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MIMS > Biomacromolecules, Protein Structure > Flashcards

Biomacromolecules, Protein Structure Flashcards

1
Q

Name the 4 macromolecules

A

Carbohydrates
Nucleic acids
Proteins
Lipids (but these are not covalently bonded)

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2
Q

What are sugars

A

Straight chain polyhydroxy alcohols, including an aldehyde or ketone group

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3
Q

What is a glucose molecule

What is its usual form

A

6 C sugar with an aldehyde group on C1

Cyclic

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4
Q

What different forms of glucose are formed when it becomes cyclic

Why

A

α glucose
β glucose

New chiral centres are formed

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5
Q

How is β glucose arranged

A

Chair conformation

NOT planar but puckered

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6
Q

What is fructose, how is it different to glucose and what ring does it form

A

A 6 C sugar with a ketone group on position 2

5 sided ring

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7
Q

What is the bind formed why two monosaccharides are linked by a condensation reaction

A

Glycosidic bond

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8
Q

Which end of a sugar chain is the reducing end

A

Where the ring can be opened to produce a free reducing group (the aldehyde end)

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9
Q

Name 2 common disaccharides

A

Lactose

Sucrose

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10
Q

What is starch a polymer of

What is starch used for

A

α glucose

To store energy in plants

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11
Q

What is glycogen a polymer of

What is glycogen used for

A

α glucose

To store energy in animals

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12
Q

Are glycogen and starch branched?

A

Yes, but starch is more tightly packed so glycogen has more free ends from which glucose can be cut

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13
Q

What is cellulose

A

Unbranched chain of glucose connected by β linkages
V strong due to H bonds
Only termites can break it down in their digestive tract

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14
Q

What are proteins and lipids coated in

A

Complex carbohydrates (oligosaccharides)

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15
Q

What is RNA

A

A working template involved in gene expression and an information store in some viruses

It has a structural role in some cellular machinery eg ribosomes

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16
Q

Describe the sugar in DNA

Where is it deoxy

A

Deoxyribose is an aldopentose whose β-anomer is used in DNA

C2

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17
Q

What is the base used in DNA

A

Purines or pyrimidines with extra groups

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18
Q

What are the purine bases

A

A

G

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19
Q

What’s re the pyrimidine bases

A

C
T
U

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20
Q

Give the complementary base pairs

A

A-T
G-C
A-U

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21
Q

How is the stranding different in RNA to DNA

A

RNA is single stranded

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22
Q

How is the double helix arranged

How often is a complete turn

A

2 poly-nucleotide strands arranged with an external phosphate backbone and bases pointed to the centre like ladder rungs

Every 3.4nm

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23
Q

Why does DNA have major and minor grooves

A

Provide access to the bases for DNA binding proteins

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24
Q

Why does a hairpin loop form in RNA

A

Some regions are complementary to other regions in same strand

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25
Q

How does the HIV virus use RNA

A

It is its genetic material containing many loops and hairpin structures, which is important to pack the RNA into the virus capsid and time control gene expression

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26
Q

What is a ribosome molecularly

What are the active sites made of

A

A complex of RNA and protein

It is a ribozyme- an RNA molecule that acts as an enzyme

RNA

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27
Q

Give the 4 levels of protein structure

A

Amino acid sequence
Local backbone arrangement
3D fold
Arrangement of subunits

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28
Q

What do all amino acids contain?

A

An amino group, a carboxyl group and a H around a central α C with a 4th R group

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29
Q

What form does the α carbon take in proteins

A

L form

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30
Q

Which amino acid has no side chain

A

Glycine

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31
Q

Give an amino acid with an aliphatic and hydrophobic side chain

A

Alanine (R group is just methyl)

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32
Q

Why is proline special

A

R group forms a ring of 3 CH2’s, linking to the N

It can therefore not form H bonds

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33
Q

Give an amino acid with

a) a negatively charged R group
b) a positively charged R group

A

a) Arginine

b) aspartic acid

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34
Q

Which amino acid has a polar and aromatic R group

A

Tyrosine (with -OH coming off the aromatic ring)

