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MIMS > Proteins and Enzymes > Flashcards

Proteins and Enzymes Flashcards

1
Q

Which are the aliphatic and hydrophobic amino acids?

A

Alanine, valine, leucine, isoleucine, glycine, proline

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2
Q

Which are the negative amino acids?

A

Aspartic acid and glutamic acid

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3
Q

Which are the positive amino acids?

A

Arginine, lysine, histidine

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4
Q

Which are the polar amino acids?

A

Asparagine, glutamine, serine, threonine, tyrosine

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5
Q

Which amino acids have aromatic side chains?

A

Phenylalanine, trypotophan

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6
Q

How is a cyclic sugar formed?

A

Nucleophilic attack on second to last carbonyl

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7
Q

What is the difference between a D and L sugar?

A

In D, 5th carbon hydroxyl is on right, in L it’s on left

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8
Q

Why does fructose form a pentagon not hexagon?

A

Ketose at second carbon so forms five-sided ring

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9
Q

Why are disaccharide sugars more reactive?

A

Have free reducing end, would make aldehyde in linear form

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10
Q

Why can’t sucrose go any further?

A

No more reducing ends

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11
Q

Why is the Haworth projection misleading?

A

Glucose is puckered not planar

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12
Q

What is the stable glucose conformation called?

A

The chair, OHs point outwards

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13
Q

Is glycogen and starch more branched?

A

Glycogen

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14
Q

What are the two kinds of starch?

A

Amylose (unbranched) and amylopectin (branched)

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15
Q

What are glucose subunits in chitin modified to have?

A

N acetyl glucosamine

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16
Q

What kind of carbohydrates are on the cell surface?

A

Oligosaccharides

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17
Q

What are cell surface carbohydrates N linked to?

A

Asparagine

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18
Q

What are cell surface carbohydrates O linked to?

A

Serine or threonine

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19
Q

How does urea work as a denaturing agent?

A

Disrupts non-covalent forces

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20
Q

How does mercaptoethanol work as a denaturing agent?

A

Reduces disulphide bonds (ethanol with SH bond)

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21
Q

What are the H bonds between in an alpha helix?

A

Between i and i+4

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22
Q

Where are the side chains in B sheets?

A

Alternatively above and below

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23
Q

Why is the hydrophobic effect entropically favourable?

A

Because water molecules would become ordered around a hydrophobic side chain and this is entropically so they just cluster together

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24
Q

Why are electrostatic interactions stronger in the centre of the protein?

A

No water to shield

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25
Q

In collagen which handedness are the helices?

A

Helix = lefthanded, superhelix = righthanded

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26
Q

What are the amino acids in collagen?

A

Glycine proline hydroxyproline

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27
Q

How do you get scurvy?

A

Enzyme that makes hydroxyproline needs Fe(II) ions - vitamin C keeps this in its reduced state so not vitamin C causes loss of collagen

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28
Q

Which bonds make up a beta-alpha-beta motif?

A

H bond and hydrophobic

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29
Q

Which bonds make up an alpha-helical hairpin?

A

Hydrophobic and ionic

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30
Q

Which bonds make up the greek key motif?

A

Hydrogen

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31
Q

How many subunits does ATP synthase have and how are they held together?

A

Six held together by hydrophobic

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32
Q

What happens to domains if not in a protein?

A

Will still form

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33
Q

What is the core of a domain?

A

Hydrophobic

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34
Q

What are the two domains in gyceraldehyde-3-phosphate?

A

One binds to NAD, one is the active site

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35
Q

How do you use xrays to get the structure of a protein?

A

Ordered protein crystals diffract X rays to get an electron density map

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36
Q

How do you use cryoEM?

A

For large assemblies, take many images then average and fit protein model

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37
Q

How do you use affinity chromatography?

A

Column contains molecule binding to protein of interest, wash the rest then add competetive ligand to elute required protein

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38
Q

How do you use ion exchange chromatography?

A

Binds depending on charge, eluted with increasing salt - separate by charge

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39
Q

What aids complex protein assemblies and unfolds misfolded proteins?

A

Chaperones

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40
Q

What are the cellular effects of Alzheimers?

A

Plaques in brain surrounded by dead neurones, amyloid fibres (misfolded proteins) in dead cells, membrane protein misfolds

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41
Q

What happens in a Prion disease?

A

Misfolding of PrP protein, forms fibres leading to neural degeneration

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42
Q

What do cofactors do?

A

Provide reactivity not found in amino acids

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43
Q

What is the cofactor in NAD?

