TOPIC 7: NUCLEIC ACIDS AND PROTEINS
7.1 DNA Structure
7.1.1: Describe the structure of DNA
 In a polynucleotide the monomers are linked
by covalent bonds called phosphodiester
linkages, between the 5' phosphate of one
nucleotide and the 3' hydroxyl of the next
monomer.
 DNA molecules consist of two
polynucleotide chains (strands) spiraled
around an imaginary axis to form a double
helix.
 The two strands of DNA are oriented in
opposite directions, an arrangement
called antiparallel.
 In each strand the monomers are linked by
covalent bonds, resulting in a polymer with a
repeating pattern of: pentose-phosphatepentose-phosphate- pentose-phosphate.
 The two sugar-phosphate backbones are on
the outside of the helix, and the bases are
on the inside.
 The two polynucleotide chains, or strands,
are held together by hydrogen bonds
between paired bases.
 There are two kinds of DNA bases: purines
(G and A) and pyramidines (C and T). G can
bond with C; and T can bond with A.
 Each DNA strand has a free 3' (three prime)
hydroxyl group at one end and a free 5'
phosphate group at the other end.
 The two strands of the double helix
are complementary, each the predictable counterpart of the other. In other words, if you know the
sequence of one DNA strand then you can easily figure out the sequence of the other strand.
7.1.2:Outline the structure of nucleosomes
 If the DNA from the 46 chromosomes in a human cell were straightened, they would be about
2m in length. Therefore, to fit inside a nucleus that is 2-3um in diameter, the DNA is tightly
wrapped around thousands of protein clusters called nucleosomes.
 Each nucleosome is a group of eight histone proteins, held together by an additional protein. By
wrapping around the histone proteins, the DNA molecule is shortened by about 10 times.
 During mitosis, the chromosomes become visible (with a light microscope) because the
nucleosomes become tightly packed together in a process called supercoiling. The supercoiled
nucleosomes are arranged in large loops to further condense the DNA.
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7.1.3: State that nucleosomes help to supercoil chromosomes and regulate transcription
7.1.4: Distinguish between single-copy genes and highly repetitive sequences
Single-Copy Genes
Satellite DNA (Highly repetitive sequences)
A single-copy gene has one locatable region on a
Satellite DNA consists of highly repetitive
DNA molecule.
sequences that can repeat up to 100,000 times in
various places on a DNA molecule.
Single-copy genes make up 1–2% of the human
Satellite DNA constitutes more than 5% of the
genome.
human genome.
A single-copy gene corresponds to a unit of
Satellite DNA is not involved with inheritance.
inheritance (i.e., a protein).
Single-copy genes are transcribed to make RNA,
Satellite DNA is not transcribed.
which in turn is translated to make a protein.
Single-copy genes are usually thousands of base
Satellite DNA is typically between 5 and 300 base
pairs in length.
pairs per repeat.
Single-copy genes are less useful for DNA profiling. Satellite DNA has a high rate of mutation making it
useful for DNA profiling.
7.1.5: State that eukaryotic genes can contain exons and introns
7.2 DNA Replication
7.2.1: State that DNA replication occurs in a 5’ 3’ direction
7.2.2: Explain the process of DNA replication in prokaryotes
Complimentary base-pairing is key to DNA replication
 The two strands of DNA are complimentary, therefore they can separate from one another and each
can serve as a template for building a new partner.
 DNA replication is semi-conservative, with each of the two daughter DNA molecules having one old
strand derived from the parent and one newly made strand.
 Complementary base pairing results in the two daughter DNA molecules being identical.
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Origins of DNA replication
 DNA replication occurs in the 5'→3' direction only, and it begins at special sites called origins of
replication where the two DNA strands first separate.
 The DNA of prokaryotes contains only one replication origin but the huge DNA molecule of a
eukaryotic chromosome has hundreds or thousands of replication bubbles.
Enzymes needed for DNA Replication
 Replication begins with an enzyme called Helicase, which unwinds the helix.
 Next, an enzyme called RNA Primase functions to provide Primers with a 3'-OH group that is needed
for synthesis to begin.
 Then, the enzyme DNA Polymerase III catalyzes the step-by-step addition of nucleotides to the free
3' OH end of a DNA chain.
 The fragments on the lagging strand are covalently joined by an enzyme called Ligase.
 Finally, DNA Polymerase I removes the RNA primers. DNA Polymerase I also functions to locate and
repair mistakes that are made during replication. DNA Polymerase requires deoxynucleoside
triphosphates as an energy source.
