Foundations of Biology

Foundations of Biology

Job 38:36 36 Who hath put wisdom in the inward parts? or who hath given understanding to the heart? 1999 Timothy G. Standish The Eukaryotic Genome Timothy G. Standish, Ph. D. 1999 Timothy G. Standish Eukaryotes Have Large Complex Genomes The human genome is about 3 x 109 base pairs or 1 m of DNA Thats a lot more than a typical bacterial genome E. coli has 4.3 x 106 bases in its genome Because humans are diploid, each nucleus contains 6 x 109 base pairs or 2 m of DNA That is a lot to pack into a little nucleus! 1999 Timothy G. Standish

It Only a Subset of Genes is Expressed at any Given Time takes lots of energy to express genes Thus it would be wasteful to express all genes all the time By differential expression of genes, cells can respond to changes in the environment Differential expression, allows cells to specialize in multicelled organisms. Differential expression also allows organisms to develop over time. 1999 Timothy G. Standish Eukaryotic DNA Must be Packaged Eukaryotic DNA exhibits many levels of packaging The fundamental unit is the nucleosome, DNA wound around histone proteins Nucleosomes arrange themselves together to form higher and higher levels of packaging.

1999 Timothy G. Standish A C T G C Packaging DNA Histone octomer GA T C A G T G T C A Histone proteins T A B DNA Helix

G C C G T 2 nm A 1999 Timothy G. Standish A C T G C Packaging DNA Histone octomer GA T

C A G T G T C A Histone proteins T A B DNA Helix G C C G T 2 nm A 1999 Timothy G. Standish A C

T G C Packaging DNA 11 nm GA T C A G T G T C A Histone proteins T A B DNA Helix Histone octomer C C G T

Nucleosome G 2 nm A 1999 Timothy G. Standish Packaging DNA A G T C A T A G C C G T A

1999 Timothy G. Standish Packaging DNA A G T C A T A G C C G T A 1999 Timothy G. Standish Packaging DNA Beads on a string

A G T C A 11 nm 30 nm T A G C C G T Tight helical fiber Looped 200 nm Domains A Protein scaffold

1999 Timothy G. Standish Packaging DNA Nucleosomes 11 nm 30 nm T G Tight helical fiber Metaphase Chromosome 700 nm 200 nm Looped Domains C A 2 nm B DNA Helix Protein scaffold 1999 Timothy G. Standish

Highly Packaged DNA Cannot be Expressed The most highly packaged form of DNA is heterochromatin Heterochromatin cannot be transcribed, therefore expression of genes is prevented Chromosome puffs on some insect chromosomes illustrate where active gene expression is going on 1999 Timothy G. Standish Control of Gene Expression Packaging Nuclear pores Cytoplasm Degradation DNA Transcription

Transportation Modification RNA G AAAAAA Nucleus Export e som mRNA G bo Ri RNA Processing Degradation etc. AAAAAA

Translation 1999 Timothy G. Standish Logical Expression Control Points DNA packaging Transcription RNA processing mRNA export mRNA masking/unmasking and/or modification mRNA degradation Translation Protein modification Protein transport Protein degradation Increasing cost The The logical logical place place to to

control control expression expression is is before before the the gene gene is is transcribed transcribed 1999 Timothy G. Standish A Simple Eukaryotic Gene Transcription Start Site 5 Untranslated Region Introns 5 Exon 1 Int. 1 Promoter/

Control Region Exon 2 3 Untranslated Region 3 Int. 2 Exon 3 Exons Terminator Sequence RNA Transcript 1999 Timothy G. Standish Enhancers DNA Many bases 5 3

Enhancer 5 Promoter TF TF 5 Transcribed Region TF 3 TF TF TF RNA RNA Pol. Pol.

5 3 RNA 1999 Timothy G. Standish Eukaryotic mRNA 5 Untranslated Region 5 G Exon 1 Exon 2 3 Untranslated Region Exon 3 AAAAA 3 Protein Coding Region 5 Cap

RNA processing achieves three things: 3 Poly A Tail Removal of introns Addition of a 5 cap Addition of a 3 tail This signals the mRNA is ready to move out of the nucleus and may control its lifespan in the cytoplasm 1999 Timothy G. Standish Junk DNA It is common for only a small portion of a eukaryotic cells DNA to code for proteins In humans, only about 3 % of DNA actually codes for the about 100,000 proteins; 50,000 in older estimates, 150,000 in more recent estimates Non-coding DNA was once called junk DNA as it was thought to be the molecular debris left over from the process of evolution

We now know that much non-coding DNA plays important roles like regulating expression and maintaining the integrity of chromosomes 1999 Timothy G. Standish The Globin Gene Family Globin genes code for the protein portion of hemoglobin In adults, hemoglobin is made Fe up of an iron-containing heme molecule surrounded by 4 globin proteins: 2 globins and 2 globins During development, different globin genes are expressed which alter the oxygen affinity of embryonic and fetal hemoglobin 1999 Timothy G. Standish

Model For Evolution Of The Globin Gene Family Ancestral Globin gene Duplication Mutation Transposition Chromosome 16 Chromosome 11

Duplication and Mutation Duplication and Mutation Embryo Fetus and Embryo Fetus Adult Adult

Pseudogenes () resemble genes, but may lack introns and, along with other differences, typically have stop codons coming soon after the start codons. 1999 Timothy G. Standish Antibody Diversity Results From Differential Splicing Humans produce antibodies to many millions of different antigens The human genome codes for less than 200,000 genes Antibodies are proteins, so how are many millions of different antibodies produced by so few genes? The answer lies in differential splicing of DNA 1999 Timothy G. Standish Antibody Structure V V sta n sta

n Light t Chain t SS Co t n ta s n SS Co n Co n SS

Antigen binding site SS V t n ta s n Antigen binding site V Light Chain Co Heavy Chains

1999 Timothy G. Standish en tig An Antigen Binding Antigen 1 Antigen 3 2 e l b a i r a V eavy H e l

b a i r a V ght Li 1999 Timothy G. Standish DNA An Antibody Gene coding for antibodies are made up of many exons referred to as genes Different exons are spliced together to make the many different antibodies V1 V2 V3 V4 J1 J2 J3 Intron Constant Random splicing of DNA as cell differentiates V1 V2 V3 J2 Intron Constant

Transcription V3 J2 Intron RNA Processing V3 J2 Translation produces a light chain V3 J2 with a variable region at one end Constant Constant Constant 1999 Timothy G. Standish Classes of Immunoglogulins IgG - A monomer - Most abundant antibody in blood. IgG easily leaves the circulatory system to fight infection and crosses the placenta conferring passive immunity to a fetus. IgD - A monomer - Found on the surface of B cells probably allowing recognition of antigens thus triggering differentiation into plasma and memory B cells IgE - A monomer - The least common antibody. The tails attach to mast cells and basophils. When antigens bind, they signal release of histamine. IgA - A dimer - Produced by cells in the mucus membranes to prevent attachment of pathogens. IgA is also found in many body secretions including milk. IgM - A pentamer - First antibody to appear following

exposure to an antigen. Because it declines rapidly in the blood, high IgM levels indicate a current infection. 1999 Timothy G. Standish Cancer Regulation of cell division is vital in multi-celled organisms Cancer can be defined as uncontrolled division of cells As regulation of cells is achieved through genes expressed in those cells, mutation of those genes can result in the loss of regulation and consequently cancer 1999 Timothy G. Standish 1999 Timothy G. Standish

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