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35
Q

What part of asparagine is polar

A

The NH2

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36
Q

Give an aromatic R group amino acid

A

Phenylalanine

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37
Q

Which amino acids contain sulphur

A

Cysteine

Methionine

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38
Q

Why are Cys residues unique

A

-SH groups can form a disulphide bond, a covalent crosslink that stabilises protein structures

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39
Q

How are peptide bonds planar

A

e- delocalisation

There is free rotation only around the α carbon

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40
Q

How does folding of a polypeptide occur

A

Rotation of φ (phi) and ψ (Psi)angles

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41
Q

Which is the N terminus and which is the C terminus

How Is an amino acid sequenced

A 
N= has a free NH3+
C= has a free COO-

Sequence is numbered from N to C

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42
Q

What was the first protein whose primary structure was determined and when

How are they now determined

A

Insulin’s structure was determined chemically in 1955

DNA sequencing

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43
Q

Describe the experiment used to show that primary structure provides all the information needed for tertiary structure

A
  • Pure RNase was dissociated by adding urea and mercaptoethanol
  • Urea disrupts non-covalent forces holding the protein together
  • mercaptoethanol reduces disulphide bonds
  • when these denaturing agents were removed, protein spontaneously refolded
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44
Q

How are secondary structures formed

What are the 2 main types of secondary structure

How are side chain interactions involved

A

H bonds between N-H and C=O groups

α helix and β sheet

They are not

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45
Q

Which amino acid doesn’t have an NH

A

Proline

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46
Q

When are H bonds strongest

A

When linear

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47
Q

What does the Ramachandran Plot show

A

The combination of φ and ψ angles found in proteins

Shaded regions are combinations found in secondary structures

Any other combination of angles leads to steric clashes

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48
Q

Describe the α helix structure

A

Backbone in the middle with side chains pointing outwards

Right handed

H bonds are between C=O of residue i and NH of residue i +4

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49
Q

2 types of β sheet

A

Anti parallel - strands go in opposite directions
Parallel - same direction ( residue makes H bonds with residue 2 and 4 of other sheet)

Side chains always point alternatively above and below the sheet

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50
Q

How are a) parallel and b) anti parallel sheets joined

A

a) long loop of protein

b) short loop forming a hairpin

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51
Q

Give the 5 major interactions that form tertiary structure

A 
H bonds
Hydrophobic effect
Electrostatic interaction
VdW forces
Disulphide bonds
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52
Q

Describe the hydrophobic effect

A

Water molecules cannot form H bonds with hydrophobic molecules
Water molecules become ordered around hydrophobic side chains, which is entropically unfavourable
To avoid this, hydrophobic molecules cluster together and interact with each other

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53
Q

Where are the hydrophobic and hydrophilic side chains usually on a protein

A

Hydrophobic in the core

Hydrophilic outside/ on surface

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54
Q

Give another name for electrostatic interactions

A

Salt bridges

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55
Q

How does water affect electrostatic interactions

A

Water molecules shield charges so interactions are stronger inside a protein as there is no water there

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56
Q

Describe disulphide bridges in proteins

A

Covalent bonds between 2 cystine side chains

Do not form inside the cell as it is a reducing environment

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57
Q

What kind of disulphide bonds do intracellular proteins form

A

They do not form disulphide bonds

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58
Q

How strong is the hydrophobic effect

A

Between VdW and H bonds

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59
Q

Give the structure of fibrous proteins and give 2 examples

A

Regular, ordered, with a strong repeating unit

Collagen
Keratin

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60
Q

Give structure of collagen

Is the collagen helix an α helix

A

Each chain forms a helix which twists around 2 others to form a right handed super helix 🧬

No it only has 3 residues and it is left handed (goes anti clockwise)

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61
Q

What is each of the 3 collagen chains made up of

A

Copies of a 3 amino acid repeat: Gly-X(usually proline)- Y(usually hydroxyproline)

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62
Q

What gives collagen its strength

A

The tightly packed triple helix structure

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63
Q

How are the 3 amino acids arranged in collagen

A

Proline on the outside of the triple helix
Gly On the inside, with its small size allowing 3 helices to pack closely
Proline hydroxylation allows another H bond to form

