exam 2 (prokaryote transcription) Flashcards
first step in the flow of genetic information
transcription
what is used to transcribe RNA to DNA
RNA polymerase
what does RNAP need to conduct RNA synthesis
normally need a DNA template strand, but sometimes they use RNA template strands
what occurs for a phosphodiester bond to form
3’ OH group of growing RNA chain makes a nucleophile attack on the alpha phosphoryl group
what drives reaction drives the phosphodiester bond to completion
hydrolysis of pyrophosphate, releasing a lot of energy
what is reverse transcription
strings deoxyribonucleotides together, just like DNA replication
what occurs during therapeutic inhibition of (reverse) transcription
retroviruses must convert their RNA genome into DNA for integration in the host cell’s genome
characteristics of nucleoside analog reverse transcriptase inhibitors
lack 3’ -OH
no attachment point
nonspecific
can be used by DNAP
how are nucleoside analog reverse transcriptase inhibitors converted into nucleotides
addition of phosphate groups
what is the difference between nucleoside/nucleotide analog reverse transcriptase inhibitors
NtARTIs (nucleotide) do not require phosphorylation to be in cells
the nascent RNA chain grows only in what direction
5’ –> 3’
what is the difference between RNAPs and DNAPs when synthesizing
RNAPs doesn’t need a primer to start synthesizing a nucleic acid chain
what direction is upstream? downstream?
upstream goes towards 3’ direction
downstream goes towards 5’ direction
the newly transcribed RNA strand is based off of what DNA strand
template strand
core bacterial RNAP contains 5 subunits, what are they?
a1, a2, b1, b’, w
what is a transcription promoter
initiation signal that is required in transcription
is downstream positive or negative? upstream?
downstream = positive upstream = negative
what are consensus sequences
sequences derived from alignments
pribnow box
-10 sequence
what is DNase
enzyme that cuts up DNA in nonspecific way and isolates the the protected DNA fragment
mutations in the -35 box result in
decreased lac expression
mutations in the -10 box result in
increased lac expression
altering the space between boxes results in
decreased expression
what are sigma factors
expressed by bacteria and RNAP
6th factor in DNAP gives brain
tells what sequences to go to and what to do
Sigma54 RNAP function
activator proteins bind enhancer elements and loop to promoters
the complete bacterial RNAP holoenzyme contains 6 subunits, which ones is added on?
sigma
what is a holoenzyme
complete form of an enzyme complex that contains all subunits for needed activity
how is DNA melted during transcription
hydrolyzing with ATP
what occurs when DNA interacts with open complex
- RNAP open complex is made
- RNAP unwinds DNA adjacent to open complex, scrunching it
- transcribes 8-10 nucleotides
- scrunched DNA is rewound
- abortive transcript is released
- builds up enough energy to spring away from promoter
why does RNAP pause
- mediated by various sequence elements
- important for proofreading the chain
- mismatches promote pausing
- cuts out extruded DNA
what are the 2 mechanisms for transcription termination
intrinsic and Rho-dependent
why does intrinsic termination depend on 2 DNA sequences
lead to specific structures in growing RNA molecule, that causes RNAP to terminate transcription
what allows for the formation of a stem loop in the RNA molecule
being G and C rich
why is having a stretch of 8-10 nucleotides, rich in U important?
release of newly generated RNA chain from RNAP
what is negative regulation
regular transcription takes place until a repressor protein binds to DNA repressor site
what is positive regulation
transcription doesn’t take place until activator protein binds to DNA activator site
what is an operon
- segment of DNA containing multiple genes regulated by a single promoter
- generates mRNA with multiple protein-coding sequences
are operons more common in eukaryotes or prokaryotes
common in prokaryotes.
rare in eukaryotes
what is B-galactosidase
breaks down lactose into galactose and glucose. produced by the lacZ gene
what is lactose permease
allows lactose to get into cells. produced by the lacY gene
what is B-galactoside transacetylase encoded by
lacA gene
how do the levels in B-galactosidase, permease, and transacetylase change as lactose is added to a previously lactose-free solution
the protein levels/synthesis increases as lactose is added to the solution
what does it mean if enzymes are repressible
their synthesis is decreased in response to a small molecule
what does it mean if enzymes are constitutive
they are always expressed and generally perform basic cellular “housekeeping” functions
what 2 classes were the mutations discovered by Monod and Jacob
lacl and lacOc
are lacOc mutations dominant or recessive
some were dominant and some were recessive
are lacl mutations dominant or recessive
recessive
what is the lac repressor
lacI encodes a factor that represses lac mRNA transcription
when can lacOc cause synthesis of lac mRNA`
when it is on the same DNA molecule as lacZ+
what is the established gene order
lacI, lacO, lacZ, lacY, lacA
what is referred to as the operator
lacO, which was later found to be the binding site for the lac repressor
describe the lac operon model
transcription occurs as the repressor binds to site and inducer attaches to fot lac mRNA to be transcribed (into the 3 proteins)
what segments are the antiterminator
2 + 3
what segments are the terminator
3 + 4
what is tryphtophan responsible for in termination
it makes sure the ribosome doesn’t get stuck at the adjacent Trp codons, therefore it’s important to have a high concentration
when transcribing trp mRNA, RNAP pauses. when and why?
it pauses as its reaches segment 2 in the ribosome, to synchronize transcription and translation
what allows the 1-2 and 3-4 hairpins to form
dissociation of the ribosome
the trpL has 4 segments, what distinct structures can be formed
terminator 3+4
antiterminator 2+3
function of the trpR protein
on/off switch for the trp operon at the level of transcription initiation
attenuation
control mechanism, involves regulation of elongation and termination via RNA and ribosome
what is the attenuator
sequence of 28 bases in the leader
what is designated as the leader of trpL
trpE, the first codon
the trp mRNA has how many nucleotides and in which direction
162 nt upstream
function of the trp operon
-encodes genes involved in tryptophan synthesis
-
structure of trp operon
promoter, operator, and 5 structural genes
trp operon is regulated at what levels of transcription
initiation, elongation, and termination
what occurs when cells grow in glucose
shut off transcription of lac genes
describe catabolite repression
cAMP forms a complex with a cAMP receptor protein, that binds to an activator site upstream of the lac promoter
what does E. coli use for fuel
glucose
what is the dimer of dimers, and binds to an operator
lac repressor
how many lac operators are there?
3
what structure does each DNA binding domain have?
supersecondary structure
purpose of the tetramerization helix
allows multiple repressor molecules to interact with one another
what is a result of low tryptophan
ribosome stalls, removes segment 1, allowing 2-3 hairpin to form, rather than 3-4
allolactose causes the lac repressor to??
to fall off the lac operator
tryptophan causes the lac repressor to??
to be able to bind to the trp operator
