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Biochemistry Monica xxx > Biochemistry Monica > Flashcards

Biochemistry Monica Flashcards

1
Q

What type of bond can carbon form with itself?

A

Covalent

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2
Q

How many covalent bonds can carbon form?

A

4

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3
Q

What does the bonding of carbon lead to?

A

A tetrahedral form

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4
Q

What can carbon also form bonds with/

A

hydrogen, nitrogen and oxygen

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5
Q

What is phosphorylation?

A

Addition/ removal of PO4

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6
Q

What is acylation?

A

Addition of C+)

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7
Q

What is carboxylation?

A

Addition of C=O, O-H

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8
Q

In condensation is water added or removed?

A

Removed

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9
Q

In hydrolysis water is added?

A

True

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10
Q

What happens in redox equations?

A

Electrons are transferred. As 1 molecule is oxidised the other molecule is reduced.

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11
Q

Oxidation is…

A

Loss of electrons

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12
Q

Reduction is…

A

Gain of electrons

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13
Q

Redox pairs are?

A

Biologically important

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14
Q

The oxidation states of carbon are?

A

alkane (in fats) > alcohol (in carbohydrates) > aldehyde > carboxylic acid > carbon dioxide (final product of catabolism)

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15
Q

Information storage location

A

DNA

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16
Q

Biomolecules structures?

A

Teeth, bones, cartilage

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17
Q

Where does energy generation occur?

A

Glycolysis, citric acid cycle, electron transport chai

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18
Q

What is the energy currency/storage location?

A

ATP

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19
Q

Where is biomolecule recognition?

A

Receptors

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20
Q

Where is biomolecule communication?

A

Hormones

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21
Q

What is biomolecule specificity?

A

Enzymes

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22
Q

What do peptides and proteins consist of?

A

Amino Acids

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23
Q

What are lipids?

A

Triglycerides, phospholipids, steroids

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24
Q

What are nucleic acids?

A

DNA, RNA

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25
Q

What are carbohydrates?

A

Mono, di, polysaccharides

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26
Q

An example of monosaccharides?

A

Glucose

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27
Q

Examples of disaccharides?

A

Lactose, maltose, sucrose, cellobiose

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28
Q

Example of polysaccharides?

A

Cellulose, glycogen

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29
Q

First law of thermodynamics?

A

Energy is neither created nor destroyed

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30
Q

Second law of thermodynamics?

A

When energy is converted from 1 form to another, some of that energy becomes unavailable to do work

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31
Q

Enthalpy?

A

Het content of a system

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32
Q

Entropy?

A

Degree of disorder of a system

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33
Q

The most important change in free energy is?

A

ΔG = ΔH – TΔS

T is the temperature in K

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34
Q

Free energy change?

A

ΔG = (energy of the products) – (energy of the reactants)

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35
Q

An exergonic reaction is defined as one in which?

A

The total free energy of the products is less than the total free energy of the reactants

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36
Q

The free energy change of an exergonic reaction is?

A

Negative

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37
Q

Exergonic reactions can occur spontaneously?

A

True

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38
Q

In an endergonic reaction?

A

The total free energy of the product is more than the total free energy of reactants

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39
Q

The free energy change of an endergonic reaction is?

A

Positive

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40
Q

Can endergonic reactions occur spontaneously?

A

Usually no, however there are exceptions to the rule

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41
Q

Endergonic reactions require an input of energy to proceed?

A

True

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42
Q

What equation is used to determine deltaG for a given reaction?

A

ΔG = ΔGo’ + RTln([C][D]/[A][B])

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43
Q

What does R stand for in the deltaG equation?

A

Universal gas constant (8.3 JK-1mol-1)

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44
Q

What does T stand for in the deltaG equation?

A

The absolute temperature (degrees Kelvin used)

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45
Q

What are the units for deltaG?

A

kJ/mol

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46
Q

What does deltaGo’ represent?

A

Change in free energy under standard conditions

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47
Q

Conditions for physical chemists?

A

T=298K
1 atmospheric pressure
1 < (1mol/l) concentration
deltaGo

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48
Q

For biochemists conditions are?

A 
T=298K
1 atmosphere pressure
1M(1 mol/l) concentration
pH=7
deltaGo'
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49
Q

DeltaG is related to the point of equilibrium?

A

True

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50
Q

The further towards completion the point of equilibrium is, the ___________ free energy is released?

A

More

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51
Q

Readily reversible reactions have deltaG values

A

Closer to zero

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52
Q

Forward and backwards reactions are balanced when?

A

The system is in equilibrium ΔG = 0 and therefore

ΔGo’ = -RTlnKeq

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53
Q

Keq =

A

[C][D]/[A][B]

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54
Q

What does increasing (A)(B) relative to (C)(D) do to deltaG?

A

(C)(D)?(A)(B) becomes smaller than 1. the ln of a smaller number smaller than 1 = negative

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55
Q

What is the effect of cellular processes that are unfavourable?

A
  1. Have to proceed in the direction of a positive deltaG
  2. Transport against a gradient
  3. Synthesis of large molecules
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56
Q

What is ATP used as?

A

A universal energy currency for driving many different cellular processes

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57
Q

How do many reactions occur within the body?

