Proteins Flashcards
(89 cards)
1
Q
The central dogma of molecular biology states that:
A
The flow of genetic information in a cell is:
DNA ⟶ mRNA ⟶ protein
2
Q
describe how the sequence of amino acids determines how a protein folds
A
amino acid sequence of each protein contains the information that specifies the native structure and the
pathway to attain that state. Shown in Anfinsen’s experiment.
3
Q
What is a protein?
A
non-branching polymer of amino acids.
4
Q
What are proteins made of?
A
specific sequence of amino acids.
5
Q
How amino acids fit together in proteins?
A
covalent bonds called peptide bonds.
6
Q
Name a protein involved in cell signalling
A
Insulin
7
Q
Name a protein involved in Oxygen transport
A
haemoglobin
8
Q
Name a protein involved in Protein digestion
A
Trypsin
9
Q
Name a protein involved in Metabolism
A
Hexokinase
10
Q
Name a protein involved in Immune protection
A
Antibodies
11
Q
Name a protein involved in Energetics
A
ATP synthase
12
Q
Name a protein involved in Replication and maintenance
A
DNA polymerase
13
Q
Name the amino acid(s) where Their side chain contains a hydroxyl group.
A
serine,
tyrosine,
threonine
14
Q
Name the amino acid(s) where Negatively charged at neutral pH.
A
acidic amino acids – Asp, Glu
15
Q
Name the amino acid(s) where Relatively poorly soluble in aqueous solution.
A
non-polar amino acids e.g. Leu,
Ala,
Val etc.
16
Q
Name the amino acid(s) where Positively charged at neutral pH.
A
basic amino acids – Lys, Arg
17
Q
Name the amino acid(s) where Side chains are capable of hydrogen bonding.
A
Ser, Asn, Gln, Trp, Thr, Cys, Tyr, His, Arg
(also Glu, Asp and Lys in their
unionised forms)
18
Q
Name the amino acid(s) where Have a basic side-chain.
A
Arg, Lys, His is sometimes included in the basic amino acids because in a protein
it’s pKa can increase to 7.4
19
Q
Name the amino acid(s) where Side chains are responsible for the hydrophobic cores of globular proteins.
A
non-polar amino acids
20
Q
Name the amino acid(s) where The amides of glutamic acid and aspartic acid.
A
glutamine,
asparagine
21
Q
The smallest amino acid (It also lacks a stereoisomer).
alanine, glycine, phenylalanine, glutamine
A
glycine
22
Q
An aromatic amino acid.
glutamic acid, tyrosine, isoleucine, serine
A
tyrosine
23
Q
A sulfur-containing amino acid.
methionine, aspartic acid, arginine, leucine
A
methionine
24
Q
An amino acid capable of forming sulfur-sulfur bonds.
methionine, proline, cysteine, tryptophan
A
cysteine
25
Which of these is not a group of amino acids?
(A) Polar
(B) Non-Polar
(C) Non-Polar Charged
(D) Polar Charged
(C) Non-Polar Charged
26
Explain the terms pKa
acid dissociation constant. pKa = -log10Ka.
The lower the value for pKa the stronger the acid, i.e. the more likely the acid is to be found in its dissociated/deprotonated state.
27
Explain pI
pH at which the net charge of a protein is zero.
28
Explain how pKa differs from pI
pKa describes the tendency for a given acid/acidic group to dissociate,
whereas pI is the isoelectric point of a molecule - the pH at which it carries no net charge.
29
List some common types of amino acid modifications.
```
Phosphorylation
Glycosylation
Methylation
Adenylation
Iodination
Metal Binding
```
30
Draw a dipeptide and circle the peptide bond.
6.)
C - N
31
Which molecule is removed during the formation of the peptide bond?
Water
32
What constraint does the planarity of the peptide bond place on the way in which
proteins can fold?
rigid nature of the planar peptide bond constrains rotations in the polypeptide chain to the bonds around the alpha-carbon.
