Proteins Flashcards

1
Q

Which AA is actually an imino acid?

A

Proline (P)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What’s supersecondary structure?

A

The close association of more than one piece of secondary structure into a functional unit.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What parts of a protein interact to stabilise the tertiary structure of a protein?

A

The side chains of the amino acids

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Which area of the Ramachandran plot are the phi-psi angles mostly found in:

  1. beta sheet
  2. alpha helix
A
  1. beta = top left

2. alpha = bottom left quadrant (closer to centre)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

Where are hydrophobic amino acids commonly found in a protein?

A

In the core

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What do the hydrophobic bonds that non polar AAs form provide energy for?

A

Protein folding

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What do chaperones do?

A

Bind to proteins and help with the correct folding of a protein (incl. preventing incorrect folding)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

What type of bond found in a protein is planar and rigid?

A

Peptide bond

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
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.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Which AA is commonly found in a beta-turn?

A

Proline

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What is quaternary structure?

A

The association of more than one polypeptide chain in a functional protein

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What is the Ramachandran plot?

A

A prediction of allowed rotations of phi and psi

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Phosphorylation is a common posttranlational modification catalysed by what?

A

Kinases

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

How does phosphorylation regulates protein activity?

A

By introducing a conformational change

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What vitamin is a required cofactor in gamma carboxylation?

A

Vitamin K

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What is the insulin receptor regulated by?

A

Phosphorylation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

Define primary protein structure.

A

Amino acid sequence

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

Define secondary protein structure.

A

3D arrangement of AAs over a short stretch of sequence.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

Define tertiary protein structure.

A

Collection of secondary structures, which make up a 3D structure

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

Define quaternary structure.

A

Made up of 2 or more tertiary structures

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

Which rotation angle does phi represent?

A

N-C bond (alpha carbon)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

Which rotation angle does psi represent?

A

C-C bond

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

What are the two Phi-Psi restrictions? (due to steric hinderance)

A
  1. Phi rotation can lead to O-O collisions

2. Psi rotation can lead to NH-NH collisions

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

Which rotation angle does omega represent?

A

C-N bond (peptide bond)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

What are the 2 characteristics of a peptide bond?

A
  • Planar

- Trans (side chains alternating sides w/ carboxyl group)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

What rotation angle does chi represent?

A

Side chain angles

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

What are the 2 types of protein secondary structure?

A
  1. Alpha helix

2. B-strand/B-sheet

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

What are the properties of the alpha-helix?

A
  • 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)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

Which 2 AA are unfavourable for alpha-helix formation?

A
  1. Proline (too bulky, introduces sharp turn)

2. Glycine (too flexible)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

What is the approximate pKa for:

  1. NH3+ groups
  2. COO- groups
A
  1. > 8

2. < 3

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

What are secondary structures stabilised by …? Formation of these are called?

A

Hydrogen bonds

Nucleation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

What is the beta structure?

A

Adjacent peptide chains (B-strands) that have an extended type structure that allows for H-bonding b/w chains

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

What are the two types of interaction in a B sheet?

A
  1. Parallel (B-strands in same direction)

2. Antiparallel (B strands in opposite direction)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

Properties of beta structure

A
  • pleated w/ right hand twist

- side chains above and below the sheet (polar on one side, non-polar on the other)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

What is the direction of a beta-strand?

A

N –> C

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

What are the bonds which stabilise the tertiary structure of a protein? (4 weak, 1 strong)

A
  1. H-bonds
  2. Electrostatic interactions
  3. Metal ion coordination
  4. Hydrophobic interactions
  5. Disulfide bonds
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

What type of bonds hold quaternary protein structures together?

A

Weak/non-covalent

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

What are 4 examples of quaternary structure? I.e. combinations

A
  1. homodimer
  2. heterodimer
  3. homotetramer
  4. hetertetramer
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
39
Q

Define super secondary structure

A

Combinations of secondary structures that form recognisable patterns. Connected by loops, turns and coils.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
40
Q

Define domains/motifs.

What is the difference b/w them?

A
  • 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)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
41
Q

What are the 3 protein types w/ regard to chaperones?

What is protein folding driven by?

A
  1. Chaperone-independent
  2. Chaperone-dependent (doesn’t require energy)
  3. Chaperonin-dependent (requires energy)

Driven by hydrophobic interactions

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
42
Q

What is the order of protein folding?

