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My ESA1 > MGD S3 - Protein Regulation, Chromosomes, Genes and DNA > Flashcards

MGD S3 - Protein Regulation, Chromosomes, Genes and DNA Flashcards

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1
Q

What does substrate availability affect?

A

Rate of enzyme activity. Some coenzymes will have limited availability

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2
Q

What are isoenzymes?

A

Different forms of the same enzyme (catalyse the same reaction) that have different kinetic properties. Different Km and Vmax - different amino acid sequences

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3
Q

Describe product inhibition

A

Accumulation of product of reaction inhibits forward reaction

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4
Q

Hexokinase and glucokinase are both involved in the first step of glycolysis. What is the difference between them?

A

Hexokinase - present in all cells and requires low glucose levels to become active. Glycolysis can occur at lowest [glucose] i.e. starvation. Important for glucose-dependent tissues Glucokinase - present in liver and pancreas. In both it acts as a glucose sensor, becoming active only when a response to high blood sugar is needed i.e. in liver glycolysis results in storage, in pancreas it results in insulin secretion

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5
Q

What does allosteric mean?

A

At a distance

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6
Q

What is the relationship between rate and substrate concentration?

A

Sigmoid, instead of the rectangular hyperbola seen for simple enzymes

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7
Q

What is the structure of allosteric enzymes?

A

Multi subunit

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8
Q

What are the two different conformations of allosteric enzymes?

A

T state - low affinity R state - high affinity

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9
Q

What is the effect of substrate binding to one subunit of an allosteric enzyme?

A

Makes subsequent binding to other subunits progressively easier

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10
Q

What does allosteric activators do?

A

Increase the proportion of (stabilise) enzyme in the R state

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11
Q

What do allosteric inhibitors do?

A

Increase the proportion of (stabilise) enzyme in the T state

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12
Q

What does phosphofructokinase do?

A

It is allosterically regulated and sets the pace of glycolysis- catalyses the third step (committing step), which can be up or down regulated depending on the energy needs of the cell

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13
Q

What are the activators and inhibitors for phosphofructokinase?

A

Activators = AMP, fructose-2,6-bisphosphate (low energy signals) Inhibitors = ATP, citrate, H+ (high energy signals)

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14
Q

What is covalent modification?

A

Post-translational modification e.g. tyrosine kinases, MAPKKK. Enzymes can be modified through the addition of an additional group

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15
Q

What groups can be added in covalent modification?

A
  • Phosphorylation by kinases (receptor tyrosine kinases) - Protein phosphatases - Carboxylation by carboxylate (FII, FVII, FIX, FX) - Acetylation (histones) - Ubiquitination (targets for protein destruction)
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16
Q

What happens in phosphorylation by kinases?

A

Transfer of terminal phosphate from ATP to -OH group if Series, Tyr, Thr. Switch enzyme on or off - different for different enzymes

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17
Q

What happens in phosphorylation by protein phosphatases?

A

Reverse effects of kinases by catalysing the hydrolytic removal (have to cut off because of covalent bond) of phosphoryl groups from proteins

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18
Q

What happens when enzymes activate enzymes?

A

The number of affected molecules increases geometrically in an enzyme cascade (enzyme 1 starts phosphorylating -> they all do)

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19
Q

Describe the action of signalling cascades

A

Amplification of signals by kinase cascades allows amplification of the initial signal by several orders of magnitude within a few milliseconds. Signalling cascades often use covalent modification to activate downstream effector proteins and amplify an extracellular signal e.g. MAPKKK pathway

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20
Q

How are glycogen breakdown and synthesis regulated?

A

Reciprocally

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21
Q

What is haemostasis?

A

Process which causes bleeding to stop via clotting cascade

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22
Q

In haemostasis, what happens before damage?

A

Heparin-like molecules released to inhibit clotting. Endothelium is naturally anti-coagulative

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23
Q

In haemostasis, what happens in activation, localisation and regulation?

A
  • Inactive zymogens become activated by substances released only at site of vascular damage (i.e. tissue factor) - Proteolytic activation in a cascading process - Feedback activation through thrombin burst (positive feedback)
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24
Q

In haemostasis, what happens during termination and resolution?

