CIS 1.5 (Science Section)

Brooklyn College

Professor Langsam

 

Assignment #6

 

The Genetic Code[1]

 

Deoxyribonucleic acid, or DNA, is a molecule that contains the instructions used in the development and functioning of all known living organisms. The main role of DNA is the long-term storage of information and it is often compared to a set of blueprints, since DNA contains the instructions needed to construct other components of cells, such as proteins and RNA molecules. DNA is a molecule in the form of a double helix (twisted-ladder) Attached to the backbone are of four types of molecules called bases – these form the rungs of the ladder. It is the sequence of these four bases along the backbone that encodes information. The four bases found in DNA are adenine (abbreviated A), cytosine (C), guanine (G) and thymine (T). RNA is similar with the base uracil (U) rather than thymine. See the figure below.

 

 

The genome of an organism is inscribed in the DNA. The portion of the genome that codes for a protein or an RNA molecule is referred to as a gene. The genetic code is the set of rules by which information encoded in genetic material (DNA or RNA sequences) is translated into proteins (amino acid sequences) by living cells. Specifically, the code defines a mapping between tri-nucleotide sequences called codons and amino acids; every triplet of nucleotides in a nucleic acid sequence specifies a single amino acid

 

 

 

Since there are 4 possible bases (A, C, G, T or U) and each codon consists of 3 bases there are 4³ = 64 different combinations possible with a triplet codon of three nucleotides. If, for example, an RNA sequence, UUUAAACCC is considered, there are three codons, namely, UUU, AAA and CCC, each of which specifies one amino acid. This RNA sequence will be translated into an amino acid sequence, three amino acids long.

The standard genetic code is shown in the following tables. Table 1 shows what amino acid each of the 64 codons specifies. Table 2 shows what codons specify each of the 20 standard amino acids involved in translation. These are called forward and reverse codon tables, respectively. For example, the codon AAU represents the amino acid asparagine, and UGU and UGC represent cysteine (standard three-letter designations, Asn and Cys respectively). Note several codons can code for the same amino acid.

 

Table 1: RNA Codon table - This table shows the 64 codons and the amino acid each codon codes for.

 

 

 

2nd base

U

C

A

G

1st
base

U

UUU (Phe/F)Phenylalanine
UUC (Phe/F)Phenylalanine
UUA (Leu/L)Leucine
UUG (Leu/L)Leucine

UCU (Ser/S)Serine
UCC (Ser/S)Serine
UCA (Ser/S)Serine
UCG (Ser/S)Serine

UAU (Tyr/Y)Tyrosine
UAC (Tyr/Y)Tyrosine
UAA Ochre (Stop)
UAG Amber (Stop)

UGU (Cys/C)Cysteine
UGC (Cys/C)Cysteine
UGA Opal (Stop)
UGG (Trp/W)Tryptophan

C

CUU (Leu/L)Leucine
CUC (Leu/L)Leucine
CUA (Leu/L)Leucine
CUG (Leu/L)Leucine

CCU (Pro/P)Proline
CCC (Pro/P)Proline
CCA (Pro/P)Proline
CCG (Pro/P)Proline

CAU (His/H)Histidine
CAC (His/H)Histidine
CAA (Gln/Q)Glutamine
CAG (Gln/Q)Glutamine

CGU (Arg/R)Arginine
CGC (Arg/R)Arginine
CGA (Arg/R)Arginine
CGG (Arg/R)Arginine

A

AUU (Ile/I)Isoleucine
AUC (Ile/I)Isoleucine
AUA (Ile/I)Isoleucine
AUG (Met/M)Methionine, Start

ACU (Thr/T)Threonine
ACC (Thr/T)Threonine
ACA (Thr/T)Threonine
ACG (Thr/T)Threonine

AAU (Asn/N)Asparagine
AAC (Asn/N)Asparagine
AAA (Lys/K)Lysine
AAG (Lys/K)Lysine

AGU (Ser/S)Serine
AGC (Ser/S)Serine
AGA (Arg/R)Arginine
AGG (Arg/R)Arginine

G

GUU (Val/V)Valine
GUC (Val/V)Valine
GUA (Val/V)Valine
GUG (Val/V)Valine

GCU (Ala/A)Alanine
GCC (Ala/A)Alanine
GCA (Ala/A)Alanine
GCG (Ala/A)Alanine

GAU (Asp/D)Aspartic acid
GAC (Asp/D)Aspartic acid
GAA (Glu/E)Glutamic acid
GAG (Glu/E)Glutamic acid

GGU (Gly/G)Glycine
GGC (Gly/G)Glycine
GGA (Gly/G)Glycine
GGG (Gly/G)Glycine

 

