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Essential Cell Biology Third Edition Chapter 5 DNA and Chromosomes Copyright © Garland Science 2010

Essential Cell Biology

Third Edition

Chapter 5 DNA and Chromosomes

Copyright © Garland Science 2010

Hereditary information is stored in genes

Hereditary information is stored in genes •   Genome is the totality of all the genetic

Genome is the totality of all the genetic information.

Human Genome

3.2 x 10 9 base pairs 24 unique chromosomes

3.2 x 10 9 base pairs 24 unique chromosomes

First Draftsequence published in 2001

~ 23000 genes = 1.5 % of DNA

Hereditary information is stored in genes

Hereditary information is stored in genes •   Genome is the totality of all the genetic

Genome is the totality of all the genetic information.

Genes are the specific information-containing elements of the genome that determine the characteristics of an organism.

Hereditary information is stored in genes

Hereditary information is stored in genes Genome is the totality of all the genetic information. Genes

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

my idea !
my
idea !
me too !
me
too !

characteristics of an organism. my idea ! me too ! •   •   Gregor Mendel
characteristics of an organism. my idea ! me too ! •   •   Gregor Mendel

Gregor Mendel

Hugo de Vries

Chromosomes

Chromosomes •   •   •   Long suspected to be involved in inherited traits 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.

DNA and proteins. Become visible ( can see with a light microscope ) as cells prepare

Condensed DNA

Extended DNA

DAPI Stained
DAPI Stained

Griffiths Experiment (1920s)

Griffith ’ s Experiment (1920s) Fred Griffith (1879 – 1941) Streptococcus pneumoniae
Griffith ’ s Experiment (1920s) Fred Griffith (1879 – 1941) Streptococcus pneumoniae

Fred Griffith (1879 – 1941)

Griffith ’ s Experiment (1920s) Fred Griffith (1879 – 1941) Streptococcus pneumoniae

Streptococcus pneumoniae

Griffiths Experiment (1920s)

Griffith ’ s Experiment (1920s) Fred Griffith (1879 – 1941)
Griffith ’ s Experiment (1920s) Fred Griffith (1879 – 1941)

Fred Griffith (1879 – 1941)

Griffith ’ s Experiment (1920s) Fred Griffith (1879 – 1941)

Griffiths Experiment (1920s)

Griffith ’ s Experiment (1920s)
Griffith ’ s Experiment (1920s)

Griffiths (transformation) Experiment (1920s)

Griffith ’ s (transformation) Experiment (1920s)
Griffith ’ s (transformation) Experiment (1920s)

DNA contains genes

DNA contains genes Oswald Avery (1877 – 1955)
DNA contains genes Oswald Avery (1877 – 1955)

Oswald Avery (1877 – 1955)

DNA contains genes Oswald Avery (1877 – 1955)

DNA contains genes

DNA contains genes •   •   •   First strong proof provided in 1944 by

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

Avery, Colin MacLeod and Maclyn McCarty. They followed up on Griffith ’ s initial findings. Received
Avery, Colin MacLeod and Maclyn McCarty. They followed up on Griffith ’ s initial findings. Received
Avery, Colin MacLeod and Maclyn McCarty. They followed up on Griffith ’ s initial findings. Received

DNA contains genes

DNA contains genes Watson & Crick expressing their gratitude to Maclyn McCarty for showing that DNA
DNA contains genes Watson & Crick expressing their gratitude to Maclyn McCarty for showing that DNA

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

DNA contains genes Watson & Crick expressing their gratitude to Maclyn McCarty for showing that DNA

DNA contains genes

DNA contains genes Alfred Hershey (1908 – 1997) Bacteriophage T4
DNA contains genes Alfred Hershey (1908 – 1997) Bacteriophage T4

Alfred Hershey (1908 – 1997)

DNA contains genes Alfred Hershey (1908 – 1997) Bacteriophage T4

Bacteriophage T4

DNA contains genes

DNA contains genes Bacteriophage T4
DNA contains genes Bacteriophage T4
DNA contains genes Bacteriophage T4

Bacteriophage T4

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

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

DNA contains genes

DNA contains genes Alfred Hershey (1908 – 1997)
DNA contains genes Alfred Hershey (1908 – 1997)

Alfred Hershey (1908 – 1997)

DNA contains genes

DNA contains genes •   •   •   Definitive evidence came in 1952 from Alfred
DNA contains genes •   •   •   Definitive evidence came in 1952 from Alfred

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

from Alfred Hershey and Martha Chase. T2 virus made of only DNA and proteins. DNA lacks

Hereditary information is stored in genes

Hereditary information is stored in genes •   Genome is the totality of all the genetic

Genome is the totality of all the genetic information.

Genes are the specific 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) à DNA is carrier of

genetic information 1953 à James Watson and Francis Crick determined the structure of DNA

DNA (Deoxyribonucleic acid)

DNA ( D eoxyribo n ucleic a cid) 1.   2 long polynucleotide chains running antiparallel

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.

