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Emma > Biochem - E2 > Flashcards

Biochem - E2 Flashcards

1
Q

What are the 6 categories of enzymes?

A

Oxidoreductases, transferases, hydrolyses, lyases, isomerases, ligases

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2
Q

What are serine proteases?

A

Proteolytic enzymes that catalyze peptide bond hydrolysis.

Dif aa residues may carry out catalysis than those that recognize substrate.

1st event after binding substrate in correct orientation –> attack of Ser-195 residue.

Exp. Pancreatic enzymes

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3
Q

What is the mechanism of serine proteases?

A
  1. bind substrate in correct orientation
  2. attack by serine 195
  3. TS stabilization
  4. Addn of H2O
  5. Prod release
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4
Q

What are 3 examples of serine proteases and which specific amino acids do they preferentially bind to?

A

Chymotrypsin –> binds large, hydrophobic aa (cleaves on c-term side) like try, tryp, phe.

Trypsin –> binds + aa residues (lysine, arginine)

Elastase –> binds small aa prevalent in elastin (gly, ala, val)

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5
Q

What is the relationship between ∆G and Keq?

A

They are constants and have the same info.

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6
Q

What does Q represent?

A

[substrate and product]

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7
Q

How does variation of Q affect Keq?

A

Q=Keq –> rxn is at equilibrium
Q>Keq –> rxn is in reverse
Q rxn goes fwd (removal of prods –> fwd)

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8
Q

When the change in free E is zero (∆G=0)…

A

the substrate and product are in equilibrium.

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9
Q

What is the mechanism of enzyme catalysis?

A

Enzymes remove barrier between substrate and product (via TS stabilization). They do NOT change equilibrium, but do change rate the equilibrium is obtained).

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10
Q

What is the Km?

A

[substrate] needed to reach 50Q% max velocity of rxn

km=1/2Vmax

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11
Q

What do lower/higher Kms indicate? (Give exp. of each)

A

Lower Km –> high affinity of enzyme for substrate
(Exp. hexokinase - in liver - has low km for glucose, binds it with higher affinity)

Higher Km –> lower affinity of enzyme for substrate
(Exp. glucokinase has high Km for glucose, binds it with less affinity)

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12
Q

What is Vmax?

A

Maximal activity for a sample. Vmax is proportional to the [enzyme]

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13
Q

As the amount of enzyme increases, what happens to Km?

A

Nothing. Km remains unchanged because not changing the properties of enzyme, there is just more of it. Vmax will increase, however.

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14
Q

What is the Kcat a measure of?

A

measures catalytic activity of enzyme - “turnover number” (how many substrate molecules can be used per sec.
Kcat = Vmax/[enzyme]

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15
Q

What are some reasons for enzyme deficiency?

A

Enzyme is not being made.
Enzyme has mutation that effects the active site.
Enzyme is made but there is insufficient substrate.
Enzyme is made, but is inhibited.

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16
Q

How would you measure substrate levels with a given amount of enzyme?

A

Use low substrate levels relative to/at the Km.

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17
Q

How would you measure enzyme activity?

A

Use saturating amounts of substrate which would give the highest activity. (subst»km).

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18
Q

In a Lineweaver-Burk plot, what do the y-int and the x-int represent?

A

y-int –> 1/Vmax (max velocity). Take reciprocal.

x-int –> -1/Km (Take inverse, Km is always +).

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19
Q

How to synthesis a needed compound that entails a Lower E anabolic rxn?

A

Couple with a high E catabolic rx.

Exp. Couple bond synthesis to peptide bond hydrolysis.

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20
Q

What are the 6 types of enzyme regulation?

A
  1. Regulation by location
  2. Activation of enzyme zymogens
  3. Protein inhibitors of enzymes
  4. Protein phosphorylation
  5. Inhibitors of enzyme activity
  6. Regulation by substrate levels & allosteric enzymes
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21
Q

The enzyme regulation of alpha-1-antitrypsin indicates what? What type of regulation is it?

A

Decrease of this protein indicates liver damage (since it is normally secreted by the liver and taken up by the lung).
Exp of regulation by location.

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22
Q

The enzyme regulation of alanine transaminase (ALT) indicates what? What type of regulation is it?

A

This enzyme is an internal liver enzyme that balances aa levels. High level of this enzyme indicates cell damage.
Exp of regulation by location.

