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Proteins Flashcards

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1
Q

At their isoelectric point (pI), what form are amino acids in?

A

Their zwitterion form.

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2
Q

Which is the only amino acid that is not chiral around its alpha carbon?

A

Glycine.

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3
Q

Name the aliphatic and hydrophobic amino acids.

A

Alanine, Valine, Leucine, Isoleucine.

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4
Q

Which amino acid has no side chain?

A

Glycine.

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5
Q

Name the only imino acid?

A

Proline.

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6
Q

Name the positively charged amino acids?

A

Arginine, Lysine and Histidine.

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7
Q

Which of the positively charged amino acids is very basic and why?

A

Arginine. The positive charge is destabilised by resonance.

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8
Q

Which amino acids are negatively charged?

A

Aspartic Acid (Aspartate) and Glutamic Acid (Glutamate).

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9
Q

Which amino acids have polar side chains? Which one is both polar and aromatic?

A

Asparagine, Glutamine, Serine, Threonine, and Tyrosine. Tyrosine is both polar and aromatic.

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10
Q

Which amino acids have sulfur-containing side chains?

A

Cysteine and Methionine.

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11
Q

Which amino acids have non-polar aromatic side chains?

A

Phenylalanine and Tryptophan.

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12
Q

What three states can an amino acid exist in?

A

Cation (at low pH), zwitterion at it’s pI (approximately neutral pH) and an anion at high pH.

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13
Q

What is the pKa?

A

The centre point of the titration for each group.

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14
Q

Why is the pKa of the carboxyl group in amino acids higher than that for carboxylic acids?

A

The amino group withdraws electrons from the carboxyl group, stabilising the negatively charged form.

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15
Q

If the amino acid has an ionisable side chain, how many pKa values will the titration curve have?

A

3

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16
Q

Which enantiomer of amino acids is found in proteins?

A

L

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17
Q

How can you tell if an amino acid is the L enantiomer?

A

If you can spell CORN with H pointing towards you, reading clockwise, then it is the L enantiomer.

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18
Q

Why is there restricted rotation around peptide bonds?

A

They have partial double bond character as they are resonance hybrids.

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19
Q

Usually, the C=O bond and the N-H bond point in opposite directions in a peptide linkage. Why?

A

Otherwise there is steric clash between R groups.

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20
Q

What does it mean to say that polypeptides are monodisperse? Is this true for polysaccharides?

A

All polypeptides of the same type are the same length. No, polysaccharides are polydisperse.

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21
Q

What is the primary structure of a protein?

A

The genetically pre-determined sequence of amino acids.

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22
Q

What is the secondary structure of a protein?

A

The folding of the protein based on the non-covalent interactions between peptide bonds.

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23
Q

What two angles are used to define the angles of bond rotation in a peptide bond? What is their range of values?

A

φ and ψ

-180 to 180 degrees.

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24
Q

Due to steric hindrance, only some angles of rotation are possible. What plot is used to show these?

A

Ramachandran plot

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25
Q

What are the values of φ and ψ in proline?

A

φ = -60 degrees, ψ = -77 degrees.

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26
Q

Why is rotation restricted in proline?

A

The bond between the alpha carbon and nitrogen is part of the pyrrolidine ring.

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27
Q

Why does glycine allow a far wider range of angles of rotation?

A

It only has a H in its side chain, so there is little to no steric hindrance.

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28
Q

What are the criteria for the formation of a stable secondary structure?

A

Peptide bonds must be planar and have favourable bond lengths and angles.
Every carbonyl carbon and amide nitrogen are involved in hydrogen bonding.
The H bonded atoms are in a straight line.
Operation to move from one residue to another is always the same.
Side-chains point out of the structure for minimal steric interference.

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29
Q

What are the two main types of secondary structure?

A

Alpha-helix and beta-pleated sheet.

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30
Q

In an alpha helix, a peptide bond ‘i’ will form hydrogen bonds with which peptide bond?

A

i+4.

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31
Q

Which end of the alpha helix do all N-H groups in peptide bonds point towards?

A

The N-terminus.

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32
Q

For L-amino acids, what is the screw-sense of the alpha-helix?

A

Clockwise when looking down from the N-terminus.

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33
Q

Another helical form is the π helix. What peptide bonds will form hydrogen bonds?

A

i, i+5.

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34
Q

What residues are often found where there is a π helix?

A

Proline, due to its limited rotation.

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35
Q

What are the values of φ and ψ in an alpha helix?

A 
φ = -60 degrees
ψ= -45 degrees
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36
Q

What are the values of φ and ψ in a beta-pleated sheet?

A 
φ = -120 degrees
ψ= 120 degrees
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37
Q

In a beta sheet, in which directions do the carbonyl and amide groups in the peptide bond point?

A

They alternate directions.

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38
Q

Why is the anti-parallel beta sheet more stable than the parallel one?

