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Semester 1 > MGD Sessions 1-6 > Flashcards

MGD Sessions 1-6 Flashcards

1
Q

Why are amino acids classified by their R group?

A

Only part of molecule not disrupted upon formation of peptide bonds

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2
Q

Which isomer are naturally occurring amino acids found?

A

L

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3
Q

Which group of amino acids do glycine, alanine, valine, leucine, isoleucine, methionine, proline, phenylalanine and tryptophan all belong to?

A

Non-polar (hydrophobic)

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4
Q

Which group of amino acids do serine, threonine, asparagine, glutamine, tyrosine and cysteine belong to?

A

Polar, uncharged (hydrophilic)

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5
Q

Which group of amino acids do lysine, arginine, histidine, aspartate and glutamate belong to?

A

Polar, charged (hydrophilic)

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6
Q

Which amino acids have positive R groups?

A

Lysine
Arginine
Histidine

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7
Q

Which amino acids have negative R groups?

A

Glutamate
As
Aspartate

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8
Q

If pH > pK what happens to the R group on an amino acid?

A

It is deprotonated

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9
Q

Which type of peptide bonds only are found in a protein?

A

Trans so side chains aren’t too close together

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10
Q

What is the isoelectric point?

A

pH at which a protein has no net charge

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11
Q

If pH

A

Protonated

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12
Q

If pH > pI what happens to the protein?

A

Deprotonated

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13
Q

How many amino acids in length are peptides/oligopeptides?

A

Few

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14
Q

Give three examples of basic proteins.

A

Chymotripsinogen
Cytochrome C
Lysozyme

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15
Q

Give four examples of acidic proteins.

A

Pepsin
Serum albumin
Urease
Haemoglobin

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16
Q

What is the pI of myoglobin?

A

7.0

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17
Q

What determines the conformation of the backbone of a polypeptide and hence how the protein folds?

A

Bond angles of peptide bonds

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18
Q

Why are not all bind angles available in a polypeptide?

A

Some will cause side group clashes

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19
Q

How many amino acids are there per turn in an alpha-helix?

A

3.6

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20
Q

What is the distance between amino acids in an alpha helix?

A

0.15 nm

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21
Q

What is the height of a turn in an alpha-helix?

A

0.54 nm

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22
Q

Is an alpha-helix right handed or left handed?

A

Right handed

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23
Q

Where are the side chains on an alpha-helix positioned so they do not affect the alpha-helix structure?

A

On the outside

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24
Q

What bonds allow an alpha-helix to be formed?

A

Carbonyl group of one residue H-binding to amine group of the residue 4 a.a. away

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25
Q

What type of residues are strong helix formers?

A

Small, hydrophobic

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26
Q

Why are small hydrophobic residues strong alpha-helix formers?

A

Keep their hydrophobic side chains out of solution

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27
Q

Why is proline an alpha-helix breaker?

A

Rotation around N-C(alpha) is impossible

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28
Q

Why is glycine an alpha-helix breaker?

A

It’s tiny R group allows for other conformations

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29
Q

How does a beta strand compare to an alpha-helix?

A

Less compact

Fully extended

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30
Q

What is the distance between amino acids in a beta-strand?

A

0.35 nm

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31
Q

How are the R groups of amino acids arranged in a beta-strand?

A

Alternate b/w opposite sides of the chain

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32
Q

What provides stability in the anti-parallel alignment of beta-strands?

A

Hydrogen bonds

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33
Q

How does a sheet with parallel alignment compare to a sheet with antiparallel alignment of beta-strands?

A

Less compact

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34
Q

What is used to illustrate beta-strands on a diagram?

A

Flat arrows

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35
Q

What is the function of fibrous proteins?

A

Provide support, shape and protection

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36
Q

How many types of repeating secondary structure make up fibrous proteins?

A

One

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37
Q

What is the structure of collagen?

A

Super helix of three alpha-helix collagen chains wrapped around each other, stabilised by hydrogen bonds

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38
Q

How does the structure of collagen allow it to form fibrils?

A

Superhelices can form covalent cross-links

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39
Q

What are globular proteins used for?

A

Catalysis

Regulation

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40
Q

How many secondary structures do globular proteins contain?

A

More than one

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41
Q

What are motifs?

A

Globular folding patterns of 1 or more secondary structure elements e.g. Beta-alpha-beta loop or beta-barrel

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42
Q

What are domains?

A

Part of a polypeptide chain that fold into a distinct shape, often with a specific functional role

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43
Q

Why do membrane proteins show an ‘inside-out’ amino acid distribution by having a hydrophobic exterior?

A

To allow it to sit in the membrane

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44
Q

How can covalent bonds in the tertiary and quaternary structure of a protein be broken?

A

Reducing agent

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45
Q

Why are most proteins with disulphide bonds secreted?

A

They are stable

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46
Q

What holds protein structures together?

A 
Covalent bonds
Electrostatic interactions b/w charged groups
H-bonds
Van der Waals
Hydrophobic effect
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47
Q

How can proteins be denatured?

A

Heat
pH
Detergents/organic solvents

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48
Q

How does pH denature a protein?

A

Alters ionisation state of a.a. and disrupts ionic/H-bonds

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49
Q

How do detergents/organic solvents cause denaturation?

A

Disrupt hydrophobic interactions

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50
Q

What determines how a sequence is folded?

