Microbial Metabolism (Enzymes) Flashcards

1
Q

What is metabolism?

A

The sum of chemical reactions within a living organism

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2
Q

Why do we need to know about microbial metabolism?

A
  • Metabolism is the basis of all life
  • Not just microbes
  • “is the set of chemical reactions that occur in living organisms to maintain life”
  • it is the chemistry of breaking down things for energy AND building or making things for cellular life
  • catobolism + anabolism = metabolism
  • metabolism forms the basis of all forms of microbiology, from environmental microbiology to medical microbiology
  • Knowledge of metabolism forms the basis of antibiotic therapy. Many antibiotics interfere with metabolic reactions
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3
Q

Catabolism is

A
  • the breakdown of complex organic molecules into simpler molecules
  • generally hydrolytic (water molecules get used)
  • Exergonic (produce energy)- energy stored in chemical bonds is released
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4
Q

Anabolism is

A
  • the synthesis of complex organic molecules from simpler molecules
  • Generally dehydration synthesis reactions (release water)
  • Endergonic (consumes energy)
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5
Q

Enzymes are:

A
  • Biological catalyst that speed up chemical reactions but is not consumed in the reaction
  • Specific for a particular substrate and reaction
  • Has a unique shape to recognize substrates
  • Very efficient- can increase the rate of a chemical reaction 10^8- 10^10 times
  • Enable metabolic reactions to proceed at a speed compatible with life
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6
Q

Enzyme Substrate Interaction

A

Enzymes have a unique active site which fits only a particular substrate

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7
Q

Turnover number:

A
  • Enzymes participate in chemical reactions but are not consumed by them (can function over and over again)
  • An enzyme’s speed (turnover number) is the maximum number of substrate molecules an enzyme molecule can convert to produce each second
  • Examples:
  • DNA polymerase (DNA synthesis)–> 250
  • Catalase (breakdown of H202–> 20,000
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8
Q

Enzyme components

A
  • Made entirely of protein
  • Conjugated enzymes consist of;
  • Apoenzyme: the protein component
  • Cofactor- non-protein component (Mg^2+ or Ca^2+ ions)
  • Apoenzyme + Cofactor = Holoenzyme
  • Without cofactor - apoenzyme is not active
  • Ex. DNA polymerase III
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9
Q

Coenzyme is

A

an organic molecule that is a cofactor

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10
Q

Naming Enzymes:

A

Enzyme names usually end in -ase

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11
Q

Factors affecting enzymatic activity:

A
  • Rate of chemical reactions increases with temperature
  • elevation above a certain temperature leads to enzyme denaturation
  • Most enzymes have a pH optimum
  • Extreme pH can result in enzyme denaturation
  • High substrate concentration leads maximal enzyme activity, the enzyme is said to be saturated
  • Under normal conditions, enzymes are not saturated
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12
Q

Metabolic pathways

A
  • Metabolic pathways usually contain many steps, each with an enzyme
  • Multienzyme systems
  • Different patterns seen
  • Linear
  • Cyclic (TCAI)
  • Branched
  • At the level of the enzymes:
  • Mess up the enzymes, pathways will not move forward
  • Control of enzyme action - competitive vs non-competitive
  • Control of synthesis - feedback loops of repression or induction
  • Enzymes activity can be controlled by inhibitors
  • controlling a microbe’s enzymes is also a good way to control growth. Why?
  • Enzyme inhibitors can be classified as
  • Competitive inhibitors
  • Non-competitive inhibitors (allosteric inhibitors)
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13
Q

Competitive Inhibitors

A
  • Fill the active site and compete with substrate
  • Similar in shape and chemical structure to the substrate
  • Does not undergo any reaction to form products

*** Inhibition of folic acid synthesis by sulfanilamide - competes with para-aminobenzoic acid (PABA) for enzymes active site

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14
Q

Non-Competitive Inhibitors

A
  • Interact with a site other than the active site
  • Binding of the inhibitor causes a change in the shape of the active site, making it non-functional
  • May bind reversibly or irreversibly
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15
Q

Feedback inhibition

A
  • The end product of a metabolic pathway is often a non-competitive inhibitor of that pathway
  • The end product inhibits one the enzymes in the pathway (often the first enzyme)j
  • Prevents the cell from wasting energy
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16
Q

Microbial Metabolism:

A

Energy production using enzymes

17
Q

Important aspects of energy production

A
  • Oxidation-reduction (redox) reactions
  • Salvages electrons (and the energy associated with them) released from the breaking of nutrient bonds
  • Mechanisms of generation of ATP (how energy is banked)
18
Q

Oxidation-reduction (redox) reactions

A
  • oxidation is the removal of electrons from a molecule
  • Reduction is the gaining of electrons by a molecule
  • OIL - RIG (oxidation is lost, reaction is gained)
  • Oxidation and reduction reactions are always coupled (redox reaction)
19
Q