The most favourable rotations produce the characteristic a-helix and b-sheet structures seen in secondary structure.
33
Name four main levels of protein structure
primary,
secondary,
tertiary,
quaternary.
34
Describe Primary structure
amino acid sequence of a protein.
35
Describe secondary structure
3D arrangement of amino acid residues over a short stretch of sequence.
36
Describe tertiary structure
3D structure of a complete protein chain.
37
Describe quaternary structure
Interchain packing and structure for a protein that contains multiple protein chains.
Not all proteins have a
quaternary structure,
38
Which level of protein structure determines the overall shape of a protein?
Primary
39
The formation of alpha helices and beta sheets early in the folding process is known
as:
Nucleation
40
What are the key properties of an alpha-helix?
3.6 residues per turn, at d = 1.5 Å with each turn having a pitch of 5.4Å.
The alpha-helix spiral is “right handed” and has all of the side chains pointing out from the helix axis.
Has a dipole. Means charges are equal and opposite.
41
Draw a parallel beta-sheet and an antiparallel beta-sheet
N - C terminus
Anti - H bonds vertical
Para - Bent / diagonal
42
How is and a-helical fold stabilised?
By hydrogen bonding between the backbone carbonyl oxygen of one amino acid and the amino hydrogen of another amino acid,
4 amino acid residues further along the polypeptide chain.
43
How might the arrangement of amino acids in an a-helix allow the helix to interact with both water and the non-polar core of a protein?
Amino acid side-chains "point out" from the helix (are perpendicular to the axis of the helix).
With an arrangement of polar amino acids on one side of the helix and non-polar residues on the other side,
a helix can interact with water on one side and the non-polar core on the other side
(in fact the non-polar residues on the internal face of the helix often form part of the non-polar core).
44
Pro is the amino acid least commonly found in a-helices but is commonly found in b-
turns. Why?
Proline forms kinks in an a-helix and cannot form H bonds, and destabilises alpha
helices.
Beta-turns provide for a change in direction in a polypeptide, thus the natural bend in proline is good for “turning a corner”.
45
What is supersecondary structure?
association of more than one element of secondary
| structure (typically in a recognisable pattern).
46
How many supersecondary structural elements make up a domain?
There is no clear answer to this. It may be one, two, three or more. What's important to
remember is that
domains form a distinct structure within a protein and have a particular function associated with them.
47
Explain how extremes of pH and detergents may cause proteins to unfold.
Extremes of pH affect the hydrogen bonding and ionic interactions that stabilise the protein.
Detergents can interact with the non-polar core of a protein and linearise (unfold) the protein.
48
How is the tertiary structure of a protein stabilised?
by interactions between amino acid side-chains.
These interactions include hydrogen bonds,
ionic interactions,
hydrophobic interactions and
disulphide bonds.
49
How is the folding of some proteins assisted in vivo?
Chaperones are proteins that help other proteins fold, and are involved in the folding of many proteins in vivo.
50
# Fill in the gaps
Haemoglobin comprises a protein component called ____
and a non-protein unit called ____.
The main structural feature of the ____ group is the metal ion ____,
which acts as a ____ carrier of ____ around the body.
```
globin
haem
haem
Fe(II) iron
reversible
oxygen
```
51
What is the specific name of the porphyrin ring found in haemoglobin?
Fe-protoporphyrin IX.
52
How is this porphyrin ring held in place by the globin chain?
via histidine F8 and hydrophobic interactions between the haem and the globin.
53
The Fe(II) in each globin chain has six coordination sites. Four of those sites complex with nitrogen atoms from the haem group. With what are the other two sites complexed?
His F8 and oxygen (in the oxyHb state).
54
How many a-helices are there in the b-haemoglobin chain?
8
55
Draw a diagram showing the relationship between O2 binding and O2 concentration
for Mb and Hb. Show on the graph the O2 concentration in the lungs and working
muscle.
Answer Lecture 7 & 8
| 6.
