Dawn Of The Proteins Flashcards
1
Q
Why did proteins evolve?
A
- better catalysts
- more chemistry
- smaller units
- hydrophobic core
2
Q
Describe the small amino acids
A
Both hydrophilic and hydrophobic
3
Q
List the small amino acids
A
- Glycine
- Proline
4
Q
Describe glycine
A
Gly, G
Flexible
5
Q
Describe proline
A
Pro, P
Inflexible, bends chain
6
Q
List the non-polar/hydrophobic amino acids
A
- Alanine
- Isoleucine
- Leucine
- Methionine
- Phenylalanine
- Tryptophane
- Tyrosine
- Valine
7
Q
Which of the non-polar/hydrophobic amino acids are aliphatic
A
- Alanine
- Isoleucine
- Leucine
- Methionine
- Valine
8
Q
Which of the non-polar/hydrophobic amino acids are aromatic
A
- Phenylalanine
- Tryptophane
- Tyrosine
9
Q
What is the hydrophobic effect?
A
Non-polar side chains tend to pack together
10
Q
List the polar, uncharged amino acids
A
- Asparagine
- Cysteine
- Glutamine
- Serine
- Threonine
11
Q
Describe cysteine
A
Cys, C
Makes disulphide bridges (S-S bonds)
12
Q
Describe polar/uncharged amino acids
A
Solvent exposed, hydrogen bridges, can be post-translationally modified
13
Q
List the charged amino acids
A
- Arginine
- Aspartate
- Glutamate
- Histidine
- Lysine
14
Q
Describe the basic amino acids in principal
A
They have a positive charge, N has an extra proton (H+)
15
Q
Describe the acidic amino acids in principal
A
Negative charge, COOH has lost proton
You then use -ate suffix
16
Q
Alanine
A
Ala, A
17
Q
Valine
A
Val, V
18
Q
Leucine
A
Leu, L
19
Q
Isoleucine
A
Ile, I
20
Q
Methionine
A
Met, M
21
Q
Phenylalanine
A
Phe, F
22
Q
Tyrosine
A
Tyr, Y
23
Q
Tryptophane
A
Trp, W
24
Q
Serine
A
Ser, S
25
Threonine
Thr, T
26
Asparagine
Asn, N
27
Glutamine
Gln, Q
28
Lysine
Lys, K
pKa = 10.53
29
Arginine
Arg, R
pKa = 12.48
30
Histidine
His, H
pKa = 6.0
31
Aspartate
Asp, D
pKa = 3.86
32
Glutamate
Glu, E
pKa = 4.25
33
List the charged amino acids
1. Arginine
2. Aspartate
3. Glutamate
4. Histidine
5. Lysine
34
Describe charged amino acids
Solvent exposed, charged at neutral pH, can co-ordinate metals/ions
35
How many AA are there?
20
36
Of which amino acids were there sufficient to be prebiotic
A, D, E, G, I, L, P, S, T, V
37
What is the prebiotic amino acid hypothesis
Proteins may have evolved with <10aa; additional aas evolved later
38
What are the qualities of an amino acid that you need to learn?
1. Aromatic/aliphatic
2. Basic/acidic
3. Polar/non-polar
4. It’s name :)
39
A peptide bond is
- Fixed in plane (cannot rotate)
- a partial double bond (resonance structure)
40
How many aas does a peptide have?
<50
41
How many aas does a protein have?
>50aa
42
Peptide/protein backbone nomenclature
NH-Cα-CO
43
Peptide/protein side chains nomenclature
R
44
Directionality of a peptide/protein
N-terminus (amino) -> C-terminus (carboxy)
45
What is the primary protein structure
Sequence of a chain of amino acids
46
What is the secondary protein structure
Local folding of the polypeptide chain into helices or sheets
47
What is tertiary protein structure?
3D folding pattern (shape) of a protein due to side chain interactions (mediated by residue side chains)
48
Quaternary protein structure
Protein consisting of more than one aa chain
49
Describe the formation of the secondary structure of proteins/peptides
- 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
Describe an α-helix
- 3.6 residues per turn
- side chains exposed outwards
51
Describe β-sheets
- can be parallel or anti-parallel
- side chains exposed outwards
52
Describe the types of tertiary structure
1. Hydrophobic effect
2. Disulphide bridges
3. H-bonds between polar aa
4. Ionic bonds between charged aa
53
What type of protein helps with folding?
