Proteins and Enzymes Flashcards
1
Q
Which are the aliphatic and hydrophobic amino acids?
A
Alanine, valine, leucine, isoleucine, glycine, proline
2
Q
Which are the negative amino acids?
A
Aspartic acid and glutamic acid
3
Q
Which are the positive amino acids?
A
Arginine, lysine, histidine
4
Q
Which are the polar amino acids?
A
Asparagine, glutamine, serine, threonine, tyrosine
5
Q
Which amino acids have aromatic side chains?
A
Phenylalanine, trypotophan
6
Q
How is a cyclic sugar formed?
A
Nucleophilic attack on second to last carbonyl
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
8
Q
Why does fructose form a pentagon not hexagon?
A
Ketose at second carbon so forms five-sided ring
9
Q
Why are disaccharide sugars more reactive?
A
Have free reducing end, would make aldehyde in linear form
10
Q
Why can’t sucrose go any further?
A
No more reducing ends
11
Q
Why is the Haworth projection misleading?
A
Glucose is puckered not planar
12
Q
What is the stable glucose conformation called?
A
The chair, OHs point outwards
13
Q
Is glycogen and starch more branched?
A
Glycogen
14
Q
What are the two kinds of starch?
A
Amylose (unbranched) and amylopectin (branched)
15
Q
What are glucose subunits in chitin modified to have?
A
N acetyl glucosamine
16
Q
What kind of carbohydrates are on the cell surface?
A
Oligosaccharides
17
Q
What are cell surface carbohydrates N linked to?
A
Asparagine
18
Q
What are cell surface carbohydrates O linked to?
A
Serine or threonine
19
Q
How does urea work as a denaturing agent?
A
Disrupts non-covalent forces
20
Q
How does mercaptoethanol work as a denaturing agent?
A
Reduces disulphide bonds (ethanol with SH bond)
21
Q
What are the H bonds between in an alpha helix?
A
Between i and i+4
22
Q
Where are the side chains in B sheets?
A
Alternatively above and below
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
24
Q
Why are electrostatic interactions stronger in the centre of the protein?
A
No water to shield
25
In collagen which handedness are the helices?
Helix = lefthanded, superhelix = righthanded
26
What are the amino acids in collagen?
Glycine proline hydroxyproline
27
How do you get scurvy?
Enzyme that makes hydroxyproline needs Fe(II) ions - vitamin C keeps this in its reduced state so not vitamin C causes loss of collagen
28
Which bonds make up a beta-alpha-beta motif?
H bond and hydrophobic
29
Which bonds make up an alpha-helical hairpin?
Hydrophobic and ionic
30
Which bonds make up the greek key motif?
Hydrogen
31
How many subunits does ATP synthase have and how are they held together?
Six held together by hydrophobic
32
What happens to domains if not in a protein?
Will still form
33
What is the core of a domain?
Hydrophobic
34
What are the two domains in gyceraldehyde-3-phosphate?
One binds to NAD, one is the active site
35
How do you use xrays to get the structure of a protein?
Ordered protein crystals diffract X rays to get an electron density map
36
How do you use cryoEM?
For large assemblies, take many images then average and fit protein model
37
How do you use affinity chromatography?
Column contains molecule binding to protein of interest, wash the rest then add competetive ligand to elute required protein
38
How do you use ion exchange chromatography?
Binds depending on charge, eluted with increasing salt - separate by charge
39
What aids complex protein assemblies and unfolds misfolded proteins?
Chaperones
40
What are the cellular effects of Alzheimers?
Plaques in brain surrounded by dead neurones, amyloid fibres (misfolded proteins) in dead cells, membrane protein misfolds
41
What happens in a Prion disease?
Misfolding of PrP protein, forms fibres leading to neural degeneration
42
What do cofactors do?
Provide reactivity not found in amino acids
43
What is the cofactor in NAD?
niacin, B3
44
What is the cofactor in FAD?
riboflavin, B2
45
What is the prosthetic group in TPP?
thiamine B1, aldehyde transfer
46
What is the prosthetic group in adenosylcobalamin and methylcobalamin?
Cobalamin B12
47
What is the cosubstrate in CoA?
Pantothenate, B5
48
What is the cosubstrate in tetrahydrofolate?
Folic acid, B9
49
What does tetrahydrofolate do?
CH3 group for thymine
50
Is reduction/oxidation of NAD/FAD endothermic or exothermic?
Reduction is endothermic, oxidation is exothermic
51
What kind of a curve does myoglobin show?
Hyperbolic
52
What is the Fe bound to in haem?
Porphyrin ring (4) and His side chain leaving one space free for O2.
53
What causes the conformational change when O2 binds?
O2 binds, Fe pulled into ring, pulls on His, conformational change
54
Which is the tense state and which is the relaxed state?
Tense = deoxy, Relaxed = oxy
55
Why do all membrane protein backbones form H bonds?
More energetically favourable than binding to water
56
What is the structure of the K+ channel?
Tetramer of identical helical subunits
57
How many alpha helices does each subunit of the K+ channel have?
3
58
How does the selectivity filter of the K+ channel work?
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
How many domains to antibodies have?
12
60
What does the carbohydrate attached to the antibody do?
Increases solubility
61
How many constants does the light chain have?
One
62
How many constants does the heavy chain have?
Three
63
What does the CH1 domain do?
Associates with CL
64
What do the CH2 and CH3 domains do?