56
Discuss the effect that exercise has on Hb oxygen binding.
As exercise intensity increases there is an increase in [CO2] and a decrease in the pH of the environment around the muscle (including the blood).
Both cause the Hb binding curve to shift to the right
57
Discuss the effect that exercise has on Hb oxygen binding. Include a description of
how the metabolites produced in active muscle affect oxygen binding and the
physiological significance of this.
CO2 and H+ promote transition to the T state (which will favour the release of oxygen).
The physiological significance is that as exercise intensity increases, the requirement for oxygen to burn fuels (carbohydrates and fats) for energy also increases.
Thus the metabolites produced by exercising muscle (CO2 and H+) promote the release of oxygen from haemoglobin so that it can be used by the muscle to oxidise fuels for energy.
The increase in CO2 also
promotes the lowering of pH because of the shift in the carbonic acid equilibrium to
bicarbonate and protons.
58
What is allosteric binding?
Binding to a site other than the active site.
59
The binding of oxygen to Hb occurs in a cooperative way. What is cooperativity?
feature of allosteric proteins.
It means that the state of one subunit in a protein influences the state of other subunits in a protein.
For example in Hb, when 1 subunit switches from the T to the R state, the remaining subunits also switch to the R state.
(and vice-versa).
60
Explain the sigmoidal shape of haemoglobin's oxygen binding curve in the context of cooperativity.
At the bottom left of the curve where it is "flatish", the rate of oxygen binding (y- axis) only increases slowly with increase in substrate concentration (x-axis) because...
the subunits of the protein have a relatively low affinity for oxygen (T-state) and so the increasing the substrate concentration doesn't have a great effect. At some point one of the subunits changes
conformation to the high affinity state (R- state) and so increases the binding of substrate.
This helps other subunits change to the high affinity state (they cooperate with each other) and you get a rapid increase in oxygen binding (steep increase in slope of the graph).
61
How does 2,3 bisphosphoglycerate (BPG) bind to Hb?
BPG has five negative charges; it binds to a positively charged site at the centre of the Hb tetramer through ionic interactions.
62
What effect does BPG have on Hb oxygen binding? How does it have this effect?
BPG decreases Hb oxygen binding. It stabilises the T-state and thus promotes the release of oxygen.
63
Fetal haemoglobin has a ____ affinity for oxygen than does adult
haemoglobin because it has a ____ affinity for 2,3 bisphosphoglycerate.
higher
| lower
64
What are two types of macromolecules that can catalyse reactions?
Proteins and RNA
65
Which features distinguish enzymes from chemical catalysts?
specificity, (usually)
faster reaction rates,
milder reaction conditions, regulated reactions
66
Enzymes lower the ____ of a reaction making it ____. Because of this the ____ is reached more easily.
activation energy
lower
transition state
67
Draw a diagram/graph illustrating how an enzyme alters the free energy of activation for a biochemical reaction.
Answer in Lecture 9 -12
| 4.)
68
In which direction does an enzyme shift the equilibrium of the reaction?
Enzymes do not affect the equilibrium of a reaction.
69
True / False
Enzymes do not show stereospecificity.
False
70
what is "Lock and Key" of enzyme-substrate interaction?
substrate fits directly into the active site of an enzyme, stabilised by surrounding residues.
71
what is “induced fit” of enzyme-substrate interaction?
there is not a perfect complementary match between the enzyme active site and the substrate.
The binding of substrate changes the shape of the enzyme (and may change the substrate shape as well), to generate an "induced fit" between the active site and substrate.
Note that enzymes may preferentially bind to something (similar to) the
transition state for the particular reaction (a feature that is one aspect of achieving rate enhancement by enzymes).
72
What types of forces hold a substrate in the active site of an enzyme?
Non-covalent interactions (though temporary covalent bonds may form as part of the
reaction sequence in changing substrate to product).
73
At low substrate concentrations (relative to enzyme concentration), what is the relationship between substrate concentration and reaction velocity?
