chapter 16 the molecular basis of inheritance updated nov. 2008
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Chapter 16
The Molecular Basis of Inheritance
Updated Nov. 2008
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Overview: Life’s Operating Instructions
In 1953, James Watson and Francis Crick shook the world With an elegant double-helical model for the
structure of deoxyribonucleic acid, or DNA
Figure 16.1
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DNA – Deoxyribonucleic acids
Nucleic acids are unique in their ability to direct their own
replication
It is the DNA program That directs the development of your biochemical,
anatomical, physiological, and (to some extent) behavioral traits
Precise replication of DNA and its transmission to offspring make up heredity
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Concept 16.1: DNA is the genetic material
Early in the 20th century After T.H. Morgan’s group showed that genes are
located on chromosomes – proteins and DNA – were the candidates for the genetic material
The identification of the molecules of inheritance loomed as a major challenge to biologists
Until 1940’s, proteins had more support
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The Search for the Genetic Material: Scientific Inquiry
Proteins as the genetic material was not consistent with bacteria and viruses
The role of DNA in heredity Was first worked out by studying bacteria and
the viruses that infect them
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Evidence That DNA Can Transform Bacteria
Frederick Griffith was studying Streptococcus pneumoniae A bacterium that causes pneumonia in mammals
He worked with two strains of the bacterium A pathogenic strain and a nonpathogenic strain Pathogenic means disease causing
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When he mixed heat-killed remains of the pathogenic strain with living cells of the harmless strain, some living cells became pathogenic
He called this phenomenon transformation, now defined as a change in genotype and phenotype due to assimilation of foreign DNA
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Fig. 16-2
Living S cells (control)
Living R cells (control)
Heat-killed S cells (control)
Mixture of heat-killed S cells and living R cells
Mouse diesMouse dies Mouse healthy Mouse healthy
Living S cells
RESULTS
EXPERIMENT
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Transformation
Now defined as a change in genotype and phenotype due to the assimilation of external DNA by a cell
Transformation also means conversion of a normal animal cell to a cancerous one (not the same meaning or process)
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Evidence That Viral DNA Can Program CellsMore evidence for DNA as the genetic
material came from studies of viruses that infect bacteria
Such viruses, called bacteriophages (or phages), are widely used in molecular genetics research (and other fields like evolutionary biology)
Animation: Phage T2 Reproductive CycleAnimation: Phage T2 Reproductive Cycle
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Viruses
Figure 16.3
Phagehead
Tail
Tail fiber
DNA
Bacterialcell
100
nm
Consist of DNA (sometimes RNA) enclosed by a protective coat of protein
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Is DNA or Protein the genetic material of phage T2?
Alfred Hershey and Martha Chase Performed experiments showing that DNA is
the genetic material of a phage known as T2
Radioactive sulfur (pink) labeled the proteins (but not DNA)
Radioactive phosphorus (blue) labeled the DNA (but not the proteins)
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Fig. 16-4-3
EXPERIMENT
Phage
DNA
Bacterial cell
Radioactive protein
Radioactive DNA
Batch 1: radioactive sulfur (35S)
Batch 2: radioactive phosphorus (32P)
Empty protein shell
Phage DNA
Centrifuge
Centrifuge
Pellet
Pellet (bacterial cells and contents)
Radioactivity (phage protein) in liquid
Radioactivity (phage DNA) in pellet
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Additional evidence that DNA is the genetic material
Prior to the 1950s, it was already known that DNA
Is a polymer of nucleotides, each consisting of three components: a nitrogenous base, a sugar, and a phosphate group
Sugar-phosphatebackbone
Nitrogenousbases
5 endO–
O P O CH2
5
4O–
HH
O
H
H
H3
1H O
CH3
N
O
NH
Thymine (T)
O
O P O
O–
CH2
HH
O
H
H
H
HN
N
N
H
NH
H
Adenine (A)
O
O P O
O–
CH2
H
HO
H
H
H
H
H H
HN
NN
OCytosine (C)
O
O P O CH2
5
4O–
H
O
H
H3
1
OH
2
H
N
NN H
ON
N HH
H H
Sugar (deoxyribose)3 end
Phosphate
