This document provides information on cell biology, organelles, microscopy techniques, the cytoskeleton, membranes, enzymes, and cell motility. Some key points covered include: 1. The definitions of a cell and subcellular organelles along with their typical sizes. 2. The basic differences between prokaryotes, eukaryotes, and viruses. 3. The scale ranges that can be seen with light vs electron microscopes. 4. The components and main functions of the cytoskeleton. 5. The fluid mosaic model of membrane structure and classes of membrane proteins. 6. Enzyme classes, kinetics, inhibitors and regulation mechanisms. 7. The roles

1. Cell Biology
Cells and Organelles
1. Define the terms (i) cell (ii) subcellular organelle with approximate dimensions1
2. What are the basic differences between prokaryotes, eukaryotes and viruses2
3. What range of scale can be seen by a light microscope vs an electron microscope3
4. What would you use a transmission electron microscope and a scanning electron
microscope for?4
5. What rule of physics defines the maximum size of a cell?5
6. How do specialist cells overcome this problem6
7. What are the components in the cytosol that make up the cytoskeleton and what
is its main function?7
8. Under what circumstance do the chromosomes of the nucleus condense?8
9. Which organelle is responsible for fusion of vesicles within the cell which are used
to deliver hormones and neurotransmitters?9
1 A cell is a semi-independent (or independent) living unit containing mechanisms for metabolism, growth
and replication (by division), size ranges from 2-100 micrometres. Organelles are subunits within a cell,
some may be membrane bound, size ranges 100nanometres-10micrometres
2 Prokaryote = a single celled organism with ribosomal DNA, e.g. bacteria, Eukaryote = has a membrane
bound ʻtrue nucleusʼ DNA expressed as chromosomes, all complex organisms are eukaryotes. Virus =
assemblage of DNA/RNA which is parasitic and incapable of replication by division alone, lack their own
plasma membrane.
3 LM = 100nm-1mm, EM = 1 angstrom - 1mm
4 TEM = to look inside a cell, SEM = to see the cellʼs surface (scattering heavy metal particles)
5 Fickʼs law, the rate of diffusion across a membrane. Diffusion is not efficient above 50 micrometres
6 In neurons and oligodendrocytes (really long cells) a system of protein filaments such as actin filaments or
microtubules, give the cell its shape and capacity for directed movement
7 Actin (thinnest), microtubules (thickest, pull daughter cells apart in division) and intermediate filaments
(mechanical strength). Cytoskeleton function = to contribute to mechanical strength and control cell shape.
8 Become condensed/visible when cell divides
9 The Golgi body - its function is the packaging of proteins

2. 10.What structure is responsible for the transmission of electrical signals between
cells?10
11.Define & give biological functions for the following:
(i) lysosome11
(ii) peroxisome12
(iii) nuclear envelope13
(iv) chromatin14
(v) nucleolus15
Autonomic Nervous System
1. Where are the ganglia of sensory fibres located?16
2. In what way is the location of motor neuron cell bodies different to sensory?17
3. What are the key differences between the anatomy of an autonomic never vs a
somatic nerve?18
4. Whereabouts in the CNS are the roots of (i) sympathetic (ii) parasympathetic
neurons found?19
5. What is the difference between white ramus and grey ramus?20
10 Actin cables
11 Electron dense spheres that contain acid hydrolase enzymes that break down waste materials in the cell
12 Found in virtually all eukaryotic cells and responsible for the breakdown of long chain or branched fatty
acids and amino acids. Involved in detoxification.
13 2 layers of membrane form the nuclear envelope which contains the nucleolus and chromatin. Nuclear
pores allow transport in and out.
14 Complex of DNA, histones and non-histone proteins found in the nucleus of eukaryotic cells
15 Where the rDNA is transcribed and ribosome subunits assembles within the nucleus
16 In posterior root ganglia of the spinal nerves, sensory ganglia of the cranial nerves.
17 Motor neurons lie in ganglia outside of the CNS, motor neurones innervate smooth muscle and glands, so
only need to be connected to the autonomic nervous system. 1 nerve leaves CNS, separate nerve
innervates the target structure.
18 Autonomics are made up of 2 neurons, 1 myelinated and rooted in the CNS, one unmyelinated and rooted
in the effector region. Somatic neurons only use Ach as neurotransmitter whereas autonomics use Ach or NE
19 Sympathetics = T1-L2 (thoracolumbar), Parasympathetics = Cranio-spinal (either end of spinal column),
S2-S4.
20 White ramus = preganglionic outflow of the sympathetic nervous system. Grey ramus = post ganglionic
and post synapse.