Linear (directly proportional).
74
An enzyme which obeys Michaelis-Menton kinetics produces a rectangular hyperbola shaped graph when velocity is plotted against substrate concentration. Explain why the curve has this shape.
At low [S] the relationship is linear,
At high [S] concentrations the enzyme is working at its maximum rate (it is saturated with substrate) and the graph levels/flattens off (rate becomes independent of concentration).
75
What does k1 represent?
rate of formation of the ES complex,
76
What does k-1 represent?
rate of dissociation of the ES complex to E + S,
77
What does k2 represent?
rate of dissociation of the ES complex to E + P (rate of product formation).
78
Give two algebraic expressions for KM (other than the Michaelis-Menton equation).
KM = (k-1+k2) / k1,
KM = [S] @ V=Vmax / 2
79
If the rate constant k2 is much smaller than k-1, what does KM approximate?
KM= k-1/k1 =Kd (Ks),
| the dissociation constant for ES
80
What is the relationship between Vmax and enzyme concentration?
Vmax is dependent on enzyme concentration.
Vmax = [E]t x kcat.
Vmax is reached when all
enzyme active sites are occupied by substrate.
81
Draw a Lineweaver-Burk plot. Make sure your graph is fully labelled, including Vmax
and KM.
Answer lecture 9 - 12
| 15.)
82
How does knowledge of enzymes enable for the development of treatments?
If we know the structure/function of an enzyme, we can take advantage of this in drug
design.
Such drugs often act as enzyme inhibitors to change disease pathology. For example, a transition state analog can be designed that will bind tightly to the enzyme active site. If this occurs, the normal substrate cannot bind, and therefore the normal enzymatic reaction will not take place.
83
What are the key differences and similarities between an enzyme and a receptor?
An enzyme
- single active site binds substrates,
- changes substrates into a product.
- membrane bound or free in cytosol.
Receptors
- several binding sites, bind ligands
- release them unchanged.
- membrane bound or free in the cytosol.
Both enzymes and receptors can be used as drug targets.
84
Describe the events that occur upon alcohol binding to its receptor.
Alcohol is an agonist of the GABAa receptor.
- inhibitory receptor, when activated, it decreases the general activity in the nervous system.
When alcohol binds to the receptor,
- opens the receptor allowing chloride ions into the cell.
- decreases nervous system activity
- loss of coordination, memory loss, slurred speech etc.
The effects are dose dependent.
85
Briefly outline the process of drug design. Using Saquinivir as an example.
Drugs work best when they are targeting a non-human factor.
If looking at HIV for
example, you need to find an enzyme that is vital to the replicative cycle of the virus, but not found in humans.
For example, HIV protease. We can then use features of the enzyme to design a drug inhibitor
Specifically, taking advantage of the active site, the fact that
enzymes have preferred substrates, and the fact that enzymes can be inhibited
competitively.
The inhibitor is then designed to mimic the transition state of the normal enzyme-substrate complex. This will hopefully bind tightly to the active site, and inhibit it.
86
```
What is the difference between a reversible and non-reversible inhibitor? What class
do competitive and non-competitive inhibitors fall into?
```
An inhibitor
- compound that binds to an enzyme and reduces its activity.
A reversible inhibitor
- binds covalently to the enzyme, which a reversible inhibitor is not covalently bound to the enzyme.
- either competitive or non-competitive.
87
What effect do competitive and non-competitive inhibitors have on Vmax and KM?
Draw a Lineweaver-Burk plot in the absence of inhibitor and in presence of both types
of inhibitor.
Competitive inhibitor – no change in Vmax, KM increases
Non-competitive inhibitor – Vmax decreases, no change in KM
88
What effect do Competitive inhibitor have on Vmax and KM?
Lineweaver-Burk plot
no change in Vmax,
| KM increases
89
What effect do non Competitive inhibitor have on Vmax and KM?
Lineweaver-Burk plot
Vmax decreases,
| no change in KM
