Lecture 13: The Genetic Code

Question 1

Ribosome reads the mRNA to

Answer 1

synthesize a polypeptide
* Ribosome reads mRNA in the 5’ to 3’ direction
* Polypeptide is synthesized in the N- to C-
terminal direction

Question 2

mRNA gets produced by

Answer 2

transcription

Question 3

Translation occurs in cytoplasm for

Answer 3

both bacteria and eukaryotes

Question 4

DNA replication and transcription

Answer 4

copies information between nucleic acids
* Synthesize new copy of DNA or RNA using dsDNA genome as template
* Base pairing rule used to determine the sequence of the new nucleic acid

Question 5

Translation synthesizes a polypeptide using

Answer 5

the information written on a nucleic acid
* Protein coding sequence must code for 20
amino acids using only 4 nucleotides

Question 6

Polypeptides are written on protein CDS using

Answer 6

a triplet-nucleotide code
* Three nucleotides represent one amino acid
* These triplet nucleotides are called codons

Question 7

Each codon corresponds to

Answer 7

one of the 20 amino acids or the stop codon

Question 8

Start codon

Answer 8

Translation start site
* AUG is the start codon for about 90 % of protein CDS

Question 9

Stop codon

Answer 9

Translation stop site
* Every protein CDS uses one of UAA, UAG, UGA
as the stop codon
* Represented by a dash in the peptide sequence

Question 10

Protein CDS always have a ______ at the 5’ end of the coding strand and a ___ at the 3’ end

Answer 10

start codon
stop codon

Question 11

Rules to read the Genetic code

Answer 11

• Read in the 5’ to 3’ direction
• Polypeptide generated N- to C-terminus
• Read codons consecutively without a break
  and without overlapping
• No punctuation exist in the genetic code
• Codons are unambiguous
• Each codon only has one meaning
• Codons are nearly universal
• Very little variation between different domains of life

Question 12

How may ways can an mRNA strand be read?

Answer 12

• mRNA can be translated in three different ways because it is read in triplets

Question 13

Reading frames

Answer 13

Even when the mRNA sequence is identical, the result of translation changes based on how you ‘frame’ the triplet-
pattern on to the sequence; these are
called reading frames

Question 14

A real gene has how many correct reading frames?

Answer 14

• A real gene only has one ‘correct’ reading frame for its protein CDS to be read in
• The other reading frames are theoretical possibilities that scientists need to account for when analyzing genes

Question 15

Reading frame is determined based on the
location of

Answer 15

the start codon (AUG)

Question 16

Once translation begins, the ribosome reads the

Answer 16

rest of the sequence in the
same frame as the start codon
* Translation ends at the first stop codon that is
in frame with the start codon
* For example, the stop codon in Frame 1 is not
recognized as the stop codon in Frame 2
because it is out of frame

Question 17

Open Reading Frame (ORFS)

Answer 17

The area flanked by the start codon and a stop codon (that are in the same frame)

Question 18

How many ways can a dsDNA strand be read?

Answer 18

• dsDNA genome contains
  two strands of ssDNA
• Both ssDNA can be the
  coding strand (theoretically), and one ssDNA can be read in three different frames
• Therefore, there are 6
  possible reading frames to
  translate a dsDNA genome
• Again, only one of these 6 is correct

Question 19

Even for a monocistronic gene, multiple _____

Answer 19

ORFs occur in all reading frames just by chance
* Only one of them is the correct protein CDS

Question 20

Determining the correct reading frame (first step)

Answer 20

• A very long ORF has a high chance of being real
• Proteins are usually 100 – 1000s of amino acids long
• It is unlikely for an ORF to be this long just by
  chance, without getting terminated by a randomly-
  generated stop codon
• Long ORFs that we observe today have survived millions of years of natural selection, resisting mutations that insert stop codons in their
  middle
• High chance of this sequence being functionally important

Question 21

Determining the correct reading frame (further steps)

Answer 21

• Check if the protein CDS is accompanied by other
  features that compose a proper gene (promoter
  sequences, etc.)
• Check if the translated CDS is homologous to
  already-known proteins in the database (BLAST
  searches etc.)
• Check if the protein CDS is actually expressed in the
  organism (Reverse-transcriptase PCR, etc.)
• Check the function of the protein coded by the
  protein CDS (mutational analysis, protein
  purification and various biochemical analysis, etc.)

Question 22

Maximum capacity triplet code can code for

Answer 22

Triplet code has capacity to code for 64 different things, but there are only 20 amino acids + 1 stop codon to code for

Question 23

Genetic code degeneracy:

Answer 23

same amino acid can be coded by more than one
codons
* Degeneracy seems to have evolved in a way to attenuate effects of some point mutations in protein CDS

Question 24

Which position does not matter in the codon as much

Answer 24

• For many amino acids, the 3rd position of their codon does not matter
• Mutation in the 3rd position of codon has
  a reasonable chance of being silent, not causing amino acid substitution

Question 25

Polarity and 2nd codon

Answer 25

* Many codons for non-polar amino acids have a 2nd position pyrimidine (U or C) * Many codons for polar amino acids have a 2nd position purine (A or G)

Question 26

Is the polarity preserved when the 2nd codon is substituted?

Answer 26

* Purine-to-purine or a pyrimidine-to- pyrimidine mutation at 2nd codon position usually causes amino acid substitution, but there is a reasonable chance for the polarity to be preserved * Not all mutations can be accounted for, of course

Question 27

T/F: Effects of point mutations at 1st codon position can not be attenuated by codon degeneracy

Answer 27

True

Question 28

Wild type

Answer 28

The unmutated version of the protein * Usually the predominant version of the protein in the population

Question 29

Silent Mutation

Answer 29

Point mutation that does not change amino acid sequence

Question 30

Missense Mutation

Answer 30

Point mutation that causes amino acid substitution

Question 31

Nonsense Mutation

Answer 31

Point mutation that generates a stop codon, thereby prematurely stopping protein synthesis

Question 32

Frameshift mutations

Answer 32

Insertion or deletion of nucleotide causes the reading frame to change after the mutation * Has huge impact on protein, since changing frame completely changes the amino acid sequence * Inserting or deleting nucleotide three at once does not cause a frameshift, but instead inserts/removes an extra amino acid to the protein

Question 33

free