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Medical Chemistry > Nikolai Scherback > Flashcards

Nikolai Scherback Flashcards

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1
Q

Apoenzym?

A

Only protein witout substrate or cofactors

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2
Q

Cofactors?

A

Molecules needed for enzyme to be catalytically active!

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3
Q

Holoenzyme?

A

Enzyme + cofactor/prosthetic group

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4
Q

Allosteric site?

A

Binding of small molecules here changes enzyme activity

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5
Q

Oxidoreductases?

A

Catalyzing oxidation, reduction reactions!

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6
Q

Transferases?

A

Catalyzing transfer of functional groups

Eg: a ketoglutarate + alanine pyruvate + glutamate

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7
Q

Hydrolases?

A

Catalyzing hydrolysis reactions, addition of water to a chemical bond

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8
Q

Lyases?

A

Catalyzing breaking apart reactions eg. Carbon carbon cleavage

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9
Q

Isomerases?

A

Catalyzing isomerisations (bond rearangements)

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10
Q

Ligases?

A

Catalyzing bond formation reactions coupled with ATP hydrolysis.

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11
Q

What is the lock and key theory?

A

The binding site is rigid and only compound with particular shape will fit

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12
Q

What is the induced fit theory?

A

Enzyme is flexible and binding of the substrate changes conformation of enzyme

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13
Q

Coenzyme? Ex?

A

Organic molecule needed for enzyme to be able to catalyze a reaction, is soluable and can difuse between different enymes

Ex ATP, NADH

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14
Q

Prosthetic groups? Ex?

A

Groups which are strongly bound to enzyme

Ex. Haem, FeS

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15
Q

What is the functionof a cosubstrate?

A

Cosubstrate is a cofactor, which never binds to the enzyme, like coenzyme NADH/NAD+

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16
Q

When metabolically altered vitamine B5 (panthenol) becomes…

A

Coenzyme A

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17
Q

When metabolically altered vitamine B2 (riboflavin) becomes…

A

FADH2

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18
Q

When metabolically altered vitamine B12 (Cobalamine)…

A

Becomes bound and moves methyl groups about in C1 metabolism (important for nucleotide synthesis)

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19
Q

When metabolically altered vitamine C (ascorbate)…

A

Moves electrons onto Fe3+ ion in prolyl hydroxylase which is needed for collagen synthesis —> hence symptoms of scurvy gums

20
Q

What is the transition state?

A

It is the state corresponding to the highest energy along the reaction coordinate. At this point colliding reactant molecules will always go on to form products.

Enzymes stabilize the transition state by lowering the energy of activation, hence speedig up the reaction

21
Q

Enzymes decrease energy activation by…

A
  • Substrate strain: induces structural rearrangments which strain substrate bonds into a position closer to the conformation of the transition state
  • Covalent catalysis: substrate forms a transient covalent bond with residues in active site
  • Entropy effect: Enzyme is lowering entropy by positioning substrates closer to eachother and in proper orientation
22
Q

What is the study of enzyme kinetics about?

A

It is the study of enzyme catalyzed reactions, and provides information on enzyme specificities and mechanisms

23
Q

What is the formula for a simple enzyme catalyzed resction?

A

S + E SE —>P

K1
K-1
K2

24
Q

What is the ping pong mechnism?

A

Substrate A binds to enzyme followed by product release. Typically, the product is a fragment of the original substrate A.

The rest of the substrate is still attached to enzyme –> E’

E’ then reacts with substrate B. Substrate B covalenly gets attached to the remaining of substrate A catalyzed by E’ and so forming poduct Q.

25
Q

Explain what Vmax is?

A

Vmax is the maximal theoretical rate of reaction, but its never reached.

It is a constant for every enzyme.

To reach Vmax would mean that everysubstrate is tightly bound to its enzyme.

26
Q

What is steady state?

A

Steady state is the state where the product formation happens at a constant rate.

27
Q

What is Km?

A

Km is 0.5 Vmax.

Km is a constant estimate for substrate binding to enzyme.

28
Q

What is the turnover number?

A

Kcat, The turnover number is the highest number of substrate molecules converted to product per enzyme molecule per units of time.

