Proteins Flashcards
(146 cards)
1
Q
Which AA is actually an imino acid?
A
Proline (P)
2
Q
What’s supersecondary structure?
A
The close association of more than one piece of secondary structure into a functional unit.
3
Q
What parts of a protein interact to stabilise the tertiary structure of a protein?
A
The side chains of the amino acids
4
Q
Which area of the Ramachandran plot are the phi-psi angles mostly found in:
- beta sheet
- alpha helix
A
- beta = top left
2. alpha = bottom left quadrant (closer to centre)
5
Q
Where are hydrophobic amino acids commonly found in a protein?
A
In the core
6
Q
What do the hydrophobic bonds that non polar AAs form provide energy for?
A
Protein folding
7
Q
What do chaperones do?
A
Bind to proteins and help with the correct folding of a protein (incl. preventing incorrect folding)
8
Q
What type of bond found in a protein is planar and rigid?
A
Peptide bond
9
Q
What was the key finding from Afinson’s experiment on protein folding?
A
All information required for a protein to fold correctly is found in the primary AA sequence.
10
Q
Which AA is commonly found in a beta-turn?
A
Proline
11
Q
What is quaternary structure?
A
The association of more than one polypeptide chain in a functional protein
12
Q
What is the Ramachandran plot?
A
A prediction of allowed rotations of phi and psi
13
Q
Phosphorylation is a common posttranlational modification catalysed by what?
A
Kinases
14
Q
How does phosphorylation regulates protein activity?
A
By introducing a conformational change
15
Q
What vitamin is a required cofactor in gamma carboxylation?
A
Vitamin K
16
Q
What is the insulin receptor regulated by?
A
Phosphorylation
17
Q
Define primary protein structure.
A
Amino acid sequence
18
Q
Define secondary protein structure.
A
3D arrangement of AAs over a short stretch of sequence.
19
Q
Define tertiary protein structure.
A
Collection of secondary structures, which make up a 3D structure
20
Q
Define quaternary structure.
A
Made up of 2 or more tertiary structures
21
Q
Which rotation angle does phi represent?
A
N-C bond (alpha carbon)
22
Q
Which rotation angle does psi represent?
A
C-C bond
23
Q
What are the two Phi-Psi restrictions? (due to steric hinderance)
A
- Phi rotation can lead to O-O collisions
2. Psi rotation can lead to NH-NH collisions
24
Q
Which rotation angle does omega represent?
A
C-N bond (peptide bond)
25
What are the 2 characteristics of a peptide bond?
- Planar
| - Trans (side chains alternating sides w/ carboxyl group)
26
What rotation angle does chi represent?
Side chain angles
27
What are the 2 types of protein secondary structure?
1. Alpha helix
| 2. B-strand/B-sheet
28
What are the properties of the alpha-helix?
- 3.6 residues/turn
- H-bond b/w n & n+4 AA
- Side chains point out from helix (polar on one side, non-polar on the other)
29
Which 2 AA are unfavourable for alpha-helix formation?
1. Proline (too bulky, introduces sharp turn)
| 2. Glycine (too flexible)
30
What is the approximate pKa for:
1. NH3+ groups
2. COO- groups
1. > 8
| 2. < 3
31
What are secondary structures stabilised by ...? Formation of these are called?
Hydrogen bonds
| Nucleation
32
What is the beta structure?
Adjacent peptide chains (B-strands) that have an extended type structure that allows for H-bonding b/w chains
33
What are the two types of interaction in a B sheet?
1. Parallel (B-strands in same direction)
| 2. Antiparallel (B strands in opposite direction)
34
Properties of beta structure
- pleated w/ right hand twist
| - side chains above and below the sheet (polar on one side, non-polar on the other)
35
What is the direction of a beta-strand?
N --> C
36
What are the bonds which stabilise the tertiary structure of a protein? (4 weak, 1 strong)
1. H-bonds
2. Electrostatic interactions
3. Metal ion coordination
4. Hydrophobic interactions
5. Disulfide bonds
37
What type of bonds hold quaternary protein structures together?
