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Michaelmas Term 1 > Dawn Of The Proteins > Flashcards

Dawn Of The Proteins Flashcards

1
Q

Why did proteins evolve?

A
  • better catalysts
  • more chemistry
  • smaller units
  • hydrophobic core
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2
Q

Describe the small amino acids

A

Both hydrophilic and hydrophobic

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3
Q

List the small amino acids

A
  1. Glycine
  2. Proline
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4
Q

Describe glycine

A

Gly, G
Flexible

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5
Q

Describe proline

A

Pro, P
Inflexible, bends chain

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6
Q

List the non-polar/hydrophobic amino acids

A
  1. Alanine
  2. Isoleucine
  3. Leucine
  4. Methionine
  5. Phenylalanine
  6. Tryptophane
  7. Tyrosine
  8. Valine
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7
Q

Which of the non-polar/hydrophobic amino acids are aliphatic

A
  1. Alanine
  2. Isoleucine
  3. Leucine
  4. Methionine
  5. Valine
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8
Q

Which of the non-polar/hydrophobic amino acids are aromatic

A
  1. Phenylalanine
  2. Tryptophane
  3. Tyrosine
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9
Q

What is the hydrophobic effect?

A

Non-polar side chains tend to pack together

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10
Q

List the polar, uncharged amino acids

A
  1. Asparagine
  2. Cysteine
  3. Glutamine
  4. Serine
  5. Threonine
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11
Q

Describe cysteine

A

Cys, C
Makes disulphide bridges (S-S bonds)

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12
Q

Describe polar/uncharged amino acids

A

Solvent exposed, hydrogen bridges, can be post-translationally modified

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13
Q

List the charged amino acids

A
  1. Arginine
  2. Aspartate
  3. Glutamate
  4. Histidine
  5. Lysine
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14
Q

Describe the basic amino acids in principal

A

They have a positive charge, N has an extra proton (H+)

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15
Q

Describe the acidic amino acids in principal

A

Negative charge, COOH has lost proton
You then use -ate suffix

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16
Q

Alanine

A

Ala, A

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17
Q

Valine

A

Val, V

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18
Q

Leucine

A

Leu, L

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19
Q

Isoleucine

A

Ile, I

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20
Q

Methionine

A

Met, M

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21
Q

Phenylalanine

A

Phe, F

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22
Q

Tyrosine

A

Tyr, Y

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23
Q

Tryptophane

A

Trp, W

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24
Q

Serine

A

Ser, S

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25
Q

Threonine

A

Thr, T

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26
Q

Asparagine

A

Asn, N

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27
Q

Glutamine

A

Gln, Q

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28
Q

Lysine

A

Lys, K
pKa = 10.53

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29
Q

Arginine

A

Arg, R
pKa = 12.48

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30
Q

Histidine

A

His, H
pKa = 6.0

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31
Q

Aspartate

A

Asp, D
pKa = 3.86

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32
Q

Glutamate

A

Glu, E
pKa = 4.25

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33
Q

List the charged amino acids

A
  1. Arginine
  2. Aspartate
  3. Glutamate
  4. Histidine
  5. Lysine
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34
Q

Describe charged amino acids

A

Solvent exposed, charged at neutral pH, can co-ordinate metals/ions

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35
Q

How many AA are there?

A

20

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36
Q

Of which amino acids were there sufficient to be prebiotic

A

A, D, E, G, I, L, P, S, T, V

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37
Q

What is the prebiotic amino acid hypothesis

A

Proteins may have evolved with <10aa; additional aas evolved later

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38
Q

What are the qualities of an amino acid that you need to learn?

A
  1. Aromatic/aliphatic
  2. Basic/acidic
  3. Polar/non-polar
  4. It’s name :)
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39
Q

A peptide bond is

A
  • Fixed in plane (cannot rotate)
  • a partial double bond (resonance structure)
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40
Q

How many aas does a peptide have?

A

<50

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41
Q

How many aas does a protein have?

A

> 50aa

42
Q

Peptide/protein backbone nomenclature

A

NH-Cα-CO

43
Q

Peptide/protein side chains nomenclature

A

R

44
Q

Directionality of a peptide/protein

A

N-terminus (amino) -> C-terminus (carboxy)

45
Q

What is the primary protein structure

A

Sequence of a chain of amino acids

46
Q

What is the secondary protein structure

A

Local folding of the polypeptide chain into helices or sheets

47
Q

What is tertiary protein structure?

A

3D folding pattern (shape) of a protein due to side chain interactions (mediated by residue side chains)

48
Q

Quaternary protein structure

A

Protein consisting of more than one aa chain

49
Q

Describe the formation of the secondary structure of proteins/peptides

A
  • backbone has a H-bond donor (N-H) and acceptor (C=O)
  • backbones folds itself in two main ways: α-helix and β-sheet
  • easy interactions through H-bonds
50
Q

Describe an α-helix

A
  • 3.6 residues per turn
  • side chains exposed outwards
51
Q

Describe β-sheets

A
  • can be parallel or anti-parallel
  • side chains exposed outwards
52
Q

Describe the types of tertiary structure

A
  1. Hydrophobic effect
  2. Disulphide bridges
  3. H-bonds between polar aa
  4. Ionic bonds between charged aa
53
Q

What type of protein helps with folding?