A

In the anti-parallel form, the atoms making up the double bond are in a straight line. In the parallel form, this is not the case.

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39
Q

Which directions do the side-chains point in a beta sheet?

A

They alternate above and below the sheet.

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40
Q

What sort of turn can reverse the direction of a beta sheet to form an anti-parallel beta sheet?

A

A reverse beta turn.

41
Q

Give the names of the interactions that hold together the tertiary structure of a protein, in order of decreasing strength.

A 
Disulfide bridges.
Ionic interactions. 
Hydrogen bonds. 
Hydrophobic interactions. 
Van der Waals interactions.
42
Q

Name the common supersecondary structures.

A

α-hairpin, β-hairpin, four-helix bundle, β-α-β motif, β meander, Greek key.

43
Q

Why are the helices in supersecondary structures often amphiphilic?

A

They can’t hydrogen bond to one another because the peptide bond groups are already hydrogen bonded to one another, so they are often held together by hydrophobic interactions.

44
Q

Where are four alpha-helix bundles often found?

A

Proteins that bind to the hydrophobic haem molecule.

45
Q

Where are β-α-β motifs found?

A

Proteins with parallel beta sheets, which can’t be connected by a beta turn.

46
Q

What is the structure called when β-α-β motifs line up so that the 2nd beta strand of one makes up the first beta strand of another. What is a protein that contains it?

A

Rossman fold.

Found in lactate dehydrogenase.

47
Q

What can the Greek key motif form? Where is this structure found?

A

A beta sandwich fold. It makes up the basis of the immunoglobulin fold (Ig fold) found in the antigen-binding domains of antibodies.

48
Q

Name the techniques that can be used to determine the structure of proteins.

A

X-ray diffraction.
NMR.
Cryo electron microscopy.
Atomic force microscopy.

49
Q

Are the forces that hold together the quaternary structure the same or different to those that hold together the tertiary structure?

A

The same.

50
Q

Some proteins can spontaneously fold (shown by experiments with ribonuclease), but more complex proteins need other types of proteins. What are these known as?

A

Chaperones.

51
Q

Describe protein folding.

A

Some secondary structural elements may be transiently formed. These may then fold to form a sub-domain that then stabilises further secondary structural elements. The structure can then be built up in stages until the native conformation is reached. Chaperones may be necessary at some point, especially to overcome energy barriers.

52
Q

What is a disease caused by protein misfolding?

A

BSE is caused by the misfolding of prion protein to form an incorrect version known as the Scrapie form. The Scrapie form then catalyses the misfolding of more prion protein, which then forms fibrils.

53
Q

What are the six major groups of enzymes? Give an example of each.

A 
Oxidoreductases - Dehydrogenase
Transferases - Acetyl transferase
Hydrolases - Protease
Lyases - Decarboxylase 
Isomerases - Epimerase
Ligases - DNA ligase
54
Q

What is a cofactor?

A

A small molecule essential for enzyme activity.

55
Q

What is a prosthetic group?

A

A small molecule tightly bound to a protein.

56
Q

What is a coenzyme?

A

Organic cofactors.

57
Q

What are coenzymes divided into?

A

Loosely bound co-substrates or tightly bound prosthetic groups.

58
Q

What is a key difference between prosthetic groups and co-substrates?

A

Co-substrates dissociate and bind again, while prosthetic groups are regenerated still attached to the enzyme.

59
Q

Give three examples of co-substrates and their vitamin source.

A

NAD+ - Niacin.
Coenzyme A - Pantothenate.
Tetrahydrofolate - Folate.

60
Q

Give three examples of prosthetic groups and their vitamin sources.

A

FAD - Riboflavin.
Thiamine Pyrophosphate (TPP) - Thiamine.
Adenosylcobalamin - Cobalamin.

61
Q

What are the 4 ways in which catalysts speed up reactions?

A 
Proximity effects. 
Acid-base catalysis. 
Covalent catalysis. 
Substrate strain.
Water exclusion.
62
Q

Describe the induced fit model of catalysis.

A

Enzyme and substrate form a weak encounter complex that isn’t that stable. The interaction is stronger with the transition state, so a transition state complex is formed via an induced conformation change, pushing substrate to the transition state so product can be formed.

63
Q

What is the Michaelis-Menten equation?

A

V_0 = (Vmax[S])/(Km + [S})

64
Q

Give the equation for Km.

A

(k1 + k3)/k1

Where k1 is rate of formation of ES from E and S,
k2 is rate of breakdown of ES to E and S,
k3 is formation of product.

65
Q

What else is k3 known as?

A

k_cat (the catalytic constant).

66
Q

What is the equation for k_cat?

A

Vmax/[E]tot

67
Q

What are the units for k_cat?

A

s^-1

68
Q

What is the ratio that gives efficiency of the enzyme?

A

k_cat/Km

69
Q

Define Vmax.

