BMB 251 Exam 3
The interior of chaperonin HSP 60 is mostly... A. Hydrophilic B. Hydrophobic C. Uncharged, neutral
A. Hydrophilic
What elongation factors are used in translation?
EF-Tu and EF-G
Wobble codon base C for bacterica and eukaryotes: what is the possible anticodon base?
G or I
Which part of an amino acid attacks the bond between an amino acid and a tRNA to form a peptide bond?
The amino acid is attached to the tRNA by its COOH end, leaving the NH2 end free. This free end attaches to the incoming tRNA. The A site reacts with the growing peptide attached to tRNA in the P site at the COOH end of the peptide attached to the tRNA.
What is the sequence of the corresponding anticodon to the initiator codon (anticodon is written in the 5' to 3' direction)?
The anticodon to the initiator codon would be CAU
What is the genetic code?
The correspondence between particular nucleotide triplets and amino acids
What part of the ribosome is responsible for catalyzing the peptidyl transferase reaction?
The large subunit
The ribosome is composed of what?
a large and a small subunit, each of which has rRNA and multiple proteins
Which RNA contains codons?
mRNA
What are the three different types of RNA involved in translation?
mRNA, tRNA, and rRNA
snoRNPs
modify rRNA
How does the stop codon cause translation to stop?
no tRNAs will base pair with the stop codons; a release factor associates with the stop codon in the A site and causes hydrolysis of the polypeptide-tRNA link and release of the polypeptide
Wobble means
not perfect base pairing
Where is the wobble position?
the wobble position corresponds to 3rd position of a codon
Why do we need the wobble base pairing?
there are some cases where multiple codons specify an amino acid so then one tRNA can associate with more than one codon
Triplet codons
three nucleotide increments; in RNA, a three-base "word" that codes for one amino acid
What determines the specific peptide produced?
where synthesis starts
What are the different features of tRNAs that are important for them to function?
1.) the 3D structure and its folding is important for it to fit into the ribsome 2.) contains some "modified" bases (not just typical A,U,G,C) 3.) anti-codon base pairs with mRNA 4.) amino acid attached to the 3' end (3' ribose sugar) 5.)D loop hear 5' end, anticodon loop, T loop near acceptor stem, amino acid attached to 3' end
How are a pattern of nucleotides translated to a pattern of amino acids?
1.) the mRNA sequence is decoded in sets of 3 nucleotides 2.) 1 of the possible 64 codons matches and specifies with an amino acid 3.) translation stops at one of three stop codons (no tRNA match)
In a ribosome the makeup is...
2/3 RNA and the rRNA forms the active site and tRNA binding sites
Wobble codon base U for bacterica and eukaryotes: what is the possible anticodon base?
A, G, or I
snoRNAs are encoded in introns of genes for other proteins especially those encoding ribosomal proteins and they are synthesized by RNA polymerase II A. True B. False
A. True
Amino acyl tRNA synthetase
Adds amino acids to tRNA
What parts of an amino acid and the tRNA are involved in forming the covalent bond between these two molecules?
Amino acids are added to the C-terminus of the chain. Growth occurs in the N to C direction
How does aminoacyl-tRNA synthase work?
Aminoacyl-tRNA synthase connects a specific amino acid to the appropriate tRNAs
tRNA synthase reminds you of... A. RNA polymerase II B. DNA polymerase C. DNA glycosylase DNA ligase
B. DNA polymerase
During protein synthesis, where is the peptidyl transferase enzyme located? A. Nucleolus B. Large subunit of the ribosome C. Small subunit of the ribosome D. Free in cytoplasm E. Bound to tRNA in the cytoplasm
B. Large subunit of the ribosome
Why is the 45 S precursor rRNA packaged into large nucleoprotein particle-containing many ribosomal proteins A. Cytoplasm B. Nucleolus C. Ribosome D. ER
B. Nucleolus
Which one of the proteins below is involved in the mRNA surveillance pathway to distinguish mRNA that are not ready for nuclear export? A. Cap-binding complex B. snRNPs used in splicing C. poly-A-binding proteins D. Export receptor
B. snRNPs used in splicing
The final maturation of tRNAs is carried out by enzymes that chemically modify the bases in the RNA. Which statement about a mature tRNA is true? A. RNA polymerase II transcribes pre-tRNA B. tRNA are modified before they are aminoacylate C. The enzymes remove thymidine bases in tRNAs D. tRNAs are processed by spliceosomes
B. tRNA are modified before they are aminoacylate
Why is the genetic code considered degenerate?
