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Phys-Pro - section 2 > Metabolism > Flashcards

Metabolism Flashcards

1
Q

What 2 kinds of energy drive all cellular reactions?

A
  1. Electrochemical

2. Chemical

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2
Q

how are electrochemical gradients established?

A

ion gradients across cellular membranes

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3
Q

What does electrochemical energy drive?

A

solute transport, ATP synthesis, flagellar rotation

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4
Q

What 3 kinds of molecules can be included under chemical energy?

A
  1. ATP and other nucleotide derivatives

2. acyl phosphates (e.g. acetyl phosphate), 3. acyl-CoA (e.g. acetyl-CoA)

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5
Q

What does chemical energy drive?

A

biosynthetic reactions like protein synthesis as well as protein transport

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6
Q

What do ATP, Acetyl-CoA, and acyl phosphates all have in their structure?

A

High energy phosphate bonds

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7
Q

What are 3 key functions of central metabolic pathways

A
  1. Generate ATP

2. Generate reducing power ( in the form of NADH, NADPH, and FADH2)

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8
Q

What are the 3 central metabolic pathways?

A
  1. The glycolytic pathway (also called the Embden-Meyerhoff-Parnas (EMP) pathway)
  2. Pentose phosphate pathway
  3. Entner-Doudoroff pathway (ED)
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9
Q

Which of the 3 central metabolic pathways is found only in prokaryotic cells?

A

Entner-Doudoroff pathway (ED)

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10
Q

All 3 pathways convert _____ to _____* and then _____* to ______**

A

glucose to phosphoglyceraldehyde (glyceraldehyde 3-phosphate)
-different reactions

and then phosphoglyceraldehyde to pyruvate
-same reaction

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11
Q

What is the overall reaction of glycolysis?

A

Glucose + 2ADP + 2NAD+ +2Pi => 2pyruvate + 2ATP + 2NADH + 2H+

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12
Q

What is the overall reaction of the pentose phosphate pathway?

A

Glucose + 6NADP+ => 3CO2 + pyruvate + 6NADPH + ATP + 6H+

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13
Q

What is the overall reaction of the Entner Doudoroff Pathway?

A

Glucose + NADP+ + NAD+ + ADP + Pi => NADPH + NADH + ATP + 2H+

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14
Q

By what method is the ATP generated in the 3 main metabolic pathways?

A

substrate level phosphorylation

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15
Q

How many molecules of ATP are produced from one molecule of glucose ?

A

2 (net)

4 ATP generated in the second part from G3P to pyruvate because this happens twice (once for each G3P). Need to subtract the initial 2 ATP invested. Net is 2 ATP

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16
Q

At which reactions are ATP generated in glycolysis ?

A
  1. Converting 1,3- bisphosphoglycerate to 3-P-glycerate

2. from PEP to pyruvate

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17
Q

How many molecules of NADH are produced during glycolysis ? At which reaction?

A

One molecule of NADH is generated, going from glyceraldehyde-3-phosphate to 1,3-bisphosphoglycerate

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18
Q

Fructose-6-phosphate is a precursor for?

A

Amino Sugars like NAG and NAM

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19
Q

DHAP is a precursor for?

A

phospholipids and fatty acid synthesis

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20
Q

Glucose-6-phosphate is a precursor for?

A

polysaccharides, pentose phosphates, aromatic amino acids

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21
Q

3-phoshphoglycerate is a precursor for?

A

serine, glycine, cysteine

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22
Q

phosphoenolpyruvate is a precursor for?

A

aromatic amino acids and muramic acid

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23
Q

What is the initial group of steps in the pentose phosphate pathway? how many times does this occur? What metabolites are generated?

A

Turns glucose-6-phosphate into ribulose-6-phosphate

Occurs 3 times

[2 NADPH and 1 CO2 each time] x3
= 6 NADPH and 3CO2

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24
Q

What can happen to the CO2 produced in the pentose phosphate pathway?