Weak/non-covalent
38
What are 4 examples of quaternary structure? I.e. combinations
1. homodimer
2. heterodimer
3. homotetramer
4. hetertetramer
39
Define super secondary structure
Combinations of secondary structures that form recognisable patterns. Connected by loops, turns and coils.
40
Define domains/motifs.
| What is the difference b/w them?
- Combinations of super secondary structures that form independently folded regions that have a specific function.
- Domains have a hydrophobic core (due to being larger/having more super secondary structures)
41
What are the 3 protein types w/ regard to chaperones?
| What is protein folding driven by?
1. Chaperone-independent
2. Chaperone-dependent (doesn't require energy)
3. Chaperonin-dependent (requires energy)
Driven by hydrophobic interactions
42
What is the order of protein folding?
1. Formation of short secondary structures
2. Several/many nuclei come together to form domains
3. Several/many domains come together to form the ALMOST final 3D tertiary configuration
4. Small conformational adjustments take place to give the final native tertiary structure
43
What are the 5 steps of the Afinsen experiment?
1. Native protein
2. Add denaturing agents
3. Denature protein
4. Remove denaturing agents
5. Protein re-folded correctly
44
Which enzyme is involved in phosphorylation?
| Which enzyme removes the phosphate group?
- Kinase
| - Phosphatase
45
What is the importance of phosphorylation?
It introduces a conformational change that either activates or inactivates protein function.
Bc the -vely charged phosphate will attract/repel nearby +ve/-ve groups
46
What are 2 examples of phosphorylation?
1. Insulin receptor
| 2. Na+/K+ pump
47
Which enzyme is involved with hydroxylation?
| Which cofactors does the enzyme need?
- Hydroxylases
| - Vitamin C and Fe2+
48
What is the importance of hydroxylation?
Facilitates H-bond formation
49
What is an example of hydroxylation?
Collagen (contains high proportion of hydroxy proline and hydroxy lysine)
50
What condition does vitamin C deficiency lead to?
Scurvy
51
What enzyme is involved in Gamma carboxylation?
| What cofactor does it need?
Carboxylase
| Vitamin K
52
What is the importance of gamma carboxylation?
Allows two COO- groups to bind to a Ca2+ ion
--> conformational change
(active form (Gla residue) differs from inactive form (Glucose residue))
53
What is an example of gamma carboxylation?
blood clotting pathway
54
What is the structure of Hb?
Tetramer
55
Which has a higher affinity for oxygen: Haemoglobin or myoglobin?
Myoglobin
56
What does the binding of oxygen do to Hb?
Changes its shape (deoxy-Hb has larger central cavity)
57
What is the function of myoglobin?
Store oxygen in muscle cells
58
What is the function of haemoglobin?
Transfer oxygen in blood
59
What 3 things contribute to the efficiency of haemoglobin in releasing oxygen? What do they all have in common (in terms of function)?
1. BPG
2. Elevated carbon dioxide
3. Elevated H+ ions
~All reduce the binding affinity of Hb
60
BPG binds to which part of haemoglobin?
The central pocket/space between the subunits
61
BPG and low pH have an effect on haemoglobin by stabilising which conformation of the globin subunits?
T-state
62
What is the common feature of tyrosine, threonine and serine, that allows them to be phosphorylated?
all have a hydroxyl (OH) in their side-chain
63
What is the pKa of the alpha-carboxyl groups in the 20 standard amino acids?
Approx. 2
64
What AAs does the structure of alpha-helices have in high frequencies?
Proline and glycine
65
What are post-translational modifications?
covalent changes to a protein
66
How does the proteolysis of proteins activate proteins?
By releasing peptides that normally inhibit function, and/or allowing for a conformational (shape) change to the active form of the protein
67
What is the configuration of most biological AAs?
L-configuration
68
What type of atoms do uncharged polar AAs have on their side chains?
Electronegative atoms (e.g. O, S)
69
What is the function of turns in protein structure?
Combine secondary structures
70
What is a domain?
