Lecture 6 Flashcards
The message is encoded in the mRNA molecule using triplets of nucleotides, called ____________
codons
True or False: Codon specify a particular amino acid
True
What are ribosomes?
The molecular machines responsible for reading the genetic code and translating it into a protein
Who hypothesized that amino acids are encoded by sequences of nucleotides (codons)?
Francis Crick
True or False: Since there are only 4 nucleotides, the length of such a codon would have to be at least 3 nucleotides to encode the 20 known amino acids since 4^2 (4^2=16) is not long enough to cover 20.
True
Which two scientists used synthetic RNAs (pU) and cell lysates to prove that RNA was the template from which the DNA code was deciphered into amino acids?
Marshall Nirenberg & Heinrich Matthaei
How many possible codons are there?
4^3=64
How many codons specify amino acids (including the start codon)?
61
How many codons specify ‘STOP’?
3
Codons are degenerate. What does this mean?
It means multiple codons can code for the same amino acid.
True or False: Codons operate universally across all species.
True
What is tRNA?
A decoder molecule that converts the language of RNA into that of proteins.
What does a tRNA look like in 2D and 3D?
It looks like a clover in 2D, and a boomerang in 3D.
What are the two functional regions of tRNA, and what is their purpose?
- Anticodon: hydrogen bonds with the RNA codon specifying an amino acid
- 3’ (acceptor) end: binds the amino acid
True or False: tRNAs contain a large number of unusual, modified bases.
True
Where is the amino acid covalently attached to in tRNA?
It is attached to the 3’ end via an ester link to the ribose of the terminal adenosine.
What type of bond does the 3 nucleotide sequence make with the RNA codon?
Hydrogen-bonds
In what fashion does the 3 nucleotide anticodon bond with the RNA codon?
It bonds in an antiparallel fashion.
True or False: Each tRNA must be charged before it encounters the ribosome.
True
What complexes are formed when the charged tRNAs bind to their corresponding amino acid?
Amino-acyl tRNA synthases
How many amino-acyl tRNA synthases are there in each cell?
20- one for every amino acid
How many subunits are ribosomes composed of?
2, each of which contain rRNA and proteins
In prokaryotes, which ribosomal subunits are combined to form the 70S ribosome?
30S & 50S
What is the 30S subunit composed of in bacteria?
16S rRNA & 21 S proteins
What is the 50S subunit composed of?
23 rRNA & 55 rRNA & 31 L proteins
How many binding sites does the 70S ribosome have? What are they?
- A (acceptor) site
- P (peptidyl-tRNA) site
- E (Exit site)
What does the A site of the 70S ribosome do?
It binds incoming aminoacyl-RNA
What does the P site of the 70S ribosome do?
Harbors the t-RNA with the growing peptide chain
What does the E site of the 70S ribosome do?
Binds a tRNA recently stripped of its polypeptide
Ribosomes have peptidyltransferase activity. What does that mean?
They make peptide bonds that bind to amino acids
What is a peptidyltransferase?
A ribozyme: RNA molecule that carries out catalytic activity.
Where is peptidyltransferase located?
It is part of the 23S rRNA of the large ribosomal subunit.
True or False: There are differences in the rRNA sequences that increase in relation to the evolutionary distance between species.
True
What does the 16S rRNA serve as?
It serves as a molecular clock.
How many potential reading frames does mRNA have?
3
What is the Shine-Dalgarno sequence?
the ribosome binding site in bacterial RNA (untranslated)
What is the consensus of the Shine-Dalgarno sequence?
Purine rich (5’-AGGAGGU-3’)
Where is the Shine-Dalgarno sequence located?
~8 bases upstream of the start codon in E.coli
True or False: The Shine-Dalgarno sequence is complementary to another sequence at the 3’ end of the 16S rRNA of the 30S subunit
True
What are the start codons?
AUG, GUG, UUG; N-formyl-methionyl-tRNA (fMet-tRNA)
What are the three steps of polypeptide synthesis?
- Initiation: brings the two ribosomal subunits together placing the first amino acid in position
- Elongation: sequentially adds amino acids as directed by mRNA transcript
- Termination: releases the completed protein and recycles ribosomal subunits
True or False: Each phase requires the use of a number of protein factors and energy in the form of GTP
True
In protein synthesis, the initiation phase consists of:
- IF3 dissociating 30S and 50S subunits
- 30S subunit binds to IF1 and mRNA
- IF2 interacts with initiator tRNA
- IF2-fMet-tRNA binds 30S subunit to the P site
- IF1 and IF3 are released. GTP hydrolysis frees IF2.
- 50S subunit associates with 30S subunit
In protein synthesis, the elongation phase consists of:
- EF-Tu-GTP binds tRNA and guides it to A site
- GTP is hydrolyzed and EF-Tu-GDP is released. EF-Tu exchanges GTP for GDP to restore EF-Tu-GTP.
3a. Peptidyltransferase activity catalyzes a peptide bond.
3b. Peptide is transferred from tRNA in P site to tRNA in A site - Translocation: EF-Tu-GTP binds; GTP is hydrolyzed; 30S subunit rotates; the 50S subunit advances on more codon. tRNA in the A site moves into the P site. Uncharged tRNA moves into the E site.
- EF-Tu-GDP exits; 30S subunit resets. The A site can receive a new charged tRNA. tRNA entering the A site triggers ejection of the E site tRNA.
What are the repeated steps during protein elongation?
- Charged tRNA enters the A site
- Amino acid in P site covalently linked to amino acid in A site
- Ribosome moves 1 codon in 5’ to 3’ direction
In protein synthesis, the termination phase consists of:
- Stop codon enters A site. Ribosome release factor 1 or 2 enters. Uncharged tRNA exits E site.
- RF1 activates peptidtransferase; protein is released from P site
- RF3 enters and ejects RF1 or RF2
- Ribosome recycling factor (RRF) and EF-G enter the A site. RF3 leaves. GTP hydrolysis unlocks 50s from 30S
- IF3 enters the 30S subunit to remove uncharged tRNA and prevent reassociation of 30S and 50S
What does Streptomycin inhibit?
70S ribosome formation
What does tetracycline do?
Inhibits amino-acyl tRNA binding to the A site
What does Chloramphenicol do?
Inhibits peptidyltransferase
What does erythromycin do?
Causes abortive translocation
Since translation and transcription are coupled in prokaryotes, the ribosomes begin translation before RNA polymerase finishes transcription resulting in the formation of __________________.
Polysomes
Where does coupled transcription and translation occur?
Nucleoid
Where does the translation of fully transcribed mRNA occur?
Cell poles
True or False: A ribosome can become stuck if it lacks a stop codon.
True
What is the consequence of a stuck ribosome?
Can lead to the accumulation of stalled ribosomes and halt translation in the cell
What is transfer-messenger RNA (tmRNA) and what is its function?
It removes stuck ribosomes and has properties of both tRNA and mRNA
