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Genome is the totality of all the genetic information.

Human Genome

3.2 x 10 9 base pairs 24 unique chromosomes

First Draft

sequence published in 2001 ~ 23000 genes = 1.5 % of DNA

Hereditary information is stored in genes

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Genes are the specic information-containing elementsof the genome that determine the characteristics of anorganism.


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Genes are the specic information-containing elementsof the genome that determine the characteristics of anorganism.

Gregor Mendel Hugo de Vries

my idea !

me too !


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Chromosomes

Long suspected to be involved in inherited traits

Chromosomes contain both DNA and proteins.

Become visible ( can see with a lightmicroscope ) as cells prepare to

divide. Chromosomes condense.

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Condensed DNA Extended DNA

DAPI Stained

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Grifth

s Experiment (1920s)

Fred Grifth (1879 1941) Streptococcus pneumoniae

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Grifth


Fred Grifth (1879 1941)

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Grifth


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Grifth

s (transformation) Experiment (1920s)

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DNA contains genes

First strong proofprovided in 1944 byOswald Avery, ColinMacLeod and MaclynMcCarty.

They followed up onGrifth

s initial ndings.

Received with skepticism.

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DNA contains genes

Watson & Crick expressing theirgratitude to Maclyn McCarty forshowing that DNA was important

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DNA contains genes

Alfred Hershey(1908 1997)

Bacteriophage T4

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DNA contains genes

Bacteriophage T4

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Figure 5-5a Essential Cell Biology ( Garland Science 2010)

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DNA contains genes

Alfred Hershey(1908 1997)

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DNA contains genes

Denitive evidence came in 1952 from AlfredHershey and Martha Chase.

T2 virus made of only DNA and proteins.

DNA lacks sulfur; proteins lack phosphorus

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Genes are the specic information-containing elementsof the genome that determine the characteristics of anorganism. In cells this is always in the DNA

In viruses, can be in either DNA (e.g.HPV) or RNA (e.g. HIV)

1940s (settled in 1952; Hersey and Chase) ! DNA is carrier ofgenetic information

1953 ! James Watson and Francis Crick determined the structure

of DNA

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DNA ( Deoxyribo nucleic acid)

1. 2 long polynucleotide chainsrunning antiparallel . Doublehelix.

2. Each DNA chain iscomposed of 4 types ofnucleotide subunits(A, C, G, T).

3. Sugar phosphate backbone(-). Bases are inside.

4. Chains held together viahydrogen bonding. Occursbetween the bases.

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Remembering your bases

5 bases:

Py rimidines: Cytosine (C), Thymine (T) andUracil (U)

Pur ines: Guanine (G) and Adenine (A)

CUT the PY (pie) PUR e As G old

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DNA (and RNA) are made of nucleotides Nucleoside = nitrogen-containing ring compound linked to a 5-

carbon sugar. The sugar can either be ribose (RNA) or deoxyribose (DNA). Nucleotide = nucleoside + 1 or more phosphates attached to its

sugar. Nitrogen-containing rings are typically called bases . Each

nucleotide is named after the base it contains. 5 bases:

Pyrimidines: Cytosine (C), Thymine (T) and Uracil (U) Purines: Guanine (G) and Adenine (A)

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DNA Double Helix

Right-handed helix.

10 bases per turn.

The coiling/winding of the2 strands creates 2 grooves.

These grooves areimportant recognitionmotifs for DNA bindingproteins.

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Figure 5-9 Essential Cell Biology ( Garland Science 2010)

Genes

encode the primary structure of proteins

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How do we t all our DNA into the nucleus?

The average bacterial genome is ~4 million base pairs. Bacteria typically carry their genes on a single, circular DNAmolecule. Some packaging occurs.

The human genome has ~3 billion base pairs.

Each human cell contains about 2 meters of DNA. Problem is cell nucleus is only 5-8 m big.

Putting all the human DNA into it

s nucleus is like trying to

shove 24 miles of ne thread into a tennis ball.

Eukaryotes package their DNA into discrete structures calledchromosomes .

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Can also tell chromosomes apart using karyotype(display of all chromosomes ) with

Giemsa

stain

Giemsa produces darkbands in regions rich inA-T bps.

Yields a surprisinglyreliable banding pattern.

Chromosomes arenumbered according tosize.

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Can also tell chromosomes apart using karyotype(display of all chromosomes ) with

Giemsa

stain

Giemsa produces darkbands in regions rich inA-T bps.

Yields a surprisinglyreliable banding pattern.

Chromosomes arenumbered according tosize.

Encode rRNA

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Karyotype with painted chromosomes

The human genome contains 23 pairs of chromosomes22

autosomal

+ 1

allosomal

(sex)

The complex of DNA and protein is called chromatin . The maternal and paternal chromosomes of a pair are called homologous

chromosomes (homologs ).