A

if the bacteria can carry out photosynthesis then it can be used there. Also can be used for carboxylation reactions

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25
Q

What is the primary role of the PPP? (2)

A

generation of reducing power of NADPH

production of precursor metabolites used in anabolic reactions
-synthesis of nucleotides for nucleic acids, of aromatic amino acids, and of glucose by photosynthesis

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26
Q

What are the two products made from ribulose-5-phosphate

A
  1. Ribose-5-phosphate

2. Xylulose-5-phosphate

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27
Q

What important metabolite is derived directly from Xylulose-5-phosphate?

A

phosphoglyceraldehyde

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28
Q

What PPP metabolites are tryptophan, tyrosine, and phenylalanine derived from?

A

erythrose-6-P

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29
Q

What are two exampled of bacteria that use the ED pathway?

A

Gram-negative Pseudomonas aeruginosa and the Gram-positive Enterococcus faecalis

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30
Q

What is the critical enzyme in the ED pathway?

A

6-phosphogluconate dehydrase

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31
Q

How is the presence of 6-phosphogluconate dehydrase of clinical relevance ?

A

provides evidence of the Entner-Doudoroff pathway to identify the presence of potential pathogens.

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32
Q

If cells are respiring, then pyruvate is….

A

Oxidized to Acetyl-CoA which then enters the TCA cycle

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33
Q

If cells are fermenting, then pyruvate is….

A

converted to fermentation end products such as: organic acids, alcohols, and solvents.

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34
Q

What enzyme catalyzes the aerobic oxidation of pyruvate?

A

Pyruvate dehydrogenase

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35
Q

What two mechanisms can ferment pyruvate under anaerobic conditions?

A
  1. Phosphotransacetylase reaction

2. Acetate kinase reaction

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36
Q

What are the three steps in the action of pyruvate dehydrogenase?

A
  1. remove CO2 from pyruvate
  2. attach remaining 2 carbon acetate to coenzyme-A
  3. Reduction of NAD+ to NADH
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37
Q

What must happen to the NADH formed by pyruvate dehydrogenase?

A

Reoxidization of NADH is absolutely required to ensure the regeneration of NAD+

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38
Q

What are the three ways in which NADH can be reoxidized?

A
  1. Respiration
  2. Fermentation
  3. Hydrogenase reaction
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39
Q

What occurs during respiratory regeneration of NADH?

A

Respiration (Aerobic and facultative anaerobic bacteria) via the electron transport chain

NADH +H+ + B + yADP + yPi => NAD+ + BH2 +yATP

-Examples of B : O2 or NO3- ; BH2 : H2O or NO2

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40
Q

What occurs during fermentation as a means of regenerating NADH?

A

Fermentation (anaerobes) using an organic compound as the electron acceptor

NADH +H+ + B (organic) => NAD+ + BH2

-Example of B : pyruvate; BH2 : lactate

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41
Q

What is the hydrogenase reaction ? In what type of bacteria dose it occur?

A

NADH +H+ => NAD+ + H2

Occurs in anaerobes

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42
Q

What is the first step of the TCA cycle? what is regenerated and what is formed?

A

Acetyl-CoA enters the Krebs cycle by joining with oxaloacetic acid to form citric acid.

Coenzyme A is regenerated

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43
Q

What are steps 2-4 in in the TCA cycle? What reactions occur and what is produced?

A

Two oxidations and decarboxylations and the addition of coenzyme A yield succinyl-CoA

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44
Q

What occurs during the 5th step of the TCA cycle? Starting with succinyl-CoA

A

Substrate-level phosphorylation produces ATP and regenerates coenzyme A.

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45
Q

What reactions occur to regenerate the cycle? What metabolite must be regenerated?

A

Further oxidations and rearrangements regenerate oxaloacetic acid, and the cycle can begin anew.