A combination of super secondary structures
| e.g. fridge, oven, microwave in a flat
71
What is protein folding guided by?
Internal hydrophobic residues (bc they try to avoid water)
72
What causes protein unfolding?
Stress on the native structure, which causes it to fold to accommodate a changing environment
73
What is a PTM?
Chemical modifications to AA side chains
74
What PTM is important for activating blood clotting cascade proteins? What is used to inhibit this activation and reduce clotting?
- Carboxylation
| - Warfarin
75
Which AAs does hydroxylation happen to?
Proline and Lysine
76
What does each subunit (in Hb and Mb) have? What are they labelled?
8 alpha-helices (A-H)
77
4 haem Fe ligand attachment sites are occupied by which atoms?
N atoms
78
In which state can haem Fe bind oxygen?
Fe2+
ferrous
reduced
79
One of the N atoms bound to haem Fe is from the side chain of which AA?
His F8
| i.e. the 8th AA of the F helix
80
What does His E7 do in terms of haem Fe?
1. Prevents oxidation of haem Fe when oxygen binds
2. Ensures weakish binding of oxygen to ensure binding is reversible
3. Prevents other gases (e.g. CO) from binding too strongly
81
How does the binding of oxygen to the haem Fe change the function of haemoglobin?
Changes the size and position of haem Fe which allows it to fit into the structural cavity; this changes the position of the other subunits; change of structure = change of function.
82
What are the relative oxygen binding affinities of the T- and R-state of Hb?
```
T-state = low oxygen affinity
R-state = high oxygen affinity
```
83
What feature does the concerted model propose for the subunits in Hb?
All subunits are ALWAYS in the same configuration (T- or R-state)
84
How does the foetus obtain oxygen from the mother's bloodstream via the placenta?
HbF has a greater affinity for oxygen than HbA bc BPG binds less tightly to HbF.
This is bc in HbF there are only 2 (+ve) His side chains interacting w/ (-ve) BPG, compared to 4 in HbA
85
STATE the 3 single AA mutations of Hb
1. HbS (sickle cell)
2. Met-Hb (HbM)
3. HbChristchurch (HbChCh)
86
Function of enzymes?
Catalyse thermodynamically favourable reactions by lowering the activation energy
87
Features of enzyme catalysed reactions?
1. Much faster reaction rate
2. Much milder reaction conditions (pH and temp)
3. Reaction specificity
4. Tightly regulated
88
What is the purpose of enzyme classification?
| Classes of enzymes and the type of reaction they catalyse?
- Clarity
LILHOT:
1. Lyases: Non-hydrolytic breaking or making of bonds
2. Isomerases: transfer of atoms/groups within a molecule to yield an isomeric form
3. Ligases: join two molecules together (form new bond, condensation reaction)
4. Hydrolases: hydrolysis reactions
5. Oxidoreductases: redox (e- transfer)
6. Transferases: transfer of functional group
89
Describe the two types of cofactor
1. Metal ions
- Acid-base catalysis (bc Lewis acids/e- acceptors)
- Form coordination compounds w/ precise geometries
2. Coenzymes
- Small organic molecules
- Co-substrates
- Carries (of electrons, atoms or functional groups)
- Often derived from vitamins
90
3 general features of enzyme active site
1. Has AA side chains projecting into it
2. Binds the substrate via several weak interactions
3. Determines the specificity of the reaction
91
Why are weak interactions b/w enzyme active site and substrate advantageous?
Ensures specificity and reversability
92
What does geometric and stereospecificity allow an enzyme to do? (provided the active site is asymmetric)
Distinguish b/w identical groups on a substrate
93
What is the induced fit model? What does it say about the nature of enzymes?
- Enzyme undergoes conformational change upon binding to the substrate; active site becomes complementary to the shape of the substrate
- Enzymes are dynamic, NOT static
94
How is the activation energy lowered in enzyme mechanisms?
