AP Bio, Chapter Sixteen, The Molecular Basis of Inheritance

UNIT THREE: GENETICS Chapter Sixteen: The Molecular Basis of InheritanceChapter Sixteen: The Molecular Basis of InheritanceChapter Sixteen: The Molecular Basis of InheritanceChapter Sixteen: The Molecular Basis of Inheritance(Text from Biology, 6th Edition, by Campbell and Reece)

The Molecular Basis of Inheritance (Chapter Sixteen)

The Search for the Genetic Material Led to DNA

DNA and protein were candidates for genetic material. Until the

1940s, most thought proteins, as the workhorses of the cell,

seemed the most likely to be the hereditary material.

Additionally, there was little knowledge about nucleic acids,

whose physical and chemical properties seemed to uniform to

account for the numerous inherited traits exhibited by every

organism.

Evidence that DNA Can Transform Bacteria

Frederick Griffith, in his studies of

mammals, discovered the genetic role of DNA. There were two strains of the bacterium: a pathogenic

S strain and a harmless R strain. When the pathogenic cells were killed with heat, and then mixed with

the harmless strain, some of the living bacteria from the harmless strain were converted to the

Evidence that Viral DNA Can Program Cells

Viruses are DNA (or RNA) enclosed in a protective coat of protein. When Alfred Hershey and Martha

Chase studied a virus that infects bacteria, they were

the genetic material. Viruses that infect bacteria are called

experiment, they worked with the T2 phage that normally infects

bacteriophages were almost completely composed of DNA and protein and that the phage could turn

an E. coli cell into a factory for producing more phages.

Chapter Sixteen: The Molecular Basis of InheritanceChapter Sixteen: The Molecular Basis of InheritanceChapter Sixteen: The Molecular Basis of InheritanceChapter Sixteen: The Molecular Basis of Inheritance Edition, by Campbell and Reece)


DNA AS THE GENETIC MATERIAL

The Search for the Genetic Material Led to DNA

DNA and protein were candidates for genetic material. Until the

1940s, most thought proteins, as the workhorses of the cell,

eemed the most likely to be the hereditary material.

Additionally, there was little knowledge about nucleic acids,

whose physical and chemical properties seemed to uniform to

account for the numerous inherited traits exhibited by every

e that DNA Can Transform Bacteria

Frederick Griffith, in his studies of Streptococcus pneumonia, a bacterium that causes pneumonia in


ss R strain. When the pathogenic cells were killed with heat, and then mixed with


pathogenic form. This new trait was then inherited by all

descendants of the transformed bacteria. Thus, some chemical

component of the dead pathogenic cells caused this change. He

called the phenomenon transformationtransformationtransformationtransformation, which is now defined as a

change in genotype and phenotype due to the assimilation of

external DNA by a cell.

His work led to Oswald Avery searching for the identity of the

transforming substance. He purified various chemicals and tried to

transform live nonpathogenic bacteria with each chemical, with only

DNA working. When he and his colleagues announced DNA a

transforming agent, they were greeted with skepticism

Evidence that Viral DNA Can Program Cells


Chase studied a virus that infects bacteria, they were able to find additional evidence that DNA was

the genetic material. Viruses that infect bacteria are called bacteriophagesbacteriophagesbacteriophagesbacteriophages, or

experiment, they worked with the T2 phage that normally infects Escherichia coli

completely composed of DNA and protein and that the phage could turn

cell into a factory for producing more phages.

1


, a bacterium that causes pneumonia in


ss R strain. When the pathogenic cells were killed with heat, and then mixed with


pathogenic form. This new trait was then inherited by all

transformed bacteria. Thus, some chemical

component of the dead pathogenic cells caused this change. He

, which is now defined as a

change in genotype and phenotype due to the assimilation of

His work led to Oswald Avery searching for the identity of the

transforming substance. He purified various chemicals and tried to

transform live nonpathogenic bacteria with each chemical, with only

DNA working. When he and his colleagues announced DNA as the

transforming agent, they were greeted with skepticism.


able to find additional evidence that DNA was

, or phagesphagesphagesphages. In their

Escherichia coli. They knew that

completely composed of DNA and protein and that the phage could turn

UNIT THREE: GENETICS Chapter Sixteen: The Molecular Basis of InheritanceChapter Sixteen: The Molecular Basis of InheritanceChapter Sixteen: The Molecular Basis of InheritanceChapter Sixteen: The Molecular Basis of Inheritance(Text from Biology, 6th Edition, by Campbell and Reece)

to infect separate samples of E. coli

centrifuge to force the bacterial cells to form a pellet, but allowing free phages to rem

the liquid (supernatant). Radioactivity was then measured in the pellet and supernatant.