A
  • Activation of plasminogen by t-PA - Removal of clotting factors by liver - Protein C (inactivates Factor Va and Factor VIIIa), Protein S (cofactor to Protein C) and AT III (anti-thrombin)
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25
What forms of short-term protein regulation are there?
1. Substrate and product concentration 2. Change in enzyme conformation: - allosteric regulation - covalent modification - proteolytic cleavage
26
What is Vitamin K?
A co-factor for gamma-glutamyl carboxylase. Adds carboxylase group to glutamate residues of proteins C, S, 2, 7, 9 and 10
27
What is specific proteolytic cleavage?
A common means of activating enzymes in biological systems - off -\> on as don't want to be active in wrong place
28
What are some examples of specific proteolysis?
- Digestive enzymes are synthesised as zymogens (inactive precursors) in the stomach and pancreas i.e. pepsinogen is zymogens of pepsin - Some protein hormones (i.e. insulin) are synthesised as inactive precursors - Blood clotting is mediated by a cascade of proteolytic activations that ensures a rapid and amplified response - Many development processes are controlled by the activation of zymogens to contribute to tissue remodelling - Apoptosis is mediated by proteolytic enzymes, caspases, which are synthesised in inactivate (procaspase) form
29
How is the activation of pancreatic proteases controlled?
By trypsin (major molecule secreted from exocrine pancreas for protein digestion). Pancreatic proteases have a wide range of specificities
30
What kind of inhibitors regulate protease activity?
Endogenous inhibitors e.g. pancreatic trypsin inhibitor binds trypsin and stops activity. Ribosomes don't work on these. Can't switch zymogen off so cell must control
31
What is α1-antitrypsin?
53kDa plasma protein that inhibits a range of proteases
32
What is emphysema?
Deficiency of α1-antitrypsin. Destruction of alveolar walls by elastase
33
What is FX -\> FXa?
Key component of clotting cascade
34
What forms of long-term protein regulation are there?
- Altering rate of protein synthesis - can be modified at numerous levels, including the degree of promotion of a gene, the rate of mRNA destruction and enzyme induction/repression - Altering rate of protein degradation - a protein can be tagged for destruction through covalent modification e.g. ubiquitin-proteasome pathway
35
Outline the blood clotting cascade
Intrinsic pathway (damages endothelial lining of blood cells promotes binding of factor XII) AND extrinsic pathway (trauma releases tissue factor, factor III) --\> Factor X activation (common endpoint for both pathways) --\> Thrombin activation --\> Formation of fibrin clot
36
How are proteins of blood coagulation (e.g. factor III = tissue factor) secreted?
As inactive precursors -\> cut off part -\> active. Triggers clotting when blood vessels damaged
37
Is fibrin an enzyme?
No, it is a protein that forms clots
38
What causes positive feedback in the coagulation cascade?
From thrombin --\> : Protein C+ -\> Active Protein C, Factor XI -\> XIa, V -\> Va, VIII -\> VIIIa, XIII -\> XIIIa
39
What causes negatie feedback in the coagulation cascade?
TFPI, Thrombomodulin, Active Protein C, Antithrombin
40
What happens in the extrinsic pathway of the coagulation cascade?
Activation of Factor VII: Membrane damage exposes extracellular domain of tissue (Factor III). Autocatalytic activation of Factor VII
41
What happens in the intrinstic pathway of the coagulation cascade?
Keeps blood clotting going. Membrane damage plays a role in pathway activation. Factor IX and X are targeted to membrane by Gla domains. Ca2+ plays a role. Required for sustained thrombin activation
42
Outline the process of clot breakdown (fibrinolysis)
43
Outline the modular structure of prothrombin
Protease function (thrombin part) is contained in the C-terminal domain. Two kringle domains help keep prothrombin in the inactive form. Gla domains (carboxyglutamate) target it to appropriate site for its activation
44
Outline the activation of thrombin
When Factor X comes. Involves proteolytic cleavage at Arg274 to release a fragment containing first 3 domains. Cleavage after Arg323 releases fully active thrombin consisting of two chains, 5kDa and 31kDa, linked by a disulphide bond
45
What is the role of gamma-carboxyglutamate (Gla) residues?
Enzymes secreted through ER. Post-translational modification of factors II, VII, IX, X in the liver. Addition of COOH groups to glutamate residues to from Gla in Golgi - patches of negative charge. Allows interaction of sites of damage and brings together clotting factors
46
Outline the role of the calcium-binding region of prothrombin
Prothrombin binds calcium ions via Gla residues. Only prothrombin next to site of damage will be activated. Clots will be localised to the site of damage
47
Outline the structure of fibrinogen (inactive form of fibrin)
