Biochemistry - Enzymes

Question 1

Biological Enzyme Properties

Answer 1

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

Question 2

Oxidoreductases

Answer 2

catalyze oxi-reducation reactions

Question 3

transferases

Answer 3

catalyze transfer of C, N or P containing groups

Question 4

Hydrolases

Answer 4

Catalyze cleveage of bonds iby addtion of water

Question 5

lyases

Answer 5

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

Question 6

Isomerases

Answer 6

Catalyze racemization of otical or geometric isomers.

Question 7

Ligases

Answer 7

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

Question 8

Holoenzyme

Answer 8

catalytically active enzyme-cofactor complex.

Question 9

Apoenzyme

Answer 9

inactive protein lacking the cofactor.

Question 10

Stereospecificity

Answer 10

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

Question 11

Free Energy

Answer 11

G - energy avaiable ot do work.

Question 12

Ground state

Answer 12

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

Question 13

Glycopeptidyl transferase

Answer 13

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.

Question 14

Catalysis by proximity

Answer 14

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

Question 15

Covalent catalysis

Answer 15

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

Question 16

Catalysis by strain

Answer 16

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

Question 17

General acid-base catalysis

Answer 17

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.

Question 18

Denaturation

Answer 18

Denaturation, Temperature, Ph

Question 19

Vo or Vi

Answer 19

Initial reaction rate. Velocity increases as [S] increases

Question 20

sigmoidal plot

Answer 20

plot characteristic o fallosteric enzymes

Question 21

hyperbolic curve

Answer 21

plot curve characteristic of Michaelis-Menten kinetics.

Question 22

Km = Michaelis-Menten constant

Answer 22

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

Question 23

saturated

Answer 23

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

Question 24

Vmax

Answer 24

upper limit value for initial velocity

Question 25

Kcat

Answer 25

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

Question 26

Isoenzymes

Answer 26

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

Question 27

Glucokinase

Answer 27

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.

Question 28

Hexokinase

Answer 28

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.

Question 29

Lineweaver-Burk plot

Answer 29

Graphs 1/Vo vs. 1/[S]

Question 30

Competitive inhibitors

Answer 30

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

Question 31

Statin drugs

Answer 31

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

Question 32

Non-competitive inhibition

Answer 32

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

Question 33

Plavix

Answer 33

a non-competitive inhibitor of platelet ADP receptors.

Question 34

Irreversible inhibitors

Answer 34

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)

Question 35

Suicide substrates

Answer 35

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.

Question 36

Disulfiram (Antabuse)

Answer 36

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

Question 37

compartmentalization

Answer 37

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).

Question 38

modes of enzyme regulation

Answer 38

compartmentalization, substrate availablilty, enzyme quantity

Question 39

regulation by enzyme quantity

Answer 39

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

Question 40

regulation of enzyme activity

Answer 40

product inhibition, allosterism, modulator proteins, covalent regulation.

Question 41

Product inhibition

Answer 41

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.

Question 42

Sigmoidal curve

Answer 42

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

Question 43

Feedback inhibition

Answer 43

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.

Question 44

Feedforward activation

Answer 44

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

Question 45

Aspartate transcarbamoylase (ATCase)

Answer 45

catalyzes the rate-limiting step in bacterial pyrimidine biosynthesis.

Question 46

Covalent regulation

Answer 46

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

Question 47

Reversible covalent modifications

Answer 47

phosphorylation, adenylation, uridylyation, ribosylation, methylation.

Question 48

Enterokinase

Answer 48

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

Question 49

proteolysis

Answer 49

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

Question 50

zymogen

Answer 50

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

Question 51

glucose 6-phosphate inhibits…

Answer 51

Hexokinase

Question 52

Homotropic

Answer 52

same chemical nature as true substrate.

Question 53

Heterotropic

Answer 53

different chemical nature from true substrate