Brainscape's Knowledge GenomeTM

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


See full index

Biochem > Exam III > Flashcards

Exam III Flashcards

1
Q

Claisen Condensation Notes

A
  • Additional of an enolate to an ester
  • Use sodium ethoxide
  • Steps 4 and 5 are irreversible
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

Oxidative Patheays

A

Glycolytic

TCA

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

Glyceraldehyde-3-phoshphate dehydrogenase

Glycolysis

A
  • Step 6
  • Inorganic Pi as pi source
  • Form NADH
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Phosphoglycerate Kinase

Glycolysis

A
  • Step 7
  • Transfers phosphate to ADP forming ATP
  • Drives reaction 6
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

Reaction 4 CAC

A

alpha-ketoglutarate to succinyl CoA

  • Enzyme = alpha-ketoglutarate dehydrogenase
  • Decarboxylation
  • Requires TPP
  • CoA is nucleophile
  • Generate NADH, very favorable
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

PFK-2

A
  • Puts phosphate at 2 position
  • Active when it is not phosphorylated
  • Stimulated by: insulin
  • Inhibited by: glucagon
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

CCK

A
  • From Small intestine
  • Stimulates release of pancreatic digestive enzymes and bile salts from gallbladder
  • Stimulates nervous system + g-coupled receptors to signal fullness
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Step 1 Glycolysis

(type, in, out, energy, enzyme, regulation)

A

Type: Phosphoryl Transfer

In: Glucose + ATP

Out: Glucose-6-phosphate + ADP

Energy: Favorable, irreversible

Enzyme: Hexokinase

Regulation: Inhibited by glucose-6-phosphate

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

Rationale for the first 5 steps of glycolysis

A
  • Investment
  • Need to generate two 3-carbon fragments
  • Do a retro aldol on fructose
  • If done on glucose would form a 2C and a 4C
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

1 Krebs Turn input

A

3 NAD+

Acetyl CoA

Pi

FAD

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

Regulation of Metabolic Pathways

A
  1. Quantity of enzyme present is regulated by gene transcription
  2. REgulated allosterically or via covalent modification in response to ATP/ADP ratio
  3. Accessibility of substrates
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Pyruvate Carboxylase

Gluconeogenesis

A

Step 1

  • Conversion by enzyme occurs in mitochondria
  • Converted to malate and transport to cytoplasm where it is reoxidized to oxaloacetate + NADH
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Fast Krebs Facts

A
  • In the mitochondria
  • Aerobic
  • Goal is to generate NADH
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

Triose Phosphate Isomerase

A
  • Step 5 Glycolysis
  • Dihydroxyacetone to g3p
  • via enediol rearrangement
  • Glutamate is general base
  • His is general acid
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

Step 8 Glycolysis

A

Type: Phosphoryl Shift

In: 3-phosphoglycerate

Out: 2-phosphoglycerate

Energy:

Enzyme: Phosphoglycerate mutase

Regulation: n/a

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

Small Intestine

A
  • Secretes sodium bicarbonate and CCk
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

NaNH2

A
  • Remove hydrogen from HC=-CH

(that thing between carbons is a triple bond)

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

Sodium Bicarb

A
  • From small intestine
  • Neutralizes acid
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

Gluconeogenesis Regulated Enzymes

A
  • Pyruvate Carboxylase
  • Phosphenol-carboxykinase
  • Fructose-1,6-bisphosphatase
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

Aldol Dehytradion

A

HEAT

  • Driving force is a conjugated product
    1. OH removes alpha hydrogen leaving a LP
    2. LP forms a double bond between alpha and beta carbons… kick off OH as LG
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

Step 4 Glycolysis

A

Type: Aldol cleavage

In: Fructose-1,6-bisphosphate

Out: Glyceraldehyde-3-phosphate + Dihydroxyacetonephosphate

Energy: not favorable

Enzyme: Aldolase

Regulation: n/a

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

Enzymes regulated in glycolysis

A

Hexokinase

Phosphofructokinase

Pyruvate Kinase

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

Pyruvate Dehydrogenase

TPP

A
  • Deprotonated TPP is a good nucleophile that is used in the PDH reactions
  • Deprotonated TPP is how you form the ylide
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