Okazaki fragments
 Recall that the strands of parental DNA are anti-parallel; hence the overall direction of DNA
synthesis must be 5|→3| for one strand and 3|→5| for the other strand. But DNA polymerases can
only synthesize DNA in the 5|→3| direction - not the 3|→5| direction.
 How then does one of the daughter DNA strands appear to grow in the 3|→5| direction? The
answer to this question was discovered by Reiji Okazaki who found DNA fragments,
called Okazaki fragments, on one of the replicating strands but not on the other. Okazaki concluded
that one DNA strand, called the leading strand, replicates continuously but the other strand, called
the lagging strand, replicates discontinuously.
 The discontinuous assembly of nucleotides in the lagging strand enables DNA polymerases to
polymerize DNA in the 5|→3| direction.
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7.2.3: State that DNA replication is initiated at many points in eukaryotic chromosomes
7.3 Transcription
7.3.1: State that transcription is carried out in a 5’ 3’ direction
7.3.2: Distinguish between the sense and antisense strands of DNA
Sense Strand
Does it get transcribed?
No
Is its base sequence the same as The sense strand has the same
mRNA?
base sequence as the mRNA
molecule, except that it contains
thymine instead of uracil.
Anti-Sense Strand
Yes
The anti-sense strand has a
complementary base sequence
to the mRNA molecule
7.3.3: Explain the process of transcription in prokaryotes
Transcription Overview
 Transcription is the process by which the genetic code is transferred from DNA to RNA.
 Transcription requires nucleoside triphosphates as an energy source.
 Transcription produces 1 molecule of messenger RNA (mRNA), the role of which is to pass
information on to transfer RNA (tRNA).
Details of Transcription
 Transcription occurs in the 5'→3' direction
only.
 RNA polymerase begins transcribing at a
site called the promoter (the beginning of a
gene).
 RNA polymerase adds RNA nucleotides to a
growing mRNA strand.
 RNA polymerase stops transcribing at the
terminator (the end of the gene).
 The terminator signals the mRNA molecule
to depart from the DNA, allowing hydrogen
bonds to reform between the 2 DNA
strands.
The 'sense' and 'anti-sense' strands
 Only one DNA strand, called the 'anti-sense' strand, is transcribed.
 The other strand, called the 'sense' strand, is not transcribed.
 The sense strand has the same sequence as mRNA and the antisense strand has the same sequence
as tRNA.
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7.3.4:State that eukaryotic RNA needs the removal of introns to form mature mRNA
7.4 Translation
7.4.1: Explain that each tRNA molecule is recognized by a tRNA-activating enzyme the tRNA
 Once in the cytoplasm, mRNA is translated from the nucleic acid language to the protein language
by transfer RNA (tRNA) which acts as an interpreter. Transfer RNA does two things: 1) it recognizes
the appropriate codons in mRNA and 2) it picks up the appropriate amino acids.
 Transfer RNA is a small molecule made up of only about 80 nucleotides. It is shaped like a cloverleaf.
One of the loops on tRNA contains a base triplet called the anticodon. The anticodon is
complementary to a codon triplet on the mRNA. At the other end of the tRNA molecule is a specific
sequence of three nucleotides (CCA). The last nucleotide is the (A) and an amino acid can attach to it.
 The type of amino acid which can attach to a tRNA molecule depends on the sequence of the
anticodon. A tRNA activating enzyme recognizes the anticodon and uses ATP to bind the appropriate
amino acid to the 3' end. Each amino acid has a specific tRNA activating enzyme, and some amino
acids have more than one tRNA because the genetic code is degenerate.
7.4.2:Outline the structure of ribosomes
 Ribosomes are made up of two subunits
(one large, one small). Each subunit is
made from protein (40% by mass) and
ribosomal RNA (60% by mass).
 Ribosomes have one mRNA binding site
and three tRNA binding sites (the P site;
the A site; the E site).
 The P site holds a tRNA that is attached to
the growing polypeptide chain; the A site
holds a tRNA that is delivering the next
amino acid to be added to the growing
polypeptide chain; and the E site binds a
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free tRNA before it exits the ribosome.
7.4.3: State that translation consists of initiation, elongation, translocation and termination
7.4.4: State that translation occurs in a 5’ 3’ direction
7.4.5: Draw and label a diagram of a peptide bond between two amino acids
7.4.6: Explain the process of translation
Translation
 Translation (polypeptide synthesis) is performed by ribosomes.
 Ribosomes can form polysomes. A polysome consists of several ribosomes attached to one mRNA
molecule, an arrangement that increases the rate of protein synthesis.
 Translation occurs in the 5’ to 3’ direction, and it can be divided into three stages: initiation,
elongation, and termination.
