Transcription + Translation Flashcards
What are tRNAs?
transfer RNAs are the intermediates between mRNA and amino acids
There should be 61 different tRNAs because of the genetic code, but why are there actually less?
because of the “Wobble Effect” where the pairing of the last position of the codon (3’ codon) is flexible and can still code for the same anticodon and amino acid
Explain the Wobble Hypothesis
the 3’ codon position of mRNA is flexible and can have a different base pair that tRNA can still recognize as coding for the same anticodon and amino acid
this makes up for the redundancy of the genetic code and allows there to be less different tRNAs than codons
How many subunits do ribosomes consist of? What are they?
2
large 50S subunit
small 30S subunit
When do the large and small subunits join together to form a functional ribosome?
when they are both attached to mRNA
What is the function of a ribosome?
to facilitate the coupling of tRNA anticodons with mRNA codons during protein synthesis
Where does mRNA bind to the ribosome?
in the small 30S subunit
What are the 3 tRNA binding sites on a ribosome?
E (Exit)
P (peptide bond formation)
A (aminoacyl-tRNA binding site)
What are the 3 tRNA binding sites on a ribosome?
E (Exit)
P (peptide bond formation)
A (aminoacyl-tRNA binding site)
Where do incoming tRNAs bind to the ribosome?
at the A site
Where is the growing peptide chain bound on the ribosome?
to a tRNA bound to the P site of the ribosome
WHere do empty tRNAs bind briefly before exiting the ribosome?
to the E site
What is the purpose of the decoding center of a ribosome?
it ensures only tRNA with the correct anticodon can enter A site
What catalyzes the formation of peptide bonds?
peptidyl transferase center
What are both the peptidyl transferase center and the decoding center made of?
rRNA
What are the 3 phases of translation?
initiation
elongation
termination
What is the main purpose of translation initiation in prokaryotes?
to place the initiator-tRNA in the P site of ribosome and establish the correct reading frame
How does the ribosome place the correct AUG start codon in the P site in prokaryotes?
the Shine-Dalgarno sequence in the 5’ UTR mRNA pairs with a sequence in the small ribosomal subunit aligns the initiator AUG codon in the P site
T or F: transcription and translation co-occur in prokaryotes
true
Where does the initiation complex form on the mRNA of prokaryotes?
near the 5’ end of mRNA that is still being transcribed
T or F: in eukaryotes, transcription and translation co-occur
false! they are spatially and temporally separated
Why does transcription happen separately from translation in eukaryotes?
because mRNA needs processing after transcription before it can be moved to the nucleus and recognized for translation
Explain translation initiation in eukaryotes?
initiation factors bind to the 5’ cap of mRNA
small ribosomal subunit and initiator tRNA form an initiation complex
complex moves 5’-3’ along mRNA while unwinding base-paired regions and the ribosome scans the mRNA for the exposed AUG codon
AUG codon aligns with initiator tRNA
large subunit binds to form complex ribosome
What 3 steps are involved in elongation?
codon recognition
peptide bond formation
translocation
What must happen in order for a tRNA to enter the ribosome?
an elongation factor binds to the tRNA outside of the ribosome
the tRNA is checked by the decoding center of the small subunit to ensure the correct anticodon is being brought in
the ribosome will change conformation and the EF will be released when the correct match is made
What happens when the tRNA bonds to the A site?
the aminoacyl from the tRNA at the P site is now very close to the aminoacyl-tRNA at the A site
methionine is transferred from the P site to the amino acid in the A site and a peptide bond forms
What happens after an amino acid is transferred from the P site to the A site and a peptide bond forms?
an EF enters A site to shift the tRNA in the A site to the P site and the tRNA from the P site into the E site as the ribosome moves one codon (3 nucleotides) towards the 3’ end of the mRNA
after the move, the EF leaves the ribosome and the A site is now open to accept another charged tRNA and cycle continues until stop codon is reached
How does termination occur?
elongation continues until a stop codon is reached
What happens when a stop codon is reached? aka describe termination
once a stop codon enters the A site, no more tRNA can enter
then release factors bind to the stop codon and hydrolyze the bond between the last amino acid and the tRNA to release the polypeptide
T or F: the genetic code is universal and all species use the same one
true
What is the purpose of the genetic code?
it allows sequences of nucleotides to be translated into sequences of amino acids
How do 4 nucleotides specify the 20 amino acids?
3 nucleotides make a codon in mRNA which specifies 1 amino acid
What is a codon?
a sequence of 3 nucleotides in mRNA which codes for an amino acid
How many different codons are possible? How many of these codons specify one of the 20 amino acids?
4^3 = 64 codons
61 code for one of 20 the amino acids
the other 3 are stop codons
Why is the genetic code redundant?
because there are 64 possible codons, of which 61 code for only one of 20 amino acids
Which direction is mRNA read in?
