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Definition of Genome

● All of the genetic information or hereditary


material possessed by an organism; the
entire genetic complement of an organism.

● All the DNA contained in an organism or a


cell, which includes both the chromosomes
within the nucleus and the DNA in
mitochondria

©2005 J.K. Pal 
Genome Size and number of genes 

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Genome size 
(Log scale)

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Genome Size And Chromosome Numbers 
Of Eukaryotic Organisms

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Organization Of Genome

Purpose?
(Structure-Function relationship)
Maintenance of genome integrity &
genome transfer (Inheritance)

Retrieval of genetic information in


relation to function

©2005 J.K. Pal 
Denaturation and Renaturation
● Heating double stranded DNA can overcome the 
hydrogen bonds holding it together and cause the 
strands to separate resulting in denaturation of 
the DNA
● When cooled relatively weak hydrogen bonds 
between bases can reform and the DNA 
renatures it on
Denatured DNA Re
na
tu ra ATGAGCTGTACGATCGTG tura
n a tio
De n
ATGAGCTGTACGATCGTG ATGAGCTGTACGATCGTG
TACTCGACATGCTAGCAC TACTCGACATGCTAGCAC

Double stranded DNA Double stranded DNA
TACTCGACATGCTAGCAC
Single stranded DNA ©2005 J.K. Pal 
DNA Reassociation Kinetics
1.0
Fraction  Prokaryotic DNA
remaining 
single­ Repetitive 
DNA Unique 
stranded  sequence 
0.5
(C/Co) complex 
Eukaryotic DNA
DNA

0
10­4   10­3   10­2   10­1    1      101    102    103    104
Cot (mole x sec./l)
©2005 J.K. Pal 
Type of DNA % of Genome Features

Single-copy (unique) ~75% Includes most genes 1

Repetitive
Interspersed ~15% Interspersed throughout genome between
and within genes; includes Alu sequences 2
and VNTRs or mini (micro) satellites

Satellite (tandem) ~10% Highly repeated, low complexity sequences


0 usually located in centromeres
fast ~10%
and telomeres
intermediate
~15%
2
Alu sequences are
about 300 bp in length
50
and are repeated about
slow (single-copy) 300,000 times in the
~75% genome. They can be
100
found adjacent to or
I I I I I I I I I
within genes in introns
or nontranslated regions.
1
Some genes are repeated a few times to thousands-fold and thus would be in
©2005 J.K. Pal 
©2005 J.K. Pal 
Organization of the human genome

©2005 J.K. Pal 
©2005 J.K. Pal 
What are Genes?
● The one gene one enzyme hypothesis has been
refined to mean each gene codes for a
polypeptide/RNA
● Things get fuzzy when a specific locus codes for
more than one polypeptide
● For the purposes of this class, we will define a
gene as the entire DNA sequence that is
necessary for the synthesis of a functional
polypeptide/RNA. In addition to the coding regions
(exons), a gene includes transcription control regions
and sometimes introns.
©2005 J.K. Pal 
©2005 J.K. Pal 
Structure of a typical eukaryotic gene

Enhancer CCAAT  TATA Enhancer


Box Box

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Protein Coding Genes May Be Solitary Or 
Belong To A Gene Family

About half of the protein coding genes in vertebrate genomic DNA 
are solitary genes (occurs only once in the haploid genome).

The remainder are duplicated genes, which arose by duplication 
of an ancestral gene and subsequent independent mutations.

Duplicated genes encode closely related proteins and generally 
appear as a cluster in a particular region of DNA.

The proteins encoded by a gene family have homologous but 
non­identical amino acid sequences and exhibit similar but slightly
different properties.
©2005 J.K. Pal 
©2005 J.K. Pal 
©2005 J.K. Pal 
The Globin Gene Family
● Globin genes code for the  α
β
protein portion of hemoglobin
● In adults, hemoglobin is made 
Fe
up of an iron containing heme 
molecule surrounded by 4 
globin proteins: 2 α globins 
and 2 β globins α β
● During development, different globin genes are 
expressed which alter the oxygen affinity of 
embryonic and fetal hemoglobin
©2005 J.K. Pal 
©2005 J.K. Pal 
©2005 J.K. Pal 
Locus Control Regions (LCR) and regulation of globin gene expression 

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MECHANISM OF FORMATION OF PROCESSED PSEUDOGENES

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β GLOBIN GENE CLUSTERS IN VERTEBRATES

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EVOLUTION OF GLOBIN GENES

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Model For Evolution Of The Globin Gene 
Family
Ancestral

Globin gene
Duplication
Mutation
α β
Chromosome 16 Transposition Chromosome 11
α β
Duplication and Mutation
ζ α ε γ β
Duplication and Mutation
ζ ψζ ψα2 ψα1 α2 α1 ψθ ε Γγ Αγ ψβ δ β
Embryo Fetus and Embryo Fetus Adult
Adult
Pseudo genes (ψ) resemble genes, but may lack introns and, along with other 
differences typically have stop codons that come soon after the start codons.
©2005 J.K. Pal 
DELETION OF β­GLOBIN GENE CLUSTERS & THALASSEMIA

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Gene Duplication By Unequal Crossing Over

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TYPES OF THALASSEMIA

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©2005 J.K. Pal 

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