A

By coupling up an unfavourable reaction with a very favourable reaction

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58
Q

What makes the ATP molecule less stable than ADP?

A

The negative charges close together

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59
Q

How is strain relieved in ADP?

A

By removing 1 or more phosphate groups

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60
Q

What type of bonds are high energy?

A

Anhydride bonds

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61
Q

Cells store large amounts of energy

A

False - it is constantly regenerated

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62
Q

Do active muscle cells for example use ATP at higher or lower rates?

A

Higher

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63
Q

Examples of ways ATP is regenerated

A

Using creatine phosphate (standard free energy of hydrolysis = -43kJ/mol
Using 2ADP ATP + AMP

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64
Q

Define metabolism

A

All reactions taking place in the body

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65
Q

Define Catabolism

A

Breaking down complex molecules into smaller ones

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66
Q

In catabolism energy is used

A

False

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67
Q

Define anabolism

A

Synthesising complex molecules out of smaller ones

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68
Q

Is energy released or required for anabolism?

A

Required

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69
Q

There are energy consuming steps in some catabolic reactions

A

True

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70
Q

What type of pathway is glycolysis an example of?

A

A catabolic pathway

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71
Q

What type of pathway os glucogenesis an example of?

A

An anabolic pathway

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72
Q

What is the purpose of glucogenesis?

A

To make new glucose from non-carbohydrate precursors

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73
Q

Reactions close to equilibrium are used as control points?

A

False

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74
Q

What kind of reactions are useful for control points?

A

Reactions with large deltaG values

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75
Q

How is flux controlled through these points?

A

By altering the activity of the enzyme involved

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76
Q

water is polar what does this mean?

A

Electrons are shared unequally

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77
Q

What does a water molecule form?

A

A dipole, tetrahedral shape

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78
Q

What are hydrophilic molecules?

A

Ionic and polar substances that dissolve in water

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79
Q

What are hydrophilic substances based on?

A

Electrostatic interactions

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80
Q

Hydrogen bonds are much weaker than covalent bonds?

A

True individually however can be strong collectively

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81
Q

Hydrogen bonding is not very important in water and biological structures?

A

False

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82
Q

What are hydrogen bonds shared between?

A

2 electronegative atoms

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83
Q

Hydrogen bonds tend to be…

A

Linear

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84
Q

Non polar substances are insoluble in water

A

True - hydrophobic

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85
Q

Attractions between water molecules are?

A

Powerful

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86
Q

Do water molecules prefer to interact with themselves or other non-polar molecules?

A

Themselves

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87
Q

Hydrocarbons are?

A

Very non-polar and hydrophobic

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88
Q

What are hydrocarbons?

A

Compounds consisting of only hydrogen and carbon

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89
Q

‘Oil and water don’t mix’ what is this often referred to as

A

Hydrophobic effect

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90
Q

Amphiphilic molecules are

A

Both hydrophilic and hydrophobic

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91
Q

Polar ‘head’ groups

A

Interact well with water

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92
Q

Non polar tails…

A

Do not interact well with water

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93
Q

Amphipathic molecules form what in water

A

Micelles

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94
Q

Examples of amphipathic molecules are?

A

Sodium palmitate

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95
Q

What is the importance of the cell membrane?

A

Aid compartmentalisation by isolating organelles

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96
Q

What are the components of the cell membrane?

A

lipids of various types
structural (lipid bilayer)
precursors of signalling
molecules (DAG, IP3)

proteins of various types
confer selectivity
involved in recognition
and more

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97
Q

All alpha carbon are bonded to?

A

An amino group (NH2)
A Carboxyl group (COOH)
A hydrogen (H)
A side chain (R)

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98
Q

D and L forms are?

A

Stereoisomers

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99
Q

Stereoisomers are?

A

Non-superimposable mirror images

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100
Q

What kind of bonds have partial double bond character?

A

Peptide bonds

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101
Q

What are characteristics of peptide bonds?

A

They are planar

They are strong and rigid - important for folding of proteins

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102
Q

Do acids donate or accept protons?

A

Donate

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103
Q

Bases are proton donators

A

False

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104
Q

How is the strength of an acid determined?

A

By how quickly it donates a proton

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105
Q

How is the strength of an acid measured?

A

Using dissociation constant Ka

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106
Q

How is Ka calculated?

A

Ka =(H+)(A-)/(HA)

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107
Q

pH=

A

pH = -log10[H+]

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108
Q

pH=

A

amount of protons in a solution

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109
Q

What does a change of one pH unit imply?

A

A tenfold change on proton concentration

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110
Q

An equivalent measure for acid strength other then pH is?

A

pKa = -log10[Ka]

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111
Q

A solution with pH=7 is?

A

Neutral

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112
Q

A solution with pH<7 is?

A

Acidic

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113
Q

A solution pH>7 is?

A

Basic

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114
Q

What is the purpose of the Henderson - Hasselbalch equation?

A

Connects the Ka of a weak acid with the pH of a solution containing this acid

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115
Q

Henderson Hasselbach equation is

A

pH=pKa + log (A-)/(HA)

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116
Q

What does the henderson hasselbalch equation allow us to calculate?

