Brainscape's Knowledge GenomeTM

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


See full index

BIOCHEM EXAMs > L13. Enzyme Structure and Function > Flashcards

L13. Enzyme Structure and Function Flashcards

1
Q

Define an enzyme

A

Proteins acting as the body’s catalysts.

They speed up time for chemical reaction without being consumed themselves

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

What would happen without enzymesi n the body?

A

The cell’s chemical reactions would either be too slow or not take place at all

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

What is an oxidoreductase and what does it do?

A

Axidoreductase is a closs of enzyme that catalyzes the transfer of electrons from one molecule, the reductant (e- donor), to another, the oxidant (e- acceptor), usually utilizes NADP+ or NAD+ as cofactors.

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

What is an example of an oxidoreductase?

A

alcohol dehydrogenase (ADH)

  • oxidizes alcohol to acetaldehyde while subsequently reducing an NAD+ cofactor to NADH.
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What is a transferase?

A

A transferase is any one of a class of enzymes that catalyse the transfer of specific functional groups (e.g. a methyl or glycosyl group) from one molecule ( donor) to another (acceptor), usually by using ATP and ADP as cofactors.

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

What is an example of transferase?

A

Hexokinase. An enzyme that phosphorylates hexoses (six-carbon sugars) from ATP to a substrate, forming hexose phosphate

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

Define lyases

A

an enzyme that catalyzes the breaking (an elimination reaction) of various chemical bonds by means other than hydrolysis and oxidation, often forming a new double bond or a new ring structure.

The reverse reaction is also possible.

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

What is Hydrolase?

A

A class of enzyme that catalyzes via the use of water to break a chemical bond, which typically results in dividing a larger molecule into smaller molecules.

Some common examples: esterases including lipases, phosphatases, glycosidases, peptidases, and nucleosidases.

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

What is Carboxypeptidase A?

A

A hydrolase enzyme that cleaves peptide bonds.

The pancreatic exopeptidase that hydrolyzes peptide bonds of C-terminal residues with aromatic or aliphatic side-chains.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Hydrolases use what type of reaction?

A

a substitution reaction

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

What is an example of a lyase enzyme?

A

Pyruvate decarboxylase.

an enzyme that catalyses the decarboxylation of pyruvic acid to acetaldehyde.

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

Define isomerases

A

a general class of enzymes that convert a molecule from one isomer to another.

Isomerases facilitate intramolecular rearrangements in which bonds are broken and formed.

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

Give an example of an isomerase.

A

maleate isomerase

responsible for catalyzing cis-trans isomerization of the C2-C3 double bond in maleate to produce fumarate, which is a critical intermediate in citric acid cycle.

The presence of an exogenous mercaptan (Thiol or thiol derivative) is required for catalysis to happen.

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

Define a ligase.

A

an enzyme that can catalyze the joining (ligation) of two large molecules by forming a new chemical bond.

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

What is Pyruvate carboxylase (PC)?

A

It is encoded by the gene PC is an enzyme of the ligase class that catalyzes (depending on the species) the physiologically irreversible carboxylation of pyruvate to form oxaloacetate (OAA).

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

What are cofactors?

A

A non-protein chemical compound or metallic ion that is required for an enzyme’s role as a catalyst. considered “helper molecules” that assist in biochemical transformations.

Cofactors can be divided into two types: inorganic ions and complex organic molecules called coenzymes.

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

What are coenzymes?

A

Small organic molecules that can be loosely or tightly bound to an enzyme that transport chemical groups from one enzyme to another

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

True or False?

At high concentration of lactate, the enzyme exhibits feedback inhibition, and the rate of conversion of pyruvate to lactate is decreased.

A

True

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

What is lactate dehydrogenase (LDH)?

A

LDH is an enzyme that catalyzes the interconversion of pyruvic acid and lactic acid with concomitant interconversion of NADH and NAD+.

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

True or False?

Without cofactor, the enzyme can’t lock the reacting substance (substrate) into its active site, so the reaction can’t take place.

A

True.

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

Most vitamin definciencies happen due to a lack of ________.

A

Cofactor

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

In many cases, the cofactor is part of the enzyme active site and thought to play a role in ________.

A

stabilizing the transition state

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

True or False?

Enzymes not only lower the activation energy of a reaction but ∆G also changes.

A

False.

Enzymes only ower the activation energy of a reaction while ∆G remains the same

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

The energy of the substrate and product are __________.

A

unaffected by an enzyme.

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

How do enzymes catalyze reactions?

A

They change the shape slightly, creating an ideal fit for catalysis.