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64
Q

What are motifs

Name some and describe how they are held together

A

Commonly observed groupings of secondary structure elements

β-α-β: H bonds between strands and hydrophobic interactions between helix and strands
α-helical hairpin: hydrophobic and ionic
Greek key: H bonds between strands

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65
Q

What is a domain

A

Part of the protein which forms a structurally Independant unit with a hydrophobic core

Often composed of several motifs put together

It is a structural and functional unit

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66
Q

How many polypeptide chains and domains do antibody molecules contain

A

4 polypeptide chains

12 domains

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67
Q

What do B lymphocytes do

A

Produce antibodies

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68
Q

What is clonal expansion

A

When an antibody recognises an antigen, the cell producing that antibody is stimulates to replicate and secrete more

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69
Q

Describe an antibody molecule

A

Tetramer
2 identical light chains and 2 identical heavy chains
Stabilised by disulphide bonds
Each chain has a variable at the N terminus which confer binding specificity

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70
Q

Describe the domains in light and heavy chains in antibody molecules

A

Light: one variable VL, one constant CL

Heavy: one variable VH, 3 constant HC

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71
Q

How do the different domains in antibody chains interact

A

VL and VH associate to be complementary to the binding site/ the epitope of the antigen
CH1 and CL associate
CH2 and 3 drive dimerisation and interact with different receptors

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72
Q

What are cofactors

A

Molecules used by proteins to provide chemical reactivity not found in amino acid side chains

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73
Q

Define prosthetic group

A

It is tightly bound to the protein

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74
Q

What is a co-substrate

A

Loosely attached and used once then released after reaction for regeneration

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75
Q

For NAD+, give the:

a) vitamin source
b) metabolic role
c) reaction role

A

a) Niacin
b) Redox reactions involving 2 e- transfer
c) Cosubstrate

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76
Q

For FAD, give the:

a) vitamin source
b) metabolic role
c) reaction role

A

Riboflavin

Redox for 1 or 2 e- transfer

Prosthetic group

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77
Q

For CoA, give the:

a) vitamin source
b) metabolic role
c) reaction role

A

Pantothenate

Acyl group transfer

Cosubstrate

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78
Q

For Tetrahydrofolate, give the:

a) vitamin source
b) metabolic role
c) reaction role

A

Folic acid

One carbon substituent transfer
Provides methyl group for T in DNA

Co- substrate

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79
Q

For TPP, give the:

a) vitamin source
b) metabolic role
c) reaction role

A

Thiamine

Aldehyde transfer

Prosthetic group

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80
Q

How are NAD and FAD reduced/ oxidised

Which is endergonic

A

Accept/ release 2 e-

Reduction is endergonic
Oxidation is exergonic

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81
Q

What does NAD+ accept

A

2 e- and a H+

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82
Q

Give an example where NADH is used for reduction

Which molecule is assayed one this experiment and why

A

Pyruvate to lactate catalysed by lactate dehydrogenase

[NADH] - only molecule that absorbed light with a wavelength of 340nm

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83
Q

How does FAD become FADH2

A

Accepts 2 e- and a H+ onto each double bonded N

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84
Q

What is haem

A

Prosthetic group used to bind to O molecules

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85
Q

Where does the O bind on a haem unit

A

Central Fe which is always Fe2+ in Oxygen carriers

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86
Q

Why can haem also carry e-

A

So Fe can be reduced to Fe2+ or Fe3+

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87
Q

How many amino acids and helices does myoglobin contain

What does it do

A

153 amino acids

8 helices

Facilitate diffusion of O2 in muscle tissue

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88
Q

Describe the graphs of saturation vs pO2 for myoglobin and haemoglobin

What does this show

A

Myoglobin- hyperbolic
Haemoglobin- sigmoidal

Cooperativity

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89
Q

What is the Fe in haem bound to

A

4 N in the porphyrin ring and 1 N on the His side chain

90
Q

How does haemoglobin change shape when it becomes oxygenated

A

In deoxy- it is done shaped with the Fe above the ring
O2 binding pulls it into the ring’s plane, pulling down the His with it
This causes changes in the whole tetramer and shifts other subunits closer to the R state, making it easier for O2 to bind