Thermodynamic Enolate

A
  • More stable
  • Removal of most sterically accessible alpha hydrogen is removed

NaOH at Room Temp

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

Ylide

A
    • and - charged on adjacent atoms
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

Irreversible steps of gluconeogenesis

A
  1. Pyruvate carboxylase
  2. Fructose-1,6-bisphosphatase
  3. Glucose-6-phosphatase
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

Crossed Claisen with Ketone Enolate as Nuc

A
  1. Deprotonation of ketone to form enolate
  2. Addition to ester

Product is a diketone

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

Glycolysis or gluconeogenesis?

A
  • Glucose abundant –> glycolysis
  • Glucose scarce –> gluconeogenesis
  • ATP required –> glycolysis
  • Glucose required –> gluconeogensis
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

Anabolic

A

Used to synthesize macromolecules and their subunits

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

Step 7 Glycolysis

A

Type: Phosphoryl Transfer

In: 1,3-BPG + ADP

Out: 3-Phosphoglycerate + ATP

Energy: favorable

Enzyme: Phosphoglycerate Kinase

Regulation: n/a

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

Catabolic

A

Used to hydrolyze macromolecules and break down subunits

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

Glucagon on PFK2

A
  • Adds a phosphate
  • Deactivates it
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

Step 6 Glycolysis

A

Type: Phosphorylation coupled to oxidation

In: Glyceraldehyde-3-phosphate + Pi + NAD+

Out: 1,3-Bisphosphoglycerate + NADH + H

Energy: Not favorable

Enzyme: Glyceraldehyde-3-phosphate dehydrogenase

Regulation: n/a

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

Aldolase

A
  • Step 4
  • Fructose-1,6-Bisphosphate –> Glyceraldehyde-3-phosphate and dihydroxyacetone phosphate
  • Retro aldol to get to g3p
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

Pyruvate –> Acetyl CoA

Reaction Type

A

Decarboxylation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

Phosphofructokinase Graph

A
  • Low ATP: MM, to the left
  • High ATP: sigmoidal, to the right

ATP binds to the T state of enzyme

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

ATP hydolysis energetics

A
  • Exergonic
  • Reduce repulsion of negative chrages when hydrolyzed
  • ADP + Pi has more resonance structures
  • Water can bond to ADP and Pi more readily offering stability
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

Debcarboxylation

A
  • Pericyclic
  • 3 arrows
  • Arrows follow one another
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
39
Q

Digesting Lipids

A
  • Gallbladder secretes bile salts to make triglycerides more accessible to lipases
  • Micelles carry triglycerides to intestinal epithelium
  • Reformed into triglycerols
  • Packed into lipoprotein chylomicron and enter blood
40
Q

PFK-1

A
  • Phosphofructokinase 1
  • Puts a phosphate at position 1
  • Stimulated by Fructose-2,6-Bisphosphate
41
Q

Gluconeogenesis Overview

A
  • Synthesis of new glucose from lactate, pyruvate, AAs
  • occurs mainly in the liver and kidneys
  • Need glucose available for brain and RBCs
42
Q

TPP

A
  • Thiamine pyrophosphate
  • Used as a coenzyme in decarbox of pyruvate
  • Contains a thiazolium ring when deprotonated
  • Forms an ylide
  • Reauired to decarboxylate an alpha ketoacid…. needs to become covalently bonded to the pyruvate so need to make TPP nucleophilic
43
Q

Reaction 1 CAC

A

Acetyl CoA –> Citrate

Aldol reaction with thioester intermediate

Very favorable b/c of thioester int.

