lecture 7: gene to protein Flashcards
what happens during transcription?
DNA to RNA
what happens during translation?
mRNA to protein
what are the differences between transcription and translation in prokaryotes and eukaryotes?
Prokaryotic transcription occurs in the cytoplasm alongside translation. Prokaryotic transcription and translation can occur simultaneously. This is impossible in eukaryotes, where transcription occurs in a membrane-bound nucleus while translation occurs outside the nucleus in the cytoplasm
what are codons?
nucleotide triplets that correspond to specific amino acids
what is the start codon?
AUG
what is transcription?
synthesis of mRNA from a DNA template
what does RNA polymerase do?
synthesizes mRNA from 5’ to 3’ by catalyzing phosphodiester bond formation between ribonucleotides
what are the three steps to transcription?
1) initiation
2) elongation
3) termination
what happens during initiation of transcription?
-RNA polymerase and transcription factors bind to the promoter
what are transcription factors?
proteins that help recruit RNA polymerase to gene
what is the promoter?
region of DNA that includes start point and TATA box
what’s the base pair sequence for the TATA box?
TATAAAA-ATATTTT
how many base pairs does RNA polymerase unwind?
10-20
all our cells have the same DNA, how can we have so many different types of cells?
all cells have same genes, but only a subset of these genes are expressed in each cell type, (depending on transcription factors). only specific genes in the cell are expressed
what happens during elongation of transcription?
-RNA polymerase synthesizes mRNA from 5’ to 3’
-reads template strand from 3’ to 5’
is a primer needed for elongation?
no
what is the coding strand of DNA and its relation to mRNA?
-its the non-template strand (mRNA not going on it directly)
-it has the same nucleotide sequences as mRNA but replace U with T
what happens during termination of transcription for prokaryotes?
-RNA polymerase transcribes a terminator sequence, causing it to detach from the mRNA
-mRNA is released and is immediately ready for translation
what happens during termination of transcription for eukaryotes?
-RNA polymerase reaches termination sequence on template strand of DNA: TTATTT
-complementary AAUAAA sequence is poly A signal sequence
-proteins are recruited to the poly A signal sequence and cut the transcript 10-35 nucleotides after the signal sequence
-mRNA is released as pre-mRNA
-DOES NOT CODE FOR STOP CODON
what do we call the AAUAAA mRNA sequence, complementary to the termination codon on the DNA template strand?
poly A signal sequence
in eukaryotes, when is mRNA processed?
after transcription (pre mRNA goes to mature mRNA)
is mature or pre mRNA longer?
pre-mRNA, because it has a whole bunch of extra stuff in the middle that gets cut out
what is added to the pre-mRNA during processing?
1) 5’ cap
2) poly A tail
what is the 5’ cap? What are its functions?
-modified guanine nucleotide is added to the 5’ end of the mRNA
functions:
-protects against degradation
-attachment of ribosomes
-facilitates transport out of nucleus
what is the poly A tail? what are its functions?
-50 to 200 adenine nucleotides are added to the 3’ end of the mRNA
functions:
-protects against degradation
-attachment of ribosomes
-facilitates transport out of nucleus
what are the three parts of mRNA processing?
-addition of 5’ cap
-additinon of poly A trail
-RNA splicing
what is RNA splicing?
-removal of nucleotides (introns) from pre-mRNA
-pre-mRNA contains coding and non-coding sequences and nucleotides
what is the difference between introns and exons?
introns: non coding sequences of nucleotides
exons: coding sequence of nucleotides
what catalyzes RNA splicing?
spliceosome
what is a spliceosome?
-its a complex of proteins and RNA (snRNA)
-removes introns and links exons
-RNA component acts as an enzyme
true or false, the RNA contained in in the spliceosome acts as an enzyme
true
what do we call an RNA that has enzymatic activity? can it catalyze a reaction?
ribozyme. yes it can
do bacteria have snRNA?
no. prokaryotes do not need their mRNA to be processed after its production. they have no introns
what are the functions of introns?
1) control of gene expression
2)regulate transport of RNA out of the nucleus
3) alternative splicing (single gene= more than one protein)
4) evolution of new proteins (through exon shuffling, which introns are involved in)
what is exon shuffling and what does it allow for?
-two different genes swap their alleles through mutation that happens during meiosis. Exons and introns mix and match to form new proteins. alternation exons and introns increase the chance that a recombinant protein will be functional because crossing over can occur anywhere in the introns an not affect the coding region
what is in the final mRNA structure before translation?
what are the three steps to translation?
1) initiation
2) elongation
3) termination
what is translation?
synthesis of polypeptide from mRNA transcript
what is the start codon and its corresponding amino acid?
AUG: methionine
what are the three stop codons?
-UAA
-UAG
-UGA
true or false, there is only one codon per amino acid
false, there are many codons for each amino acid, therefore if a mutation occurs, the same protein will still be produced
what are the three types of RNA involved in translation?
-ribosomal RNA (rRNA)
-transfer RNA (tRNA)
-messenger RNA (mRNA)
what are ribosomes formed by?
rRNA and ribosomal proteins
what are the 2 subunits for ribosomes?
-small unit
-large unit
in what direction do ribosomes read mRNA?
