Gene expression I from gene to RNA Flashcards
what’s a UTR?
an untranslated region
what’s a spacer?
region of non-coding DNA between genes (introns are non-coding within genes)
what’s a cistron?
sections of DNA or RNA molecule that codes for a specific polypeptide in protein synthesis in prokaryotic DNA– same as a gene
what is RNA polymerase?
an enzyme that synthesizes RNA on a DNA or RNA template
what’s a promoter?
nucleotide sequence, upstream of a gene, to which RNA polymerase binds to initiate transciption
define intron
a non coding region within a discontinuous gene in eukaryotes
define exon
a coding region within a discontinuous gene in eukaroytes
define genome
the entire genetic sequence of a living organism
what’s the sense strand?
DNA strand directed in the 3’ to 5’ direction and is not transcribed into RNA (it has the same nucleotide sequence to RNA but with T instead of U)
what’s the antisense strand?
DNA strand directed in the 5’ to 3’ direction which is transcribed into RNA (contains the complementary nucleotide sequence to RNA)
what is a gene?
a genetic unit containing information to make a functional product (RNA and/or protein)
what 4 bits of information does a gene contain?
- structural
- temporal
- positional
- inducible
what’s structural information?
coding DNA
what’s temporal information?
when genes should be on or off
what’s positional information?
where genes should be on or off
what’s inducible information?
when gene is responsive to external stimuli e.g. environmental
what type of genetic information is in all organisms?
structural and inducible
what type of genetic information is in more developed/ multicellular organisms?
structural
temporal
positional
inducible
is it true that more complex/ developed organisms have more genes?
yes– to an extent
not always true e.g. humans have less genes than pieris japonica (a plant)
what components are seen in a prokaryotic gene?
transcription start promoter leader coding regions (cistrons) spacers transcription termination
are transcription start/stop sites the same as translation start/stop sites?
no
what is a leader?
apparently useless part of DNA
where are spacers found?
between cistrons
what’s lost during transcription? (in prokaryotes)
promoter
what’s lost during translation? (in prokaryotes)
leader
promoter
terminator
what does the promoter contain?
TATA boxes (A-T rich)
what components are seen in a eukaryotic gene?
enhancer introns promoter transciption start exons transcription termination
what word describes enhancers and promoters?
they’re regulatory
where are UTRs found?
at the end of each section of mature mRNA
what is mature mRNA?
mRNA which has had introns spliced out
where does mature mRNA go?
transported out of the nucleus and into the cytoplasm to make proteins
what 2 factors affect the direction in which the polymerase travels?
- promoter
- directionality of the sequence
what’s the transcription bubble?
section of unwound DNA found during transcription
what happens at the transcription bubble?
RNA polymerase binds to DNA
melts double strand
polymerase polymerises from template strand in the 5’ to 3’ direction
how does the polymerase know where and when to bind to DNA, start transcription, stop transcription etc.?
it’s all in the gene
what is TBP?
TATA binding Protein- a component of the transcription factor TEIID with ancillary roles in the recognition of the TATA box
how many subunits is the Prokaryotic RNA polymerase made up of?
6
which subunits and how many is prokaryotic RNA polymerase made up of?
1 sigma (O) 2 alpha (a) 2 beta (B) 1 omega (w)
what is sigma in prokaryotic RNA polymerase for?
promoter recognition
what is alpha in prokaryotic RNA polymerase for?
involved in assembly and activation
what is beta in prokaryotic RNA polymerase used for?
catalysis and termination of transcription
what is omega in prokaryotic RNA polymerase used for?
involved in assembly and folding of some genes
which is the largest part of prokaryotic RNA polymerase?
betas
what’s an enzyme called when it has all of its subunits?
Holoenzyme
is prokaryotic RNA polymerase fairly large?
yes- covers around 70bp of DNA
which subinit can polymerase function without?
omega
what does the polymerase do first on DNA?
opens up DNA at the transcription site
what happens to the sigma once the polymerase begins to polymerise?
it is lost/ discarded
why is the sigma discarded?
it allows the polymerase to bind to the promoter site, however after this the polymerase has no use for it and needs to be able to bind to other sequences
where does the lost sigma go?
to join up with another polymerase
what is the polymerase called when the sigma has gone?
the core enzyme (aaBBw)
how many type of RNA polymerase do prokaryotes have?