A

The properties of buffer solutions - dependent on the concentrations of acid and conjugate base

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117
Q

What is a buffer?

A

A solution used to control the pH of a reaction mixture

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118
Q

what equations exhibit when the concentration of an acid equal the concentration of a base?

A

[HA] = [A-]
[A-]/[HA] = 1
log [A-]/[HA] = 0
pH = pKa

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119
Q

what happens at buffers pKa values?

A

They tend to resist a change of pH on moderate addition of acid or base

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120
Q

What do titration curves do?

A

Plot pH as a function of a base added to an acid

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121
Q

What happens close to the pKa on a titration curve?

A

The pH remains relatively unchanged in response to addition of a base

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122
Q

What do AA without charged side groups exist as _______ in neutral solution?

A

Zwitterions - n net charge

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123
Q

What do zwitterions contain?

A

2 titratable groups

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124
Q

What is the pH called when the molecule has no net charge?

A

The isoelectric pH

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125
Q

What is special about AA that have 2 titratable groups?

A

They have 2 pKa values

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126
Q

The ends of proteins can be ionised

A

True

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127
Q

Can proteins act as buffers?

A

Yes - e.g. haemoglobin in blood

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128
Q

A change in pH can change ionisation of a protein. What can this lead to?

A

A change in structure, thereby function

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129
Q

Primary structure of proteins

A

The sequence of amino acid residues

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130
Q

Secondary sequence of proteins

A

The localised conformation of the polypeptide backbone

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131
Q

Tertiary structure of proteins

A

3D structure
Entire polypeptide
Includes all side reactions

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132
Q

Quaternary structure of proteins

A

Spatial arrangement
Polypeptide chains
Multiple subunits

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133
Q

Polypeptides can rotate around angles between…

A

the α carbon and the amino group

the α carbon and the carboxyl group

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134
Q

what are the three types of secondary structures?

A

alpha (α) helix

beta (β) strands and sheets

triple helix

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135
Q

Give points about hydrogen bonded 3D arrangements of a polypeptide chain?

A

Localised

Only considers backbone of polypeptide

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136
Q

Alpha helix is rod like

A

True

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137
Q

Alpha helix has how many polypeptide chains

A

1

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138
Q

Are alpha helixes normally right or left handed

A

Right

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139
Q

How do alpha helixes arrise

A

C-O group of one amino acid forms a hydrogen bond with the -N-H group of an amino acid four residues away

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140
Q

Polypeptide backbone almost completely extended

A

True

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141
Q

How many chains can B sheets involve

A

1 or more

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142
Q

What directions are possible in B sheets

A

Parallel and anti-parallel

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143
Q

B sheets do not contain turns

A

False

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144
Q

What is the most abundant protein in vertebrates?

A

Collagen triple helix

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145
Q

The collagen triple helix is a component of what?

A

Bone and connective tissue

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146
Q

Collagen triple helix contains water soluble fibres

A

False water insoluble fibres

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147
Q

What kind of bonds does collagen triple helix exhibit?

A

Covalent inter and intra molecules

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148
Q

What are twisted round each other in a collagen triple helix?

A

Three left-handed helical chains to form a right-handed superhelix

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149
Q

Inter chain hydrogen bonds of a collagen triple helix involve

A

hydroxylysine and hydroxyproline

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150
Q

Collagen triple helix is repeating sequences of

A

X-Y-Gly in all strands
X = any amino acid
Y = proline or hydroxyproline
also contains hydroxylysine

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151
Q

Why is collagen relevant?

A

influences strength of connective tissue

weakened collagen results in bleeding gums

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152
Q

Covalent crosslinking increases with age what does this explain?

A

meat from older animals is tougher

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153
Q

What is skurvy?

A

Bleeding gums, skin discolourisation

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154
Q

What is the term used to describe the arrangement of all atoms of a polypeptide chain in space?

A

Tertiary structures

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155
Q

What do tertiary structures consist of?

A

Local regions with distinct secondary structures

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156
Q

What are examples of tertiary structures?

A

Fibrous proteins

Globular proteins

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157
Q

Fibrous molecules contain

A

Polypeptide chains organised approximately parallel along a single axis.

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158
Q

What are 4 characteristics of fibrous molecules?

A

consist of long fibers or large sheets
tend to be mechanically strong
are insoluble in water and dilute salt solutions
play important structural roles in nature

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159
Q

Give examples of fibrous proteins

A

wool + hair keratin

collagen of connective tissue of animals including cartilage, bones, teeth, skin, and blood vessels

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160
Q

Give 4 characteristics of globular proteins?

A

they tend to be soluble in water and salt solutions
most of their polar side chains are on the outside and interact with the aqueous environment by hydrogen bonding and ion-dipole interactions
most of their nonpolar side chains are buried inside
nearly all have substantial sections of alpha-helix and beta-sheet

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161
Q

Examples of globular proteins include

A

Myoglobin

Haemoglobin

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162
Q

List forces stabilising tertiary structures?

A 
Covalent disulphide bonds
Electrostatic interactions = salt bridges
Hydrophobic interactions
Hydrogen bonds
backbone
side chain
Complex formation with metal ions
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163
Q

Repulsion occurs

A

Between similar charges

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164
Q

Where are charged molecules normally located?

