Title: DNA Structure and Function
1- Chapter 8
- DNA Structure and Function
2Eukaryotic Chromosomes
- The DNA in a eukaryotic cell nucleus is organized
as one or more chromosomes that differ in length
and shape - Chromosome
- A structure that consists of DNA and associated
proteins - Carries part or all of a cells genetic
information
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4Chromosome Organization
- During most of the cells life, each chromosome
consists of one DNA strand. - When the cell prepares to divide, it duplicates
all of its chromosomes, so that both offspring
get a full set - Each duplicated chromosome has two DNA strands
(sister chromatids) attached to one another at
the centromere
5centromere
one chromatid
its sister chromatid
a chromosome (unduplicated)
a chromosome (duplicated)
p134
6Chromosome Structure
- A duplicated, condensed chromosome consists of
two long filaments bunched into a characteristic
X shape - Each filament consists of a coil of DNA wrapped
around spools of proteins called histones - Each DNA-histone spools is a nucleosome, the
smallest unit of chromosomal organization in
eukaryotes - Stretched out end to end, the DNA molecules in a
human cell would be about 2 meters (6.5 feet)
long. That is a lot of DNA to fit into a nucleus
that is less than 10 micrometers in diam- eter!
Proteins structurally organize the DNA and help
it pack tightly into a small nucleus.
7The DNA molecule consists of two strands twisted
into a double helix
DNA molecule
Zooming in on chromosome structure. Tight packing
allows a lot of DNA to fit into a very small
nucleus.
Figure 8-2b p134
85
6
Figure 8-2c2 p134
9Chromosome Number
- The total number of chromosomes in a eukaryotic
cell (chromosome number) is characteristic of the
species human body cells have 46 chromosomes - Human body cells have two of each type of
chromosome their chromosome number is diploid
(2n) - A karyotype shows how many chromosomes are in an
individual cell, and reveals major structural
abnormalities
10A karyotype. This one shows 22 pairs of autosomes
and a pair of X chromosomes.
Figure 8-3a p135
11Chromosome Numbers
Source http//plantcellbiology.masters.grkraj.org
/html/Plant_Cell_Genetics1-Chromosomes.htm
12Autosomes and Sex Chromosomes
- In a diploid organism, one chromosome in a
chromosome pair is inherited from the mother and
one from the father - All except one pair of chromosomes are autosomes
pairs of chromosomes with the same length,
shape, and centromere location - Pairs of sex chromosomes differ between females
and males human females have two X chromosomes
(XX) human males have one X and one Y chromosome
(XY)
13Stepped Art
Figure 8-3b p135
14The Discovery of DNAs Functions
- Investigations that led to our understanding that
DNA is the molecule of inheritance reveal how
science advances
15Discovery of DNA
- 1800s Johannes Miescher found DNA
(deoxyribonucleic acid) in nuclei, though its
function was unknown
16Griffiths Experiments
- Pneumococci has two general formsrough (R) and
smooth (S). The virulent S form, when injected
subcutaneously into mice succumbed to pneumonia
and died within a couple of days. The avirulent R
form that does not prompt pneumonia. - When Griffith injected heat-killed S into mice,
as expected no disease ensued. When mice were
injected with a mixture of heat-killed S and live
R, however, pneumonia and death ensued. The live
R had transformed into Sand replicated as such.
17Griffiths Experiments
Summary of results from Fred Griffiths
experiments. The hereditary material of harmful
Streptococcus pneumoniae cells transformed
harmless cells into killers. 1 Mice injected with
live cells of harmless strain R do not die. Live
R cells in their blood. 2 Mice injected with live
cells of killer strain S die. Live S cells in
their blood. 3 Mice injected with heat- killed S
cells do not die. No live S cells in their
blood. 4 Mice injected with live R cells plus
heat-killed S cells die. Live S cells in their
blood.