Enzyme = Citrate synthase

44
Q

Retro Aldol in Glycolysis

A
  • Step 4
    1. Ketone condenses with lysine to make iminium ion at C2. Due to increase acidity of beta hydroxy, H is removed via a tyrosine
    2. C-C bond cleavage… aldehyde and enamine
    3. Enamine hydrolysis to yield dihydroxyacetone phosphate
45
Q

NaOH and enolates

A
  • NaOH can remove an alpha hydrogen from a double enolate
46
Q

Step 10 Glycolysis

A

Type: Phosphoryl Transfer

In: PEP + ADP + H

Out: Pyruvate + ATP

Energy: Very favorable, irreversible

Enzyme: Pyruvate kinase

Regulation: Inhibited by excess ATP

47
Q

Aldol Condensation

A
  1. Hydroxide removes alpha hydrogen forming a resonance stabilized enolate anion
  2. Nucleophilic addition to carbonyl carbon… 2 arrows
  3. O- removes hydrogen from water to generate a neutral aldol product
48
Q

Alpha Amylase

A

Breaks down alpha 1,4 bonds

49
Q

Why enediol?

A
  • Easily convert between ketones and aldehydes
50
Q

What gets oxidized and reduced with PDH?

A
  • Oxidize pyruvate
  • Reduce NADH
51
Q

Step 5 Glycolysis

A

Type: Isomerization

In: Dihydroxyacetonephosphate

Out: Glyceraldehyde-3-phosphate

Energy: not favorable

Enzyme: Triose phosphate isomerase

Regulation: N/a

52
Q

Acid Catalyzed Enolization

A
  1. Protonation of carbonyl oxygen from acid H
  2. A- removes hydrogen from alpha carbon and form c=c double bond and break c=o pi bond
53
Q

Pathways for Fructose and Galactose

A
  • Undergo glycolysis

Gal –> Glucose 6P

Fru –> Fructose 6P

54
Q

Step 3 Glycolysis

A

Type: Phosphoryl Transfer

In: Fructose-6-phosphate + ATP

Out: Fructos-1,6-bisphosphate + ADP

Energy: Favorable, irreversible

Enzyme: Phosphofructokinase

Regulation: + from ADP, - from ATP

55
Q

Kinetic Enolate

A
  • Formed fasted
  • Removal of the more sterically accessible alpha H

LDA at -78 C

  • Less stable
56
Q

Suctase and Lactase

A

Digests sucrose and lactose respectively

57
Q

Net effects of reactions 6 and 7 in glycolysis

A

Aldehyde –> Carboxylate

58
Q

Insulin on PFK2

A
  • Stimulates
  • Removes phosphate
59
Q

Dieckmann Condensation

A
  • Intramolecular Claisen
  • Closes 5 or 6 membered rings
  • NaOEt and acidic workup
60
Q

Reaction 3 CAC

A

Oxidation of OH in isocitrate and isomerization

  • Isocitrate dehydrogenase
  • NAD+ reduced
  • Isocitrate oxidized
  • Decarboxylation of beta-keto

isocitrate - alpha-ketoglutarate

61
Q

Goal of metabolism

A

Generate ATP

62
Q

Reaction 6 CAC

A

Succinate to Fumarate

  • Enzyme is Succinate Dehydrogenase
  • Reduce FAD to FADH2
63
Q

Crossed Claisen with Esters

A
  1. Pre-form enolate
  2. Reaction of enolate with a different ester
64
Q

Pyruvate Kinase

A
  • Step 10
  • ADP attacks PEP
  • Tautomerization of enol to ketone
  • Very favorable/ irreversible
  • Drives step 9
  • Inhibited by excess ATP
65
Q

Carbon oxidation state and energy

A

higher oxidation state of carbon, less energy you get out when you convert to CO2

66
Q

Hexokinase

A
  • Step 1 glycolysis
  • ATP is phosphate source, not energy source
  • Inhibited by Glucose-6-phosphate
67
Q

LDA and ketone

A
  • Can remove a hydrogen from a CH3 on a ketone
68
Q

1 Krebs Output

A

3 NADH

1 GTP

2 CO2

1 FADH2

69
Q

alpha-olextrinase

A

Cleaves alpha 1,6 bonds

70
Q

Tautommers

A

Structural isomers that are readily interconverted

Ketones and enols

71
Q

Why does gluconeogenesis only occur in the liver and kidney?