Hersey and Chase found that when the bacteria were infected with the phages containing

radioactively labeled protein, most of the radioactivity was f

phage protein did not enter the bacterial cells. However, when DNA was tagged with radioactive

phosphorus, most of the radioactivity was found in the pellet.

Their experiment showed that DNA was injected into the

information to make the cells produce new viral DNA and protein.

Additional Evidence that DNA is the Genetic Material of Cells

In eukaryotes, DNA is exactly doubled before mitosis, and then distributed equal

cells during mitosis. Additionally,

sets.

Erwin Chargaff was able to provide more evidence. At the time, scientists

were already aware that DNA was a polymer of nucleotides,

nitrogenous base, pentose sugar (deoxyribose), and a phosphate group. The

base could be either adenine (A), thymine (T), guanine (G), or cytosine (C).

Chargaff noticed that DNA composition is different depending on the species

of an organism. This molecular diversity made DNA a more credible

candidate for the genetic material. He also discovered that the number of

adenines approximately equals the number of thymines, and the number of

guanines approximately equaled the number of cytosine

C equalities later became known as


They used different radioactive isotopes

to tag phage DNA and protein. Since

protein contains sulfur, they grew

phages with radioactive sulfur, so that

the radioactive atoms would be

incorporated into the

a separate batch, phage DNA was

labeled with radioactive phosphorus and

protein was left unlabeled (DNA

unlabeled in first batch).

In each experiment, the protein

and DNA-labeled batches were allowed

E. coli cells. After being infected, the cultures were agitated in a

centrifuge to force the bacterial cells to form a pellet, but allowing free phages to rem



radioactively labeled protein, most of the radioactivity was found in the supernatant


phosphorus, most of the radioactivity was found in the pellet.

Their experiment showed that DNA was injected into the host cell during infection, providing genetic

information to make the cells produce new viral DNA and protein.

Additional Evidence that DNA is the Genetic Material of Cells

In eukaryotes, DNA is exactly doubled before mitosis, and then distributed equal

cells during mitosis. Additionally, diploid sets of chromosomes have twice as much DNA as haploid

Erwin Chargaff was able to provide more evidence. At the time, scientists

were already aware that DNA was a polymer of nucleotides, containing a

nitrogenous base, pentose sugar (deoxyribose), and a phosphate group. The

base could be either adenine (A), thymine (T), guanine (G), or cytosine (C).

Chargaff noticed that DNA composition is different depending on the species

m. This molecular diversity made DNA a more credible

candidate for the genetic material. He also discovered that the number of

adenines approximately equals the number of thymines, and the number of

guanines approximately equaled the number of cytosines. The A = T and G =

C equalities later became known as Chargaff’s rules.

2

They used different radioactive isotopes

to tag phage DNA and protein. Since

protein contains sulfur, they grew

phages with radioactive sulfur, so that

the radioactive atoms would be

incorporated into the phage protein. In

a separate batch, phage DNA was

labeled with radioactive phosphorus and

protein was left unlabeled (DNA

unlabeled in first batch).

periment, the protein-labeled

labeled batches were allowed

cells. After being infected, the cultures were agitated in a

centrifuge to force the bacterial cells to form a pellet, but allowing free phages to remain suspended in



ound in the supernatant – indicating that


host cell during infection, providing genetic

In eukaryotes, DNA is exactly doubled before mitosis, and then distributed equally to two daughter

diploid sets of chromosomes have twice as much DNA as haploid

3 UNIT THREE: GENETICS Chapter Sixteen: The Molecular Basis of InheritanceChapter Sixteen: The Molecular Basis of InheritanceChapter Sixteen: The Molecular Basis of InheritanceChapter Sixteen: The Molecular Basis of Inheritance (Text from Biology, 6th Edition, by Campbell and Reece) Watson and Crick Discovered the Double Helix by Building Models To Conform to X-Ray Data