1
2
3
4
18Griffiths Experiments
- Early 1900s Griffith transferred hereditary
material from dead cells to live cells - Mice injected with live R cells lived
- Mice injected with live S cells died
- Mice injected with killed S cells lived
- Mice injected with killed S cells and live R
cells died live S cells were found in their
blood
19Avery and McCarty Find the Transforming Principle
- 1940 Avery and McCarty separated deadly S cells
(from Griffiths experiments) into lipid,
protein, and nucleic acid components - When lipids, proteins, and RNA were destroyed,
the remaining substance, DNA, still transformed R
cells to S cells - Conclusion DNA is the transforming principle
20Confirmation of DNAs Function
- 1950s Hershey and Chase experimented with
bacteriophages (viruses that infect bacteria) - Protein parts of viruses, labeled with 35S,
stayed outside the bacteria - DNA of viruses, labeled with 32P, entered the
bacteria - Conclusion DNA, not protein, is the material
that stores hereditary information
21Bacteriophages
The HersheyChase experiments. Alfred Hershey
and Martha Chase tested whether the genetic
material injected by bacteriophage into bacteria
is DNA, protein, or both. The experiments were
based on the knowledge that proteins contain more
sulfur (S) than phosphorus (P), and DNA contains
more phosphorus than sulfur.
DNA inside protein coat
tail fiber
hollow sheath
22Stepped Art
Figure 8-6 p137
23The Discovery of DNAs Structure
- James D. Watson and Francis Cricks discovery of
DNAs structure was based on 150 years of
research by other scientists
24The Discovery of DNAs Structure
- DNA structure was discovered through the work of
many scientists. - One crucial piece of evidence came from X-ray
crystallography. - A purified substance can be made to form
crystals the pattern of diffraction of X rays
passed through the crystallized substance shows
position of atoms. - Rosalind Franklin
- Prepared crystallographs from uniformly oriented
DNA fibersher images suggested a spiral model
25The Short Story of Rosalind Franklin
- In science, as in other professions, public
recognition does not always include everyone who
contributed to a discovery - Rosalind Franklin was first to discover the
molecular structure of DNA, but did not share in
the Nobel prize which was given to Watson and
Crick. - Franklin died of cancer at age 37 probably caused
by extensive exposure to x-rays during her work
26Rosalind Franklin and Her X-Ray Diffraction
Image of DNA
27X-Ray Crystallography Helped Reveal the Structure
of DNA
28DNAs Building Blocks
- Nucleotide
- A nucleic acid monomer consisting of a
five-carbon sugar (deoxyribose), three phosphate
groups, and one of four nitrogen-containing bases - DNA consists of four nucleotide building blocks
- Two pyrimidines thymine and cytosine
- Two purines adenine and guanine
29Four Kinds of Nucleotides in DNA
adenine (A) deoxyadenosine triphosphate, a purine
30Four Kinds of Nucleotides in DNA
guanine (G) deoxyguanosine triphosphate, a purine
31Four Kinds of Nucleotides in DNA
thymine (T) deoxythymidine triphosphate, a
pyrimidine
32Four Kinds of Nucleotides in DNA
cytosine (C) deoxycytidine triphosphate, a
pyrimidine
33DNA Structure Reflects Its Role as the Genetic
Material
Chargaffs rule
- In 1950 Erwin Chargaff found that in the DNA from
many different species - Amount of A amount of T
- Amount of C amount of G
- Or, the abundance of purines the abundance of
pyrimidines Chargaffs rule.
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35- Francis Crick and James Watson used model
building and combined all the knowledge of DNA to
determine its structure. - Franklins X-ray crystallography convinced them
the molecule was helical. - Modeling also showed that DNA strands are
anti-parallel.
36- Watson and Crick suggested that
- Nucleotide bases are on the interior of the two
strands, with a sugar-phosphate backbone on the
outside. - Per Chargaffs rule, a purine on one strand is
paired with a pyrimidine on the other. - These base pairs (A-T and G-C) have the same
width down the helix.
37Watson and Crick Model of DNA
38Franklin, Watson and Crick
- Rosalind Franklins research in x-ray
crystallography revealed the dimensions and
shape of the DNA molecule an alpha helix - This was the final piece of information James
Watson and Francis Crick needed to build their
model of DNA
39Watson and Cricks DNA Model
- A DNA molecule consists of two nucleotide chains
(strands), running in opposite directions and
coiled into a double helix - Base pairs form on the inside of the helix, held
together by hydrogen bonds (A-T and G-C)
40DNAs Base-Pair Sequence
- Bases in DNA strands can pair in only one way A
always pairs with T G always pairs with C - The DNA sequence (sequence of bases) is the
genetic code that varies between species and
individuals
one base pair
41Base Pairs in DNA Can Interact with Other
Molecules
42DNA Structure Reflects Its Role as the Genetic
Material
- Four key features of DNA structure
- (see next slide)
- It is a double-stranded helix of uniform
diameter. - It is right-handed.