5’-3’ as a series of nonoverlapping codons
What ensures translation begins in the correct reading frame?
the start codon
Describe the structure of an RNA nucleotide
there are 4: Uracil Adenine Guanine Cytosine
describe the structure of an RNA polymer
a nucleic acid composed of a ribose sugar, nucleotide bases (A, U, G, C) and 1+ phosphate groups
sugar-phosphate backbone and RNA strands assembled by phosphodiester bonds between adjacent nucleotides
What is the difference between informational (aka coding) RNA and functional RNA?
informational: coding RNA that is translated into protein (aka mRNA)
functional: RNA that do not code for proteins and have other functional roles in the cell (ex. tRNA, rRNA, etc.)
What is mRNA and its function?
messenger RNA
coding RNA that is made from protein producing genes and undergoes translation
What is rRNA and its function?
ribosomal RNA combines with proteins from the small and large ribosomal subunits to make a ribosome for translation
What is tRNA and its function?
transfer RNA carries amino acids from the cytoplasm to the ribosome where they can bind to mRNA by complementary base pairing and elongate polypeptides
What is telomerase RNA and its function?
functional RNA that provides a template for synthesis of repetitive DNA telomere sequences
What is snRNA and its function?
small nuclear RNA joins with proteins to form spliceosome subunits which remove introns from pre-mRNA during mRNA processing in eukaryotes
What is siRNA and its function?
small interfering RNA interferes with the expression of specific genes by degrading mRNA after transcription and preventing translation
What is miRNA and its function?
micro RNA regulates eukaryotic gene expression by degrading mRNA by shortening its poly-A tail or decreasing translation efficiency
What is XIST and its function?
X-inactivation specific transcript coats one mammalian female X chromosome in each nucleus to establish and maintain chromosome compaction and to repress gene expression
What are the 2 major stages of protein synthesis?
transcription: production of RNA from DNA template
translation: synthesis of polypeptide
What direction does transcription always occur?
in 5’-3’
What direction is the template strand always read?
3’-5’
What is the function of RNA polymerase in transcription?
it catalyzes the addition of each ribonucleotide via phosphodiester bonds to the 3’ end of the growing RNA chain
When are all RNAs produced?
during transcription
How is RNA produced?
by synthesizing a complementary strand to one DNA strand of a gene (the template strand)
Which is the template strand?
the strand of DNA used to synthesize RNA transcript
Which is the coding strand?
the strand that is complementary to the template strand
What is transcription?
the synthesis of a single-stranded RNA molecule by RNA polymerase
What are the 4 stages of bacterial transcription?
promoter recognition
initiation
elongation
termination
What does RNAP use the template strand for?
to assemble a complementary, antiparallel strand of ribonucleotides
What is the promoter and where is it located?
it is a DNA sequence located immediately upstream (+1 nucleotide toward the 5’) of the transcription start
it controls the access of RNAP to the gene
Describe the coding region of a gene
the portion of the gene that contains the information needed to synthesize the protein product
What is the termination region of a gene?
the portion of a gene downstream (3’) of the coding region that regulates termination of transcription
Nucleotide positions upstream of the initiation site are indicated by what sign?
negative
Nucleotide positions downstream of the initiation site are indicated by what sign?
positive
How many types of RNAP are required to catalyze transcription of all RNAs in bacteria?
only one
What is bacterial RNAP made of?
5 subunits that bind a 6th (sigma)
What forms the holoenzyme? What does this mean?
when bacterial RNAP core binds with the sigma subunit
the core enzyme can now efficiently bind to the promoter region to initiate transcription
T or F: the same sigma subunit recognizes all promoter sequences
false, different sigmas recognize different promoters
What is the purpose of different sigma subunits being able to recognize different promoter sequences?
this allows different genes to be transcribed at different stages in bacterial life cycle
What is the promoter?
a double-stranded DNA sequence which RNAP can recognize and bind to
How does RNAP bind to the promoter?
the RNAP core enzyme + sigma subunit bind to the consensus sequences at -10 and -35 location of the promoter bind to RNAP so that RNAP can bind to the promoter
Where are the consensus sequences located?
at -10 and -35 positions on the promoter
What is the -10 consensus sequence?
Pribnow’s box: 5’-TATAAT-3’ on the coding DNA strand
What is the -35 consensus sequence?