91
Q

Is T state oxy or deoxy

A

Deoxy

92
Q

How do ion channels work

A

Allow hydrophilic ions to cross membranes through a pore

93
Q

True or false: the K channel is a dimer

A

False it is a tetramer if identical helices

94
Q

How does the selectivity filter work in a K channel

A

It strips the aqueous shell from K ions and provides C=O O atoms that allows the loss of hydration shell without the loss of energy

Na is too small to contact C=O so it stays hydrated and is too large

95
Q

How can you determine protein structure

A

X Ray crystallography

NMR

96
Q

How does x Ray crystallography work

A

Ordered molecule crystals distract x Rays and an electron density map is calculated

97
Q

What is cryoEM

A

Cyroelectron Microscopy

Many images are taken and averaged to generate a single image

98
Q

Describe affinity chromatography

A

The column material contains a molecule that specifically binds to the protein of interest. When the sample passes through only that protein will bind and others wash away.

The protein can then be eluted from the column, usually by adding a competitive ligand

99
Q

Describe ion exchange chromatography

A

Uses a column of charges materials
Proteins will bind to different degrees depending on their charge
Proteins are eluted with increasing salt which disrupts electrostatic attractions
Highly charged proteins elute at higher salt concentrations

100
Q

Describe gel filtration chromatography

A

Column contains a gel of porous beads. Small proteins can pass through the pours into the beads, while larger proteins pass around them.
Therefore small proteins take longer to pass through

101
Q

What is another name for gel filtration chromatography

A

Size exclusion chromatography

102
Q

What diseases can be caused by misfolding

A

Parkinson’s
Alzheimer’s
CJD
BSE

103
Q

What are the brain plaques in Alzheimer’s disease patients surrounded by

A

dead neurons

Amyloid fibres of a misfolded protein Aβ are found in these dead cells

104
Q

What is protein Aβ

A

Aβ is a degradation product of amyloid precursor protein

105
Q

What test shows that proteins are the infectious agent in Alzheimer’s

What causes Aβ to misfold

A

Injection of amyloid fibrils into animals leads to development of disease

Unknown

106
Q

What are prion diseases such as kuru caused by

A

Misfolding of the PrP protein -

PrP^c is normal, PrP^sc is misfolded Scrapie form

Misfolding is catalysed by PrP^sc, leading to infectivity

107
Q

How much protein?

A

Use the Bradford assay

Use a standard/ calibration curve of [protein] vs absorbance

108
Q

When would you use SDS PAGE

A

To determine which protein

109
Q

How does SDS PAGE work

A

DeNature protein by heating and SDS binds to hydrophobic regions of protein to make it negatively charged (it needs to be charged) so you know which way it will run
You compare the marks with proteins of known mass

110
Q

Describe ELISA

A

Antibody 1 is on plate
Add sample with >2 domains
Bind antibody 2 to sample to check it has stuck
Antibody 2 is covalently bonded to an enzyme
When a substrate is added, the enzyme converts into a product that can be detected

Done in 96 well plate

111
Q

What is used in HIV testing

A

ELISA

112
Q

Reactions catalysed by enzymes show what properties

How do enzymes drive energetically unfavourable reactions

A

Increases rates
Great reaction specificity
Capacity for regulation

Haha TRICK QUESTION enzymes cannot drive energetically unfavourable reactions

113
Q

How can enzymes provide a driving force for reactions

A

Coupling a favourable to the unfavourable one

114
Q

What is a more realistic model of enzyme function

A

Induced fit

Where both enzyme and substrate change conformation when they interact

115
Q

Describe a case study for the induced fit model

A

Carbonic anhydrase

Active site of carbonic anhydrase contains a zinc ion coordinated with 3 His side chains and a water in 4th position

Binding to zinc deforms water, polarising the e- and His64 accepts this e-

116
Q

Why are HIV proteases important for HIV

Why is this a important for treatment

A

HIV makes its molecules as ‘polyproteins’ which must be cleaved by HIV protease (an Asp protease) to be functional

Human cells do not do this cleavage so the protease is an excellent drug target

117
Q

How are inhibitors designed generally

A

To block to enzyme’s active site and binding of the protein substrate

118
Q

How were HIV protease inhibitors developed

A

Designed to be similar to substrate and to mimic tetrahedral transition state of cleavage reaction. However they cannot be cleaved.

