This document discusses gene discovery and DNA structure. It defines key terms like genotype, phenotype, genes and genomes. It describes the double helix structure of DNA and how DNA is composed of nucleotides. Genes are located on chromosomes and encode proteins. DNA is transcribed into mRNA and then translated into proteins. Eukaryotic and prokaryotic genome annotation aims to find genes, exons, transcripts and predict function. DNA must replicate before cell division to produce double-stranded chromosomes from single-stranded ones.
3. Understanding the words
• Gene
• Genome
• Genotype and Phenotype
• Bioinformatics
• Gene Annotation, Genome annotation
• Proteome
4. Genotype and Phenotype
• Genotype and phenotype are very similar-
sounding words that are related, but actually
mean different things. The genotype is the set
of genes in our DNA which is responsible for a
particular trait. The phenotype is the physical
expression, or characteristics, of that trait.
5. The DNA molecule
• Composed of 2
polymers of
nucleotides
• Polymers are oriented
in antiparallel
• Molecule resembles a
spiral staircase of
complementary base
pairs
6. Nucleotide structure of DNA
• Each nucleotide of
DNA contains:
– Deoxyribose
– Phosphate
– Nitrogen base (either
A, G, C, T)
7. Nucleotide structure of RNA
• Each nucleotide of
RNA contains:
– Ribose
– Phosphate
– Nitrogen base (either
A, G, C, U*)
*contains Uracil instead
of Thymine
8. DNA structure
• “Double helix”
propsed by Watson
and Crick (1953)
• Antiparallel backbones
• Complementary base
pairing:
– Adenine to Thymine
– Cytosine to Guanine
10. Chromosomes vs Genes
• A chromosome
constitutes an entire DNA
molecule + protein
– Protein = histones
– Supercoiled DNA in
nucleosomes
– Humans contain 46 such
molecules (23 pairs)
• 44 somatic chromosomes
• 2 sex chromosomes (X +Y)
11. Chromosomes vs Genes
• Genes constitute
distinct regions on the
chromosome
• Each gene codes for a
protein product
• DNA -> RNA-> protein
• Differences in proteins
brings about differences
between individuals and
species
17. DNA, genes & chromosomes
The objectives of this presentation are to:
• Understand the role and structure of DNA, genes and
chromosomes.
• Understand that proteins are encoded by genes
• Be aware that alterations in genetic material can cause disease
18. Gene Annotation
• Finding RNA-only genes
• Gene prediction
– Prokaryotes vs. eukaryotes
– Introns and exons
– Transcription signals
– ESTs
• Functional annotation
• Biochemical pathways and subsystems
• Metabolic reconstruction of whole organisms
19. Types of exons
5’
3’
Start Stop
Transcription start
Translation
StoppolyA
5’ untranslated
region
3’ untranslated
region
5’ 3’
Protein
coding
region
promoter
GT AG GT AG GT AG GT AG
Open reading frame
Gene
mRNA
Translation
Initial exon
Internal exon
Internal coding exon
Terminal exon
20. Eukaryote genome annotation
20
Genome
ATG STOP
AAAn
A B
Transcription
Primary Transcript
Processed mRNA
Polypeptide
Folded protein
Functional activity
Translation
Protein folding
Enzyme activity
RNA processing
m7G
Find locus
Find exons
using transcripts
Find exons
using peptides
Find function
21. Prokaryote genome annotation
21
Genome
START STOP
A B
Transcription
Primary Transcript
Processed RNA
Polypeptide
Folded protein
Functional activity
Translation
Protein folding
Enzyme activity
RNA processing
Find locus
Find CDS
Find function
START STOP
22. Therefore, prior to dividing, any cell
must first replicate DNA
• Each single-stranded (SS)
chromosome duplicates
to become a double-
stranded (DS)
chromosome
• Example:
– A human cell is formed
with 46 SS chromosomes
– Each chromosome
replicates to produce 46
DS chromosomes
