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ABI 102 WINTER QTR > Finals > Flashcards

Finals Flashcards

1
Q

Why is glycolysis the most important metabolic pathway?

A
  • found in nearly all cells
  • starts catabolism of glucose
  • sole course of ATP and NADH for some cells/condition
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2
Q

How many steps does glycolysis have?

A

10 steps to oxidize glucose to pyruvate

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3
Q

How many important products does glycolysis have?

A

3 important products:
- 2 pyruvate
- 2 ATP
- NADH

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4
Q

What are the two phases in glycolysis?

A
  • preparatory phase
  • payout phase
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5
Q

What happens in the preparatory phase?

A

2 ATP consumed in steps 1 and 3

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6
Q

What happens in the payout phase?

A

4 ATP produced in steps 7 and 10
2 NADH produced in step 6

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7
Q

What is the Net in Glycolysis?

A
  • 2 ATP generated
    = 4 payout - 2 preparatory
  • 2 NADH generated
    = 2 payout
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8
Q

What is step 1 in glycolysis?

A
  • phosphorylation of glucose to glucose 6P
  • uses ATP
  • traps glucose inside cell
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9
Q

What is the enzyme that phosphorylates glucose into Glucose 6- phosphate?

A

hexokinase

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10
Q

What happens during phosphorylation?

A

once phosphorylated it will be trapped in the cell

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11
Q

What happens in step 2 in glycolysis?

A
  • isomerization of Glucose -6P
  • rearranges molecules to make step 3 easier
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12
Q

What enzyme used during the process of isomerization of glucose-6P to fructose 6-phosphate?

A

phosphohexose isomerase

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13
Q

What happens in step 3 in glycolysis?

A
  • phosphorylation of fructose-6P
  • uses ATP
  • first committed step of glycolysis
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14
Q

what enzyme is used during the phosphorylation of fructose -6P to Fructose 1,6-biphosphate

A

phosphofructokinase -1 (PFK-1)

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15
Q

Why is step 3 the first committed step in glycolysis?

A
  • earlier intermediates can be used in other pathways
  • highly regulated (e.g inhibited by ATP)
    = signals the cell that it does not need more ATP
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16
Q

What happens in step 4 in glycolysis?

A
  • cleavage of fructose 1,6P2
  • creates two triose phosphates
    • phosphate sugars with 3 carbons
  • Lysis step that gives pathway its name
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17
Q

What enzyme is used during the cleavage of fructose 1,6P2 to the following:

Dihydroxyacetone phosphate
Glyceeraldehyde 3-phosphate

A

aldolase

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18
Q

What does lysis mean?

A

molecules that are broken down into two

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19
Q

What happens in step 5 in glycolysis?

A
  • isomerization of dihydroxyacetone-P
  • Only glyceraldehyde-3P can be used in later steps
    = dihydroxyacetone - P must be converted to it.
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20
Q

what enzyme is used in isomerization of dihydroxyacetone -P to Glyceraldehyde 3- phosphate?

A

triose phosphate isomerase

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21
Q

What step does payout phase start?

A

step 6

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22
Q

What happens in step 6 in glycolysis?

A
  • phosphorylation and oxidation glyceraldehyde-3P
  • uses Pi, NOT ATP
    • allows for later ATP production, with no ATP investment
  • produces NADH
    • 1 per glyceraldehyde-3P
    • 2 per glucose
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23
Q

What enzyme is being used during phosphorylation and oxidation of glyceraldehyde -3P to 1,3 Biphosphoglycerate

A

Glyceraldehyde 3-phosphate dehydrogenase

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24
Q

What happens in step 7 of glycolysis?

A
  • transfer of phosphoryl group to ADP
  • 1st production of ATP
    • 1 per 1,3-biphosphoglycerate
    • 2 per glucose
  • enzyme name (phosphoglycerate kinase) is confusing
    - named fro reverse reaction (phosphorylation of 3-phosphoglycerate)

This is the first time getting ATP back

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25
Q

What happens in step 8 of glycolysis?