1. Ground state destabilisation and transition state stabilisation (by active site having shape/charge complementary to the TRANSITION state, not the substrate)
2. Alternate reaction pathway with a lower transition state
95
State/explain the 5 catalytic mechanisms
1. Preferential binding of the transition state
2. Proximity and orientation effects (molecules must be close together and in the right orientation)
3. Acid-base catalysis (involves H+ transfer)
4. Metal ion catalysis
- metal ions: provide substrate orientation, polarise H2O or other functional groups (bc can act as e- acceptor), provide site for redox reactions
5. Covalent catalysis
- involves the formation of a reactive, short-lived intermediate which is covalently attached to the enzyme
96
What is K(M)?
| M is subscript
- The conc. of substrate needed to reach half Vmax. (maximum reaction rate)
- Low Km = high affinity b/w E and S
97
What is Kcat?
| cat is subscript
- Is a measure of catalytic activity
I.e. is the no. of substrate molecules converted to product per enzyme per unit of time (when E is saturated with substrate)
98
What is the overall efficiency of an enzyme given by?
Kcat / Km
99
Irreversible vs. reversible inhibitors
Irreversible: binds covalently to the enzyme and permanently inactive it
Reversible: Non-covalently binds to the enzyme, and can be released after binding to leave the enzyme in its original condition
100
Compare the two types of reversible inhibitors (incl. changes to enzyme kinetics)
1. Competitive:
- competes directly w/ the substrate for the active site
- No change in Vmax (infinite substrate conc. outcompetes inhibitor)
- Increases Km (more substrate is needed to get to V=Vmax/2)
2. Non-competitive inhibitors
- bind at different site to the substrate
- enzyme can bind to substrate, inhibitor, or both
- Change in kinetics depends on which inhibitor it is (pure or mixed)
101
Compare the two types of non-competitive inhibitor
1. Pure
- Binding has no effect on binding of S, but slightly changes active site so not optimal fit
- Vmax decreases, Km stays the same
2. Mixed
- Binding has effect on binding of S
- Vmx decreases, Km increases
102
Why is feedback inhibition important in enzyme regulation?
Prevents the synthesis of unnecessary metabolic intermediates
103
What are the two types of allosteric enzyme and how do they act?
Allosteric inhibitor - stabilises T form (need more substrate to reach the same velocity)
Allosteric activator - stabilises R state (need less substrate to reach the same velocity)
Both undergo conformational change when a substrate binds.
104
How are recombinant human proteins made?
1. DNA encoding gene of interest
2. Clone DNA into an expression plasmid
3. Transfer plasmid into cell (of choice)
4. Let the cell multiply
- gene expressed
- gene transcribed (into mRNA)
- gene translated (into protein)
- lots of protein made
105
Advantages & disadvantages of prokaryotic systems for recombinant human proteins
```
Advantages:
1. Cheap
2. High yield (protein)
3. Pathogen free
Disadvantages
1. Proteins often partially folded
2. Can't perform PTMs
```
106
What type of cell is used to create therapeutic proteins in eukaryotic animal cells?
Chinese Hamster Ovary cells (CHO cells)
107
What type of cell is used to create proteins that require PTMs? What's an example of one of these proteins?
- Eukaryotic animal cells (CHO cells)
| - Example: EPO (needs glycosylation)
108
Advantages & disadvantages of Eukaryotic systems for recombinant human proteins
```
Advantages:
- Can do most PTMs
- Proteins usually folded
Disadvantages:
- Expensive
- Low yield
- Potential for pathogens
- Can't do some PTMs
```
109
Advantages and disadvantages of using whole animals to make recombinant proteins & an example of protein made this way
Advantages:
1. All types of PTMs
2. Easy extraction of protein from animals' milk is possible
3. Large quantities of protein produced
Disadvantages
1. Expensive, labour intensive, time consuming
2. Some approaches require sacrifice of animal
Example: Antithrombin (anti-blood clotting factor)
110
What is gene therapy and how does it work?
- provides a cure for a disease/condition (permanent fix)
- Gene that encodes the recombinant protein is placed into the patient using viral vectors (plasmids) so they can produce their own proteins
111
How does CRISPR-Cas work?
