Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Biochemistry Final > Enzyme Mechanisms > Flashcards

Enzyme Mechanisms Flashcards

1
Q

What is the active site of a molecule?

A

The place where the enzyme binds. Often a pocket or cleft surrounded by amino acid residues that help bind the substrate (and other residues that play a role in catalyst).

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

How does a substrate recognize the active site?

A

Through complimentarity.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What is the Lock and key hypothesis of enzyme binding and why did it suck?

A

The enzyme accommodates the specific substrate as a lock does a specific key. Increased understanding in enzyme specificity but didn’t help our understanding of catalyst because a lock does nothing to its key

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What is the Induced fit hypothesis?

A

The enzyme doesn’t just accept the substrate it, the enzyme also demands that the substrate be distorted into something close to the transition state.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What must an efficient catalyst do in regards of the transition state?

A

An efficient catalyst will stabilize the transition state and thereby lower its free energy relative to other states.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What are the four basic steps in enzyme binding? [enzyme (E), substrate (S), product (P)]

A

E+S -> ES -> EP -> E+P

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What are the three genera l things that all enzymes do?

A

1.) binds to substrate or substrates. 2.) Lowers the energy of the transition state. 3.) Directly promotes the catalytic event. when the catalytic processes is over the enzyme must be able to release its original product and return to its original state

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Is formation of the enzyme-substrate complex thermodynamically favorable? Why?

A

Oh yeah, because of complementarity.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What are the 6 ways an enzyme may achieve rate enhancement?

A
  1. ) preferred binging to the transition state through complementarity noncovalent bonding interactions (H-bonds, charge-charge, etc.) (NC- bonds are electrostatic in nature so this is called electrostatic catalysis.)
  2. ) Distortion of the substrate and/or active site which premotes reduction of the activation energy (induced fit)
  3. ) binding of substrates to optimize proximity & orientation (making ΔS °# more favorable)
  4. )altering the reaction pathway to include intermediate states. (typical of covalent catalysis)
  5. ) general acid/base catalysis (GABC) important in reactions involving proton transfer.
  6. ) metal ion catalysis
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Whats a general acid in enzyme hell?

A

Donates an H+ to an atom that develops a negative charge in the transition state.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

Whats a general base in enzyme hell?

A

Removes an H+ from a atom that develops a positive charge in the transition state

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Whats special about histadine in GABC?

A

It can donate protons at a physiological pH.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

What are Metalloenzymes?

A

Enzyme with a metal ion at its active site.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

Where is the active site of lysozyme located?

A

In a deep cleft

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

How many glycosyl residues bind to lysozyme?

A

6 reidues bind to substituents A-F

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

Where does lysozyme cleave the glycosidic bond?

A

In between residues D-E

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

How to describe an amino acid mutation of glutamic acid replacing glutamine at residue 35 in single letter code?

A

E35Q

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

What is Lysozymes optimum pH?

A

~5

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

Whats a serine protease?

A

Important class of enzymes. Called protease because they catalyze the hydrolysis of peptide bonds in polypeptides and proteins. This general class of protease is unique because they all have a critical serine nuleophine in the active site. Hydrolyze a large variety of esters.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

What is a scissile bond in a serene protease?

A

A very specific binding of a particular amino acid that serves to place the active site serine very close to the carbonyl group of the bond to be cleaved.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

What is a catalytic triad?

A

Common feature of serine protease. Has a nucleophile, general base, and acid (in many theyre composed of serine, histidine, and aspartic acid residues presented in similar 3D orientation in the active site.)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

What is a Low-barrier hydrogen bond?

A

Shorter, 3-6 times stronger, w/ more covalent character.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

What is conformational selection (selected fit)?

A

Implies that the unbound enzyme has multiple conformations but the substrate can only bind to an unbound enzyme with the same conformation.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

What are the two general categories of “tailor made” catalyst?

A

Rational design and directed evolution

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

Example of tailoring a catalyst by James Wells.

A

Research focused on a specificity pocket in a protease (subtilisn). The site is usually occupied by gly. Protease comes thru and cleaves the “polypeptide chains next to the bulky hydrophobic residue”. When gly is replaced with lys this cleavage happens 500x faster.

26
Q

What are fusion proteins?

A

Proteins coded for by genes that have been spliced together in vitro from two or more sources.

27
Q

What are cofactors?

A

A cofactor is a non-protein chemical compound or metallic ion that is required for a protein’s biological activity to happen.

Cofactors are not irreversibly changed during catalysis; they are either unmodified or regenerated.

28
Q

How do cofactors relate to organisms in general?

A

Cofactors often have complex organic structures that cannot be synthesized by some organisms – mammals in particular.

29
Q

What is the vitamin-B complex?

A

The collective name for the water soluble vitamins that are metabolic precursors of several cofactors in the body.

B1, B2, B12, Niacin, and more.

30
Q

What is NAD+?

A

NAD+ is nicotinamide adenine dinucleotide

It is derived from the vitamin niacin

31
Q

What is the active part of NAD+?

A

The nicotinamide portion is capable of being reduced and serves as an oxidizing agent to which two eletrons and a proton are added to the nicotinamide ring

32
Q

What does alcohol dehydrogenase do?