5’ to 3’
where is the ribosomal binding spot for mRNA?
small subunit
where is the ribosomal binding spot for tRNA?
3 sites, large subunit:
- E-site (exit site)
- P-site (peptidyl-tRNA binding site)
- A-site (aminoacyl-tRNA binding spot)
how many nucleotides are in tRNA?
approx 90 nucleotides
what is the anticodon?
a sequence of 3 bases that are complementary to a codon on the mRNA strand
where is the amino acid attached on the tRNA?
on the amino acid attachment site (3’ end)
by what enzyme is the the attachment of amino acid to tRNA catalyzed by?
aminoacyl-tRNA synthetase
true or false, all amino acids have the same aminoacyl-tRNA synthetase
false. each amino acid has its own
how many aminoacyl-tRNA synthetases are there?
20 (1 per amino acid)
is the attachment of amino acid to tRNA an endergonic or exergonic reaction?
endergonic (requires energy)
what happens during initiation of translation of translation?
3 steps:
-small ribosomal subunit binds to mRNA
-initiator tRNA binds to mRNA (UAC anticodon binds to AUG start codon on mRNA
-large ribosomal subunit binds to small subunit
where is the initiator tRNA positioned in the large ribosomal subunit?
positioned in P-site (EPA)
true or false, for the large ribosomal subunit to bind to small subunit, GTP is required.
true!
what is GTP?
guanosine triphosphate. it’s hydrolysis is used as an energy source
what does the hydrolysis of GTP give us?
GDP+Pi
what are elongation factors?
set of proteins that facilitate the elongation part of translation
in what direction is the mRNA read during the elongation part of transcription
5’ to 3’
what are the 3 steps of elongation for translation?
-codon recognition (mRNA codon at A-site forms H-bonds with anticodon of incoming tRNA)
-peptide bond formation (growing polypeptide transferred from tRNA in P-site to tRNA in A-site, peptide bond is formed)
-translocation (growing peptide in A-site is moved to P-site)
what is the bond between the mRNA codon and the anticodon of the incoming tRNA?
H-bond
for which steps of the elongation part translation is GTP required?
the first and the last step! codon recognition and translocation
do we need ATP to link amino acid to tRNA?
yes
what does the elongation cycle look like for translation?
what happens during termination of translation?
-stop codon reaches mRNA
-release factor binds to the stop codon (not a stop codon!)
-bond between tRNA (in p-site) and the polypeptide chain is hydrolyzed (broken)
-polypeptide is released
-ribosome dissociates and leaves mRNA
what type of bond is formed between tRNA and the amino acid?
covalent bond
where does translation happen?
in the cytoplasm
what are the 2 types of ribosomes?
-free (cytosolic proteins)
-bound to the rough endoplasmic reticulum
where does the synthesis of ALL proteins start?
-all start on free ribosomes
what directs the ribosome to the ER? How does it work?
signal peptides
which type of proteins have signal peptides?
membrane proteins and secreted proteins
what does the signal peptide consist of?
-approximately 20 hydrophobic amino acids at N-terminus of growing polypeptide
what does SRP stand for? what does it do?
-signal recognition particle (SRP)
-it binds to the signal peptide, which causes protein synthesis pause, then it binds to the SRP receptor bringing the growing polypeptide AND ITS RIBOSOME to the ER for protein synthesis to continue there
what is the SRP comprised of?
protein and RNA
what is the SRP receptor?
-protein complex built into the ER membrane (integral membrane protein)
after the continuation of the synthesis of membrane/secreted proteins in the ER ribosomes, what happens once the protein is done synthesizing?
-secreted proteins remain in the ER lumen
-membrane proteins are embedded in the ER membrane
-signal peptide is usually removed by an enzyme
what are the 2 types of mutations in genes?
-base pair substitution (point mutation, replacement of one nucleotide with another)
-insertions or deletions (addition or loss of nucleotides)
what is a mutation?
any change in the sequence of bases at the DNA level
what are the 4 types of base pair substitution mutations? what do they mean?
-silent (no change of amino acid)
-missense (change of amino acid)
-neutral/conervative missense mutation (chang to similar amino acids)
-nonsense (amino acid to stop codon, change in DNA that causes a protein to terminate or end its translation earlier than expected)
what are the 2 types of base pair insertion/deletion mutations?
-frameshift mutations
-no frameshift mutations
what is a frameshift mutation?
-alter reading frame of mRNA
-insertion or deletion is not a multiple of 3
-all codons after mutation are changed
what is a non-frameshift mutation?
-does not alter reading frame of mRNA
-insertion or deletion is multiple of 3
-codons are either added or removed but codons before and after mutation are unchanged
which strand of DNA is directly involved in transcription?
template strand (non-coding strand)
(NOT coding strand)
what is the nucleotide sequence on the template strand for the TATA box?
ATATTT
where does pre-mRNA splicing happen?
in the nucleus (before its released)
what does UTR stand for?
untranslated region
what is required for initiation (translation)?
initiation factors
what is required for elongation (translation)?
elongation factors
what is required for termination (translation)?
release factors and GTP
all steps of translation require protein factors and energy. what are the protein factors required for translation?
-initiation factors
-elongation factors
-release factors