After most biologists were convinced of DNA’s identity as the

genetic material, scientists began to focus on discovering its

three-dimensional structure. James Watson and Francis Crick

were able to discover that DNA was in the shape of a double helix

after viewing X-ray diffraction images of DNA, as produced by

Rosalind Franklin. Since Watson was familiar with the types of

patterns helical molecules produce, looking at Franklin’s

diffraction photo allowed him to figure out the width of the helix

and spacing of the nitrogenous bases. The width of the helix

showed that it was made out of two strands – a double helixdouble helixdouble helixdouble helix.

Watson and Crick began building models of a double helix that

would conform to the X-ray diffraction images. They established

that the sugar-phosphate chains were on the outside of the

molecule, with the nitrogenous bases swiveling in the interior of

the double helix. The helix makes one full turn every 3.4 nm along

its length, with the bases stacked .34 nm apart (ten layers per

turn of the helix).

Adenine is always paired with thymine, and cytosine is always

paired with guanine. Since the double helix had a uniform

diameter, a purine must pair with a pyrimidine. Adenine and

guanine are purines, nitrogenous bases with two organic rings.

Thymine and guanine are pyrimidines, which have a single ring.

Watson and Crick also noticed that each base has chemical

side groups form hydrogen bonds with its partner. Guanine

forms three hydrogen bonds with cytosine, and adenine forms

two hydrogen bonds with thymine.

This model explained Chargaff’s rules. Since A was always

paired with T, and C with G, there would be equivalent

amounts of A and T, C and G in any DNA. Since the linear

sequence of the four can be varied in countless ways, each

gene has a unique order.

4 UNIT THREE: GENETICS Chapter Sixteen: The Molecular Basis of InheritanceChapter Sixteen: The Molecular Basis of InheritanceChapter Sixteen: The Molecular Basis of InheritanceChapter Sixteen: The Molecular Basis of Inheritance (Text from Biology, 6th Edition, by Campbell and Reece)

DNA REPLICATION AND REPAIR

During DNA Replication, Base Pairing Enables Existing DNA Strands to Serve as Templates for New

Complementary Strands

Watson and Crick believed that the model for DNA

was a pair of complementary templates. Prior to

duplication, the hydrogen bonds would unwind and

allow each chain to act as a template for the

formation of two new companion chains. By

referring to the base-pairing rules, it is possible to

construct a new pair of chains from just one strand.

Their model predicts that when a double helix

replicates, each of the two daughter molecules will

have one strand – one from the parent molecule

and one brand new strand. This semiconservative semiconservative semiconservative semiconservative

model model model model can be distinguished from a conservative

model, in which the parent molecule emerges

intact. In the dispersive model, all four strands of

DNA have a mixture of old and new DNA.

In the late 1950s, Meselson and Stahl devised

experiments to test the three models. Their

experiments supported the semiconservative model.

A Large Team of Enzymes and Other Proteins Carries Out DNA Replication

Getting Started: Origins of Replication

Replication of a DNA molecule begins at origins of replicationsorigins of replicationsorigins of replicationsorigins of replications. In the circular bacterial chromosome,

there is a single origin. Proteins that initiate DNA replication recognize a special sequence marking the

origin and attach to the DNA to separate the two strands and form a replication “bubble.” Replication

then proceeds in both directions until the entire molecule is copied.

In a eukaryotic chromosome, there can be thousands of replication origins. Individual bubbles form and

eventually fuse, which speeds up replication of very long DNA molecules. At the end of each

replication bubble is a replication forkreplication forkreplication forkreplication fork, a Y-shaped region where the new strands of DNA are

elongating.

UNIT THREE: GENETICS Chapter Sixteen: The Molecular Basis of InheritanceChapter Sixteen: The Molecular Basis of InheritanceChapter Sixteen: The Molecular Basis of InheritanceChapter Sixteen: The Molecular Basis of Inheritance(Text from Biology, 6th Edition, by Campbell and Reece) Elongating a New DNA Strand

Elongation of new DNA at a replication fork is catalyzed by

enzymes called DNA polymerasesDNA polymerasesDNA polymerasesDNA polymerases

complementary bases, polymerase adds them on to the growing

end of the new DNA strand.