Guanine (G)
DNA nucleotide
2
N
Figure 16.5
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Nitrogenous bases
In 1947, Edwin Chargaff developed a set of rules based on a survey of DNA
composition in organisms
Evidence of molecular diversity among species Made DNA a more credible candidate for the
genetic material
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Chargaff’s rules
In all organisms, the number of adenines was approximately equal to the number of thymines
The number of guanines was approximately equal to the number of cytosines
The basis for these rules remained unexplained but were key to solving the genetic code
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Building a Structural Model of DNA: Scientific Inquiry
Once most biologists were convinced that DNA was the genetic material The challenge was to determine how the
structure of DNA could account for its role in inheritance
Three of the scientists working on this were Linus Pauling (California), Rosalind Franklin (London) and Maurice Wilkins (London)
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Maurice Wilkins and Rosalind Franklin
Were using a technique called X-ray crystallography to study molecular structure
Rosalind Franklin Produced a picture of the DNA molecule using
this technique
(a) Rosalind Franklin Franklin’s X-ray diffractionPhotograph of DNA
(b)Figure 16.6 a, b
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Rosalind Franklin
Concluded that DNA Was composed of two antiparallel sugar-
phosphate backbones With relatively hydrophobic nitrogenous bases
paired in the molecule’s interior
The nitrogenous bases Are paired in specific combinations: adenine with
thymine, and cytosine with guanine
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Watson and Crick deduced that DNA was a double helix
Figure 16.7a, c
C
T
A
A
T
CG
GC
A
C G
AT
AT
A T
TA
C
TA0.34 nm
3.4 nm
(a) Key features of DNA structure
G
1 nm
G
(c) Space-filling model
T
Through observations of the X-ray crystallographic images of DNA
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Uniform diameter along the helix
O
–O O
OH
O
–OO
O
H2C
O
–OO
O
H2C
O
–OO
O
OH
O
O
OT A
C
GC
A T
O
O
O
CH2
OO–
OO
CH2
CH2
CH2
5 end
Hydrogen bond3 end
3 end
G
P
P
P
P
O
OH
O–
OO
O
P
P
O–
OO
O
P
O–
OO
O
P
(b) Partial chemical structure
H2C
5 endFigure 16.7b
O
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Watson and Crick
Reasoned that there must be additional specificity of pairing
Dictated by the structure of the bases
Each base pair forms a different number of hydrogen bonds
Adenine and thymine form two bonds, cytosine and guanine form three bonds
In April 1953, Watson and Crick published their model in Nature
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Hydrogen bondsN H O CH3
N
N
O
N
N
N
N H
Sugar
Sugar
Adenine (A) Thymine (T)
N
N
N
N
Sugar
O H N
H
NH
N OH
H
N
Sugar
Guanine (G) Cytosine (C)Figure 16.8
H
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Concept 16.2: Many proteins work together in DNA replication and repair
The relationship between structure and function Is manifest in the double helix
The Basic Principle: Base Pairing to a Template Strand Since the two strands of DNA are complementary
each strand acts as a template for building a new strand in replication
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In DNA replication
The parent molecule unwinds, and two new daughter strands are built based on base-pairing rules
(a) The parent molecule has two complementary strands of DNA. Each base is paired by hydrogen bonding with its specific partner, A with T and G with C.
(b) The first step in replication is separation of the two DNA strands.
(c) Each parental strand now serves as a template that determines the order of nucleotides along a new, complementary strand.
(d) The nucleotides are connected to form the sugar-phosphate backbones of the new strands. Each “daughter” DNA molecule consists of one parental strand and one new strand.
A
C
T
A
G
A
C
T
A
G
A
C
T
A
G
A
C
T
A
G
T
G
A
T
C
T
G
A
T
C
A
C
T
A
G
A
C
T
A
G
T
G
A
T
C
T
G
A
T
C
T
G
A
T
C
T
G
A
T
C
Figure 16.9 a–d
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Figure 16.10 a–c
Conservativemodel. The twoparental strandsreassociate after acting astemplates fornew strands,thus restoringthe parentaldouble helix.
Semiconservativemodel. The two strands of the parental moleculeseparate, and each functionsas a templatefor synthesis ofa new, comple-mentary strand.
Dispersivemodel. Eachstrand of bothdaughter mol-ecules containsa mixture ofold and newlysynthesizedDNA.