A

On the outside of the protein

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165
Q

Charged molecules interact with water

A

True

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166
Q

What kind of bonds does water form with other molecules?

A

Hydrogen

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167
Q

Are attractions between water and hydrocarbon stronger or weaker?

A

Weaker

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168
Q

Attractions between hydrocarbon and hydrocarbon are weakest

A

True

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169
Q

Explain the hydrophobic effect

A

Strong organising influence

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170
Q

Where do amino acids with hydrophobic side chains tend to cluster?

A

In the centre of globular proteins

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171
Q

What can a change from glutamic acid to valine potentially lead to?

A

Significant functional changes

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172
Q

What would you expect if a mutation in a given protein changes a glutamic acid into a valine?

A

glutamic acid is negatively charged at physiological pH
can form ionic bonds or hydrogen bonds with water or other amino acid side chains
valine is hydrophobic
interacts with other hydrophobic amino acids

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173
Q

Primary structure of a protein does not contain all the information needed for its 3D shape

A

False it does contain all information required

174
Q

How may proteins fold into their correct shape?

A

Spontaneously

175
Q

Why may protein folding be a slow and erroneous process?

A

protein may begin to fold incorrectly before it is completely synthesised
it may associate with other proteins before it is folded properly

176
Q

Give examples of processes that are slow and erroneous?

A

Alzheimer’s, Parkinson’s, CJD

177
Q

What are the other specialised proteins that aid in the folding of proteins?

A

Chaperones

178
Q

What term the process when types of physical conditions or chemical agents disrupt the various protein structures?

A

Denaturation

179
Q

What does heat increase?

A

Vibration in proteins

180
Q

What is the result of pH extremes?

A

Electrostatic interactions interrupted

181
Q

What is the result of detergents, urea, guanidine hydrochloride?

A

Disrupt hydrophobic interactions

182
Q

Thiol agents and reducing agents disrupt protein structures in what way?

A

Reduce and thereby disrupt disulphide bonds

183
Q

Give examples of tertiary structures?

A

Lysozyme

Myoglobin

184
Q

Give characteristics of myoglobin as a globular protein?

A

Contains a haem group
Haem group contains an iron ion Fe (2)
Prosthetic group

185
Q

Myoglobin stores oxygen in muscle

A

True

186
Q

Heam groups bind to what?

A

Oxygen

187
Q

How many oxygen molecules bind per myoglobin protein?

A

1

188
Q

Outline the main characteristic of quaternary structures

A

Contain more than one polypeptide chain

189
Q

Are subunits identical or different?

A

Can be either

190
Q

Give an example of a quaternary structure?

A

Haemoglobin

191
Q

What can haemoglobin transport?

A

Oxygen in blood

192
Q

Outline 4 main characteristics of haemoglobin

A

4 subunits
2 alpha and 2 beta chains
Each contain a haem group
Each subunit can bind 1 oxygen molecule

193
Q

How many subunits are present in polypeptide chains?

A

Between 2 and more than a dozen subunits

194
Q

Binding of 1 oxygen changes what?

A

The affinity of the other subunits - refer to allosteric regulation

195
Q

What is ‘The central dogma’?

A

Total DNA in each cell which constitutes the DNA

196
Q

What does the central dogma carry?

A

The genetic info required for making the whole organism

197
Q

Where is the information of the central dogma stored?

A

Nucleotide sequence of the genome

198
Q

What does the DNA nucleotide sequence determine?

A

AA sequences of polypeptide chains

199
Q

How is information transmitted?

A

Via an intermediate, RNA

200
Q

Nucleotide—-> Nucleotode

A

DNA——>RNA = transcription

201
Q

Nucleotide ——> AA

A

RNA——-> Protein = Translation

202
Q

What kind of sugar is in RNA?

A

Ribose

203
Q

What kind of sugar is in DNA?

A

Deoxyribose

204
Q

What is a nucleoside?

A

A base + sugar

205
Q

What is a nucleotide?

A

Nucleoside + phosphate group

206
Q

What are the 4 bases of DNA?

A

A, C, G, T

207
Q

What are the 4 bases in RNA?

A

A, C, G, U

208
Q

List the building blocks of nomenclature

A 
base 	 nucleoside
adenine 	 adenosine
cytosine	 cytidine
guanine	 guanosine
thymine	 thymidine
uracil 	 uridine
209
Q

List the building blocks of DNA

A

dATP, dCTP, dGTP, dTTP

deoxy-adenosine-triphosphate etc.

210
Q

List the building blocks of RNA

A

ATP, CTP, GTP, UTP

adenosine-triphosphate etc.

211
Q

What is a phosphodiester bond formed between?

A

A free 3’ OH group and 5’ triphosphate

212
Q

Polymerisation consumes 2 high energy bonds

A

True

213
Q

Where are new nucleotides added?

A

Only to a free 3’end

214
Q

Nucleotide strands are parallel

A

False - ant-parallel - one 5’ t 3’ other 3’ to 5’

215
Q

Where is the sugar phosphate backbone?

A

On the outside

216
Q

What bond exists between base pairs?

