Structure and Function of Proteins Flashcards
1
Q
What are the 5 groups of amino acids?
A
Hydrophobic, aromatic, polar, negatively charged, positively charged
2
Q
Do hydrophobic acids contain polar groups?
A
No
3
Q
Where are hydrophobic amino acids found?
A
the hydrophobic core of proteins
4
Q
Which amino acid group does glycine belong to?
A
Hydrophobic
5
Q
What is the one letter code for glycine?
A
G
6
Q
What is the three letter code for glycine?
A
Gly
7
Q
Which amino acid group does alanine belong to?
A
Hydrophobic
8
Q
What is the one letter code for alanine?
A
A
9
Q
What is the three letter code for alanine?
A
Ala
10
Q
Which amino acid group does valine belong to?
A
Hydrophobic
11
Q
What is the one letter code for valine?
A
V
12
Q
What is the three letter code for valine?
A
Val
13
Q
Which amino acid group does leucine belong to?
A
Hydrophobic
14
Q
What is the one letter code for leucine?
A
L
15
Q
What is the three letter code for leucine?
A
Leu
16
Q
Which amino acid group does isoleucine belong to?
A
Hydrophobic
17
Q
What is the one letter code for isoleucine?
A
I
18
Q
What is the three letter code for isoleucine?
A
Ile
19
Q
Which amino acid group does methionine?
A
Hydrophobic
20
Q
What is the one letter code for methionine?
A
M
21
Q
What is the three letter code for methionine?
A
Met
22
Q
Which amino acid group does proline belong to?
A
Hydrophobic
23
Q
What is the one letter code for proline?
A
P
24
Q
What is the three letter code for proline?
A
Pro
25
Name the 7 hydrophobic amino acids
Glycine, Alanine, Leucine, Isoleucine, Valine, Methionine, Proline
26
What do all aromatic amino acids contain?
A ring of delocalised electrons
27
Which amino acid group does phenylalanine belong to?
Aromatic
28
What is the one letter code for phenylalanine?
F
29
What is the three letter code for phenylalanine?
Phe
30
Which amino acid group does tyrosine belong to?
Aromatic
31
What is the one letter code for tyrosine?
Y
32
What is the three letter code for tyrosine?
Tyr
33
Which amino acid group does tryptophan belong to?
Aromatic
34
What is the one letter code for tryptophan?
W
35
What is the three letter code for tryptophan?
Trp
36
Are polar amino acids hydrophilic or hydrophobic?
Hydrophilic
37
Where are polar amino acids usually found?
On the surface of proteins
38
Which amino acid group does serine belong to?
Polar
39
What is the one letter code for serine?
S
40
What is the three letter code for serine?
Ser
41
Which amino acid group does threonine belong to?
Polar
42
What is the one letter code for threonine?
T
43
What is the three letter code for threonine?
Thr
44
Which amino acid group does cysteine belong to?
Polar
45
What is the one letter code for cysteine?
C
46
What is the three letter code for cysteine?
Cys
47
Which amino acid group does asparagine belong to?
Polar
48
What is the one letter code for asparagine?
N
49
What is the three letter code for asparagine?
Asn
50
Which amino acid group does gluamine belong to?
Polar
51
What is the one letter code for gluamine?
Q
52
What is the three letter code for gluamine?
Gln
53
Name the 3 aromatic amino acids
Phenylalanine, tyrosine, tryptophan
54
Name the 5 polar amino acids
Serine, threonine, cysteine, asparagine, gluamine
55
Which amino acid group does aspartate belong to?
Negatively charged
56
What is the one letter code for aspartate?
D
57
What is the three letter code for aspartate?
Asp
58
Which amino acid group does glutamate belong to?
Negatively charged
59
What is the one letter code for glutamate?
E
60
What is the three letter code for glutamate?
Glu
61
Name the 2 negatively charged amino acids
Aspartate, glutamate
62
Which amino acid group does lysine belong to?
Positively charged
63
What is the one letter code of lysine?
K
64
What is the three letter code of lysine?
Lys
65
Which amino acid group does arginine belong to?
Positively charged
66
What is the one letter code for arginine?
R
67
What is the three letter code for arginine?
Arg
68
Which amino acid group does histidine belong to?
Positively charged
69
What is the one letter code for histidine?
H
70
What is the three letter code for histidine?
His
71
Name the 3 positively charged amino acids
Lysine, arginine, histidine
72
Name the 7 uses of proteins
```
catalysis
transport and storage
motion
mechanical support
immune protection
signal transduction
growth and development control
```
73
Which amino acid is the most common replacement in mutation?
Alanine (she fit)
74
Why is hydrogen bonding limited in proline?
Lack of hydrogen on the nitrogen
75
What is the largest amino acid?
Tryptophan
76
Which amino acid contains an imidazole ring?
Histidine
77
Name the two processes by which protein structures can be determined
X-ray crystallography and Nuclear Magnetic Resonance (NMR)
78
What are the three types of protein structure?
Globular, Membrane, and Fibrous
79
Are globular proteins soluble in water?
Yes
80
What makes globular proteins soluble in water?
They have a hydrophobic core and a hydrophilic surface
81
What are possible protein structures limited by?
Properties of the peptide bond
82
What is the hierarchy of protein structure?
Primary: amino acid sequence
Secondary: secondary structure elements and motifs
Tertiary: whole protein/domain structure
Quaternary: whole protein structure
83
Can rotation occur around a peptide bond?
No
84
Which amino acid can form cis bonds?
Proline
85
Which bond is between C(alpha) and the amide group?
Phi
86
Which bond is between the carbonyl carbon and the C(alpha)
Psi
87
What does a Ramachandran plot show?