5’-TTGACA-3’ on the coding DNA strand
What does the sigma subunit do in transcription initiation?
it helps separate the DNA strands near the transcription start site so that RNAP can bind tightly to the promoter
How is the 5’ UTR produced? What does UTR stand for?
initiation of transcription occurs upstream of the translation initiation (AUG) sequence and produces the 5’ Untranslated Region
What happens to the sigma subunit after transcription initiation?
it dissociates as the core enzyme continues transcription
T or F: shortly after one round of transcription is initiated in bacteria, a second round begins
true
T or F: RNAP unwinds DNA ahead of it and rewinds DNA that has already been transcribed
true
What is a transcription bubble
a region of single-strand DNA (unwinded DNA)
How is the RNA chain lengthed?
as RNAP unwinds the DNA strand and forms the bubble, RNAP monitors the binding of free nucleotides to the exposed DNA template strand and adds a complementary nucleotide to the RNA chain at the 3’ end
How is the RNA strand extruded from the RNAP as it’s being transcribed?
the complementary base pairs between the template DNA strand and the lengthening RNA strand are broken at the point of exit
How is the 3’ UTR region created?
transcription continues past the protein coding segment of a gene to create the 3’ untranslated region
What is a DNA duplex?
another term for the 2 DNA strands
When does elongation of transcription end?
when RNAP reaches one of the 3 terminal sequences
How is the RNA transcript released from RNAP?
When the termination sequence is reached, the core enzyme/RNAP dissociates from the DNA and the RNA is released
How does most bacterial termination occur?
by intrinsic termination
What does intrinsic termination depend on?
the presence of an inverted repeating sequence followed by many adenine nucleotides
Describe intrinsic termination
common bacterial termination
mRNA containing inverted repeated sequences form into a short stem-loop structure (hairpin) which is followed by a series of U’s in the mRNA (As in the DNA template strand) which causes the RNAP to slow down and destabilize
the instability causes RNAP to release the transcript and separate from DNA
How many RNAPs do eukaryotes have? Do they recognize the same or different types of promoters?
3
they recognize different promoters and produce different types of RNA
Why is eukaryotic transcription more complex than bacterial?
because eukaryotes have a larger genome = more genes to be identified and transcribed, there’s more noncoding regions
T or F: bacteria have a single RNAP with multiple different sigma subunits
true
What do eukaryotic genes carry that need to be processed?
introns must be spliced
exons must be ligated
How is chromatin formed?
eukaryotic DNA associating with proteins
Composition of what in a gene affects its transcription?
chromatin
What are the 3 most common eukaryotic promoter sequence?
the TATA box at -25 bp
CAAT box at -80 bp
GC-rich box ~-90 bp
How does the RNAP bind to the promoter region in eukaryotes?
transcription factors are proteins that bind to the consensus sequences within a promoter and help RNAP recognize the promoter and bind for transcription initiation
what are the 3 modifications made to pre-mRNA in eukaryotes before translation can occur?
5’ capping
3’ polyadenylation
intron splicing
describe 5’ capping of pre-mRNA
an enzyme adds a guanine to the 5’ end of the pre-mRNA and another enzyme methylates the guanine to form the cap
What are the functions of the 5’ cap?
protection of mRNA from rapid degradation by nucleases
facilitates transport of mRNA out of the nucleus
facilitates intron splicing
properly orients the ribosome on the mRNA = improves translation
Describe the 3’ polyadenylation of pre-mRNA
a string of adenine bases are added to the 3’ end of pre-mRNA when transcription termination occurs
What are the functions of polyadenylation?
facilitates the transport of mature mRNA into the cytoplasm
protects mRNA from degradation
helps the ribosome recognize the mRNA for translation
What are exons vs introns?
exons are segments of the mRNA that code for protein segments
introns are intervening segments that need to be removed during splicing / processing
What is a consequence of errors in intron removal?
incorrect protein sequences
What is the 5’ splice site? What is the 3’ splice site?
the 5’ barrier of an intron which contains a GU sequence at the 5’ end
the 3’ barrier of an intron which has an 11-nucleotide consensus sequence with AG at the 3’ end
What is the branch site?
a third consensus sequence that is upstream of the 3’ splice site of an intron
What is required for accurate intron splicing?
all 3 intron consensus sequences:
5’ splice site
3’ splice site
branch point
What removes the introns from pre-mRNA and ligates the exons?
an snRNA-protein complex called the spliceosome
T or F: it is common for large eukaryotic genomes to express more protein types than there are genes in the genome
true
Why is it common for large eukaryotic genomes to express more protein types than there are genes in the genome?
alternate pre-mRNA splicing can cause more than one polypeptide to be produced from a single gene
Describe alternative RNA splicing and how it leads to the production of different polypeptides from a single gene
identical pre-mRNA transcripts are spliced different which results in mature mRNA with different combinations of exons which when translated will produce different polypeptides
When is alternative splicing common?
in different cell types or at different stages of development when different polypeptides are required
Approximately how many human genes are thought to undergo alternative splicing?
70%
T or F: alternative splicing is just as common in other animals and plants as it is in humans
false! it is less common in other animals and rare in plants
