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MGD > Part 1 > Flashcards

Part 1 Flashcards

0
Q

What do transferases do?

A

Transfer a C, N or P containing group

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1
Q

What do catalyst do?

A

Increase the rate of reaction without changing the overall process. Stabilises formation of high energy transition state.

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2
Q

What do Hydrolases do?

A

Break bonds by addition of water

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3
Q

What do Lyases do?

A

Breaking C-C, C-S AND SOME C-N bonds

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4
Q

What do isomerases do?

A

Racemizationm of optical isomers

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5
Q

What do ligases do?

A

Formation of bonds between C to O, S, N coupled to hydrolyse of high energy phosphate (using ATP)

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6
Q

What are ribozymes?

A

Act like enzymes, catalysing the cleavage of the synthesis of phosphodiester bonds in RNA

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7
Q

What is the ACTIVE SITE?

A

Folding of proteins with AA side chain, substrate binds to for, ES complex. Conformational change in structure (induced fit) allows better catalysism as substrate held to proteins with more weak bonds hence enhanced bonding.
ES coverts into Enzyme-product complex. Product not complementary hence dissociates leaving the enzyme.

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8
Q

What is specificity?

A

Enzymes are highly specific hence interact with 1 or a few substrates. Catalyse only one type of chemical reaction.
Set on enzymes determine cell type

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9
Q

What is Catalytic Efficiency?

A

Increases rate by a million.

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10
Q

What is the Turnover Rate?

A

Kcat = # substrate molecules converted to product per enzyme molecule per second

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11
Q

What is regulation?

A

Activity regulated to increase or decrease so rate of product matches cellular need

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12
Q

What is location?

A

Enzymes are compartmentalised in the cells to isolate substrate and products of other reactions, and to provide the optimal environment for efficiency.

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13
Q

What is Holdenzyme?

A

ACTIVE enzyme with non-protein molecules for enzyme activity

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14
Q

What is APOENZYME?

A

Enzyme with non-protein hence metal CO-FACTOR becomes inactive

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15
Q

What is a co-factor?

A

Non-protein. Hence metal ion for enzyme regulation

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16
Q

What is a Co-enzyme?

A

Small organic protein for enzyme regulation

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17
Q

What is a prosthetic group?

A

A permanent group covalently bonded to the enzyme

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18
Q

What is a protoporphyrin ring?

A

Fe bound to 4 N, via the histidine residue. Fe2+ then forms two bonds to an O2 molecule. The binding causes the Fe to rise from below the plN to into the plane

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19
Q

Describe myoglobin?

A 
In the muscle
153AA 
Compact
Hyperbolic ppO2 curve
Only 1 molecule of O2 binds
Fe bound to Histidine 93 on 8th alpha helix covalently
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20
Q

Describe Heamoglobin?

A

Tetrameric
4 O2 bind
2 polypeptide chains of alpha and beta
Each chain contains a prosthetic Haem group

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21
Q

Describe the T and R state of Hb?

A

T state occurs in deoxygenated Hb, hence tense and low affinity for O2.

O2 binds when there is a high O2 conc. this causes a change in the structure to promote the stabilisation of the R state.
Hence as each O2 binds, the Hb becomes more R state hence has a higher affinity hence O2 binds more easily. This is called co-operative binding.

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22
Q

What is co-operative binding?

A

The binding of one O2 molecule to Hb promotes the binding of subsequent molecules. Hence the affinity increases hence sigmoid shape.

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23
Q

Why must O2 be carried?

A

It is non-polar hence is not water-soluble.

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24
Q

What is the passage of O2?

A

In the lungs, there is high [O2] hence Hb picks up O2, it travels in the blood to aerobic ally respiring tissues that have utilised their O2 hence the low [O2] levels means O2 diffuse out to the cells.

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25
Q

What is 2,3-BPG?

A

2,3-busphophategylcercate.
It decreases Hb affinity for O2 by forcing Hb into the T state, hence promoting the dissociation of O2 to deliver into tissue. This is important for higher altitudes when low ppO2 meaning O2 dissociates.

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26
Q

If 2,3-BPG decreases affinity what happens to the curve?

