BIOMG 3320 LEC 19

How many combinations of bases are in DNA and messenger RNA

4 bases

How many combinations of amino acids are in proteins

20

Why is a triplet code required

Because 4^2=16 combinations is not enough for 20 amino acids || Thus, a triplet code (of 3 nucleotides) is required since 4^3 = 64 combinations is enough for 20 amino acids

What is a codon?

Triplet of nucleotides that codes for a specific amino acid

What are the characteristics of the triplet code

It has no punctuation, it is non-overapping, and it has directionality as the sequence of bases is read sequentially from a fixed starting point

What is the reading frame

A way of dividing the sequence of nucleotides in a nucleic acid (DNA or RNA) molecule into a set of consecutive, nonoverlapping triplets

What is an Open Reading Frame (ORF)

It is a reading frame without a termination codon among 50 or more consecutive codons

How was the genetic code cracked?

Using artificial mRNA templates

What was the experiment that led to the genetic code being cracked?

Poly-U RNA mixed with E.Coli Extract, GTP, ATP, and a mixture of 20 radioactively labeled amino acids. They reaction was repeated in 20 test tubes and each had a different amino acid radioactively labeled

What was the result of the experiment that led to genetic code cracking

Radioactive polypeptide was formed in only one of 20 tubes, which contains phenylalanine. Thus, the triplet codon UUU encodes phenylalanine.

How many codons correspond to amino acids? How many codes for chain termination?

61 codons correspond to amino acids and three code for chain termination

What codons are used as start codons in bacteria

AUG and GUG

What codon is used as a start in eukaryotes?

Only AUG

How are eukaryotic and bacterial (prokaryotic) start codons different

Bacteria use AUG and GUG as start codons, while eukaryotes use only AUG as start codons. (both use AUG as start codons, but bacteria also has GUG)'

What does degenerate mean?

Multiple codons encode the same amino acid

What does a degenerative code refer to?

An amino acid may be specified by more than one codon

Is the genetic code degenerate?

Yes, an amino acid may be specified by more than one codon

What is the biological significance of the degenerate code?

1.) if the code was not degenerate, 20 codons would designate 20 amino acids, and then 44 codons would lead to chain termination. Degeneracy of codons minimizes the deleterious effects of mutations || 2.)Flexibility in codon usage allows DNA base composition to vary over a wide range without altering the amino acid sequence of proteins coded by DNA || E.g.e [G+C] of bacteria ranges form about 30% to 70%

What minimizes the deleterious effects of mutations

Degeneracy of codons

What does flexibility in codon usage allow for?

It allows DNA base composition to vary over a wide range without altering the amino acid sequence of proteins coded by DNA

What does it mean for the Genetic Code to be Mutation-Resistant?

It means that some mutations do not change the encoded amino acid sequence || For example, ACA, ACU, ACC, ACG all encode Thr. A change in sequence at position three of any Thr codon does not alter encoding

Which amino acids would not be altered by a change in sequence at position three of a codon?

Thr(ACN), Leu(CUN), Gly(GGN), Ala(GCN), Val(GUN), Pro(CCN), Ser (UCN), Arg (CGN)

What does a synonymous mutation mean?

There is no change in codon encoded for

What does a non-synonymous mutation mean?

There are changes in the amino acid encoded for

What is the common feature of all amino acids in the first column of the codon table

All amino acids are hydrophobic

What does changing the 3rd position of a codon do to amino acids in the first column and why is this important

Changing the third position of the codon changes them to a different HYDROPHOBIC amino acid. This is important because it protects against mutations since hydrophobic amino acids have similar function and could be swapped without impacting overall protein function

Does codon usage vary from species to species? example?

Yes, in E.Coli most arg are coded for by CGC/CGU but in humans most arg are encoded by AGA/AGG

Are Degenerate codons used equally?

No, degenerate codons are not used equally . THis is called codon bias

What do frequently used codons correspond to? And what can this do?

tRNAs present at higher levels. This can impact expression of human proteins in E.COli. If rare codons are used, it is difficult to efficiently translate the mRNA

Does codon bias differ between species

Yes, codon bias differs between species

What problems does Codon Bias Create?

Codon Bias creates problems for Recombinant Protein Expression || If rare codons are used, it is difficult to efficiently translate the mRNA (e.g. making a human protein in E. Coli)

Who discovered how the mRNA sequence translated to amino acid sequence?

Bob

Describe the structure of tRNAs

tRNAs can have 4-5 arms. The anticodon arm recognizes codons on mRNA and the amino acid arm's last A on CCA attaches to amino acids

What does the anticodon arm of tRNAs do?

It recognizes codons on mRNA

What does the amino acid arm do?

it s last A on CCA attaches to amino acid

What are facts about tRNAs

They have 73 -93 bases || They contain many unusual bases || They are L shaped || Half base paired (A form) || 5 unpaired regions that provide the structural diversity so that teh tRNAs can be uniquely distinguished || The 5' end is phosphorylated || Amino acid is attached to the 3'CCA || The anticodon loop contains the anticodon

What allows tRNAs to be uniquely distinguished

5 unpaired regions which provide structural diversity?

What end of tRNAs are phosphorylated?

The 5' end is phosphorylated

Where are amino acids attached in tRNAs?

To the 3' CCA

What does the anti codon loop contain?

The anticodon

What is the shape of t-RNAs

L-shaped

Do we need 61 tRNAs, each for a specific amino acid coding codon?

No, synonymous codons differing in the thrid base are often read by the same tRNA

Does the wobbling of the third base require specific rules?

Yes

What does wobble allow for?

It allows some tRNAs to recognize more than one codon

What is the minimum number of tRNAs required to translate all 61 codons?

A minimum of 32 tRNAs are required

What is the biological significance of Wobble-ing?

1. Wobble allows a minimum number of tRNAs needed for protein translation (32) || 2. It permits rapid dissociation of the tRNA from its codon during protein synthesis.

How do wobble bases increase the speed of translation

Because it is easier for the tRNA to dissociate || There is weak attachment of the third nucleotide (as compared to the first two)]

What do mutations of the 5' base of codons lead to?

Amino acids with similar chemical properties || I.e.Hydrophobic residues turn into similar hydrophobic residue (or vice versa)