TOPIC 7 – Nucleic Acids & Proteins-Notes
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7.1.1 Describe the structure of DNA, including the antiparallel strands, 3' - 5'
linkages and hydrogen bonding between purines and pyrimidines
[4 max]
The carbon atoms in deoxyribose are numbered, with the nitrogenous bases attach to
C1 and the phopshate group is attached to C5
Nucleotides are joined by a covalent phosphodiester bond between the C 5 phosphate
group and the C3 hydroxyl group
Hence one nucleotide strand runs 5' - 3'
The nitrogenous bases interact via hydrogen bonding (complementary base pairing)
Adenine (A) and thymine (T) share 2 hydrogen bonds
Guanine (G) and cytosine (C) share 3 hydrogen bonds
In order for the bases to associate (i.e. face each other), one strand must run
antiparallel to the other (this antiparallel strand runs 3' - 5')
Double stranded DNA forms a double helix, with 10 nucleotides per turn and the
structure containing both major and minor grooves
Structural Organisation of DNA
7.1.2 Outline the structure of nucleosomes
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[usually 1, 2 max]
The DNA double helix contains major and minor grooves on its outer diameter, which
expose chemical groups that can form hydrogen bonds
The DNA of eukaryotes associates with proteins called histones
DNA is wound around an octamer of histones (146 bases and 1.65 turns of the helix per
octamer) The octamer and DNA combination is secured to a H1 histone, forming a
nucleosome
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7.1.3 State that nucleosomes help to supercoil DNA and help to regulate
transcriptio
[Usually 1, at most 2]
Nucleosomes serve two main functions:
They protect DNA from damage
They allow long lengths of DNA to be packaged (supercoiled) for mobility during mitosis
/ meiosis
When supercoiled, DNA is not accessible for transcription
Cells will have some segments of DNA permanently supercoiled (heterochromatin) and
these segments will differ between different cell types
7.1.4 Distinguish between unique or single copy genes and highly repetitive
sequences in nuclear DNA
[2]
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7.1.5 State that eukaryotic genes contain introns and exons
[1]
Intron: A non-coding sequence of DNA within a gene (intervening sequence) that is cut
out by enzymes when RNA is made into mature mRNA
Exon: The part of the gene which codes for a protein (expressing sequence)
Eukaryotic DNA contains introns but prokaryotic DNA does not
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7.2.1 State that DNA replication occurs in a 5' - 3' direction
[1, at most 2]
DNA replication is semi-conservative, meaning that a new strand is synthesised from an
original template strand
DNA replication occurs in a 5' - 3' direction, in that new nucleotides are added to the C3
hydroxyl group such that the strand grows from the 3' end
This means that the DNA polymerase enzyme responsible for adding new nucleotides
moves along the original template strand in a 3' - 5' direction
Direction of DNA Replication
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7.2.2 Explain the process of DNA replication in prokaryotes, including the role of
enzymes (helicase, DNA polymerase, RNA primase and DNA ligase), Okazaki
fragments and deoxynucleoside triphosphates
[6 max]
DNA replication is semi-conservative and occurs during the S phase of interphase
Helicase unwinds and separates the double stranded DNA by breaking the hydrogen
bonds between base pairs
This occurs at specific regions (replication origins), creating a replication fork of two
polynucleotide strands in antiparallel directions
RNA primase synthesises a short RNA primer on each template strand to provide an
attachment and initiation point for DNA polymerase III
DNA polymerase III adds deoxynucleoside triphosphates (dNTPs) to the 3' end of the
polynucleotide chain, synthesising in a 5' - 3' direction
The dNTPs pair up opposite their complementary base partner (adenine pairs with
thymine ; guanine pairs with cytosine)
As the dNTPs join with the DNA chain, two phosphates are broken off, releasing the
energy needed to form a phosphodiester bond
Synthesis is continuous on the strand moving towards the replication fork (leading
strand)
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Synthesis is discontinuous on the strand moving away from the replication fork (lagging
strand) leading to the formation of Okazaki fragments
DNA polymerase I removes the RNA primers and replaces them with DNA
DNA ligase joins the Okazaki fragments together to create a continuous strand
Overview of DNA Replication