A

The curve shifts Right!

27
Q

What effect does CO2 and H+ have?

A

The Bohr Effect.

Binding to Hb, lowers the affinity forcing Hb into T state hence cure shifts right. This promotes dissociation to muscles and tissue. CO2 present in aerobically respiring tissue. H+ present in anaerobic respiring tissue.

28
Q

What does a shift to the right of the curve mean?

A

You need a higher ppO2 for the Hb to become saturated, aka for O2 to bind to Hb because it has a lower affinity.

29
Q

How is 2,3-BPG fit into glycolysis?

A

It is an intermediate.

1,3-BPG converts to 2,3-BPG by BISPHOPHOGLYCERATE MUTASE

30
Q

Affects of CO on Hb?

A

Poisoning. Combines to ferromyoglobin and ferrohaemoglobin blocking O2 transport.
Binds 250X readily than O2.
CO shifts curve LEFT to increase affinity hence O2 doesn’t dissociate! Tissue gets deprived!

31
Q

Foetal Hb?

A

Curve shifted left. Higher affinity for O2 than Hb hence O2 transferred from mother to fetus.

32
Q

Beta Thalasseamia?

A

Low or no Beta Globin chain hence alpha unable to form stable Tetrameric hence symptoms after birth.

33
Q

Alpha thalasseamia?

A

Low or no alpha Globin so more severe as multiple copies of alpha present. Beta can still form stable Tetrameric but high affinity hence O2 not deposition to growing cells hence symptoms before birth

34
Q

What is HbS?

A

Sickle Cell Anaemia.
1 base substitution leads to Glutamate –> Valine
So clump together in blood and crystallise and polymerise out of solution.

35
Q

What are isoenzymes?

A

Different forms of the same enzyme with different kinetic properties hence different Km values.
They differ in AA sequence. Up catalyse the same reactions.

36
Q

What is Vmax?

A

Maximum rate of system achieved when substrate is at maximum conc.

37
Q

What is Km?

A

The substrate conc when the reaction rate is half Vmax.
A high Km means that greater [S] required in order to reach 1/2 of Vmax. So at [S] = X in high Km, it has a slower rate than X in low Km.

38
Q

Is an enzyme has low Km, what does that mean to the rate?

A

High affinity for substrate. Hence fast rate of reaction.

39
Q

What does Allosteric Inhibitors do?

A

Enzyme in T state hence AS has low affinity to S

40
Q

What does Allosteric Activators do?

A

Enzyme in R state hence high affinity for S

41
Q

Short-term regulation of protein activity?

A
  • Substrate/Product conc
  • Allosteric
  • Covalent Modification
  • Phosphorylation
  • Proteolytic Activation
42
Q

What is Proteolytic Activation?

A

Inactive enzymes precursors - zymogen, activated by the removal of a part of the enzyme.

43
Q

When does Proteolytic Activation occurred?

A
  • Blood clotting cascade
  • Development of tissue remodelling
  • some hormones - insulin
  • Apoptosis
44
Q

What is covalent modification?

A

Protein covalently attached to enzyme

45
Q

What is phosphorylation?

A

Kinase.
P from ATP added onto the -OH GROUPS OF Serine, Tyrosine, Thr. As P is bulky and charged, affects confirmation and binding.

46
Q

What is Hydrolytic?

A

Removal of P with phosphatase.

47
Q

Regulation of Protease Activity?

A

Trypsin is inhibited when pancreatic trypsin inhibitor - alpha1 anti-trypsin, binds.
Deficiency of anti-trypsin leads to destruction of alveolar walls by elastase - EMPHYSEMA
Trypsinogen –> trypsin by ENTEROKINASE/ENTEROPEPSIDASE which breaks the peptide bonds between N-terminal to form a mature trypsin.

48
Q

What are long-term protein regulation?

A

Rate of protein synthesis
by increase/decrease rate of transcription of
mRNA
Rate of protein degradation
Proteins tagged for destruction by small
UBIQUITIN molecules

49
Q

Regulation in metabolic pathways?

A

End product inhibits enzymes

50
Q

What is Feedback Inhibition!