- 340kDa protein - 2 sets of tripeptides - alpha, beta, gamma - joined at N-termini by disulphide bonds - 3 globular domains linked by rods - N-terminal regions of alpha and beta chains are highly negatively charged and prevent aggregation of fibrinogen (they repel)
48
Outline the formation of a fibrin clot
- Thrombin cleaves fibrinopeptides A and B from the central globular domain of fibrinogen - Globular domains at the C-terminal ends of the beta and gamma chains interact with exposed sequences at the N-termini of the cleaved beta and alpha chains to form a fibrin mesh or clot - Newly formed clot stabilised by formation of amide bonds between side chains of lysine and glutamine residues in different monomer - a cross-linking reaction
49
How is the formation of a fibrin clot catalysed?
By transglutaminase, which is activated from protransglutaminase by thrombin
50
What causes haemophilia A (classic haemophilia)?
A defect in factor VIII (antihaemophilic factor) - not a protease, but markedly stimulates activity of factor IXa, a serine protease. Activity of factor VIII is markedly increased by limited proteolysis by thrombin and factor Xa. This positive feedback amplifies clotting signal and accelerates clot formation. Treat with recombinant factor VIII
51
What causes haemophilia B?
A defect in factor IX
52
Outline the stopping of the clotting process
- Localisation of (pro)thrombin. Dilution of clotting factors by blood flow, and removal by liver. - Digestion by proteases i.e. factors Va and VIIIa degraded by protein C, which is activated by thrombin binding to endothelial receptor, thrombomodulin. Defects in protein C can cause thrombotic disease. - To stop clotting: specific inhibitors. Antithrombin III (AT3), enhanced by heparin binding. AT3-heparin does not act n thrombomodulin-bound thrombin
53
What is the shade of each form of chromatin in the nucleus?
Heterochromatin = dark Euchromatin = light
54
Is a nucleosome a rigid molecule?
No, it is flexible
55
What does heterochromatin consist of?
Solenoid 30nm fibre Genes not expressed
56
What does euchromatin consist of?
Beads on a string - histone core and linker DNA of nucleosome Genes expressed
57
Are genes expressed in a chromosome?
No, DNA too tightly wound
58
What are genes?
They carry the code for proteins and have a chromosomal location
59
How many genes are there?
Humans have about 25,000 Fruitfly has about 15,000 E.coli has about 4,500 (Our regulation is far more complex)
60
What is a genome?
The entire DNA sequence. Human Genome is 24 chromosomes (22 autosomes plus 2 sex chromosomes X and Y)
61
How many base pairs are there in a genome?
Human: 3,200,000,000 bp Fruitfly: 140,000,000 bp E.coli: 4,600,000 bp Studies re. bp needed for life: ~500
62
What are DNA and RNA?
Nucleic acids
63
What are nucleic acids?
Polynucleotides = linear polymers of nucleotides
64
What is a nucleo**_s_**ide?
Base + sugar
65
What is a nucleo**_t_**ide?
Base + sugar + phosphate
66
What is the difference between ribonucleic acid (RNA) and deoxyribonucleic acid (DNA)?
RNA contains ribose (OH at carbon-2) and DNA contains 2-deoxyribose (H at carbon-2)
67
What are the two types of nitrogenous base?
Purine - 2 rings Pyrimidine - 1 ring
68
What are the two types of main purines?
In both DNA and RNA: adenine and guanine
69
What are the three types of main pyrimidines?
Cytosine (in RNA/DNA), uracil (in RNA) and thymine (in DNA) There are derivatives in other molecules that we can use to interfere with, for example, transcription/replication
70
Give examples of nucleic acid nomenclature in order: Base, Nucleoside, Nucleotide
In RNA: Adenine, Adenosine, Adenosine Monophosphate (AMP) Cytosine, Cytidine, Cytidine Monophosphate (CMP) In DNA: Adenine, Deoxyadenosine, Deoxyadenosine Monophosphate (dAMP)
71
How are nucleotides joined?
By phosphodiester bonds DNA and RNA are polymers Chain has polarity - 5' to 3' Chain has distinct ends - 5'P and 3'OH
72
What happens during base pairing?
Purine is flipped G-C: 3 H bonds (all bonds almost same length, so logical that they bond) A-U or A-T: 2 H bonds. Distance too far to form 3rd H bond
73
When can nucleic acids form duplex structures?
When antiparallel (1 is flipped) and complementary
74
What types of duplex structures can be formed?
DNA-DNA, RNA-RNA and DNA-RNA Stable or temporary In vivo and in the laboratory
75
Describe the structure of RNA stem-loops, i.e. in tRNA
UUUC loop then 2 complementary stems. Hydrogen bonds are formed between anti-parallel, complementary sequences
76
Describe the structure of the DNA double helix
Right-handed double helix Anti-parallel strands of DNA Major groove = rigid Minor groove = flexible Major and minor groove are asymmetrical
77
How is a polynucleotide sequence depicted?
5' A C C U 3' (Can leave numbers off) By convention, 5' to 3' from left to right
78
How is a duplex sequence depicted?
5' A C C T C G 3' 3' T G G A G C 5' (Can leave off 2nd strand) Anti-parallel, complementary strands By convention, top strand 5' to 3' from left to right

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