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46
Q

How many molecules of ATP, NADH, NADPH, and FADH2 are produced in the TCA cycle? (per 1 molecule of glucose)

A

ATP: 2
NADH: 4
FADH2: 2
NADPH: 2

(reflects 2 turns of the cycle because each glucose molecule forms 2 acetyl-CoA molecules

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47
Q

How many CO2 are produced in the TCA cycle

A

2

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48
Q

Oxaloacetate is a precursor for….?

A

Aspartate

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49
Q

Aspartate itself is a precursor for?

A

asparagine, threonine, isoleucine, methionine, and lysine.

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50
Q

α-ketoglutarate is a precursor for …?

A

Glutamate

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51
Q

glutamate itself is a precursor for?

A

glutamine, proline, and arginine

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52
Q

What kind of regulation controls the TCA cycle?

A

Feedback inhibition by intermediates and end products

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53
Q

What inhibits citrate synthase?

A

NADH and α-ketoglutarate

-signal that the cycle is already saturated

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54
Q

What 4 things can oxaloacetate be generated from?

A
  1. Amino acids
  2. Malic acid
  3. PEP
  4. Pyruvate
  • PEP and pyruvate occur by carboxylation using CO2
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55
Q

what is the role of the catabolite-control protein A (CcpA)?

A

It’s a global regulator that represses several catabolic operons involved in the degradation of secondary carbon sources

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56
Q

What are the 2 levels at which enzymes in glycolysis and TCA cycle can be inhibited?

A
  1. Enzyme activity level

2Gene expression level

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57
Q

What cycle do aerobic bacteria require to grow on fatty acids and ?

A

The Glyoxylate Cycle

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58
Q

What else is the Glyoxylate Cycle important for?

A

other living things including some germinating seeds and developing nematodes from eggs.

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59
Q

What cycle is the Glyoxylate Cycle comparable to?

A

The TCA cycle?

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60
Q

What TCA cycle steps does the Glyoxylate Cycle omit?

A

Those that lead to a loss of CO2

61
Q

How many steps in the Glyoxylate Cycle bypass are there?

A

2

62
Q

What are the two enzymes involved in the bypass and what do they accomplish ?

A
  1. Isocitrate lyase
    - converts isocitrate to succinate and glyoxylate
  2. Malate synthase
    - condenses glyoxylate and another molecule of acetyl-CoA to malate
63
Q

What are the final products of the glyoxylate cycle?

A

1 molecule of succinate, 1 NADH, and regeneration of oxaloacetate

64
Q

What is the general definition of gluconeogenesis?

A

Synthesis of hexose sugars from pyruvate via the reversal of carbon flow

65
Q

What can be formed from the hexoses made in gluconeogenesis?

A

Polymers like starch and peptidoglycan

66
Q

What situation fuels gluconeogenesis?

A

growth on carbon poor environments

-need hexoses in order to maintain cell wall and make nucleic acid

67
Q

What are the 3 non reversible reactions in glycolysis? (in reverse order)

A
  1. Pyruvate to Phosphoenolpyruvate (PEP)
  2. Fructose-1,6-bisphosphate to Fructose-6-P
  3. Glucose-6-P to Glucose
68
Q

What are the 4 specialized enzymes that are used in gluconeogenesis to bypass the irreversible steps and what do they do?

A
  1. PEP carboxykinase and pyruvate carboxylase
    - go from pyuvate to PEP via oxaloacetate
  2. Fructose-1,6-bisphosphatase
    - forms fructose-6-phosphate from the dephosphorylation of fructose-1,6-bisphosphate
  3. Glucose-6-phosphatase
    - dephosphorylates glucose-6-phosphate to glucose
69
Q

What is the major regulatory step in gluconeogenesis?

A

catabolite repression of PEP carboxykinase

70
Q

What does catabolite repression of PEP carboxykinase mean?

A

Means that gluconeogenesis is inhibited when glucose or other carbohydrate sources are available

71
Q

What is the definition of a fermentation pathway?

A

a pathway in which the reduced electron acceptor (e.g. NADH) generated by oxidative reactions is re-oxidized by metabolites produced by the pathway.

72
Q

Where does NADH reoxidation occur?

