Unit 8 Flashcards
Given that there are four different bases, what is the minimum number of nucleotides per amino acid required to specify all 20 amino acids?
3 nucleotides because 4^3 is the first number that is above
Define codon
A sequence of 3 adjacent nucleotides in a nucleic acid that codes for a specific amino acid
Is the code overlapping or non-overlapping?
The code is non-overlapping
Distinguish between a nonoverlapping code and overlapping code
Non Overlapping:
AUA - CGA - GUC
Overlaping:
AUA CGA GUC
UAC
ACC
Define reading frame
A specific way of dividing a sequence of nucleotides into a series of consecutive, non-overlapping codons during the process of translation
Are individual codewords delimited, as for example words in a sentence are delimited by spaces?
No. There is no punctuation between codons for successive amino acids.
What establishes the reading frame?
It is established by the start of translation of an mRNA molecule. In mRNA, this starting point is typically the first AUG (start codon) which encodes methionine
Given a sequence of RNA, an indication of the correct reading frame, and the genetic code, deduce the relevant polypeptide sequence encoded in the reading frame
- The third base of each codon plays a letter role in specifying an amino acid than the first two
- The three termination codons are shaded in red and the initiation codon, AUG, in green
What are the expected consequences of a one or two base addition or deletion within the above sequence?
- Inserting or deleting one base pair alters the sequence of all amino acids coded by the mRNA following the change
- However, if there is a combined insertion and deletion mutation, it will only affect some amino acids but eventually the reading frame will be restored to the correct amino acid
Why are such additions or deletions (when they occur in DNA) called frameshift mutations?
Because they alter the reading frame
Initiation codon
AUG is the most common signal for the beginning of a polypeptide in all cells, in addition to coding for Met residues in internal positions of polypeptides
Termination codon
UAA, UGA, UAG; in protein synthesis, these codons signal termination of polypeptide synthesis and do not code for any known amino acid
Open reading frame
A reading frame without a termination codon among 50 or more consecutive codons are referred to as an open reading frame. But it does have a stop codon at the end
What does degeneracy refer to in the context of coding?
Degeneracy means that an amino acid may be specified by more than one codon
ex. Arg is coded by 6 codons
Describe how aminoacyl tRNA interact with mRNA
- Transfer RNAs base-pair with mRNA codons at a three-base sequence on the tRNA called the anticodon. The first base of the codon in mRNA (read in the 5’ to 3’ direction) pairs with the third base of the anticodon
- Alignment of the two RNAs are antiparallel
*draw this out to see if you can do it
Is the genetic code almost universal
Genetic code is not quite as universal as once believed, but that is flexibility is severely constrained. The variations are obviously derivatives of the cellular code, and no example of a completely different code has been found
*basically the differences are that some codons do not code for the same amino acids in other animals
The genetic code has been conserved through evolutionary time because it is resistant to the deleterious effects of mutations. Discuss and give an example of, how the genetic code protects against missense mutations at both the 5’ and 3’ nucleotide positions in the codon
- A mutation in the first position of the codon will usually produce an amino acid coding change, but the change often results in an amino acid with similar chemical properties
(ex. Val’s codon is GUU. A change to AUU would substitute Ile for Val, but they are both still hydrophobic) - A mutation in the last position is also protected due to the wobble hypothesis. The wobble hypothesis states that only the first two amino acids bind tightly, so the third can be variable
Discuss the meaning of “wobble”
- The wobble (or third) base of the codon contributes to specificity, but because it pairs only loosely with its corresponding base in the anticodon, it permits rapid dissociation of the tRNA from its codon during protein synthesis
- If all three bases of a codon engaged in strong pairing with the 3 bases of the anticodon, tRNAs would dissociate too slowly and this would limit the rate of protein synthesis
What is degeneracy a feature of?
The genetic code (some amino acids are encoded for by more than one codon)
What is wobble a feature of?
The tRNA (some tRNAs can bind to more than one codon)
Show how guide RNAs can be used as templates to direct the addition or removal of specific nucleotides from an mRNA transcript
- RNA editing is a post-transcriptional editing process that can alter the meaning of one or more codons during translation
- The insertions require a special class of guide RNAs that act as a template for the editing process
- The base pairing between the initial transcript and the guide RNA includes several G-U base pairs which are common in RNA molecules
*the guide RNA will not be able to form strong base pairs with mismatched amino acids so amino acids that can base pair strongly with the guide RNA will be inserted in
Show how deaminases can alter specific nucleotides in an mRNA transcript.
- The adenosine deamination reactions are carried out by adenosine deaminases that act as RNA (ADARs). Turns Adenosine into Inosine
- The Cytidine deaminations (to Uridine) are carried out by apoB mRNA editing catalytic peptide (APOBEC)
*deamination means the top NH2 is turning into a C=O bond
How does RNA editing by deaminases can regulate the production of two related but different products from a single transcript in a tissue specific manner
RNA editing deaminates a specific cytidine to uridine (only occurring in the intestine) changing a Gln code to a stop codon and producting a truncated protein (shortened protein)
Summarize the key events that occur during each of the following stages of protein synthesis
- Activation of amino acids
- Initiation of protein synthesis
- Elongation
- Termination and ribosome recycling
- Folding and post-translational processing
Activation of amino acids
The tRNA is aminoacylated
Initiation of protein synthesis
the mRNA and the aminoacylated tRNA bind to the small ribosomal subunit. The large subunit then binds
Elongation
Successive cycles of aminoacyl-tRNA binding and peptide bond formation occur until the ribosome reaches a stop codon
Termination and ribosome recycling
Translation stops when a stop codon is encountered. The mRNA and protein dissociate, and the ribosomal subunits are recycled