This is done by:

  1. Provides a reaction surface (the active site) and a suitable environment (hydrophobic)
  2. Positions the substrate in the correct orientation and weakens bonds in the substrates
  3. Lowers the activation E and promotes its rapid progression (easier reaction)
  4. Return to the original state at the completion of the reaction
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

What does the binding wtih induced fit involve and how is it helpful?

A

The binding involves intermolecular bonds between functional groups in the substrate and functional groups in the active site.

The substrate also changes shape to maximize bonding interactions.

This results in tighter bonding to the active site.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

In the binding of of pyruvic acid into LDH, what bond is weakened to facilitate induced fit?

A

The pi bond on the alpha carbon to Oxygen 1. This happens so that oxygen 1 can hydrogen bond to LDH.

28
Q

True or False?

The binding interactions must be sufficiently strong to hold the substrate for the subsequent reaction, but they cannot be too strong.

A

True.

If the binding interactions were too strong, the product might also be bound strongly and fail to depart the active site.

29
Q

If the binding interactions between a substrate and enzyme were too strong, making the product fail to depart the active site, what would happen?

A

This would block the active site of the enzyme and prevent it from completeing another reaction.

30
Q

True or False?

With transition-state inhibitors, the enzyme also binds to the transition state involved in the enzyme-catalyzed reaction, which is not as strong as the binding interactions with the substrate.

A

False.

Binding to the transition state is stronger than substrate binding. This is what stabilizes the intermediate.

31
Q

True or False?

The transition state is more stabilized than the substrate. This results in a lower activation energy compared with the non-catalyzed reaction

A

True

32
Q

In acid/base cataylsis, The Imidazole ring exists in _______ between its protonated and base forms.

A

equilibrium

33
Q

In acid/base cataylsis, the non-ionized enzyme acts as a ______ catalyst, called the ________.

A

Basic; proton ‘sink’

34
Q

In acid/base catalysis, the ionized enzyme acts as a _______ and is the ________.

A

Acid cataylst; proton source

35
Q

The ionized Imidazole ring is stabilizes by _______.

A

The resonance stabilization of the charge.

36
Q

What is the catalytic triad?

A

Serine (Ser) is H-bonded to Histidine (His), which is further H-bonded to Aspartic acid (Asp).

37
Q

Define Serine protease

A

Cleaves peptide bonds in proteins, in which serine serves as the nucleophile (donate an e- pair to an electrophile to form a chemical bond).

38
Q

What is an example of a Serine protease?

A

Chymotrypsin.

39
Q

How is the catalytic triad formed?

A

As the O of Serine attacks the carbonyl C of a peptide bond, the H-bonded Histidine functions as a general base to abstract the Serine proton.

The negatively charged Aspartic acid stabilizes the positive charge that forms on the Histidine. This prevents the development of a very unstable positive charge on the Serine hydroxyl and increases its nucleophilicity.

40
Q

How are enzyme regulated and why are they regulated?

A

Via feedback inhibition, which uses allosteric deactivation.

The final product of multiple enzymes binds to the allosteric site of the first enzyme and switches off the enzyme which shuts off all the following enzymes.

This prevents too much build-up of product and provides a means of self-regulating in a system.

41
Q

What is an oxyanion hole?

A

A pocket which stabilizes a deprotonated O of the tetrahedral intermediate formed by

the Two peptide NH groups of the polypeptide backbone by donating H-bonds to the negatively charged O of the tetrahedral intermediate

42
Q

What is allosteric control?

A

It is inhibition or activation of an enzyme by a small regulatory molecule that interacts at a site (allosteric site) other than the active site (at which catalytic activity occurs).

43
Q

What is the difference between positive and negative modulation?

A

Positive allosteric modulators do not exhibit intrinsic agonism but facilitate agonist-mediated receptor activity.

Negative allosteric modulators include both non-competitive antagonists and inverse agonists.

Positive modulators are allosteric activators while negative modulators are allosteric inhibitors.

44
Q

What is an agonist?

A

Agonist is a substance which initiates a physiological response when combined with a receptor.

45
Q

Hemoglobin contains ________, each with an iron-containing heme group that loosely binds with an ____ molecule

A

4 subunits; O2

46
Q

The binding of oxygen to one subunit induces a conformational change in that subunit that interacts with the remaining active sites to __________.

A

enhance their oxygen affinity.

47
Q

Because oxygen enhances the affinity of a hemoglobin subunit, this makes oxygen both a _________ and _______.

A

substrate and allosteric activator

48
Q

True or False?

External signals cannot regulate the activity of enzymes.

