Microbial Metabolism Flashcards
1
Q
What is metabolism
A
- Refers to the thousands of chemical reactions that occurs in a living cell, transformation of nutrients into energy, fundamental basis of life (prokaryotes and eukaryotes)
- Catabolism and anabolism
- Metabolic Pathways: Is a sequence of enzymatically catalysed chemical reactions in a cell, determined by enzymes, enzymes are encoded by genes on DNA
2
Q
What is catabolism
A
- Breaking down macromolecules to their smaller component parts, provide the building blocks for anabolic reactions
- Catabolic reactions are coupled to ATP synthesis
- Generates the energy in the form of ATP that is needed to drive the anabolic reactions
- When the terminal phosphate group is released from ATP energy is released, ATP to ADP + Pi + energy
- Energy from catabolic reactions combines ADP and Pi to re-synthesise ATP, ADP + Pi + energy ATP
3
Q
What is anabolism
A
- The building of complex molecules from simpler ones (sugars, proteins and nucleic acids), anabolic reactions are coupled to ATP degradation
4
Q
What are enzymes
A
- Biological catalysts, accelerate chemical reactions by lowering activation energy, typically proteins (some RNAs), highly specific, may not consist entirely of proteins
- Active site is the region of an enzyme that binds the substrate, classified by the type of chemical reaction they catalyse
- Some require co-factors to become functional e.g. metal ions (Fe, Mg, Zn)
- If the cofactor is an organic molecule = a coenzyme
- Many enzymes contain small non-protein, non-substrate molecules that participate in catalysis
- Prosthetic Groups: Tightly bound, usually bind covalently and permanently (haeme in cytochromes)
- Coenzymes: Loosely bound, most are derivatives of vitamins
- Catalysis depends on substrate binding position of substrate relative to catalytically active amino acids in active site, endergonic and exergonic reactions coupled (ATP hydrolysis or proton motive force)
5
Q
What are electron donors and acceptors (ATP, FAD, NAD, NADP)
A
- Redox: Energy from oxidation–reduction reactions is used in synthesis of energy-rich compounds (ATP), redox reactions occur in pairs (two half reactions)
- Electron donor: oxidised
- Electron acceptor: reduced
- Redox Couple: Either electron donors or acceptors under different circumstances
- Redox Tower: Range of possible reduction potentials, the farther the electrons “drop,” the greater the amount of energy released (ΔE0′)
- O2 is the strongest significant natural electron acceptor
- NAD+ and NADH: Facilitate redox reactions without being consumed, they are recycled, allows many different donors and acceptors to interact, coenzyme acts as intermediary
- NADP+/NADPH facilitate anabolic (biosynthetic) redox reactions
6
Q
What are factors that affect enzymatic activity
A
Temp:
- Increasing temp, will increase the RoR and enzymatic activity, eventually reach a temp when enzyme denatures and reaction stops (~60-70°C), thermal denaturation is time dependent
- Denature: Damages protein structure, alter shape of substrate site, optimal temperature for most disease causing bacteria (mesophiles) is 35 – 40 °C,
pH:
- Increased enzymatic activity at optimum pH, above or below optimum pH causes enzymatic decline
- Extreme changes in pH can cause denaturation of an enzyme
- Acids and bases can alter the 3D structure of a protein
- The H+ and OH- ions can compete with hydrogen and ionic bonds in an enzyme
Substrate Concentration:
- There is a max rate at which a certain conc of enzyme can catalyse a specific reactions
- If conc of substrate is high (saturation), the enzyme catalyses at its maximum rate
7
Q
What are enzyme inhibitors
A
- Molecules which stop or slow down enzyme reactions, 4 classes (reversible, allosteric, irreversible covalent, enzyme catalysed covalent)
- Competitive: Fill active site of an enzyme and compete with the substrate
- Noncompetitive: Binds to enzyme altering shape of enzymes active site (functions less effectively)
- Metabolic Pathway: A series of chemical reactions where products of one reaction become reactants (substrate) for next reaction, different enzyme catalyses each step
- Feedback Inhibition: Final product of metabolic pathway inhibits an earlier reaction in the sequence, by inhibiting the first enzyme in the pathway this will prevent metabolites from accumulating in the cell
8