A
  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
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
43
Q

What are the 5 steps of the Afinsen experiment?

A
  1. Native protein
  2. Add denaturing agents
  3. Denature protein
  4. Remove denaturing agents
  5. Protein re-folded correctly
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
44
Q

Which enzyme is involved in phosphorylation?

Which enzyme removes the phosphate group?

A
  • Kinase

- Phosphatase

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
45
Q

What is the importance of phosphorylation?

A

It introduces a conformational change that either activates or inactivates protein function.
Bc the -vely charged phosphate will attract/repel nearby +ve/-ve groups

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
46
Q

What are 2 examples of phosphorylation?

A
  1. Insulin receptor

2. Na+/K+ pump

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
47
Q

Which enzyme is involved with hydroxylation?

Which cofactors does the enzyme need?

A
  • Hydroxylases

- Vitamin C and Fe2+

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
48
Q

What is the importance of hydroxylation?

A

Facilitates H-bond formation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
49
Q

What is an example of hydroxylation?

A

Collagen (contains high proportion of hydroxy proline and hydroxy lysine)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
50
Q

What condition does vitamin C deficiency lead to?

A

Scurvy

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
51
Q

What enzyme is involved in Gamma carboxylation?

What cofactor does it need?

A

Carboxylase

Vitamin K

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
52
Q

What is the importance of gamma carboxylation?

A

Allows two COO- groups to bind to a Ca2+ ion
–> conformational change
(active form (Gla residue) differs from inactive form (Glucose residue))

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
53
Q

What is an example of gamma carboxylation?

A

blood clotting pathway

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
54
Q

What is the structure of Hb?

A

Tetramer

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
55
Q

Which has a higher affinity for oxygen: Haemoglobin or myoglobin?

A

Myoglobin

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
56
Q

What does the binding of oxygen do to Hb?

A

Changes its shape (deoxy-Hb has larger central cavity)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
57
Q

What is the function of myoglobin?

A

Store oxygen in muscle cells

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
58
Q

What is the function of haemoglobin?

A

Transfer oxygen in blood

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
59
Q

What 3 things contribute to the efficiency of haemoglobin in releasing oxygen? What do they all have in common (in terms of function)?

A
  1. BPG
  2. Elevated carbon dioxide
  3. Elevated H+ ions
    ~All reduce the binding affinity of Hb
60
Q

BPG binds to which part of haemoglobin?

A

The central pocket/space between the subunits

61
Q

BPG and low pH have an effect on haemoglobin by stabilising which conformation of the globin subunits?

A

T-state

62
Q

What is the common feature of tyrosine, threonine and serine, that allows them to be phosphorylated?

A

all have a hydroxyl (OH) in their side-chain

63
Q

What is the pKa of the alpha-carboxyl groups in the 20 standard amino acids?

A

Approx. 2

64
Q

What AAs does the structure of alpha-helices have in high frequencies?

A

Proline and glycine

65
Q

What are post-translational modifications?

A

covalent changes to a protein

66
Q

How does the proteolysis of proteins activate proteins?

A

By releasing peptides that normally inhibit function, and/or allowing for a conformational (shape) change to the active form of the protein

67
Q

What is the configuration of most biological AAs?

A

L-configuration

68
Q

What type of atoms do uncharged polar AAs have on their side chains?

A

Electronegative atoms (e.g. O, S)

69
Q

What is the function of turns in protein structure?

A

Combine secondary structures

70
Q

What is a domain?

A

A combination of super secondary structures

e.g. fridge, oven, microwave in a flat

71
Q

What is protein folding guided by?

A

Internal hydrophobic residues (bc they try to avoid water)

72
Q

What causes protein unfolding?

A

Stress on the native structure, which causes it to fold to accommodate a changing environment

73
Q

What is a PTM?

A

Chemical modifications to AA side chains

74
Q

What PTM is important for activating blood clotting cascade proteins? What is used to inhibit this activation and reduce clotting?

A
  • Carboxylation

- Warfarin

75
Q

Which AAs does hydroxylation happen to?

A

Proline and Lysine

76
Q

What does each subunit (in Hb and Mb) have? What are they labelled?

A

8 alpha-helices (A-H)

77
Q

4 haem Fe ligand attachment sites are occupied by which atoms?

A

N atoms

78
Q

In which state can haem Fe bind oxygen?