Chaperones
54
Proteins naturally seek the
Lowest energy state
55
List some things that cause dénaturation
1. Acids
2. Bases
3. Detergents
4. Heat
5. Salt
6. Solvent
56
What does dénaturation cause?
Protein to go from folded to unfolded
57
List the two forms of conformational change
1. Induced fit
2. Allosteric regulation
58
Describe allosteric regulation
- binding of a molecule at a site other than the active site
59
What is allosteric regulation more generally described as
Enzyme regulation
60
Give an example of induced fit
Fructose binding to rhamnulose kinase
61
Give an example of allosteric regulation
- Binding of O2 to one subunit in homotetramer of hémoglobin promotes O2 binding to other subunits
- Co-operatic it’s via conformational change
62
Give an example of conformational change
Human α-macroglobin traps proteases
63
Give examples of metal ions as cofactors
- Zn2+ in zinc finger protein
- Zn2+ in carboxypeptidase
- Ca2+ in calmodulin
- 2Fe-2S cluster in redox protein
64
Give an example of a non-metal ion based cofactor
NADPH cofactor bound to aldehyde dehydrogenase
65
Define post-translational modifications (PTMs)
- Covalent modification of proteins
- often reversible and enzymatic
- regulate proteins by altering surface proteins
66
Give examples of PTMs
1. Acetylation
2. Acylation/lipidation
3. Glycosylation
4. Hydroxylation
5. Methylation
6. Nitrosylation
7. Phosphorylation
67
Phosphorylation
Addition of a phosphate group
68
Nitrosylation
Addition of N=O onto cysteine residues
69
Acylation/lipidation
Addition of lipid onto cysteine residue
70
Hydroxylation
Addition of a H onto an O
71
Glycosylation
Addition of a glucose onto -NH
72
Acetylation
Addition of an acetyl group onto -NH
73
Methylation
Addition of methyl groups onto -NH
74
Describe the chemistry of RNA
- 4 bases
- ~340Da
- no hydrophobic core
75
Describe the chemistry of proteins
- 20 various bases
- ~110Da
- yes hydrophobic core
76
Describe proteins relative to RNA
‘Smaller molecular machines with more chemistry; better for catalysis’
77
Does protein self-replicate
- no
- interactions in antiparallel β-sheets (that might look like DNA) are between backbones, not residues
78
How are cyclic peptides made?
- non-ribosomal peptide synthétases (NRPS)
- polyketide synthases (PKS)
79
Give an example of a cyclic peptide
Antibiotics
80
Describe cyclic peptides
- unusual aas
- D-enantiomers
- cyclisation
81
What happens to amino acids in water?
Proton donation from carboxyl to amine group
82
Why does steric hindrance arise?
From side chains
83
Where is proline found?
- in loops and bends
- small; little steric hindrance
84
What is interesting about the smallness of glycine and proline?
Can be found in hydrophilic and hydrophobic environments
85
Why is Tryptophane apolar?
Benzyl group
86
Why is tyrosine polar?
Hydroxyl group gives polarity
87
Where does the hydrophobic effect occur?
In the core of the protein
88
What does the hydrophobic effect entail?
Protein cannot interact with water
89
Why are disulphide bridges good?
They are strong; stabilise proteins
90
Why are polar, uncharged amino acids generally involved in interactions with water?
Due to polarisation and hydrogen bonds
91
What is the special capability of N?
It can carry an extra proton
92
What happens if you go above pKa?
- Protons are taken
- residues become uncharged
93
Papain =
An enzyme
94
Define backbone
Coupled amino acids without side chains
95
Define residues
Amino acids when bonded, because there are no longer amino or acid groups
96
Folding reduces
Steric hindrance
97
Cofactors help in:
1. Catalysis
2. Structure
98
Hydrogen bonds do what to a molecule?
Stabilise it
99
Methylation does what?
Reduces positive charge of lysine
100
What does the hydrophobic core allow?
Embedding in membranes
101
Why is peptide size restricted initially?
Lack of translation machinery