29
Q

Can you say how an enzyme is regulated by covalent modification?

A

A covalent modification can be a phosphorylation, where the protein is either activated or deactivated by the phosphorylation

30
Q

Can you say how an enzyme is regulated by allosteric binding?

A

non covalent reversible binding to the enzyme by cofactors or ligands and changes proteins conformation without getting changed themselves. They are called effectors or modifiers.

31
Q

What is the alkaline Bohr effect?

A

Hb + 4O2 = Hb(O2) 4 + nH+

32
Q

How is isohydric transport carried out and what enzyme is active and what does it do?

A

CO2 + H2O =
H2CO3 + Hb(O2)4 —>
HCO3- + HbH+ + 4O2

Carbonic anhydrase is the enzyme! It fuses CO2 + H2O.

33
Q

What is the second transport (less usual) called through which CO2 is carried through?

A

It is the nonenzymatic transport through carbamino hemoglobin, where CO2 reacts with the NH2 terminal amino groups of the Hb polypeptide chains.

HbNH2 + CO2 HbNHCO2- + H+

34
Q

What is BPGs function?

A

It is an important modulator of the hemoglobin equilibium.

BPG conc are equimolar to that of Hb.
It binds to deoxy T but not to the oxy R conformation.

Binding of BPG to Hb stabilizes the T conformation and increases its conc relative to the R- conformation. BPG dissociates as deoxy Hb is converted to oxy- Hb.

H+BPG x Hb + 4O2 Hb(O2)4 + BPG + nH+

35
Q

What is a potential solution to use serineproteases in case of myochardial infarction?

A

Increased t-PA, so that plasminogen is formed –> plasmin

Plasmin breaks down fibrin –> releases clot.

36
Q

Metastasis has been correlated with urokinase activation. What is the reason?

A

Urokinase is an activator of plasminogen —> plasmin

Plasmin degrades fibrin. This causes greater metastasis of cells being transported more easy.

37
Q

What causes cystathioninuria?

A

Excess cystathionine in urea and other tissues.

Gamma-cystathionase that catalyzes the reaction is defect.

Solution: addition of co-enzyme pyridoxal phosphate partially restored gamma-cystathionase activity

38
Q

Cause of gout?

A

PRPP synthase had a threefold greater activity than normal producing much more PRPP.

Km the same, but Vmax three fold. This shows how Km and Vmax are independently changing.

39
Q

What is the reason that asian people get much more easily affected by alcohol than other ethnic groups?

A

ALDH pointmutation in active site —> Km increases as well as low activity of enzyme
—> acetylaldehyde does not bind to aldehyde dehydrogenase and very low activity, therefore becomes acculumated and is toxic.

40
Q

Why does one feel ill after drinking alcohol and then eating the mushroom black ink?

A

Because mushroom contains corpine which binds covalently to aldehyde dehydrogenase. It is a competitive inhibitor —> greater levels of acetylaldehyde —> becomes toxic —> feeling sick

41
Q

Alcohol and rubber, why feeling sick?

A

Disulfaram is an antioxidant and is contained in rubber. Permanetly binds to ALDH (aldehyde dehydrogenase) —> greater levels of acetylaldehyde —> feeling sick!

42
Q

What happens in hereditary orotic aciduria?

A

OPRT and OMPDC are deficient —> decreased CTP and TTP pyrimidins which are required for dCTP and dTTP —> no DNA synthesis —> no cell division

Patients are pale and weak. Elevated levels of orotic acid in urine.

Solution: addition of uridine and cytidine.
Uridine leads to synthesis of CTP and TTP.
Cytidine represses by feedback inhibition carbamoyl phosphate synthetase, resulting in decrease of orotate production.

43
Q

What enzymes are widely used in diagnostics and why?

A
  • Lactate dehydrogenase (LDH)
  • Creatine phosphokinase (CPK)
  • Alkaline phosphatase (AP)

They have different isoenzymes existing in different areas of the body!

44
Q

What is the function of papain?

A

Cleavage of antibody into its big parts: Fab and Fc!

45
Q

What is the function of pepin when it comes to immunoglobulins?

A

It cuts the fragments ino much smaller pieces.

Medical Chemistry (9 decks)

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