A
  • isomerization of 3-phosphoglycerate
  • moves phosphoryl group to position better for later steps

(shifting phosphoryl group to a better location)

  • performed by phosphoglycerate mutase
    • involves an intermediate with two phosphoryl groups (2,3-biphosphoglycerate)
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26
Q

What enzyme is used during isomerization of 3-phosphoglycerate to 2-phosphoglycerate?

A

phosphoglycerate mutase

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27
Q

What happens in step 9 of glycolysis?

A
  • dehydration of 2-phosphoglycerate
  • creates a compound with high phosphoryl group potential
    -∆rG’˚ for PEP hydrolysis = 61.0 kj/mol = really favorable
    • makes it possible to synthesize ATP in step 10
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28
Q

What enzyme is used during the dehydration of 2-phosphoglycerate to phosphoenolpyruvate

A

enolase

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29
Q

what happens in step 10 in glycolysis?

A
  • transfer of phosphoryl group to ADP
  • 2nd production of ATP
    • 1 per PEP
    • 2 per glucose
  • production of pyruvate
    • 1 per PEP
    • 2 per glucose
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30
Q

what enzyme is used during the transfer of phosphoenolpyruvate to pyruvate?

A

pyruvate kinase

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31
Q

Glycolysis has energetically favorable and unfavorable steps. Give examples :)

A
  • some steps are highly favorable (∆ rG’ «0) = easy to carry out
    • example: phosphorylation of glucose (step 1; ∆rG’ =-33 kj/mol)
  • other steps are not (∆rG’ ~ 0) = difficult to carry out
    • example: isomerization of glucose-6P ; ∆rG’ ~ 0 kj/mol)
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32
Q

_______ speeds up during cancer?

A

Glycolysis

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33
Q

Why does glycolysis speed up during cancer?

A
  • cancerous tissues have 10x faster glycolysis
    • warbug effect
    • provides pyruvate faster to support anabolism
  • detectable by PET scan
    • detects tissues taking up glucose analog (FdG)
    • high uptake -> cancer
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34
Q

Why does glycolysis speed up during cancer?

A
  • cancerous tissues have 10x faster glycolysis
    • warbug effect
    • provides pyruvate faster to support anabolism
  • detectable by PET scan
    • detects tissues taking up glucose analog (FdG)
    • high uptake -> cancer
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35
Q

What continues the catabolism of glucose?

A

Pyruvate metabolism and TCA cycle

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36
Q

why is pyruvate metabolism and TCA cycle continue catabolism of glucose important to take note of?

A
  • completes oxidation of pyruvate (from glycolysis) to CO2
  • produces most NADH and FADH2 available to cell
    • used to generate ATP by oxidative phosphorylation
  • present in all cells that respire (use O2 during catabolism)
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37
Q

_______ has a single step with two important products?

A

Pyruvate metabolism

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38
Q

Pyruvate metabolism is a single step with two important steps

A
  • connects glycolysis with the TCA cycle
  • pyruvate is oxidized to acetyl - CoA
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39
Q

What are the two important products of pyruvate metabolism?

A

1 Acetyl - CoA
1 NADH

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40
Q

What enzyme is used during the oxidization of pyruvate to acetyl - CoA?

A

pyruvate dehyrdogenase complex (E1+ E2 + E3 )

41
Q

What is the center of metabolism?

A

Acetyl -CoA

  • catabolized during TCA cycle but is also used in anabolism
42
Q

How many steps are there in the TCA cycle?

A

8 steps to oxidize 1 acetyl-CoA to 2 CO2

43
Q

How many important products are there in the TCA cycle?

A

3 important products
- 3 NADH
- 1 FADH
- 1 GTP

44
Q

What is step 1 in the TCA cycle?

A
  • condensation of acetyl-CoA (2 carbons) with oxaloacetate (4 carbons)
  • product (citrate) is 6 carbons
45
Q

what enzyme is being used during the condensation of acetyl-coa and oxaloacetate?