The only non-homologous pair are the sex chromosomes in males.

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Karyotypes can be used to detect chromosomaldeletions, amplications and translocations

This is common inmany genetic disorders

and some types ofcancer.

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Detection of the

Philadelphia Chromosome

inChronic Myelogenous Leukemia (CML)

A genetic translocation event leads to afusion chromosome (Philadelphia) thatexpresses BCR-ABL, a constitutiveactive tyrosine kinase.

BCR-ABL cause of 95% of CML cases.

e

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Gleevec was rst targeted therapy

!"# %&'( )* !"#$%&'()*"+ -"+).)&" +

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Chromosomes carry genes

Genes are segments of DNA containing instructions formaking RNA. Usually the RNA is translated into proteins.

Only one strand encodes the information to make theRNA.

Can be either strand.

Regardless, a gene is generally denoted to contain boththe coding strand and its complementary strand.

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Organisms vary greatly in their DNAcontent & number of genes

Some bacteria only have ~500 genes. Humans have ~23,000 genes. Single-celled Amoeba has ~60x amount of DNA of humans

Greatest difference in genomes between simple vs complexorganisms is inclusion of

junk

DNAbut

junk

DNA might not be

junk

after all

ENCODE Project

vs

3 billion bps180 billion bps

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and chromosomes

24 uniquechromosomes

5 uniquechromosomes

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Muntiacus reevesi Muntiacus muntjak

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Chromosomes have to replicate themselves

Cells replicate their chromosomes, and therefore their genome,through a process of ordered events that occur during the cell cycle .

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The cell cycle

Less condensed ! access for

gene expression

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3 elements are required for theeukaryotic DNA replication

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Telomeres form special caps at eachchromosome end

Contain repeated nucleotide sequences that enable thechromosome ends to be duplicated.

Prevent misrecognition as broken DNA. Contribute to overall chromosome stability. Continually shortening telomeres may play a role in aging

and may limit lifespan.

Telomere shorting can also lead to chromosome instability,leading to abnormal fusions/gene rearrangements which canlead to cancer.

Elizabeth Blackburn, Carol Greider, and Jack Szostak wereawarded the 2009 Nobel Prize in Physiology or Medicinefor the discovery of how chromosomes are protected by

telomeres and the enzyme telomerase.

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Interphase DNA

Condensed Chromosome 22 (10000 fold more compact)

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During interphase, chromosomesoccupy distinct regions in the nucleus

Note: Homologs not located near one another.This limits unwanted interchromosomal recombinations.

Prevents unwantedentanglement

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During interphase , the nucleolus is themost prominent structure in the nucleus

euchromatin

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Nucleosomes are the basic units ofchromosome structure

Chromosomes are made of DNA and proteins (collectivelycalled chromatin ). 2 types of proteins: histones and non-histone chromosomal proteins

Histones are responsible for the rst level of DNApackaging, nucleosomes .

nucleosomes

30 nm ber

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Figure 5-22 (part 1 of 2) Essential Cell Biology ( Garland Science 2010)

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Figure 5-22 (part 2 of 2) Essential Cell Biology ( Garland Science 2010)

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1.7 turns per

histone octet

(nucleosome)

= 147 bp

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Intermediate structures

leading tochromosomalcondensation prior tomitosis

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Chromatin packing has multiple levels

How this occurs is

not well know.

Requires histone H1

Interphasechromosome

Mitoticchromosome

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Chromatin packing has multiple levels

A linker histone that helps pull nucleosomes

together to form the 30 nm ber.

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Various types of machinery are needed toadjust the structure of chromatin rapidly

Chromatin-remodeling complexescan decondense chromatin

Needed for both replicationand gene expression .

Hence, chromatin structureis dynamic .

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Covalent modications of histones regulatechromatin structure ( histone code )

These modications function, in part, by recruiting otherchromatin-remodeling complexes.

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Covalent modications of histones regulatechromatin structure ( histone code )

These modications function in part by recruiting otherchromatin-remodeling complexes.

Can also modify corehistones to help alterchromatin (e.g., HATs)

Still learning whatthe

codes

mean

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Interphase chromosomes contain bothcondensed and more extended chromatin

Euchromatinmore extended, higher gene expression

Heterochromatincondensed, low gene expression ~10% of interphase chromatin Located around centromere and telomeres There are heterochromatin-specic proteins

Heterochromatin canspread to coding regionsand

silence

the gene.

Barrier DNA preventsheterochromatin spread

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Maternal Gene Silencing

One must be silenced,so that expression infemales and males issimilar.

Selection appears tobe random

Silenced X is passedalong the cell lineage

Females are Mosaics

h b h d

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Chromatin structure can be inherited(epigenetic inheritance )

Specic histone modications are passed on. DNA methylation patterns are passed on. This process occurs during differentiation of cells (committed)

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END

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Rea Lec 7 DNA