A

Vmax is the maximum rate at the given enzyme concentration.

70
Q

What is Km equal to? What information does it give?

A

The substrate concentration at 1/2Vmax. It gives a measure of the enzyme’s affinity for the substrate.

71
Q

What can be used to linearise the Michaelis-Menten Plot and what is its equation?

A

The Lineweaver-Burk Plot.

1/v = ((Km/Vmax) x (1/[S])) + 1/Vmax

72
Q

What three aspects of catalysis can lysozyme be used as an example of?

A

Substrate strain.
Acid-base catalysis.
Water exclusion.

73
Q

Why is the pKa of glutamic acid 35 in lysozyme so high (6.7) compared to in solution, where it ranges from 2.0 to 4.2?

A

In lysozyme, it is opposite to a negatively charged aspartate residue. If glutamate lost its proton below the optimum pH of the enzyme (around 5) then it would destabilise the enzyme due to repulsion between the two negative charges.

74
Q

What is the pKa of aspartic acid 52 in lysozyme?

A

3.8

75
Q

Where does a competitive inhibitor bind on an enzyme?

A

The active site.

76
Q

What is the effect on Vmax with a competitive inhibitor?

A

No change.

77
Q

On a graph of initial rate against substrate concentration, what is the effect of a competitive inhibitor?

A

Shifts the curve to the right because you need higher substrate concentration to reach the same activity.

78
Q

What is the effect on the gradient (Km/Vmax) of a Lineweaver-Burk plot when a competitive inhibitor is present?

A

The gradient is increased.

79
Q

What is the effect on the apparent Km when a competitive inhibitor is added?

A

Increased.

80
Q

Give an example of a competitive inhibitor.

A

Methotrexate. It binds to the active site of dihydrofolate reductase 1000 times more strongly than the substrate (dihydrofolate), preventing the production of tetrahydrofolate. Tetrahydrofolate is an intermediate in the transfer of a 1-carbon unit in thymine synthase, so methotrexate is a good anti-cancer drug.

81
Q

Give an example of an irreversible inhibitor.

A

Sarin. It inhibits acetylcholine esterase by forming covalent bonds with a serine residue in the active site. This prevents the hydrolysis of acetylcholine at neuromuscular junctions, causing paralysis.

82
Q

What are suicide inhibitors?

A

Inhibitors that exploit the enzyme’s catalytic activity, making the enzyme begin to catalyse the reaction, forming a covalent bond with the inhibitor, hence preventing the enzyme working.

83
Q

Give an example of a suicide inhibitor.

A

Penicillin, which inhibits the formation of peptide bonds in bacterial peptidoglycan cell walls, so the bacteria can’t divide.

84
Q

Give the most common example of reversible covalent modification enzymes.

A

Phosphorylation.

85
Q

Which enzymes are used to add phosphate to another enzyme?

A

Kinases.

86
Q

Which enzymes are used to hydrolyse the bond between a phosphate and another enzyme?

A

Phosphatases.

87
Q

What are the two possible effects of phosphorylating an enzyme?

A

Activation or inhibition.

88
Q

What factor of enzyme control is due to genetics?

A

Enzyme concentrations, which alter Vmax.

89
Q

Give an example of a negative feedback loop in enzyme control.

A

ATP and citrate allosterically inhibit phosphofructokinase-1 in muscle cells, so glycolysis is reduced when there is already enough ATP.

90
Q

What are zymogens?

A

Enzymes that produced in a precursor form, then activated by proteolysis when needed.

91
Q

Give an example of when zymogens are important.

A

Blood clotting cascade. The first protease is activated by damage at the surface, which then activates more enzymes and so on. There is no way to stop this cascade, other than by destroying the enzymes.

92
Q

Enzymes that have multiple subunits often bind substrates in what way?

A

Cooperatively.

93
Q

What effect does cooperative binding have on a graph of initial rate against substrate concentration?

A

Curve becomes sigmoidal.

94
Q

Explain cooperative binding.

A

The allosteric activator binds at an allosteric site on one subunit, inducing a conformational change in the other subunit that increases the enzyme’s affinity for the substrate.

95
Q

ADP and AMP are allosteric activators of which enzyme?

A

Phosphofructokinase-2.

96
Q

Give a non-enzymatic example of cooperative binding.

A

Haemoglobin.

97
Q

What are the two models for cooperative binding in Haemoglobin?

A

Concerted model. In the concerted model, haemoglobin’s subunits can switch between the low- and high-affinity conformations, but the conformational changes induced by the oxygen result in the high-affinity state being favoured the more oxygen is bound.

Sequential model. The binding of one oxygen results in a conformational change in the next which increases its affinity for oxygen and so on.

98
Q

In terms of enzymatic control, what is the benefit of compartmentation in eukaryotic cells?

A

Competing forward and reverse reactions can be maintained in different parts of the cell.

Biology of Cells (7 decks)

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