- It is antiparallel.
- Outer edges of nitrogenous bases are exposed in
the major and minor grooves.
43DNA Is a Double Helix
Grooves. The strand backbones are closer together
on one side of the helix than on the other. The
major groove occurs where the backbones are far
apart, the minor groove occurs where they are
close together and the grooves twist around the
molecule on opposite sides. Certain proteins
bind to DNA to alter its structure or to regulate
transcription (copying DNA to RNA) or replication
(copying DNA to DNA). It is easier for these DNA
binding proteins to interact with the bases on
the major groove.
44Structure of DNA
0.34 nanometer between each base pair
2-nanometer diameter
3.4-nanometer length of each full twist of the
double helix
Figure 8-8b p139
45- Surfaces of A-T and G-C base pairs are chemically
distinct. - Binding of proteins to specific base pair
sequences is key to DNAprotein interactions, and
necessary for replication and gene expression.
46- DNA has three important functions
- double-helical structure is essential
- Storage of genetic informationmillions of
nucleotides base sequence encodes huge amounts
of information - Precise replication during cell division by
complementary base pairing - Expression of the coded information as the
phenotypenucleotide sequence is transcribed into
RNA and determines sequence of amino acids in
proteins
47DNA Replication
- DNA replication is the energy - intensive process
by which a cell copies its DNA - A cell copies its DNA before it reproduces
- Each of the two DNA strands in the double helix
is replicated - DNA replication requires many enzymes, including
DNA polymerase, and other molecules
48DNA Replication
- A cells genetic information consists of the
order of nucleotide bases (the DNA sequence) of
its chromosomes - Descendant cells must get an exact copy of that
information - Each chromosome is copied entirely the two
chromosomes that result are duplicates of the
parent molecule
49Semiconservative DNA Replication
- Each strand of a DNA double helix is a template
for synthesis of a complementary strand of DNA - One template builds DNA continuously the other
builds DNA discontinuously, in segments - Each new DNA molecule consist of one old strand
and one new strand (semiconservative replication)
50Primers for DNA Polymerase
- There are several types of DNA polymerases
- All types require a primer in order to initiate
DNA synthesis - Primer
- A short, single strand of DNA or RNA that is
complementary to a targeted DNA sequence
51Enzymes of DNA Replication
- DNA helicase breaks hydrogen bonds between DNA
strands - Topoisomerase untwists the double helix
- DNA polymerase joins free nucleotides into a new
strand of DNA - DNA ligase joins DNA segments on the
discontinuous strand
52Discontinuous Replication
- DNA polymerases attach a free nucleotide only to
the 3' end of a DNA strand (not the 5' end) - Only one of the two new strands of DNA can be
synthesized continuously during DNA replication - Synthesis of the other strand occurs in segments,
in the direction opposite that of unwinding - DNA ligase joins segments into a continuous
strand of DNA
53DNA Replicates Semiconservatively
- Semiconservative replication means that each
parental strand serves as a template for a new
strand. - Conservative replication would show that the
intact parental DNA (both strands) serves as a
template. - Evidence from radioactively-labeled strands
supports semiconservative replication.
54DNA Replicates Semiconservatively
- Two steps in DNA replication
- The double helix is unwound, making two template
strands available for new base pairing. - New nucleotides form base pairs with template
strands and linked together by phosphodiester
bonds. Template DNA is read in the 3'-to-5'
direction.
55DNA Replicates Semiconservatively
- During DNA synthesis, new nucleotides are added
to the 3' end of the new strand, which has a free
hydroxyl group (OH). - Deoxyribonucleoside triphosphates (dNTPs), or
deoxyribonucleotides, are the building blockstwo
of their phosphate groups are released and the
third bonds to the 3' end of the DNA chain (see
next slide). A bond forms between the 3' carbon
on the end of a DNA strand and the phosphate of a
new nucleotides 5' carbon.