1
How many types of RNA polymerase do eukaryotes have?
3
what are the 3 eukaryotic RNA polymerases?
polymerase I
polymerase II
polymerase III
what does polymerase I transcribe? (1)
ribosomal RNA genes (rRNA)
what does polymerase II transcribe?(2)
protein coding genes (mRNA)
small nuclear RNA (snRNA)
what does polymerase III transcribe? (3)
transfer RNA (tRNA) ribosomal RNA (rRNA) Small nuclear RNA (snRNA)
which eukaryotic RNA polymerase are simple?
I and III
which eukaryotic RNA polymerase are complex?
II
Genes which make different types of RNA have: (3)
- different architecture
- use different RNA polymerases
- each type of RNA polymerase needs a distinct set of accessory factors
what is meant by genes having different architecture?
different promoter and coding regions
what is meant by each type of RNA polymerase needing a distinct set of accessory factors?
needs other factors to work as well as their main subunits
what are the first subunits of the RNA polymerase II to bind to the DNA to be transcribed?
TFIID (Transcription Factor Polymerase II D)
TFIIA
TFIIB
what does TFIID do?
recognises a specific region of the promoter
acts as a saddle for another set of factors- TBP (TATA Binding Region)
what is TFIID?
a TATA (region of DNA) Binding Protein (TBP)
what is TBP similar to?
the sigma factor in Prokaryotic RNA polymerase
what part of the DNA is the TBP associated with?
minor-groove
what part of the DNA do most DNA proteins interact with?
major-groove
What does TFIIA do?
helps TFIID to bind to DNA
what was TFIIB do?
sets distance from TATA element to start site
how many subunits make up the entirety of RNA polymerase II?
10
what are the important subunits of RNA polymerase II?(8)
TFIID TFIIA TFIIB TFIIF TFIIE TFIIJ TFIIH Pol II
What do TFIIE, F, H, J and K do? (6)
interact with D-A-B complex
blocks non-specific binding of polymerase II (like sigma factor)
promoter clearance- (helping the polymerase move of the promoter and start transcribing the gene)
Helicase activity (unwinding DNA)
Processivity/ elongation- (Polymerase will polymerise a section then stop, but the other factors alllow the polymerase II to keep going for longer)
transcription- coupled DNA repair
what sort of RNA do the genes that RNA polymerase II transcribe make?
rRNA
what sort of RNA do the genes that RNA polymerase II transcribe make?
rRNA
generally, what is the apparatus and promoter sequence of the RNA polymerase I like?
simple
generally, what is the apparatus and promoter sequence of the RNA polymerase I like?
simple
RNA polymerase I cannot access DNA without specific…
accessories
RNA polymerase I cannot access DNA without specific…
accessories
what is the polymerase I promoter made up of?
2 sequences- core and UCE
what is the polymerase I promoter made up of?
2 sequences- core and UCE
in RNA polymerase I, what is SL1?
another general factor, like TFIID, multi subunit protein, containing TBP
what is TFIIIB made up of?
TBP (TATA Binding Protein) + 2 polymerase III specific TAFs
what is the upstream binding factor in RNA polymerase I?
factor that binds to UCE and core element in DNA
what is the upstream binding factor in RNA polymerase I?
factor that binds to UCE and core element in DNA
when is transcription started in RNA polymerase I?
when RNA polymerase I binds to the complex
when is transcription started in RNA polymerase I?
when RNA polymerase I binds to the complex
in RNA polymerase III, where is the promoter?
within the coding region
what happens at RNA polymerase III for initiation?
- TFIIIC binds to the B box
then recruits TFIIIB
once TFIIB is recruited, TFIIIC is dispensable
RNA polymerase III is rectruited and initiates transcription
what is TFIIIB made up of?
