Microbial Metabolism (Enzymes) Flashcards
1
Q
What is metabolism?
A
The sum of chemical reactions within a living organism
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
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
4
Q
Anabolism is
A
- the synthesis of complex organic molecules from simpler molecules
- Generally dehydration synthesis reactions (release water)
- Endergonic (consumes energy)
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
6
Q
Enzyme Substrate Interaction
A
Enzymes have a unique active site which fits only a particular substrate
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
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
9
Q
Coenzyme is
A
an organic molecule that is a cofactor
10
Q
Naming Enzymes:
A
Enzyme names usually end in -ase
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
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)
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
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
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
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