56Each New DNA Strand Grows by the Addition of
Nucleotides to Its 3' End
57DNA Replicates Semiconservatively
- DNA replication begins with the binding of a
large protein complexthe pre-replication
complexto a specific site on the DNA molecule. - The complex contains DNA polymerase, which
catalyzes addition of nucleotides. - The complex binds to a region on the chromosome
called the origin of replication (ori).
58DNA Replicates Semiconservatively
- When the pre-replication complex binds to ori,
the DNA unwinds and replication proceeds in two
directions. - The replication fork is the site where DNA
unwinds to expose bases. - Eukaryotic chromosomes are linear and have
multiple origins of replication, which speed up
replication. (Compare the next two slides)
59The Origin of DNA Replication Prokaryote
60The Origin of DNA Replication Eukaryote
61DNA replication. Two double-stranded DNA
molecules form one strand of each is parental
(old), and the other is new, so DNA replication
is said to be semiconservative. Green arrows show
the direction of synthesis for each strand. The
Y-shaped structure of a DNA molecule undergoing
replication is called a replication fork. 1 As
replication begins, many initiator proteins
attach to the DNA at certain sites in the
chromosome. Eukaryotic chromosomes have many of
these origins of replication DNA replication
proceeds more or less simultaneously at all of
them. 2 Enzymes recruited by the initiator
proteins begin to unwind the two strands of DNA
from one another. 3 Primers base-paired with the
exposed single DNA strands serve as initiation
sites for DNA synthesis. 4 Starting at primers,
DNA polymerases ( green boxes) assemble new
strands of DNA from nucleotides, using the parent
strands as templates. 5 DNA ligase seals any gaps
that remain between bases of the new DNA, so a
continuous strand forms. 6 Each parental DNA
strand ( blue ) serves as a template for assembly
of a new strand of DNA ( magenta ).
1
initiator proteins
topoisomerase
2
helicase
3
primer
4
DNA polymerase
5
DNA ligase
6
Figure 8-9 p140
62DNA Replicates Semiconservatively
- DNA replication begins with a short primera
starter strand. - The primer is complementary to the DNA template.
- Primasean enzymesynthesizes DNA one nucleotide
at a time. - Primase catalyzes the synthesis of a short RNA
(or DNA in some organisms ) segment called a
primer complementary to a DNA template. - Primase is important in DNA replication because
no known DNA polymerases can initiate the
synthesis of a DNA without an initial RNA or DNA
primer . - DNA polymerase adds nucleotides to the 3' end.
63- Topoisomerases are enzymes that regulate the
overwinding or underwinding of DNA. -
- As DNA Helicase moves along the DNA opening the
replication fork the DNA can become over twisted
or coiled preventing the further movement of the
enzyme. In order to help overcome this
topological problem caused by the double helix,
topoisomerases bind to either single-stranded or
double-stranded DNA and cuts the phosphate
backbone of the DNA. - This break allows the DNA to be untangled or
unwound, and, at the end of these processes, the
DNA backbone is resealed again.
64DNA Forms with a Primer
65DNA Replicates Semiconservatively
- DNA polymerases are larger than their substrates,
the dNTPs, and the template DNA. - The enzyme is shaped like an open right handthe
palm brings the active site and the substrates
into contact. - The fingers recognize the nucleotide bases.
66DNA Polymerase Binds to the Template Strand
67DNA Polymerase Binds to the Template Strand
68DNA Replicates Semiconservatively
- A single replication fork opens up in one
direction. - The two DNA strands are antiparallelthe 3' end
of one strand is paired with the 5' end of the
other. - DNA replicates in a 5'-to-3' direction.
69DNA Replicates Semiconservatively
- One new strand, the leading strand, is oriented
to grow at its 3' end as the fork opens. - The lagging strand is oriented so that its
exposed 3' end gets farther from the fork. - Synthesis of the lagging strand occurs in small,
discontinuous stretchesOkazaki fragments.
70DNA Replicates Semiconservatively
- Each Okazaki fragment requires its own primer,
synthesized by the primase. - DNA polymerase adds nucleotides to the 3' end,
until reaching the primer of the previous
fragment. - A different DNA polymerase then replaces the
primer with DNA. - The final phosphodiester linkage between
fragments is catalyzed by DNA ligase.