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Initiation
 Initiation begins when a mRNA
attaches its 5’ end to the small
subunit of a ribosome. Next, a tRNA
attaches by hydrogen bonding its
anticodon to the first mRNA codon,
which is positioned in the P site. At
this point we have a functional
ribosome and elongation can begin.
Elongation
 Elongation is the stage of translation when amino acids are added one by one to the growing
polypeptide chain. During elongation, the ribosome moves along the mRNA (codon by codon)
towards the 3’end.
 In the first step of elongation, the mRNA in the A site of the ribosome forms hydrogen bonds with
the anticodon of an incoming tRNA molecule carrying its amino acid.
 In the second step a peptide bond forms between the amino acid at the P site and the newly arriving
amino acid in the A site. At the same time, the bond between the amino acid and the tRNA in the P
site breaks and the tRNA is released from the ribosome.
 In the third step the tRNA in the A site (which is now carrying the growing polypeptide chain) is
translocated to the P site. The codon and anticodon remain hydrogen bonded allowing the mRNA
and tRNA to move as a unit. This movement in turn, brings the next codon on the mRNA into the A
site and it too gets translated. Elongation continues (codon by codon) until the polypeptide is
complete.
Termination
 Termination, the third stage of protein synthesis, occurs when a stop codon enters the A site of the
ribosome. Stop codons (UAA, UAG and UGA) do not code for proteins but instead act as signals to
stop elongation. A protein binds to the stop codon in the A site which results in a water molecule
being added to the polypeptide chain instead of an amino acid. This causes the polypeptide to be
released from the ribosome.
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
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7.5 Proteins
7.5.1: Explain the four levels of protein structure indicating the significance of each level
 The shape of a protein can be described by four levels of structure: primary, secondary, tertiary and
quaternary.
Primary Structure
 Primary structure is the unique and linear sequence of amino acids in a protein. It is the sequence in
which amino acids are added to a growing polypeptide during translation.
 With 20 different amino acids, the number of primary sequences is almost infinite.
 It is the primary structure that determines how (and where) the polypeptide will fold to give a
protein its shape. Thus, primary structure determines the higher levels of protein structure.
 Small changes in primary structure can result in large changes in protein shape and function.
Secondary Structure
 Secondary structure describes regions where the polypeptide is folded into localized shapes. There
are two types of secondary structure (alpha helix and Beta pleated sheet).
 The alpha helix is a delicate coil formed by hydrogen bonding between a hydrogen atom on one
amino acid and an oxygen atom on the fourth amino acid away.
 The beta sheet results from hydrogen bonding between different polypeptide chains or between
different sections of the same polypeptide.
Tertiary Structure
 Tertiary structure is the overall shape of the protein. Most proteins (e.g. lysozyme, hemoglobin and
insulin) have a compact, globular tertiary structure.
 Some proteins are fibrous. Fibrous proteins like collagen (tendons, cartilage) and keratin (hair,
feathers, horns, hoofs, etc.) have the alpha helix formation over their entire length. Other fibrous
proteins like fibroin (the structural protein of silk) are dominated by beta sheets.
 Tertiary structure is influenced by ionic bonds between opposite charged R-groups, hydrogen bonds
between R-groups bearing opposite partial charges, and hydrophobic interactions resulting from the
tendency of nonpolar R-groups to stay close together in an aqueous solution.
 Another important bond affecting tertiary structure occurs in proteins that contain the amino acid
cysteine. Where two cysteine monomers are close together, the sulfur of one cysteine bonds to the
sulfur of the other, forming strong covalent bonds known as disulfide bridges.
Quarternary Structure
 Quaternary structure occurs in proteins that are made up of more than one polypeptide chain.
 Combining different polypeptides leads to a greater range of biological activity. Collagen, for
example, is made of three subunits intertwined into a triple helix, and hemoglobin is made of four
heme groups, each a different polypeptide.
 An influence on the quaternary structure of some proteins is the presence of a prosthetic group: a
small molecule that is not a peptide but that tightly binds to the protein and plays a crucial role in its
function. For example, the four heme groups on a hemoglobin protein are prosthetic and they
function to carry oxygen.
 Proteins with prosthetic groups are called conjugated proteins.
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7.5.2: Outline the difference between fibrous and globular proteins
 Most proteins (e.g. lysozyme, hemoglobin and insulin) have a compact, globular tertiary structure.
Enzymes are usually globular.
 Some proteins are fibrous. Fibrous proteins like collagen (tendons, cartilage) and keratin (hair,
feathers, horns, hoofs, etc.) have the alpha helix formation over their entire length. Other fibrous
proteins like fibroin (the structural protein of silk) are dominated by beta sheets.