Other chemical groups were also added to improve solubility and stability of drug

119
Q

Name a HIV drug

Have such drugs been useful?

Are there any problems?

A

Saquinavir

HIV drugs have led to a 70% reduction in AIDS deaths in areas where they are available

Virus can develop resistance through mutation of residues in drug-binding pocket

120
Q

Give the 6 classes of enzymes according to IUBMB

A 
Oxioreductases
Transferases
Hydrolases
Lyases 
Isomerases
Ligases
121
Q

Give the function and an example of oxioreductases

A

Catalyse oxidation and reduction reactions (ie removal and addition of e-)

Alcohol dehydrogenase removes hydrogen from alcohol

122
Q

Give the function and an example of transferases

A

Transfer a functional group from a donor to acceptor molecule

Protein kinases transfer a phosphate group onto a protein molecule

123
Q

Give the function and an example of hydrolases

A

Catalyse hydrolytic cleavage

Eg HIV protease
 or DNase (which cuts DNA
124
Q

Give the function and an example of lyases

A

Break (covalent) bonds by means other than hydrolysis or oxidation, creating new double bonds or rings

Aldolase yin glycolysis which breaks fructose-1.6-bisphosphate and generate a C=O bond

125
Q

Give the function and an example of isomerases

A

Catalyse geometric changes

Proline racemase

Triose phosphate isomerase in glycolysis

126
Q

Give the function and an example of ligases

A

Join molecules together using ATP

DNA ligase which joins 5’ end of one DNA molecule to the 3’ end of another

127
Q

Give the order of glycolysis

A

Glucose➡️ glucose-6-phosphate ➡️ fructose-6-phosphate ➡️ fructose-1,6-bisphosphate
⬇️⬇️
GADP↔️DHAP

128
Q

Where do you find glucokinase and hexokinase

What are the different properties

A

Glucokinase = liver
Hexokinase - muscle

When blood glucose is low:
Glucokinase has low activity so does not uptake glucose
Hexokinase: active so muscles continue to use glucose

129
Q

Give the Michaelis-Menten equation for enzyme to product

Why is ES —> E+ P irreversible

A

E+S 🔁 ES ➡️ E + P

Under initial conditions, [P]=0 and reverse reaction is therefore minimal

130
Q

What is the actual Michaelis Menten Equation

A

Vo = Vmax[S]
—————
Km + [S]

131
Q

What is Vmax and Km

Which axis is each on

A

Vmax= maximum rate at this enzyme concentration
Y axis

Km= substrate concentration where rate is Vmax/2
X axis

132
Q

What happens if you put Vo= Vmax/2

A

[S] = Km

133
Q

What is the steady state assumption for michaelis menten

A

[ES] is constant

Ie rate of formation=rate of breakdown

134
Q

Vmax=?

A

K2x[E]t

135
Q

2 requirements for mechalis menten equation

A

Only [S] is changed when Vo is measured

[E]«

136
Q

When is Vmax achieved

What is the equation for Vo here? Therefore what is a simple way to increase Vmax

A

When [S] is infinite
There is no free enzyme, it is all within the ES complex

Vo=k2[E]total= Vmax

Increase [E] by making more enzyme

137
Q

What is the equation for the catalytic constant when Vmax is achieved

Why

A

Vmax
———-
[E] total

K2=Kcat

138
Q

What is the turnover number

A

Number of reactions per second at active site

139
Q

In relation the the Michaelis Menten graph and ES complexes, what happens as the [substrate] increases

A

The percentage of enzyme in the ES complex increases and the rate increases towards Vmax