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23
Q

What is a zymogen and how do they regulate enzyme activity?

A

Zymogens are the inactive form of enzymes that are rapidly activated by peptide bond cleavage. This cleavage causes the proper formation of the active site.

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24
Q

Where is prothrombin converted to thrombin?

A

On a membrane surface. (variety of Dif cell types: monocytes, platelets, endothelial cells)

25
Q

What triggers the conformational change of prothrombin so that it will bind to a membrane surface along with its activating enzyme?

A

Gamma carboxylation (occurs as a post-translational mod) of certain glutamate residues on prothrombin which enables CA 2+ binding.

26
Q

What is gamma carboxylation of prothrombin dependent on and what interferes with this process?

A

Vitamin K dependent rxn.

Vitamin K antagonists, Coumadin, warfarin - all interfere with this.

27
Q

The irreversible activation of thrombin is accomplished by 2 proteolytic cleavages. What do each of the cleavages entail?

A

1 cleavage: releases enzyme from membrane

1 cleavage: allows for proper active site formation & releasing of enzyme away from the membrane

28
Q

Describe the clotting cascade including the role of thrombin.

A

The initial trigger is a few damaged molecules but results in millions of molecules activated.

Prothrombin is cleaved to thrombin on a membrane surface.
Fibrinogen (soluble) in the blood is cleaved by thrombin into fibrin monomers.
Fibrin monomers form an initial clot. The clot cross-links.

29
Q

T or F: protein inhibitors of enzymes are reversible.

A

F. These inhibitors bind so tightly that entire enzyme-inhibitor complex is degraded as a whole. Inhibition is irreversible.

30
Q

alpha-1-antirypsin inhibits what? Why is this important in the liver?

A

alpha-1-antirypsin inhibits elastase. This is important because it prevents destruction of elastin in the lung.

31
Q

What does mutated alpha-1-antitrypsin lead too?

A

Overactive elastase –> destroyed elastin –> lung scarring and emphysema.

32
Q

Give an example of a commonly rx’d short-acting anti-coagulant and its mechanism.

A

Heparin –> promotes anti-thrombin-thrombin complex formation.

33
Q

If a protein is phosphorylated or dephosphorylated, what could happen?

A

The charge of an amino acid residue of the protein can be modified. If serine/threonine/tyrosine is in or near the enzyme active site - enzyme activity may be changed.

34
Q

Which type of enzyme inhibition does this describe?

Inhibition at binding site only (inhibitor usually resembles substrate in structure).

Km is changed, but Vmax remains the same.

Inhibition is reversible.

An example is ethanol.

A

Competitive inhibition

35
Q

Which type of enzyme inhibition does this describe?

Do not bear resemblance to the substrate.

Bind to the enzyme in a location other than the active site irrespective of whether substrate is present and affect the amino acid residues of the enzyme involved in the catalysis of the reaction. (A type of allosteric inhibitor.)

Vmax is reduced (because these inhibitors effectively reduce the amount of enzyme present. Vmax can’t be reached no matter how much substrate is added).
Km is unchanged.

These inhibitors can be reversible or irreversible.

A

Non-competitive inhibition

36
Q

Which type of enzyme inhibition does this describe?

This type of inhibition kills the enzyme (because can form very tight complexes, even at substrate binding site but also affect catalytic residues)

Vmax is reduced (because these inhibitors effectively reduce the amount of enzyme present. Vmax can’t be reached no matter how much substrate is added).
Km is unchanged.
(Same kinetics as non-competitive inhibition.)

A

Irreversible inhibition.

37
Q

What does Ki represent?

A

The inhibitory constant.
It is inversely related to the affinity constant of inhibitor for enzyme. (The lower the Ki, the tighter the inhibitor binds to the enzyme and the more effective that inhibitor is.)

38
Q

Describe the mechanism of allosteric enzymes. Where are they often located?

A

These are more sensitive to [substrate]. They usually contain multiple subunits and can exist in T or R forms.

Substrate binds with high affinity to R and low affinity to T. The binding of substrate increases the likelihood that the allosteric protein is in the relaxed form.

Highly regulated by [substrate] and often control rxn pathway (often located at beginning of dedicated rxn pathway).

Do not usually follow Michaelis-Menten kinetics; can define an ‘apparent’ Km.