TBP (TATA Binding Protein) + 2 polymerase III specific TAFs
define operon
a cluster of genes transcribed by the same promoter that give rise to polycistronic mRNA (encodes several proteins)- genes usually related
define lac operon
a complete genetic unit containing genes for all the enzymes for a particular pathway and gene(s) which regulate it
what is the Plac?
promoter
what is the Olac?
operator
in the lac operon, what are the 3 subunits for a polyamide?
lacZ, lacY, lacA
what protein does lacZ translate to?
B- Galactosidase
what does B-Galactosidase do?
hydrolyses lactose to galactose and glucose
what’s the main source of energy for bacteria?
glucose
what sort of sugar is lactose?
Disaccharide
what monosaccharides is lactose made up of?
Galactose and glucose
in what situation is the lac operon activated?
when there’s no glucose available but there’s lactose available
what does the lac repressor tetramer do under normal conditions?
prevents the transcription of the gene required when lactose is present
what happens when lactose isn’t present?
lac operon repressed
repressor binds to lacO
prevents RNA polymerase from clearing promoter
what does lacA translate to?
lactose transacetylase
what is lactose in terms of how it affects the operon?
an inducer
what happens to the lac operon when lactose runs out
the system will switch off
what is the lacI?
lac repressor
what does lacY translate to?
lactose permease
what does lactose permease do?
facilitates the entry of lactose into cell
what does lacA translate to?
lactose transacetylase
what does a cis-acting factor do?
regulates DNA it’s directly joined to
what does a trans-acting factor do?
regulates DNA anywhere
is a cis-acting factor dominant or recessive?
dominant
is a trans-acting factor dominant or recessive?
recessive
what is the CRP?
Catabolite Repression Protein
what does a lacOc (constitutive) mutation cause?
the lac operon to be permanently switched on, as the operon isn’t repressed
is a lacOc mutation dominant or recessive?
dominant
is a lacOc mutation cis or trans- dominant?
cis
in a lacOc mutation, would adding a repressor make a difference?
no
what does a lacI- mutation cause?
the lacI gene be permanently switched on as the repressor is mutated
if glucose is low,
cAMP is high, so CRP is active
what is catabolite repression?
repression of the lac-operon in the presence of glucose
what is CRP?
Catabolite Repressor Protein
what is CAP?
Catabolite Activator Protein
what does the Trp repressor do?
binds to operator when tryptophan is present- prevents transcription
how does the CRP bind?
using cyclic AMP (cAMP)
if glucose is high…
cAMP is low, so CRP is inactive
if glucose is low,
cAMP is high, so CRP is active
is catabolite repression an example of a cis or trans- acting repressor?
trans
what is the Trp operon used to make?
Tryptophan
what’s different about promoters and enhancers positionally?
enhancers are independent of position and orientation, whereas promoters can be affected by these factors
what does the Trp repressor do?
binds to operator when tryptophan is present- prevents transcription
how is eukaryotic DNA organised?
into chromatin
what does DNA coated in chromatin do in terms of transcription factors?
it presents a physical barrier
when a gene is transcribed what happens to the chromatin around it?
it changes
what’s the chain of events in the signal tranduction pathway, starting with the ligand-receptor interaction at the cell plasma membrane?
there’s then the generation of a 2nd messenger small molecule
this activates protein kinases
causing the regulation of transcription factor activity
charge, structure and protein-protein interactions
DNA binding activation nuclear localisation, degradation
affects DNA activation
where is the regulatory information situated?
the enhancer
what’s different about promoters and enhancers positionally?
enhancers are independent of position and orientation, whereas promoters can be affected by these factors
in transcription of eukaryotes, how is the issue of a large distance between the enhancer and promoter solved?
they are looped out
how does histone acetylation make DNA acceptable for transcription?
changes the lysine tails from positive to negatively charged, causing the histones to be repelled by the negatively changed DNA
what do ATP- dependent chromatin modification complexes do?
also make DNA to be transcribed accessible
what are signal transduction pathways?
how a signal from outside a cell can interact with the cell and which then interacts with the nucleus and affect transcription factors