3. 6. What are the sympathetic chains/trunks?21
7. What are the main differences in the structure of a parasympathetic neuron vs. a
sympathetic neuron?22
8. What are the basic functions of the:
(i) Pons23
(ii)Medulla24
(iii)Hypothalamus25
(iv)Thalamus26
Lipids and Membrane Structure
1. How are (i) proteins (ii) carbohydrates (iii) lipids expressed in the fluid mosaic
model of membrane structure?27
2. List the 4 main functions of lipids in the body28
3. What do serine, choline, ethanolamine and inositol have in common with
reference to phospholipids?29
4. Describe the structure of a phospholipid30
5. What does it mean if something is amphiphatic?31
21 Paired (either side of spinal cord) which run from the skull to the coccyx and allow sympathetic neurons to
interconnect. Interacts with the spinal nerves via rami communicantes.
22 Sympathetics synapse far from the target and their postsynaptic (unmyelinated) neurons are longer.
Parasympathetics synapse at the target organ so their longest neuron is myelinated. Sympathetics may
induce their effects by stimulating an endocrine gland which then induces the target response by hormone
secretion into the circulation, the PNS does not use hormones.
23 Higher levels of respiratory control
24 Processing centres for complex visceral reflexes
25 Sympathetic and parasympathetic HQ
26 Emotions and sensory input
27 Proteins are ʻislandsʼ in the membrane and may be membrane spanning channels or only sit on one side
of the membrane. Carbohydrates visible as ribose or chains attached to the end of phosphoglycoproteins.
Phospholipids (hydrophilic head, hydrophobic tail) chains make up the majority of the membrane.
28 1/ Energy stores - triglycerol, 2/ Precursors for vitamins/hormones, 3/ Cholic acid (bile salts) for
emulsification of fat in the GI tract, 4/ Membrane structure (phospholipid bilayer)
29 These are all amino acids which commonly form the polar heads of phospholipid molecules.
30 A polar head (amino acid) attached to a glycerol backbone via a phosphate group. The glycerol is attached
to 2 fatty acid chains by ester bonds.
31 Where the same molecule is both hydrophobic (lipophilic) and hydrophilic

4. 6. Describe the structure of sphingomyelin32
7. What is the difference between fully saturated, mono-unsaturated and
polyunsaturated fatty acids and give one example of each33
8. How does lipid content affect the fluidity of a membrane?34
9. List 5 classes of membrane proteins35
10.What is the difference between (i) integral/intrinsic proteins, (ii) anchored
proteins (iii) peripheral proteins36
11.What type of protein in (10) are (i) RAS, (ii) alkaline phosphatase (iii) spectrin37
12.Name the 4 classes of phospholipase and where they break bonds on
phospholipids38
13.What classes of membrane protein can be removed by (i) high salt substances, (ii)
detergent, (iii) phospholipase 39
Functional Organisation of the Respiratory System
1. What is minute ventilation (V)?40
32 One of a class of lipids that contain a sphingosine backbone in the place of glycerol. It still contains the
phosphate group and amino acid (in this case choline) and has one fatty acid chain attached to the NH group
on the sphingosine.
33 Fully saturated = no double bonds (Stearic, Palmitic or Myristic acid), mono unsaturated = one double
bond (Oleic acid), polyunsaturated = several double bonds (arachidonic acid)
34 Fluidity is the ease with which lipid molecules move about in the plane of the bilayer. Short chain fatty
acids and unsaturated fats increase fluidity. High cholesterol and saturated fats decrease fluidity.
35 Structural (e.g. cytoskeleton/cell-cell contact), receptors, ion channels, transporters (e.g. GLUT-4),
enzymes (may be found on membrane)
36 Integral = embedded in the bilayer and usually span across the bilayer (alpha helixes or beta pleated
sheets), Anchored = membrane covalently bound to glycolipids fatty acids (inside edge), although the protein
itself is not deeply embedded 3/ Peripheral - attach to the membrane surface by ionic interactions with
integral proteins or polar head (outside edge)
37 RAS and alkaline phosphatase = anchored (attached to lipid), Spectrin = peripheral (attached to polar
group)
38 PLA 1 and 2 = the ester bonds between fatty acids and glycerol backbone, PLC = phosphate to glycerol,
PLD = polar group to phosphate
39 High salt = peripheral (breaks bond with polar group), Detergent = all (degrades bilayer int detergent
micelles), phospholipase = anchored (breaks polar group bond with fatty acids)
40 volume entering the lungs per minute