Parent cellFirstreplication
Secondreplication
DNA replication is semiconservative
Each of the two new daughter molecules will have one old strand, derived from the parent molecule, and one newly made strand
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Experiments performed by Meselson and StahlSupported the semiconservative model of
DNA replication
Figure 16.11
Matthew Meselson and Franklin Stahl cultured E. coli bacteria for several generations on a medium containing nucleotide precursors labeled with a heavy isotope of nitrogen, 15N. The bacteria incorporated the heavy nitrogen into their DNA. The scientists then transferred the bacteria to a medium with only 14N, the lighter, more common isotope of nitrogen. Any new DNA that the bacteria synthesized would be lighter than the parental DNA made in the 15N medium. Meselson and Stahl could distinguish DNA of different densities by centrifuging DNA extracted from the bacteria.
EXPERIMENT
The bands in these two centrifuge tubes represent the results of centrifuging two DNA samples from the flask in step 2, one sample taken after 20 minutes and one after 40 minutes.
RESULTS
Bacteriacultured inmediumcontaining15N
Bacteriatransferred tomediumcontaining14N
21
DNA samplecentrifugedafter 20 min(after firstreplication)
3 DNA samplecentrifugedafter 40 min(after secondreplication)
4Lessdense
Moredense
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CONCLUSION Meselson and Stahl concluded that DNA replication follows the semiconservative model by comparing their result to the results predicted by each of the three models in Figure 16.10. The first replication in the 14N medium produced a band of hybrid (15N–14N) DNA. This result eliminated the conservative model. A second replication produced both light and hybrid DNA, a result that eliminated the dispersive model and supported the semiconservative model.
First replication Second replication
Conservativemodel
Semiconservativemodel
Dispersivemodel
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DNA Replication: A Closer Look
The copying of DNA Is remarkable in its speed and accuracy
More than a dozen enzymes and other proteins Participate in DNA replication
A human cell can copy 6 billion base pairs and divide in only a few hours with only 1 error per 10 billion nucleotides
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Getting Started: Origins of ReplicationMuch more is known about replication in
prokaryotes (specifically bacteria) than is known about eukaryotes
But the processes appear to be similarThe replication of a DNA molecule
Begins at special sites called origins of replication, where the two strands are separated
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Bidirectional Circular DNA Replication in Bacteria (a prokaryote)
DNA replication occurs in both directions from the origin of replication in the circular DNA found in most bacteria.
In eukaryotes, there may be hundreds or thousands of origin sites per chromosome.
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Fig. 16-12a
Origin of replication Parental (template) strand
Daughter (new) strand
Replication fork
Replication bubble
Double-stranded DNA molecule
Two daughter DNA molecules
(a) Origins of replication in E. coli
0.5 µm
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Fig. 16-12b
0.25 µm
Origin of replication Double-stranded DNA molecule
Parental (template) strandDaughter (new) strand
Bubble Replication fork
Two daughter DNA molecules
(b) Origins of replication in eukaryotes
Animation: Origins of ReplicationAnimation: Origins of Replication
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Proteins in DNA replication
At the end of each replication bubble is a replication fork, a Y-shaped region where new DNA strands are elongating
Helicases are enzymes that untwist the double helix at the replication forks
Single-strand binding protein binds to and stabilizes single-stranded DNA until it can be used as a template
Topoisomerase corrects “overwinding” ahead of replication forks by breaking, swiveling, and rejoining DNA strands
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Fig. 16-13
Topoisomerase
Helicase
PrimaseSingle-strand binding proteins
RNA primer
55
5 3
3
3
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Initiation
DNA polymerases cannot initiate synthesis of a polynucleotide; they can only add nucleotides to the 3 end
The initial nucleotide strand is a short RNA primer An enzyme called primase can start an RNA chain
from scratch and adds RNA nucleotides one at a time using the parental DNA as a template
The primer is short (5–10 nucleotides long), and the 3 end serves as the starting point for the new DNA strand
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Figure 16.13
New strand Template strand5 end 3 end
Sugar A TBase
C
G
G
C
A
C
T
PP
P
OH
P P
5 end 3 end
5 end 5 end
A T
C
G
G
C
A
C
T
3 endPyrophosphate
2 P
OH
Phosphate
Synthesizing a New DNA Strandat a replication fork is catalyzed by
enzymes called DNA polymerases, which add nucleotides to the 3 end of a growing strand
Nucleosidetriphosphate
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DNA Polymerase
The rate of elongation is about 500 nucleotides per second in bacteria, 50 per second in human cells
E. coli has DNA polymerase I and IIIEukaryotes have at least 11 different types
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Antiparallel Elongation
How does the antiparallel structure of the double helix affect replication?