A

Primary structure

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51
Q

What may be required for a protein to fold?

A

Chaperone

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52
Q

What happens when mis folding occurs?

A

Molecules cluster to form accumulations of denatured proteins which disrupt cell and its function

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53
Q

Give three examples of degenerative neurological disorders caused by misfolded proteins.

A

BSE (mad cow disease)
CJD
Kuru

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54
Q

What can happen when soluble proteins misfold?

A

Create insoluble form

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55
Q

What causes Alzheimer’s disease?

A

Amyloid beta-protein tail misfolding to form a highly ordered structure w/a high degree of beta-sheet which disrupts the rest of the protein formation

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56
Q

What is the inter-chain assembly in Alzheimer’s disease stabilised by?

A

Hydrophobic interactions b/w aromatic a.a.

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57
Q

What does synthetase require to function?

A

ATP

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58
Q

Does synthase require ATP?

A

Nope

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59
Q

How does phosphatase work?

A

Uses water to remove phosphoryl group

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60
Q

How does phosphorylase work?

A

Phosphate breaks bond and makes phosphorylated products

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61
Q

What does dehydrogenase accept?

A

Electrons

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62
Q

Are the oxygen atoms in the substrate for an oxidase?

A

Nope

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63
Q

Where are the oxygen atoms in oxygenase?

A

One or both in substrate

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64
Q

What are ribozymes?

A

RNAs which act like enzymes to catalyse cleavage and synthesis of phosphodiester bonds

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65
Q

What is Kcat?

A

Turnover number

Molecules of substrate to product pre enzyme per second

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66
Q

If the additional molecule needed for an enzyme to function is present, what name is given to the enzyme?

A

Holoenzyme

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67
Q

If the additional molecule an enzyme needs to function is not present, what name is given to the enzyme?

A

Apoenzyme

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68
Q

What is a cofactors?

A

Metal ion needed for enzyme function

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69
Q

What is a coenzyme?

A

Small organic molecule

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70
Q

What is a co substrate?

A

Co enzyme that makes a transient association and dissociates from the enzyme in an altered state

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71
Q

What is the name given to a coenzyme permanently associated with an enzyme which is returned to its original form?

A

Prosthetic group

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72
Q

Where are coenzymes often derived from?

A

Vitamins

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73
Q

What is the free energy of activation?

A

Peak energy difference b/w product and high energy intermediate

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74
Q

Does an enzyme change the equilibrium of a reaction?

A

No, just reached it quicker

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75
Q

What is transition-state stabilisation in enzyme action?

A

Enzyme stabilises structure in which the bonds are neither product or substrate and therefore greatly increase conversion to product

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76
Q

Can the transition state caused by enzymatic action be isolated?

A

Nope

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77
Q

How can the presence of catalytic groups increase enzyme action?

A

Enhance probability of transition state formation

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78
Q

What happens in visualisation of transition state during enzyme action?

A

ES formed –> conform into product shape –> product shape formed

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79
Q

What is Vmax?

A

Maximal velocity - when all available active sites are blocked

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80
Q

What kind of curve is formed by an enzyme that follows Michaelis-Menten kinetics when you plot V0 versus [S]?

A

Hyperbolic

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81
Q

What kind of curve is created by an allosteric enzyme when V0 is plotted against [S]?

A

Sigmoid all

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82
Q

What is Km?

A

Affinity of an enzyme for its substrate

[S] at 1/2 Vmax

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83
Q

Does Km vary with [E]?

A

Nope

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84
Q

What do a small and large Km indicate?

A 
Small = high affinity
Large = low affinity
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85
Q

When [S]&raquo_space; Km, what can be said about the reaction kinetics?

A

0 order w.r.t. [S]

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86
Q

What is used to graphically calculate Km, Vmax and mechanism of action of enzyme inhibitors?

A

Lineweaver-Burk plot

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87
Q

What does the y-intercept of a Lineweaver-Burk plot give?

A

1/Vmax

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88
Q

What does the gradient of a Lineweaver-Burk plot give?

A

Km-Vmax

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89
Q

What are suicide inhibitors?

A

Conversion of molecule to form which covalently bonds to active site of enzyme by the enzyme itself

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90
Q

Is competitive inhibiting reversible?

A

Yes

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91
Q

What kind of bonds are formed in competitive inhibition?

A

Non-covalent

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92
Q

What is observed at high [S] in competitive inhibition?

A

Vmax

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93
Q

What happens to Km in competitive inhibition?

A

Increases

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94
Q

What effect does competitive inhibition have on the Lineweaver-Burk plot?

A

Rotates anti-clockwise

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95
Q

How does non-competitive inhibition affect Vmax and Km?

A

Decreases Vmax

Km unaffected

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96
Q

What affect does non competitive inhibition have on the Lineweaver-Burk plot?

A

Rotates clockwise

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97
Q

How do you distinguish between competitive and non-competitive inhibition by using a graph?

A

Plot 1/V0 v.s. 1/[S] and see Vmax decrease and Km remain constant if non-competitive inhibitor

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98
Q

How do captopril, enalapril and lisinopril cause vasodilation?

A

Block conversion of angiotensin I to II

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99
Q

What action does aspirin have?

A

Irreversibly inhibits prostaglandin and thromboxane synthesis

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100
Q

What are allosteric enzymes regulated by?

