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Bacterial Physiology (BIOL 471) > Ch. 8 > Flashcards

Ch. 8 Flashcards

1
Q

What are the 2 different kinds of energy that drive all cellular reactions?

A
  1. Electrochemical energy (ion gradients)
  2. Chemical energy (high-energy molecules)
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2
Q

List the high-energy molecules cells use.

A
  • ATP and nucleotide derivatives
  • Phosphoenolpyruvate (PEP)
  • Actyl-CoA and derivatives
  • Acyl-phosphates
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3
Q

High-energy molecules have bonds that have a _____.

A

high free energy of hydrolysis

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4
Q

What does the squiggle (~) denote?

A

A high negative free energy of hydrolysis

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5
Q

Explain what having a “high group transfer potential” means.

A

Chemical group attached to the “squiggle” is transferred with a large free energy release to acceptor molecules

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6
Q

Explain what happens in a generic phosphoryl group transfer.

A
  1. Positively charged phosphorus is attacked by a nucleophile
  2. Chemical group Y is displaced with its bonding electrons, and the phosphoryl group is transferred to the hydroxyl, forming ROP
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7
Q

Why does the phosphorus atom in all phosphate groups carry a positive charge?

A

Because phosphorus forms double bonds poorly –> electrons in the bond are shifted toward the electron-attracting oxygen

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8
Q

What is a nucleophile?

A

An attacking atom with a pair of electrons seeking a positive center

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9
Q

Group transfer reactions are what type of reaction?

A

Nucleophilic displacements

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10
Q

What is the group transfer potential defined as?

A

The negative of the standard free energy of hydrolysis at pH 7
- Tendency of a molecule to donate the chemical group to a nucleophile
- Not really a potential in an electrical sense, but a free energy change per mole of substrate hydrolyzed

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11
Q

What are group transfer potentials used to estimate?

A

The direction in which a reaction will proceed

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12
Q

What types of modifications to metabolites can ATP make?

A
  • Phosphorylation
  • Pyrophosphorylation
  • Adenylation
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13
Q

Transfers chemically activate metabolites for _____.

A

future steps

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14
Q

Why is ATP the central energy currency in the cell?

A

Because phosphate transfer releases a lot of energy

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15
Q

Why is so much energy released during ATP hydrolysis? (Hint: look at its structure)

A
  • At pH 7 the phosphate groups are ionized
  • This produces electrostatic repulsion between the negatively charged phosphates
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16
Q

Why are reactions during which phosphate is removed from ATP favored?

A

Because the electrostatic repulsion is decreased as a result of the hydrolysis

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17
Q

Any group that is _____ can attack the _____ phosphorus shown and result in phosphoryl group transfer. Give an example.

A
  1. electronegative
  2. electropositive
  3. Ex. Hydroxyl groups in sugars
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18
Q

Enzymes that catalyze phosphoryl group transfer reactions are called _____.

A

kinases

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19
Q

What is the difference between bond energy vs. free energy of hydrolysis?

A
  • Bond energy = energy required to break a bond
  • Free energy of hydrolysis = energy released when a bond is broken
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20
Q

What is the more energetic phosphoryl donor: ATP or PEP?

A

PEP

21
Q

Why does PEP have a high phosphoryl group transfer potential?

A

Hydrolysis removes the phosphate allowing the enol form of pyruvic acid to tautomerize into the keto form
- Energy is released because the keto form is more stable than the enol form

22
Q

The formation of a molecule with _____ bond energy will result in the release of energy.

A

higher

23
Q

Why do acyl derivatives have high group transfer potentials?

A

Because they do not resonate well
- In a normal ester, 2 electrons shift from the oxygen to form a double bond during resonance –> oxygen acquires a positive charge

24
Q

Why is resonance hindered in phosphate esters and thioesters?

A
  1. Because the positive charge on the phosphorus atom prevents electrons from shifting in from the oxygen to form a double bond –> would leave 2 adjacent positive centers
  2. Thioesters don’t resonate as well
    as normal esters     because sulfur doesn’t form double bonds with carbon
25
Q

Why is the hydrolysis of acyl derivatives energetically favored?

A

Because it leads to products stabilized by resonance with respect to the reactants

26
Q

Match the enzymes to the reaction they catalyze. Why are these important?

Reaction (groups donated):
1. Acyl groups
2. CoA groups
3. Phosphoryl groups

Enzymes:
a. Kinases
b. CoA transferases
c. Transacylases

A
  1. Acyl groups = transacylases
  2. CoA groups = CoA transferases
  3. Phosphoryl groups = kinases
    Importance: very versatile
    - Fatty acids and proteins are synthesized via acyl group transfer reactions
    - CoA transfer takes place during fermentative reactions in bacteria
    - Acyl phosphates donate their phosphoryl groups to ADP to form ATP
27
Q

Why are group transfer reactions central to all metabolism?