A

niacin, B3

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44
Q

What is the cofactor in FAD?

A

riboflavin, B2

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45
Q

What is the prosthetic group in TPP?

A

thiamine B1, aldehyde transfer

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46
Q

What is the prosthetic group in adenosylcobalamin and methylcobalamin?

A

Cobalamin B12

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47
Q

What is the cosubstrate in CoA?

A

Pantothenate, B5

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48
Q

What is the cosubstrate in tetrahydrofolate?

A

Folic acid, B9

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49
Q

What does tetrahydrofolate do?

A

CH3 group for thymine

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50
Q

Is reduction/oxidation of NAD/FAD endothermic or exothermic?

A

Reduction is endothermic, oxidation is exothermic

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51
Q

What kind of a curve does myoglobin show?

A

Hyperbolic

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52
Q

What is the Fe bound to in haem?

A

Porphyrin ring (4) and His side chain leaving one space free for O2.

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53
Q

What causes the conformational change when O2 binds?

A

O2 binds, Fe pulled into ring, pulls on His, conformational change

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54
Q

Which is the tense state and which is the relaxed state?

A

Tense = deoxy, Relaxed = oxy

55
Q

Why do all membrane protein backbones form H bonds?

A

More energetically favourable than binding to water

56
Q

What is the structure of the K+ channel?

A

Tetramer of identical helical subunits

57
Q

How many alpha helices does each subunit of the K+ channel have?

A

3

58
Q

How does the selectivity filter of the K+ channel work?

A

Strips aqueous shell and the C=O mimics hydration water so no energy lost, sodium is too small to touch C=O so stays hydrated and is too big

59
Q

How many domains to antibodies have?

A

12

60
Q

What does the carbohydrate attached to the antibody do?

A

Increases solubility

61
Q

How many constants does the light chain have?

A

One

62
Q

How many constants does the heavy chain have?

A

Three

63
Q

What does the CH1 domain do?

A

Associates with CL

64
Q

What do the CH2 and CH3 domains do?

A

Drive dimerisation, recruit macrophages

65
Q

Where do small and large molecules bind to antibodies?

A

Small bind into grooves, large bind in flat surfaces

66
Q

What is IgE for?

A

Histamine, allergic responses

67
Q

What is IgA for?

A

Saliva, tears, breast milk

68
Q

What is IgG for?

A

Immunity, therapeutics

69
Q

What is the first antibody?

A

IgM

70
Q

What is the other antibody?

A

IgD

71
Q

What are complementarity determining regions?

A

Hypervariable loops on variable domains

72
Q

Why is the lock and key model wrong?

A

ES complex too stable

73
Q

What is the Zn ion bound to in carbonic anhydrase?

A

3 His and water

74
Q

What accept the proton from bound water in carbonic anhydrase?

A

His64

75
Q

What is the catalytic triad in serine proteases?

A

Ser195, His57, Asp102

76
Q

What does the Ser195 do in the serine protease?

A

Performs nucelophilic attack on C in substrate

77
Q

What does the His57 do in the serine protease?

A

Acts as base

78
Q

What does the Asp102 do in the serine protease?

A

Stabilises positive charge at His57

79
Q

What is the selectivity pocket?

A

Oxyanion hole only filled when transition state formed to select correct substrate using residue before bond to be cleaved

80
Q

What is in the chymotrypsin selectivity pocket?

A

Bulky hydrophobic residues

81
Q

What is in the trypsin selectivity pocket?

A

Positively charged residues

82
Q

What is in the elastase selectivity pocket?

A

Small residues

83
Q

What is the structure of HIV protease?

A

Dimer with active site at interface

84
Q

What are flaps in HIV protease made from?

A

Two stranded beta sheet

85
Q

What does HIV protease substrate have either side of the bond to be broken?

A

Phe and Pro

86
Q

How do HIV protease inhibitors work?

A

Mimic transition state but can’t be cleaved

87
Q

What are the six different enzyme classes?

A

Oxidoreductases, transferase, hydrolases, lyase, isomerases, ligases

88
Q

What does Km measure?

A

E+S affinity - large if affinity is low

89
Q

What is the catalytic constant (turnover number)?

A

k2

90
Q

How do competetive inhibitors alter Vmax and Km?

A

Don’t alter Vmax but affect Km

91
Q

What does proline racemase do?

A

Convert L-proline to D-proline, reaction happens in flat pocket

92
Q

Which HIV protease drugs mimic transition state?

A

Sequinavir and Ritonavir

93
Q

How do non-competetive inhibitors alter Vmax and Km?