Q
What is carbohydrate catabolism
A
- Most microorganisms oxidise carbohydrates as their primary source of cellular energy, glucose is the most common source, however lipids and proteins can also be catabolised
- Microorganisms use two processes to generate energy from glucose cellular respiration (anaerobic or aerobic) or fermentation
9
Q
Describe the steps of glycolysis
A
- Multistep biochemical pathway of enzyme conversions, oxidation of glucose to pyruvic acid, produces 2 ATP, 2 NADH, 2 Pyruvate
- Ubiquitous, substrate-level phosphorylation, conversion of glucose to form two pyruvic acid molecules (pyruvate, 3 carbon molecule) and 2 ATP, used by mitochondria, splitting of sugar
- Releases a small amount of energy stored in glucose, much energy still locked up in pyruvate (C-H)
- Further Processing occurs via anaerobic (fermentation) or aerobic (citric acid cycle and electron transport chain / chemiosmosis respiration)
10
Q
Describe the steps of the Krebs cycle / TCA
A
- Oxidation of acetyl (derivative of pyruvic acid) to CO2, complete oxidation of glucose for energy, produces 2 ATP, 6 NADH, 2 FADH2
- Pyruvate to Acetyl CoA (2 NADH)
- Acetyl CoA (2 C) combines with oxaloacetic acid (4 C) to produce citrate / citric acid (6 C), subsequent decomposition / oxidation of citrate to produce oxaloacetic acid
- Transfers high energy e- to carriers, harvested electrons are directed to the electron transport chain (ETC) to drive ATP synthesis
11
Q
Describe how the TCA is regulated and oxidative phosphorylation
A
- High levels of ADP and Pi (inorganic phosphate) relative to ATP, stimulate ATP production
- Citrate (which also inhibits glycolysis), succinyl-CoA and a high ratio of NADH to NAD+ inhibit ATP production
12
Q
Describe the steps of the electron transport chain
A
- Multi protein complexes and mobile carriers in cell membrane of bacteria, each compound in the sequence has a higher affinity for electrons
- Involves oxidative phosphorylation of NADH and FADH2 to 3 and 2 ATP produced in glycolysis and citric acid cycle
- Produces 30 ATP (from 10 NADH), 4 ATP (from 2 FADH2)
- The phospholipid membrane is normally impermeable to protons, one directional pumping establishes a proton gradient across the membrane, excess H+ makes one side of membrane positively charged
- Protons can diffuse across membrane, only through special protein channels = ATP synthase, when this flow occurs energy is released and is used by ATP synthase to generate ATP
13
Q
Describe chemiosmotic energy coupling
A
- Proton gradient needed for ATP synthesis can be stably established across a topologically closed membrane (plasma membrane in bacteria)
- Membrane must contain proteins that couple the “downhill” flow of electrons in the electron transfer chain with the “uphill” flow of protons across the membrane
- Membrane must contain a protein that couples “downhill” flow of protons to the phosphorylation of ADP
14
Q
What are the different types of energy pathways
A
- Three different biochemical pathways used to generate ATP, different pathways are not used by all cells under same conditions, one of the biggest issues is the availability of oxygen
- Glycolysis: The process where a single molecule of glucose is broken down into two molecules of Pyruvate, can happen with or without oxygen, produces a net yield of 2ATP.
- Anaerobic Fermentation: Cells need to get rid of the Pyruvate, no ATP produced in this process, waste products in the form acids [not just lactic acid]
- Aerobic Respiration: Oxygen available, occurs in mitochondria, produces 36-38 ATP
15
Q
What is a pure culture, where did it originate and some related terms
A
- Robert Koch (1843-1910): Developed the germ theory of disease (1 microorganism = 1 disease)
- Lead to attempts to isolate microorganisms
- Not all microbes are easy to culture (non-cultivatable strains), must isolate the bacterium and inoculate
- Nature: Attach to surfaces, secrete polysaccharide matrix and live in communities called biofilms
- Beneficial Properties of Environment: Acidic / low pH, high salt, fastidious nutrient requirements, chemicals and antibiotics
- Pure Culture: Contains only one species or strain
- Colony: Population of cells arising from a single cell or spore or from a group of attached cells, bacterium are often called colony-forming units (CFU)
- Streak Plate: Used to isolate single colonies