A

+ve and -ve effectors which bind noncovalently to an allosteric site

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101
Q

What can binding of an effector do to an allosteric enzyme?

A

Affect affinity of enzyme for its substrate
Modify Vmax
Both

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102
Q

What do allosteric enzymes often catalyse?

A

Early committed step early in a pathway

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103
Q

What form are amino acids always written in?

A

Ionised

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104
Q

What is the structure of haemoglobin?

A

Tetramic - 2 alpha and 2 beta subunits

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105
Q

Why does haemoglobin have a sigmoidal binding curve?

A

Has cooperativity

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106
Q

What conformational change occurs between the T and R states of haemoglobin?

A

Twisted through 15 degrees

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107
Q

How does binding of an oxygen molecule affect the affinity of haemoglobin for oxygen?

A

Increases it

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108
Q

What does 2-3 bisphosphoglycerate do to a molecule of haemoglobin?

A

Sits in the middle of the 4 subunits to interact with histidine and lysine residues

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109
Q

How does 2-3BPG affect the oxygen binding curve for haemoglobin?

A

Shifts it to the right

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110
Q

When is 2-3BPG released into the tissues?

A

High altitude

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111
Q

What action does 2-3BPG have on the affinity of haemoglobin for oxygen?

A

Lowers it

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112
Q

How can the charge on 2-3BPG be described?

A

V. negative

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113
Q

What change in residues is seen in sickle cell anaemia?

A

Glutamate is replaced by valine in the beta-global chain

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114
Q

What does the ‘sticky’ hydrophobic pocket created in SCA do?

A

Polymerises deoxygenated HbS

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115
Q

What is beta-thalassaemia?

A

Decreased or absent beta globin chains

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116
Q

Why are beta-thalassaemia patients symptomatic after birth?

A

Alpha globin chains cannot form stable tetramers

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117
Q

What is alpha-thalassaemia?

A

Lack of alpha globin chains

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118
Q

What is the function of the Bohr effect?

A

Ensure delivery is coupled to demand

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119
Q

What causes the Bohr effect?

A

Local increase in hydrogen ions and carbon dioxide

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120
Q

What does the Bohr effect cause?

A

Reduction in affinity for oxygen therefore release of oxygen into metabolising tissues

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121
Q

Why is carbon monoxide toxic?

A

Binds 250x more readily to haemoglobin than oxygen and upon binding increases the affinity of haemoglobin for oxygen so it is not released

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122
Q

What effect does carbon monoxide have on the oxygen binding curve?

A

Shifts left

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123
Q

How can haemoglobin be used to measure diabetes?

A

Measure HbA1c levels

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124
Q

Which type of haemoglobin has the highest affinity for oxygen?

A

Foetal

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125
Q

How many amino acids form a molecule of myoglobin?

A

153

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126
Q

What percentage of a myoglobin molecule is alpha-helical

A

75

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127
Q

How many polypeptide chains make up a myoglobin molecule?

A

1

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128
Q

Where is iron located in deoxymyoglobin?

A

Slightly below plane of ring

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129
Q

How is deoxymyoglobin transformed into its ferric from?

A

Binding of oxygen moves iron into the plane of the ring

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130
Q

What shape is the binding curve of myoglobin?

A

Hyperbolic

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131
Q

What happens to myoglobin in the presence of carbon monoxide?

A

Combines which blocks oxygen transport

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132
Q

What does the saturation of myoglobin depend on?

A

Partial pressure of oxygen

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133
Q

What structural changes to the myoglobin molecule cause it’s change into the ferric form?

A

Movement of His F8

Small overall conformation change

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134
Q

How do allosteric activators and inhibitors affect V v.s. [S] curves for allosterically controlled enzymes?

A

Activator: shifts to left
Inhibitor: shifts to right

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135
Q

Where can phosphate groups be added to enzymes?

A

-OH of serine, threonine and tyrosine

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136
Q

What is addition of a phosphate group catalysed by?

A

Kinase

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137
Q

What is removal of a phosphate group catalysed by?

A

Phosphatase

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138
Q

What are zymogens?

A

Inactive precursor enzymes

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139
Q

How are zymogens activated?

A

Removal of part of the polypeptide chain

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140
Q

What do zymogens allow?

A

Safe transportation of inactive form without causing premature effects e.g. preventing premature proteolytic cleavage by proteases

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141
Q

How is the rate of enzyme synthesis regulated?

A

Increase or decrease in the rate of mRNA transcription

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142
Q

What is the function of ubiquitin?

A

Added to proteins to tag them for destruction

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143
Q

What is feedback inhibition?

A

End product inhibits enzymes earlier in pathway

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144
Q

What is feedforward activation?

A

Increase in initial substrate increases first pathway step

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145
Q

What is counter regulation of opposing metabolic pathways?

A

Catabolic pathway breaking down A inactivates anabolic pathway making A e.g. glycogenolysis and glycogenesis

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146
Q

What are the main mechanisms which regulate the blood clotting cascade?

A

Inactive zymogens at low conc
Amplification of initial signal
Localisation of clotting factors to site of damage
Feedback activation of thrombin
Termination of clotting by multiple processes

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147
Q

What does activated thrombin enhance activation of?

A

Factors V, VIII and XI

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148
Q

How are clotting factors localised to the site of damage?