A

citrate synthase

46
Q

what is step 2 in the TCA cycle?

A

-isomerizarion of citrate to isocitrate
- involves intermediate cisaconitrate
- sometimes it is considered in two separate steps

47
Q

what enzyme is used during the isomerization of citrate to isocitrate?

A

citrate -> aconitae -> (intermediate ) cis-aconitrate ->aconitase -> isocitrate

48
Q

what is step 3 in the TCA cycle?

A
  • oxidation and carboxylation of isocitrate
    -forms NADH or NADPH
    -one isoenzyme forms NADH, and another form NADPH
  • product (∂- ketoglutarate) is 5 carbons
49
Q

what enzyme is being used in the oxidation and carboxylation of isocitrate to ∂ ketoglutarate

A

isocitrate dehydrogenase

50
Q

What is step 4 in the TCA cycle?

A
  • oxidation and decarboxylation of ∂-ketoglutarate
  • forms NAGH
    -product (succinyl - CoA) is 4 carbons
    • no more carbons are lost during cycle
51
Q

What enzyme is being used during the oxidation and decarboxylation of ∂ - ketoglutarate?

A

∂- ketoglutarate dehydrogenase complex

52
Q

what is step 5 of TCA cycle?

A
  • conversion of succinyl-CoA to succinate
  • from GTP or ATP
    • depending on isoenzyme used!!!!!
  • only step that directly forms NTP
    • rest are formed during oxidative phosphorylation

bacteria = atp not gtp

53
Q

what enzyme is used during the conversion of succinyl - CoA to succinate?

A
  • succinyl-CoA synthethase
54
Q

what is step 6 in the TCA Cycle?

A
  • oxidation of succinate
  • forms FADH2
    • remains bound to enzyme (unlike NADH)
    • enzyme is part of respiratory chain in oxidative phosphorylation
55
Q

What enzyme is being used during the oxidation of succinate to fumarate?

A

succinate dehydrogenase

56
Q

what is step 7 in TCA Cycle?

A

hydration of fumarate
- product is L- malate not D- malaate (stereospecific)

57
Q

What enzyme is being used in the hydration of fumarate to L-malate?

A

fumarase

fumarate -> carbanion transition state -> L-malate

58
Q

what is step 8 in the TCA cycle?

A
  • oxidation of malate
    • forms NADH
    • product is oxaloacetate which is the substrate for first step
    • completes the cycle
59
Q

what enzyme is used during the oxidation of L-malate to oxaloacetate?

A

L-malate dehydrogenase

60
Q

T/F: TCA cycle generates large numbers of reduced enzymes

A

True because it does the following:
- generates more than other steps of glucose catabolism
- fate of reduced coenzyme is oxidative phosphorylation
- Or fermentation (in anaerobic organisms)

61
Q

What are the other roles of the TCA cycle?

A
  • involved in the catabolism of other nutrients
    • amino acids
    • fatty acids
    • anything else that produces acetyl-CoA
  • involved in anabolism
    • intermediates are siphoned off for anabolic pathways
      • amino acid synthesis
62
Q

How does oxidative phosphorylation complete glucose catabolism?

A
  • oxidizes reduced coenzymes (NADH and FADH2), completing catabolism of glucose
  • generates most ATP available to cell
  • Present in all cells that respire (use O2 during catabolism)
  • Reason why we breath oxygen :))))))
63
Q

How many protein complexes do oxidative phosphorylation involve?

A

5 protein complexes in total

  • first 4 complexes
    + oxidize reduced coenzyme (e- donors) with O2
    + generate H+ gradient
  • Last complex (ATP synthase)
    + uses H+ gradient to synthesize ATP
64
Q

Where does the Oxidative phosphorylation occur?

A

+ Mitochondria
- protein complexes are in inner membrane
- TCA cycle enzymes are in the matrix
- Glycolysis enzymes are the cytosol (not in the mitochondria)

65
Q

What are the two different paths of oxidative phosphorylation?