Nucleotides that serve as substrates for DNA polymerase are

actually nucleoside triphosphates

groups, much like ATP. However, the nucleoside triphosphate has a sugar component (deoxyribose in

DNA and ribose in RNA). These monomers are chemically reactive because of their phosphate tails

negative charge. When each monomer joins the growing end of a DNA strand, it loses two phosphate

groups as a molecule of pyrophosphate

The Antiparallel Arrangement of the DNA Strands

The two DNA strands are antiparallel

carbons of a deoxyribose sugar are numbered from 1’ to 5’, with the phosphate group

attached to the 5’ end, the 3’ end is attached to another nucleotide’s phosphate group,

and the 1’ carbon is bonded to the nitrogenous base. At a DNA

group attached to the 3’ carbon of the ending deoxyribose. At the 5’ carbon of the last nucleotide,

there is a phosphate group.

One strand runs in the 5’ → 3’ end, while the other runs counter to the 5’

polymerases can only add nucleotides to the free 3’ end of an existing DNA strand

can only elongate in the 5’ → 3’ direction. Along one strand of DNA, the

polymerase can just continue adding nucleotid


at a replication fork is catalyzed by

DNA polymerasesDNA polymerasesDNA polymerasesDNA polymerases. As the nucleotides align with

complementary bases, polymerase adds them on to the growing

Nucleotides that serve as substrates for DNA polymerase are

ly nucleoside triphosphates – they contain three phosphate


DNA and ribose in RNA). These monomers are chemically reactive because of their phosphate tails


groups as a molecule of pyrophosphate .

The Antiparallel Arrangement of the DNA Strands

antiparallel, meaning they run in opposite directions.



and the 1’ carbon is bonded to the nitrogenous base. At a DNA strand’s 3’ end, there is a hydroxyl (OH)


3’ end, while the other runs counter to the 5’ → 3’ direc

polymerases can only add nucleotides to the free 3’ end of an existing DNA strand

3’ direction. Along one strand of DNA, the leading strandleading strandleading strandleading strand

polymerase can just continue adding nucleotides as the replication fork opens up.

To elongate the other strand of DNA, polymerase

must work in the direction away

fork – this strand is referred to as the

As a replication bubble opens, a polymerase molecule

must work away from the fork and synthesize a short

segment of DNA. As the fork continues to open, it

can go back to the fork and make another short

segment. These series of segments are called Okazaki

fragments and are about 100 to 200 nucleotides long

in eukaryotes. Another enzyme,

the sugar-phosphate backbones of the Okazaki

fragments to create a single DNA strand.

5


DNA and ribose in RNA). These monomers are chemically reactive because of their phosphate tails’


irections. The five



strand’s 3’ end, there is a hydroxyl (OH)


3’ direction. Since DNA

polymerases can only add nucleotides to the free 3’ end of an existing DNA strand, a new DNA strand

leading strandleading strandleading strandleading strand, DNA

es as the replication fork opens up.

To elongate the other strand of DNA, polymerase

away from the replication

this strand is referred to as the lagging strandlagging strandlagging strandlagging strand.

As a replication bubble opens, a polymerase molecule

ork away from the fork and synthesize a short

segment of DNA. As the fork continues to open, it

can go back to the fork and make another short

segment. These series of segments are called Okazaki

fragments and are about 100 to 200 nucleotides long

aryotes. Another enzyme, DNA ligaseDNA ligaseDNA ligaseDNA ligase, joins

phosphate backbones of the Okazaki

fragments to create a single DNA strand.

6 UNIT THREE: GENETICS Chapter Sixteen: The Molecular Basis of InheritanceChapter Sixteen: The Molecular Basis of InheritanceChapter Sixteen: The Molecular Basis of InheritanceChapter Sixteen: The Molecular Basis of Inheritance (Text from Biology, 6th Edition, by Campbell and Reece)

Priming DNA Synthesis

DNA polymerase cannot immediately start synthesis of a new strand – it can only add nucleotides to

the end of an already existing chain that is base-paired with the template strand. As a result, an

enzyme called primaseprimaseprimaseprimase joins together RNA nucleotides to make a primerprimerprimerprimer, a short strip of 10

nucleotides that attaches to the parental DNA. DNA polymerase can then continue adding

nucleotides as normal. Another DNA polymerase will replace the RNA primer with DNA. For the

lagging strand, primers are required for each Okazaki fragment.

