Midterm 2

Question 1

3 ways regulation of promotor region by DNA modification

Answer 1

1. methylation
2. DNA inversion
3. local sequence variation

Question 2

3 mechanisms for sigma factor release from antisigma factor

Answer 2

1. proteolytic cleavage
2. chemical interaction
3. partner swapping

Question 3

3 sites in ribosome

Answer 3

aminocyl site
peptidyl site
exit site

Question 4

translation control: growth rate-dependent control of 70S ribosome

Answer 4

ribosomal proteins can bind to their won mRNA and prevent translation.
Higher levels of ATP promote translation. Lower levels inhibit.

Question 5

translation consensus sequence

Answer 5

AGGAGG- critical for ribosome binding.

Question 6

two types of M tRNA

Answer 6

initiator tRNA, elongator tRNA

Question 7

translation - 3 elongation steps

Answer 7

aminoacyl-tRNA binding
transpeptidation
translocation

Question 8

trigger factors

Answer 8

-ensure proper de novo protein folding
-2-3x more TF than ribosomes in cells
-

Question 9

DnaK

Answer 9

hydrophobic core

sandwich subdomain, helical lid domain which compose the substrate binding domain.

Question 10

DnaJ

Answer 10

cystein rich

zn finger domain

Question 11

DnaK, DnaJ, GrpE - mechanism

Answer 11

DnaK is a holdase
DnaK is bound to ATP. DnaJ brings in protein to be folded. ATP is used to fold protein. DnaJ is released. GrpE facilitates the ADP ATP exchange.

Question 12

signal sequence

Answer 12

N terminal marks the protein for secretion

Question 13

tat system

Answer 13

transports proteins out of the cell - usually with cofactor.
powered by the PMF

Question 14

how does the N terminus affect protein turnover

Answer 14

some AA are unstable (RKFLWY) and have a short half life.

Question 15

4 reasons for protein degradation

Answer 15

1. misfolded/unfolded
2. denatured or damage
3. missing their partner
4. not needed anymore by the cell (process is complete

Question 16

AAA protease

Answer 16

ATPases Assocated with a number of cellular activites

Question 17

sspB

Answer 17

modulate kinetics of substrate binding y the protease

Question 18

RssB

Answer 18

absolutely required for substrate recognition and proteolysis

Question 19

regulated proteolysis mechanism

Answer 19

1. truncated protein
2. tagged with SsrA by tmRNA
3. SspB binds to substrate to mark for the protease
4. Proteolysis in protease with RssB and ATP.

Question 20

enzyme regulation

Answer 20

activity

amount

Question 21

allosteric effect

Answer 21

end product acts as an allosteric effector for the enzyme that is catalyzing the reaction, binding and changing the conformation of the enzyme.

Question 22

covalent modifications of enzymes

Answer 22

methylation, AMP/ADP addition, phosphate group addition

Question 23

corepressor

Answer 23

a repressor may need a corepressor to bind to it so it cna bind and block transcription.

Question 24

inducer

Answer 24

bind to repressor and prevent them binding to DNA, allowing transcription

Question 25

lac operon

Answer 25

-needs lactose present and high cAMP-CRP | -

Question 26

arabinose operon

Answer 26

AraC is both activator and repressor can for loop through dimerization can bind to I and promote transcription of araBADa

Question 27

Embdem-Meyerhof Pathway

Answer 27

glucose is used as precursor to form precursors for TCA. gluconeogenesis - formation of glycogen/starch can produce pyruvate, lactate, glycerol etc.

Question 28

net yield of glycolysis

Answer 28

2ATP 2 pyruvate 2NADH 2 H2O

Question 29

Cra and regulatory pathways

Answer 29

when glucose and lactose are present: Cra is off - repression of gluconeogenesis, ED and EM activated when lactose is present: Cra is off- same as above when neither is present: Cra is on - gluconeogenesis is activated, ED and EM off.

Question 30

Cra - where does it bind? how do catabolites affect function

Answer 30

upstream of RNAP activator, downstream = inhibitor. | -catabolites bind and repress gluconeogenic genes and activate glycolytic genes.

Question 31

CsrA

Answer 31

going to activate anything relating to growth - glyocolysis and pathogenesis

Question 32

ED Net

Answer 32

1 ATP | 1NADH

Question 33

ED genes

Answer 33

all genes are not essential

Question 34

ED genes

Answer 34

all genes are not essential

Question 35

Pentose phosphate NET

Answer 35

ribulose 5-P, CO2, 2NADPH, 1ATP

Question 36

TCA NET (including the pre step)

Answer 36

``` 2 pyruvvate 6 CO2 8. NADH 2FADH2 2 GTP ```

Question 37

FNR

Answer 37

Fumarate and nitrate reductase | TCA regulator

Question 38

ArcA

Answer 38

aerobic respiration control, member o two component regulatory system responding to oxygen availability.