Essential Cell Biology

Third Edition

Chapter 5 DNA and Chromosomes !

Copyright Garland Science 2010

Hereditary information is stored in genes!

! Genome is the totality of all the genetic information.! !
!

Human Genome! ! ! 3.2 x 109 base pairs! ! ! !24 unique chromosomes! ! First Draft sequence published in 2001! ! ! ~ 23000 genes = 1.5 % of DNA! ! !

Hereditary information is stored in genes!

! Genome is the totality of all the genetic information.! ! ! Genes are the specic information-containing elements of the genome that determine the characteristics of an organism.!

Hereditary information is stored in genes!

! Genome is the totality of all the genetic information.! ! Genes are the specic information-containing elements of the genome that determine the characteristics of an organism.!
my! idea !! me! too !!

Gregor Mendel!

Hugo de Vries!

Chromosomes!
! Long suspected to be involved in inherited traits! ! Chromosomes contain both DNA and proteins.!

! Become visible (can see with a light microscope) as cells prepare to divide. Chromosomes condense.!

Condensed DNA !

Extended DNA !

DAPI Stained!

Grifths Experiment (1920s) !

Fred Grifth (1879 1941)!

Streptococcus pneumoniae!

Grifths Experiment (1920s) !

Fred Grifth (1879 1941)!

Grifths Experiment (1920s) !

Grifths (transformation) Experiment (1920s) !

DNA contains genes !

Oswald Avery (1877 1955)!

DNA contains genes !

! First strong proof provided in 1944 by Oswald Avery, Colin MacLeod and Maclyn McCarty. ! ! They followed up on Grifths initial ndings.! ! Received with skepticism.!

DNA contains genes !

Watson & Crick expressing their gratitude to Maclyn McCarty for showing that DNA was important!

DNA contains genes !

Alfred Hershey ! (1908 1997)!

Bacteriophage T4!

DNA contains genes !

Bacteriophage T4!

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

DNA contains genes !

Alfred Hershey ! (1908 1997)!

DNA contains genes !

! ! ! Denitive evidence came in 1952 from Alfred Hershey and Martha Chase.! T2 virus made of only DNA and proteins.! DNA lacks sulfur; proteins lack phosphorus!

Hereditary information is stored in genes!

! Genome is the totality of all the genetic information.! ! Genes are the specic information-containing elements of the genome that determine the characteristics of an organism.!
! ! ! ! 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 of genetic information! 1953 ! James Watson and Francis Crick determined the structure of DNA!

DNA (Deoxyribonucleic acid) !

1.! 2 long polynucleotide chains running antiparallel. Double helix.!
!

2.! Each DNA chain is composed of 4 types of nucleotide subunits ! !(A, C, G, T).!
!

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

!

4. Chains held together via hydrogen bonding. Occurs between the bases.!

Nucleotides are the precursors of nucleic acids DNA and RNA !

! RNA consists of A, G, C & U! ! Transient carrier of instructions!
!

! DNA consists of A, G, C & T! ! More stable! ! Long-term storage of information!

!

DNA !

! Nucleic acids have directionality.! 1.! 5 end! 2.! 3 end!

Remembering your bases !

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

CUT the PY (pie) !

PURe As Gold !

DNA (and RNA) are made of nucleotides !

! Nucleoside = nitrogen-containing ring compound linked to a 5carbon 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)!

The hydrogen bonding between antiparallel chains always occurs as either A-T or G-C base pairs (bps); complementary base-pairing !
! ! ! ! Watson-Crick base pairing! Always between purine and pyrimidine! G-C bps are more stable than A-T bps! Energetically most favorable also aided by twisting!

DNA Double Helix ! ! Right-handed helix.! ! 10 bases per turn.! ! The coiling/winding of the 2 strands creates 2 grooves.! ! These grooves are important recognition motifs for DNA binding proteins.!

Genes encode the primary structure of proteins !

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

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 DNA molecule. 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 its nucleus is like trying to shove 24 miles of ne thread into a tennis ball. ! ! Eukaryotes package their DNA into discrete structures called chromosomes. !

Can also tell chromosomes apart using karyotype (display of all chromosomes) with Giemsa stain !
! Giemsa produces dark bands in regions rich in A-T bps.! ! Yields a surprisingly reliable banding pattern.! ! Chromosomes are numbered according to size.!

Can also tell chromosomes apart using karyotype (display of all chromosomes) with Giemsa stain !
! Giemsa produces dark bands in regions rich in A-T bps.! ! Yields a surprisingly reliable banding pattern.! ! Chromosomes are numbered according to size.! ! Encode rRNA!

The human genome contains 23 pairs of chromosomes 22 autosomal + 1 allosomal (sex) !

Karyotype with painted chromosomes

! 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.

