What is a genome? Genome: set of DNA Difference between Genomics and genetics Genetics: deals with heriditory Genomics deals with the organisms gimones in entirety

DNA: Deoxyribonucleic acid

DNA contains:

• A : Adenine
• T : Thymine
• C : Cytosine
• G : guanine

pairs:

• A <-> T
• C <-> G

RNA: Ribonucleic acid

• A : Adenylate
• U : Uridylate
• C : Cytidylate
• G : Guanylate

pairs:

• A <-> U
• C <-> G

DNA pairing

Paring between the top and bottom layeris inverted

5' ATCGGCTA 3'
     | | | | | | | | |
3' TAGCCGAT 5'

3' and 5' represent the numner pf sugar backbones. 5' -> Phosphate group 3' -> hydroxly group

GC content

the persentage that amots the amount of C and G in a given DNA formula: (No of C + No of G)/(len of DNA)

Codons

They are the codes for amino acids. Pairs of 3 taken in the genome
https://en.wikipedia.org/wiki/DNA_codon_table ![alt text]( Codons table

'M' - START, '_' - STOP
"GCT": "A", "GCC": "A", "GCA": "A", "GCG": "A",
"TGT": "C", "TGC": "C",
"GAT": "D", "GAC": "D",
"GAA": "E", "GAG": "E",
"TTT": "F", "TTC": "F",
"GGT": "G", "GGC": "G", "GGA": "G", "GGG": "G",
"CAT": "H", "CAC": "H",
"ATA": "I", "ATT": "I", "ATC": "I",
"AAA": "K", "AAG": "K",
"TTA": "L", "TTG": "L", "CTT": "L", "CTC": "L", "CTA": "L", "CTG": "L",
"ATG": "M",
"AAT": "N", "AAC": "N",
"CCT": "P", "CCC": "P", "CCA": "P", "CCG": "P",
"CAA": "Q", "CAG": "Q",
"CGT": "R", "CGC": "R", "CGA": "R", "CGG": "R", "AGA": "R", "AGG": "R",
"TCT": "S", "TCC": "S", "TCA": "S", "TCG": "S", "AGT": "S", "AGC": "S",
"ACT": "T", "ACC": "T", "ACA": "T", "ACG": "T",
"GTT": "V", "GTC": "V", "GTA": "V", "GTG": "V",
"TGG": "W",
"TAT": "Y", "TAC": "Y",
"TAA": "_", "TAG": "_", "TGA": "_"

open reading frames (ORF)

These frames are read by ribosomes. open reading frame is a portion of DNA molecule that when translated to an amino acid contains no "stop"codon.

Sturcture of open Reading frame START - Codon - Stop Codons give mRNA mRNA gives functional protein

for eg:- given DNA sequence: AGTATAAGGTGCTGGCACATCAGTATGGCTTACTGAGCGTGGGCGCGAAG

output for amino acids for entire seq: ['S', 'I', 'R', 'C', 'W', 'H', 'I', 'S', 'M', 'A', 'Y', '_', 'A', 'W', 'A', 'R']

output ORF:
['S', 'I', 'R', 'C', 'W', 'H', 'I', 'S', 'M', 'A', 'Y', '', 'A', 'W', 'A', 'R']
['V', '', 'G', 'A', 'G', 'T', 'S', 'V', 'W', 'L', 'T', 'E', 'R', 'G', 'R', 'E']
['Y', 'K', 'V', 'L', 'A', 'H', 'Q', 'Y', 'G', 'L', 'L', 'S', 'V', 'G', 'A', 'K']
['L', 'R', 'A', 'H', 'A', 'Q', '', 'A', 'I', 'L', 'M', 'C', 'Q', 'H', 'L', 'I']
['F', 'A', 'P', 'T', 'L', 'S', 'K', 'P', 'Y', '', 'C', 'A', 'S', 'T', 'L', 'Y']
['S', 'R', 'P', 'R', 'S', 'V', 'S', 'H', 'T', 'D', 'V', 'P', 'A', 'P', 'Y', 'T'].

First row continue with the 3 letter set with the numbering starting from the first letter onwards

the 'S' in the first row is the amino acid corresponding to the 3 letters set starting form the second letter in the DNA sequence "AGT"

Second row continue with the 3 letter set with the numbering starting from the Seond letter onwards.

the 'V' in the first row second letter is the amino acid corresponding to the3 letters set starting form the second letter in the DNA sequence "GTA"