140
Q

Give a simple operational definition of Km

A

The substrate concentration at which the enzyme works at half of its maximum rate

141
Q

What is Kd and what does it measure

A

K1/K-1 (ie the rate of E+S —>ES divides by the rate of ES—-> E+S)

The affinity of E and S

142
Q

What is the formal definition of Km

A

K-1+K2
———-
K1

K1= E+S—-> ES
K2= ES—->E+P
K-1= ES—-> E+S
143
Q

An enzyme with a low Km has a ____ affinity

A

High

144
Q

Give the units of Km

A

M or moldm-3

145
Q

What is the Lineweaver Burk plot

A

If we measure the initial rate for a series of different substrate concentrations and plot 1/Vo against 1/[S] we will get a straight line

146
Q

Give the rearranged equation of the Michaelis Menten equation as
y=Mx+c

A

Y= 1/Vo
M=Km/Vmax
X=1/[S]
C=1/Vmax

147
Q

How do competitive inhibitors work

A

Bind to active site of enzyme, blocking access for the substrate

Binding is transient ie inhibition is reversible

148
Q

What is the best competitive inhibitor

A

One that resembles the transition state

149
Q

Talk about the inhibition of proline racemase

A

It is an enzyme that interconverts L-proline and D-proline with a planar transition stage

Inhibitors mimic the transition state and bind with 160x the affinity than proline (the substrate)

150
Q

How does Ritonavir work

A

It is a competitive inhibitor of HIV protease designed to mimic its transition state

151
Q

Why does a competitive inhibitor increase Km without affecting Vmax

A

More substrate is needed to reach Vmax/2

152
Q

How does a non-competitive inhibitor affect Vmax and Km

Explain

A

Changes Vmax but not Km

It binds to both E and ES
It does not affect substrate binding but reduces catalytic activity

153
Q

How do irreversible inhibitors work

A

They form covalent bonds with essential active site residues, preventing substrate entry

154
Q

Describe the cell wall of bacteria, it’s enzyme and the effect of penicillin

A

Bacteria are protected by a peptidoglycan cell wall of cross linked sugars and peptides

Glycopeptide transpeptidase cross links peptidoglycan chains during cell wall synthesis but is inhibited by penicillin so the bacteria continues to grow but the cell wall doesn’t form correctly and bursts due to osmotic pressure

155
Q

How does penicillin inhibit glycopeptide transpeptidase

A

It is a suicide inhibitor

Penicillin binds to the O on glycopeptide transpeptidase’s Ser and the reaction cannot be completed

156
Q

Talk about Sarin gas

A

It inhibits acetylcholine esterase at the NMJ
Irreversible inhibitor
Deadly

157
Q

Why does sarin bond more readily to acetylcholine esterase

A

Acetylcholine as there is a
HO-C=O
(making the C δ positive for the enzyme to bind to)
Sarin has a
F-P=O
In the same place so the more electronegative F is lost more easily

158
Q

When is reversible covalent modification useful and what is a common example

A

Enzyme control

Phosphorylation

159
Q

Which residues can phosphate groups be added to

A

The -OH of Ser, Thr, and Tyr

160
Q

Give the structure of a phosphate group

A 
O-
      |
O=P-O-
      |
     O
      |
161
Q

How is cyclin dependent kinase 2 controlled

A

Phosphate is inserted onto Tyr preventing binding of ATP

This must be removed for activation

162
Q

How can phosphorylation activate an enzyme

Give the example of zymogens

A

Allosteric changes

Zymogens are generated in an inactive form and are activated by proteolytic cleavage

163
Q

Which state is Oxy for haemoglobin

A 
Oxy= R
Deoxy= T
164
Q

Give an example of a monomeric allosteric enzyme

A

Glucokinase (found in pancreatic β cells)

It has a binding cleft between two domains which reorientate when the substrate binds (from super-open (inactive) to closed (active))
In the presence of glucose an intermediate state is slowly formed but then this quickly becomes closed when ATP is present

165
Q

What forms of Diabetes is glucokinase associated with

A

MODY and noenatal diabetes (if the enzyme is mutated)

