Exam 3 Flashcards
- Starch utilization occurs on the exterior of Bacteriodes, Why are degradative enzymes outside, how are they consolidated and how do the end products get into the cell.
Starch must be broken down before entering the cell by degradative enzymes. They are concentrated near a transporter that gets energy from TonB which allows the degraded branches of starch to enter the cell. All enzymes and transporters are regulated together.
- Define and relate the processes of anabolism, catabolism and amphibolic pathways.
Catabolism breaks down nutrients to create energy, anabolism uses nutrients to build biomass, amphibolic reactions can go either way depending on what the cell needs. Some enzymes can go both ways, others have different enzymes for each direction the pathway goes.
- How are glycolysis, entner deuderoff, and pentose phosphate linked through metabolites?
Metabolites made in one pathway can switch to other pathways and be used to synthesize the end products of that pathway instead of the product of the pathway it started in. They become less energy efficient as you go.
- How is amino acid formation linked to pyruvate?
Pyruvate enters the TCA cycle and intermediates of the cycle can be used to synthesize amino acids. Pyruvate can also go backwards in the pathway that generated it to synthesize other amino acids.
- Glyceraldehyde 3-Phosphate is part of which catabolic pathways? Which anabolic pathways?
Catabolic- Glycolysis
Anabolic- Calvin Cycle
- What two activities are carried out by pyruvate kinase?
Enzymatic: Catalyzes the phosphorylation of ADP from PEP which forms ATP and pyruvate.
Regulatory: Fructose 1,6-bisphosphate binds an allosteric site on pyruvate kinase which locks it in a conformation that increases its enzymatic activity.
- What is catabolite repression and how does CRP and CAP fit with this system of regulation?
Catabolite repression is the repression of a pathway that’s using a less efficient energy source when a better energy source is available or a pathway that is no longer needed. CRP complexes with cAMP to bind the CRP binding site and initiate transcription.
- What is cyclic AMP? What does it do?
When the cell is starved of glucose, ATP production stops. This triggers an increase in cAMP by adenylate cyclase, which converts the ATP to cAMP. cAMP complexes with catabolite repressors and binds to promoter to prevent synthesis of the product.
- When is pentose phosphate pathway used? How does it work with anabolistic pathways?
During a growth phase, the pentose phosphate pathway uses nutrients from glycolysis to fuel the synthesis of biomass.
- What are the main outcomes of the citric acid cycle in terms of energy production and biosynthesis of complex molecules.
Each cycle generates 1 ATP, and the intermediates of the cycle can be used in the synthesis of amino acids and other cell components.
- How does electron transport generate ATP?
Protons are moved outside the cell to cause a proton motive force. They can only re-enter the cell through an ATP synthase, which generates energy. The PMF drives the protons through the ATP synthase.
- How are electrons moved from active sites in electron transport cytochromes?
NADH contains cofactors like FMN, that “pass” electrons to each other. Quinone binds the electrons and 2 hydrogens at the end of the chain. The reduction of quinone and oxidation of NADH generates the energy needed to move 4 protons across the membrane.
- Review the complexes of the electron transport. Why are there different terminal electrons acceptors under aerobic and anaerobic conditions?
Oxygen is the preferred electron acceptor, so nitrogen isn’t used as the terminal electron acceptor in the presence of oxygen. The electron acceptor that will be used also determines the cytochromes present.
- How does proton motive force generate ATP? How does the location of the PMF relate to the activity in generating ATP?
ATP synthase generates ATP from protons flowing through in the direction determined by the proton gradient. The location of the PMF determines what direction the proton gradient flows in.
- How does light generate ATP?
Bacteriorhodopsin generates a proton gradient from harvested light which is converted to chemical energy
- How is cycling of glutamine and glutamate important in Nitrogen metabolism?
NtrC is phosphorylated in the presence of low nitrogen, which triggers glutamine synthesis. Excess glutamine signals the cell to stop converting glutamate to glutamine to maintain a balance.
- How is glutamine synthesis linked to oxygen levels?
Glutamine synthesis increases as oxygen increases because nitrogen fixation is suppressed by oxygen.
- How does 3-phosphoenol pyruvate lead to aromatic amino acid synthesis?
It goes through a pathway which creates chorismate, which is used to synthesize the aromatic amino acids.
- What are the main benefits of using and reusing key metabolites for biosynthesis and metabolic pathways?
It is energetically favorable to recycle metabolites rather than making more.
- Briefly describe how tryptophan levels change expression of tryptophan biosynthesis genes.
Tryptophan levels impact the secondary structure of the RNA encoding the tryptophan operon. Low tryptophan causes the ribosome to pause on the mRNA so the 2-3 loop forms and transcription continues. High tryptophan causes the ribosome to pause on the mRNA so the 3-4 terminator loop forms.
- How are Non-ribosomal peptide synthase (NRPS) pathways similar to polyketide synthesis pathways? How are they different? What is meant by “modular design” and what does PCP stand for in NRPS ?
Both contribute building blocks for peptide synthesis, but NRPS contributes amino acids and polyketide synthases contribute organic acids, modular means there are repeating domains that form a molecule, peptide carrier protein.
- What is a postulated reason why antibiotic structures not ribosomally encoded? What part of antibiotic synthase is encoded in the genome?
Antibiotic structures aren’t ribosomally encoded because it makes it harder for the bacterial cells to recognize them, PCP is encoded in the genome.
