1. Chapter 8 DNA Structure and Function

2. 8.1 A Hero Dog’s Golden Clones
James Symington and his search dog Trakr located the last living survivor of the 9/11 attack on the World Trade Center
Trakr later died of a degenerative neurological disease, probably due to toxic smoke exposure at Ground Zero
Trakr’s DNA lives on in his clones – genetic copies produced by inserting his DNA into donor eggs

3. The Cloning Controversy
Few cloned mammal embryos result in a live birth – many of the clones that survive have serious health problems
The problem: 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

4. 8.2 The Discovery of DNA’s Function
1869: Johannes Miescher found DNA (deoxyribonucleic acid) in nuclei, though its function was unknown
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
Mike 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

5. Griffith’s Experiments
Figure 8.3 Fred Griffith’s experiments with two strains (R and S) of Streptococcus pneumoniae bacteria.
A Griffith’s first experiment showed that R cells were harmless. When injected into mice, the bacteria multiplied, but the mice remained healthy.
B The second experiment showed that an injection of S cells caused mice to develop fatal pneumonia. Their blood contained live S cells.
C For a third experiment, Griffith killed S cells with heat before injecting them into mice. The mice remained healthy, indicating that the heat-killed S cells were harmless.
D In his fourth experiment, Griffith injected a mixture of heat-killed S cells and live R cells. To his surprise, the mice became fatally ill, and their blood contained live S cells. A B C D

6. Avery and McCarty Find the Transforming Principle
1940: Avery and McCarty separated deadly S cells (from Griffith’s 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”

7. Confirmation of DNA’s 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

8. Bacteriophages DNA inside protein coat tail fiber hollow sheath
Figure 8.4 The Hershey–Chase experiments. Alfred Hershey and Martha Chase carried out experiments to determine the composition of the hereditary material that bacteriophage inject into bacteria. The experiments were based on the knowledge that proteins contain more sulfur (S) than phosphorus (P), and DNA contains more phosphorus than sulfur.
A Left, a model of a bacteriophage. Right, micrograph of three viruses injecting DNA into an E. coli cell.

9. DNA being injected into bacterium
Virus particle coat proteins labeled with 35S
35S remains
outside cells
Labeled DNA being injected into bacterium
Virus DNA labeled with 32P
32P remains inside cells
Figure 8.4 The Hershey–Chase experiments. Alfred Hershey and Martha Chase carried out experiments to determine the composition of the hereditary material that bacteriophage inject into bacteria. The experiments were based on the knowledge that proteins contain more sulfur (S) than phosphorus (P), and DNA contains more phosphorus than sulfur.
B In one experiment, bacteriophage were labeled with a radioisotope of sulfur (35S), a process that makes their protein components radioactive. The labeled viruses were mixed with bacteria long enough for infection to occur, and then the mixture was whirled in a kitchen blender. Blending dislodged viral parts that remained on the outside of the bacteria. Afterwards, most of the radioactive sulfur was detected outside the bacterial cells. The viruses had not injected protein into the bacteria.
C In another experiment, bacteriophage were labeled with a radioisotope of phosphorus (32P), which makes their DNA radioactive. The labeled viruses were allowed to infect bacteria. After the external viral parts were dislodged from the bacteria, the radioactive phosphorus was detected mainly inside the bacterial cells. The viruses had injected DNA into the cells—evidence that DNA is the genetic material of this virus.
Stepped Art
Figure 8-6 p137

10. The Hershey–Chase Experiments
35S remains outside cells
Virus particle coat proteins
labeled with 35S DNA being
injected into
bacterium
Virus DNA
Figure 8.4 The Hershey–Chase experiments. Alfred Hershey and Martha Chase carried out experiments to determine the composition of the hereditary material that bacteriophage inject into bacteria. The experiments were based on the knowledge that proteins contain more sulfur (S) than phosphorus (P), and DNA contains more phosphorus than sulfur.
labeled with 32P
32P remains inside cells
Labeled DNA being injected into bacterium

11. 8.4 The Discovery of DNA’s Structure
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

