Chapter 8

Question 1

How are cells differentiated? Give the two most common methods.

Answer 1

Differences in which genes are transcribed/translated

Combinations of transcriptional regulators
Epigenetic maintenance

Question 2

What are the three ways epigenetics are passed on?

Answer 2

Positive feedback loops (remember signal even after replication)

Inheritance of condensed chromatin structure

DNA methylation by maintenance methyltransferse to match template (silencing, on cytosine)

Question 3

What are the three purposes of controlling gene expression?

Answer 3

cell differentiation
adapting to the environment
efficiency

Question 4

How do transcription regulators bind to DNA? How do they know where to bind? What are their partners?

Answer 4

Bind (H-bond, hydrophobic) to specific DNA sequences

Recognize AT/GC by availability of H bond donors/acceptors

Needed as well as transcription factors to get high expression

Question 5

How do repressors work for prokaryotes (transcription)? Where do they bind?

Answer 5

Repressors bind on operator, can block sigma factor

Question 6

What does the TRP operon control? What repressors/activators are involved?

Answer 6

Codes for enzymes needed for tryptophan biosynthesis

Off when trp (tryptophan) is high

Trp binds to and activates repressor (allosteric), which blocks sigma factor

Question 7

What does the Lac operon control? When is it off and when is it on?

Answer 7

Codes for galactoside permease and B-galactosidase (needed to make lactose glucose)

On when lactose is high and glucose is low (has both activator and repressor)

Question 8

Describe the activator/repressor in the Lac operon

Answer 8

Repressed when lactose is absent
Lactose converts repressor to inactive form (allosteric)

Active when cAMP (signaling molecule, made from ATP) is high
(cAMP produced when glucose is low)
Binds/Activates (allosteric) activator protein (CAP, activates RNA polymerase)

Question 9

What is the area where activators bind called? How do they interact with the gene? How do they activate?

Answer 9

Enhancers are binding sites for activator proteins

Work from a distance by bends and loops in the DNA and recruiting mediators

Stabilize RNA polymerase complex and increase rate of transcription

Question 10

Can prokaryotes, eukaryotes, or both control gene expression by histones?

Answer 10

Only eukaryotes, prokaryotic DNA is naked

Question 11

Match histone acetal transferase (HAT) and histone deacetylase (HDAC) to gene activation and gene repression

Answer 11

Histone Acetal Transferase (HAT) → gene activation

Histone DeACetylase (HDAC) → gene repression

Question 12

What are the three ways activators can function?

Answer 12

stabilize transcription preinitiation complex through proteins (ex:Mediator)
Chromatin remodeling complexes
HAT

Question 13

Describe MyoD

Answer 13

MyoD forms a complex with other regulators and binds to DNA to turn on muscle specific sequences, can convert fibroblasts to muscle cells

Question 14

What are the three ways repressors can function?

Answer 14

block or destabilize transcription preinitiation complex
Chromatin remodeling complexes
HDAC

Question 15

Describe gene regulation by steriods

Answer 15

Steroid hormones/receptors can regulate DNA, need regulatory sequence + activator protein (one of the ways regulation can be grouped)

Question 16

Describe grouped regulation in prokaryotes and eukaryotes

Answer 16

Prokaryotes have many proteins under the same promoter (operon)

Eukaryotes have one promoter per gene, but may have shared regulatory sequence (combinatorial control, control by committee)

Question 17

Describe the involvement of UTRs in control of gene translation in both prokaryotes and eukaryotes

Answer 17

Both prokaryotic and eukaryotic mRNAs contain UnTranslated Regions

Pro → RBS
Eu → 5* cap, Poly A tail (controls mRNA stability)

Question 18

Describe translational control in prokaryotes

Answer 18

Translation repressor protein hides RBS from small ribosomal subunit, binds to hair-pin loop formed by base-pairing

Question 19

Describe translational control in eukaryotes

Answer 19

Repressor proteins hide start codon from small ribosomal subunit, binds to hair-pin loop

Question 20

Describe negative regulation of eLF2 (and what it does)

Answer 20

Repressor proteins hide start codon, binds to hair-pin loop

Helps tRNA bind to ribosome

Question 21

Give a short description of miRNA and how it is made

Answer 21

Noncoding, 20-22 bp, made by processing precursor miRNA with dicer

Question 22

What does miRNA do and how does it work?

Answer 22

Complementary base pair (3/5 UTR) with mRNA to target for degradation
Form RISC (RNA induced silencing complex) before searching for matches
Involved in fate decisions

Question 23

Describe siRNA and its role in the cell

Answer 23

small interfering RNA
Foreign double-stranded RNA cleaved by dicer to form siRNAs
Those siRNAs used to search for complementary RNA

Question 24

What are the similarities and differences between miRNA and siRNA?

Answer 24

Same active complex, same dicer protein

miRNA is cell-produced single stranded RNA

siRNA is invader double-stranded RNA

Question 25

Describe protein phosphorylation (include enzymes, reversibility, and effects)

Answer 25

Kinase adds P, phosphatase removes P (P comes from ATP) Rapid and reversible, can activate or inactivate (depends on protein) Affects binding to ligands, catalytic activity, cellular localization, ubiquitination and destruction

Question 26

Describe the degradation of proteins (enzyme, identification, purpose)

Answer 26

Degradation by proteasome is controlled by ubiquitination Breaks peptide bonds and uses ATP to unfold protein Targets misfolded proteins and is used for quick regulation Enzymes (E1, E2, E3) and ATP is used to attach ubiquitin proteins to target Short peptides are recycled into amino acids

Question 27

Describe the specificity and possible levels of interaction of miRNA

Answer 27

Milder effects if not a complete base pairing | Each one targets multiple mRNAs (only need to pair short sequences)