Definition of Genome

q

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

q

©2005 J.K. Pal 

Genome Size and number of genes 

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Genome size  (Log scale)

©2005 J.K. Pal 

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 

Heating double stranded DNA can overcome the  hydrogen bonds holding it together and cause the  strands to separate resulting in denaturation of  the DNA q When cooled relatively weak hydrogen bonds  between bases can reform and the DNA  Denatured DNA Re renatures na ion t
q
De n a tur a
ATGAGCTGTACGATCGTG tura tio n ATGAGCTGTACGATCGTG TACTCGACATGCTAGCAC ATGAGCTGTACGATCGTG TACTCGACATGCTAGCAC TACTCGACATGCTAGCAC

Denaturation and Renaturation

Double stranded DNA

Double stranded DNA
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Single stranded DNA

DNA Reassociation Kinetics
1.0

Fraction  remaining  single­ stranded  0.5 (C/Co)

Prokaryotic DNA
Repetitive  DNA

Eukaryotic DNA

Unique  sequence  complex  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
Single-copy (unique) Repetitive Interspersed ~75% ~15%

Features

Includes most genes 1 Interspersed throughout genome between and within genes; includes Alu sequences 2 and VNTRs or mini (micro) satellites

Satellite (tandem) 0

50

100

Highly repeated, low complexity sequences usually located in centromeres fast ~10% and telomeres intermediate 2 Alu sequences are ~15% about 300 bp in length and are repeated about 300,000 times in the slow (single-copy) genome. They can be ~75% I I I I I I I I I

~10%

found adjacent to or within genes in introns or nontranslated regions. 1 ©2005 J.K. Pal  Some genes are repeated a few times to thousands-fold and thus would be in

©2005 J.K. Pal 

Organization of the human genome

©2005 J.K. Pal 

©2005 J.K. Pal 

What are Genes?
q

q

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

q

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  Box

TATA Box

Enhancer

©2005 J.K. Pal 

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 q In adults, hemoglobin is made  Fe up of an iron containing heme  molecule surrounded by 4  globin proteins: 2 α globins  β α and 2 β globins q During development, different globin genes are  expressed which alter the oxygen affinity of  embryonic and fetal hemoglobin
q
©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

©2005 J.K. Pal 

Model For Evolution Of The Globin Gene  Family
Ancestral Duplication Mutation Chromosome 16 Globin gene

α

β β γ Αγ ψβ Chromosome 11 β δ β

α α

Transposition Duplication and Mutation ε Duplication and Mutation Γγ α1 ψθ ε

ζ ζ
Embryo

ψζ

ψα2 ψα1 α2

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

©2005 J.K. Pal 

Gene Duplication By Unequal Crossing Over

 

©2005 J.K. Pal 

TYPES OF THALASSEMIA

©2005 J.K. Pal 

©2005 J.K. Pal 

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