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7.2.3 State that DNA replication is initiated at many points in eukaryotic
chromosomes
[1-2 max]
Because eukaryotic genomes are (typically) much larger than prokaryotic genomes,
DNA replication is initiated at many points simultaneously in order to limit the time
required for DNA replication to occur
The specific sites at which DNA unwinding and initiation of replication occurs are called
origins of replication and form replication bubbles
As replication bubbles expand in both directions, they eventually fuse together, two
generate two separate semi-conservative double strands of DNA
Origins of Replication
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7.3.1 State that transcription is carried out in a 5' - 3' direction
Transcription is carried out in a 5' - 3' direction (of the new RNA strand)
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[1]
7.3.2 Distinguish between the sense and antisense strands of DNA
[2 max]
DNA consists of two polynucleotide strands, only one of which is transcribed into RNA
The antisense strand is transcribed into RNA
Its sequence will be complementary to the RNA sequence and will be the "DNA version"
of the tRNA anticodon sequence
The sense strand is not transcribed into RNA
Its sequence will be the "DNA version" of the RNA sequence (identical except for T
instead of U)
7.3.3 Explain the process of transcription in prokaryotes, including the role of the
promoter region, RNA polymerase, nucleoside triphosphates and the terminator
A gene is a sequence of DNA which is transcribed into RNA and contain three main
parts:
[6 marks]
Promoter: Responsible for the initiation of transcription (in prokaryotes, a number of
genes may be regulated by a single promoter - this is an operon)
Coding Sequence: The sequence of DNA that is actually transcribed (may contain
introns in eukaryotes)
Terminator: Sequence that serves to terminate transcription (mechanism of
termination differs between prokaryotes and eukaryotes)
Transcription is the process by which a DNA sequence (gene) is copied into a
complementary RNA sequence and involves a number of steps:
RNA polymerase binds to the promoter and causes the unwinding and separation of the
DNA strands
Nucleoside triphosphates (NTPs) bind to their complementary bases on the antisense
strand (uracil pairs with adenine, cytosine pairs with guanine)
RNA polymerase covalently binds the NTPs together in a reaction that involves the
release of two phosphates to gain the required energy
RNA polymerase synthesises an RNA strand in a 5' - 3' direction until it reaches the
terminator
At the terminator, RNA polymerase and the newly formed RNA strand both detach from
the antisense template, and the DNA rewinds
Many RNA polymerase enzymes can transcribe a DNA sequence sequentially,
producing a large number of transcripts
Post-transcriptional modification is necessary in eukaryotes
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Overview of Transcription
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7.3.4 State that eukaryotic RNA needs the removal of introns to form mature
mRNA
[1]
Euakaryotic genes may contain non-coding sequences called introns that need to be
removed before mature mRNA is formed
The process by which introns are removed is called splicing
The removal of exons (alternative splicing) can generate different mRNA transcripts
(and different polypeptides) from a single gene
Splicing
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TRANSLATION:
7.4.1 Explain that each tRNA molecule is recognized by a tRNA-activating
enzyme that binds a specific amino acid to the tRNA, using ATP for
energy.
[ 7 max]
There are many different types of tRNA and each tRNA is recognised by a tRNA-activating enzyme.
This enzyme binds a specific amino acid to the tRNA by using ATP as an energy source. The tRNA
molecule has a specific structure. It contains double stranded sections (due to base pairing via
hydrogen bonds) and loops. It has an anticodon loop which contains the anticodon and two other
loops. The nucleotide sequence CCA is found at the 3' end of the tRNA and allows attachment for an
amino acid. Each type of tRNA has slightly different chemical properties and three dimensional
structure which allows the tRNA-activating enzyme to attach the correct amino acid to the 3' end of
the tRNA. There are 20 different tRNA-activating enzymes as there are 20 different amino acids. Each
enzyme will attach a specific amino acid to the tRNA which has the matching anticodon for that amino
acid. When the amino acid binds to the tRNA molecule a high energy bond is created. The energy from
this bond is used later on to bind the amino acids to the growing polypeptide chain during translation.