A

Hydrogen bonds

217
Q

What are the DNA base pairs?

A

A=T

C=-G (triple bond)

218
Q

What must DNA undergo before cell division?

A

Must be replicated

219
Q

Why must DNA be replicated before cell division?

A

So the daughter cells have a complete complement of the genome

220
Q

Replication is semi-conservative?

A

True

221
Q

What catalyst is used for DNA replication?

A

DNA polymerase

222
Q

Outline the requirements of DNA polymerase

A

Can only add to existing nucleic acids
Inability to start DNA synthesis on their own
Requires an RNA primer to start replication

223
Q

Eukaryotic genomes have many origins of what?

A

Replication

224
Q

Replication does not start simultaneously at several points in the genome

A

False - it does start simmultaneously

225
Q

Replication is in one direction?

A

False - bidirectional

226
Q

What is the importance of replication starting simultaneously at several points in the genome?

A

Ensures replication completed in reasonable time

227
Q

Explain why replication is discontinuous?

A

Nucleotides can only be added to feee 3’ end

228
Q

What does a leading strand always exhibit?

A

A free 3’ end

229
Q

Lagging strand must be replicated in what?

A

Short segments - Okazaki fragments

230
Q

Outline the steps of DNA replication

A

Helicase unwinds DNA
Primase synthesises an RNA primer
DNA polymerase synthesises a complementary DNA strand
The lagging strand is replicated as Okazaki fragments
The second Okazaki fragments is synthesised
A third okazaki fragment is synthesised
The tail end of another okazaki fragment
RNA primers are degraded
Gaps are filled in by DNA polymerase

231
Q

What can incorporating the wrong nucleotide create?

A

Mutations

232
Q

Mutations can…

A

Be deleterious

Lead to errors occurring once every 10^4 to 10^5 base pairs

233
Q

What kind of exonuclease activity does DNA polymerase exhibit?

A

3’ ——->5’

234
Q

What does 3’ to 5’ exonuclease activity remove and improve?

A

Remove incorrect nucleotide

Improve error rate to one in 10^9 to 10^10 base pairs

235
Q

Further repair systems do not exist

A

False

236
Q

RNA is usually single stranded

A

True

237
Q

What are stem loops?

A

Local stretches of intramolecular base-pairing

238
Q

Name the 3 main classes of RNA

A 
Ribosomal RNA (rRNA)
Transfer RNA (tRNA)
Messenger RNA (mRNA)
239
Q

What RNAs are considered stable RNAs?

A

rRNA and tRNA

240
Q

What is the purpose of rRNA?

A

Combines with proteins to form ribosomes where protein synthesis take space (80%)

241
Q

What is the purpose of tRNA?

A

Carries AA to be incorporated into the protein(15%)

242
Q

What is the purpose of mRNA?

A

Carriers the genetic info for protein synthesis(5%)

243
Q

What does RNA contain instead of thymine?

A

Uracil

244
Q

Adapters are between…

A

Nucleic acid code and AA code

245
Q

Anticodons consist of how many nucleotides?

A

3

246
Q

What is attached to 3’ end?

A

Specific AA (dependent on AA sequence)

247
Q

What kind of RNA have a distinct 3D structure?

A

tRNA molecules

248
Q

What structure arrises when tRNA is flattened into 2D?

A

Cloverleaf structure

249
Q

RNA is made by…

A

RNA polymersaes

250
Q

How many types of RNA polymerases are exhibited by prokaryotic cells?

A

1 type

251
Q

Eukaryotic cells have 5 types of RNA polymerase

A

False - 3 types

252
Q

What polymerase synthesises all mRNA

A

Poll (II)

253
Q

How can polymerases be distinguished?

A

By their sensitivity to toxins like alpha-amanitin (derived from fungus)

254
Q

List the steps of transcription

A 
RNA polymerase binding
DNA chain separation
Transcription initiation
Elongation
Termination
255
Q

Explain RNA polymerase binding

A

Initiation sites detected on DNA

256
Q

Explain DNA chain separation

A

Local unwinding of DNA

Gain access to nucleotide sequence

257
Q

Explain transcription initiation

A

Selection of the first nucleotide of the growing RNA

258
Q

Explain elongation

A

Adding further nucleotides to the RNA chain

259
Q

Explain termination

A

Release of finished RNA

260
Q

TBP=

A

TATA box Binding Protein

261
Q

What is TFIID?

A

A general transcription factor

262
Q

What is TFIID required for?

A

All Pol II transcribed genes

263
Q

TBP introduces a kink into DNA what does this determine?

A

Transcriptional start and direction

264
Q

Initiation of transcription requires additional general transcription factors

A

True

265
Q

Initiation of transcription requires a _______ order of assembly

A

Precise

266
Q

What extends transcription on their own?

A

Pol II and TFIIF

267
Q

TFIID remains at promoter, a new initiation complex can assemble. What does this allow?

A

Transcription at low, basal rates

268
Q

New RNA sequences are complementary to the template strand

A

True

269
Q

Is RNA sequence complementary to the template strand

A

YES

270
Q

What is identical to the coding strand?

A

New RNA sequences (U instead of T)

271
Q

In Transcription termination what does newly synthesised RNA make?

