AP Biology, Chapter 18 pt.2[focus on operons]Microbial Models: The Genetics of Viruses and Bacteria

The control of gene expression enables individual bacteria to adjust their metabolism to environmental change

1. Briefly describe two main strategies that cells use to control metabolism.a. Regulate enzyme activity

i. End product of the pathway feedback to stop its productionii. Binds to 1st enzyme in the pathway; non-competitive or allosteric

b. Regulate gene expressioni. Turn genes on and off by controlling the initiation of transcriptionii. Takes longer

2. Explain the adaptive advantage of genes grouped into an operon.a. Operon = operator, promoter, and the genes they controlb. Puts functionally related genes under the control of a single on-off switch

3. Using the trp operon as an example, explain the concept of an operon and the function of the operator, repressor, and co-repressor.

a. Separate repressor gene is expressed constitutivelyb. Corepressor = tryptophanc. Repressor + tryptophan binds to operator and blocks transcriptiond. When tryptophan is low, repressor alone releases from operator

4. Distinguish between structural and regulatory genes.a. Structural genes code of enzymes in a biosynthetic pathwayb. Regulatory genes code for proteins that turn operons on or off

5. Describe how the lac operon functions and explain the role of the inducer, allolactose.a. Separate repressor gene is expressed constitutivelyb. Repressor alone binds to operator, blocks transcriptionc. Inducer allolactose binds to repressor and it releases from the operatord. RNA polymerase can the transcribe the genes required for lactose digestion

6. Explain how repressible and inducible enzymes differ and how those differences reflect differences in the pathways they control.

a. Respressiblei. Small molecule binds respressor and turns off the operonii. Useful for anabolic pathways; enough product turns off pathway

b. Induciblei. Small molecule binds repressor and turns on the operonii. Useful for catabolic pathways; presence turns on genes to digest

7. Distinguish between positive and negative control and give examples of each from the lac operon.

a. Negativei. Operon switched off by active repressorii. Lac repressor without allolactose binds to operator, blocks transcription

b. Positivei. Operon switched on by active regulatory proteinii. CRP protein + cAMP binds to DNA, helps RNA polymerase bind to promoter

8. Explain how cyclic AMP and the cyclic AMP receptor protein are affected by glucose concentration.

a. Glucose plentifuli. cAMP is not made in the cytoplasmii. CRP doesn't bind to DNA, RNA polymerase doesn't bind as much

b. Glucose lowi. cAMP madeii. cAMP + CRP bind and increase transcription

19.2 Eukaryotic gene expression is regulated at many stagesDifferential Gene Expression

1. Define differentiation and describe at what level gene expression is generally controlled.a. Differentiation = cellular change in form and functionb. Control

i. At transcriptional levelii. Involves DNA-binding proteinsiii. Coordinated by external signals

Regulation of Chromatin Structure2. Histone acetylation

Loosens nucleosome associations, promotes transcriptionAcetyltransferases may be associated with transcription factorsRemoval causes nucleosomes to bind

3. Methylation condenses chromatinPhosphorylation loosensCombination and order of modification may be important

DNA Methylation4. DNA methylation

i. Methyl groups may be added/removed especially to Cii. Inactive DNA is often highly methylated; demethylation activatesiii. Methyl inactivation during development is passed on after mitosisiv. Methylating enzymes recognize methylation on one strand, add methyl to opposite strandv. Explains genomic imprinting

Regulation of Transcription Initiation5. Describe an example of a general transcription factors.

General are required to transcribe all protein-coding genesEx: protein that binds the TATA box

6. How may nuclear architecture affect gene expression?Chromosomes are mainly segregatedActive chromatin loops may associate in transcription factories

7. Describe the eukaryotic processing of pre-mRNA.a. 5'-cap and poly(A) tail addedb. Introns removed

8. Define control elements and explain how they influence transcription.a. Noncoding sequencesb. Regulate by binding transcription factorsc. Don’t vary muchd. Combination of proteins bound determines time and place of expressione. May be close or far away(proximal vs. distal)

9. Explain the role that promoters, enhancers, activators, and repressors play in transcriptional control.a. Promoters

i. RNA polymerase binding sites; transcription initiation sites ii. Depends on previous binding of transcription factors

b. Enhancersi. Distant (distal) control elements where proteins bindii. DNA folds so their bound transcription factors contact initiation complex(RNA pol)iii. May require specific proteins

c. Activatorsi. Transcription factors bound to enhancersii. DNA folding brings them to the transcription complex

d. Repressorsi. Proteins that block transcription ii. Bind to silencer control elements

10. Describe the two basic structural domains of transcription factors.a. Sequence-specific DNA binding domainb. Protein-binding domain(s) to interact with other transcription factors and RNA polymerase

11. Explain how eukaryotic genes can be coordinately expressed and give some examples of coordinate gene expression in eukaryotes.

a. Some operons (gene clusters giving a single transcript) in eukaryotic cellsb. Coordinately controlled genes have the same combination of control elements

i. Steroid receptor in a transcriptional activatorii. Signal-transduction pathways can activate common activators