1.2: Regulation of Genome Expression

Question 1

describe a genome

Answer 1

encodes the information to construct and maintain an organism. most genomes are made of DNA.

Question 2

what is the exception to the idea that genomes are made of DNA

Answer 2

viruses have RNA genomes - but viruses aren’t considered living things

Question 3

describe the transcriptome

Answer 3

the repertoire of RNA molecules present in a cell at a particular time. it is maintained by the process of transcription

Question 4

how can you visualize a transcriptome

Answer 4

DNA microarray. read like a table where rows are genes and columns are samples. there are diff color coding but red/black/green from most to least of RNA imaged

Question 5

these days, fewer researchers are using DNA microarrays. what is the alternative

Answer 5

RNA sequencing

Question 6

describe the proteome

Answer 6

collection of proteins in a cell which then defines the biochemical functions of the cell

Question 7

how can you visualize the proteome

Answer 7

2d gel electrophoresis. read it like a graph. the splotches are proteins the x axis is acidic - isoelectronic point - basic and the y axis is the molecular weight. you can also use color analysis to compare the presence of proteins in different samples (matching or not)

Question 8

what process maintains the transcriptome and which maintains the proteome

Answer 8

transcriptome: transcription
proteome: translation

Question 9

what is the central dogma of molecular bio

Answer 9

genome (dna) -> transcriptome (rna) -> proteome (protein)

Question 10

diff cell types of a multicellular organism contain the same genome, how do we produce different cell types?

Answer 10

differences in genome expression

Question 11

regulation of gene expression is crucial for (2)

Answer 11

1. defining cell types (multicellular organism): brain v liver
2. responses to extracellular stimuli (both multicellular and unicellular organisms)

Question 12

what enzyme transcribes DNA into RNA

Answer 12

RNA polymerase

Question 13

describe prokaryotic transcription, recall the following key terms: sigma factor, promoter, rnap

Answer 13

sigma factor goes to rnap, promoter is region of dna that positions rnap and indicates transcription start site. rnap holoenzyme (sigma factor + rnap love enzymes), rnap unwinds dna, transcription begins, once ~10 nucleotides synthesized, sigma factor is released (needs it to get started), transcription elongation occurs, then transcription termination occurs

Question 14

gene expression in both prokaryotes and eukaryotes is regulated by _________________ which bind specifically to ____________________

Answer 14

gene expression in both prokaryotes and eukaryotes is regulated by gene regulatory proteins (transcription factors - prot that controls how much rna u make from a gene) which bind specifically to regulatory regions of dna (cis elements)

Question 15

what are cis elements

Answer 15

dna seq on same dna double helix as the gene

Question 16

describe the operon system

Answer 16

multiple genes can be transcribed into a single rna molecule in a prokaryote. in e coli many genes are transcriptionally regulated by food availability

Question 17

describe the trp (tryptophan) operon

Answer 17

5 genes, encode enzymes for trp biosynthesis, transcription regulated by a single promoter

Question 18

for which organism do you assume the trp operon is apart of (unless stated otherwise)

Answer 18

e coli

Question 19

what are the two potential protein bound states of the trp operon

Answer 19

bound by rnap: trp gene expression ON
bound by tryptophan repressor protein: trp gene expression off

Question 20

what does a trp repressor bind to

Answer 20

a specific dna sequence of the promotor called an operator

Question 21

how does a trp repressor function

Answer 21

blocks promoter access through preventing rnap cannot bind, negatively regulates trp expression

Question 22

how is the trp repressor dna binding activity regulated

Answer 22

the repressor must bind two molecules of trp to bind to dna – the repressor and operator provide a simple switch to control trp biosynthesis according to the availability of free trp

Question 23

trp repressor contains which dna binding motif (most common) and binds to major

Answer 23

helix turn helix, binds in the major groove of the dna helix

Question 24

what does trp binding induce

Answer 24

• conformational change
• protein fits into the major groove

Question 25

describe the e coli lac operon

Answer 25

• 3 genes required for transport of lactose into the cell and for its catabolism
• enables use of lactose in the absence of glucose
• dual regulation: both both positive and negative control