166
Q

How big is an angstrom

A

10^-10m

167
Q

What does the allosteric site do In glucokinase

A

Stabilises active state

168
Q

How do glucokinase activators work as drugs

A

Reduce the Km (so there is a higher binding affinity) and therefore increase glucose sensitivity thus increases insulin secretion

169
Q

Why do you not want to affect the Vmax of glucokinase activators

A

The enzymes don’t work faster overall, causing hypoglycaemia

170
Q

What kind of curve would an allosteric enzyme have

Why

A

Sigmoidal

All enzymes initially in T state
Eventually enough are in R state for sudden increase in rate (when there is a very high affinity)

171
Q

Why can you not use Michaelis Menten for allosteric enzymes

Can you talk about Vmax

A

No single Km is always correct

Yes - it will reach a maximum rate

172
Q

Where does an enzyme want to be on a [S] vs [activity] graph

A

At the steep bit so a small change in [S] causes a large change In Activity

173
Q

What does an activator do

Ditto for inhibitor

Discuss their respective graphs

A

Stabilises the high activity form (curve becomes hyperbolic)

Stabilises low activity form (still sigmoidal but higher [S] is required to switch to high activity form)

174
Q

What does PFK do

A

Binds fructose-6-phosphate and ATP

175
Q

Does ATP inhibit PFK

why

A

Yes

If ATP levels are high you do not need energy so glycolysis is inhibited

176
Q

Give the structure of PFK

A

4 subunits with each monomer contributing to the active site and allosteric sites at each subunit interface
ATP inhibits by being to allosteric site

177
Q

ATP can never be v low in cells so how can PFK be regulated

Give experimental proof

A

AMP

Even the addition of 0.1mM of AMP to 1mM of ATP pushes the sigmoidal curve to the left into a hyperbolic curve

178
Q

Give the equation for the reaction that glycogen phosphorylase controls

A

Glycogen(n residues)+phosphate ——> glucose-1-phosphate + glycogen (n-1 residues)

179
Q

How is glycogen phosphorylase controlled

A

ATP and glucose-6-phosphate inhibit
AMP activates

Phosphorylation of Ser-14 stabilises high activity form (stabilising phosphorylase a form)

(a for active)

180
Q

What must a successful drug have (3)

A 
High selectivity
High affinity 
High bioavailability (stays in the patient)
181
Q

What must an influenza virus do to infect a cell

A

Haemagglutinin binds to Salic acid on the host cell surface and then get inside to hijack cell’s machinery

The neurominidase is necessary to release new virus particles as it cuts the Salic acid off the surface so the new virus doesn’t get stuck

182
Q

How were influenza drugs designed

What was the problem

A

To mimic Sialic acid transition state - it had 1000x more affinity

Poor selectivity so attacked human cells

183
Q

How was the influenza drug improved

A

Chemical groups were added including a positively charged group to form hydrogen bonds with 2 glutamate side chains

Further, parts of the molecule that didn’t interact with the enzyme were removed to make it more lipophilic and therefore could pass through membranes (improving bioavailability)

184
Q

Why do we think bird flu is resistant to Tamiflu

A

There is a large cavity in the neuraminidase

185
Q

What is the story of Viagra

A

Initially developed as angina treatment (a planned phosphodiesterase block)
But after trial ended, test subjects did not want to give back the drug
Was this discovered to have an effect on erectile dysfunction

186
Q

What was the idea behind viagra

A

If you inhibit breakdown of cGMP, it should lead to vasodilation

cGMP leads to activation of PKG which leads to vasodilation

Eventually it was changed so that Viagra is now basically an analogue of the substrate (cGMP)

187
Q

What are the characteristic angles associated with α helices

A

Dihedral angles

188
Q

Which molecules decrease enzyme activity by increasing Km without changing Vmax

A

Competitive

189
Q

How many carbon atoms in citric acid

A

6

190
Q

Which gene is most strongly associated with a predisposition to cancer

A

APC

191
Q

Which DSB repair is vital in G0 and G1

A

NHEJ

192
Q

Which DNA repair stalled replication forks

A

HR

193
Q

What is the initial step in mRNA degradation in eukaryotes

A

Deadenylation

194
Q

How do you convert nucleotides in RNA editing reactions

A

Hydrolytic deamination

195
Q

What are a category of genetic markers comprising repeats of 1-5 nucleotides in length