Other Proteins Assisting DNA Replication

HelicaseHelicaseHelicaseHelicase is an enzyme that untwists the double helix at the replication fork, separating the two old

strands. Molecules of singlesinglesinglesingle----strand binding proteinstrand binding proteinstrand binding proteinstrand binding protein then line up along the unpaired DNA strands to

hold them apart.

The DNA Replication Machine as a Stationary Complex

While DNA polymerase molecules are represented as moving along the DNA, this model is inaccurate.

The various proteins participating in replication actually form a single large complex that is stationary

during the replication process. The multiple copies of the machine are anchored to the nuclear matrix.

The DNA is what really moves through the replication machinery.

Enzymes Proofread DNA During Its Replication And Repair Damage in Existing DNA

During DNA replication, DNA polymerase proofreads each nucleotide as soon as it is added to the

growing strand. If it finds a mistake, it will remove the nucleotide and then resume synthesis.

Mismatched nucleotides are sometimes missed by DNA polymerase or arise after DNA synthesis is

completed. In mmmmiiiissssmmmmaaaattttcccchhhh rrrreeeeppppaaaaiiiirrrr, cells use special enzymes to fix incorrectly paired nucleotides. The

importance of such proteins was shown when researchers found that a hereditary defect in one of the

proteins is associated with a form of colon cancer. The defect allows cancer-causing errors to

accumulate in the DNA.

DNA molecules are constantly subjected to potentially harmful chemical and physical agents. For

example, reactive chemicals, radioactive emissions, X-rays, and ultraviolet light can change

nucleotides in ways that affect encoded genetic information. DNA bases often undergo spontaneous

chemical changes. Each cell continuously monitors and repairs its genetic material to correct such

changes.

Most mechanisms for repairing DNA depend on the base-paired structure of DNA. Usually, a segment

of the strand containing the damage is cut out by a DNA-cutting enzyme, nnnnuuuucccclllleeeeaaaasssseeee, and the resulting

gap is filled in with the correct nucleotides. The enzymes involved in filling the gap are a DNA

polymerase and ligase. This type of DNA repair is called nnnnuuuucccclllleeeeoooottttiiiiddddeeee eeeexxxxcccciiiissssiiiioooonnnn rrrreeeeppppaaaaiiiirrrr.

7 UNIT THREE: GENETICS Chapter Sixteen: The Molecular Basis of InheritanceChapter Sixteen: The Molecular Basis of InheritanceChapter Sixteen: The Molecular Basis of InheritanceChapter Sixteen: The Molecular Basis of Inheritance (Text from Biology, 6th Edition, by Campbell and Reece) The Ends of DNA Molecules Are Replicated By a Special Mechanism

For linear DNA, there is a potential problem resulting from the fact that a DNA polymerase can only

add nucleotides to the 3’ end of a preexisting polynucleotide. There is now way to complete the 5’

ends of daughter DNA strands. Repeated rounds of replication continually shorten the DNA molecules.

To solve this problem, eukaryotic chromosomal DNA molecules have special nucleotide sequences

called tttteeeelllloooommmmeeeerrrreeeessss at their ends. Instead of containing genes, they consist of multiple repetitions of one

short nucleotide sequence. The number of repetitions varies between 100 and 1,000. Telomeric DNA

protects the organism’s genes from being eroded.

Since eukaryotic organisms need a way of restoring their telomeres, the enzyme tttteeeelllloooommmmeeeerrrraaaasssseeee catalyzes

the lengthening of telomeres. It has a short molecule of RNA along with its protein, that RNA contains

a nucleotide sequence serving as the template for new telomere segments. Telomerase and DNA

polymerase can then work together to lengthen telomeres.

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AP Bio, Chapter Sixteen, The Molecular Basis of Inheritance