Lecture 9

Question 1

Where is the most effective place to regulate protein concentration and why?

Answer 1

transcription rates because it is the beginning of information flow and translation is energetically expensive therefore at transcription we save more energy

Question 2

lac operon

Answer 2

(bacteria) contains genes needed for synthesis or degradation of lactose; transcription control region

Question 3

Why do bacteria prefer glucose over lactose?

Answer 3

glucose = monosaccharide, lactose = disaccharide = require more energy

Question 4

when do bacteria use lactose over glucose?

Answer 4

when glucose levels are low or nonexistent

Question 5

Components of the operon

Answer 5

CAP site, promoter, operator, the lac genes

Question 6

CAP site

Answer 6

binds catabolite activator protein = increases rates of transcription | activation site

Question 7

lac promoter

Answer 7

binds to RNA polymerase, promotes transcription

Question 8

lac operator

Answer 8

binds to the repressor: repressor + operator = transcription off

Question 9

CAP

Answer 9

activated when bound to cAMP = complex will then bind to CAP site

Question 10

lac repressor

Answer 10

binds to operator and acts as a road block for RNA Pol

Question 11

What is the co-inducer

Answer 11

lactose, binds to repressor to remove it from operator and induces transcription

Question 12

What increases the rate of transcription in the lac operon?

Answer 12

CAP + cAMP on CAP site

Question 13

What is the co-activator?

Answer 13

cAMP as it activates CAP and co-activates transcription

Question 14

2 components of a regulatory system

Answer 14

sensor protein & response regulator

Question 15

Sensor protein

Answer 15

senses stimulus| ie: histidine kinase

Question 16

regulator protein

Answer 16

drives response due to stimulus; transcription factors

Question 17

purpose of the 2-component regulatory system

Answer 17

enables bacteria to easily respond to a changing environment

Question 18

transcription factors

Answer 18

activate or repress transcription of a gene

Question 19

example of a 2-component regulatory system

Answer 19

low levels of Gln = no Gln bound to sensory domain = activates system to activate transcription of Gln

Question 20

Are RNA polymerases conserved or not conserved throughout all domains of life

Answer 20

Conserved

Question 21

what is the open structure of RNA pol

Answer 21

clamp domain

Question 22

What does it mean when RNA polymerase has a high processivity?

Answer 22

the clamp holds down the DNA strand via closed conformation to the polymerase = increases how long the polymerase can stay on a template and add bases (processivity)

Question 23

3 types of promoter sequences in eukaryotic DNA

Answer 23

initiator promoter, CpG islands, TATA box

Question 24

TATA box

Answer 24

AT rich region, prevalent in highly transcribed genes

Question 25

benefit of eukaryotic gene expression having more elements/parts to the process

Answer 25

gives a lot of variability in levels of control

Question 26

where are recognition elements found on genes

Answer 26

upstream and downstream from initiation sequences

Question 27

What does RNA pol II have that is significant

Answer 27

a C-terminal Tail Domain (CTD) = important for 5’ capping

Question 28

TFIIH - function and components

Answer 28

consists of a Helicase and Kinase domain || kinase domain phosphorylates CTD and separates DNA strands

Question 29

PPE (promoter proximal element)

Answer 29

located closer to promoter and can be within introns

Question 30

Enhancers

Answer 30

far from promoter region

Question 31

Domains of transcription activation factors

Answer 31

activation domain (AD) and DNA-binding domain (DBD)

Question 32

heterodimerization

Answer 32

allows for different number of combinations to increase with limited number of factors || hetero = different , dimer = 2 proteins linked together

Question 33

How is diversity created with the factor monomers

Answer 33

dimerize = increase # of combos || order of factors (AB vs BA) | combo of DNA binding domains and factor domains

Question 34

inhibitory factors

Answer 34

inhibitory factors can dimerize with a factor to inhibit interaction with a site

Question 35

repression factors (histone deacetylase)

Answer 35

histone deacetylase interacts with repression factor (RD repression domain) to tightly bind DNA

Question 36

activator factors

Answer 36

interacts with kinase, acetylene, etc