9 Flashcards
3’ untranslated region (3’UTR)
the region between the stop codon and the 3’ end of an mRNA.
Contains sequences associated with transcription termination and, in eukaryotes, with modifying the 3’ end
N-terminal
terminal end of a protein that corresponds with the most 5’ end of mRNA that is translated
C-terminal
terminal end of a polypeptide that corresponds with the most 3’ end of an mRNA to be translated
5’ UTR
the region between the 5’ end of mRNA and and the start codon
contains sequences that help initiate translation (ex: shine-dalgarno sequence)
large ribosomal subunit
joins the small ribosomal subunit to form a ribosome.
contributes to the formation of the A site, P site, and E site
50 S in bacteria
small ribosomal subunit
binds with the large subunit to form a ribosome
contributes to formation of A site, P site, and E site
30 S in bacteria
Peptidyl site (P-site)
part of the ribosome
holds a tRNA to which the nascent polypeptide is being attached or is already attached to
(i.e. the tRNA that holds the most recently added amino acid. it holds the tRNA until the A-site brings in a new amino acid to be attached and then takes in that tRNA. the old tRNA leaves from the E-site)
Aminoacyl site (A site)
the site on a ribosome that binds a tRNA with the next amino acid to go on the polypeptide
Exit site (E site)
provides an avenue of exit for tRNAs as they leave the ribosome after their amino acid has been added to the polypeptide chain.
initiator tRNA
in translation initiation, the initiator tRNA carries the first amino acid of the polypeptide to be generated by the ribosome.
This is added to the small ribosomal subunit after it recognizes the start sequence
this tRNA actually binds with the start sequence, and THEN the large subunit joins the whole shebang with the help of initiation factor proteins.
guanosine triphosphate provides energy for translation.
charged tRNA
used during translation
each carries a specific amino acid
uncharged tRNA
a tRNA without an amino acid attached to it.
specialized enzymes recognize uncharged tRNA’s and attach them to their corresponding amino acids
what are the six critical components to translation initiation in E. coli?
1) mRNA
2) small ribosomal subunit
3) large ribosomal subunit
4) initiator tRNA
5) three essential initiation factor proteins
6) GTP
initiation factor protein (IF)
in bacteria, its called IF3
is affiliated with small ribosomal subunit for most of translation initiation
prevents the binding of 30 S with 50 S subunit
preinitiation complex
forms when the authentic start codon sequence is identified by base pairing that occurs between the 16S rRNA in the 30S ribosome and a short mRNA sequence located a few nucleotides upstream of the start codon in the 5’ UTR
(Shine-Dalgarno sequence)
Shine-Dalgarno sequence
a short mRNA sequence located a few nucleotides upstream of the start codon in the 5’ UTR of mRNA.
the small ribosomal subunit-initiation factor complex recognizes this to initiate formation of the preinitiation complex
purine rich sequence
six nucleotides located three to nine nucleotides upstream of the start codon.
complementary sequence on 3’ end of 16S rRNA
what is the amino acid on the initiator tRNA?
N-formylmethionine
(fMet)
the charged tRNA is abreviated tRNA^(fMet)
30S initiation complex
consists of mRNA bound to 30S subunit, tRNA^(fMet), 3 initiation factors, and a molecule of GTP
initiation factors are
IF-2, IF-1 (which forestalls attachment of 50S subunit), and the IF3 protein is already there
70S initiation complex
50S subunit joins 30S initiation complex to form intact ribosome.
energy for the union of two subunits comes from one GTP hydrolosis to GDP
Eukaryotic initiation factor(eIF)/preinitiation complex
the eukaryotic 40S(small) ribosomal subunit complexes with the eIF proteins eIF1A, eIF3, and a charged tRNA to form the preinitiation complex
Eukaryotic initiation complex
consists of:
preinitiation complex
-recruited to 5’ cap region of mRNA, located at the end of the 5’ UTR
-the preinitiation complex joins the eIF4 complex, a group of at least four eIF4 proteins that assembles at the 5’ cap independently of translational initiation.
all of this together forms the Initiation Complex
scanning
Initiation embarks on this process after formation
it uses ATP hydrolysis to move the small ribosomal subunit through the 5’ UTR in search of the start codon.