A

A stem loop structure

272
Q

What follows the creation of a stem-loop structure?

A

A stretch of Us

273
Q

What happens when a specific enzyme cleaves RNA?

A

RNA = release

Polymerase dissociates

274
Q

Specific regulation of transcription

A

Go back to slide 45

275
Q

What does coordinated gene expression act in response to?

A

Specific stimuli e.g. hormones, cellualr stress

276
Q

What are coding regions interrupted by?

A

Non coding regions (between 1 and more than 50 introns per gene)

277
Q

What must be removed before translation into protein and by what process?

A

Introns by splicing

278
Q

How are the ends of mRNAS processed?

A

Addition of poly(A) tail

Addition of 5’ cap

279
Q

What do all anticodons of tRNA molecules form during translation?

A

Base pairs with codons on mRNA

280
Q

The genetic code is based on pairs

A

False - based on triplets

281
Q

How many different nucleotides are available?

A

4

282
Q

How many possible combinations are there?

A

64

283
Q

How many amino acids do they code for?

A

20

284
Q

Define degenerate

A

Many AA have more than 1 codon

285
Q

Define unambiguous

A

Each codon codes for only 1 AA (or a top)

286
Q

ATP and GTP act as

A

Sources of energy

287
Q

How many rRNA molecules do ribosomes contain?

A

4

288
Q

What are the3 tRNA binding sites?

A 
E = exit
P = peptidyl
A = aminoacyl
289
Q

What does initiation require?

A

Initiation factors

290
Q

What molecule is hydrolysed to provide energy for initiatuin?

A

GTP

291
Q

What binds to the 5’ end of mRNA?

A

Small ribosomal subunits

292
Q

What is AUG?

A

Start codon

293
Q

Moves along mRNA until AUG is found. What is this process is dependent on?

A

ATP

294
Q

What base pairs with the start codon? And what does this carry?

A

Special initiator tRNA with UAC anticodons - Carriers methionine

295
Q

What does the large subunit join?

A

Assembly and initiator tRNA

296
Q

Where is tRNA located?

A

In P site

297
Q

What does an elongation factor bring?

A

The next aminoacyl-tRNA to the A site

298
Q

Name the anticodon which pairs with codon during elongation

A 
Anticodon = CGU
Codon = GCA
299
Q

What is hydrolysed during elongation?

A

GTp

300
Q

What is released from tRNA during elongation?

A

tRNA

301
Q

What does a second elongation factor regenerate?

A

EF1α to pick up the next aminoacyl-tRNA

302
Q

What is the role of peptidyl transferase?

A

Catalyses peptide bond formation between AA in P and A sites

303
Q

Where is the peptide bond located after peptide bond formation?

A

Now located in A site

304
Q

Where and what does does the elongation factor move?

A

Ribosome along the RNA - by 1 triplet

305
Q

Where does empty tRNA move?

A

To the E site

306
Q

‘Empty’ tRNA can move to E site and…

A

Exit and become reloaded with AA

307
Q

Where foes tRNA with the growing peptide move?

A

From the A to the P site

308
Q

When does termination occur?

A

When the A site of the ribosome encounters a stop codon

309
Q

Name 3 stop codons

A

UAA, UAG, UGA

310
Q

Aminoacyl-tRNA base pairs with stop codons

A

False

311
Q

What does a release factor bind to?

A

Stop codon - GTP hydrolysis

312
Q

What happens to the finished protein?

A

It’s cleaved off tRNA

313
Q

What components dissociate from each other?

A

rRNA, mRNA and tRNA

314
Q

Explain termination starting over again?

A

Small subunit being bound by IF = ready for translation of a new protein

315
Q

What is a point mutation?

A

A change in single base in DNA

316
Q

What is a missense mutation?

A

Results in a change of AA sequence

Can change protein function

317
Q

What does a nonsense mutation create?

A

A new termination codon

318
Q

What does a nonsense mutation change and how does it do this?

A

Length of a protein due to premature stop of translation

319
Q

A silent mutation causes a change of AA sequence

A

False - no change

320
Q

What are silent mutations due to?

A

Degeneracy of the genetic code

321
Q

What is the effect of a silent mutation on the proteins function?

A

No effect

322
Q

Define frameshift mutation?

A

Deletion or addition of a single base (or 2)

323
Q

List 4 chromosomal mutations

A

Deletions
Duplications
Inversions
Translocations

324
Q

Chromosomal mutations affect smaller portions of the genome

A

False - affect larger portions of the genome

325
Q

What does a targeting move?

A

A protein to its final cellular destination

326
Q

Where can targeting take place?

A

Many possible locations within a cell

327
Q

What is targeting dependennt on?

A

The presence of specific AA sequences within the translate protein

328
Q

What term is used to describe addition of further functional chemical groups?

A

Modification

329
Q

What happens during degradation?

A

Unwanted or damaged proteins have to be removed

330
Q

What do free ribosomes in the cytosol make proteins destined for?

A

Cytosol
Nucleus
Mitochondria
Translocated post-translationally

331
Q

What do bound ribosomes on the rough ER make proteins destined for?