71The Lagging Strand Story (Part 1)
72The Lagging Strand Story (Part 2)
73The Lagging Strand Story (Part 3)
74DNA Replicates Semiconservatively
- DNA polymerase works very fast
- It is processiveit catalyzes many sequential
polymerization reactions each time it binds to
DNA - Okazaki fragments are added to RNA primers to
replicate the lagging strand. - When the last primer is removed no DNA synthesis
occurs because there is no 3' end to extenda
single-stranded bit of DNA is left at each end. - These are cut after replication and the
chromosome is slightly shortened after each cell
division.
75DNA Replicates Semiconservatively
- Telomeres are repetitive sequences at the ends of
eukaryotic chromosomes. - These repeats prevent the chromosome ends from
being joined together by the DNA repair system. - Telomerase contains an RNA sequenceit acts as a
template for telomeric DNA sequences. - Telomeric DNA is lost over time in most cells,
but not in continuously dividing cells like bone
marrow and gametes.
76Telomeres
- The DNA molecules in eukaryotic chromosomes are
linear i.e., have two ends. - The DNA molecule of a typical chromosome contains
a linear array of genes (encoding proteins and
RNAs) interspersed with noncoding DNA. - Included in the noncoding DNA are long stretches
that make up the centromere and stretches at the
ends of the chromosome, the telomeres. - Telomeres keep the ends of the chromosomes from
accidentally becoming attached to each other.
77Telomeres
- Replication of linear chromosomes results in a
special problem. - DNA polymerase can only synthesize a new strand
of DNA as it moves along the template strand in
the 3' gt 5' direction. This is fine for the 3'
gt 5' strand of a chromosome as the DNA
polymerase moves uninterrupted from an origin of
replication until it meets another bubble of
replication or the end of the chromosome. - Synthesis of the 5' gt 3' strand is
discontinuous. DNA polymerase synthesizes
sections of complementary strand (Okazaki
fragment) followed by a DNA ligase stitching the
Okazaki fragments together. - This continues until close to the end of the
chromosome where there is no longer enough
template to continue forming Okazaki fragments.
So the 5' end of each newly-synthesized strand
cannot be completed. Thus each of the daughter
chromosomes will have a shortened telomere. - It is estimated that human telomeres lose about
100 base pairs from their telomeric DNA at each
mitosis. At this rate, after 125 mitotic
divisions, the telomeres would be completely
gone. - Is this why normal somatic cells are limited in
the number of replications and thus cell
divisions.
78Telomeres and Telomerase (Part 1)
79DNA Replicates Semiconservatively
- DNA polymerases can make mistakes in replication,
but most errors are repaired. - Cells have two major repair mechanisms
- Proofreadingas DNA polymerase adds nucleotides,
it has a proofreading function and if bases are
paired incorrectly, the nucleotide is removed. - Mismatch repairafter replication other proteins
scan for mismatched bases missed in proofreading,
and replace them with correct ones.
80DNA Repair Mechanisms (Part 1)
81DNA Repair Mechanisms
- DNA repair mechanisms correct most replication
errors - DNA polymerases proofread DNA sequences during
DNA replication and repair damaged DNA - When proofreading and repair mechanisms fail, an
error becomes a mutation a permanent change in
the DNA sequence
82Mutations Are Heritable Changes in DNA
- Mutations are changes in the nucleotide sequence
of DNA that are passed on from one cell, or
organism, to another. - Mutations occur by a variety of processes.
- Errors that are not corrected by repair systems
are passed on to daughter cells.
83Mutations Are Heritable Changes in DNA
- Mutations are of two types
- Somatic mutations occur in somatic (body)
cellspassed on by mitosis but not to sexually
produced offspring. - Germ line mutations occur in germ line cells that
give rise to gametes. A gamete passes a mutation
on at fertilization.
84Mutations Are Heritable Changes in DNA
- Most genomes include genes and regions of DNA
that are not expressed - Genes are transcribed into RNAs, for translation
into amino acid sequences or into RNAs with
catalytic functions. - The coding regions of a gene contain sequences
within the transcribed region that are
translated. - Genomes also contain regions of DNA that are not
expressed.