A

Gla domains on factors bind to damaged endothelial cell lining and allow rapid activation of downstream effectors

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149
Q

What is heterochromatin?

A

Solenoid 30 nm fibres which are not used in gene expression

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150
Q

What is euchromatin?

A

‘Beads on a string’ DNA used for gene expression

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151
Q

Describe the structure of chromosomes.

A

Double DNA strand –> nucleosomes (around histones) –> sole lids –> hierarchical loops

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152
Q

What is a nucleoside?

A

Base+sugar

153
Q

What is a nucleotide?

A

Base + sugar + phosphate

154
Q

What is DNA a polymer of?

A

Deoxyribonucleotides

155
Q

What is RNA a polymer of?

A

Ribonucleotides

156
Q

What secondary structure does DNA form?

A

RH double helix

157
Q

What secondary structure does RNA form?

A

Stem loops

158
Q

What is at the 5’ and 3’ ends of a single stranded chain of polynucleotides?

A 
5' = phosphate
3' = OH
159
Q

What are purines?

A

2 ring nitrogenous bases

160
Q

What are pyrimidines?

A

Single ring nitrogenous bases

161
Q

Which bases are purines?

A

A and G

162
Q

Which bases are pyrimidines?

A

C, T and U

163
Q

What types of duplex structure can form by complementary antiparallel arrangement?

A

DNA-DNA
RNA-RNA
DNA-RNA

164
Q

What is the convention for writing polynucleotide sequences?

A

5’ –> 3’ left to right (complementary strand underneath 3’ –> 5’ for duplex structures)

165
Q

Describe mitosis.

A

Forms 2 genetically identical diploid daughter cells
Somatic
One round of replication and one round of division
Homologous pairs

166
Q

Describe meiosis.

A 
4 haploid daughter cells - gametes
One round of replication, 2 rounds of division
Crossing over essential
Homologous pairs form tetrads
Generates genetic diversity
167
Q

Where are the checkpoints in the cell cycle located?

A

End of G1 and G2

168
Q

What is G0?

A

Resting phase where cell carries out its normal function

169
Q

What method is used for DNA replication?

A

Semi-conservative

170
Q

What is the function of DNA polymerase?

A

Control ribose-phosphate bind formation in semi-conservative replication of DNA

171
Q

What happens when two facing DNA replication forks meet in semi-conservative replication?

A

DNA lipase joins fragments

172
Q

Describe the process of DNA replication in prokaryotes.

A

Circular ‘naked’ chromosome –> initiation: strands separate –> elongation –> termination

173
Q

Which enzyme gives DNA polymerase a kick start?

A

Primate

174
Q

Why are Okazaki fragments formed in DNA replication?

A

Helical arrangement of DNA

175
Q

What joins Okazaki fragments?

A

Lipase

176
Q

Which ends of the DNA strand does DNA polymerase extend?

A

3’ only

177
Q

How does the definition of a chromosome differ before and after replication?

A

Before 1 chromosome = 1 DNA molecule

After 1 chromosome = 2 DNA molecules = 2 identical sister chromatids

178
Q

What is the function of DNA helicase?

A

Unwind double helix

179
Q

How are chromosomes classified?

A

Position of centromeres

180
Q

Describe the passage of neurones in the cell cycle.

A

Enter G0 and do not undergo mitosis after specialisation

181
Q

What happens in mitotic prophase?

A

23 pairs of highly condensed chromosomes present
Kinetochore present for spindle connection
Nuclear membrane broken down

182
Q

What happens in mitotic prometaphase?

A

Spindle fibres attach to chromosomes

Centrioles move to poles

183
Q

What happens in mitotic metaphase?

A

Chromosomes randomly align along metaphase plate

184
Q

What happens in mitotic anaphase?

A

Spindle moves to equator of cells
Sister chromatids pulled to opposite poles
Centromeres divide

185
Q

What happens in mitotic telophase?

A

Nuclear envelope forms around both sets of separated chromatids
Nucleolus forms in both
Chromosomes decondense
Spindle fibres disappear

186
Q

What happens in mitotic cytokinesis?

A

Cytoplasm divides

Parent cell becomes two daughter cells w/identical genetic information

187
Q

What happens during metaphase I in meiosis?

A

Maternal and paternal chromosomes find each other to arrange in a tetrad
Crossing over incl. sister chromatids

188
Q

Does crossing over of sister chromatids have a consequence?

A

No as they are identical

189
Q

What happens in anaphase I during meiosis?

A

Homologous pairs separate

190
Q

What happens in prophase II during meiosis?

A

Random arrangement of chromosomes

Retention of swapped over parts of chromatid

191
Q

Why is there random arrangement of chromosomes in prophase II?

A

No homologous pairs

192
Q

What happens in metaphase II of meiosis?

A

Chromosomes align along equator at 90 degrees to metaphase plate and spindle attaches

193
Q

What happens in anaphase II of meiosis?

A

Chromosomes pulled to opposite poles

194
Q

Give an overview of meiosis I and meiosis II.

A

I: homologous chromosomes of each chromosome pair divided
II: chromatids of each chromosome divided

195
Q

What happens in spermatogenesis?

A

Spermatogonium (2n) –> primary soermatocyte (2n) –> spermatids (n) –> mature sperm

196
Q

How long does spermatogenesis take?