Drive dimerisation, recruit macrophages
65
Where do small and large molecules bind to antibodies?
Small bind into grooves, large bind in flat surfaces
66
What is IgE for?
Histamine, allergic responses
67
What is IgA for?
Saliva, tears, breast milk
68
What is IgG for?
Immunity, therapeutics
69
What is the first antibody?
IgM
70
What is the other antibody?
IgD
71
What are complementarity determining regions?
Hypervariable loops on variable domains
72
Why is the lock and key model wrong?
ES complex too stable
73
What is the Zn ion bound to in carbonic anhydrase?
3 His and water
74
What accept the proton from bound water in carbonic anhydrase?
His64
75
What is the catalytic triad in serine proteases?
Ser195, His57, Asp102
76
What does the Ser195 do in the serine protease?
Performs nucelophilic attack on C in substrate
77
What does the His57 do in the serine protease?
Acts as base
78
What does the Asp102 do in the serine protease?
Stabilises positive charge at His57
79
What is the selectivity pocket?
Oxyanion hole only filled when transition state formed to select correct substrate using residue before bond to be cleaved
80
What is in the chymotrypsin selectivity pocket?
Bulky hydrophobic residues
81
What is in the trypsin selectivity pocket?
Positively charged residues
82
What is in the elastase selectivity pocket?
Small residues
83
What is the structure of HIV protease?
Dimer with active site at interface
84
What are flaps in HIV protease made from?
Two stranded beta sheet
85
What does HIV protease substrate have either side of the bond to be broken?
Phe and Pro
86
How do HIV protease inhibitors work?
Mimic transition state but can't be cleaved
87
What are the six different enzyme classes?
Oxidoreductases, transferase, hydrolases, lyase, isomerases, ligases
88
What does Km measure?
E+S affinity - large if affinity is low
89
What is the catalytic constant (turnover number)?
k2
90
How do competetive inhibitors alter Vmax and Km?
Don't alter Vmax but affect Km
91
What does proline racemase do?
Convert L-proline to D-proline, reaction happens in flat pocket
92
Which HIV protease drugs mimic transition state?
Sequinavir and Ritonavir
93
How do non-competetive inhibitors alter Vmax and Km?
Alter Vmax but not Km
94
Which enzyme does penicillin inhibit?
Glycopeptide transpeptidase
95
How does penicillin work?
Cross links in bacteria cell wall can't form, cell bursts due to osmosis, suicide inhibitor
96
What does Sarin gas inhibit?
ACh esterase
97
Why is sarin gas a good inhibitor?
Has good F leaving group and complex formed is very stable
98
How is CDK2 activated?
Phosphate residue of Tyr15 of active site prevents binding, removed when activated
99
What does allosteric inhibitor stabilise?
T state
100
What does allosteric activator stabilise?
R state
101
What is homotropic allostery?
Binding of substrate causes conformational change from low to high affinity
102
What is heterotropic allostery?
At high activator concs, curve becomes hyperbolic and all subunits in high-affinity form
103
What are the stages of glucokinase activation?
Superopen to intermediate open to closed
104
What happens to glucokinase in high glucose?
Doesn't go super-open after
105
Why is there no Km in allostery?
Because it measures affinity and affinity is changing
106
What's the structure of phosphofructokinase?
Tetrameric, each monomer has active site and allosteric site at interfaces
107
What are the substrates of PFK?
F6P and ATP
108
What is an allosteric activator and inhibitor of PFK?
ATP inhibits, AMP activates
109
What does glycogen phosphorylase do?
glycogen + phosphate makes G1P and glycogen
110
What is the structure of glycogen phosphorylase?
Dimeric
111
What activates and inhibits glycogen phosphorylase?
AMP activates, ATP and G6P inhibit
112
What are the activated and inactivated types of glycogen phosphorylase?
Phosphorylated active form = phosphorylase a, dephosphorylated form = phosphorylase b
113
What is phosphorylated in glycogen phosphorylase?
Ser14
114
Binding of what to glycogen phosphorylase causes the same conformational change?
Phosphorylation and AMP binding
115
What does tamiflu target?
Neuraminidase
116
What does neuraminidase do?
Releases new particles
117
What does haemagglutinin do?
Binds to sialic acid on host cell
118
What do transition state analogues like tamiflu do?
Bind competitively with sialic acid
119
How was tamiflu improved?
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
What was viagra supposed to do?
Planned phosphodiesterase 5 block - smooth muscle relaxation and increased blood flow
121
How many times does glucose transporter polypeptide span the membrane?
12
122
What is in the 4 co-ordination positions of Zn in carbonic anhydrase?
3 His, one polarised water
123
What accepts the electron of the polarised water in CA?
His64
124
What is the mechanism of carbonic anhydrase?
Oxygen of water does nucleophilic attack on C of CO2
125
What are serine proteases used for?
Clotting, digestion and development
126
What's the mechanism of serine proteases?
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
Which Asp is protonated and which is deprotonated in Asp proteases?
Asp1 is protonated, Asp2 is deprotonated
128
Where is the water molecule in an Asp protease?
Coordinated between the Asp residues
129
What is the mechanism of an Asp protease?
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
Two requirements for MM?
Only [S] changed when Vo measured and [E]
131
What does Km measure?
rate of breakdown/formation of ES (how tightly enzyme binds to substrate)
132
MM equation?
Vo = Vmax[S]/Km+[S]
133
Vmax/[E] = ?
k2 = kcat