3. Sugar phosphate backbone (-). Bases are inside. 4. Chains held together via hydrogen bonding. Occurs

Nucleotides are the precursors of nucleic acids DNA and RNA

Nucleotides are the precursors of nucleic acids DNA and RNA DNA •   RNA consists of
Nucleotides are the precursors of nucleic acids DNA and RNA DNA •   RNA consists of

DNA

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

Nucleic acids have directionality.

1. 5’ end

2. 3’ end

Remembering your bases

Remembering your bases •   5 bases: •   Py rimidines: Cytosine (C), Thymine (T) and

5 bases:

Py rimidines: Cytosine (C), Thymine (T) and Uracil (U) Pur ines: Guanine (G) and Adenine (A)

Thymine (T) and Uracil (U) •   Pur ines: Guanine (G) and Adenine (A) CUT the

CUT the PY (pie)

Thymine (T) and Uracil (U) •   Pur ines: Guanine (G) and Adenine (A) CUT the

PUR e A s Gold

DNA (and RNA) are made of nucleotides

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

Nucleoside = nitrogen-containing ring compound linked to a 5-

Nucleotide = nucleoside + 1 or more phosphates attached to its

carbon sugar. The sugar can either be ribose (RNA) or deoxyribose (DNA).

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

A-T or G-C base pairs (bps); complementary base-pairing •   Watson-Crick base pairing •   Always

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

pyrimidine •   G-C bps are more stable than A-T bps •   Energetically most favorable

DNA Double Helix

DNA Double Helix •   Right-handed helix. •   10 bases per turn. •   The

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.

of the 2 strands creates 2 grooves. •   These grooves are important recognition motifs for

Genesencode the primary structure of proteins

“ Genes ” encode the primary structure of proteins Figure 5-9 Essential Cell Biology (© Garland
“ Genes ” encode the primary structure of proteins Figure 5-9 Essential Cell Biology (© Garland

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

How do we fit all our DNA into the nucleus?

How do we fit all our DNA into the nucleus? •   The average bacterial genome

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 µ m big.

Putting all the human DNA into its nucleus is like trying to shove 24 miles of fine 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 Giemsastain

( display of all chromosomes ) with “ Giemsa ” stain •   Giemsa produces dark
( display of all chromosomes ) with “ Giemsa ” stain •   Giemsa produces dark

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 Giemsastain

( display of all chromosomes ) with “ Giemsa ” stain •   Giemsa produces dark
( display of all chromosomes ) with “ Giemsa ” stain •   Giemsa produces dark

Giemsa produces dark bands in regions rich in A-T bps.

Yields a surprisingly reliable banding pattern.

Chromosomes are numbered according to size.

a surprisingly reliable banding pattern. •   Chromosomes are numbered according to size. •   Encode

Encode rRNA

The human genome contains 23 pairs of chromosomes

22 autosomal+ 1 allosomal(sex)

22 “ autosomal ” + 1 “ allosomal ” (sex) •   •   •  

Karyotype with “painted” chromosomes

•   •   Karyotype with “painted” chromosomes The complex of DNA and protein is called

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, amplifications and translocations

chromosomal deletions, amplifications and translocations •   Figure 5-12 Essential Cell Biology (© Garland
chromosomal deletions, amplifications and translocations •   Figure 5-12 Essential Cell Biology (© Garland

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

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

Detection of the Philadelphia Chromosomein Chronic Myelogenous Leukemia (CML)

Chromosome ” in Chronic Myelogenous Leukemia (CML) •   A genetic translocation event leads to a
Chromosome ” in Chronic Myelogenous Leukemia (CML) •   A genetic translocation event leads to a

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.

e
e

Gleevec was first targeted therapy

Gleevec was first targeted therapy The Dawn of Personalized Medicine .
Gleevec was first targeted therapy The Dawn of Personalized Medicine .
Gleevec was first targeted therapy The Dawn of Personalized Medicine .
Gleevec was first targeted therapy The Dawn of Personalized Medicine .

The Dawn of Personalized Medicine.

Gleevec was first targeted therapy The Dawn of Personalized Medicine .

Chromosomes carry genes

Chromosomes carry genes •   Genes are segments of DNA containing instructions for making RNA. Usually

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

for making RNA. Usually the RNA is translated into proteins. •   Only one strand encodes

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

vary greatly in their DNA content & number of genes •   Some bacteria only have

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

  Single-celled Amoeba has ~60x amount of DNA of humans 3 b i l l i

3 billion bps

vs

of DNA of humans 3 b i l l i o n b p s vs

180 billion bps

Greatest difference in genomes between simple vs complex organisms is inclusion of junkDNA……but junkDNA might not be junkafter all …

ENCODE Project

……and chromosomes

……and chromosomes 24 unique chromosomes Figure 5-14 Essential Cell Biology (© Garland Science 2010) 5 unique
……and chromosomes 24 unique chromosomes Figure 5-14 Essential Cell Biology (© Garland Science 2010) 5 unique