Summary:
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Each tRNA activating enzyme recognises a specific tRNA molecule
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The tRNA molecule is made up of double stranded sections and loops
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At the 3' end of the tRNA there is the nucleotide sequence CCA to which the amino acid attaches to
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The different chemical properties and three dimensional structure of each tRNA allows the tRNAactivating enzymes to recognise their specific tRNA
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Each tRNA enzyme binds a specific amino acid to the tRNA molecule
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The tRNA-activating enzyme will bind the amino acid to the tRNA with the matching anticodon
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Energy from ATP is needed during this process
7.4.2 Outline the structure of ribosomes, including protein and RNA
composition, large and small subunits, three tRNA binding sites and
mRNA binding sites.
[2]
Ribosomes have a particular structure. They are made up of proteins and ribosomal RNA. They have
two subunits, one large the other small. On the surface of the ribosome there are three sites to which
tRNA can bind to. However not more than two tRNA molecules can bind to the ribosome at one time.
Also there is a site on the surface of the ribosome to which mRNA can bind to.
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7.4.3 State that translation consists of initiation, elongation, translocation
and termination.
[1]
Translation consists of initiation, elongation, translocation and termination.
7.4.4 State that translation occurs in a 5? → 3? direction.
[1]
Translation occurs in a 5'→3' direction.
7.4.5 Draw and label a diagram showing the structure of a peptide bond
between two amino acids.
[2]
7.4.6 Explain the process of translation, including ribosomes, polysomes,
start codons and stop codons.
[10 max]
Translation occurs in the cytoplasm. It starts off with the tRNA containing the matching anticodon for
the start codon AUG binding to the small subunit of the ribosome. This tRNA carries the amino acid
methionine and is always the first tRNA to bind to the P site. The small subunit of the ribosome then
binds to the 5' end of the mRNA. This is because translation occurs in a 5'→3' direction. The small
subunit will move along the mRNA until it reaches the start codon AUG. The large subunit of the
ribosome can then binds to the small subunit. The next tRNA with the matching anticodon to the
second codon on the mRNA binds to the A site of small subunit of the ribosome. The amino acids on
the two tRNA molecules then form a peptide bond. Once this is done, the large subunit of the
ribosome moves forward over the smaller one.The smaller subunit moves forward to join the larger
subunit and as it does so the ribosome moves 3 nucleotides along the mRNA and the first tRNA is
moved to the E site to be released. The second tRNA is now at the P site so that another tRNA with
the matching anticodon can then bind to the A site. As this process continues the polypeptide is
elongated. Once the ribosome reaches the stop codon on the mRNA translation will end as no tRNA
will have a matching anticodon to the stop codon. The polypeptide is then released. Many ribosomes
can translate the same mRNA at the same time. They will all move along the mRNA in a 5'→3'
direction. These groups of ribosomes on a single mRNA are called polysomes.
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Summary:
1. The tRNA containing the matching anticodon to the start codon binds to P site of the small subunit
of the ribosome
2. The small subunit binds to the 5' end of the mRNA and moves along in a 5'→3' direction until it
reaches the start codon
3. The large subunit then binds to the smaller one
4. The next tRNA with the matching anticodon to the next codon on the mRNA binds to the A site
5. The amino acids on the two tRNA molecules form a peptide bond
6. The larger subunit moves forward over the smaller one
7. The smaller subunit rejoins the larger one, this moves the ribosome 3 nucleotides along the mRNA
and moves the first tRNA to the E site to be released
8. The second tRNA is now at the P site so that another tRNA with the matching anticodon to the
codon on the mRNA can bind to the A site
9. As this process continues, the polypeptide is elongated
10. Once the ribosome reaches the stop codon on the mRNA translation ends and the polypeptide is
released
11. Many ribosomes can translate a single mRNA at the same time, these groups of ribosomes are
called polysomes
7.4.7 State that free ribosomes synthesize proteins for use primarily
within the cell, and that bound ribosomes synthesize proteins primarily
for secretion or for lysosomes.
