Study your flashcards anywhere!

Download the official Cram app for free >

  • Shuffle
    Toggle On
    Toggle Off
  • Alphabetize
    Toggle On
    Toggle Off
  • Front First
    Toggle On
    Toggle Off
  • Both Sides
    Toggle On
    Toggle Off
  • Read
    Toggle On
    Toggle Off

How to study your flashcards.

Right/Left arrow keys: Navigate between flashcards.right arrow keyleft arrow key

Up/Down arrow keys: Flip the card between the front and back.down keyup key

H key: Show hint (3rd side).h key

A key: Read text to speech.a key


Play button


Play button




Click to flip

59 Cards in this Set

  • Front
  • Back
  • 3rd side (hint)
In the cloverleaf structure of tRNA, the inverted sequences form _____ double-helical segments.
On the tRNA, where does the amino acid bind during amino acid activation?
At the 3' end, where there is a single strand sequence -CCA- The terminal A is coupled to the amino acid during activation.
During amino acid activation, the amino acid couples with the terminal ___ base on the 3' end of the tRNA.
A; this is invariant - the CCA is almost a consensus sequence
What are the four 'arms' on tRNA molecule (3' to 5')?
1. T(psi)C arm - named for sequence T(psi)C that occurs on this arm in almost all tRNAs (psi is a modified U)
2. The variable arm; may contain between 4 and 21 nucleotides
3. Anticodon arm; contains 3 nucleotide anticodon that pairs with the codon during translation.
4. DHU arm; named for the occurence of dihydrouridine in all tRNAs
How is a charged tRNA attached to the amino acid?
It is covalently bonded.
What type of RNA can have modified bases after post-transcription modifications?
Mature tRNAs can contain modified bases other than normal A,U,G, and C.
Where is the wobble position on a tRNA molecule?
On the anticodon arm at the 5' end.
What is the significance of the wobble position?
It allows one tRNA to bond to multiple different codons.
True or False: All tRNA go through translation sites in the order of A-P-E.
False; the initial tRNA carrying methionine binds to the P site, then the E site. This is the only tRNA to do so.
The ribosome and tRNAs move in relation to the ______.
mRNA; the ribosome moves along the mRNA for the space of a single codon - the A site become the P site and the new tRNA enters and bonds to the new A site.
What is a peptidyltransferase reaction?
The transfer of the growing peptide chain from the peptidyl site to the amino acid on the aminoacyl site.
What is (approximately) the rate of peptide elongation in a ribsome?
Three to five amino acids added per second
True or false: When an mRNA stop codon is reached during translation, tRNA sends the termination base to end elongation.
False; no tRNA molecules respond to the stop codon - elongation ceases upon reaching the stop codon due to termination factors.
In translation, interaction with release factors results in ______ of the complete protein chain from the tRNA in the __ site.
Cleavage; P-site
What are chaperones?
Proteins responsible for folding a new protein into its three-dimensional shape.
What is a 'charged' tRNA molecule?
A tRNA that has been covalently attached to the correct AA on its 3' end.
What is another term meaning 'charged tRNA'?
What enzyme charges aminoacyl-tRNA?
Aminoacyl-tRNA synthetase
What are the two major points at which the fidelity of translation is determined?
1. Synthesis of cognate amino acid/tRNA pairs by aminoacyl-tRNA synthetase in an aminoacylation reaction
2. The accuracy of aminoacyl-tRNA selection by the ribosome.
____________ are the only components of the translation machinery that really know the genetic code and are thus crucial guarantors of the ______ of protein synthesis.
Aminoacyl tRNA sythetases; fidelity
The first blank is three words
True or False: There is more than one amino acid for one codon.
False; there is more than one codon for each amino acid
How many different aminoacyl-tRNA synthetases do cells usually make?
20 - one for each type of amino acid
True or false: All aaRS are homodimers.
False; aaRS can be homodimers, small or large monomers, or tetramers (or more) of one or more different types of subunits.
What is the significance of an aaRS being a homodimer?
It can charge two tRNAs at once.
What (in general) are the differences between Class 1 and Class 2 aminoacyl-tRNA synthetases?
Class 1 is generally made up of monomers or homodimers (less complex).
Class 2 aaRS always have 2 or more subunits that are often different types (more complex).
Which of the following aaRS would be class 1? Class 2?
1. alpha
2. alpha2beta2
#1 is class 1, and #2 is class two.
Class 2 is more complex.
What are characterisics of Class 1 aminoacyl-tRNA synthetases?
-mostly monomeric
-approach tRNA along the minor groove and add AA to the 2' hydroxy of the tRNA
-class 1 aaRS have a catalytic domain structure in common (Rossmann fold)(different from class 2)
What are characteristics of Class 2 aminoacyl-tRNA synthetases?
-mostly dimeric or multimeric
-add the AA to the 3' hydroxyl site on the last tRNA base
-Class 2 aaRS have similar domain structures
Why can both class 1 and class 2 synthetases bind to tRNA?
All tRNAs have conserved domains - tRNA binding involves the alpha-helical structure conserved between class 1 and class 2 sythetases
Has to do with domains
In tRNAs, what do positive and negative interactions do?
Positive interactions match up the proper tRNA with the proper enzyme (synthetase).
Negative interactions block the binding of improper pairs.
How many active sites do aminoacyl-tRNA sythetases have? What are they?
aaRS have two active sites:
1. Acylation site (aka catalytic site): rejects AA that are larger than the correct one (and/or too hydrophobic/hydrophilic)
2. Editing (or "hydrolytic") site: cleaves activated species that are smaller than the correct one
What are the two basic steps in aminoacylation?
1. The AA and ATP form aminoacyl-AMP. (diphosphate product)
2. The tRNA covalently bonds to the AA, displacing AMP
In an aminoacylation reaction, what is the intermediate?
Aminoacyl-AMP (plus diphosphate)
Complete the two reactions from step one and two of an aminoacylation reaction:

