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Biochemistry > Biochemistry - Enzymes > Flashcards

Biochemistry - Enzymes Flashcards

1
Q

Biological Enzyme Properties

A

Higher reaction rates, milder reaction conditions, great specificity, capacity for regulation.

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2
Q

Oxidoreductases

A

catalyze oxi-reducation reactions

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3
Q

transferases

A

catalyze transfer of C, N or P containing groups

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4
Q

Hydrolases

A

Catalyze cleveage of bonds iby addtion of water

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5
Q

lyases

A

catalyze cleveage of C-C, C-S, and certain C-N bonds

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6
Q

Isomerases

A

Catalyze racemization of otical or geometric isomers.

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7
Q

Ligases

A

Catalyze formation of bonds between O, S, N coupled to hydrolysis of high energy phosphates.

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8
Q

Holoenzyme

A

catalytically active enzyme-cofactor complex.

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9
Q

Apoenzyme

A

inactive protein lacking the cofactor.

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10
Q

Stereospecificity

A

The active site is not only specific for the right substrate but also for the correct steroisomer. E.g., lactate dehydrogenase.

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11
Q

Free Energy

A

G - energy avaiable ot do work.

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12
Q

Ground state

A

The normal energetically favorable state of a molecule. Lower the free egenrgy, the more stable the molecule.

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13
Q

Glycopeptidyl transferase

A

essential bacterial protein involved in the synthesis of the cel wall, necessary for srowth and survival. Catalyzes a cross linking reaction where the substrate is an Alanine-Alanine dipeptide. Penicillin iis a TS analog that binds covalently, inactivating it.

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14
Q

Catalysis by proximity

A

Molecules need to come within bond-forming distance. High concentration, more likely. Enzyme creates a high local concentratino in correct orientation.

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15
Q

Covalent catalysis

A

enzyme forms a transient bond with substrate. Common in transferases.

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16
Q

Catalysis by strain

A

Mechanism used by anzymase that catalyze “-lytic” reactions, binding substrate in an unfavorable conformation, making it more vulnerable to change.

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17
Q

General acid-base catalysis

A

Side chains of the protein residues or some prosthetic groups mediate proton transfer or proton binding between the enzyme and substrate or transition state. Histidine is typical as a proton donor/acceptor. E.g., cat. By fructose 2,6 biphosphatase.

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18
Q

Denaturation

A

Denaturation, Temperature, Ph

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19
Q

Vo or Vi

A

Initial reaction rate. Velocity increases as [S] increases

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20
Q

sigmoidal plot

A

plot characteristic o fallosteric enzymes

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21
Q

hyperbolic curve

A

plot curve characteristic of Michaelis-Menten kinetics.

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22
Q

Km = Michaelis-Menten constant

A

The concentration of substrate [S] that give us Vmax/2. An intrinsic property measuring the binding affinity of an enzyme for its substrate.

23
Q

saturated

A

all enzyme active sites are filled, and cannot convert product any faster. Rate said to be zero order with respect to substrate concentration.

24
Q

Vmax

A

upper limit value for initial velocity

25
Q

Kcat

A

the turnover number, and represents the efficiency of an enzyme. Formation of product per second per enzyme of molecule. Vmax/[E]tot

26
Q

Isoenzymes

A

different enzymes able to catalyze the same reaction but differing other areas: different genes, primary sequence, kinetic properties, cofactor dependence etc. Hexokinase vs. Glucokinase.

27
Q

Glucokinase

A

works mainly in the liver and B-pancreatic cells and has a high Km (low affinity) for glucose. - Activity usually low, but increases when glucose leves high and liver needs to store glucose.

28
Q

Hexokinase

A

Found in most tissues, and has a low Km (high affinity) for glucose. Activity is constant under most concentrayions of glucose, supplying need of tissues. Especially important in brain.

29
Q

Lineweaver-Burk plot

A

Graphs 1/Vo vs. 1/[S]

30
Q

Competitive inhibitors

A

Vmax is unaffected and apparent Km increases (lower affinity for the substrate), because it takes more substrate ot reach Km.(Statin drugs)

31
Q

Statin drugs

A

Competitive inhibitors of HMG CoA reductase, the enzyme that catalyzes the rate-limiting step in cholesterol biosynthesis

32
Q

Non-competitive inhibition

A

Bind the enzyme at a site different from the active site, producing a conformational change. Vmax decreases, apprent Km remains the same. E.g., plavix

33
Q

Plavix

A

a non-competitive inhibitor of platelet ADP receptors.

34
Q

Irreversible inhibitors

A

Binding through covalent bonds produces a permanent loss of enzyme activity. Some toxic (e.g., Hg2+, Pb2+, insecticides.) Some good drugs (e.g., penicillin, aspirin)

35
Q

Suicide substrates

A

Relatively unreactive until they bind to the active site of a specific enzyme. Inert in ingested form, modified by enzyme into irreversible inhibitor. Makes for very effective drugs.

36
Q

Disulfiram (Antabuse)

A

An irreversible inhibitor of aldehyde dehydrogenase. Leads to accumulation of acetaldehyde when person consumes ethanol (have really bad hangover).

37
Q

compartmentalization

A

Preventing a futile cycle by separation of processes in space and time in different organelles and with different rate limiting steps. Provides different conditions (e.g., lysosomes).

38
Q

modes of enzyme regulation

A

compartmentalization, substrate availablilty, enzyme quantity

39
Q

regulation by enzyme quantity

A

More enzyme, greater Vmax. Depends on gene expression, slow process.

40
Q

regulation of enzyme activity

A

product inhibition, allosterism, modulator proteins, covalent regulation.

41
Q

Product inhibition

A

When the concentration of product from an enzyme-catalyzed reaction builds up, the product may inhibit the enzyme. Products can bind reversibly to the active site. Response immediate.

42
Q

Sigmoidal curve

A

hyperbolic curve typical of allosteric enzymes. Km is called K0.5, not M-M kinetics.

43
Q

Feedback inhibition

A

downstream product of a multi-enzyme pathway inhibits an upstream enzyme pathway inhibits an upstream enzyme. Binding occurs in a regulatory site. No need for structural similarity.

44
Q

Feedforward activation

A

upstream substrate of a multi-enzyme pathway activates a downstream enzyme

45
Q

Aspartate transcarbamoylase (ATCase)

A

catalyzes the rate-limiting step in bacterial pyrimidine biosynthesis.

46
Q

Covalent regulation

A

the addition or removal of specific chemical groups via covalent bonding. Has an immediate effect, reversible or irreversible.

47
Q

Reversible covalent modifications

A

phosphorylation, adenylation, uridylyation, ribosylation, methylation.

48
Q

Enterokinase

A

membrane bound protease on duodenal cells that catalyzes the formatino of trypsin.

49
Q

proteolysis

A

One-time irreversible removal of a portion of a polypeptide chain. Fast, prevents auto-digestion by proteases (dietary).

50
Q

zymogen

A

inactive form of an enzyme. E.g., Trypsinogen -> trypsin.

51
Q

glucose 6-phosphate inhibits…

A

Hexokinase

52
Q

Homotropic

A

same chemical nature as true substrate.

53
Q

Heterotropic

A

different chemical nature from true substrate

54
Q
A

Biochemistry (12 decks)

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