[1]
Free ribosomes synthesise proteins for use primarily within the cell while bound ribosomes synthesise
proteins primarily for secretion or for lysosomes.
Proteins
7.5.1 Explain the four levels of protein structure, indicating the
significance of each level.
[7 max]
There are four levels of protein structure:
Primary Structure: The primary structure of a protein is its amino acid sequence. This amino acid
sequence is determined by the base sequence of the gene which codes for the protein.
Secondary Structure: Secondary structures have α-helices and β-pleated sheets. These form as a
result of hydrogen bonds between the peptide groups of the main chain. Therefore, proteins that
contain secondary structures will have regions that are cylindrical (α-helices) and/or regions that are
planar (β-pleated sheets).
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Tertiary Structure: The tertiary structure of a protein is its three-dimensional conformation which
occurs as a result of the protein folding. This folding is stabilised by hydrogen bonds, hydrophobic
interactions, ionic bonds and disulphide bridges. These intramolecular bonds form between the R
groups of different amino acids.
Quaternary Structure: A quaternary structure is formed when two or more polypeptide chains
associate to form a single protein. An example is haemoglobin which consists of four polypeptide
chains. In some cases, some proteins can have a non-polypeptide structure called a prosthetic group.
These proteins are called conjugated proteins. The haem group in haemoglobin is a prosthetic group.
7.5.2 Outline the difference between fibrous and globular proteins, with
reference to two examples of each protein type.
[2]
Protein shape can be categorised as either fibrous or globular. Fibrous proteins tend to be elongated,
physically tough and insoluble in water. Collagen found in the skin and keratin found in hair are
examples of fibrous proteins. Globular proteins tend to be compact, rounded and water soluble.
Haemoglobin and enzymes are examples of globular proteins.
7.5.3 Explain the significance of polar and non-polar amino acids.
[6]
Amino acids have different R groups. Some of these R groups will be hydrophilic, making the amino
acid polar, while others will be hydrophobic, making the amino acid non-polar. The distribution of the
polar and non-polar amino acids in a protein influences the function and location of the protein within
the body. Non-polar amino acids are found in the centre of water soluble proteins while the polar
amino acids are found at the surface.
Examples of how the distribution of non-polar and polar amino acids affect protein function and
location:
Controlling the position of proteins in membranes: The non-polar amino acids cause proteins to
be embedded in membranes while polar amino acids cause portions of the proteins to protrude from
the membrane.
Creating hydrophilic channels through membranes: Polar amino acids are found inside
membrane proteins and create a channel through which hydrophilic molecules can pass through.
Specificity of active site in enzymes: If the amino acids in the active site of an enzyme are nonpolar then it makes this active site specific to a non-polar substance. On the other hand, if the active
site is made up of polar amino acids then the active site is specific to a polar substance.
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7.5.4 State four functions of proteins, giving a named example of each.
[4]
Function
Example
Structural
Collagen strengthens bones, skin and tendons.
Movement
Myosin found in muscle fibers causes
contraction of the muscle which results in
movement.
Transport
Haemoglobin transports oxygen from the lungs
to other tissues in the body.
Defense
Immunoglobulin acts as an antibody.
Enzymes
7.6.1 State that metabolic pathways consist of chains and cycles of
enzyme- catalysed reactions.
[1]
Metabolic pathways consist of chains and cycles of enzyme-catalysed reactions.
7.6.2 Describe the induced-fit model.
[4]
Initially the substrate does not fit perfectly into the active site of the enzyme. When the substrate
binds to the active site, this changes the shape of the active site and only then does it perfectly fit the
substrate. As the substrate binds it changes the shape of the active site and this weakens the bonds in
the substrate and therefore reduces the activation energy. This model is a more precise version of the
lock and key one. The reason for this is that it explains why some enzymes can bind to many different
substrates. If the shape of the active site changes when a substrate binds, this allows many different
but similar substrates to bind to the one enzyme.
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Figure 7.6.1 - The induced-fit model
7.6.3 Explain that enzymes lower the activation energy of the chemical
reactions that they catalyse.