Question 26

3 big rules of the lac operon

Answer 26

• e coli’s first choice is to use glucose
• when there is low glucose and high lactose, it’ll then use lactose - both conditions must be there to use lactose
• the lac operon is what is turned on when it wants to use lactose

Question 27

describe the activator/repressor (of transcription) of the lac operon

Answer 27

activator: catabolite activator protein (CAP) promotes lac expression: low glucose/high lactose
repressor: lac repressor protein, inhibits lac expression: low lactose

Question 28

where does cap bind

as in CAP not the cap on mRNA

Answer 28

cis regulatory sequences for cap

Question 29

first gene of lac operon encodes for what and what does it do

Answer 29

b galactosidase; breaks down lactose to glucose and galactose

Question 30

when lactose levels are ___, the lac repressor is bound to the operator = lac operon gene expression is ___

Answer 30

low, off

Question 31

increased lactose __________ the repressor from the operator

Answer 31

increased lactose removes the repressor from the operator

Question 32

increases in lactose increase levels of ________, related to lactose; requires __________

Answer 32

allolactose, b galactosidase

Question 33

describe the relationship between lactose and allolactose

Answer 33

direct relationship

Question 34

allolactose binds to lac repressor and does what

Answer 34

conformational change, decreases dna-binding activity, release from the operator

Question 35

+glucose and -lactose has the lac repressor on/off the strand which leads to the operon being on/off
+glucose and + lactose has the lac repressor on/off the strand which leads to the operon being on/off

Answer 35

+glucose and -lactose has the lac repressor on the strand which leads to the operon being off
+glucose and + lactose has the lac repressor off the strand which leads to the operon being off (bc it has to be low gluc and high lac)

Question 36

why is the activator needed in lac operon regulation

Answer 36

• rnap binding is inefficient to the lac promoter
• efficient rnap binding to lac promoter requires CAP to be bound
• CAP contains a helix turn helix dna binding motif == can bind to dna

Question 37

compare the lac operon and trp operon in regards to regulation

Answer 37

trp: if no repressor, rnap sigma factor can just bind to the desired seq
laq: need activator (another prot) to get rnap to bind to apt dna seq

Question 38

cap dna binding activity is activated by ____ glucose

Answer 38

low

Question 39

how is cap regulated

Answer 39

decreasing glucose levels increase the levels of the signaling molecule called cyclic AMP
cAMP binds CAP protein: conformational change, increases dna binding activity, binds to cap binding site

Question 40

where does cap recruit rnap to

Answer 40

the lac promoter

Question 41

describe the relationship between glucose and cAMP levels

Answer 41

inverse relationship

Question 42

describe the conditions which facilitate the overall binding of rnap

in the lac operon

Answer 42

high lactose=high allolactose = allolactose binds to the repressor, the repressor cannot bind to dna, rnap can bind
low glucose = high cAMP = cAMP binds cap = cap binds dna = rnap can bind
=== operon on

Question 43

the bacterial toxin cycloheximide inhibits eukaryotic translation. which of the following would you expect to be most affected in human cells treated with cycloheximide?
a. genome
b. transcriptome
c. proteome

Answer 43

c. proteome bc it stops translation

Question 44

the bacterial toxin cycloheximide inhibits eukaryotic translation. if a scientist wants to compare differences in cycloheximide treated vs cycloheximide untreated animal cells, which of the following techniques should the scientist use?
a. dna seq
b. dna microarrays
c. 2d gel electrophoresis
d. rna seq

Answer 44

c

Question 45

under conditions where both glucose and lactose levels are low, the expression of the lac operon should be:
a. on
b. off
and explain

Answer 45

b. off
this is not met: high lactose=high allolactose = allolactose binds to the repressor, the repressor cannot bind to dna, rnap can bind
even if the following is met (low glucose = high cAMP = cAMP binds cap = cap binds dna = rnap can bind) both conditions must be accepted so overall rnap can bind