A

In the cytosol

73
Q

How is ATP produced in fermentation reactions?

A

Solely by substrate level phosphorylation

74
Q

What is the main function of fermentation reactions?

A

Get rid of reducing power i.e. reoxidation of NADH

75
Q

What is the phosphoclastic reaction and what does it produce?

A

An example of substrate level phosphorylation

-oxidation of pyruvate to acetate via acetyl-CoA

76
Q

What do all common fermentations use as a substrate?

A

Pyruvate

77
Q

What do all common fermentations use as an electron donor?

A

NADH

78
Q

What 2 enzymes are used to anaerobically reduce pyruvate to acetyl-CoA?

A

Pyruvate-formate lyase

and

Pyruvate ferredoxin oxireductase

79
Q

What is a common type of product from fermentation reactions?

A

Alcohols

-many of which are useful for us like ethanol and isopropanol

80
Q

What are some examples of food products that rely on fermentation?

A

cheese, yogurt, soy sauce, wine, beer, nail polish remover, rubbing alcohol and vinegar, *swiss cheese (has CO2 bubble holes), chocolate (bacteria ferment the carbohydrates around the chocolate seed)

81
Q

Fermentation also plays an important role in which food chain?

A

The anaerobic food chain

82
Q

What are the three main reactions of the anaerobic food chain?

A
  1. fermentations
  2. acetogenic reactions
  3. methanogenic reactions
83
Q

What is the overall breakdown in the anaerobic food chain (reactants to products)

A

organic compounds to methane gas (CH4) and CO2

84
Q

Fermentation reactions are performed by?

What products are formed?

A

fermentors

-break down convert to acids, alcohols, H2, and CO2

85
Q

Acetogenic reactions are performed by?

What products are formed?

A

Obligate proton reducers and sulphate reducers

-convert to acetate, H2, and CO2

86
Q

Methanogenic reactions are performed by? What products are formed?

A

methanogens

-convert to CH4 and CO2

87
Q

Autotrophs are?

A

prokaryotes that use CO2 as the sole/major carbon source for growth

88
Q

What are examples of autotrophs?

A

nitrifying, nitrogen-fixing, and iron bacteria

89
Q

What are the 3 major autotrophic carbon fixation pathways in prokaryotes?

A
  1. Via the Calvin-Benson pathway
  2. Acetyl-CoA pathway
  3. Reductive TCA pathway
90
Q

Which bacteria use the Calvin-Benson carbon fixation pathway ?

A

cyanobacteria, photosynthetic bacteria, some nitrifying bacteria.

91
Q

In the Calvin-Benson cycle pathway of fixing carbon, 3 CO2 are converted to ?

A

phosphoglyceraldehyde

92
Q

What energy sources/reducing powers are required for the Calvin-Benson pathway of carbon fixation? How much?

A

9 ATP and 6 NAD(P)H

93
Q

What is the fate of phosphoglyceraldehyde?

A

can then enter the glycolytic pathway and pentose phosphate pathway

94
Q

What are the 3 main steps of the Calvin-Benson cycle?

A
  1. Three molecules of RuBP combine with three molecules of CO2.
  2. The resulting molecules are reduced to form six molecules of Glyceraldehyde-3-phosphate (G3P).
  3. Five molecules of G3P are converted to three molecules of RuBP, which completes the cycle.
95
Q

How many turns of the PPP are required to generate one molecule of gluocose-6-phosphate?

A

2

- Two turns of the cycle yield two molecules of G3P, which are polymerized to synthesize glucose 6-phosphate.

96
Q

What bacteria use the acetyl-CoA pathway of fixing carbon?

A

methanogens, acetogenic bacteria, and autotrophic sulfate-reducing bacteria

97
Q

What occurs during the acetyl-CoA pathway of fixing carbon? What special enzyme is required?

A

CO2 is converted to acetyl-CoA by an unique enzyme called carbon monoxide dehydrogenase.