[5 max]
Reactants of a chemical reaction need to gain energy before they can undergo the reaction. This
required energy is called the activation energy of the reaction and it is needed to break bonds within
the reactants. At a later stage in the reaction energy will be released as new bonds form. The majority
of biological reactions are exothermic. In exothermic reactions the energy released by the new bonds
formed is greater than the activation energy. In other words, the reaction releases energy. Enzymes
make it easier for reactions to occur by decreasing the activation energy required in the reactions that
they catalyse.
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Figure 7.6.2 - Activation energy of an exothermic reaction
7.6.4 Explain the difference between competitive and non-competitive
inhibition, with reference to one example of each.
[8-10 max]
Enzyme inhibitors are substances which inhibit enzyme activity. There are competitive enzyme
inhibitors and non-competitive inhibitors.
Competitive Inhibitors
These are structurally similar to the substrate of the enzyme and bind to the active site. This means
that when a competitive inhibitor binds to the active site of an enzyme, it prevents the substrate from
binding to the active site. Only once the inhibitor has been released from the active site can the
substrate bind. The inhibitor is called a competitive inhibitor as it competes with the substrate for the
active site.
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Figure 7.6.3 - Competitive inhibition
The effects of a competitive inhibitor can be reduced by increasing the substrate concentration. More
substrate would successfully bind to the active site than inhibitor and therefore reducing the effect of
the inhibition. The maximum rate of reaction or a level very close to the maximum rate of reaction can
be reached.
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Figure 7.6.4 - The effect of increasing substrate concentration on a competitive inhibitor
An example of a competitive inhibitor is malonate. Malonate is structurally similar to the substrate
succinate. Succinate is found in the Krebs cycle of aerobic respiration and binds to the active site of
the dehydrogenase enzyme. Malonate can compete with succinate for the active site and in doing so it
can prevent succinate from binding.
Non-Competitive Inhibition
These are not similar to the substrate and they do not bind to the active site of the enzyme. Instead
they bind to a different site on the enzyme and change the conformation of the active site. The
substrate may still be able to bind to the active site however the enzyme is not able to catalyse the
reaction or can only do so at a slower rate.
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Figure 7.6.5 - Non-competitive inhibition
In the presence of a non-competitive inhibitor, increasing the substrate concentration cannot prevent
the inhibitor from binding to the enzyme as the two bind to different sites. Therefore, no matter how
high the concentration of substrate is, some of the enzymes will still be inhibited. The maximum rate
of reaction will always be lower in the presence of a non-competitive inhibitor.
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Figure 7.6.6 - The effect of increasing substrate concentration on a non-competitive inhibitor
An example of a non-competitive inhibitor is ATP. When ATP accumulates it binds to a site other than
the active site on the enzyme phosphofructokinase. In doing so it changes the enzyme conformation
and lowers the rate of reaction so that less ATP is produced.
7.6.5 Explain the control of metabolic pathways by end-product
inhibition, including the role of allosteric sites.
[5]
Metabolic pathways are made up of many chemical reactions and these reactions are catalysed by
enzymes. Often, the product of the last reaction in the pathway inhibits the enzyme that catalyses the
first reaction of the pathway. This is called end-product inhibition and it involves non-competitive
inhibitors.
The product of the last reaction of the metabolic pathway will bind to a site other than the active site
of the enzyme that catalyses the first reaction. This site is called the allosteric site. When it binds to
the allosteric site it acts as non-competitive inhibitor and changes the conformation of the active site.
Therefore, it makes the binding of the substrate to the enzyme unlikely. Once the inhibitor is released
from the allosteric site, the active site returns to its original conformation and the substrate is able to
bind again.
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There is a clear advantage in using end-product inhibition for controlling metabolic pathways. When
there is an excess of end-product, the whole metabolic pathway is shut down as the end product
inhibits the first enzyme of the pathway. Therefore less of the end product gets produced and by
inhibiting the first enzyme it also prevents the formation of intermediates. When the levels of the end
product decrease, the enzymes start to work again and the metabolic pathway is switched on.
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