Karyotypes can be used to detect chromosomal deletions, amplications and translocations !

! This is common in many genetic disorders and some types of cancer. !

Figure 5-12 Essential Cell Biology ( Garland Science 2010)

Detection of the Philadelphia Chromosome in! Chronic Myelogenous Leukemia (CML) !

! A genetic translocation event leads to a fusion chromosome (Philadelphia) that expresses BCR-ABL, a constitutive active tyrosine kinase.! BCR-ABL cause of 95% of CML cases.!

Gleevec was rst targeted therapy !

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Chromosomes carry genes

! Genes are segments of DNA containing instructions for making RNA. Usually the RNA is translated into proteins.!

! Only one strand encodes the information to make the RNA.! ! Can be either strand.! ! Regardless, a gene is generally denoted to contain both the coding strand and its complementary strand.!

Organisms vary greatly in their DNA content & number of genes!

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

vs !
180 billion bps !

3 billion bps !

! Greatest difference in genomes between simple vs complex organisms is inclusion of junk DNAbut junk DNA might not be junk after all ! ! ENCODE Project !

and chromosomes!

24 unique ! chromosomes!
Figure 5-14 Essential Cell Biology ( Garland Science 2010)

5 unique ! chromosomes!

Muntiacus reevesi!

Muntiacus muntjak!

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.!

The cell cycle!

Less condensed !access for gene expression !

3 elements are required for the eukaryotic DNA replication!

Figure 5-16 Essential Cell Biology ( Garland Science 2010)

Telomeres form special caps at each chromosome end!

! Contain repeated nucleotide sequences that enable the chromosome 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 can lead to cancer.! ! ! Elizabeth Blackburn, Carol Greider, and Jack Szostak were awarded the 2009 Nobel Prize in Physiology or Medicine for the discovery of how chromosomes are protected by telomeres and the enzyme telomerase.!

Interphase DNA! ! ! ! ! ! ! ! ! ! Condensed Chromosome 22! (10000 fold more compact)!

Figure 5-20 Essential Cell Biology ( Garland Science 2010)

During interphase, chromosomes occupy distinct regions in the nucleus!

Prevents unwanted entanglement !

Note: Homologs not located near one another. ! This limits unwanted interchromosomal recombinations.!
Figure 5-18 Essential Cell Biology ( Garland Science 2010)

During interphase, the nucleolus is the most prominent structure in the nucleus!

(low gene expression)!

! Where parts of chromosomes encoding rRNAs cluster together. This is where rRNAs are thus made and combined with proteins to form ribosomes.!
euchromatin

(active gene expression) !

During interphase, the nucleolus is the most prominent structure in the nucleus!

euchromatin

Nucleosomes are the basic units of chromosome structure!

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

! Histones are responsible for the rst level of DNA packaging, nucleosomes.! 30 nm ber!

nucleosomes!

The Nucleosome!
Contain lots of lysines and arginines (+) !

Have long N-terminal tails that are highly modied (histone code) !

Histones are extremely well conserved. Even in archaea!!!

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

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

1.7 turns per histone octet! (nucleosome)! ! = 147 bp!

Figure 5-23 Essential Cell Biology ( Garland Science 2010)

Intermediate structures leading to chromosomal condensation prior to mitosis!

Figure 5-25 Essential Cell Biology ( Garland Science 2010)

Chromatin packing has multiple levels!

Requires histone H1!

Interphase chromosome !

How this occurs is not well know.!

Mitotic chromosome !

Figure 5-24 Essential Cell Biology ( Garland Science 2010)

Chromatin packing has multiple levels!

A linker histone that helps pull nucleosomes together to form the 30 nm ber.!

Figure 5-26 Essential Cell Biology ( Garland Science 2010)

Various types of machinery are needed to adjust the structure of chromatin rapidly!
! Needed for both replication and gene expression.! ! Hence, chromatin structure is dynamic.!

! Chromatin-remodeling complexes can decondense chromatin!

Covalent modications of histones regulate chromatin structure (histone code)!

! These modications function, in part, by recruiting other chromatin-remodeling complexes.!

Covalent modications of histones regulate chromatin structure (histone code)!

! These modications function in part by recruiting other chromatin-remodeling complexes.!

Can also modify core histones to help alter chromatin (e.g., HATs)! Still learning what the codes mean!

Interphase chromosomes contain both condensed 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 can spread to coding regions and silence the gene.!
!

Barrier DNA prevents heterochromatin spread!

Figure 5-29 Essential Cell Biology ( Garland Science 2010)

Maternal Gene Silencing!

One must be silenced, so that expression in females and males is similar.! ! Selection appears to be random! ! Silenced X is passed along the cell lineage! ! Females are Mosaics!

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)!

END!