- Uses DNA to correct genome
- Process:
1. Recruitment of Cas9 (enzyme) via guide RNA, which binds complementary DNA sequence
2. Cas9 cleaves DNA --> double strand breaks
3. Repair of DNA by non-homologous end-rejoining (often causing mutations)
4. If a donor sequence (desired gene) is present in the nucleus, homologous recombination can occur (either to fix or create mutations or inserted DNA)
112
Uses of CRISPR-Cas
1. Create a disease model (can be used to study the disease)
| 2. Correct mutations caused during DNA repair
113
Melanin:
- What is it?
- Produced by? How?
- Pigment (quantity determines colour of skin)
- Produced by melanocytes
- Enzymatic conversion of tyrosine by tyrosinase
114
What is keytruda and how does it work?
- Therapeutic antibody which targets the immune system (used to treat melanoma)
- How melanoma tumour cells act:
1. T cell recognises antigen on tumour cell
2. Tumour cell fights back by up-regulating expression of membrane protein PDL-1
- the interaction of PDL-1 with PD1 down-regulates (silences) T cell and thus prevents it from activating the immune system and destroying the tumour cell
- How keytruda treats melanoma:
Interferes with PD1/PDL-1 interaction, which allows the T cell to continue functioning; does this using an antibody that binds to PD1 on the T cell
(antibodies produced using CHO cells)
115
What are the variants of tyrosinase (Tyr) and their causes?
1. Albinism (loss of function of Tyr)
2. Vitaligo (autoimmune loss, antibodies target Tyr)
3. Siamese (temperature-sensitive mutant)
116
How does the activity of tyrosinase influence risk of melanoma?
Less activity = fairer skin = less pigment (melanin) = increased risk of melanoma
117
Explain the 3 core principles of toxicology using nitrates as an example
1. Dose: nitrates are toxic at high levels (higher risk in rural areas where more fertiliser is used)
2. Route of exposure: oral exposure from contaminated water is the most likely ROE for nitrates
3. Who you are: size is important, i.e. babies and foetus' are more at risk (HbF more readily oxidised), and fish & cattle can suffer nitrate poisoning
118
How can we be exposed to nitrogen?
1. Drinking contaminated water
- fertiliser contamination
- formula reconstituted w/ contaminated water (infants)
2. Diet
- Preservatives in food contain nitrates and nitrites
- Fruit and veg (accumulate N from fertiliser)
119
Toxicity of nitrate vs. nitrite
Nitrate (NO3)
- Least toxic; only toxic when converted to nitrite
Nitrite
- toxic:
- reacts w/ Fe2+ and converts it to Fe3+, i.e. prevents O2 from binding to Hb
120
Symptoms of nitrite poisoning
- Correlate to lack of O2 carrying ability: difficulty breathing, blue skin around lips, increased pulse, dizziness
121
What is used to treat nitrite poisoning and how does it work?
- Methylene blue
- Reduces Fe3+ in MetHb to Fe2+
(acts in the same way as metHb reductase)
122
Why are infants more susceptible to nitrite poisoning?
1. Have a high GI pH (increases conversion of nitrate to nitrite)
2. MetHb reductase system not fully developed --> lower MetHb reductase activity
123
Why are foetus' more susceptible to nitrite poisoning?
HbF has different subunits to HbA, therefore:
1. Has a higher affinity for oxygen
2. Is more readily oxidised by NO2 to MetHb
124
How are cattle and fish exposed to nitrite poisoning?
Cattle: consume toxic amounts of nitrate
Fish: eutrophication and directly (formation of MetHb, same as humans)
125
What's a receptor
receives chemical signals from outside the cell
126
Enzyme vs. receptor
- Enzymes have 1 active site, receptors have several binding sites
- Enzymes bind substrates, receptors bind ligands
- Enzyme changes substrate to form product, receptors release ligand unchanged
127
How does Aspirin work? Why does it have side effects? How can these be prevented?