A

Micro satellites

196
Q

What causes Prader Willi syndrome

A

A deletion of the paternal 15q11b

Commonly associated with eating disorders and short stature

197
Q

What causes VFCS

A

Non allelic recombination between related repetitive sequences in chromosome 22

198
Q

How do enzymes catalyse a reaction

A

Stabilising the transition state

199
Q

How do serine proteases work

A

They use a reactive serine residue to perform nucleophilic attack on the substrate molecule

200
Q

Which B vitamin are vegans likely to be deficient in

A

Vitamin B12 (cobalamin)

201
Q

What is a physiological activator of guanylyl Cyclase

A

NO

202
Q

What are riboswitches

A

RNA sequences that directly interact with small molecules to control translation

203
Q

True or false

Eukaryotic PIC is defines as a set of specific DNA binding transcription factors bound to an enhancer element

A

False

204
Q

How does the glucocorticoid receptor bind to promoters

A

As a dimer

205
Q

What does AKT

A

Phosphorylates the target of mTOR protein

206
Q

What is the action of β catenin in the Wnt pathway

A

It trans locates from the cytoplasm to the nucleus

207
Q

What increases due to increased IP3

A

Ca2+

208
Q

What substance increases inside the cell due to generation of nitric oxide

A

cGMP

209
Q

Which infectious protease contains 2 essential Asp residues in its active site

A

HIV protease

210
Q

Name an enzyme inhibited by penicillin

How is it inhibited

A

Glycopeptide transpeptidase

Suicide inhibition

211
Q

Which enzyme uses a catalytic Zn ion for transition state stabilisation

A

Carbonic anhydrase

212
Q

Which is the only amino acid that can form a covalent bond with another amino acid

A

Cysteine (because it has a -SH group that can link to another -SH group in a disulphide Bridge )

213
Q

Which amino group can’t form H bonds

A

Proline

214
Q

Describe the reaction mechanism of serine proteases

A

1) Ser performs nucleophilic attack on C in substrate
2) His accepts the new Ser H+
3) Asp stabilises positive charge on His. The tetrahedral intermediate is now formed
4) tetrahedral decomposes, accepting His H+, and the first product is formed and is replaced by H2O. The Ser is now separate, bound to acyl-enzyme
5) His accepts H+ from H2O and OH in the water attacks C=O of acyl enzyme. This forms a second tetrahedral which decomposes to release the enzyme

215
Q

What are the roles of the catalytic triad

What is the oxyanion hole

A

This is important in serine proteases

Ser- nucleophilic attack
His- acid/base
Asp- stabilises charge on His

The hole is only filled when the transition state is formed on the way to making the tetrahedral intermediate

216
Q

What does the active site of carbonic anhydrase contain (3)

How does the reaction work

A

Zn coordinated by 3 His side chains.
The H2O substrate occupies the 4th coordination position
Active site also binds CO2

Binding to Zn deforms H20 so His can take a H+
The remaining OH- attacks the C of CO2, generating HCO3-, which is released

217
Q

What kind of enzyme is HIV protease

How do these enzymes work

A

Asp protease

Use Aspartic acid as reactive groups

There are 2 Asp: 1 in an environment favourable for protonation (A) and 1 in aq environment (B)
H2O is coordinated between them
B removes a H+, allowing the water to nucleophilic attack the C=O at the peptide bond
The CN bond is broken and the N pulls B’s H+ towards it and the products are released

218
Q

How many molecules of Acetyl CoA does 1 palmitoyl CoA

A

8

219
Q

How many e- are involved in Vit C redox reactions

A

2

220
Q

Where are the H bonds on an α helix

A

Between C=O of i and NH of i+4

221
Q

What are α helical hairpins held together by

A

Mostly hydrophobic (and some ionic) interactions

MIMS (12 decks)

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