 

Table 2: Inverse table

 

Ala/A

GCU, GCC, GCA, GCG

Leu/L

UUA, UUG, CUU, CUC, CUA, CUG

Arg/R

CGU, CGC, CGA, CGG, AGA, AGG

Lys/K

AAA, AAG

Asn/N

AAU, AAC

Met/M

AUG

Asp/D

GAU, GAC

Phe/F

UUU, UUC

Cys/C

UGU, UGC

Pro/P

CCU, CCC, CCA, CCG

Gln/Q

CAA, CAG

Ser/S

UCU, UCC, UCA, UCG, AGU, AGC

Glu/E

GAA, GAG

Thr/T

ACU, ACC, ACA, ACG

Gly/G

GGU, GGC, GGA, GGG

Trp/W

UGG

His/H

CAU, CAC

Tyr/Y

UAU, UAC

Ile/I

AUU, AUC, AUA

Val/V

GUU, GUC, GUA, GUG

START

AUG

STOP

UAG, UGA, UAA

 

 

Note that a codon is defined by the initial nucleotide from which translation starts. For example, the string GGGAAACCC, if read from the first position, contains the codons GGG, AAA and CCC; and if read from the second position, it contains the codons GGA and AAC; if read starting from the third position, GAA and ACC. Partial codons have been ignored in this example. Every sequence can thus be read in three reading frames, each of which will produce a different amino acid sequence (in the given example, Gly-Lys-Pro, Gly-Asp, or Glu-Thr, respectively).

 

The actual frame of a protein is translated in is defined by a start codon, usually the first AUG codon in the mRNA sequence. There are three stop codons (UAG, UGA, UAA) which signal then end of a sequence.

 

Proteins are large organic compounds made of amino acids arranged in a linear chain. The sequence of amino acids in a protein is defined by a gene and encoded in the genetic code. Proteins are essential parts of organisms and participate in every process within cells.

 

The entire process may be represented by the following diagram:

 

 

 

                                                      

Write a program that examines a sequence of bases in a strand of RNA and prints the amino acid sequence for each protein coded within that strand. For example, given the following portion of an RNA strand:

 

 

…AAUUGUAUGAAAUUUCCUGAAUAUUAGGAUGCUCAAAAAAUGUGGUUUUUGUUGGAACAAGACUAAUACUUUU…

 

Your program should print the following:

 

Protein #1: KFPEY

Protein #2: WFLLEQD

 

Note that each protein begins with a start codon and ends with a stop codon. The sequence in between the stop codon and the next start codon does not code for any protein and is known as junk DNA. An actual protein may be hundreds or thousands of amino acids long. Also note that we are using the one letter abbreviations of the 20 amino acids that make up all proteins.

Strategy

 

  1. Create a data file that contains the information given in Table 2. The table should have one entry per line:

                                                       GCU         A

                                                       GCC         A

                                                       GCA         A

                                                       GCG         A

                                                       CGU         R

                                                       CGC         R

                                                            . . .

 

  1. Write a function, readRNACodonTable, that reads this data file into a two dimensional array.
  2. Write a function, sort, that sorts this array in codon order.
  3. Write a function, codonLookup, that given a three character codon returns the one-letter abbreviation for the corresponding amino acid by searching the table you created in step 2.
  4. The main function should:
    1. Read the RNA strand from a file one character at a time until a start codon is encountered.
    2. Continue to read the RNA strand three characters at a time and call the function codonLookup to identify the corresponding amino acid.
    3. Print the one-letter abbreviation returned by codonLookup.
    4. Repeat step 5b-c until a stop codon is returned.
    5. Continue scanning the RNA strand (steps 5a-d) until the end of the strand is reached.

 

 

Extra Credit:

  1. Have the main function print the junk DNA sequence.
  2. Write a reverse function that accepts an amino acid sequence and prints each of the possible codon sequences that would code this protein. (There may be more than one. Why?) – Use this function on each protein that you have found in the original assignment.

 

 

Data: (copy this carefully – you may also download it from the web at:

            http://eilat.sci.brooklyn.cuny.edu/cis1_5/CISClassPage.htm )

 

 

 

…AACAAUAUUAUGCAACAGUGUCCUCCCUUAUGAGCGUGUGGUUAGAAUUGUAUGAAAUUUCCUGAAUAUUAGGAUGCUCAAAAAAUGUGGUUUUUGUUGGAACAAGACUAAUACUUUUUUGUUGAUGAGAAUGAAACCCCCCAAAUUUAGAGCUGCCAGACAUCAACCCUUUAAACCCCCCUAGUUUCCCAAA…