5. 2. What is alveolar ventilation (Va)?41
3. What is the approximate volume of dead space in a typical respiratory system?42
4. What is approximate alveolar ventilation at rest?43
5. What is ‘Helium dilution’44
6. What happens to the lower six ribs in forced breathing once the limit of
abdominal compliance is reached and central tendon of the diaphragm is fixed?45
7. What would alveolar pressure be at functional residual capacity?46
8. What is the function of alpha-1 antitrypsin?47
Amino Acids and Proteins
1. What defines something as an essential amino acid?48
2. What are the two stable forms of secondary protein structure?49
3. What is the basic structure of a basic amino acid?50
41 volume taking part in gas exchange per minute
42 150ml
43 5L/min
44 Used for measuring lung volume. Subject inhlaes helium (which is poorly aborbed by the blood), the gas
volume that was originally in the lungs can be deduced from the fall in helium concentration as the inhaled
gas and original lung gas mix.
45 Lower 6 ribs can be raised upwards and outwards to allow lungs to thorax to expand further
46 Although pressure in the airways would be negative alveolar pressure is maintained at zero by the surface
tension created by surfactant. It is negative when breathing in and positive when breathing out.
47 A protease inhibitor which protects lung tissue in particular from the enzymes of inflammatory cells. For
example, it is responsible for protecting elastin from the damaging effects of neutrophil elastase. (COPD/
emphysema can be a result of deficiency)
48 An amino acid that cannot be synthesised by the body and therefore has to be supplied in the diet
49 Alpha helix and B pleated sheet
50 All amino acids have an amine group (NH2) at one end, a COOH group at the other and a carboxyl group
in-between with an R group attached (H = glycine, CH = alanine).

6. 4. What are the special properties of a peptide bond?51
5. What happens when a protein becomes denatured?52
6. What is the difference between primary structure and secondary structure?53
7. How is solubility affected by globular or fibrillar structure?54
8. What is the difference between tertiary and quaternary structure?55
9. Hydrogen bonds are formed by electronegative elements in the protein structure,
what are H-bond donors and what are acceptors?56
10.Where will you find the R groups in a b-pleated sheet?57
11.What kind of fibrillar proteins have B-pleated sheets and what characteristic does
this give them?58
12.Describe the nature of the peptide bond between amino acids59
13.Describe the main structural features of an alpha helix60
51 Contains some features of a double bond, shorter than a C-N bond, no rotation, partial -ve charge on O
atom, partial +ve charge on N atom
52 Hydrogen bonds which gave the protein its original formation have been broken, although basic protein
structure remains.
53 Primary = arrangement of amino acids in chain, secondary = hydrogen bonding between water and/or
other protein chains to give protein either an alpha helix or b-pleated sheet.
54 Globular = soluble, fibrillar = insoluble
55 tertiary = peptide chain (in alpha helix or beta pleated sheet) folds in on itself, Quaternary = folded peptide
chains join together, held together by hydrogen and S-S bonds.
56 Nitrogen and oxygen can be donors or acceptors
57 either side of the plane of the sheet (alternating)
58 Fibrillar proteins such as fibroin - gives them high tensile strength but little elasticity
59 A covalent chemical bond formed between two molecules when the carboxyl group of one binds to the
amino group of the other molecule
60 Secondary structure brought about between hydrogen bonding between N-H groups and C=O group.

7. Properties of Enzymes and Enzyme Kinetics
1. What are the 6 classes of enzyme and their main function?61
2. Give an example of a ligase enzyme62
3. Describe the basics of enzyme structure63
4. What is the ‘induced fit’ model64
5. What are the co-enzymes for:
(i) alcohol + NAD+65
(ii)succinate + FAD66
(iii)Glucose + ATP67
6. What is the Michaelis menton reaction model?68
7. What is the Michaelis-Menton equation?69
8. Define the terms:
(i) Initial velocity70
(ii) Km71
(iii)Vmax72
61 Oxoreductases (redox reactions, catalyse transfer of hydrogens), transferases (transfer functional groups),
hydrolases (cleave bonds using water), lysases (add groups to C=C bonds), Lysases (form C-C or C-N
bonds using ATP)
62 DNA ligase - joins DNA molecules together with C-C or C-N bonds using ATP
63 Enzymes are proteins composed of 1 or more folded peptide chains, stabilized by hydrogen bonds. Weak
bonds between protein chains mean enzymes are highly sensitive to their environment.
64 Where one molecule changes the structure of an enzyme so that the binding site can be filled.
65 Alcohol dehydrogenase
66 Succinate dehydrogenase
67 Glucokinase
68 Enzyme + Substrate <-k1/k-1-> Enzyme/Substrate complex <-k2-> Enzyme + Product
69 Initial reaction velocity = Vmax x [S]
# # # Km + [S]
70 written as V0 initial velocity is measured as soon as enzyme and substrate are mixed so no substrate has
been used up yet
71 Km is the substrate concentration at which the initial velocity is half the Vmax
72 Vmax is the maximum velocity of an enzyme catalysed reaction when all active sites are fully saturated
with substrate