Because it is redundant since most amino acids match with more than one codon
Wobble codon base G for eukaryotes: what is the possible anticodon base?
C
Wobble codon base G for bacterica: what is the possible anticodon base?
C or U
Why do you think the process of rRNA processing is not like that of pre-mRNAs? A. It occurs in the nucleus B. Sequences of the end product is shorter C. The cleaved RNA are not pieced together D. It does not require protein complexes
C. The cleaved RNA are not pieced together
Prokaryotic mRNAs can be polycistronic because they have internal ribosome entry sites. How does this work? A. The sequences form a hairpin and prevent ribosome movement B. Bacteria don't use translation initiation factors C. The ribosome binding site contains a sequence complementary to an RNA in the small subunit of the ribosome D. It contains multiple start codons (AUG) so it has a high affinity for the ribosome
C. The ribosome binding site contains a sequence complementary to an RNA in the small subunit of the ribosome
What does EF-Tu do?
Carries aminoacyl-tRNA's to the ribosome and positions them in the empty A site; helps ensure a correct match to the codon in the mRNA; contributes to proofreading; hydrolyzes GTP to function
How does the cell recognize the rare mature mRNA versus the debris created by RNA processing?
Debris are degraded by nuclear RNA exosome that has RNAase activity
What factor recognizes the 5' cap?
El-F4 binds the 5' CAP and recruits the small subunit of the ribosome
True or false: mRNAs are translated once?
False, one mRNA is often translated by multiple ribosomes beginning in succession
True or False: mRNAs are the only RNAs that are processed/modified in eukaryotes. Justify your response.
False. tRNAs and rRNAs are also processed and have roles in protein synthesis, but they are not just translated themselves
What is a hnRNP?
Heterogeneous nuclear ribonucleoproteins: complexes of RNA and protein present in the cell nucleus during gene transcription and subsequent post-transcriptional modification of the newly synthesized RNA (pre-mRNA)
What would prevent an mRNA from leaving the nucleus?
If mRNA does not "pass" all of its quality control checks, it will not become mature, and it will not leave the nucleus.
What is different about how eukaryotic ribosomes find the start codon versus the way a prokaryotic ribosome finds the start codon?
In bacteria, the small unit of the ribosome associates with specific sequences located adjacent to start codons which then allows ribosomes to initiate translation at multiple places on an mRNA. Eukaryotic is only one protein per mRNA.
RNA pol 1
In eukaryotes, transcribes 5.8s, 18s, 28s rRNA
Describe wobble base pairing.
In some cases where multiple codons specify an amino acid, one tRNA can associate with more than one codon that varies at the wobble position, or the 3rd position of a codon
What is aminoacyl-tRNA synthetase?
It connects a specific amino acid on the correct tRNA. each amino acid has a specific aminoacyl-tRNA synthase. it reads the nucleotide at several different positions of the tRNA. has proofreading activity
How does tRNA splicing endonuclease work?
It is produced bu eukaryotic RNA pol III, cut and paste mechanism of intron splicing, it is docked on to a precursor tRNA, and tRNA ligase joins them together
What would happen to an mRNA if it is not properly processed/modified?
It will not leave the nucleus
Which end of a polypeptide chain is encoded by information nearest the 5' end of a gene: N or C terminus?
N terminus
Mature mRNA associates with numerous proteins and is exported from the nucleus to the cytoplasm through what?
Nuclear pores
Where does the initiator tRNA bind?
P site of the small subunit
Peptidyl transferase
Peptide bond formation
How does the polyadenylation signal contribute to completion of an mRNA?
Poly-A polymerase adds a poly-A tail to complete the synthesis of mRNA. The poly-A tail is not encoded in the DNA and is not synthesized by RNA pol.
What is meant by the terms poly and monocistronic?
Polycistronic refers to an mRNA that directs synthesis of multiple proteins (Bacteria). Moncistronic refers to an mRNA that only synthesizes one protein
What RNA polymerase is responsible for synthesizing rRNA?
RNA Pol 1 for most and RNA Pol III for 5s rRNA
Sites of rRNA processing are selected by ..
RNA-protein complexes by base-pairing
Describe the movement of the creation of the ribosome subunits?