(Antiparallel – oriented in opposite directions to each other)
DNA polymerases add nucleotides Only to the free 3end of a growing strand
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Directions
3’ end has a free hydroxyl group which is the only place a nucleotide can be added
Along one template strand of DNA, the leading strand DNA polymerase III can synthesize a
complementary strand continuously, moving toward the replication fork
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Elongation
To elongate the other new strand of DNA, the lagging strand DNA polymerase III must work in the direction
away from the replication fork
The lagging strand Is synthesized as a series of segments called
Okazaki fragments, which are then joined together by DNA ligase
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Fig. 16-15
Leading strand
Overview
Origin of replicationLagging strand
Leading strandLagging strand
Primer
Overall directions of replication
Origin of replication
RNA primer
“Sliding clamp”
DNA poll IIIParental DNA
5
3
3
3
3
5
5
5
5
5
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Synthesis of DNA
Okazaki fragments are 1,000 – 2,000 nucleotides long in E. coli
They are 100-200 nucleotides long in eukaryotes
DNA ligase joins the fragments together so they form a single DNA strand
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Priming DNA Synthesis
DNA polymerases cannot initiate the synthesis of a polynucleotide They can only add nucleotides to the 3 end
The initial nucleotide strand Is an RNA or DNA primer
Primase (and RNA polymerase) joins RNA nucleotides into a primer
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Synthesis of the lagging strand
Only one primer is needed for synthesis of the leading strand But for synthesis of the lagging strand, each Okazaki
fragment must be primed separately
DNA pol III adds to the 3’ end of the primer and continues
DNA pol I replaces the RNA nucleotides with DNA versions
DNA ligase forms the bonds between the fragments
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Fig. 16-16a
Overview
Origin of replication
Leading strand
Leading strand
Lagging strand
Lagging strand
Overall directions of replication
12
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Overall direction of replication
3
3
3
35
35
35
35
3
5
3
5
3
5
3 5
5
1
1
21
12
5
5
12
35
Templatestrand
RNA primer
Okazakifragment
Figure 16.15
Primase joins RNA nucleotides into a primer.
1
DNA pol III adds DNA nucleotides to the primer, forming an Okazaki fragment.
2
After reaching the next RNA primer (not shown), DNA pol III falls off.
3
After the second fragment is primed. DNA pol III adds DNAnucleotides until it reaches the first primer and falls off.
4
DNA pol 1 replaces the RNA with DNA, adding to the 3 end of fragment 2.
5
DNA ligase forms a bond between the newest DNAand the adjacent DNA of fragment 1.
6 The lagging strand in this region is nowcomplete.
7
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Table 16-1
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Fig. 16-17
OverviewOrigin of replication
Leading strand
Leading strand
Lagging strand
Lagging strandOverall directions
of replication
Leading strand
Lagging strand
Helicase
Parental DNA
DNA pol III
Primer Primase
DNA ligase
DNA pol III
DNA pol I
Single-strand binding protein
5
3
5
5
5
5
3
3
3
313 2
4
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The DNA Replication ComplexThe proteins that participate in DNA
replication form a large complex, a “DNA replication machine”
The DNA replication machine is probably stationary during the replication process
Recent studies support a model in which DNA polymerase molecules “reel in” parental DNA and “extrude” newly made daughter DNA molecules
Copyright © 2008 Pearson Education Inc., publishing as Pearson Benjamin Cummings
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Proofreading and Repairing DNA
Mistakes happen at a rate of 1 per 100,000 base pairs
DNA polymerases proofread newly made DNA Replacing any incorrect nucleotides
In mismatch repair of DNA Repair enzymes correct errors in base pairing
Final error rate is 1 in 10 billion (but 6 billion base pairs in a human chromosome)
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Mismatched nucleotides sometimes evade proofreading
In mismatch repair, special enzymes fix incorrectly paired nucleotides
DNA can be damaged by reactive chemicals, radioactive emissions, X-rays and UV light
DNA bases can also undergo spontaneous chemical changes
A hereditary defect in one of these enzymes is responsible for a form of colon cancer
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Figure 16.17
Nuclease
DNApolymerase
DNAligase
A thymine dimerdistorts the DNA molecule.1
A nuclease enzyme cutsthe damaged DNA strandat two points and thedamaged section isremoved.
2
Repair synthesis bya DNA polymerasefills in the missingnucleotides.
3
DNA ligase seals theFree end of the new DNATo the old DNA, making thestrand complete.