8. 9. What is Kcat?73
10.What is the difference between competitive inhibitors and non-competitive
inhibitors?74
11.Give an example of clinical use of enzyme inhibitors75
12.List 3 biological mechanisms for the regulation of enzyme activity76
Cell Motility and the Cytoskeleton
1. What functions/characteristics of the cell can be determined by the cytoskeleton?
77
2. What are the 3 components of the cytoskeleton?78
3. What is required for the growth of an actin filament?79
4. What are the 3 main functions of actin within the cell?80
5. Where in the cell are the intermediate filaments most dense?81
6. What are dimers and tetramers?82
73 The turnover number - equivalent to the number of substrate molecules converted to product in a given
unit of time on a single enzyme molecule when the enzyme is saturated with substrate. Two enzymes may
have the same Kcat but different Km.
74 Competitive Inhibitors block the enzyme active site (alter the apparent Km not the Vmax. Non-competitive
interfere with mechanism in any other way (e.g. allosteric)
75 1/ Control of angiotensin production by treatment of heart failure with ACE inhibitors to reduce blood
pressure and edema.
76 Allosteric modification (e.g. ATP and citrate affecting phosphofructokinase), covalent modification by other
enzymes (e.g. kinase adding a phosphate), increase or repression of enzyme synthesis (e.g. adrenaline can
regulate the amount of insulin and release glucagon).
77 Cell shape and polarity, tissue structure, adhesion, cell movement, intracellular movement of vesicles or
chromosomes
78 Actin (microfilaments, actin binding proteins, double helix), Intermediate filaments (fibrillar), microtubules
(literally small tubes)
79 ATP can add actin monomers to either end, it is much easier to add to the +ve end, ADP remains bound.
80 Mechanical support, cell shape changes and maintenance, cell motility
81 Nearest the membrane, they then extend out into the periphery
82 Helical dimers are formed by intermediate filament monomers, helical dimers then form the basis for
tetramers which link in a staggered formation to form a multilayered fibrillar intermediate filament.

9. 7. What is the monomer unit for microtubules?83
8. Which organelles polymerize microtubules?84
9. What are the functions of intermediate filaments?85
10.Give an example of an actin-based cell movements?86
11.Describe the mechanism by which actin moves cells?87
12.What is a lamellipodium?88
13.What is the microtubule associated protein which initiates movement?89
14.What are the functions of microtubules?90
15.Which two proteins are associated with the movement of vesicles along
microtubules?91
16.What is a processive motor?92
17.Give examples of drugs/therapeutic agents given to stabilise or destabilise
microtubules and inhibit cell division93
18.Give examples of diseases caused by actin abnormalities94
83 Tubulin monomers (alpha tubulin and beta tubulin)
84 centromeres (+ve end of microtubule faces outwards towards the periphery, -ve
85 For support of cells which need to be a particular shape for their function: microvilli, actin sheets in
erythrocytes, stereocilia in inner ear, axons.
86 Migration of neutrophils to sites of infection
87 Cell pushes out protrusions at the front edge of cell, protrusions adhere to the surface on which the cell is
moving. Actin filaments drag the cell towards anchorage points, actin depolymerizes at the rear of the cell
88 Name for the actin projection from the motile side of a cell used to move the cell and sample the
environment. Actin joins to myosin and forms cross bridge.
89 dyenin (a -ve end directed motor protein)
90 Support, anchoring cells together, transport of organelles between cells or along axons to synapses.
91 Kinesin and dyenin
92 A motor protein which stays attached throughout the ATP hydrolysis cycle (unlike myosin which completely
detaches at end of cross bridge cycle), and is therefore capable of moving long distances.
93 Colchicine (destabilize), vinblastine (stabilize) and taxol (stabilises)
94 Muscular dystrophy, Usherʼs syndrome (deafness and blindness)

10. 19.Give examples of diseases caused by intermediate filament abnormalities95
20.Give examples of diseases caused by microtubule abnormalities96
Regulation of the Cell Cycle and Cancer
1. What is the criteria for a cell to be considered capable of ‘the cell cycle’?97
2. What are the stages of mitosis?98
3. What is interphase?99
4. What are the 3 stages of interphase?100
5. What is the restriction point?101
6. What is G0/quiescence?102
7. How does the length of the cell cycle vary for embryonic tissues?103
8. What proteins must be activated in order to move from one stage to another?104
9. What causes the proteins in (8) to activate at the correct time?105
95 Epidermolysis bullosa symplex (skin is sensitive to mechanical injury, blistering, sloughing), Amyotophic
lateral scletosis
96 Alzheimerʼs, Herediary Spastic Paraplegia (mutations in spastin, a microtubule severing protein)
97 Division into 2 daughter cells
98 1/ Prophase (condensation of chromosomes), 2/ Prometaphase (breakdown of nuclear envelope), 3/
Metaphase (chromosomes assemble on the spindle of the centre of the cell 4/ Anaphase (separation of
chromosomes to opposite ends of the cell, 5/ Telophase (reformation of nuclear envelopes) 6/ Cytokinesis
(separation of the 2 daughter cells)
99 The time between cell division of a particular cell (20 hours), DNA synthesis & chromosome replication
100 G1 (12 hours) cell determines whether the environment is favourable or has had growth signals i.e.
correct DNA, is cell big enough to divide, S (6-8 hours) the stage of chromosome replication (chromosomes
x2), G2 (4 hours) more checkpoints, is the cell big enough to divide & have all the chromosomes been
replicated
101 The ʻcheckpointʼ of G1
102 If the cell decides that it cannot divide in G1 and remains static without dividing.
103 As little as 8 hours (22-24 when born), as the G1 phase is reduced
104 Cyclin dependent protein kinases. Present in cell all the time but active when moving between G1/S and
G2/M
105 Dependent on a family of proteins called cyclins. Cyclin E controls G1-S phase, cyclin A S-G2 phase and
cyclin B controls G2/M phase

