Genetic Regulation

Question 1

Cost of making proteins

Answer 1

1 ATP per base for transcription + 3 ATP per Amino Acid for translation

Question 2

Cost per second in Bacteria

Answer 2

E.Coli -> 20 AA/sec
Divide cost by time

Question 3

Constitutive

Answer 3

Genes that are always on, therefore never regulated

Question 4

Where does regulation occur?

Answer 4

Every step, but trade-off between energy savings and speed at which the change takes effect

Question 5

Most frequent level of regulation

Answer 5

Transcription Initiation

Question 6

Operon

Answer 6

Multiple protein-coding regions under control of a single promoter, transcribed as a polycistronic (encodes multiple different proteins) mRNA

Question 7

beta-galactosidase

Answer 7

cleaves lactose into galactose (isomerized into glucose) and glucose (main food source)

Question 8

lac permease

Answer 8

Pokes holes in cell to allow lactose in

Question 9

lacZ

Answer 9

beta-galactosidase gene

Question 10

lacY

Answer 10

lac permease gene

Question 11

lacI

Answer 11

constitutively expressed gene that codes for lac repressor protein

Question 12

lac repressor protein

Answer 12

binds to operator region of the lac operon, inhibiting transcription (RNA polymerase can’t bind to site)

Question 13

lacA

Answer 13

codes for transacetylase protein

Question 14

transacetylase protein

Answer 14

detoxifies cell when lac permease brings in unwanted materials

Question 15

Expression on lac operon -> absence of LACTOSE

Answer 15

lacI gene enabled to a high degree = lots of lac repressor proteins = not a lot of binding to lac operon = not as much beta-galactosidase

Question 16

Expression on lac operon -> presence of LACTOSE

Answer 16

lactose binds to lac repressor genes = lac repressors can’t bind to lac operon = lacZ expressed

Question 17

Expression on lac operon -> presence of LACTOSE + GLUCOSE

Answer 17

Not as efficient transcription of lac repressor protein, but still there, mainly due to cAMP

Question 18

cAMP (cyclic AMP)

Answer 18

Concentration inversely related to glucose, binds to lac promoter and ENHANCES RNA polymerization = higher lac expression

Question 19

cAMP Receptor Protein (CRP)

Answer 19

Creates a complex with cAMP and bind to the lac promoter region, increasing efficiency of RNA Polymerase binding

Question 20

Expression of lac operon -> presence of NO GLUCOSE + Some LACTOSE

Answer 20

cAMP + CRP complex positively regulates promoter region = LOTS OF BETA-GALACTOSIDASE

Question 21

Ratio of Beta-gal:Permease:Transacetlyase

Answer 21

10:5:2

Question 22

After transcription, how can the mRNA be adjusted?

Answer 22

1) Level of mRNA STABILITY
2) Level of Transition Initiation (“Strength” of Shine-Dalgarno Sequence)
3)

Question 23

What end of lac mRNA is preferably degraded?

Answer 23

3’ end

Question 24

Inducible Operons

Answer 24

Operons that can be induced if needed

Question 25

Repressible Operons

Answer 25

Operans that can be repressed if needed

Question 26

trp operon vs. lac operon

Answer 26

trp operon's repressor protein is off by default, meaning that the binding of tryptophan to it enables it to bind to the operator site, which prevents transcription

Question 27

Eukaryotic vs. Prokaryotic transcriptional regulation

Answer 27

Promoter is made up a "core" and a "promoter proximal sequence"

Question 28

Pre-initiation complex

Answer 28

"core" promoter bound by transcription factors (NO OTHER FACTORS); Eukaryotes only

Question 29

Mediator Protein

Answer 29

Allows for the communication between two different sets of proteins

Question 30

Gene-specific transcription factors

Answer 30

Assists for specific purposes of THAT gene for the binding of RNA Poly II, connected to the general transcription factors and RPII by Mediator Protein

Question 31

Upstream Transcription Factor Binding

Answer 31

1) Activator binds to enhancer 2) TFIID binds to TATA Box 3) Pre-initiation complex is assembled 4) Mediator Protein binds to complex 5) Another activator binds to some other enhancer sequence 6) A Co-activator binds to the activator 7) The mediator protein binds to the co-activator to initiate elongation

Question 32

TFIID

Answer 32

general transcription factor that promotes assembly of pre-initiation complex

Question 33

Chromatin Remodeling Complexes

Answer 33

Change accessibility of chromatin (beads), ATP-dependent

Question 34

Functions of Chromatin Remodeling Complexes

Answer 34

1) Change nucleosome positions 2) Histone eviction 3) Histone variant replacement

Question 35

Tendencies for various types of histone modifications

Answer 35

Acetylation -> Loosen up histone's hold on DNA; enhances expression Methylation -> Tightens histone's hold on DNA; leads to silencing

Question 36

Amino terminal tail

Answer 36

Sequence of about 20 amino acids at the start of the 4 core histone proteins that can be modified to change its properties

Question 37

4 Core Histone Proteins

Answer 37

1) H2A 2) H2B 3) H3 4) H4

Question 38

Iron Regulatory Process

Answer 38

Binding of Iron Regulatory Protein (IRP) binds to Iron Regulatory Element (IRE), inhibits translation of Ferritin mRNA Excess iron binds to IRP, changing confirmation that releases it from IRE, allowing Ferritin mRNA to be translation

Question 39

Ferritin

Answer 39

Iron-storing protein