Transcription + Translation Flashcards
where does transcription occur?
the nucleus
where does translation occur?
cytoplasm or RER
where does RNA processing occur?
the nucleus
gene definition
the stretch of DNA that is transcribed into RNA also called transcription
what are the main stages of transcription
initiation, elongation, termination
what is the promoter region?
where the RNAP first binds and RNAP starts transcribing and has the transcription start point
how many promoters do prokaryotes have?
one RNAP
how many promoters do eukaryotes have? Name them and what do they do
3:
RNAP I makes rRNA
RNAP II involves in transcription (makes mRNA)
RNAP III makes tRNA
Where is the promoter located?
upstream ofthe gene
what is the promoter composed of?
an AT rich region
why is the promoter composed of AT rich region
AT have fewer hydrogen bonds, meaning they require less energy to have
describe the pribnow box
is the AT rich region in prokaryotes that is located -10
consensus sequence: TATAAT
decribe the TATA box
the AT rich region in eukaryotes located at -15
consesus sequence: TATAAA
Describe the transcription initiation in prokaryotes
- RNAP recognizes and binds to the promoter
- unwind the DNA
- begin transcription at start site
describe transcription initiation in eukaryotes
a transcription pre initiation complex is formed that consists of the following components in binding order
- transcription factors: protein that help initiate and regulate transcription
- inactive (dephosphorylated) RNAP II on promoter
- RNAP phosphorylated the C-terminal domain (CTD)
- transcription beings one the CTD on RNAP is phosphorylated
sense strand
the coding strand
antisense strand
the template and noncoding strand
transcript
newsly synthesized RNA
describe the transcription termination in prokaryotes
two inverted repeats of GC regions on DNA, once on the RNA they form complementary bonds with each other which results in a GC hairpin loop which causes the RNAP to stall, from there the adenine on DNA transcribe into uracil on RNA results in a dA/U rich region with weak interactions so RNAP stops transcribing and RNA released from RNAP
describe the termination process of a eukaryote in transcription
dephosphorylation of CTD on RNAP II which reduces rate of elongation and increases pausing
has a terminator sequence AAUAAA on the nascent RNA, which stalls/pauses RNAp II but the RNAP II can still continue for a few bases to thoushands of bases past the sequence
40-60 nucleotides downstream of terminator sequence GU righ sequence with signals the cleavage of RNA by an endonuclease
in what types of cells does RNA processing occur?
eukaryotes
what are the 3 types of RNA processing?
capping, polyadenylation, splicing
Describe the RNA processing capping: Where, When, Purpose, Mechanism
Where: 5’ end
When: con transcriptional (at the same time as others)
Purpose: protect and facilitate ribosome binding
Mechanism: addition of modeified guanine
Describe the RNA processing polyadenylation: Where, When, Purpose, Mechanism
Where: 3’ end
When: post transcriptional (after transcription)
Purpose: protect and facilitate mRNA export
Mechanism: addition of many adenine nucleotides
Describe the RNA processing splicing: Where, When, Purpose, Mechanism
Where: introns
When: co or post transcriptional
Purpose: alternatice splicing, exon shuffling
Mechanism: intron is excised
describe the 5’ cap
modified guanine added to the 5’ end that is added by capping enzyme complex to protect mRNA from degradation and signal ribosome attachment
what adds the adenine to the 3’ end? what does it do?
poly-A polymerase to protect mRNA from degradation and facilitate export of mRNA from nucleus
what are introns
INtervening sequences interspersed between exons
exons
coding sequences EXpressed
what is the protein component of splicing? What do they do?
snRNP = snRNA + protein
it binds to the splice site (snRNA is complementary to the splice site) and forms a spliceosome and exices (cuts out) the intron then rejoins the exons
what is the function of an intron?
it allows for a single gene to encode for multiple polypeptides by removing different regions to form different polypeptides (which segments are treated as exons), they have a regulatory role and occurs at the RNA level
What are the four steps in translation initiation?
- ribosome (small subunit) finds and binds to the mRNA strand
- ribosome locates translation start site (AUG codon)
- intator tRNA binds
- ribosome large subunit binds
describe step 1 of translation initiation: ribosome finds and binds to the mRNA strand in PROKARYOTES
the 5’ end of the mRNA transcript has a Shine-Dalgarno sequence and the rRNA on the ribosome small subunit has a complementary anti Shine-Dalgarno sequence which helps it find and bind to the 5’ end of the mRNA
describe step 1 of translation initiation: ribosome finds and binds to the mRNA strand in EUKARYOTES
ribosome small subunit recognizes and binds to mRNA at 5’ cap
what is a ribonucleoprotein composed of?
ribosomal RNA and a protein
where is the ribosome made in eukaryotes?
nucleolus
what are the 2 subunits of the ribosome?
the large subunit (60s) and the small (40s)
what are the 4 binding sites of a ribosome?