11. 10. What are the functions of activated CDK?106
11.What makes transformed or neoplastic cells different to normal cells?107
12.What is the role of p53 in preventing damage?108
13.What is the intrinsic error rate of the DNA replication machinery (mutations/
gene/division)?109
14.How many times does a single gene mutate in a lifetime?110
15.What gene which regulates actin and microtubule skeletons could cause
transformation of cell type (e.g. epithelial to mesothelial)?111
Structure and Properties of Nucleoacids
1. What are the components of a DNA molecule?112
2. What are the names of the 4 nitrogenous bases?113
3. What is the common unit shared by AMP, ADP and ATP?114
4. What type of bond strings together DNA nucleotides in a chain?115
5. How many OH groups can a single nucleotide (in a chain) be attached to?116
106 Activates DNA polymerase, Phosphorylated histones and lamins and stimulates kinetochore formation
107 They cannot be regulated because they divide in the absence of growth factors and exhibit density
independent growth when cultured (loss of contact inhibition).
108 p53 is a tumour supressor gene, it is phosphorylated (activated) following DNA damage and induces
transcription of p21 which inhibits the activation of cyclin dependent kinase preventing entry into the S phase
or M phase.
109 1x 10^-6 mutations/gene/division
110 10^10 per lifetime
111 Ras
112 Deoxyribose H (no OH). Ribose OH. Phosphate. Nitrogenous base (A, C, T or G)
113 Adenine, Guanine, Thymine and Cytosine
114 Adenosine, 5
115 Phosphodiester bonds between nucleotide. O (from OH on ribose) to P (on phosphate group)
116 3, bound to the ribose

12. 6. What is the 5 end and the 3 end?117
7. What is X-ray diffraction?118
8. What is the diameter of the DNA helix and the length of one full twist?119
9. What is the nature of the bonds between C-G and A-T?120
10.What is done to DNA to make it into chromosomes?121
11.Approximately what length of DNA is stored in a single nucleus?122
12.What is chromatin?123
13.What are histones?124
14.What is a nucleosome?125
15.How many chromosomes and genes are there in the human genome?126
16.What are introns?127
17.What proportion of human DNA actually codes for proteins?128
DNA Transcription
117 5 end = phosphate, 3 end = hydroxyl group
118 Firing a DNA sample with X rays to project an image of it onto a photographic plate, the X ray imaging
shows diffraction in an X pattern consistent with the DNA being a helix, also showed the spacing of the
nitrogenous bases.
119 2nm diameter, 3.4nm one full twist
120 2 hydrogen bonds for A-T, 3 hydrogen bonds for G-C
121 DNA packaged by proteins into chromosomes so that it can fit into the nucleus (chromosomes consist of
DNA plus protein)
122 1.8 metres of DNA in a single nucleus
123 The combination of DNA proteins that make up a cell nucleus
124 Proteins which package DNA into nucleosomes for storage in nucleus
125 Densely packed DNA on a chromatin fibre for storage in a nucleus. Tightly wound but can be unwound for
transcription.
126 23 pairs of chromosomes, 23,000 genes
127 Non-coding areas of DNA, present in eukaryotic genes but not prokaryotic ones
128 Only about 2%