A

Fe2+
ferrous
reduced

79
Q

One of the N atoms bound to haem Fe is from the side chain of which AA?

A

His F8

i.e. the 8th AA of the F helix

80
Q

What does His E7 do in terms of haem Fe?

A
  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
Q

How does the binding of oxygen to the haem Fe change the function of haemoglobin?

A

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
Q

What are the relative oxygen binding affinities of the T- and R-state of Hb?

A
T-state = low oxygen affinity
R-state = high oxygen affinity
83
Q

What feature does the concerted model propose for the subunits in Hb?

A

All subunits are ALWAYS in the same configuration (T- or R-state)

84
Q

How does the foetus obtain oxygen from the mother’s bloodstream via the placenta?

A

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
Q

STATE the 3 single AA mutations of Hb

A
  1. HbS (sickle cell)
  2. Met-Hb (HbM)
  3. HbChristchurch (HbChCh)
86
Q

Function of enzymes?

A

Catalyse thermodynamically favourable reactions by lowering the activation energy

87
Q

Features of enzyme catalysed reactions?

A
  1. Much faster reaction rate
  2. Much milder reaction conditions (pH and temp)
  3. Reaction specificity
  4. Tightly regulated
88
Q

What is the purpose of enzyme classification?

Classes of enzymes and the type of reaction they catalyse?

A
  • 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
Q

Describe the two types of cofactor

A
  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
Q

3 general features of enzyme active site

A
  1. Has AA side chains projecting into it
  2. Binds the substrate via several weak interactions
  3. Determines the specificity of the reaction
91
Q

Why are weak interactions b/w enzyme active site and substrate advantageous?

A

Ensures specificity and reversability

92
Q

What does geometric and stereospecificity allow an enzyme to do? (provided the active site is asymmetric)

A

Distinguish b/w identical groups on a substrate

93
Q

What is the induced fit model? What does it say about the nature of enzymes?

A
  • 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
Q

How is the activation energy lowered in enzyme mechanisms?

A
  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
Q

State/explain the 5 catalytic mechanisms

A
  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
Q

What is K(M)?

M is subscript

A
  • The conc. of substrate needed to reach half Vmax. (maximum reaction rate)
  • Low Km = high affinity b/w E and S
97
Q

What is Kcat?

cat is subscript

A
  • 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
Q

What is the overall efficiency of an enzyme given by?

A

Kcat / Km

99
Q

Irreversible vs. reversible inhibitors

A

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
Q

Compare the two types of reversible inhibitors (incl. changes to enzyme kinetics)

A
  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
Q

Compare the two types of non-competitive inhibitor

A
  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
Q

Why is feedback inhibition important in enzyme regulation?

A

Prevents the synthesis of unnecessary metabolic intermediates

103
Q

What are the two types of allosteric enzyme and how do they act?

A

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
Q

How are recombinant human proteins made?

A
  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
Q

Advantages & disadvantages of prokaryotic systems for recombinant human proteins

A
Advantages:
1. Cheap
2. High yield (protein)
3. Pathogen free
Disadvantages 
1. Proteins often partially folded
2. Can't perform PTMs
106
Q

What type of cell is used to create therapeutic proteins in eukaryotic animal cells?

A

Chinese Hamster Ovary cells (CHO cells)

107
Q

What type of cell is used to create proteins that require PTMs? What’s an example of one of these proteins?

A
  • Eukaryotic animal cells (CHO cells)

- Example: EPO (needs glycosylation)

108
Q

Advantages & disadvantages of Eukaryotic systems for recombinant human proteins

A
Advantages:
- Can do most PTMs
- Proteins usually folded
Disadvantages:
- Expensive 
- Low yield 
- Potential for pathogens
- Can't do some PTMs
109
Q

Advantages and disadvantages of using whole animals to make recombinant proteins & an example of protein made this way

A

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
Q

What is gene therapy and how does it work?

A
  • 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
Q

How does CRISPR-Cas work?

A
  • 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
Q

Uses of CRISPR-Cas

A
  1. Create a disease model (can be used to study the disease)

2. Correct mutations caused during DNA repair

113
Q

Melanin:

  • What is it?
  • Produced by? How?
A
  • Pigment (quantity determines colour of skin)
  • Produced by melanocytes
  • Enzymatic conversion of tyrosine by tyrosinase
114
Q

What is keytruda and how does it work?