90% of the time the first AUG encountered by the initiation complex is used as the start codon
10% of the time, the second or third is used.
Able to accurately find the start codon because it is embedded in a sequence called the Kozak sequence
Kozak sequence
5’ - ACCAUGG - 3’
location via scanning leads to attachment of 60S subunit to complex, then dissociation of eIF proteins to form a fully functional ribosome.
Elongation
second phase of translation
-energy provided by GTP
Elongation Factor (EF) proteins
are recruited into the initiation complex to initiate Elongation
occurs in 3 steps:
1) Recruitment of charged tRNAs to the A site
2) Formation of a peptide bond between sequential amino acids
3) Translocation of the ribosome in the 3’ direction along mRNA
peptidyl transferase
catalyzes peptide bond formation between the amino acid at the P site and the newly recruited amino acid at the A site.
stop codons
UAG, UGA, or UAA
release factors (RF)
they bind stop codons in the A site.
initiates release of the polypeptide bound to the tRNA at the P site via hydrolysis of GTP, which is complexed with the RF. Polypeptide release causes ejection of the RF from the P site and leads to the seperation of the ribosomal subunits.
polyribosomes
structures containing groups of ribosomes that are all actively translating the same mRNA
each ribosome in the structure independently synthesizes a polypeptide, markedly increasing the efficiency of utilization of an mRNA
monocistronic mRNA
each polypeptide producing gene in eukaryotes produces this mRNA.
it directs the synthesis of a single kind of polypeptide.
polycistronic mRNA
produced as part of operon systems that regulate the transcription of sets of bacterial genes functioning in the same metabolic pathway.
one mRNA molecule = several different polypeptides
one Shine-Dalgarno sequence for each polypeptide
one ribosome can translate multiple polypeptides one after another because the intercistronic spacer is only 3 or 4 nucleotides long which allows the ribosome to recognize the next start codon before it splits up
cistron
polypeptide producing segment of mRNA
synonymous codons
codons that specify the same amino acid
can be grouped into pairs that have the same two nucleotides in the first and second positions nd differ only at the third base, where the synonymous codons either both carry a purine (A or G) or both carry a pyrimidine (C or U).
Amino acids specified by four synonomous codons are represented by two pairs of synonymous codons.
the members of each pair differ in the third position only, by carrying the alternating purine or pyrimidine.
isoaccepting tRNAs
transfer RNA molecules with different anti-codon sequences for the same amino acid
3’ base wobble
the name given to the mechanism that relaxes the requirement for complementary base pairing between the third basee of a codon and the corresponding nucleotide of its anticodon.
the third codon is shared as either a purine or pyramidine
Inosine
a modified wobble nucleotide
pairs with purines and pyramidines
aminoacyl-tRNA synthetases
or just tRNA synthetases
they catalyze the chargine of tRNAs.
catalyzes a two-step reaction that forms a bond between the carboxyl group of the amino acid and the 3’ hydroxyl group of adenine in the CCA terminus.
the tRNA acceptor stem fits into an active site of tRNA synthetase which contains the amino acid to be added. ATP provides the energy for this.
it proof reads, causing the mischarging rate to be 1 in 50,000 to 1 in 100,000
reading frame
refers to the specific codon sequence as determined by the points at which the grouping of nucleotides into triplets begins
frameshift mutation
every codon in the reading frame changes due to insertion or deletion of a nucleotide
reversion mutation
the reversal of a frameshift mutation due to the addition or deletion of a nucleotide
posttranslational polypeptide processing
modifies polypeptides into functional proteins through the removal or chemical alteration of amino acids after translation is completed
protein sorting
uses signal sequences to sort proteins and direct them to their cellular destinations.
signal sequences
also called leader sequences
short sequences of amino acids at the N-terminal end of a polypeptide
insulin formation
review later
signal hypothesis
proposes that the first fifteen to 20 amino acids of many polypeptides contain an address label in the form of a signal sequence that designates the protein’s destination in the cell.
chaperones
molecules within the ER that identify and bind with misfolded proteins.
they affiliate with proteins during the folding process and dissociate when the correctly folded structure is attained
if correct folding doesnt happen, they remain irreversibly bound to the misfolded proteins, resulting in the sequestration of such proteins in the ER. the sequestrations are usually destroyed.