13. 1. Which enzyme synthesizes RNA strands?129
2. Describe the direction of addition of RNA nucleotides130
3. What are the three main steps of transcription?131
4. What happens at stage 1?132
5. What is sigma factor?133
6. What happens at stage 2?134
7. What happens at stage 3?135
8. What is a stop sequence?136
9. How is RNA transcription different in prokaryotes?137
10.What is an exon?138
11.What is an intron?139
12.What is gene splicing?140
129 RNA polymerase - forms strand from nucleotides by phosphodiester bonds
130 Synthesis can only occur from the 5 end (phosphate group) towards the 3 end (hydroxyl group)
131 Initiation, elongation, termination
132 Initiation - RNA polymerase is directed to the start site of transcription on the double stranded DNA,
enzyme finds the transcription start site
133 A bacterial factor that enables RNA polymerase to bind to coding strand
134 Elongation - Reading of DNA sequence on a synthesis of a messenger RNA
135 Termination - Reaching of transcriptional termination site, mRNA synthesis finishes, controlled by STOP
sequences
136 GC rich region of the DNA which forms a hairpin loop, preventing further trasncription by RNA polymerase
137 More complex, more proteins involved - includes polymerases, initiation factors, elongation factors and
additional mRNA processing,
138 A region of DNA within a gene unit that is found in mature mRNA “expressed” regions
139 Regions of DNA within a gene unit that are not found in mature mRNA i.e. are not coding regions
140 Removal of intronic segments and collation of exon coding regions

14. 13.What is 5’ capping?141
14.What is polyadenylation?142
15.What additional processes are involved in eukaryotic transcription as opposed to
prokaryotic transcription?143
Translation and the Genetic Code/Protein Synthesis
1. What are the three STOP codons?144
2. What is the start codon with which all proteins begin?145
3. What are the functions of mRNA, tRNA and Ribosomes?146
4. What are the 4 ends/loops of a ‘clover leaf’ tRNA molecule?147
5. What is wobble pairing?148
6. What is the reaction equation for activation of an amino acid from tRNA?149
7. What is the basic difference between 70S and 30S subunits?150
141 Process for getting mRNA out of the nucleus to be translated (after having been transcribed). Stabilises
immature mRNA making it mature so methyl group is added to guanine position.
142 Addition of AAAAA chain to the 3 (hydroxyl) end of an RNA chain. Happens at the end of a gene
transcription.
143 Despite less proteins involved, eukaryotic transcription involves the additional processes of capping,
splicing and 3 polyadendation.
144 UAG, UGA and UAA
145 AUG (Met)
146 mRNA = carries sequence of information to make protein, tRNA = bring individual amino acids to sites of
protein synthesis, Ribosomes = contain ribosomal RNA, machinery of protein synthesis and bind mRNA and
tRNA
147 3 end (where amino acid attached), D loop, T loop, anticodon loop
148 Last base on anticodon part of anticodon loop can form non Watson-crick base pair. Allows a single tRNA
species to recognize more than one codon without changing the amino acid sequence, because its
anticodon can vary.
149 Amino acid + tRNA + ATP --> aminoacyl-tRNA + PPi + AMP (energy for addition of amino acid to tRNA
comes from hydrolysis of ATP)
150 These are two parts (subunits) of the ribosomal DNA, the 50S is the larger subunit and the 30S is the
smaller one

15. 8. What are the 3 binding sites on the prokaryotic ribosome?151
9. Describe the initiation stage of translation in prokaryotic cells152
10. What is the Shine-Dalgarno sequence?153
11. Describe the elongation stage of translation in prokaryotic cells154
12.What are the main differences between prokaryotic and eukaryotic transcription?
155
Protein Targeting
1. How is an mRNA molecule in the cytosol coupled to its corresponding place in
on the endoplasmic reticulum membrane?156
2. What is responsible for cleaving the signal sequence protein?157
151 E site, P site and A site
152 Initiation = formation of initiation complex comprising of the ribosome, mRNA and initiator tRNA. Initiation
proteins IF1, IF2 and IF3 are required. GTP dependent. 30S subunit binds factors, binds mRNA and 1st
tRNA. Once bound to IF2 the 50S subunit arrives and binds to the whole complex, releasing energy (Pi) from
GTP to GDP
153 Sequence in a gene upstream of the ʻstartʼ (AUG) sequence. It is basically the initiation sequence. So
every time you want to start translation you need 1/ Ribosome binding site, 2/ Shine Dalgarno sequence, 3/
AUG start codon
154 The activated tRNA binds to EF (elongation factor) and GTP, ʻproof readingʼ (GTP to GDP). Peptidyl
transferase then makes a bond between the first and second amino acids and the ribosome moves one over
and one RNA strand is released.
155 Prokaryotic has and Eukaryotes ribosome. mRNA translated as soon as synthesised.
Prokaryotes Eukarotes
Ribosome: 30S + 50S (70S) Ribosome: 40S + 60S (80S)
mRNA translated as soon as synthesised hnRNA has to be modified by capping, splicing and
polyadendation before leaving nucleus
Initiator: fmet-tRNA Initiator: met-tRNA
Start: Shine-Dalgano sequence (start) Start: Cap 5 and mRNA
mRNA codes for multiple proteins mRNA codes for one protein
156 ER signal sequence grows out of side of mRNA, joined to a signal recognition particle. SRP picked up by
a receptor on the ER membrane which pulls the mRNA into a translocation channel.
157 Signal peptidase