39
Q

Give an example of an allosteric enzyme that plays a role in glycolysis. Explain its mechanism.

A

PFK1: catalyzes F6P –> F-1,6-BP. (committed step of glycolysis, which makes ATP).

Increased AMP –> R state
Increased ATP –> T state
(^ATP made at end of glycolysis)

40
Q

What are the hallmarks of cancer (a genetic disease, many caused by mutations)?

A

Disordered proliferation/growth/differentiation of cells.

41
Q

What is the function of the Rb gene?

A

Rb is a tumor suppressor that is frequently missing in cancers (including retinoblastoma).

Rb gene encodes pRB. pRB…

  • located in the nucleus, regulates cell cycle
  • then NOT phosphorylated, binds to E2F (tFac) and blocks its ability to transcribe genes whose prods are required for S-phase of cell cycle.
42
Q

What inheritance patterns cause retinoblastoma?

A

No retinoblastoma –> 2 Rb alleles on chromosome 13
Predisposal to retinoblastoma –> deletion of 1 Rb + allele
Induced tumor formation –> loss of other Rb+ allele in somatic cells

43
Q

What is responsible for the phosphorylation of pRB and what outcome does this cause?

A

At right point of cell cycle, Cdk/cyclin complexes will phosphorylate pRB (via phosphate from ATP) and release it from E2F.

E2F is now available to stimulate production of proteins required for S phase. (like pol-alpha-primase complex)

Relatives of pRB –> p107 & p130

44
Q

What nuclear protein is a substrate for many “stress-related” phosphorylation events, and is found to be mutated in 50% human cancers?

A

p53

45
Q

p53 may be involved in transcription regulation via targeting of ____. Describe this mechanism.

A

Upon DNA damage, p53 can induce p21 gene transcription. p21 binds to Cdk1 cyclin complexes and halts cell cycle in G1.

This allows time to repair DNA damage prior to S phase.

p21 also binds to PCNA (clamp) and inhibits progression of replication forks.

46
Q

Mutations in p53 lead to ….

A

sarcomas, carcinomas

47
Q

Mutations in NF1 lead to ….

A

Neuroblastoma

48
Q

Mutations in APC lead to ….

A

colon, stomach cancer

49
Q

BRCA1

A

Breast Cancer

50
Q

What is the differentiation between oncogenes and tumor suppressors?

A

Oncogenes are seen as accelerators of cell growth.

Tumor suppressor genes are seen as brakes.

51
Q

Most oncogenes are derived from proto-oncogenes, which normally encode…

A

growth factors proteins, etc.

52
Q

Oncogenes activate cell division in response to…

A

growth factor stimulation

53
Q

How many of cell’s gene copies need to be altered for aberrant oncogene function?

A

Just one of the cells two copies (dominant effect)

54
Q

To accomplish signal transduction, there are membrane receptors with intrinsic enzymatic activity. Explain the mechanism of PDGF receptors.

A

PDGF receptors are tyrosine kinase receptors. Phosphorylation of tyrosine residues allows for interactions with other members of the cascade. (frequently, signals meant to be transient)

55
Q

What are 4 examples of alterations in the signal transduction cascade that are linked to cancers?

A
  1. excess growth factors
  2. defective growth factor receptors
  3. defective signaling molecules
  4. altered regulation of transcription factors
56
Q

The simian sarcoma (sis) oncogene is an example of an altered growth factor. Explain its method of inducing signal transduction.

A

The sis gene encodes part of the PDGF molecule, thus, it induces Tyrosine kinase receptor signal transduction pathways.

57
Q

ErbB and HER2 are examples of altered growth factor receptors. Why do they lead to constant stimulation of growth?

A

Epidermal growth factor (EGF) is a small protein that stimulates epidermal and various other cells to divide.

These encode a modified form of the EGF receptor. The receptor is mutated such that the intracellular stimulatory signal is produced con- stantly, even in the absence of EGF.

58
Q

~25% of human cancers have mutant RAS (a signaling molecule). What is the mechanism behind this abnormality?

A

When bound to GTP, RAS is active.
When bound to GDP, RAS is inactive.
(GAPs - GTPase activating proteins - switch RAS from on and off)

When mutated, RAS is looked into the GTP form –> always activated and excessive signal transduction to nucleus occurs.

Emma (18 decks)

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