Which Phi and Psi bond combinations are possible
88
What types of bonding are in proteins?
- ionic interactions: between acidic and basic side chain groups of opposite charge
- hydrogen bond: between donor and acceptor groups
- disulphide bridges
- hydrophobic interactions: between aliphatic and aromatic side chain groups
- pi stacking between aromatic groups
89
What are domains built from?
Motifs
90
What can domains be stabilised by?
Disulphide bondes
91
What are two ways in which proteins can be post translationally modified?
Covalent and non-covalent
92
What are some examples of covalent modification?
Disulphide bridge formation, cleavage of peptide bonds, the N-terminus, the C-terminus, amino acid residues (side chains)
93
What are some examples of non-covalent modification?
Addition of metals, addition of cofactors
94
Why are proteins modified?
Stability, regulation of activity, localisation, ageing
95
Are alpha helices left-handed or right handed?
Right-handed
96
Do protein adopt the most thermodynamically stable or unstable structure?
Stable
97
Name the four methods of denaturation
Chemical denaturants, heat, acid/base, force/kinetic energy
98
What do protein disulphide isomerases (PDI) do?
Accelerate the formation of native disulphide bridging arrangements allowing disulphide shuffling and attacks incorrectly formed disulphide bonds
99
What do Peptidyl Prolyl Cis-Trans Isomerases (PPIs) do?
Catalyse the rotation around peptide bonds preceding proline
100
What do molecular chaperones do?
Prevent the improper folding and aggregation of proteins and prevent or reverse improper associations between proteins
101
What are the two types of molecular chaperones?
DnaK/DnaJ/GrpE (or Hsp70) family and chaperonin family (GroE chaperonin)
102
What do the DnaK/DnaJ/GrpE (or Hsp70) family do?
Prevent premature folding: bind to growing polypeptide chains while they are being synthesised on ribosomes
103
What do the chaperonin family do?
Bind to the solvent-exposed hydrophobic surfaces of an unfolded or aggregated protein and release them
Assist post-translational folding
104
What are proteopathies?
Diseases caused by misfolded proteins
105
What are the two classes if proteopathies?
Hereditary and acquired
106
Define hereditary proteopathies
Mutation causes loss of function or gain of function leading to disease
107
Define acquired proteopathies
Infectious prion disease caused by exposure to misfolded proteins from other organisms
108
Give two examples of a hereditary proteopathy
Cystic fibrosis and Alzheimer's disease
109
Give two examples of an acquired proteopathy
Bovine spongiform encephalopathy (BSE) and vCJD
110
Why is Alzheimer's disease associated with neuronal loss?
Due to deposition of amyloid plaques
111
What did Anfinsen's experiment on Ribonuclease A demonstrate about protein folding?
1. All of the information for folding to the correct structure is in the amino acid sequence
2. Proteins will fold to the most thermodynamically stable conformation
112
Give 3 reasons why proteins might need to be purified
Protein characterisation, use in drugs & diagnostics, for commercial use esp. enzymes
113
Give 3 examples of when protein characterisation might be needed
Assay to investigate function, investigate post-translational modifications, to study structure-function relationships
114
What are the two sources of proteins?
Native (extracted from host organism) and heterologous protein expression systems
115
How do heterologous protein expression systems work?
1. Gene cloned into a vector
2. Inserted into an organism
3. Produces the protein via constitutive expression or inducible expression (AraBAD promoter and arabinose)
116
Name the 6 characteristics used to separate proteins
```
Size
Charge
Specific binding
Specific epitope
Purification tag
Hydrophobicity
```
117
How are proteins separated by size?
Size exclusion chromatography
118
How are proteins separated by charge?
Ion exchange chromatography
119
How are proteins separated by specific binding?
Affinity chromatography
120
How are proteins separated by specific epitope?
Affinity chromatography
121
How are proteins separated by purification tag?
Affinity chromatography
122
How are proteins separated by hydrophobicity?
Hydrophobic interaction chromatography
123
How can proteins be engineered for purification and detection?
1. Add signal sequence that causes secretion into culture medium
2. Add sequence of protein that helps the target protein fold and stay soluble
3. Add a sequence that aids detection
4. Add an affinity tag
124
How does hydrophobic interaction chromatography work?
1. Add bacterial lysate to column matrix in high salt buffer (hydrophobic proteins will stick to column)
2. Wash less hydrophobic proteins from column with low salt buffer (less hydrophobic proteins elute from column)
3. Elute protein from column by adding salt-free buffer
125
What are the two techniques for analysing protein size?
Gel electrophoresis and mass spectrometry
126
What is the difference in the mass given by gel electrophoresis vs mass spectrometry?
Gel electrophoresis gives approximate mass; mass spectrometry gives accurate mass
127
What is the aim of polyacrylamide gel electrophoresis (PAGE)?
Separating mixtures of proteins by their relative rates of migration through a matrix in an electrical field
128
What type of PAGE should be used for denatured protein?
SDS-PAGE
| relative migration rate based on mass of protein
129
What type of PAGE should be used for native proteins?
Native PAGE
| relative migration rate based on both mass of protein and charge at the pH used
130
What is isoelectric focusing (IEF) used for?
To separate proteins according to their overall charge
131
What are the three basic components of a mass spectrometer?
Ioniser, mass analyser, detector
132
What is the proteome?
The primary sequence of all proteins
133
How can proteins be identified in complex mixtures?
Proteomics
1. extract mixture of proteins from cells/tissue and 2D-PAGE
2. extract proteins from gel and digest with trypsin
3. identify by peptide mass fingerprinting