16. 3. What are the products of the transport vesicles given off by the endoplasmic
reticulum once they have passed through the Golgi body?158
4. Name the receptor regions on the protein vesicle and plasma membrane that
intertwine to cause the vesicle and membrane to fuse together159
5. What are the processes of protein folding and glycosylation that occur in the
endoplasmic reticulum and Golgi body?160
6. Which organelle receives unfolded proteins (not vesicles) from the cytoplasm and
folds them up for its own use?161
7. What are the locations within the cell of transcription and translation?162
8. Name the protein responsible for carrying other proteins into the nuclear
envelope163
9. What is the function of a lysosome?164
10.Which receptor/tag molecule is added to lysosomal proteins when they are
packaged into vesicles in the Golgi body165
11.What could cause waste proteins to be secreted instead of going into lysosomes?
166
12.How are proteins transported:
(i) across the organelle membrane to ER or mitochondria167
158 Secretory vesicles, lysosomes, peroxisomes.
159 v-SNARE on the vesicle and t-SNARE (target) on the membrane, vesicle fuses into membrane to release
proteins
160 Protein folding = formation of tertiary protein structure (disulphide bridges), Glycosylation = processing of
sugars to give diversity, adding sugar residues to protein
161 Mitochondria
162 Transcription (RNA synthesis) = nucleus, Translation = cytoplasm/ER ribosomes
163 Importin
164 To degrade unwanted proteins, RNA etc. (enzymes require acidic pH)
165 Mannose-6-phosphate
166 Defective mannose-6-phosphate tagging mechanism. Inclusion-cell disease caused by mutant enzyme
for phosphorylating mannose. Named because waste accumulates in ʻinclusion bodiesʼ.
167 Protein translocators/ signal recognition particles

17. (ii)from the ER to lysosomes or plasma membrane168
(iii)Into the nucleus from the cytosol169
Antibiotics and Protein Synthesis Control
1. List the stages at which protein synthesis can be controlled170
2. How many genes are there in the human genome?171
3. How does transcriptional control work?172
4. What is the Leucine zipper?173
5. What is negative regulation?174
6. What is positive regulation?175
7. What mechanism of negative feedback could occur in protein synthesis control?176
8. List examples of translational/post translational control177
9. What are the actions of transcription factors?178
168 In vesicles which may fuse with the target membrane
169 Free diffusion of small molecules through nuclear pores, larger ones transported by protein ʼimportinʼ
170 Transcription, RNA processing in nucleus, RNA transport, mRNA degradation, translation, protein activity
(i.e. protein may be synthesised but not activated (by phosphorylation, acidic conditions etc.), folding of
protein etc.
171 22,000
172 transcription factors act on a promoter and distort the DNA allowing RNA polymerase to work better. Can
be based on hnRNA synthesis rate, processing/export rate or mRNA degradation
173 Is a 3D structural motif in proteins which is part of the DNA binding domain, they regulate gene
expression.
174 Where an inhibitor binds to the DNA, inhibiting its transcription
175 transcription only occurs when the transcription factor binds to the DNA
176 Where the protein being synthesised or a molecule associated with it contains the ligand for switching the
DNA polymerase off and stops too much of itself being synthesised
177 Regulating the efficiency of translation, the folding/maturing of proteins, the protein degradation of
proteins, the targeting of proteins to sites of activity
178 Distort double helix, allow RNA polymerase to recognize the start site for transcription, repress ability of
RNA polymerase to transcribe the gene (e.g. Leucine Zipper)

18. 10.Name the glucocorticoid hormone released in the starving state which stimulates
the liver to increase production of glucose?179
11.Explain what is meant by chromatin remodeling180
12.What is micro-RNA181
13.What is the mechanism behind protein degradation?182
14.What is the cytoplasmic site of proteolysis?183
15.What is the mechanism of the following antibiotics:
(i) Actinomycin184
(ii)Rifamycin185
(iii)Streptomycin186
(iv)Erythromycin187
(v)Chloramphenicol188
(vi)Tetracyclines189
16. Describe the mechanisms of these other translational inhibitors:
(i) Puromycin190
(ii) alpha-aminitin191
179 cortisol
180 The dynamic modification of chromatin architecture (packaged chromosomes) to allow access of
condensed genomic DNA to the regulatory transcription machinery proteins, controlling gene expression.
181 A small, non-coding molecule, form base pairs within mRNA molecules which silences the target gene
(about 1/3 of human genes are targeted).
182 Turnover/lifespan of protein may be affected by transcription factors. Proteolysis is the breakdown of
proteins into inactive fragments by enzymes, occurs in lysosomes (where unwanted proteins are disposed
of) also in cytoplasm.
183 Proteosome - a cap within this recognises and binds proteins destined for digestion and they are digested
back down into peptides within the proteosomeʼs cylindrical structure.
184 binding DNA at transcription initiation complex
185 Inhibition of DNA dependent RNA synthesis through binding to prokaryotic RNA polymerase
186 Affects initiation of prokaryotic 30S subunit and causes misreading of codons
187 Binds to 50S subunit
188 Inhibits peptidyl transferase by binding on 50S subunit
189 Inhibit binding of aminoacyl tRNAs to ribosome
190 causes premature chain termination during translocation
191 Inhibits RNA polymerase