A
  • 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
Q

What are the variants of tyrosinase (Tyr) and their causes?

A
  1. Albinism (loss of function of Tyr)
  2. Vitaligo (autoimmune loss, antibodies target Tyr)
  3. Siamese (temperature-sensitive mutant)
116
Q

How does the activity of tyrosinase influence risk of melanoma?

A

Less activity = fairer skin = less pigment (melanin) = increased risk of melanoma

117
Q

Explain the 3 core principles of toxicology using nitrates as an example

A
  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
Q

How can we be exposed to nitrogen?

A
  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
Q

Toxicity of nitrate vs. nitrite

A

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
Q

Symptoms of nitrite poisoning

A
  • Correlate to lack of O2 carrying ability: difficulty breathing, blue skin around lips, increased pulse, dizziness
121
Q

What is used to treat nitrite poisoning and how does it work?

A
  • Methylene blue
  • Reduces Fe3+ in MetHb to Fe2+
    (acts in the same way as metHb reductase)
122
Q

Why are infants more susceptible to nitrite poisoning?

A
  1. Have a high GI pH (increases conversion of nitrate to nitrite)
  2. MetHb reductase system not fully developed –> lower MetHb reductase activity
123
Q

Why are foetus’ more susceptible to nitrite poisoning?

A

HbF has different subunits to HbA, therefore:

  1. Has a higher affinity for oxygen
  2. Is more readily oxidised by NO2 to MetHb
124
Q

How are cattle and fish exposed to nitrite poisoning?

A

Cattle: consume toxic amounts of nitrate
Fish: eutrophication and directly (formation of MetHb, same as humans)

125
Q

What’s a receptor

A

receives chemical signals from outside the cell

126
Q

Enzyme vs. receptor

A
  • 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
Q

How does Aspirin work? Why does it have side effects? How can these be prevented?

A
  • 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
Q

How can you reduce the side effects of a drug?

A

Increase its selectivity

129
Q

How does alcohol (ethanol) work?

Effects of low/high dose?

A
  • 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
Q

How does marijuana work?

A
  • (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
Q

Composition of phospholipid and respective hydrophobicity. What causes variation?

A
  • 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
Q

What determines the speed of movement of phospholipids? I.e. lateral and rotational movement is fast, whereas transverse movement is very slow

A

The interaction b/w the hydrophobic and hydrophilic regions

133
Q

What factors affect membrane fluidity? How?

A
  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
Q

How can membrane proteins stay in the membrane?

A
  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
Q

What factors effect the transport of non polar molecules across the membrane?

A
  1. Hydrophobicity (incr. = incr. permeability)

2. Concentration (incr. = incr. rate of transport)

136
Q

Define non-mediated transport

A

Doesn’t require protein

137
Q

What are the nonpolar amino acids?

A

Ala, Cys, Gly, Isoleucine, Leu, Met, Phenylalanine, Tryptophan, Val

138
Q

What are the uncharged polar AAs?

A

Asparagine, Glutamine, Ser, Tyr, Threonine

139
Q

What are the charged polar AAs?

A

Glu, aspartic acid, arginine, His, Lys

140
Q

Define agonist

A
  • Agonist: chemical which increases action of receptors
141
Q

Define ligand

A

Any molecule that binds to a receptor

142
Q

Define mediated transport

A

Uses protein

143
Q

Define co-transport (symport and antiport)

A

Movement of 2 molecules by a transporter; no ATP used

  • symport = both move in same direction
  • antiport = molecules move in opposite directions
144
Q

Describe the HbS (sickle cell) AA mutation

  • AA change
  • What it causes
  • Significant or insignificant change
A
  • 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
Q

Describe the Met-Hb (HbM) AA mutation

  • AA change
  • What it causes
  • Significant or insignificant change
A
  • Fe2+ oxidised to Fe3+
  • Causes poor binding of Oxygen, since the Fe is no longer electrochemically held in the Fe2+ state
  • Dramatic change
146
Q

Describe the HbChristchurch (HbChCh) AA mutation

  • AA change
  • What it causes
  • Significant or insignificant change
A
  1. HbChristchurch (HbChCh)
    - Phe (large, non polar) –> Ser (small, polar)
    - Slightly destabilises haem
    - Has less severe effect than (1) and (2)