- Competitive inhibitor of the COX-2 enzyme, which stops the production of inflammatory signals
- Also inhibits COX-1, which helps regulate the release of stomach acid. Thus, inhibition causes stomach ulcers
- Make it more selective (i.e. only bind to COX-2)
128
How can you reduce the side effects of a drug?
Increase its selectivity
129
How does alcohol (ethanol) work?
| Effects of low/high dose?
- acts as an agonist at the GABA receptor (a ligand-gated Chloride channel)
- Process
1. Opens the channel (via binding)`
2. Influx of Cl- into cell
3. decreased activity in the NS (brain)
4. Loss of coordination, slurred speech, etc.
- low dose = relaxation, loss of inhibitions
- high dose = coma or death
130
How does marijuana work?
- (THC) acts as an agonist at the cannabinoid (CB) receptor
- CB receptor:
* G-protein coupled receptor (thus has inhibitory and stimulatory effects simultaneously)
* Two forms:
1. CB1 - high conc. in brain; activation causes psychoactive effects (hallucinations, appetite stimulation, euphoria, anxiety, relaxation)
2. CB2 - found in the body (spleen and pancreas)
131
Composition of phospholipid and respective hydrophobicity. What causes variation?
- Composition:
Head: phosphate connected to glycerol, hydrophilic
Tail: two fatty acids, hydrophobic
- Variation:
Differ by what's on the side chain of the phosphate group
132
What determines the speed of movement of phospholipids? I.e. lateral and rotational movement is fast, whereas transverse movement is very slow
The interaction b/w the hydrophobic and hydrophilic regions
133
What factors affect membrane fluidity? How?
1. Temperature
- High temp = high KE = breaking of Van der Waals interactions = increased fluidity
- Low temp = low KE = close packing = decreased fluidity
2. Type of fatty acid
- Chain length of hydrocarbon tails = strength of interaction bc of VdW interactions (short chain = less intrctn = more fluid)
3. Presence of cholesterol
- effect depends on temp:
* low temp = maintains fluidity (prevents close packing)
* high temp = maintains integrity (prevents excessive movement)
134
How can membrane proteins stay in the membrane?
1. Anchored by hydrophobic AAs
2. Partially inserted proteins (a hydrophobic domain inserted into the membrane)
3. Fatty acids (post-translational addition of lipids)
135
What factors effect the transport of non polar molecules across the membrane?
1. Hydrophobicity (incr. = incr. permeability)
| 2. Concentration (incr. = incr. rate of transport)
136
Define non-mediated transport
Doesn't require protein
137
What are the nonpolar amino acids?
Ala, Cys, Gly, Isoleucine, Leu, Met, Phenylalanine, Tryptophan, Val
138
What are the uncharged polar AAs?
Asparagine, Glutamine, Ser, Tyr, Threonine
139
What are the charged polar AAs?
Glu, aspartic acid, arginine, His, Lys
140
Define agonist
- Agonist: chemical which increases action of receptors
141
Define ligand
Any molecule that binds to a receptor
142
Define mediated transport
Uses protein
143
Define co-transport (symport and antiport)
Movement of 2 molecules by a transporter; no ATP used
- symport = both move in same direction
- antiport = molecules move in opposite directions
144
Describe the HbS (sickle cell) AA mutation
- AA change
- What it causes
- Significant or insignificant change
- Glu (polar) --> Val (non-polar)
- The mutation enables hydrophobic interaction b/w Hb molecules, causing polymerisation of Hb into chains that distort RBCs; RBCs then get stuck in capillaries
- Dramatic change
145
Describe the Met-Hb (HbM) AA mutation
- AA change
- What it causes
- Significant or insignificant change
- Fe2+ oxidised to Fe3+
- Causes poor binding of Oxygen, since the Fe is no longer electrochemically held in the Fe2+ state
- Dramatic change
146
Describe the HbChristchurch (HbChCh) AA mutation
- AA change
- What it causes
- Significant or insignificant change
3. HbChristchurch (HbChCh)
- Phe (large, non polar) --> Ser (small, polar)
- Slightly destabilises haem
- Has less severe effect than (1) and (2)