A

NADH is the electron donor
I-III-IV-V
FADH2 (succinate) is the electron donor
II-III-IV-V

66
Q

NADH pathway: what happens in complex I?

A
  • oxidizes NADH
    -Reducs quinone (Q), forming QH2
  • Builds up gradient of 4 H+
    • 4H+ pumped out of the matrix into the intermembrane space
    • An additional 2H+ is consumed during quinone reduction, but this is canceled out by 2H+ released by dehydrogenases
67
Q

NADH pathway: what happens in complex II?

A

SKIPPED

68
Q

NADH & FADH2pathway: what happens in complex III?

A
  • Oxidizes QH2
  • reduces cytochrome C (Cyt c)
  • builds up gradient of 2H+
    • 2H+ pumped out
69
Q

NADH & FADH 2pathway: what happens in complex IV?

A
  • oxidizes Cyt c
    -Reduced O2 to water
  • Builds up gradient of 4 H+
    • 2H+ pumped out
    • 2H+ consumed with water formation
70
Q

NADH pathway: what happens in complex V?

A
  • ATP synthase (complex V)
  • synthesizes ATP from H+ gradient
    • 1 ATP/ 4H+
      = 2.5 ATP / 1 NADH
71
Q

NADH pathway summary

A
  • complexes I, III, IV
  • oxidize NADH with O2
  • pump/consume 10H+

COMPLEX II = NOT INVOLVED

ATPase
- synthesizes 2.5 ATP/NADH

72
Q

FADH2 pathway: what happens in complex I?

A

SKIPPED

73
Q

FADH2 pathway: what happens in complex II?

A
  • succinate reduces FAD+ to FADH2
  • FADH2 reduces Q to QH2
  • part of TCA cycle (succinate dehydrogenase)
74
Q

FADH2 pathway: what happens in complex V?

A
  • Same as NADH but H+ gradient is smaller
    – 6H+ FADH2 vs 10 H+ NADH
  • less ATP is synthesized
    • 1.5 ATP/ 1 FADH2
75
Q

FADH2 pathway summary

A
  • complexes I1, III, IV
  • oxidize NADH with O2
  • pump/consume 6H+

COMPLEX I = NOT INVOLVED

ATPase
- synthesizes 1.5 ATP/NADH

76
Q

How many ATPs are yielded in the whole catabolism of glucose?

A

~32

77
Q

What are the other roles of oxidative phosphorylation?

A

Involved in catabolism of other nutrients
- Amino Acids
- Fatty Acids
- Anything else that produces NADH or FADH2

78
Q

What are the two ways to synthesize ATP?

A
  • Electron transport phosphorylation
  • Substrate level phosphorylation
79
Q

What is Electron Transport Phosphorylation?

A

ATP formed by ATP synthase
Example: ATP synthase in oxidative phosphorylation

80
Q

What is substrate-level phosphorylation?

A

ATP formed by via substrate with phosphoryl group
example: pyruvate kinase in glycolysis

81
Q

In glucose catabolism how many ATPs are from oxidative phosphorylation vs substrate level phosphorylation?

A
  • 28 ATP from oxidative phosphorylation
  • 4 ATP from substrate level phosphorylation
    === We breathe O2 to make most of our ATP
82
Q

Why is fermentation important in absence of O2?

A
  • No O2 as final electron acceptor = cells cant perform oxidative phosphorylation
  • reduced coenzymes (NADH and FADH2) from glycolysis and TCA cycle quickly build up
  • Oxidized coenzyme (NAD+ and FAD+) are quickly depleted
  • metabolism cant continue
  • fermentation is an alternative
    • used pyruvate or other organic compounds as electron acceptor
83
Q

why is fermentation to lactate important in many organisms?