A

~48 days

197
Q

What happens in oogenesis?

A

Oogonium –> primary oocyte –> 3 polar bodies + 1 ovum –> mature ovum

198
Q

How does the immature ovum compare to the three polar bodies formed during its genesis?

A

It has all of the energy stored within it

199
Q

How long does oogenesis take?

A

12-50 years

200
Q

Why is crossing over essential?

A

Ensures correct number of chromosomes in each cell by preventing chromosomes from sticking to each other

201
Q

What does faulty meiosis lead to?

A

1/3 of all identified miscarriages
Infertility
Mental retardation

202
Q

What is the frequency of faulty meiosis?

A

30 in 100

203
Q

What gives 2^n possible arrangement of chromosomes where n is the number of chromosomes?

A

Independent assortment of chromosomes

204
Q

What pattern of inheritance does Cystic Fibrosis show?

A

Autosomal recessive

205
Q

How does an autosomal recessive inheritance pattern appear on a pedigree chart?

A

Appears to ‘come out of nowhere’
Can skip generations
Makes and females equally affected

206
Q

What pattern of inheritance does Huntingdon’s disease show?

A

Autosomal dominant

207
Q

What is the probability of heterozygotes with an autosomal recessive having affected offspring?

A

25%

208
Q

What is the probability of heterozygotes with an autosomal dominant disease having affected offspring?

A

50%

209
Q

Why are autosomal dominant diseases rare in the homozygous state?

A

Likely to result in termination

210
Q

How do autosomal dominant inheritance patterns appear on a pedigree diagram?

A

Present in ever generation unless de novo

Males and females equally affected

211
Q

What pattern of inheritance does Haemophilia A show?

A

X-linked recessive

212
Q

Who is affected by an X-linked recessive inheritance pattern disease?

A

Hemizygous males and homozygous females

213
Q

How does an X-linked recessive inheritance pattern appear on pedigree diagram?

A

More common in males
Every affected female has carrier mother and affected father
Daughters of affected males always at least carriers

214
Q

What is the probability of a female carrier of an X-linked recessive genetic disease having an affected son?

A

50%

215
Q

What is co-dominance?

A

New phenotype is formed when neither allele is dominant over another

216
Q

Use blood groups to describe co-dominance.

A

A and B both dominant over O but neither dominant over the other –> AB blood type

217
Q

What codes for glycoproteins on RBC surface which determine blood group?

A

Human isoglutamin gene

218
Q

Which antigens are present on the RBCs of blood group O?

A

None

219
Q

Which blood those can be given to AB blood group patients?

A

All

220
Q

How can receive blood transfusion of type O?

A

All blood groups

221
Q

What is a gene?

A

Stretch of DNA at a specific chromosomal locus

222
Q

What are genes condensed into?

A

Chromatin

223
Q

What are the types of RNA?

A 
Messenger
Ribosomal
Transfer
Micro
Noncoding
224
Q

What is microRNA used for?

A

Control of gene expression in eukaryotes

225
Q

What enzymes are needed for DNA replication, transcription and translation?

A

Replication: DNA polymerase
Transcription: RNA polymerase
Translation: ribosome

226
Q

Describe the process of initiation in transcription.

A

Initiation: sequence dependent promoter recognition, transcription initiation factors, RNA polymerase

227
Q

Describe the process of elongation in transcription.

A

5’ to 3’ chain growth

228
Q

What does the termination of transcription depend on?

A

Sequence

229
Q

What happens in the initiation stage of transcription?

A

TATA box recognised in 5’ –> 3’ direction
General transcription factors recruit polymerase II
RNA polymerase II phosphorylated

230
Q

How does initiation of transcription vary between eukaryotes and prokaryotes?

A

Eukaryotes: TATA box at -30, variety of upstream sequences, complex regulation
Prokaryotes: Pribnow box at -10, upstream sequences at -35, simple regulation

231
Q

How is transcription regulated?

A

Protein-DNA and protein-protein interactions

Promoters have numerous sequence activators

232
Q

What happens to the DNA molecule during the elongation stage of transcription?

A

Opens to allow for gene expression the closes when DNA polymerase is finished

233
Q

In which direction does mRNA synthesis take place?

A

5’ –> 3’

234
Q

What is capping?

A

Methylated guanine creates a 5’-5’ triphosphate bridge immediately after transcription to prevent degradation

235
Q

What is polyadenylation?

A

Addition of large numbers of adenine residues to 3’ end of mRNA

236
Q

What is the function of polyadenylation?

A

Protect against degradation

Signal export from nucleus

237
Q

What does the length of the polyadenine tail on a mature mRNA molecule indicate?

A

Half-life

238
Q

What is splicing?

A

Removal of introns and some exons depending on sequence

239
Q

What is likely to happen to a protein if splicing goes wrong?

A

Likely to be ineffective

240
Q

Give an example of a condition where there is an error with splicing.

A

PKU

241
Q

Describe the structure of a mature mRNA molecule.

A

5’ cap –> 5’ UTR –> ORF –> 3’ UTR –> 3’ poly A tail

242
Q

Where in the cell does translation take place?

A

Cytoplasm

243
Q

How many kinds and copies of rRNA are present in a eukaryotic cell?

A

6-8 kinds

Many copies of each

244
Q

Which type of RNA polymerase is associated with rRNA?