85Mutations Are Heritable Changes in DNA
- At the molecular level there are two categories
of mutations - A point mutation results from the gain, loss, or
substitution of a single nucleotide. - Chromosomal mutations are more extensivethey may
change the position or cause a DNA segment to be
duplicated or lost.
86Mutations Are Heritable Changes in DNA
- Chromosomal mutations
- Deletionsresult in the removal of part of the
genetic material and can have severe or fatal
consequences. - Duplicationshomologous chromosomes break in
different places and recombine with wrong
partners one may have two copies of segment and
the other may have none
87Chromosomal Mutations
88Mutations Are Heritable Changes in DNA
- Chromosomal mutations
- Inversionsresult from breaking and rejoining,
but segment is flipped - Translocationssegment of DNA breaks off and is
inserted into another chromosome this can lead
to duplications and deletions
89Chromosomal Mutations
90Mutations Are Heritable Changes in DNA
- Mutations are caused in two ways
- Spontaneous mutations occur with no outside
influence, and are permanent. - Induced mutations are due to an outside agent, a
mutagen.
91Mutations Are Heritable Changes in DNA
- Induced mutationcaused by mutagens
- Chemicals can alter nucleotide bases (e.g.,
nitrous acid can cause deamination) - Some chemicals add other groups to bases (e.g.,
benzopyrene adds a group to guanine and prevents
base pairing). DNA polymerase will then add any
base there.
92Environmental Causes of Mutations
- Ionizing radiation (gamma rays, x-rays, most UV
light) - Knocks electrons out of atoms
- Breaks chromosomes into pieces that get lost
during DNA replication - Creates free radicals in tissues
- UV light (320-400 nm)
- Forms pyrimidine dimers that kink the DNA strand
- Causes skin cancer
93thymine dimer
An example of a pyrimidine dimer. This type of
DNA damage can be caused by exposure to light
with a wavelength shorter than about 400 nm.
Pyrimidine dimers result in mutations because
they interfere with DNA replication.
Figure 8-12 p142
94Environmental Causes of Mutations
- At least fifty-five carcinogenic (cancer-causing)
chemicals in tobacco smoke transfer small
hydrocarbon groups to the nucleotide bases in DNA - Many environmental pollutants are converted by
the body to other compounds that bind
irreversibly to DNA, causing replication errors
that lead to mutation
95- Mutations can have benefits
- Provide the raw material for evolution in the
form of genetic diversity - Diversity may benefit the organism immediatelyif
mutation is in somatic cells - May cause an advantageous change in offspring
96Animal Cloning
- Various reproductive interventions produce
genetically identical individuals
97Cloning
- Clones
- Exact copies of a molecule, cell, or individual
- Occur in nature by asexual reproduction or embryo
splitting (identical twins) - Reproductive cloning technologies produce an
exact copy (clone) of an individual
98What is cloning?
- Reproductive cloning technologies produce clones
genetically identical individuals - The DNA inside a living cell contains all the
information necessary to build a new individual - Somatic cell nuclear transfer (SCNT) is a
reproductive cloning technology in which nuclear
DNA of an adult donor is transferred to an egg
with no nucleus the hybrid cell develops into an
embryo that is genetically identical to the adult
donor - Therapeutic cloning uses SCNT to produce human
embryos for research
99Reproductive Cloning Technologies
- Somatic cell nuclear transfer (SCNT)
- Nuclear DNA of an adult is transferred to an
enucleated egg - Egg cytoplasm reprograms differentiated (adult)
DNA to act like undifferentiated (egg) DNA - The hybrid cell develops into an embryo that is
genetically identical to the donor individual
100Somatic Cell Nuclear Transfer (SCNT)
101A Clone Produced by SCNT
102Therapeutic Cloning
- Therapeutic cloning uses SCNT to produce human
embryos for research purposes - Researchers harvest undifferentiated (stem) cells
from the cloned human embryos - Such research may ultimately lead to treatments
for people who suffer from fatal diseases
103The Cloning Controversy
- Few cloned mammal embryos result in a live birth
many of the clones that survive have serious
health problems - One problem is, the DNA in adult cells is
controlled differently than the DNA in embryonic
cells - Perfecting methods for cloning animals brings us
closer to the possibility of cloning humans, both
technically and ethically