A

End product inhibits enzymes so decreases own production rate

51
Q

What is Feedforward Activation?

A

Increase in Substrate induces the first steps of the pathway by inducing enzymes

52
Q

What is Counter Regulation?

A

Catabolic pathways hydrolysing substrate, hence synthesis is deactivated.
Eg the production of glycogen inhibits glycogenolysis.

53
Q

What is the Blood Clotting Cascade?

A

The tightly regulated mechanism for clotting factors to aggregate at a site of damage to prevent blood lose. It comprises of positive feedback, cofactors, a cascade of enzymes that amplify the response and Proteolytic activation.

54
Q

What is the Intrinsic Pathway?

A

Damage to the epithelial lining of blood vessels leads to the binding of Factor 11 which converts Factor 10 into 10a which is proteolytically activated.

Also release of Ca2+ targeting Gla domains if a Factor 9 and 10 to site

55
Q

What is the Extrinisic Pathway?

A

Vascular damage and Trauma releases tissue factor due to membrane damage. Factor 3 converts Factor 10 into 10a which is proteolytically activate.

Exposes extra cellular domain of Factor 3 which Cleaves 7–> 7a. Which converts 10 –> 10a

56
Q

What happens after Factor 10 is activated?

A

Factor 10a converts prothrombin attached to site of damage into thrombin which converts Fibrinogen into activated form Fibrin which cross links to form a clot.

57
Q

How does thrombin activate fibrin?

A

Cleaves fibrinogen A & B feet and stalks from the central globular domain (n-terminal regions of alpha and beta are highly negative regions so repelled each other preventing aggregation of fibrinogen hence once cut off can aggregate) 2 tripeptide join at N-terminal by disulphide bonds, 3 globular linked by rod. These are stabilised by aimed bonds catalysed by transglutaminase.

58
Q

Characteristic of Fibrin Clot?

A

Insoluble.

59
Q

Characteristics of BCC?

A
  • Fast
  • Efficient
  • Occurs at site of damage and no where else
  • Cascade allows clot formation to induce from very small amounts of initial factor.
60
Q

In real life, now what happens in BCC?

A

-inactive zymogen in low conc in blood
-amplification of initial signal, blood vessel damaged triggers cascade of activation to form fibrin clot
-localisation of clotting factors to damage site. Factors with Gla bind to damaged endothelial cells lining causing rapid activation of downstream effector molecules
-feedback activation by thrombin
Activated enhances activation of Factor 5,8&11

61
Q

How is the BCC terminated?

A

Removal of activated proteins by
Proteolytic digestion - streptokinase.
Dilution by blood flow to liver
Binding of inhibitors molecules (antithrombin 3 HEPARIN. and protein C activated when thrombin binds to receptor, thrombomodulin, and digests a Factor 5a and 8a)

62
Q

What is Gla and why is it important?

A

Gamma-carboxyglutamate residue.
Added in post-transcription modification of Factor 2,7,9&10.
Addition of COOH groups to glutamate residue to form Gla which is now negative. This carboxylation is vitamin K dependant!
Gla interacts to sites of damage where Ca2+ is released, and aggregates the clotting factors together.
Prothrombin binds Ca2+ to Gla so only activated next to site of damage.
Requires Vitamin K as co-factor

63
Q

Examples of Zymogens?

A

Pepsinogen + pH –>Pepsin (Stomach)

Trypsinogen + Enteropeptidase –> Trypsin (pan.)

Proelastase + trypsin –> Elastase (Pancreas)

64
Q

Examples of positive feedback in BCC?

A

Fibrinogen to Fibrin acts positively on the production of cofactor 5, the conversion of co-factor 8–>co-factor 8a and 11 (which starts the intrinsic pathway)

Thrombin positive in Factor 13 to 13a which promotes cross-linking

65
Q

What is Wafarin?

A

An anti-coagulant.
It blocks the formation of vitamin K dependant clotting factors by inhibiting actions of vitamin K, hence clot unable to form.

66
Q

What is Heamophillia?

A

X-linked recessive. Defect of Factor 8 or 9 hence Factor 9a not activated hence no clotting occurs.

MGD (5 decks)

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