A

False

Examples would be neurotransmitters or hormones

49
Q

What is an example of an external signal regulating enzyme activity?

A

Adrenaline is an external chemical messenger that initiates a signal cascade which activates enzymes protein kinases.

The protein kinases phosphorylates the inactive enzyme phosphorylase B to become active (phosphorylase A). This is covalent modification.

50
Q

True or False?

with respect to an enzyme’s ability to catalyze a reaction, An enzyme allows the reaction to go through a less stable transition state than would normally be the case.

A

False.

An enzyme makes the transition state MORE STABLE

51
Q

True or False?

An active site is normally hydrophilic in nature.

A

False.

The active site is hydrophobic

52
Q

True or False?

An active site contains amino acids which are important to the binding process and the catalytic mechanism.

A

True

53
Q

The process by which a substrate binds to an active site and alters the shape of the active site is called ________.

A

Induced fit

54
Q

A non-protein organic molecule that is bound covalently to the active site of an enzyme, and which is required if the enzyme is to catalyze a reaction on a substrate is called a ________.

A

PROSTHETIC GROUP

55
Q

Consider the following enzyme-catalyzed reaction:

A. What is the substrate?

B. What is the product?

C. What is the enzyme and what type is it?

D. What is the enzyme modulator that activates the enzyme?

A

A. Glycogen

B. Glucose-1-phosphate.

C. Phosphorylase a. This is a phosphorylase, type of transferase

D. AMP

56
Q

What chemical messenger triggers a cascade of cellular event that eventually activates the enzyme involved in this reaction?

A

Adrenaline

57
Q

Which amino acid commonly acts as a nucleophilic group in enzyme-catalyzed reaction mechanisms?

A

Serine

58
Q

Which of the following will change the ∆G of an enzyme catalyzed reaction?

A. Decreasing product concentration

B. Increasing temperature

C. ∆G is a constant and cannot be readily changed

D. Increasing enzyme concentration

A

B. Increasing temperature

59
Q

Which of the following statements regarding enzymes is NOT true?

A. Enzymes increase the kinetic barrier.

B. Enzymes speed up reactions by lowering the energy of activation.

C. Enzymes are not used up during reactions.

D. Enzymes do not affect the thermodynamics of a reaction.

A

A. Enzymes increase the kinetic barrier.

Enzymes decrease the kinetic barrier, not increase it

60
Q

In which of the following situations would there be the greatest yield of products at equilibrium following the addition of an enzyme?

A. A reaction favoring reactants and large activation energy.

B. A reaction with more stable reactants and small activation energy.

C. A reaction with less stable reactants and large activation energy.

D. A reaction favoring reactants and small activation energy.

A

C. A reaction with less stable reactants and large activation energy.

The greater the stability of the reactants, the more they are favored at equilibrium and the greater the stability of products, the more they are favored at equilibrium.

61
Q

What best explains the reason for the inability of the human intestinal tract to digest cellulose?

A. β(1,4) linkages

B. (1,6) linkages at branch points

C. 5’-3’ phosphodiester bonds

D. φ-ψ peptidyl linkages

A

A. β(1,4) linkages

Humans are unable to digest cellulose due to the large numbers of β(1,4) glycosidic linkages. These cannot be cleaved by human amylases and pass though the GI tract undigested.

62
Q

What is an agonist?

A

a substance which initiates a physiological response when combined with a receptor

63
Q

Compounds A and B react very slowly to form Compound C. Addition of a very small quantity of Enzyme X doubles the reaction rate. Addition of twice as much Enzyme X would most likely:

A. Increase the reaction rate by the same amount as the first addition of enzyme.

B. Have no effect, since reaction rate is independent of enzyme concentration.

C. Have no effect since the enzyme will be saturated with substrate

D. Increase the reaction rate by increasing the equilibrium constant.

A

A. Increase the reaction rate by the same amount as the first addition of enzyme.

Doubling the amount of enzyme doubles the number of available active sites, and so doubles the rate of the reaction.

64
Q

Define decarboxylation

A

Decarboxylation is a chemical reaction that removes a carboxyl group and releases carbon dioxide

65
Q

What is Chymotrypsin?

A

A serine protease produced by the pancreas that hydrolyzes the peptide bonds of tryptophan, leucine, tyrosine, and phenylalanine.

Two forms of chymotrypsin (1 and 2) are synthesized by the pancreas as inactive chymotrypsinogens.

66
Q

What is carboxylation?

A

Carboxylation is a chemical reaction in which a carboxylic acid is produced by treating a substrate with carbon dioxide.

BIOCHEM EXAMs (10 decks)

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