Week 7 Flashcards
Transcription and Translation
define: transcription
process by which the polymerization of ribonucleotides guided by complementary base pairing produces an RNA transcript of a gene (DNA -> RNA)
in which direction are nucleotides added
5’-to-3’
what is in place of thymine in RNA
uracil
which enzyme catalyzes transcription
RNA polymerase
define: promoters
DNA sequences near the beginning of genes that signal RNA polymerase where to begin transcription
define: terminators
sequences in the RNA produces that tell RNA polymerase where to stop (encoded by DNA)
define: open reading frame (ORF)
region between the start and stop codons
are the start and stop codons located at the ends of mRNA
no, since they are nested within the promoter and terminator regions
what are the three steps of transcription
initiation, elongation, and termination
define: RNA polymerase holoenzyme
RNA polymerase + sigma factor
what two things does the sigma factor do
- reduces RNA polymerase’s general affinity for DNA
- increases RNA polymerase’s affinity for the promoter
what happens when RNA polymerase binds to the promoter
the RNA polymerase unwinds part of the double helix
define: open promoter complex
complex formed between the RNA polymerase holoenzyme and an unwound promoter
when does the sigma factor get released
after the first few nucleotides of the RNA are synthesized
what is the average speed of RNA synthesis
50 nucleotides per second
define: transcription bubble
region of DNA unwound by RNA polymerase
what causes the RNA to get displaced during transcription
reformation of DNA helix
when can the next instance of transcription happen on a strand of DNA
once RNA polymerase has moved off the promoter
on which strand of DNA does transcription occur
the template strand
define: coding strand
the strand of DNA that has the same sequence as mRNA (with T replaced by U)
are the promoter and terminator sequences present in mRNA
no
what are the two methods of transcription termination
- rho-dependent
- rho-independent
what causes a hairpin loop to be formed in rho-independent termination
transcription of six adenines
what bonds are primarily present in a hairpin loop
C-G bonds
why does the hairpin loop form
hydrogen bonds between A-U are weaker than C-G
what happens after a hairpin loop is formed
the RNA polymerase becomes weakly associated with the DNA and falls off
does a frame shift mutation in one gene affect the sequence of another gene
no, since each genes has its own transcription start/stop
in which type of cell does RNA processing occur
only in eukaryotes
what is added to the 5’ end of eukaryotic mRNA
a methylated cap
what is the structure of a methylated cap
a guanidine triphosphate in reverse orientation to the 5’ end with a methyl group, and methyl groups to one or more of the succeeding nucleotides in the RNA
what is at the 5’ end of prokaryotic mRNA
a triphosphate
what is added to the 3’ end of eukaryotic mRNA
poly-A tail
what is the structure of a poly-A tail
100-200 adenosines
how does the poly-A tail get added
ribonuclease cleaves the primary transcript (11-30 nucleotides downstream of the polyadenylation signal) to form a new 3’ end and the poly-A polymerase adds As onto this new 3’ end
define: polyadenylation
the addition of the poly-A tail to the 3’ end
what is the purpose of the cap and tail in eukaryotic RNA
- prevent degradation since it has to be transported to the cytoplasm
- to enable ribosomes to initiate translation
what are the forms of mRNA processing
- addition of methylated cap
- addition of poly-A tail
- RNA splicing
define: RNA splicing
the removal of introns
define: exons
coding sequences for the protein product
what carries out splicing
spliceosome
why don’t some RNA transcripts require a spliceosome
they are self-splicing
where are introns found
in the DNA and primary transcript, not in the mature RNA
what are the three short regions used for splicing
splice donors, splice acceptors, and branch sites
define: alternative splicing
a single mRNA transcript can be spliced in different ways to produce different mature mRNA molecules
in what phyla is alternative splicing the highest
in mammals
does the number of genes indicate complexity
no, but alternative splicing may
define: trans-splicing
form of alternative splicing in which an exon from one transcript can be joined to an exon from a different transcript
define: translation
process in which the genetic code carried by mRNA directs the synthesis of proteins from amino acids
how long are tRNA
74 to 95 nucleotides long
what do tRNA carry
- some modified bases produced by chemical alterations of the A, G, C, and U nucleotides
- one particular amino acid
what is an example of a modified base that tRNA contains
inosine, a modification of adenosine
what does aminoacyl-tRNA synthetase catalyze
the attachment of a tRNA to its cognate amino acid
how is the correct order of amino acids determined
base pairing between an mRNA codon and a tRNA anticodon
what do the wobble rules refer to
the ability for some tRNAs to recognize more than one codon for the amino acid they carry
where can inosine be found in tRNA
in the anticodon when more than one codon can be recognized
what are ribosomes composed of
protein and rRNA
what is the function of ribosomes
the sites of protein synthesis
what are the three function sites of ribosomes
- A: aminoacyl binding site
- P: peptidyl binding site
- E: exit tRNA binding site
what is the E. coli Shine-Dalgarno sequence
AGGAGG
what recognizes the E. coli Shine-Dalgarno sequence
complimentary sequences in the 16S rRNA of the 30S subunit
what are Shine-Dalgarno sequences usually rich in
purines
what are the three steps of translation
initiation, elongation, termination
how does initiation happen in prokaryotes
30S ribosomal subunit binds to Shine-Dalgarno sequence in presence of tRNA carrying formylmethionine and then the 50S ribosomal subunit binds
what are 30S ribosomal subunits escorted by
initiation factor (IF) proteins
compare tRNA-FMet and tRNA that carries unmodified methionine
- they have the same anti-codon
- rest of the tRNA is unique
what is an example of another start codon used in prokaryotes
Mycobacterium tuberculosis occasionally uses GUG
where does the 50S ribosomal subunit get placed in prokaryotic initiation
binds in a way such that tRNA-FMet is placed in the P site of the ribosome
what escorts the next tRNA into the A site of the ribosome
elongation factors (EFs)
what catalyses the formation of peptide bonds between amino acids
peptidyl transferase
when does the amino acid get released from its tRNA in P site
after the peptide bond between the amino acids in the P and A sites are formed
what happens to a free tRNA when it enters the E site
it gets released
what recognizes stop codons
a release factor
what is a nonsense codon
a stop codon (there is no corresponding tRNA)
how does initiation happen in eukaryotes
the 40S ribosome subunit recognizes and binds to the 5’ methylated cap, it then scans along the mRNA unit it find the initiation of translation sequence
what amino acid does the initiator tRNA carry in eukaryotes
Met
define: polyribosome
complex of several ribosomes translating from the same mRNA
where does replication, transcription, and translation occur in prokaryotes
in the cytoplasm
where does replication, transcription, and translation occur in eukaryotes
- replication and transcription: in the nucleus
- translation: in the cytoplasm
how long does mRNA live in prokaryotes vs eukaryotes
- prokaryotes: seconds
- eukaryotes: minutes to hours
what is included in posttranslational processing
- enzyme removes methionine
- cleavage of long polypeptides into smaller polypeptides
- addition of chemical constituents to an amino acids (e.g. phosphorylation)
what are the four types of mutations on gene expression
- silent mutation
- missense mutation
- nonsense mutation
- frameshift mutation
where are the two locations mutations can occur
- within the coding sequence
- outside the coding sequence
