1.2: Regulation of Genome Expression Flashcards
describe a genome
encodes the information to construct and maintain an organism. most genomes are made of DNA.
what is the exception to the idea that genomes are made of DNA
viruses have RNA genomes - but viruses aren’t considered living things
describe the transcriptome
the repertoire of RNA molecules present in a cell at a particular time. it is maintained by the process of transcription
how can you visualize a transcriptome
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
these days, fewer researchers are using DNA microarrays. what is the alternative
RNA sequencing
describe the proteome
collection of proteins in a cell which then defines the biochemical functions of the cell
how can you visualize the proteome
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)
what process maintains the transcriptome and which maintains the proteome
transcriptome: transcription
proteome: translation
what is the central dogma of molecular bio
genome (dna) -> transcriptome (rna) -> proteome (protein)
diff cell types of a multicellular organism contain the same genome, how do we produce different cell types?
differences in genome expression
regulation of gene expression is crucial for (2)
- defining cell types (multicellular organism): brain v liver
- responses to extracellular stimuli (both multicellular and unicellular organisms)
what enzyme transcribes DNA into RNA
RNA polymerase
describe prokaryotic transcription, recall the following key terms: sigma factor, promoter, rnap
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
gene expression in both prokaryotes and eukaryotes is regulated by _________________ which bind specifically to ____________________
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)
what are cis elements
dna seq on same dna double helix as the gene
describe the operon system
multiple genes can be transcribed into a single rna molecule in a prokaryote. in e coli many genes are transcriptionally regulated by food availability
describe the trp (tryptophan) operon
5 genes, encode enzymes for trp biosynthesis, transcription regulated by a single promoter
for which organism do you assume the trp operon is apart of (unless stated otherwise)
e coli
what are the two potential protein bound states of the trp operon
bound by rnap: trp gene expression ON
bound by tryptophan repressor protein: trp gene expression off
what does a trp repressor bind to
a specific dna sequence of the promotor called an operator
how does a trp repressor function
blocks promoter access through preventing rnap cannot bind, negatively regulates trp expression
how is the trp repressor dna binding activity regulated
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
trp repressor contains which dna binding motif (most common) and binds to major
helix turn helix, binds in the major groove of the dna helix
what does trp binding induce
- conformational change
- protein fits into the major groove
describe the e coli lac operon
- 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
3 big rules of the lac operon
- 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
describe the activator/repressor (of transcription) of the lac operon
activator: catabolite activator protein (CAP) promotes lac expression: low glucose/high lactose
repressor: lac repressor protein, inhibits lac expression: low lactose
where does cap bind
as in CAP not the cap on mRNA
cis regulatory sequences for cap
first gene of lac operon encodes for what and what does it do
b galactosidase; breaks down lactose to glucose and galactose
when lactose levels are ___, the lac repressor is bound to the operator = lac operon gene expression is ___
low, off
increased lactose __________ the repressor from the operator
increased lactose removes the repressor from the operator
increases in lactose increase levels of ________, related to lactose; requires __________
allolactose, b galactosidase
describe the relationship between lactose and allolactose
direct relationship
allolactose binds to lac repressor and does what
conformational change, decreases dna-binding activity, release from the operator
+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
+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)
why is the activator needed in lac operon regulation
- 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
compare the lac operon and trp operon in regards to regulation
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
cap dna binding activity is activated by ____ glucose
low
how is cap regulated
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
where does cap recruit rnap to
the lac promoter
describe the relationship between glucose and cAMP levels
inverse relationship
describe the conditions which facilitate the overall binding of rnap
in the lac operon
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
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
c. proteome bc it stops translation
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
c
under conditions where both glucose and lactose levels are low, the expression of the lac operon should be:
a. on
b. off
and explain
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