A 
Plasma membrane
ER
Golgi apparatus
Secretion
Translocated co-translationally
332
Q

Define glycosylation

A

Addition and processing of carbohydrates in the ER and Golgi

333
Q

What forms in the ER?

A

Disulfide bonds

334
Q

Where does folding and assembly of multi-subunit proteins take place?

A

In the ER

335
Q

What is contained in the ER, golgi and secretory vesicles?

A

Specific proteolytic cleavage

336
Q

What is the cause of hereditary forms of emphysema?

A

Misfolding of the protein α1-antitrypsin in the ER

337
Q

Small changes in the abundance, efficiency or distribution in tissue of enzymes can have what effect?

A

Major complications for disease

338
Q

Enzymes are non-specific

A

False

339
Q

What characteristic of enzymes makes them useful in diagnosing diseases?

A

Their catalytic behaviour

340
Q

What type of reaction do enzymes control?

A

Well defined chemical reactions

341
Q

Enzymes can be used to investigate and develop a wide range of diagnaostic kits and therapeutic drugs

A

True

342
Q

What must we know to understand how an enzyme works?

A

The concentration of substrate (S)

The rate of the catalysed reaction (V)

343
Q

What 2 parameters are used to describe the relationship of enzyme behaviour?

A

Vmax and Km

344
Q

What model is used to explain the relationship between Vmax and Km

A

The Michaelis Menten model

345
Q

What makes the enzyme-substrate complex inherently unstable?

A

The activation energy barrier

346
Q

The enzyme substrate complex is only in 1 direction

A

false - can go forwards or backwards

347
Q

Write the relationship described by the Michaelis constant Km

A

Km=(k-1 + k2)/k1

348
Q

What is K1?

A

The forward rate constant for enzyme associate with the substrate

349
Q

What is K-1?

A

The backwards rate constant for enzyme dissociation from the substrate

350
Q

What is K2?

A

The forward rate constant of an enzyme conversion of substrate to product

351
Q

How are Vmax and Km measured?

A

Measure initial reaction velocity, Vo at a known sunstrate conc.
Repeat at inccreasing substrate conc.

352
Q

How are initial reaction rates Vo plotted?

A

As a function of the substrate concn.

353
Q

What does the initial reaction rate at infinite substrate concn approach?

A

A maximal rate (Vmax)

354
Q

What is . Michaelis constant Km equivalent to?

A

Substrate concn. where initial rate = 1/2 maximal

355
Q

Why is is not straight forward to determine Vmax and Km from certain graphs?

A

Because the kinetics = not linear. Hence reaction velocity never quite reaches true Vmax

356
Q

What does the michaelis menten equation describe?

A

The rate of catalysis as a function of substrate concn.

357
Q

Instead of V against S how is the graph plotted?

A

As 1/V against 1/S

358
Q

What term describes the plotting of linweaver burk plot?

A

A double reciprocal plot

359
Q

What does a lineweaver burk plot enable?

A

Accurate determination of Vmax and Km

360
Q

What is the intersection of the straight line with the Y axis?

A

Vmax

361
Q

What is intersection with the X axis?

A

Km

362
Q

What does Vmax equal?

A

The maximum velociety of a reaction

363
Q

What does Km equal?

A

Concentration in moles of S which gives 1/2 Vmax

Km=(S) at 0.5 Vmax

364
Q

What is the effect of a low Km?

A

The enzyme only needs a little substrate to work at 1/2 maximal velocity

365
Q

what is the effect of a high Km?

A

An enzyme needs a lot of substrate to work at 1/2 maximal velocity

366
Q

Enzymes with the same Vmax can have different?

A

Km values

367
Q

What type of inhibition is reversible?

A

Competitive

Non-competitive

368
Q

What type of inhibition is irreversible?

A

Non-competitive

369
Q

How do competitive inhibitors act?

A

Inhibitor binds to active site + blocks substrate access

370
Q

Define orthosteric inhibition

A

At the same site

371
Q

How do non competitive inhibitors act?

A

Bind to a site other than the catalytic centre; inhibits enzyme by changibng its conformation

372
Q

Define allosteric inhibition?

A

At a different site

373
Q

What does non-competitive inhibition usually involve?

A

Formation of breakage of covalent bonds in the enzyme complex

374
Q

In competitive inhibition what remains the same and what varies?

A 
Vmax = does not change
Km = varies
375
Q

In non-competitive inhibition what remains the same and what varies?

A 
Vmax = varies
Km = no change
376
Q

Define feedback inhibition

A

Inhibition of rate limiting enzymes by end product is a common mechanism of allosteric control

377
Q

Allosteric enzymes follow Michaelis-Menten kinetics?

A

false - do not follow

378
Q

What does increasing substrate concn. result in?

A

SIgmoidal curve, instead of a hyperbola

379
Q

How can allosteric enzymes be controlled?

A

By allosteric inhibitors and allosteric activators

380
Q

What type of behaviour do allosteric enzymes exhibit?

A

Co-operative behaviour

381
Q

What modulates enzyme kinetic behaviour?

A

Allosteric factors

382
Q

Outline and describe an important example for allosteric regulation

A

Binding of O2 to haemoglobin
Positive co-operativity
Controlled by - H+, CO2, 2,3 bisphosphoglycerate (side product of glycolysis)

383
Q

What process do enzymes make up?