4
In nucleotide excision repair
Enzymes cut out and replace damaged stretches of DNA
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Inherited disorder xeroderma pigmentosum
Having this disorder means hypersensitivity to sunlight
UV light can produce thymine dimers between adjacent thymine nucleotides
Buckles the DNA and interferes with DNA replication
The repair enzyme doesn’t work in this disorder so the mutations are left uncorrected and cause skin cancer
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The ends of eukaryotic chromosomal DNA get shorter with each round of replication
Figure 16.18
End of parentalDNA strands
Leading strandLagging strand
Last fragment Previous fragment
RNA primer
Lagging strand
Removal of primers andreplacement with DNAwhere a 3 end is available
Primer removed butcannot be replacedwith DNA becauseno 3 end available
for DNA polymerase
Second roundof replication
New leading strand
New lagging strand 5
Further roundsof replication
Shorter and shorterdaughter molecules
5
3
5
3
5
3
5
3
3
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Linear DNA
Prokaryotes don’t have this problem because their DNA is circular
The ends of eukaryotic chromosomal DNA have special nucleotide sequences called telomeres
Telomeres do not contain genes, but multiple repetitions of one short nucleotide sequence
In humans, it is repeated 100 to 1,000 times
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Telomeres
postpone the erosion of genes near the ends of DNA molecules
May be connected with aging
Figure 16.19 1 µm
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Telomeres and gametes
If the chromosomes of germ cells became shorter in every cell cycle Essential genes would eventually be missing from
the gametes they produce
An enzyme called telomerase Catalyzes the lengthening of telomeres in germ
cells
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Telomeres and cancer
Normal shortening of telomeres may protect against cancer by limiting the number of divisions a somatic cell can undergo
Active telomerase has been found in some somatic cells
Telomerase may provide a useful target for cancer diagnosis and chemotherapy
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Concept 16.3 A chromosome consists of a DNA molecule packed together with proteinsThe bacterial chromosome is a double-
stranded, circular DNA molecule associated with a small amount of protein
Eukaryotic chromosomes have linear DNA molecules associated with a large amount of protein
In a bacterium, the DNA is “supercoiled” and found in a region of the cell called the nucleoid
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Chromatin is a complex of DNA and protein, and is found in the nucleus of eukaryotic cells
Histones are proteins that are responsible for the first level of DNA packing in chromatin
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Animation: DNA PackingAnimation: DNA Packing
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Fig. 16-21a
DNA double helix (2 nm in diameter)
Nucleosome(10 nm in diameter)
Histones Histone tailH1
DNA, the double helix Histones Nucleosomes, or “beads on a string” (10-nm fiber)
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Fig. 16-21b
30-nm fiber
Chromatid (700 nm)
Loops Scaffold
300-nm fiber
Replicated chromosome (1,400 nm)
30-nm fiber Looped domains (300-nm fiber)
Metaphase chromosome
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Chromatin is organized into fibers
10-nm fiber DNA winds around histones to form
nucleosome “beads” Nucleosomes are strung together like beads on
a string by linker DNA
30-nm fiber Interactions between nucleosomes cause the
thin fiber to coil or fold into this thicker fiber
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300-nm fiber The 30-nm fiber forms looped domains that
attach to proteins
Metaphase chromosome The looped domains coil further The width of a chromatid is 700 nm
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Chromatin
Most chromatin is loosely packed in the nucleus during interphase and condenses prior to mitosis
Loosely packed chromatin is called euchromatin During interphase a few regions of chromatin
(centromeres and telomeres) are highly condensed into heterochromatin
Dense packing of the heterochromatin makes it difficult for the cell to express genetic information coded in these regions
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Histones
Histones can undergo chemical modifications that result in changes in chromatin organization For example, phosphorylation of a specific
amino acid on a histone tail affects chromosomal behavior during meiosis
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You should now be able to:
1. Describe the contributions of the following people: Griffith; Avery, McCary, and MacLeod; Hershey and Chase; Chargaff; Watson and Crick; Franklin; Meselson and Stahl
2. Describe the structure of DNA
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3. Describe the process of DNA replication; include the following terms: antiparallel structure, DNA polymerase, leading strand, lagging strand, Okazaki fragments, DNA ligase, primer, primase, helicase, topoisomerase, single-strand
4. Describe the function of telomeres
5. Compare a bacterial chromosome and a eukaryotic chromosome
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