A

Alter Vmax but not Km

94
Q

Which enzyme does penicillin inhibit?

A

Glycopeptide transpeptidase

95
Q

How does penicillin work?

A

Cross links in bacteria cell wall can’t form, cell bursts due to osmosis, suicide inhibitor

96
Q

What does Sarin gas inhibit?

A

ACh esterase

97
Q

Why is sarin gas a good inhibitor?

A

Has good F leaving group and complex formed is very stable

98
Q

How is CDK2 activated?

A

Phosphate residue of Tyr15 of active site prevents binding, removed when activated

99
Q

What does allosteric inhibitor stabilise?

A

T state

100
Q

What does allosteric activator stabilise?

A

R state

101
Q

What is homotropic allostery?

A

Binding of substrate causes conformational change from low to high affinity

102
Q

What is heterotropic allostery?

A

At high activator concs, curve becomes hyperbolic and all subunits in high-affinity form

103
Q

What are the stages of glucokinase activation?

A

Superopen to intermediate open to closed

104
Q

What happens to glucokinase in high glucose?

A

Doesn’t go super-open after

105
Q

Why is there no Km in allostery?

A

Because it measures affinity and affinity is changing

106
Q

What’s the structure of phosphofructokinase?

A

Tetrameric, each monomer has active site and allosteric site at interfaces

107
Q

What are the substrates of PFK?

A

F6P and ATP

108
Q

What is an allosteric activator and inhibitor of PFK?

A

ATP inhibits, AMP activates

109
Q

What does glycogen phosphorylase do?

A

glycogen + phosphate makes G1P and glycogen

110
Q

What is the structure of glycogen phosphorylase?

A

Dimeric

111
Q

What activates and inhibits glycogen phosphorylase?

A

AMP activates, ATP and G6P inhibit

112
Q

What are the activated and inactivated types of glycogen phosphorylase?

A

Phosphorylated active form = phosphorylase a, dephosphorylated form = phosphorylase b

113
Q

What is phosphorylated in glycogen phosphorylase?

A

Ser14

114
Q

Binding of what to glycogen phosphorylase causes the same conformational change?

A

Phosphorylation and AMP binding

115
Q

What does tamiflu target?

A

Neuraminidase

116
Q

What does neuraminidase do?

A

Releases new particles

117
Q

What does haemagglutinin do?

A

Binds to sialic acid on host cell

118
Q

What do transition state analogues like tamiflu do?

A

Bind competitively with sialic acid

119
Q

How was tamiflu improved?

A

Add more groups to fill active site, add +ve group to form H bonds with glutamate side chain, make it more lipophilic to pass through membranes

120
Q

What was viagra supposed to do?

A

Planned phosphodiesterase 5 block - smooth muscle relaxation and increased blood flow

121
Q

How many times does glucose transporter polypeptide span the membrane?

A

12

122
Q

What is in the 4 co-ordination positions of Zn in carbonic anhydrase?

A

3 His, one polarised water

123
Q

What accepts the electron of the polarised water in CA?

A

His64

124
Q

What is the mechanism of carbonic anhydrase?

A

Oxygen of water does nucleophilic attack on C of CO2

125
Q

What are serine proteases used for?

A

Clotting, digestion and development

126
Q

What’s the mechanism of serine proteases?

A

Ser195 does nucleophilic attack on the C in the substrate, forms tetrahedral intermediate with substrate covalently bound to enzyme, the intermediate decomposes, the peptide bond breaks and you get the first product (an amine), product leaves and is replaced by water, reaction then happens in reverse - His57 accepts a proton from the water, the water OH nucleophilic attacks the C=O and another tetrahedral intermediate forms, this breaks down to give carbonyl product and enzyme

127
Q

Which Asp is protonated and which is deprotonated in Asp proteases?

A

Asp1 is protonated, Asp2 is deprotonated

128
Q

Where is the water molecule in an Asp protease?

A

Coordinated between the Asp residues

129
Q

What is the mechanism of an Asp protease?

A

Activated water performs nucleophilic attack on the C=O of the bond to be broken forming a tetrahedral intermediate, the C-N bond breaks and the -NH- forms -NH2 using the proton from Asp2

130
Q

Two requirements for MM?

A

Only [S] changed when Vo measured and [E]

131
Q

What does Km measure?

A

rate of breakdown/formation of ES (how tightly enzyme binds to substrate)

132
Q

MM equation?

A

Vo = Vmax[S]/Km+[S]

133
Q

Vmax/[E] = ?

A

k2 = kcat

MIMS (8 decks)

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