ATP- The Energy Bank

A

ATP has “high energy” or unstable bonds which allows the energy to be released quickly and easily

20
Q

Mechanisms of ATP generation

A
  • Substrate-level phosphorylation
  • Oxidative phosphorylation
  • Photophosphorylation
21
Q

Substrate-Level phosphorylation

A

ATP is generated when a high energy phosphate is transferred directly to ADP from a phosphorylated substrate

22
Q

Oxidative phosphorylation

A
  • Electrons are transferred from organic compounds through a series of electron carriers to O2 or other oxidized inorganic or organic molecules
  • This sequence is called the electron transport chain
  • Energy is released during the transfer of electrons from one carrier and is used to make ATP from ADP
23
Q

Photophosphorylation

A
  • Occurs in photosynthetic cells
  • contain light trapping pigments such as chlorophyll
  • Light causes chlorophyll to give up electrons
  • Energy released from the transfer of electrons (oxidation) of chlorophyll through a system of carrier molecules is used to generate ATP
24
Q

Carbohydrate catabolism

A

Microbes use two general processed to generate energy from carbohydrates:

  • Cellular respiration
  • Fermentation
  • Both start with glycolysis
25
Cellular Respiration
* Glycolysis - Glycose is oxidized to pyruvic acid with ATP and NADH produced. NADH and FADH2 are energy-containing * Intermediate step - Pyruvic acid is converted to acetyl CoA with NADH produced * TCA cycle (Kreb's cycle) - Acetyl CoA is oxidized to CO2 with ATP, NADH and FADH2 produced * Electron Transport Chain - NADH and FADH2 are oxidized through a series of redox reactions and a considerable amount of ATP is produced
26
Glycolysis
* Starting point for cellular respiration (also fermentation) * 10 step catabolic pathway - Every ( ) is a carbon - Every ( ) is a step along the process
27
Glycolysis: Preparatory Stage: Steps 1-5
1. ) Glucose 2. ) Hexokinase-----ATP 3. ) Phosphoglucoisomerase 4. ) Phosphofructokinase-----ATP 5. ) Aldolase
28
Glycolysis: Energy Stage: Steps 6-10
6. ) Triose phosphate dehydrogenase-----NAD+--->NADH & NAD+--> NADH 7. ) Phosphoglycerokinase----ADP--->ATP & ADP--->ATP 8. ) Phosphoglyceromutase 9. ) Enolase 10. ) Pyruvate kinase-----ADP--->ATP & ADP---> ATP
29
Summary of glycolysis
* Glucose is split and oxidized through a ten step pathway to two molecules of pyruvic acid (C3H4O3) * Net gain of 2 ATP molecules, 4 from energy phase (by substrate level phosphorylation) minus 2 from preparatory stage * 2 NADH molecules produced - will be used to make more ATP! * Pyruvic acid can now undergo either fermentation or respiration
30
Glycolysis- the universal pathway
* Glycolysis is an almost universal metabolic pathway - humans and animals - plants? - Eukaryotic microbes - Archaea - Bacteria- mostly * There are some organisms that don't use glycolysis - some are asaccharolytic - Campylobacter jejuni, Bordetella pertussis - some have alternative pathways
31
Alternatives to glycolysis
* Many bacteria have an alternative pathway to glycolysis for the oxidation of glucose - Phosphogluconate pathway - - breakdown of 5 carbon sugars - - makes important intermediates (nucleic acids) - - not as efficient as glycolysis * Entner-Doudoroff reaction - - Glucose breakdown for organisms that don't ahe all the necessary enzymes for glycolysis (Pseudomonas spp.) - - not as efficient as glycolysis
32
What happens after glycolysis?
* After glucose is broken down to pyruvic acid, pyruvic acid can be channeled into either: - fermentation OR - - Cellular Respiration: - ---* Aerobic respiration - requires O2 and the final electron acceptor is O2 - --* Anaerobic respiration - No O2 and final electron acceptor is an inorganic molecule other than O2
33
Aerobic Respiration
* Tricarboxylic acid (TCA) cycle - Kreb's cycle or citric acid cycle - A large amount of potential energy stored in acetyle CoA is released by a series of redox reactions that transfer electrons to the electron carrier coenzymes (NAD+ and FAD)
34
Acetyl CoA
* where does it come from? - intermediate step * Pyruvic acid is converted to a 2-carbon compound (decarboxylation) * The 2 carbon acetyle group then combines with Coenzyme A through a high energy bond * NAD+ is reduced to NADH
35
Cellular Respiration: Intermediate Step
Pyruvic acid is converted to acetyle CoA with NADH produced
36
TCAC cylce
* for every molecule of glucose (2 acetyl CoA) the TCA cycle generates - 4 CO2 - 6 NADH - 2 FADH2 - 2 ATP * TCA cycle begins and ends with Oxaloacetate and acetyl CoA - count carbons! - follow the pathway