Starts at 12:05 pm pst on 3/15/2021
Study Guide
Module 4: Molecular Regulation
- Constitutive/responsive genes. Define and recognize all key structural elements of gene expression: promoter, operator, activator binding site, operon and intrinsic terminator. Key parts: list cis and trans elements. Major modes of regulation. Describe how the syntheses of proteins are controlled at DNA and RNA levels. Define regulatory networks, and related elements- operon, cluster and regulon.
- Regulatory proteins. Negative and positive controls of transcription. Two main types of regulatory proteins (e.g., DNA-binding proteins): repressors and activators. Compare and contrast the activities of an activator protein and a repressor protein. Describe what happens when a repressor binds DNA; what happens when an activator binds DNA. Describe differences between inducer, co-repressor, and inhibitor. How do activators and repressors work during transcription? Compare and contrast LacR and TrpR.
- Two component regulators, sensor kinase, response regulator. Describe how a two-component regulatory system works. What is signal transduction?
- Global regulators. Catabolite repression. What is Catabolite Repression; define diauxic growth; describe the function of cyclic AMP. How is cAMP formed? What is CRP? Describe the overall regulation of the lac-system (lac-operon, lacZ, lacY, lacI). Which part of the lac-operon expression is controlled by a repressor; which part is controlled by an activator.
- Describe attenuation; explain how the formation of one stem-loop in the RNA can block the formation of another. Describe the regulation of trp-operon in E.coli.
- Regulatory RNAs: describe the major differences between using a repressor protein versus small RNAs to control gene expression/translation. Describe basics of a riboswitch – mediated control of gene expression.
- Phase variation – define and be able to explain role of invertases.
- What changes in the network s will be observed in ______
lacI mutant?
LacZ mutants?
Lac Y mutant?
CRP mutant ?
PTS mutant?
Adenylate cyclase mutant?
trpR mutant?
Attenuator mutants: i.e. no region 1, or 2, or 3, or 4
- What levels of GFP ( assessed as green fluorescence -high, medium, no) will you observed in cells expressing GFP from the Plac promoter?
Consider different substrates (glucose only, lactose only, glucose + lactose, etc) and genotypes (lacI-mutants, etc)
- What levels of GFP (assessed as green fluorescence -high, medium, no) will you observed in cells expressing GFP from the Ptrp promoter? Consider different levels of tryptophan (high, low, no tryptophan)
- What would be outcomes of fljA mutation?
Module 5: Metabolic pathways: Integration and design
- Which reactions can be used in catabolic pathways? Provide examples of environmental factors, which influence the reaction ΔG. Refresh phototrophy and chemotrophy, organotrophy and lithotrophy, autotrophy and heterotrophy terms, and predict function based on the description (i.e. H2 utilization and CO2 fixation is an example of chemolithoautotrophy).
- Energy carriers, reducing (or redox) power carriers and the proton motive force: Compare and contrast energy carriers versus reducing (or redox) power carriers: what is the main difference between an energy carrier (ATP) and a reducing power carrier (NADH)? The proton motive force (PMF) components: concentration difference (ΔpH) and the charge difference.
- List cellular functions supported by ATP. What other molecules can carry energy for metabolic reactions? Kinases and their main functions. List cellular functions supported by
- Describe two main pathways for ATP synthesis. List biochemical reactions which produce ATP via substrate level phosphory Describe chemiosmotic coupling. ATP-synthase: structure, function and reversibility. Describe how the redox power carriers (NADH, FADH2, cytred and Fdred) are generated and used. Compare and contrast cytred and cytox, Fdred and Fdox, NADH/H (or NADH) and NAD+, ATP and ADP.
- Carbohydrate catabolism pathways: Utilization of complex carbohydrates (lignin, cellulose, starch) with extracellular enzymes. Describe function of Sus-enzymes. Know key steps and enzymes specific for EMP pathway, EDD pathway, Pentose Phosphate pathway (PPP) and TCA cycle. Which enzymes are unique to each pathway? Which pathway provides the highest energy yield? Describe the connection between sugar catabolism pathways and fermentation.
- How is the conversion of NADH back to NAD+ linked to fermentation? Role of reducing (or redox) power carrier pool in fermentation. Know some examples of fermentation products: ethanol, acetate, lactate, succinate, and formate.
- Electron transport systems: List key components of the electron transport systems (ETS). How many protons may be pumped per one NADH in coli during aerobic vs. anaerobic respiration? What is the function of NADH dehydrogenase? What are (ubi)quinones? Compare ETS in E.coli with ETS in iron-reducing bacteria. What parts of the ETS are similar and what parts are different. Describe the function of nitrate reductase (NAR) in anaerobic respiration. What compounds could be used as electron acceptors. Describe reverse electron transfer. What is the main function of reverse electron transfer?
- Photosynthesis: Describe photoexcitation. Describe direct proton pumping. Know the general function of (bacterio)rhodopsins. Is the rhodopsin-mediated generation of PMF linked to electron transfer? how is it linked to ATP-production? Describe the key parts of the photosystem machinery: chlorophyll, antenna, and the reaction center. Compare and contrast PSI versus PSII. Name examples of electron donors for photosystem I, photosystem II and oxygenic photosynthesis.
- Anabolism (biosynthesis, assimilation): Know the main elements (C, N, S, P, Fe, Mg) essential for biosynthesis. Key building blocks for biosynthesis and their main sources. Define the central metabolic pathways and primary metabolites. Define the metabolic role of anaplerotic reactions. Name two examples. Gluconeogenesis and PPP roles in biosynthesis. What challenges microbes grown on acetate might have compared to those grown on glucose. What decarboxylation reactions contribute to conversion of acetyl-CoA into pyruvate? What are secondary products (metabolites)?
- CO2 Name pathways for CO2-fixation. Compare intermediates. What are the two main steps of the Calvin cycle. Name the key enzyme. Compare and contrast the Calvin cycle and gluconeogenesis and PPP pathway. Compare and contrast TCA and rTCA cycles.
- Metabolic engineering concept. What is genome-based modeling? How it could be applied.
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