24 unique chromosomes

Figure 5-14 Essential Cell Biology (© Garland Science 2010)

5 unique chromosomes

Muntiacus reevesi
Muntiacus reevesi
Muntiacus muntjak
Muntiacus muntjak
Muntiacus reevesi Muntiacus muntjak

Chromosomes have to replicate themselves

Chromosomes have to replicate themselves •   Cells replicate their chromosomes, and therefore their genome, through

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

their chromosomes, and therefore their genome, through a process of ordered events that occur during the
their chromosomes, and therefore their genome, through a process of ordered events that occur during the

The cell cycle

The cell cycle Less condensed à access for gene expression
The cell cycle Less condensed à access for gene expression
The cell cycle Less condensed à access for gene expression

Less condensed à access for gene expression

The cell cycle Less condensed à access for gene expression
The cell cycle Less condensed à access for gene expression

3 elements are required for the eukaryotic DNA replication

3 elements are required for the eukaryotic DNA replication Figure 5-16 Essential Cell Biology (© Garland

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

Telomeres form special caps at each chromosome end
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 (©

Interphase DNA

Interphase DNA Condensed Chromosome 22 (10000 fold more compact) Figure 5-20 Essential Cell Biology (© Garland

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

chromosomes occupy distinct regions in the nucleus Prevents unwanted entanglement Note: Homologs not located
Prevents unwanted entanglement
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

the nucleolus is the most prominent structure in the nucleus euchromatin (low gene expression) •  
euchromatin
euchromatin

(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.

(active gene expression)

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

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

Nucleosomes are the basic units of chromosome structure

Nucleosomes are the basic units of chromosome structure •   Chromosomes are made of DNA and

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 first level of DNA packaging, nucleosomes.

proteins •   Histones are responsible for the first level of DNA packaging, nucleosomes . 30

30 nm fiber

nucleosomes

The Nucleosome

The Nucleosome Contain lots of lysines and arginines (+) Have long N-terminal tails that are highly

Contain lots of lysines and arginines (+)

Have long N-terminal tails that are highly modified (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 1 of 2) Essential Cell Biology (© Garland Science 2010)

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

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

Figure 5-23 Essential Cell Biology (© Garland Science 2010) 1.7 turns per histone octet (nucleosome)

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

1.7 turns per histone octet (nucleosome)

= 147 bp

Figure 5-25 Essential Cell Biology (© Garland Science 2010) Intermediate structures leading to chromosomal condensation

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

Intermediate structures leading to chromosomal condensation prior to mitosis

Chromatin packing has multiple levels

How this occurs is not well know.
How this occurs is
not well know.

Requires histone H1

Interphase

chromosome

Mitotic

chromosome

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

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

Chromatin packing has multiple levels

Chromatin packing has multiple levels A linker histone that helps pull nucleosomes together to form the
Chromatin packing has multiple levels A linker histone that helps pull nucleosomes together to form the
Chromatin packing has multiple levels A linker histone that helps pull nucleosomes together to form the

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

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

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

Various types of machinery are needed to adjust the structure of chromatin rapidly

are needed to adjust the structure of chromatin rapidly •   Needed for both replication and
are needed to adjust the structure of chromatin rapidly •   Needed for both replication and

Needed for both replication and gene expression. Hence, chromatin structure is dynamic.

Chromatin-remodeling complexes can decondense chromatin

Covalent modifications of histones regulate chromatin structure (histone code)

of histones regulate chromatin structure ( histone code ) •   These modifications function, in part,

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

( histone code ) •   These modifications function, in part, by recruiting other chromatin-remodeling complexes.
( histone code ) •   These modifications function, in part, by recruiting other chromatin-remodeling complexes.

Covalent modifications of histones regulate chromatin structure (histone code)

of histones regulate chromatin structure ( histone code ) •   These modifications function in part

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

in part by recruiting other chromatin-remodeling complexes. Can also modify core histones to help alter chromatin

Can also modify core histones to help alter chromatin (e.g., HATs)

Still learning what the codesmean

Interphase chromosomes contain both condensed and more extended chromatin

contain both condensed and more extended chromatin •   Euchromatin—more extended, higher gene

Euchromatin—more extended, higher gene expression

Heterochromatin—condensed, low gene expression ~10% of interphase chromatin Located around centromere and telomeres There are heterochromatin-specific proteins

•   There are heterochromatin-specific proteins Heterochromatin can spread to coding regions and “

Heterochromatin can spread to coding regions and silencethe gene.

Barrier DNA prevents heterochromatin spread

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

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

Maternal Gene Silencing

Maternal Gene Silencing One must be silenced, so that expression in females and males is similar.
Maternal Gene Silencing One must be silenced, so that expression in females and males is similar.

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)

structure can be inherited ( epigenetic inheritance ) •   Specific histone modifications are passed on.

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

END