A

Because biological molecules are synthesized as a result of group transfer reactions

28
Q

How does ATP donating other parts of the molecule contribute to biosynthesis?

A
  • When these groups are transferred to an acceptor molecule, the acceptor molecule itself becomes a high-energy donor for subsequent biosynthetic reactions
  • Energy from ATP can be transferred to other molecules, which can then drive biosynthetic reactions
29
Q
  1. What happens if the α phosphate is attacked?
  2. What happens if the γ phosphate is attacked?
A
  1. AMP is the group transferred and PPi is the leaving group
  2. The phosphoryl group is transferred forming the phosphorylated derivatives and ADP as the leaving group
30
Q

What determines the specificity of the attack?

A

The reaction depends upon which enzyme catalyzes the reaction

31
Q

What are some bonds that ATP can form?

A
  • Amide linkages
  • Thioesters
  • Esters
32
Q

How is ATP made (2 pathways)? Where does each pathway occur?

A
  1. Oxidative phosphorylation (ATP synthase)
    - Occurs in membrane
  2. Substrate-level phosphoylation (SLP)
    - Occurs in cytosol
33
Q

Define substrate level phosphorylation (SLP).

A

Phosphorylation of ADP in the soluble part of the cell by means of a high-energy phosphoryl donor

34
Q

SLPs are catalyzed by enzymes called _____.

A

kinases

35
Q

What is the general reaction for SLP?

A
36
Q

Diagram what happens during SLP.

A
  1. An oxygen in the β phosphate of ADP acts as a nucleophile and bonds to the phosphate phosphorus in the high-energy donor
  2. The phosphoryl group is transferred to ADP –> makes ATP
37
Q

Phosphoryl donors for ATP synthesis during SLPs include _____.

A
  • 1,3-bispohosphoglycerate (BPGA)
  • Phosphoenolpyruvate (PEP)
  • Succinyl-phosphate
  • Acetyl-phosphate
38
Q

What are the 4 major SLPs? What metabolic pathways do they occur in?

A
  1. 1,3-BPGA + ADP –> 3-PGA + ATP
    - Glycolysis
  2. PEP + ATP –> pyruvic acid + ATP
    - Glycolysis
  3. acetyl-P + ADP –> acetic acid + ATP
    - Acetyl-P formed form acetyl-CoA formed from pyruvate
  4. succinyl-CoA + Pi + ADP –> succinic acid + ATP + CoASH
    - Citric acid cycle
39
Q

How is 1,3-bisphosphoglycerate (BPGA) formed?

A

Phosphoglyceraldehyde dehydrogenase oxidizes phosphoglyceraldehyde (PGALD) into 1,3-BPGA

40
Q

How does 1,3-BPGA make ATP?

A
  • Donates a phosphoryl group to ADP in SLP
  • Forms ATP and 3-phosphoglycerate
  • Catalyzed by phosphoglycerate kinase
41
Q

How is acetyl-CoA formed from pyruvate?

A

Usually made by the oxidative decarboxylation of pyruvate

42
Q

What are the 3 enzyme systems in bacteria that decarboxylate pyruvate –> acetyl-CoA? Which are in aerobic vs. anaerobic bacteria?

A
  1. Pyruvate dehydrogenase
    - Aerobic
  2. Pyruvate-ferrodoxin oxidoreductase
    - Anaerobic
  3. Pyruvate-formate lyase
    - Anaerobic
43
Q

Pyruvate dehydrogenase is not usually found in fermenting bacteria. Why might this be?

A
  • Pyruvate dehydrogenase reaction produced NADH
  • Would be disadvantageous to fermenting bacteria because there is often no external electron acceptor that can reoxidize NADH into NAD+
44
Q

What is acetyl phosphate made from?

A

Made from pyruvate via acetyl-CoA

45
Q

Explain what happens in the pyruvate dehydrogenase reaction.

A
  1. 2 electrons that bond the carboxyl group to the molecules are transferred to NAD+
  2. CoA attached to the carbonyl group to form the acylated CoA derivative
46
Q

How is succinyl-CoA made?

A

Made by oxidative carboxylation of α-ketoglutarate
- Occurs in the citric acid cycle

47
Q

How is phosphoenolpyruvate (PEP) made?

A

Formed by a dehydration reaction catalyzed by enolase

48
Q

What is PEP used for?

A

Used to regenerate ATP which is used to phosphorylate sugars in glycoslysis

Bacterial Physiology (BIOL 471) (15 decks)

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