A
  • pyruvate reduced to lactate in single step using lactate dehydrogenase
  • consumes 1NADH/pyruvate
  • allows glycolysis to continue with no O2
    • Glycolysis produces 1 NADH/pyruvate
84
Q

why is fermentation to lactate important in animals

A
  • muscles during intense exercise
    • not enough O2 to sustain oxidative phosphorylation
  • erythrocytes
    • lack mitochondria for TCA cycle
  • cancerous cells
    -Warburg effect
85
Q

why is fermentation to lactate important in microbes?

A
  • bacteria in yogurt and other fermented products
  • microbes from cow rumen during lactic acidosis
    • produce lactate when quickly changed to high grain
    • lower rumen pH to dangerous levels (< 5.2)
    • can kill host
86
Q

why is fermentation to ethanol important to microbes?

A
  • pyruvate reduced to ethanol in two steps
    • consumes glycolysis to continue with no O2
    • same as lactate
  • important to microbes
    • yeast = used in production of most alcohol
    • Zymomonas mobilis = bacterium used in production of tequila
87
Q

why is fermentation to VFA important to cattle?

A
  • Volatile Fatty Acids (VFA)
    • Acetate
    • Propionate
    • Butyrate
  • formed by microbes in the rumen of cattle from feed carbohydrate
  • absorbed and metabolized by cow
    • fulfill up to 70% of total energy needed by host
88
Q

VFA: what is propionate

A
  • formed by phosphoenilpyvruate in 9 steps
  • consumes NADH (NAD red)
  • also produces ATP

(TCA cycle in reverse)

89
Q

VFA: what is acetate

A
  • formed from pyruvate in 3 steps
  • produces ATP
  • produces reduced ferredoxin (Fd red)
  • does not consume NADH
    • does not have the same role as other fermentation pathways
  • can be formed using a second pathway
    • forms. some products as first pathway, but last two enzymes differ
90
Q

VFA: what is butyrate?

A
  • formed from pyruvate in 7 steps
  • produces ATP
  • Consumes NADH and produces reduces ferredoxin
91
Q

What are the industrial importance of other fermentations

A
  • fermentation to produce biofuels and chemicals
    – ethanol
    – butanol
    – acetone
  • dome with microbes at a large scale in tanks
92
Q

what are the other alternatives to oxidative phosphorylation?

A
  • anaerobic respiration
    – respiration without O2
    — uses inorganic electron acceptors other than O2
    + Nitrate (forms nitrite)
    + Sulfate ( forms sulfide)
    + CO2 (forms methane)
    — important in microbes

methanogen = type of microbe in the rumen that forms CO2

93
Q

what are the two important sources of glucose?

A

-gluconeogenesis and glycogen

94
Q

why are the two important sources of glucose important?

A
  • some organs can use only glucose, not other nutrients
    – example : brain
  • glucose can come from die, but used up within hours of fasting
    -body used two glucose sources to meet needs
    – glycogen (polysaccharide of glucose)
    – gluconeogenesis (glucose synthesis)
95
Q

_______ is mobilized to and from glycogen

A

Glucose

96
Q

What is glucose degradation?

A
  • mobilizes glucose during fasting
  • also called glycogenolysis
  • glycogen phosphorylase breaks (∂1->1) bonds
    – release glucose 1P
    — conserves 1 ATP equivalent by releasing glucose - 1P, not glucose
    – stops when near branch point with (∂1->6) bond
  • debranching enzyme breaks (∂1->6) bonds
    – also has a transferase activity shown
    – sets up glycogen phosphorylase to break remaining (∂1–>4) bonds
97
Q

what is glycogen synthesis?

A
  • replenishes stores of glycogen during well-fed state
  • also called glycogenesis
98
Q

what happens during glycogen synthase elongates (∂1->4) chains

A

– uses UDP-glucose as precursor
– requires an input of 2 ATP equivalents

99
Q

what happens during the glycogen-branching enzyme forms (∂1->6) bonds

A
  • makin more non-reducing ends
    — increases sites for synthesis and degradation
  • makes glycogen more water-soluble

ABI 102 WINTER QTR (4 decks)

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