A

I

245
Q

How many kinds and copies of mRNA are there in a cell?

A

100,000s of kinds

Few copies of each only present when proteins need to be made

246
Q

Which type of RNA polymerase is associated with mRNA?

A

II

247
Q

How many kinds and copies of tRNA are there in a cell?

A

~100 kinds

Lots of copies of each

248
Q

Which type of RNA polymerase is associated with tRNA?

A

III

249
Q

How many rRNAs are present in a eukaryotes?

A

4

250
Q

How many proteins are there in eukaryotes?

A

82

251
Q

Describe the structure of a eukaryotic ribosome.

A

40S and 60S subunits

80S ribosome

252
Q

Describe a prokaryotic ribosome.

A

30S and 50S subunits

70S ribosome

253
Q

How many rRNAs are there in prokaryotes?

A

3

254
Q

How many proteins are there in prokaryotes?

A

56

255
Q

In which direction is the template read during translation?

A

5’ to 3’

256
Q

In what direction does the polypeptide extend during translation?

A

Amino to carboxyl

257
Q

What initiates translation?

A

AUG

258
Q

Which codons terminate translation?

A

UAA
UAG
UGA

259
Q

Why is the genetic code said to be degenerate?

A

More than one codon codes for the same amino acid

260
Q

What differences in bacterial translation give opportunity for attack?

A 
Simple promoter
Different transcription factors
1 RNA polymerase
Coupled transcription and translation
No post transcriptional processing
Short lived mRNAs
Simpler ribosomes
Distinctive translation initiation
Different translation factors
261
Q

What is the wobble position on a tRNA molecule?

A

5’ base of anticodon and 3’ base of codon which allows single tRNA to recognise more than one codon

262
Q

What is inosine?

A

Purine derived aspecific nucleotide

263
Q

What is the function of inosine?

A

Give extra degeneracy

Less susceptibility to mutation

264
Q

What happens during initiation of translation?

A

5’ cap recognised –> (40S subunit) methionyl recognises AUG –> phosphorylation (60S subunit) –> fully functional subunit

265
Q

What happens during the elongation stage of translation?

A

tRNA occupies P site –> tRNA w/correct codon binds to A site –> peptidyl transferase forms peptide bond –> ribosome moves –> empty A site

266
Q

What happens during termination in translation?

A

P site full –> stop codon recognised by uncharged tRNA which physically moves ribosome along –> water, peptide and tRNA formed

267
Q

When do ribosomes attach to the ER membrane?

A

If protein is destined for membrane or secretory pathway

268
Q

How do ribosomes attach to the ER?

A

Co-translational insertion

269
Q

When do ribosomes remain in the cytosol during protein synthesise?

A

If the protein is destined for the cytosol or posttranslational import into organelles

270
Q

How are proteins directed to the correct destinations?

A

Intrinsic signal
Receptor recognises signal and directs to correct membrane
Translocation machinery transports across membrane
Energy available to transport protein to new place

271
Q

Where can proteins exist in mitochondria?

A

All areas

272
Q

How are mitochondrial matrix proteins directed?

A

Chaperone keeps protein folded –> signal binds to receptor –> protein through TOM –> protein through TIM –> targeting signal cleaved

273
Q

Where is the signal sequence on a mitochondrial matrix protein located?

A

N-terminus

274
Q

What are TOM and TIM?

A

Channels which allow passage of a mitochondrial matrix protein mRNA across the outer and inner mitochondrial membranes

275
Q

What causes pyruvate dehydrogenase deficiency?

A

Mutation at codon 10 in precursor protein

276
Q

What does the mutation in pyruvate dehydrogenase deficiency cause in the precursor protein?

A

Pro replaces Arg
Lose basic residue on hydrophilic face of amphipathic helix
Reduce mitochondrial uptake

277
Q

What supplies the energy for nuclear import of proteins destined for the nucleus?

A

GTP hydrolysis

278
Q

What happens in the cytosol before nuclear import?

A

Importin binds cargo containing a nuclear localisation signal

279
Q

After migrating the rough the nuclear pores, what happens to importin?

A

Ran-GTP binds –> conformational change –> cargo released –> importin w/bound Ran-GTP recycled to cytoplasm

280
Q

What binds with cargo that has a peroxisomal targeting signal?

A

Peroxisomal import receptor

281
Q

What happens to the peroxisomal protein as the receptor integrated into the translocon?

A

Remains folded

282
Q

What happens when the receptor integrates with the translocon in peroxisomal protein synthesis?

A

Translocon opens
PTS dissociated from receptor
Receptor uses ATP to move to cytosol

283
Q

Where can a mutation occur in peroxisomal protein synthesis?

A

In receptor for subset of peroxisomal proteins

284
Q

How are proteins for the ER or secretory pathway directed?

A

Co translational transport

285
Q

Describe how proteins destined for the secretory pathway are synthesised.

A

Produced by ER ribosomes w/ co translational transport in/across ER membrane –> bud off in vesicles –> fuse w/Golgi –> cisternae progression –> trans-Golgi network –> lysosome or secretion

286
Q

What is another name for cisternae progression in the secretory pathway?

A

Retrograde transport

287
Q

What is constitutive cellular secretion?

A

Proteins always secreted e.g. extracellular matrix enzymes

288
Q

What kind of cellular secretion do specialist cells carry out?