A

Chaperones

54
Q

Proteins naturally seek the

A

Lowest energy state

55
Q

List some things that cause dénaturation

A
  1. Acids
  2. Bases
  3. Detergents
  4. Heat
  5. Salt
  6. Solvent
56
Q

What does dénaturation cause?

A

Protein to go from folded to unfolded

57
Q

List the two forms of conformational change

A
  1. Induced fit
  2. Allosteric regulation
58
Q

Describe allosteric regulation

A
  • binding of a molecule at a site other than the active site
59
Q

What is allosteric regulation more generally described as

A

Enzyme regulation

60
Q

Give an example of induced fit

A

Fructose binding to rhamnulose kinase

61
Q

Give an example of allosteric regulation

A
  • Binding of O2 to one subunit in homotetramer of hémoglobin promotes O2 binding to other subunits
  • Co-operatic it’s via conformational change
62
Q

Give an example of conformational change

A

Human α-macroglobin traps proteases

63
Q

Give examples of metal ions as cofactors

A
  • Zn2+ in zinc finger protein
  • Zn2+ in carboxypeptidase
  • Ca2+ in calmodulin
  • 2Fe-2S cluster in redox protein
64
Q

Give an example of a non-metal ion based cofactor

A

NADPH cofactor bound to aldehyde dehydrogenase

65
Q

Define post-translational modifications (PTMs)

A
  • Covalent modification of proteins
  • often reversible and enzymatic
  • regulate proteins by altering surface proteins
66
Q

Give examples of PTMs

A
  1. Acetylation
  2. Acylation/lipidation
  3. Glycosylation
  4. Hydroxylation
  5. Methylation
  6. Nitrosylation
  7. Phosphorylation
67
Q

Phosphorylation

A

Addition of a phosphate group

68
Q

Nitrosylation

A

Addition of N=O onto cysteine residues

69
Q

Acylation/lipidation

A

Addition of lipid onto cysteine residue

70
Q

Hydroxylation

A

Addition of a H onto an O

71
Q

Glycosylation

A

Addition of a glucose onto -NH

72
Q

Acetylation

A

Addition of an acetyl group onto -NH

73
Q

Methylation

A

Addition of methyl groups onto -NH

74
Q

Describe the chemistry of RNA

A
  • 4 bases
  • ~340Da
  • no hydrophobic core
75
Q

Describe the chemistry of proteins

A
  • 20 various bases
  • ~110Da
  • yes hydrophobic core
76
Q

Describe proteins relative to RNA

A

‘Smaller molecular machines with more chemistry; better for catalysis’

77
Q

Does protein self-replicate

A
  • no
  • interactions in antiparallel β-sheets (that might look like DNA) are between backbones, not residues
78
Q

How are cyclic peptides made?

A
  • non-ribosomal peptide synthétases (NRPS)
  • polyketide synthases (PKS)
79
Q

Give an example of a cyclic peptide

A

Antibiotics

80
Q

Describe cyclic peptides

A
  • unusual aas
  • D-enantiomers
  • cyclisation
81
Q

What happens to amino acids in water?

A

Proton donation from carboxyl to amine group

82
Q

Why does steric hindrance arise?

A

From side chains

83
Q

Where is proline found?

A
  • in loops and bends
  • small; little steric hindrance
84
Q

What is interesting about the smallness of glycine and proline?

A

Can be found in hydrophilic and hydrophobic environments

85
Q

Why is Tryptophane apolar?

A

Benzyl group

86
Q

Why is tyrosine polar?

A

Hydroxyl group gives polarity

87
Q

Where does the hydrophobic effect occur?

A

In the core of the protein

88
Q

What does the hydrophobic effect entail?

A

Protein cannot interact with water

89
Q

Why are disulphide bridges good?

A

They are strong; stabilise proteins

90
Q

Why are polar, uncharged amino acids generally involved in interactions with water?

A

Due to polarisation and hydrogen bonds

91
Q

What is the special capability of N?

A

It can carry an extra proton

92
Q

What happens if you go above pKa?

A
  • Protons are taken
  • residues become uncharged
93
Q

Papain =

A

An enzyme

94
Q

Define backbone

A

Coupled amino acids without side chains

95
Q

Define residues

A

Amino acids when bonded, because there are no longer amino or acid groups

96
Q

Folding reduces

A

Steric hindrance

97
Q

Cofactors help in:

A
  1. Catalysis
  2. Structure
98
Q

Hydrogen bonds do what to a molecule?

A

Stabilise it

99
Q

Methylation does what?

A

Reduces positive charge of lysine

100
Q

What does the hydrophobic core allow?

A

Embedding in membranes

101
Q

Why is peptide size restricted initially?

A

Lack of translation machinery

Michaelmas Term 1 (42 decks)

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