosalind Franklin’s X-ray diffraction investigation, the diffraction pattern

DNA Structure Suggests Semi-conservative Replication YOUR NOTES

Semi-conservative replication of DNA

7.1.2 Mechanism of DNA Replication YOUR NOTES

Enzymes Involved in DNA Replication YOUR NOTES

Direction of Replication YOUR NOTES

7.1.3 Non-coding DNA YOUR NOTES

DNA Profiling YOUR NOTES

7.1.4 DNA Sequencing YOUR NOTES

High-throughput method of carrying out the chain termination method

7.1.5 Skills: The Hershey & Chase Experiment YOUR NOTES

7.1.6 Skills: Nucleosomes & Molecular Visualisation Software YOUR NOTES

7.2 Transcription & Gene Expression YOUR NOTES

The Promoter Region

Gene Expression Regulated by Proteins YOUR NOTES

Exam Tip YOUR NOTES

7.2.2 Environment & Gene Expression YOUR NOTES

Epigenetics YOUR NOTES

7.2.3 Transcription YOUR NOTES

Acetylation of the Nucleosome

7.2.4 Post-transcriptional Modification YOUR NOTES

mRNA Splicing YOUR NOTES

Alternative splicing YOUR NOTES

7.2.5 Skills: Analysing DNA Methylation Patterns YOUR NOTES

DNA methylation involves the addition of a methyl group to a cytosine nucleotide

DNA Methylation analysis showing reduced methylation of tumour-specific genes in

7.3 Translation YOUR NOTES

Elongation of the Polypeptide

Termination of Translation YOUR NOTES

tRNA-activating Enzymes YOUR NOTES

7.3.2 Ribosomes YOUR NOTES

A diagram of a ribosome, showing the small and large subunits

Bound Ribosomes YOUR NOTES

7.3.3 Translation in Prokaryotes YOUR NOTES

Transcription and translation occur simultaneously in prokaryotes due to the absence of a

7.3.4 Bioinformatics YOUR NOTES

Bioinformatics allows for large amounts of biological data to be available instantly to

7.3.5 Levels of Protein Structure YOUR NOTES

Secondary Structure YOUR NOTES

Tertiary Structure YOUR NOTES

Quaternary Structure YOUR NOTES

The quaternary structure of haemoglobin

7.3.6 Skills: Polysomes & Ribosomes YOUR NOTES

Electron micrograph of prokaryotic polysomes, the image shows simultaneous

Electron micrograph of eukaryotic polysomes, polypeptide chains can be seen emerging

Visualising the Structure of Ribosomes YOUR NOTES

Structure of yeast tRNA

You might also like