A

Regulated

289
Q

What are secretory cells polarised?

A

So secretory granules at apical side and nucleus basal

290
Q

What prevents damage caused by secretion of enzymes into tissue?

A

Polarisation of secretory cells

291
Q

Signal sequences at which terminus of secretory proteins are hydrophobic?

A

N

292
Q

What does the pre- prefix of a protein indicate?

A

Activator sequence still attached

293
Q

What are hydrophobic signal sequences rich in?

A

Basic side groups

294
Q

What is signal recognition protein?

A

Multi domain riboprotein that mediates 3-way association w/SRP-receptor in the ER, ribosome, and signal peptide

295
Q

What is the structure of the SRP receptor in the ER membrane?

A

Alpha-beta tetradimer

296
Q

What happens after SRP and GTP bind to SRP receptor in synthesis of secretory proteins?

A

Translocon is opened, sequence enters –> signal peptidase cleaves signal –> protein synthesis –> released into cell

297
Q

Where must proteins destined for plasma membrane or internal membrane of secretory pathway insert?

A

ER membrane

298
Q

What exists in a membrane protein which anchors it during protein synthesis and prevents further transfer into the ER lumen?

A

Second hydrophobic sequence

299
Q

What sequence in a membrane protein remains in the cytosol during its synthesis?

A

Stop transfer anchor sequence

300
Q

What are the functions of ER in protein synthesis?

A 
Insertion of proteins into membrane
Glycosylation
Proper protein folding
Hydroylation of selected Lys and Pro residues
Specific proteolytic cleavage
Formation of disulphide bonds
Assembly of multi subunit protein
301
Q

Why is N-linked glycosylation of proteins important?

A

Correct protein folding
Protein stability
Deficiency –> sever congenital disorder

302
Q

What is the oligosaccharide preassembled on in N-linked glycosylation?

A

Lipid carrier - dolichol

303
Q

What is the oligosaccharide in N-linked glycosylation transferred to after preassembly?

A

Asparagine

304
Q

Is the same oligosaccharide always used in N-linked glycosylation?

A

Yes

305
Q

How is the oligosaccharide in N-linked glycosylation extensively modified in the ER and Golgi?

A

Trimming and addition of further sugars

306
Q

What is the function of peptidyl-prolyl isomerases?

A

Accelerate inter conversion of cis/trans isomers of proline residues

307
Q

What is the role of protein disulphide isomerase in the ER lumen?

A

Form disulphide bonds

308
Q

How does protein disulphide isomerase carry out its role?

A

It is itself oxidised and can then be reduced by oxidising the substrate protein

309
Q

What prevents secretion of ER lumen proteins from the ER during their synthesis?

A

Specific signal

310
Q

What recognises Lys-Asp-Glu-Leu sequence in soluble ER resident proteins to return them back to ER from cis-Golgi cisternae?

A

KDEL receptor

311
Q

What is anterograde transport?

A

KDEL receptor points to vesicle formation –> pH prevents direct KDEL binding –> secreted protein w/out KDEL

312
Q

What is retrograde transport?

A

Decrease in Golgi pH causes KDEL binding –> higher ER pH causes dissociation of ER resident protein

313
Q

What folding problems can arise during protein secretion?

A

Trapped in mis-folded conformation
Protein contains mutation resulting in misfolding
Protein incorrectly assoc. w/other subunits

314
Q

How does the ER respond to misfolded proteins?

A

Chaperone attempts to correct protein

Retained unfolded proteins in ER –> downregulates protein synthesis

315
Q

What happens to proteins if misfolding cannot be corrected?

A

Protein –> cytosol for degradation

Protein accumulates to toxic levels in ER

316
Q

What diseases arise as a result of protein misfolding?

A

Parkinson’s

Wilson disease

317
Q

What happens to lysosomal enzymes as they pass through the Golgi?

A

Phosphate group added to hydroxyl group of C6 mannose sugar

318
Q

Which enzymes are found in the Golgi body that act on lysosomal enzymes?

A

Glucosamine phosphotransferase

Phosphodiesterase

319
Q

What mediates lysosomal enzyme delivery by determining whether vesicle buds off from trans-Golgi network?

A

Mannose-6-phosphate receptor

320
Q

What is O-linked glycosylation?

A

Attachment of sugar to hydroxyl group of serine (mainly) or threonine

321
Q

What type of molecule is O-linked glycosylation important in?

A

Proteoglycans

322
Q

Where is O-linked glycosylation prevalent?

A

Extracellular matrix and mucus secretions

323
Q

Where is O-linked glycosylation prominent?

A

ER and Golgi

324
Q

Give an example of a protein released by the unregulated constitutive secretory pathway.

A

Collagen

325
Q

Give an example of a protein released by the regulated secretory pathway.

A

Insulin

326
Q

Which action in the secretory pathway determines whether a protein is released by regulated or constitutive pathway?

A

Whether membrane fusion is regulated or not

327
Q

Which protein is the most abundant in the body?

A

Collagen

328
Q

What secretes collagen in connective tissue?

A

Fibroblasts

329
Q

What is the basic unit of collagen?

A

Tropocollagen

330
Q

What is the repeating structure in collagen?

A

Gly-X-Y

331
Q

How many polypeptide alpha chains are in one molecule of tropocollagen?