Amino acid + ATP -->

Aminoacyl-AMP + tRNA -->
AA + ATP = aminoacyl-AMP + PPi

Aminoacyl-AMP + tRNA = aminoacyl-tRNA + AMP
In an acylation reaction, what type of bond is created between the carboxyl group of an AA and the 2' (class 1) or 3' (class 2) OH of the tRNA? What catalyzes this reaction?
An ester bond; catalyzed by aminoacyl-tRNA sythetase
What happens in step 1 of an acylation reaction? In step 2?
Step 1:
-the enzyme (sythetase) binds ATP and the AA, catalyzing the formation of an aminoacyl-adenylate intermediate (Aminoacyl-AMP).
-the intermediate is formed by a covalent linkage between the 5' phosphate group of ATP and the carboxyl end of the AA.
-when ATP is hydrolyzed, the aminoacyl tRNA sythetase uses the energy to activate the amino acid, forming the intermediate.
-the sythetase remains associated with the intermediate.

Step 2:
-the 2' or 3' OH of the terminal adenosine of tRNA attacks the amino acid carbonyl carbon atom, and the amino acid is transferred to the appropriate tRNA.
-The amino acid is covalently bonded to either the 2' OH or 3'OH (depending on sythetase) of the INVARIANT 3' adenosine terminal of the tRNA molecule.
-The energy in the aminoacyl-AMP is used to transfer the amino acid to the tRNA, forming aminoacyl-tRNA.
After step 1 of an acylation reaction, why is the amino acid call an 'activated' amino acid?
Because when ATP is hydrolyzed, the high energy bonds between the phosphate groups are broken, and the energy is trapped in the aminoacyl-AMP intermediate.
How many subunits make up aaRS (sythetase)?
At least two, as aaRS have two active sites.
What are the two byproducts of an acylation reaction?
Pyrophosphate (diphosphate) and adenosine monophosphate
What eukaryotic RNAP is primarily responsible for making rRNA?
What is a ribosome made up of (basically)?
A collection of ribosomal RNAs and proteins
What do the following subunits refer to (in a ribosome)?
a. 30S
b. 40S
c. 80S
d. 50S
e. 60S
f. 70S
a. the small subunit of the prokaryotic ribosome
b. the small subunit of the eukaryotic ribosome
c. the eukaryotic ribosome (whole)
d. the large subunit of the prokaryotic ribosome
e. the large subunit of the eukaryotic ribosome
f. the prokaryotic ribosome (whole)
If in eukaryotic ribosomes, the large subunit is 60S and the small subunit is 40S, what is the entire ribosome referred to as?
If in prokaryotic ribosomes, the large subunit is 50S and the small subunit is 30S, what is the entire ribsome referred to as?
What is the dominant activity of almost all cells?
Ribosomal activity (90% of cell energy in prokaryotes)
What are some characteristics of the large subunit of the ribosome?
-composed of two RNA strands
-contains the active site (where the new peptide bonds are created when proteins are synthesized)
-dozens of proteins bind on the surface of the ribosome
-the interaction of the RNA and proteins give the ribosome its structural integrity.
What are some characteristics of the small subunit in a ribosome?
-in charge of information flow during protein synthesis
-initially finds mRNA strand
-after combining with large subunit, ensures each codon in message is paired with the anticodon in the proper tRNA
During translation, the mRNA enters through a small hole in the ______ ribosomal subunit.
Small; enters then extends up into 'decoding center'
What is the main evidence that a ribosome is actually a ribozyme?
The ribosome appears to use an adenine RNA nucleotide to perform its synthetic task (catalyze chemical reaction - enzymes typically use amino acids to catalyze chemical reactions)
How does mRNA enter the small subunit?
Through a small hole formed by a loop of rRNA, which can open and admit the messenger.
How many active sites exist in a ribosome? What are they?
3 active sites:
Two sites for binding charged tRNA:
1. A (aminoacyl/acceptor) site: exposes the codon for the next AA to be added to the growing chain, then binds to the incoming aminoacyl-tRNA.
2. P (peptidyl/donor) site: occupied by the peptidyl-tRNA, a tRNA carrying the growing polypeptide chain

Site for uncharged tRNA:
3. the E (exit) site: where tRNA exits after being separated from its AA
What order do tRNA (except the initial Met. tRNA) follow in translation (active sites)?
A-P-E; A and P hold charged tRNAs, E releases uncharged tRNA
What is a polysome?
An mRNA with more than one ribosomal subunit
What direction, 3' to 5' or 5' to 3', does translation move in?
5' to 3'
In translation, proteins are sythesized from the _________ end to the __________ terminus.
Amino (N); Carboxy (C) - relative to the protein
What is the translational start codon?
You should know this
What are the two types of tRNA (methionine) molecules in the cell? What type of tRNA sythetases charge these tRNAs?
1. Initiating tRNA^Met
-tRNA^fMet in bacteria, mitochondria, and chloroplasts
-specific tRNA^Met in eukaryotes
2. tRNA^Met for internal methionines

Usually, both are charged by the same methionyl-tRNA synthetases.
During an aminoacylation reaction, the Class 1 aaRS adds the activated AA to the 2' OH of the 3' terminal adenylate in the tRNA. How does the AA end up on the 3' OH?
A trans-esterfication reaction moves the AA
When is 5' aminoacyl-adenylate made?
In an aminoacylation reaction, when ATP is hydrolyzed by the aaRS and the energy is put into the intermediate product.