RNAs start in the nucleus, are transported out through nuclear pores to the cytoplasm (proteins) and are completed in the nucleus (assembly)
What is splicing?
Removing introns from RNA and sealing exons together
What is responsible for forming the nucleolus?
Ribosomal RNA genes congregate in the site that becomes the nucleolus
What do the proteins that coat the mRNA do?
Survey for essential modifications and processing
What is the complementary tRNA anticodon sequence to this 5' to 3' mRNA sequence ATG AAA AAC CCA AAG AAA TCC GGA GGA TTC
TAC TTT TTG GGT TTC TTT AGG CCT CCT AAG
When does the large subunit of the ribosome associate with the small subunit during translation?
The large subunit of the ribosome associates after the small subunit and the initiator tRNA finds the start codon by scanning
What is the sequence of the initiator codon in mRNA?
The most common starting codon sequence is AUG
What is the ribosome made of?
The ribosome is made of a large and small subunit, each of which has rRNA and multiple proteins.
What role does the 5' cap play in translation initiation?
The small subunit associates with the 5' cap on the mRNA. The small subunit then scans until the first AUG (start codon) and base pairs with the initiator-tRNA
Wobble codon base A for eukaryotes: what is the possible anticodon base?
U
Wobble codon base A for bacterica: what is the possible anticodon base?
U or I
What are codons?
a sequence of three nucleotide units that together form a unit of genetic code in a DNA or RNA molecule.
What sets the reading frame for translation?
a start codon
unusual nucleotides found in tRNA
about 10% of nucleotides are modified in tRNA molecules; over 50 different types of tRNA modifications are known
Poly A polymerase
add adenosine monophosphate to RNA
RNA pol 2
all mRNA, snoRNA, miRNA, siRNA, lncRNA, snRNA
Why is the reading frame important?
because it will determine which amino acids will be encoded by a gene
How does aminoacyl-tRNA synthase achieve specificity?
by recognizing the structure/shape of various amino acid binding sites
tRNA (transfer RNA)
central to protein synthesis as adaptors between mRNA and amino acids
capping, splicing, and 3' end processing occur...
co-transcriptionally
mRNA (messenger RNA)
code for proteins
RNA polymerase terminates transcription ..... from the poly-A signal
downstream
Ribosomal RNA is ...... processed
extensively
rRNA (ribosomal RNA)
form the basic structure of the ribosome and catalyze protein synthesis (translation)
snRNAs (small nuclear)
function in a variety of nuclear processes, including the splicing of pre mRNA
snoRNA (small nucleolar RNA)
helps to process and chemically modify rRNAs
What is the function of rRNA during translation?
it associates with a set of proteins to form ribosomes. they move along the mRNA molecule and catalyze amino acids into protein chains
What does elF2 do and how does it work?
it escorts the initiator tRNA into the P site
What is a ribozyme?
it is an RNA that can act as catalyst like a protein enzyme
What is the nuclear pore complex?
it is located in the nuclear double bilayer and transport through it includes nuclear RNA and ribosomes funneled into the cytoplasm and cytoplasmic proteins, signaling molecules and lipids moving into the nucleus.
What is the function of tRNA during translation?
it is the adaptor that allows a codon to specify a particular amino acid
What is the function of mRNA during translation?
it is used as a guide for establishing the order of amino acid attachment when the ribosome catalyzes amino acid addition
What molecules must aminoacyl-tRNA synthase recognize?
it must recognize anticodons but also use segments on the acceptor and bases elsewhere in the molecule.
How does decoding the genetic code work?
it requires codon-anticodon specificity and amino acid-tRNA specificity
What does mRNA do in the cytoplasm?
it serves as the template for protein synthesis (translation)
GTPase of EF-Tu
proofreading in ribosome
What RNA is the most abundant RNA in the cell?
rRNA (~90%)
tRNA ligase
rRNA splicing
An RNA sequence can be translated into 3 different.....
reading frames
What happens in the nucleolus?
ribosomal RNA is synthesized; the site of ribosomal assembly and rRNA transcription and processing
What does EF-G do?
stimulates the movement of the ribosome along the mRNA. Hydrolyzes GTP to function.
Which RNA contains anticodons?
tRNA
RNA pol 3
tRNA and 5S rRNA, some snRNA
During polypeptide synthesis, amino acids are added to what?
the c-terminus of the chain via peptide bonds, growths occurs in the N to C direction