12. Four Kinds of Nucleotides in DNA
ADENINE (A)
deoxyadenosine triphosphate
GUANINE (G)
deoxyguanosine triphosphate HC
BASE SUGAR
THYMINE (T)
deoxythymidine triphosphate
CYTOSINE (C)
deoxycytidine triphosphate
Figue 8.5 The four nucleotides in DNA. Each has three phosphate groups, a deoxyribose sugar (orange), and a nitrogen-containing base (blue) after which it is named. Adenine and guanine bases are purines; thymine and cytosine, pyrimidines. Biochemist Phoebus Levene identified the structure of these bases and how they are connected in nucleotides in the early 1900s. Levene worked with DNA for almost 40 years.

13. Chargaff’s Rules
The amounts of thymine and adenine in DNA are the same, and the amounts of cytosine and guanine are the same
A = T
G = C
The proportion of adenine and guanine differs among species

14. Franklin, Watson, and Crick
Rosalind Franklin’s 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

15. Watson and Crick’s 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)
Insert image left column page 137

16. 0.34 nanometer between each base pair
2-nanometer diameter
3.4-nanometer length of each full twist of the double helix
Figure 8.7 Double helix structure of DNA, as illustrated by a composite of different models. Numbering carbons in the deoxyribose sugars (see Figure 8.5) allows us to keep track of the orientation of each DNA strand. This orientation is important in DNA replication.

17. 8.4 Eukaryotic 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 cell’s genetic information

18. Chromosome Organization
During most of the cell’s life, each chromosome consists of one DNA strand
When the cell prepares to divide, it duplicates all of its chromosomes, so that both offspring receive a full set
Each duplicated chromosome
Has two DNA strands (sister chromatids) attached to one another at the centromere
Consists of two long filaments bunched into a characteristic X shape

19. Chromosomes and Chromatids
DNA inside protein coat
centromere
one chromatid
tail fiber
hollow sheath
a chromosome (unduplicated)
a chromosome (duplicated)
Figure on page 138, right-hand column

20. Chromosome Structure
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
The DNA molecule consists of two strands twisted into a double helix

21. Chromosome Structure – Illustrated
DNA inside protein coat
Two strands of DNA twist into a double helix.
At regular intervals, the DNA (blue) wraps around a core of histone proteins (purple).
The DNA and proteins associated with it twist tightly into a fiber.
The fiber coils and then coils again to form a hollow cylinder.
At its most condensed, a duplicated chromosome has an X shape.
The DNA in the nucleus of a eukaryotic cell
is typically divided into a number of chromosomes.
Figure 8.8 Chromosome structure
1 Two strands of DNA twist into a double helix.
2 At regular intervals, the DNA (blue) wraps around a core of histone proteins (purple).
3 The DNA and proteins associated with it twist tightly into a fiber.
4 The fiber coils and then coils again to form a hollow cylinder.
5 At its most condensed, a duplicated chromosome has an X shape.
6 The DNA in the nucleus of a eukaryotic cell is typically divided into a number of chromosomes.

22. Chromosome Packing DNA inside protein coat
Figure 8.9 Chromosome packing. Left, beads-on-a string appearance of DNA–histone spools. Middle, coiled coils of a DNA fiber. Right, a duplicated chromosome just before cell division.
Andrew Syred/Science Source.

23. Chromosome Number
The total number of chromosomes in a eukaryotic cell (chromosome number) is characteristic of the species
Human body cells have:
Forty-six chromosomes
Two of each type of chromosome – so their chromosome number is diploid (2n)
A karyotype shows how many chromosomes are in an individual cell, and reveals major structural abnormalities

24. Karyotypes DNA inside protein coat Figure 8.10 Karyotypes
A Karyotype of a female human, with identical sex chromosomes (XX)

25. Autosomes and Sex Chromosomes
In a diploid organism, one chromosome in a pair is inherited from the mother and one from the father
All except one pair of chromosomes are autosomes – 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)

26. 8.5 DNA 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

27. Replication of the DNA Sequence
A cell’s 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

28. Enzymes 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

29. Primers for DNA Polymerase
Several types of DNA polymerases exist
Each requires a primer to initiate DNA synthesis
A primer is a short, single strand of DNA or RNA that is complementary to a targeted DNA sequence
Insert image middle right column, page 140