A

Turns ethanol to aldehyde

33
Q

How does NAD+ act as a cofactor? Example

A

When it is reduced to NADH and then reoxidized to regenerate the NAD+ all within the same enzyme/catalytic reaction

34
Q

How does NAD+ act as a substrate? Example

A

When it is turned into NADH and then has to go to another enzyme to be reoxidized and become NAD+ again

35
Q

What are metalloenzymes?

A

They are enzymes that contain one or more metal ions

Usually held by coordinate covalent bonds from amino acid side chains, but sometimes bound by a prosthetic group like heme.

36
Q

What are the six major classes of enzymes?

A
  • Oxidoreductases
  • Transferases
  • Hydrolases
  • Lyases
  • Isomerases
  • Ligases
37
Q

What do oxidoreductases do?

A
  • Catalyze oxidation-reduction reactions
38
Q

What do transferases do?

A

Catalyze transfer of functional groups from one molecule to another

39
Q

What do hydrolases do?

A

Catalyze hydrolytic cleavage

40
Q

What do lyases do?

A

Catalyze removal of a group from or addition of a group to a double bond, or other cleavages involving electron rearrangement

41
Q

What do isomerases do?

A

Catalyze intramolecular rearrangement

42
Q

What do ligases do?

A

Catalyze reactions in which two molecules are joined

43
Q

What are ribozymes?

A

RNA molecules that can act as enzymes

44
Q

What is ribonuclease P and what does it do?

A

Ribonuclease P is an RNA-protein complex that catalyzes the hydrolysis of a phosphodiester bond which is involved in the production of tRNA from pre-tRNA.

The RNA portion can do this by itself.

45
Q

Are there DNA that act as enzymes?

A

None have been found in nature.

Some have been developed in labs

46
Q

What is substrate-level control?

A

A type of enzyme regulation that occurs when the products of an enzyme interact with the substrate of that enzyme itself.

Usually inhibits

47
Q

What is feedback inhibition?

A

An increase in the concentration of E leads to a decrease in its rate of production by inhibiting the enzyme that converts A to B

A->B->C->D->E

48
Q

What is allosteric regulation?

A

Allosteric regulation is the regulation of an enzyme by binding an effector molecule at a site other than the enzyme’s active site.

49
Q

What is homoallostery?

A

Cooperativity in substrate binding. Binding of one substrate favors binding of additional substrates.

For example, hemoglobin

50
Q

What is heteroallostery?

A

If an enzyme can exist in two conformational states, T and R, then:

Allosteric inhibitors shift the equilibrium toward T

Allosteric activators shift the equilibrium toward R

51
Q

What is ATCase?

A

An enzyme called aspartate transcarbamoylase

52
Q

What is covalent modification in the context of enzymes?

A
  • Some enzymes are inactive until they are covalently modified
  • Some enzymes are inactivated by the covalent modification
  • Some covalent modifications can be reversed, others not.
53
Q

What are protein kinases?

A

Protein kinases are ATP-dependent enzymes that add a phosphoryl group to the OH group of a Tyr, Ser, or Thr on some target protein

54
Q

What are phosphatases?

A

They reverse the process of protein kinases: phosphatases hydrolyze side chain phosphate esters, releasing Pi

55
Q

What is acetylation?

A

The transfer of an acetyl group from acetyl-coenzyme A

56
Q

What is a zymogen?

A
  • Catalytically inactive molecules that must be cleaved in order to yield active enzymes
57
Q

How does stereospecificity come into play with enzymes?

A

The asymmetric surface of an enzyme can confer stereospecificity in the reaction of a symmetric substrate.

If the substrate molecule X2 makes at least make three contacts with unique complementary groups on the enzyme, its two X atoms are no longer equivalent.

Only a specific one of the two X atoms can contact the surface properly.

58
Q

What is the proposed mechanism for UDP-galactose epimerase?

A
  1. UDP-galactose is bound to the enzyme, which carries the coenzyme NAD+.
  2. Hydride is transferred to NAD+ from C4 of the galactose ring to produce the carbonyl intermediate.
  3. Hydride is then transferred back to C4 to give the opposite stereochemistry.
  4. The product, UDP-glucose, is released
59
Q

How do ATP and CTP regulate ATCase?

A
  • ATP is an activator.

- CTP is an inhibitor.

60
Q

Activation of chymotrypsinogen:

A

A series of cleavages produces the enzyme chymotrypsin, with the disulfide bonds continuing to hold the structure together.

The initial cleavage between amino acids 15 and 16 (arrow) results in the formation of p-chymotrypsin.

Subsequent removal of the segments shown in black yields a-chymotrypsin.

61
Q

What sort of catalytic activation does blood clotting use?

A

Blood clotting involves a cascade of proteolytic activation of specific proteases, culminating in the transition of fibrinogen to fibrin.

62
Q

Where does the proteolytic activation to blood clotting start?

A

Intrinsic pathway: The cascade of proteolytic activations starts from exposure of blood at damaged tissue surfaces.

Extrinsic pathway: The cascade of proteolytic activations starts from internal trauma to blood vessels.

Biochemistry Final (4 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions