Brainscape's Knowledge GenomeTM

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


See full index

Biochemistry II > Recap Test 1 > Flashcards

Recap Test 1 Flashcards

1
Q

Glycolysis

In the preparatory phase of glycolysis, the hexose molecule ___________________ is phosphorylated at carbons ___ and ___ and then cleaved to form two molecules of __________________________.

A

Glucose

C1

C6

Glyceraldehyde-3-phosphate

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

Glycolysis

The conversion of glucose-6-phosphate to fructose-6-phosphate plays a critical role in the overall chemistry of the glycolytic pathway. Why?

A

Because the rearrangement of the carbonyl and hydroxyl groups at C-1 and C-2 is a necessary prelude to the next two steps: (1) the formation of fructose-1,6-bisphosphate requires the carbonyl group at C-1 be converted to an hydroxyl group and (2) the following step requires a carbonyl group at C-2 for the cleavage of the bond between C-3 and C-4

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

Glycolysis

The phosphohexose isomerase reaction uses general acid base catalysis to convert glucose-6-phosphate to fructose-6-phosphate via an _________________ intermediate.

A

Enediol

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

Glycolysis

Aldolase, which cleaves fructose-1,6-bisphosphate, requires two critical amino acid residues for functioning. What are they?

A

Lysine

Aspartate

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

Glycolysis

What is an overview of the aldolase mechanism?

A
  1. The carbonyl reacts with active site lysine residue to form an amine, which is then converted to an imine or Schiff base
  2. Condensation occurs
  3. Bond cleavage releases G3P
  4. The resulting enamine covalently linked to the enzyme is isomerized to a protonated Schiff base
  5. Hydrolysis of the Schiff base generates DHAP
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Glycolysis

What is the mechanism of aldolase?

A
  1. Lys attacks carbonyl and protonates O
  2. Hydrogen atom of Lys “kicks back,” forms double bond between N and C, and releases H2O
  3. Asp deprotonates O on C4, breaking C3 and C4 bond and yielding G3P and an ENAMINE intermediate
  4. Lone pair of Lys “kicks back” and protonates alkene (C2=C3) via Asp
  5. Water deprotonates and attacks the carbon of the enamine
  6. Hydroxyl group “kicks back,” forming a carbonyl group that expels Lys and forms DHAP
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

Glycolysis

What is the name of this strucutre?

A

Dihydroxyacetone phosphate

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

Glycolysis

What is the name of this structure?

A

Glyceraldehyde-3-phosphate

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

Glycolysis

What is the mechanism for GAP dehydrogenase?

A

Oxidation-reduction

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

Glycolysis

What cofactor does GAP dehydrogenase require?

A

NAD+

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

Glycolysis

What amino acid residue acts as the nucleophile in GAP dehydrogenase catalysis?

A

Cysteine

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

Glycolysis

What is the mechanism for glyceraldehyde-3-phosphate (GAP) dehydrogenase?

A
  1. Cys acts as a nucleophile and attacks carbonyl C (C1)
  2. Hydride released and forms NADH
  3. Inorganic phosphate attacks the carbonyl C (C1) and expels enzyme
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Glycolysis

Why is GAP dehydrogenase important in glycolysis?

A

Because it catalyzes the formation of NADH

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

Glycolysis

GAP dehydrogenase requires the cofactor NAD+ and what other molecule to form 1,3-bisphosphoglycerate from glyceraldehyde-3-phosphate?

A

Inorganic phosphate

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

Glycolysis

Phosphoglycerate mutase requires a phosphorylated amino acid residue in its active site to function. What amino acid residue is it?

A

Histidine

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

Glycolysis

What is of phosphoglycerate mutase?

A
  1. Deprotonated His abstracts proton from hydroxyl on C2
  2. O acts as nucleophile and attacks electrophilic phosphorus on phosphohistidine residue
  3. Dephosphorylated His attacks phosphate group on C3, restoring phosphorylated status, and O picks up proton from other protonated His residue
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

Glycolysis

What intermediate produced via phosphoglycerate mutase is also important in regulating hemoglobin?

A

2,3-bisphosphoglycerate

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

Glycolysis

What is the mechanism of action for enolase?

A

Dehydration and general-acid catalysis

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

Glycolysis

Enolase requires a metal ion. What metal ion does it require?

A

Mg2+

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

Glycolysis

What is the role of Mg2+ in the enolase mechanism?

A

It makes the proton even more acidic

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

Glycolysis

What is the point of forming phosphoenolpyruvate?

A

It is a high energy compound that can be used to make ATP - 2-phosphoglycerate cannot

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

Glycolysis

What is the mechanism for enolase?

A
  1. Lys abstracts proton from C2, forming unstable carbanion
  2. Lone pair delocalizes to O atom of carbonyl, which is stabilized by Mg2+
  3. O “kicks back” and expels water from C3 by deprotonating Glu
  4. Phosphoenolpyruvate is formed
23
Q

Glycolysis

What two amino acid residues are required for enolase activity?

A

Lysine

Glutamate

24
Q

What is the limiting reagent in glycolysis?

A

NAD+

25
Q

Fermentation

In alcoholic fermentation, pyruvate must first be decarboxylated into acetaldehyde and carbon dioxide by what enzyme?

A

Pyruvate decarboxylase

26
Q

Fermentation

Alcoholic fermentation requires two steps. What are they?

A
  1. Decarboxylation of pyruvate to acetaldehyde and carbon dioxide
  2. Reduction of acetaldehyde to ethanol
27
Q

Fermentation

What coenzyme is required for the functioning of pyruvate decarboxylase?

A

Thiamine pyrophosphate or TPP

28
Q

Fermentation

What part of the coenzyme thiamine pyrophosphate or TPP is the “business end” or the chemically reactive part regarding the decarboxylation of pyruvate?

A

The thiazolium ring

29
Q

Fermentation

What is the mechanism for pyruvate decarboxylase?

A
  1. Thiazolium ring is deprotonated
  2. Carbanion functions as nucleophile and attacks the carbonyl C of pyruvate, reducing carbonyl to hydroxyl
  3. O “kicks back,” releases carbon dioxide, and forms C=C, causing electrons to move on to N of thiazolium ring
  4. Lone pair “kick back” and double bond between thiazolium ring and C is protonated, leaving behind a hydroxyl group
  5. Hydroxyl group loses its H, “kicks back” and reforms the carbonyl, and expels enzyme, leaving behind acetylaldehyde
30
Q

Fermentation

Does the non-enzymatic decarboxylation of an alpha-keto acid work? Why or why not?

A

No, it does not work; non-enzymatic decarboxylation will only occur with a beta-keto acid as the products of decarboxylation of an alpha-keto acid are unstable

31
Q

Fermentation

What enzyme reduces acetaldehyde to ethanol in alcoholic fermentation?

A

Alcohol dehydrogenase

32
Q

Fermentation

What metal ion is required for alcoholic fermentation?

A

Zinc is required in the reduction of acetaldehyde to ethanol by alcohol dehydrogenase

33
Q

What is the first bypass reaction in gluconeogenesis?

A

Pyruvate is transported into the mitochondrial matrix via pyruvate transporter and acted upon by pyruvate carboxylase with the help of biotin, its covalently attached coenzyme

34
Q

Pyruvate is first transported from the cytosol into mitochondria where pyruvate carboxylase, a mitochondrial enzyme that requires the coenzyme ____________, converts pyruvate to oxaloacetate. The reaction involves the coenzyme as a carrier of activated ______________.

A

Biotin

Bicarbonate

35
Q

What are the two steps to the pyruvate carboxylase mechanism?

A
  1. Bicarbonate activation & carboxybiotinyl-enzyme formation: bicarbonate is activated via phosphorylation (at expense of ATP); biotin attacks C carbonyl, which releases inorganic phosphate and leaves carbon dioxide
  2. Oxaloacetate formation: carbon dixode is carried to next catalytic site, where it is released and reacts with pyruvate, forming oxaloacetate and regenerating the biotinyl-enzyme.
36
Q

Is the conversion of pyruvate to oxaloacetate via pyruvate carboxylase energy-requiring or energy-producing?

A

Energy-requiring; it requires ATP

37
Q

What reactant is required for pyruvate to be converted to oxaloacetate via pyruvate carboxylase?

A

Carbonate

38
Q

How is biotin covalently linked to pyruvate carboxylase?

A

Via an amide linkage at a lysine residue

39
Q

What is the mechanism for pyruvate carboxylase?

A
  1. O on bicarbonate attacks gamma P of ATP, releasing ADP and a proton (“activated molecule of carbon dioxide”)
  2. N of biotin attacks C carbonyl, ultimately “kicking out” phosphate, which is a good leaving group
  3. H from pyruvate’s methyl group deprotonates, forming carbanion that attacks the carbonyl C of carboxy-biotin, ultimately kicking out biotin and reforming the enzyme by protonating N on its way out
40
Q

How many active sites does biotin have?

A

Two - in one active site, biotin picks up carbon dioxide; in the other active site, biotin transfers carbon dioxide

41
Q

The product of catalysis by pyruvate carboxylase is oxaloactetate, which must be moved back into the cytosol to continue gluconeogensis. How does the cell accomplish this?

A

Through the malate-oxaloacetate shuttle system

42
Q

Identify this compound.

A

Oxaloacetate

43
Q

How does the malate-oxaloacetate shuttle system function?

A
  1. Oxaloacetate is converted to malate via malate dehydrogenase
  2. Malate is transported out of the mitochondria via the malate transporter
  3. Once in the cytosol, malate is converted back into oxaloacetate by malate dehydrogenase
44
Q

Once oxaloacetate moves back into the cytosol it is acted up by which enzyme?

A

PEP carboxykinase

45
Q

Oxaloacetate is converted to _________________________ via PEP carboxykinase.

A

Phosphoenolpyruvate

46
Q

What is the mechanism of PEP carboxykinase?

A

It is a decarboxylation followe by a phosphoryl transfer (from GTP)

47
Q

What cofactor is required for PEP carboxykinase to function?

A

GTP

48
Q

What chemical changes does pyruvate carboxylase catalyze? In other words, what happens to pyruvate?

A

A carbon dioxide molecule (COO-) is added to pyruvate, resulting in a four carbon molecule with an additional terminal COO- group

49
Q

Does PEP carboxykinase facilitate a carboxylation or decarboxylation?

A

Decarboxylation

50
Q

What is the first step in the PEP carboxykinase mechanism?

A

Removal of CO2

51
Q

What is the second step in the PEP carboxykinase mechanism?

A

Phosphoryl transfer from GTP

52
Q

PEP carboxykinase catalyzes the conversion of oxaloacetate to what intermediate of glycolyis?

A

Phosphoenolpyruvate

53
Q

Describe the mechanism of PEP carboxykinase?

A
  1. O anion on C4 kicks back and expels CO2
  2. Carbanion forms on C3, which then kicks back, forming an alkene with C2, and the carbonyl oxygen becomes phosphorylated
54
Q

Note that the carbon dioxide added to pyruvate in the _____________ ___________________ step is the same molecule that is lost in the _______ _______________ reaction. This carboxylation-decarboxylation sequence represents a way of “activating” pyruvate, in that the decarboxylation of oxaloacetate facilitates PEP formation.

A

Pyruvate carboxylase

PEP carboxykinase

Biochemistry II (19 decks)

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