A

3

332
Q

Why are the alpha chains of tropocollagen highly extended?

A

Presence of proline and hydroxyproline in X and some Y parts of the repeating structure

333
Q

What are the structural features of the RH triple helix which forms collagen?

A

Non-extensible
Non-compressible
High tensile strength

334
Q

What stabilises the structure of the RH triple helix in collagen?

A

H binds b/w alpha chains

335
Q

Which type of collagen accounts for 90% of all body collagen?

A

I

336
Q

Which unites are present in collagen type I?

A

2 x alpha-1

1 x alpha-2

337
Q

Where is type II collagen found?

A

Cartilage

Intervertebral discs

338
Q

Which units make up type II collagen?

A

3 x alpha-1 units

339
Q

Where is type III collagen found?

A

Foetal skin

CVS

340
Q

Which units make up collage type III?

A

3 x alpha-1

341
Q

Where is type IV collagen found?

A

Basement membrane

342
Q

Where is type V collagen found?

A

Placenta and skin

343
Q

What is associated with protein disulphide isomerase in the ER and is used for collagen synthesis?

A

Prolly hydroxylase

344
Q

What dos prolyl hydroxylase require to function?

A

Vitamin C

Iron(II) ions

345
Q

How does prolyl hydroxylase increase the stability of collagen?

A

Creates hydrogen bonds

346
Q

What happens to the tropocollagen triple helices in scurvy?

A

They are weak

347
Q

Why is collagen not synthesised within the cell?

A

Molecules too long

348
Q

Give the first four stages of the modification and synthesis of collagen in the ER.

A

Synthesis and entry of chain into ER lumen
Cleavage of signal peptide
Hydroxylation of selected proline and lysine residues
Addition of N-linked oligosaccharides

349
Q

What causes the transition of prepro-alpha to pro-alpha in collagen synthesis?

A

Signal peptidase

350
Q

What causes hydroxylation of selected proline and lysine residues in collagen synthesis?

A

Prolyl hydroxylase

351
Q

Where are N-linked oligosaccharides added in collagen synthesis?

A

C-terminal propeptide

352
Q

Give an example of a sugar that can be added to collagen when N-linked oligosaccharides are added to the C-terminus.

A

Galactose

353
Q

What is added to hydroxylysine residues in collagen synthesis?

A

Galactose

354
Q

What occurs in chain alignment of 3 alpha chains during collagen synthesis?

A

Formation of disulphide bonds

355
Q

How is the triple helical procollagen assembled in collagen synthesis?

A

From C to N terminus

356
Q

What is found at both the N and C termini of a collagen molecule?

A

Extra amino acids that do not form the triple helix

357
Q

How is completion of O-linked oligosaccharide chains achieved?

A

Addition of glucose

358
Q

What links the N and C terminal extensions in the transport vesicle?

A

Disulphide

359
Q

What happens to the N and C terminal propeptides extracellularly?

A

Extensions removed

Alpha-chain formation stimulated

360
Q

How is a collagen fibre formed once the N and C terminal propeptides have been cleaved?

A

Lateral association of molecules

Followed by covalent cross linking

361
Q

How do collagen fibrils form a fibre?

A

Aggregation

362
Q

What is formed by lateral association of individual collagen units?

A

Form 50 nm fibrils

363
Q

Why does collagen have a striated appearance?

A

Formed of 50 nm fibrils

364
Q

What happens when heavy metal staining is used on collagen?

A

Sit in gaps b/w molecules giving striated appearance

365
Q

How is an aldol cross-link formed?

A

Lysine residues –> aldehyde derivatives –> potentially spontaneous aldol cross-links

366
Q

Which enzyme converts lysine residues to aldehyde derivatives?

A

Lysyl oxidase

367
Q

Which enzyme is affected in Ehlers Danlos syndrome?

A

Lysyl oxidase

368
Q

What is needed for lysyl oxidase function?

A

Vitamin B6

Copper(II) ions

369
Q

What is the action of lysyl oxidase?

A

Form covalent cross-links

370
Q

What are the two steps in insulin processing that take place in the ER?

A

Hydrophobic sequence cleaved from proinsulin

Specific folding stabilised by 3 sulphide group bonds

371
Q

What happens post-Golgi to leave a complete two-chain insulin molecule?

A

Connecting peptide removed

372
Q

Which three enzymes are involved in the ER processing of insulin?

A

PC3 endoprotease
PC4 endoprotease
Carboxypeptidase

373
Q

Where is the proinsulin antibody found?

A

Secretory glands waiting to mature

374
Q

What is the third sulphide bond in an insulin molecule important for?

A

Structure

375
Q

Why is proteolytic processing needed for small secretory products such as enkephalins in the secretory pathway?

A

They are too short to enter the ER via co-translational mechanism

376
Q

What would happen if hydrolytic enzymes were activated in the cell instead of being proteolytically processed in the secretory pathway?

A

They would be destructive to the cell

377
Q

How are multiple bio active products produced from the same polypeptide?

A

Proteolytic processing in the secretory pathway

378
Q

How is activation of the insulin receptor avoided in the secretory pathway?

A

Proteolytic processing

379
Q

How are bio active growth factor and insulin prevented from acting at the same time?

A

Proteolytic processing in the secretory pathway

Semester 1 (7 decks)

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