7.5.3: Explain the significance of polar and non-polar amino acids
 The 20 different amino acids vary in their R groups; some R groups are non-polar, others are polar.
 Polar amino acids have R groups that carry either a (+) or a (-) charge.
 Polar amino acids are hydrophilic and non-polar amino acids are hydrophobic.
 Hydrophobic R-groups stay close together in water.
 Proteins with a lot of polar amino acids are soluble in water, and those with many non-polar amino
acids do not dissolve in water.
 The hydrophilic and hydrophobic properties of amino acids cause proteins to twist into useful
shapes. This ability of proteins is important for cellular membranes.
 Membrane proteins are firmly anchored in the phospholipid bilayer because they have two polar
ends and a non-polar center. One end of a membrane protein contacts the watery extracellular fluid
and the other end extends to the watery cytoplasm. The non-polar center remains inside the
membrane because it is hydrophobic.
 Protein channels facilitate the passage of polar molecules across cellular membranes because the
polar amino acids line the inside of the channel and non-polar amino acids line the outside.
 The polarity of R groups plays a role in the tertiary structure of globular proteins. Thus, polarity plays
a role in shaping enzymes and their active sites.
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7.5.4: State four functions of proteins giving a named example of each
 Muscle contraction (Actin and Myosin)
 Transport of other substances (e.g. Haemoglobin)
 Membrane Proteins (e.g. Glycoproteins, channel proteins)
 Hormones (e.g. Insulin)
 Enzymes (e.g. Catalase, Lactase, Amylase)
7.6 Enzymes
7.6.1: State that metabolic pathways consist of chains and cycles of enzyme catalyzed reactions
7.6.2: Describe the induced-fit model
 The 'lock and key' model explains the high specificity of most enzymes. It states that each enzyme
has a unique 'shape' at its active site that compliments the particular substrate it acts upon.
 The 'induced fit' model explains the broad specificity of some enzymes (i.e. why some enzymes can
work on many different substrates provided they are similar in structure).
 Each substrate has a unique 'shape' that almost (but not quite) fits into it's enzymes active site.
 An enzyme-substrate complex is formed when the active site undergoes a small change of shape
that causes the substrate to be held tightly.
 The change of shape may strain chemical bonds thereby lowering the activation energy.
7.6.3: Explain that enzymes lower activation energy
 One challenge for a cell is to produce certain
products quickly when they are needed. This
control is achieved by enzymes, which are
biological catalysts that speed up reactions in cells.
 Enzymes are not altered by the reactions they
speed up so they can be used over and over. One
enzyme may catalyze thousands of reactions per
second.
 Enzymes accelerate reactions by: 1) bringing
substances together at the active site; 2)
weakening bonds in the substrate; and 3) reducing
the activation energy required to make a reaction
proceed.
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
Only a small part of an enzyme molecule (called the active-site) comes into contact with the
substrate(s) it acts upon. The rest of the enzyme molecule functions to position the active site in the
correct location for it to function.
7.6.4: Explain the difference between competitive and
non-competitive inhibition
 Enzyme reaction rates can be affected by inhibitors.
There are competitive inhibitors and noncompetitive inhibitors.
Competitive inhibitors
 Competitive inhibitors are so similar in structure to
the substrate that they can bind to the active site,
thereby preventing the substrate from binding.
 Prontosil is a competitive inhibitor that is used as
an antibiotic because it inhibits folic acid synthesis
in bacteria.
Non-competitive inhibitors
 Non-competitive inhibitors also bind to enzymes
but not at the active site. When a non-competitive
inhibitor binds to an enzyme it changes the
enzymes shape and deactivates the active site.
 Nerve gases like Sarin function by inactivating the
enzyme ethanoyl (acetyl) cholinesterase.
7.6.5: Explain the control of metabolic pathways by end-product inhibition
End-product inhibition
 Many metabolites (end products of
metabolic pathways) act as allosteric
inhibitors of enzymes earlier in a
metabolic pathway. This is called
feedback inhibition.
 In feedback inhibition, an increase in the
level of a metabolite results in a decrease
in the production of that metabolite.
 One example of negative feedback is
phosphofructokinase, an important
enzyme in glycolysis that is allosterically
inhibited by ATP and allosterically activated by ADP.
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Allostery
 Allostery is a form of non-competitive inhibition.
 All allosteric enzymes consist of two or more polypeptides whose shape can be altered.
 Allosteric activators activate allosteric enzymes.
 Allosteric inhibitors de-activate allosteric enzymes.
 Allosteric inhibitors bind to the allosteric site, the enzyme changes shape, and its active site is
deactivated.
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