- A site, aminoacyl tRNA binding site
- P site, peptidyl-tRNA binding site
- E site, exit site
- mRNA binding site
Describe the second step of translation initiation
the ribosome small subunit moves along 5’ leader of mRNA until reach translation start site (start codon AUG)
in prokaryotes what factors help ribosome small subunit find start codon?
initiation factors
in eukaryotes what factors help the ribosome small subunit find the start codon? where is it
Kozak sequence on the mRNA
describe step 3 of translation initiation
anticodon
complementary sequence of a codon on tRNA
what does tRNA do?
carries the amino acid to make the polypeptide chain
what is the starting amino acid in prokaryotes?
fmet - formyl methionine
what is the starting amino acid in eukaryotes?
met, regular methionine
what does the A site on the ribosome do?
holds the aatRNA carrying the next amino acid to be added
what does the P site on the ribosome do?
holds the tRNA molceule carrying the growing polypeptide chain
what does the E site on the ribosome do?
where the tRNA molecules leave the ribosome
what type of bond is formed between the amino acids on the P site and A site?
a peptide bond
translocation requires energy
what are the 3 main steps of polypeptide elongation?
- codon recognition
- peptide bond formation
- translocation
describe the termination process for translation
a stop codon called a release factor binds to the A site, it adds a water molecule instead of amino acid to polypeptide the polypeptide in the P site is hydrolyzed from tRNA in P site and released and the translation complex disassembles
polyribosomes
when 1 molecule of mRNA has multiple ribosomes simultaneously translating the mRNA
what direction do ribosomes go in
from 5’ to 3’
if the ribosome is free/unbound where are the proteins that it produces?
cytoplasmic proteins
if a ribosome is bound to the ER and goes to the golgi where are the proteins it produces?
secretory proteins
describe cytoplasmic proteins
- water soluble
- folds spontaneously on its own into its tertiary structure
- but sometimes cytosol does not necesarily provide the right environment for the protein to fold
what is the role of chaperon proteins?
provides the ideal microenvironment for folding and keep the cytoplasmic proteins separated from other influences in the cytosol
describe the environment the chaperon protein provides and why it is the way it is.
hydrophilic since the cytoplasmic protein exists in the hydrophilic cytoplas
describe signal sequences
5-30 hydrophobic amino acids at the leading end/N terminus of a polypeptide and makes the polypeptide destined for the ER aka signal peptide
describe the stop-transfer sequence
it is located on the nascent polypeptide and achors into the membrane so the polypeptide does not get released into the lumen
what does an signal recognition particle (SRP) do?
binds to the signal sequence stopping translation
it binds to an SRP receptor on the ER membrane bringing an entire translation complex with it and the ribosome is docked on the ER membrane
translocon
similar to a channel protein in which the signal seuqnce is oriented into threading the polypeptide into the ER lumen making the SRP is released and translation resumes
what does a signal peptidase do?
cleaves (like cleavage) the signal sequence
describe the pathway of secretory proteins
- the stop transfer sequence on the nascent polypeptide anchors into the membrane so that the polypeptide does not get released into the lumen
- vesicles pinch off from ER and fuse onto the golgi with polypeptide attached to membrane
- vesicles pinch off from golfi and exocytose to cell membrane where polypeptide becomes incorporated onto the cell surface
name all the organelles in the endomembrane system
- vesicles
- lysosome
- smooth endoplasmic reticulum
- rough endoplasmic reticulum
- golgi apparatus
what dose a vesicle (or transport vesicle)
takes lipids to golgi apparatus
what does the lysosome do?
contains digestive enzymes that break down cell parts or substances entering by vesicles
what does the smooth ER do?
synthesizes lipids and has various other functions
what does the rough ER do?
synthesezes proteins and packages them in vesicles
what does the golgi apparatus do?
modifies lipids and proteins from the ER sorts and packages them in vesicles
what are the post-translation modifications?
- addition
- removal
- polymertization
- folding
describe the post translational modification addition
adding sugards, lipids, sulfate or phosphate groups
describe the post translational modification removal
cleavage - some amino acids such as methionie or whole polypeptide chains are separated
describe the post translational modification polymerization
two or more polypeptides may join together to form a protein like hemoglobin