A
  • No other cell type shave the glucose-6-phosphatase enzyme
  • Enzyme transported to ER lumen
  • Useful for glycogen synthesis
72
Q

Fermentation

A
  • Anaerobic respiration
  • Only do when we need NAD+
  • Reduce pyruvate to lactate and oxize NADH –> NAD+ via lactate dehydrogenase
  • Makes 2ATP per glucose
  • Replenishes NAD+ supply for glycolysis
73
Q

Claisen Condensation Mechanism

A
  1. Remove alpha hydrogen
  2. Addition of enolate to another molecule of neutral ester
  3. Regenerate carnoyl, kick off LG
  4. Deprotonation of extremely acidic alpha H which is alpha to two carbonyls
  5. Acidic workup to reprotonate
74
Q

Phosphoglycerate Mutase

Glycolysis

A
  • Step 8
  • A different phosphate is put on C2 than what was on C3
  • Creates beta-hydroxycarboxylate for next reaction
75
Q

Step 9 Glycolysis

A

Type: Dehydration

In: 2-phosphoglycerate

Out: PEP + H20

Energy:

Enzyme: Enolase

Regulation: n/a

76
Q

Crossed Aldol****

A
77
Q

Reaction 7 CAC

A
  • Fumarate to Malate
  • Enzyme is fumarase
  • Conjugate addition of water
78
Q

Decarboxylation reactions in biochemistry

A

Krebs

isocitrate –> alpha-ketoglutarate

Alpha-ketoglutarate –> succinyl CoA

Pyurvate –> Acetyl CoA

79
Q

Phosphoglucose Isomerase

Glycolysis

A
  • Step 2 Glycolysis
  • Glucose –> Fructose
  • Converts aldehyde to ketone via enediol intermediate
  • Lysine+ is acid catalysit
  • His is base catalist
  • Glutamate+ is base catalyst
  • First step is ring opening
80
Q

ATP is energy rich

A
  • Charge repulsion
  • Resonance
  • Hydration
81
Q

Oxidation in CAC Overall

A

Carbon oxidized from -2 to +2

Generate NADH

82
Q

Enolase

A
  • Step 9
  • Dehydration reaciton
  • Water formed
  • Not super favorable
83
Q

Reaction 5 CAC

A
  • Convert Succinyl CoA to Succinate
  • Generates a GTP from GDP + Pi
  • Looks like hyrdolysis but inorganic phosphate instead of water
  • Hydrolysis, phosphorylation, dephosphorylation in this step
84
Q

Step 2 Glycolysis

A

Type: Isomerization

In: Glucose-6-phosphate

Out: Fructose-6-phosphate

Energy: unfavorable

Enzyme: Phosphoglucose isomerase

Regulation: n/a

85
Q

Phosphoryl-Transfer Potential

A
  • Higher PTP than ATP means you can use it to make ATP
  • Lower PTP than ATP means you cannot use it to make ATP
86
Q

Reaction 2 CAC

A

Isomerization of citrate to isocitrate

  • Enzyme = cis-aconitase
  • Isomerization, dehydration, then conjugate addition
87
Q

Retro Aldol

A
  1. OH deprotonates alcohol
  2. O- reforms C=O pi bond… kick enolate out as LG
  3. Enolate anion steals H from water generating neutral product

3 drives 2.

88
Q

Basic Enolization Mechanism

A
  1. Remove alpha hydrogens
  2. Form c=c pi bond
  3. Protonation of O- with water
89
Q

Reaction 8 CAC

A

Malate to oxaloacetate

  • Enzyme is malate dehydrogenase
  • Oxidation of secondary alcohol to ketone
  • Generates NADH
  • not very favorable, driven by reaction 1
90
Q

Amphibolic

A

Intermediary pathways which can syntehsize or break down molecules

91
Q

NaOEt in Claisen

A
  • One of the esters has no alpha hydrogens and must be the electrophile
  • Will form two products
92
Q

Step of glycolysis that uses NAD+

A

Step 6

93
Q

Step of CAC that uses NAD+

A

3

4

8

94
Q

Step of CAC that uses FAD

A

6

95
Q

Pyruvate Dehydrogenase

Lipoate

A
  • Lipoate acts as an oxidizing agent in the second reaction of the PDH complex
  • Contains a disulfide
  • Enables you to do the transthioesterification with coenzyme A
96
Q

Glycolysis Steps that generate ATP

A

7

10

Biochem (2 decks)

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