A

Metabolism

384
Q

What is the main purpose of enzymes?

A

To speed up the rate at which a reaction reaches equilibrium

385
Q

Enzymes affect the position of equilibrium

A

False

386
Q

What are enzymes?

A

Biological catalysts

387
Q

What are enzymes most made of?

A

Protein - exception (some types of RNA - ribozymes - are catalysts)

388
Q

When are enzymes efficient?

A

At body temperature, in aqueous solution, near neutral pH

389
Q

Efficient enzymes can increase the rate of a reaction by a. factor of up to what?

A

10^20

390
Q

What is meant by enzymes being specific?

A

Each enzyme == limited rage of substrates

391
Q

What does the specific nature of enzymes allow?

A

Some can distinguish stereoisomers

392
Q

What does the potent nature of enzymes allow?

A

Each molecule can convert many substrate molecules into product per second

393
Q

What do enzymes bind and stabilise?

A

The transition state

394
Q

What is the transition state?

A

Reaction intermediate species which has greatest free energy

395
Q

How do enzymes reduce activation energy?

A

Provide alternative reaction pathways

396
Q

Explain glycogen storage disease

A

Enzyme deficiency

Glycogen fails to enter transition “phosporylated” state

397
Q

What is the cause of glycogen storage disease?

A

Defective glycogen synthesis/breakdown in muscle, liver and kidney

398
Q

What are the symptoms of glycogen storage disease

A 
Hypoglycaemia
Hepatomegaly
Skin and mouth ulcers
Bacterial and fungal infections
Bowel inflammation + irritability
399
Q

What is the treatment of glycogen storage disease?

A

Slow release glucose meal

Feed little and often

400
Q

What does the catalytic activity of many enzymes depend on?

A

The presence of small molecules called cofactors or coenzymes

401
Q

Metal ions are inorganic and termed

A

Cofactors

402
Q

Organic molecules are termed

A

Co-enzymes

403
Q

What do metal cofactors form?

A

A metal co-ordination centre in the enzyme (AKA metalloprotein)

404
Q

How do coenzymes mostly associate with the enzyme?

A

Transiently

405
Q

Are coenzymes regenerated

A

Yes

406
Q

What do coenzymes change during the course of a reaction?

A

Charge or structure

407
Q

Define a prosthetic group

A

Tightly bound coenzyme

408
Q

Give an example of a prosthetic group

A

Haem in haemoglobin

409
Q

What are enzymes without a cofactor called?

A

Apoenzymes

410
Q

What are enzymes with a cofactor called?

A

Haloenzymes

411
Q

Holoenzymes are the result of

A

Apoenzyme + cofactor

412
Q

Examples of metal ions

A

Zinc, iron, copper
Involved in redox reactions
Stabilise transition state

413
Q

Give exmapes of coenzymes

A

Many derived from vitamins
Many involved in redox reactions (NAD+, FAD)
Others involved in group transfer processes (ATP transfers phosphate group)

414
Q

WHat do substrates binf to?

A

An active site

415
Q

Why do substrates contain AA’s?

A

Essential for catalytic activity

Highly specidc interactions

416
Q

Discuss the lock and key model

A

Active site of unbound enzyme = complementary to substrate shape

417
Q

Discuss the induced fit model

A

Binding = induced conformational change in enzyme = complementary fit

418
Q

What are isozymes?

A

Isoforms of enzymes

419
Q

What do isozymes catalyse

A

Same reaction but have diff properties and structure

420
Q

When can different isozymes be sunthesised?

A

During different stages of foetal and embryonic development

421
Q

Where are differennt isozymes present?

A

In different tissues

In different cellular locations

422
Q

What are relative amount of isozymes useful for?

A

Diagnostic purposes

423
Q

How many enzymes are typically used in the clinical lab to diagnose disease?

A

More than 20

424
Q

What can side groups of serine, theronine and tyrosine form?

A

Phosphate esters

425
Q

What can phosphorylation convert?

A

Enzymes to active or inactive form

426
Q

What kind of reactions do protein kinases carry out?

A

Phosphorylation reactions

427
Q

Give characteristics of phosphorylation reactions

A

Very fast
Reversible
Found in all cells - especiallu energy generating processes

428
Q

What does the Regulation of enzyme activity by irreversible covalent modification result in?

A

Activation of enzymes

429
Q

Define zymogens

A

inactive precursors of an enzyme

430
Q

Zymogens are irreversibly transformed into active enzymes. How is this achieved?

A

By cleavage of a covalent bond

431
Q

Give examples of zymogens

A

Digestive enzymes
Blood clotting enzymes
Clot-dissolving enzymes
Pancreas = trypsinogen and chymotrypsinogen, inactive precursors, are formed
Small intestine = enteropeptidase cleaves trypsinogen to form active trypsin which cleaves chymotrypsinogen to form active chymotrypsin

432
Q

List irreversible proteolytoc enzymes

A

Digestive enzymes
Blood coagulation enzyme
Enzymes involved in dissolving blood clots
Enzymes involved in programmed development

Biochemistry Monica xxx (1 decks)

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