30. Semiconservative 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)

31. 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.
Enzymes recruited by the initiator proteins begin to unwind the two strands of DNA from one another.
Primers base-paired with the exposed single DNA strands serve as initiation sites for DNA synthesis.
Starting at primers, DNA polymerases (green boxes) assemble new strands of DNA from nucleotides, using the parent strands as templates.
DNA ligase seals any gaps that remain between bases of the “new” DNA, so a continuous strand forms.
Each parental DNA strand (blue) serves as a template for assembly of a new strand of DNA (magenta). Both strands of the double helix serve as templates, so two double- stranded DNA molecules result. One strand of each is parental (old), and the other is new, so DNA replication is said to be semiconservative.
initiator proteins
Topoisomerase
(untwists the double helix) 2
Helicase
(breaks hydro gen bonds between bases) 3 4
primer
DNA polymerase 5
Figure 8.11 DNA replication, in which a double-stranded molecule of DNA is copied in its entirety. 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.
nucleotide 6
DNA ligase

32. Discontinuous Replication
DNA polymerases attach a free nucleotide only to the 3′ end of a DNA strand
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

33. Discontinuous Replication
unwinding
A During DNA synthesis, only one of the two new strands can be assembled in a single piece. The other strand forms in short segments, which are called Okazaki fragments after the two scientists who discovered them. DNA ligase joins Okazaki fragments where they meet.
DNA inside protein coat
B DNA synthesis proceeds only in the 5′ to 3′ direction because DNA polymerase catalyzes only one reaction: the formation of a bond between the 3′ carbon on the end of a DNA strand and the phosphate on a nucleotide’s 5′ carbon.
Figure 8.12 Discontinuous synthesis of DNA. This close-up of a replication fork shows that only one new DNA strand is assembled continuously.

34. 8.6 Mutations: Cause and Effect
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

35. Electromagnetic Agents of DNA Damage
Ionizing radiation (gamma rays, X-rays, most UV light)
Knocks electrons out of atoms
Breaks chromosomes into pieces that may get lost
Creates free radicals in tissues
UV light ( nm)
Forms pyrimidine dimers that kink DNA strands
Causes skin cancer

36. Chemical Agents of DNA Damage
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

37. Rosalind Franklin, X-Rays, and Cancer
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, Crick, and Wilkins
Franklin died of cancer at age 37, probably caused by extensive exposure to x-rays during her work

38. 8.7 Cloning Adult Animals Clones
Exact copies of a molecule, cell, or individual
Occur in nature by asexual reproduction or embryo splitting (identical twins)
As cells develop, they become differentiated
Different in form and function
Usually a one-way process in animal cells
Reproductive cloning technologies produce an exact copy (clone) of an individual

39. Cloning in the Laboratory
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

40. Somatic Cell Nuclear Transfer (SCNT)
A A cow’s egg is held in place by suction through a hollow glass tube called a micropipette. DNA is
identified by a purple stain.
D The micropipette
enters the egg and delivers the skin cell to a region between the cytoplasm and the plasma membrane.
E After the pipette is withdrawn, the donor’s skin cell is visible next to the cytoplasm of the egg. The transfer is now complete.
B Another micropipette punctures the egg and sucks out the DNA. All that remains inside the egg’s plasma membrane is cytoplasm.
Figure 8.15 Somatic cell nuclear transfer, using cattle cells. This series of micrographs was taken by scientists at Cyagra, a company that specializes in cloning livestock.
F An electric current causes the foreign cell to fuse with and deposit its nucleus into the cytoplasm of the egg. The egg begins to divide, and an embryo forms.
C A new micropipette pre- pares to enter the egg at the puncture site. The pipette contains a cell grown from the skin of a donor animal.

41. Therapeutic 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

42. Points to Ponder
One of the problems consistently encountered with cloned organisms is their rapidly declining health. Why do you think this is happening?
What are some reasons DNA is double-stranded instead of single-stranded?
What are some advantages of semiconservative replication?