19. (iii) Cycloheximide192
(iv) Diptheria toxin193
DNA Replication/Mutation/Analysis
1. What are the respective time periods for the following parts of the cell cycle in
eukaryotic cells: G1, S phase, G2 and Mitosis194
2. What is semi conservative replication195
3. What is the function of DNA helicase?196
4. What is the difference between the leading and lagging strands?197
5. What are Okazaki fragments?198
6. What is positive supercoiling?199
7. What are the functions of DNA primase and DNA polymerase III?200
8. What is the function of DNA ligase?201
9. What is the function of nuclease enzyme?202
192 Inhibits protein biosynthesis by interfering with translocation step (in eukaryotes)
193 Inhibits RNA translation by inactivating elongation factor 2
194 G1 = 6-9 hours, S phase = 8-9 hours, G2 = 5-6 hours, Mitosis = 1-2 hours, TOTAL = 20-26 hours
195 Each DNA molecule contains one parent and one daughter strand
196 Separation of 2 strands of DNA, breaking hydrogen bonds to form 2 replication forks (one ʻ3 and one ʻ5)
197 The replication fork strand moving in the 3 to 5 direction (from the hydroxyl 3 towards the phosphate 5),
so the original strand it is being synthesised from is in the opposite 5 to 3 direction. It is called leading
because it is being synthesised in the same direction as the fork opening, i.e. the newest synthesised DNA is
that nearest the junction of the fork. Lagging is the opposite (synthesised 3-5), its synthesis is furthest away
from the activity of the DNA helicase.
198 DNA primase forms these short fragments on the lagging strand, since its movement is not continuous
with DNA helicase
199 Where the separation of the two strands by DNA helicase makes the coils tighter further down the helix
200 Primase makes the RNA primer so that DNA synthesis can begin. DNA polymerase III synthesizes new
DNA strand
201 Joins discontinuous fragments together making a phosphodiester bond
202 Removes wrong/miscopied nucleotides so correct gene is copied without mutation, can work as a
standalone enzyme or as a function of DNA polymerase III

20. 10.What are the functions of the following types of DNA polymerase in prokaryotic
replication: alpha, delta, beta, epsilon?203
11.How is mitochondrial DNA replication different to that of other eukaryotic
organelles?204
12.What is a telomere?205
13.What enzyme catalyses the formation of telomeres?206
14.What kind of cells have the ability to lengthen their telomeres (and so prevent
cell aging)?207
15.Define (i) point mutation (ii) silent mutation (iii) missense mutation (iv) Nonsense
mutation208
16.What are the 4 types of gross mutation?209
17.How does mutation happen from replication slippage?210
18.What is deamination?211
19.How does UV radiation cause DNA damage?212
20.List some causes of induced mutations (physical and chemical)213
203 A = assembles primers and synthesizes lagging strand, D = synthesizes lagging strand and has
proofreading ability. B & E = Involved in DNA repair
204 Mitochondrial DNA have their own circular chromosome. Synthesised by DNA polymerase gamma.
205 A region of repetitive nucleotide sequences at the end of each chromatid, protects the end of the
chromosome from deterioration from fusion with neighboring chromosomes because the end of each
chromosome shortens with every round of replication.
206 Telomerase, acts by extending the 3ʼ end of the chromosomal DNA
207 Gametes and most tumor cells (85%)
208 Point = single base changed, Silent = mutation that still codes for the same amino acid, Missene =
mutation that codes for a different amino acid, Nonsense = change in code from amino acid to a stop codon
209 Inversion, translocation, deletion, duplication
210 Where a part of one of the coding strand slips backwards or sideways so that the strand being
synthesised misses that part of the code
211 Deletion of one amine group from a sequence
212 Forms a dimer between adjacent thymidine residues
213 Ionising radiation, UV light, various agents that react with bases (nitrous acid, alkylating agents, free
radicals)

21. 21.How does 06 methylguanine act to repair DNA?214
22.What is Xeroderma pigmentosum?215
23.What virus has the highest mutation rate of anything observed to date?216
214 directly repair the damage by removing damaged region and re-synthesize it
215 Genetic disorder causing defective repair of UV damage and over 1000x risk of skin cancer from sunlight
216 HIV, this is why it is so difficult to treat. HIV reverse transcriptase does not possess a 3-5 exonuclease so
is unable to proofread/correct mutations