98
Q

What type of bacteria makes use of the reductive TCA pathway

A

strict anaerobes (e.g. Desulfobacter), photosynthetic green bacteria, and the aerobic bacterium Hydrogenobacter

99
Q

What is the difference between the normal TCA and the reductive TCA?

A

Normal TCA cycle is oxidative: this is reverse TCA so ‘reductive TCA’

100
Q

What is achieved by the reductive TCA cycle?

A

Synthesis of oxaloacetate from 4CO2 via the carboxylation of PEP

101
Q

Which microorganisms are able to carry out photosynthesis?

A 
cyanobacteria, 
purple sulfur bacteria, 
green sulfur bacteria, 
green nonsulfur bacteria, 
purple nonsulfur bacteria, 
algae, 
and a few protozoa
102
Q

What is the basic composition of a chlorophyll?

A

A pigment composed of a hydrocarbon tail attached to light-absorbing active site centered around a Mg2

103
Q

Why is it beneficial for different bacteria to have the ability to be activated at different wavelengths of light ?

A

This allows them to live together in the same ecosystem and not rely all on the same wavelength of light

104
Q

What is the hierarchy of photosynthetic structures within an organism ?

A

Pigments are arranged within protein matrices called photosystems

Photosystems are embedded in cellular membranes called thylakoids

105
Q

What are thylakoids in bacteria?

A

Invaginations of the cytoplasmic membrane

106
Q

What is a reaction centre of a photosystem? how does energy arrive there? Where does the energy go from there?

A

Many chlorophylls absorb light energy and transfer it to neighbouring molecules until the energy eventually arrives at a special chlorophyll molecule called the reaction centre chlorophyll

This excites electrons in the reaction centre chlorophyll causing the passage of electrons to the electron acceptor in reaction centre

From there the electrons are passed through the ETC

  • during this process protons are pumped out to generate a PMF
  • ATP can then be generated
107
Q

What is photosystem I? How does it function? What phosphorylations are involved?

A
  • generates a proton gradient across the membrane and ATP is generated as protons are brought back in via ATPase.
  • involves both cyclic and non-cyclic photophosphorylations
108
Q

What is photosystem II? how does it function? What phosphorylations are involved?

A
  • generates O2 and a proton gradient.

- involves non-cyclic photophosphorylation only.

109
Q

What is Cyclic photophosphorylation ? Where does it occur?

A

occurs when the original electron donor is the final electron acceptor

Occurs in PSI

110
Q

What is non-cyclic phosphorylation?

A

Light energy hitting PSII excites electrons which are passed to PSI through ETC
-establishes a proton gradient

Further excitation of e’s at PSI and transfers them through an electron transport chain to reduce NADP+ to NADPH (via ETC)

NADPH is then used in glucose synthesis or CO2 fixation in the Calvin-Benson cycle

111
Q

How are the electrons replenished in non-cyclic phosphorylation?

A

Electrons must be constantly replenished to the reaction center of PS II and this is achieved via photolysis of H2O.

112
Q

What is the electron donor and what is the electron acceptor in non cyclic phosphorylation?

A

H20 is the electron donor, NADP+ is the electron acceptor

113
Q

Which two groups of microorganisms can engage in non-cyclic phosphorylation?

A

Only eukaryotes and cyanobacteria

114
Q

How do prokaryotes typically conduct the first step in the process of protein catabolism?

A

By secreting proteases and peptidases in to the extracellular fluid

  • hydrolyze proteins into peptides and amino acids.
  • because proteins are too large to cross cytoplasmic membranes
115
Q

What is deamination?

A

removal of amino groups from amino acids by special enzymes

116
Q

What happens to the remaining carbon amino acid skeletons after deamination?

A

enter the TCA cycle

117
Q

What happens to the removed amino groups after deamination?

A

either recycled to synthesize other amino acids (via amination, see later) or excreted as nitrogenous wastes

118
Q

What are 2 nitrogenous waste forms?

A

ammonia (NH3), or trimethylamine oxide (TMAO).

119
Q

When is TMAO used as a final electron acceptor?

A

In anaerobic respiration

120
Q

What is responsible for the fishy smell of non-fresh fish?

A

Activity of anaerobic bacteria reducing TMAO to trimethyl amine (TMA), a compound with a very definite “fishy” odor

121
Q

NO3- is first reduced to _____ , which is then incorporated into _______.

A

Ammonia (NH3), Glutamate

122
Q

The 1st step in the reduction from NO3- to NH3is done by ? Where? What intermediate is formed?

A

By nitrate reductase in the cytoplasm

converts NO3- to nitrite (NO2-)

123
Q

The 2nd step in the reduction from NO3- to NH3is done by ? Where?

A

cytoplasmic nitrite reductase, which reduces nitrite to NH3.

124
Q

What 3 electron donors are used in the assimilation of nitrate?

A

NADH, NADPH, Ferredoxin

125
Q

What two enzymes can perform the incorporation of NH3 into glutamate?

A

either glutamate dehydrogenase or by glutamine synthase (aka. GOGAT enzyme)

126
Q

Under what conditions is glutamate dehydrogenase used?

A

When NH3 is in excess

127
Q

under what conditions is glutamine synthase used?

A

When NH3 is limiting

128
Q

How is N2 assimilated?

A

N2 is reduced to NH3, which is then incorporated into glutamine or alanine.

129
Q

What 5 bacteria can fix nitrogen?

A

Azotobacter, Rhizobium, Clostridium, cyanobacteria (Anabaena), and Klebsiella

130
Q

How do Rhizobium interact with legumes? What kind of relationship is it?

A

The bacteria infect the roots and form root nodules, within which the bacteria fix nitrogen for the plants and the plants in turn feed organic nutrients to the bacteria.
-example of a symbiotic relationship

131
Q

Anabaena fixes nitrogen for what plants

A

Non-leguminous water fern plants

132
Q

What does nitrogenase do?

A

reduces nitrogen to ammonia

133
Q

How many components is nitrogenase composed of? What are they called?

A

2

Component I and component II (wow fun names)

134
Q

What is the structure of component I ?

A

molybdenum-iron-containing tetrameric protein

135
Q

What is the structure of component II ?

A

dimeric iron-containing protein

136
Q

Why is nitrogenase sensitive to oxygen?

A

The iron sulphur complex of component II is very exposed and the irons can easily be attacked by oxygen

137
Q

Do both of the components contain FeS centres?

A

yep

138
Q

You need a lot of ___ and ___ to fix nitrogen into ammonia

A

energy (ATP) and reducing power

139
Q

What modification do bacteria have to protect nitrogenase from oxygen?

A

specialized cells called heterocysts

- in addition to vegetative cells

140
Q

What is the structure of heterocysts?

A

Heterocysts have a very thick cell wall as a barrier to atmospheric oxygen and have a photosystem I that produces only ATP but not oxygen.

141
Q

What fixations are occurring in each type of cell?

A

CO2 fixation in the vegetative cell

N2 fixation in the heterocyst

142
Q

Whats a free living soil bacteria that can fix nitrogen?

A

Clostridium

143
Q

What coenzyme is used in all transamination reactions? From what is it derived?

A

Pyrodoxal phosphate

-derived from vitamin B6

144
Q

What amino acid is derived from oxaloacetate?

A

Aspartate

145
Q

What amino acid is derived from alpha ketoglutarate?

A

Glutamate

146
Q

The PPP provides what precursors that can be used for amino acid synthesis?

A

ribose 5-phosphate as well as erythrose 4-phosphate

147
Q

What occurs during amination? is it reversible or not?

A

amine group from ammonia is added to a precursor metabolite (an alpha keto acid)
-not reversible

148
Q

What occurs during transamination? is it reversible or not?

A

the amine group is derived from an existing amino acid
-transferred by transaminase with pyrodoxal phosphate

Yes it is reversible

Phys-Pro - section 2 (5 decks)

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