AP Bio Chapter 16

Transformation

a change in genotype and phenotype due to the assimilation of external DNA by a cell

Antiparallel

DNA's subunits run in opposite directions

Semiconservative

when a double helix replicates, each daughter molecule will have one old strand and one newly made strand

Replication bubble

it is where the DNA strands begin separating

Replication fork

a Y-shaped region where the parental strands of DNA are being unwound.

DNA ligase

joins the sugar-phosphate backbones of all the Okazaki fragments into a continuous strand

Leading strand

runs from the 5' to 3' direction

Lagging Strand

runs in the 3' to 5' direction

Griffith's experiment

He studied two strains of the bacterium Streptococcus pneumoniae. The S strain can cause pneumonia in mice; it is pathogenic because the cells have an outer capsule that protects them from an animal's immune system. Cellf of the R strain lack a capsule an

Chargaff

Chargaff analyzed the base composition of a number of different organisms. He reported that the base composition of DNA varies from one species to another. Chargaff's evidence of molecular diversity among species made DNA a more credible candidate for the

Hershey and Chase

Hershey and Chase used radioactive sulfur and phosphorus to trace the fates of protein and DNA, respectively, of T2 phages that infected bacterial cells. They wanted to see which of these molecules entered the cells and could reprogram them to make more p

What did Watson and Crick and Rosalind Franklin contribute to our knowledge of DNA?

Watson and Crick introduced an elegant double-helical model for the structure of deoxyribonucleic acid. Rosalind Franklin was an X-ray crystallographer, and she produced the X-ray diffraction photograph of DNA.

Compare and Contrast RNA and DNA

DNA has deoxyribose sugar, a thymine, and is a double helix. RNA has ribose sugar, uracil, and is single-stranded.

Which bases are purines

adenine and guanine

Which bases are pyrimidines?

uracil, cytosine, and thymine

In general, how do purines and pyrimidines vary in structure?

Purines have a double ring structure and pyrimidines have a single ring structure.

Adenine _____ bonds with thymine and cytosine ______ bonds with guanine.

double; triple

What type of bonds form between the bases?

hydrogen

What type of bonds form in the backbone?

covalent

Helicase

enzymes that untwist the double helix at the replication forks.

Single strand binding proteins

bind to and stabilize single-stranded DNA.

Topoisomerase

corrects "overwinding" ahead of replication forks by breaking, swiveling, and rejoining DNA strands.

What are two different functions of DNA polymerase?

DNA polymerase adds the nucleotides with the complementary bases to the 3' end of the DNA molecule and it proofreads newly made DNA, replacing any incorrect nucleotides.

What is mismatch repair?

repair enzymes correct errors in base pairing.

What is the function of a nuclease?

cuts out and replaces damaged stretches of DNA.

How does DNA polymerase play a role in proofreading and repair of DNA?

DNA polymerases proofread each nucleotide against its template as soon as it is covalently bonded to the growing strand. Upon finding an incorrectly paired nucleotide, the polymerase removes the nucleotide and then resumes synthesis.

What is the average number of errors in a completed DNA molecule.

The average number of errors in a completed DNA molecule is one in 1010 (10 billion) nucleotides.

What contributes to DNA damage?

exposure to harmful chemical or physical agents such as cigarette smoke and X-rays; it can also undergo spontaneous changes

What is the significance of mutations that are permanently found in daughter cells?

Mutations can change the phenotype of an organism. The vast majority of such changes either have no effect or are harmful, but a very small percentage can be beneficial. Mutations are the original source of the variation on which natural selection operate

Why are eukaryotes unable to complete the 5' ends of daughter cells? What is the consequence?

Eukaryotes are unable to complete the 5' ends of daughter strands because DNA polymerase can add nucleotides only to the 3' end of a preexisting polynucleotide. As a result, repeated rounds of replication produce shorter and shorter DNA molecules with sta

Why isn't the shortening of DNA molecules an issue in prokaryotes?

Prokaryotes have a circular chromosome, with no ends, so shortening of DNA does not occur.

Describe telomeres. Do telomeres contain genes?

Eukaryotic chromosomal DNA molecules have special nucleotide sequences called telomeres at their ends. Telomeres do not contain genes; instead, the DNA typically consists of multiple repetitions of one short nucleotide sequence.

Describe two factors associated with telomeres

They prevent the staggered ends of the daughter molecule from activating the cell's systems for monitoring DNA damage. Also, telomeric DNA acts as a kind of buffer zone that provides some protection against the organism's genes shortening.

Why is it believed that telomeres are associated with the aging process?

Telomeres become shorter in every round of replication, and the shortening is said to be connected to aging

Germ cells do not become shorter with each cell cycle. Germ cells are located in the testes in males and the ovaries of females and produce sperm and egg cells. How does the enzyme telomerase play a role in germ cells?

It catalyzes the lengthening of telomeres in eukaryotic germ cells, thus restoring their original length and compensating for the shortening that occurs during DNA replication. The activity of telomerase in germ cells results in telomeres of the maximum l

Why doesn't telomerase carry out the same process in somatic cells?

Telomerase is not active in most human somatic cells, but its activity varies from tissue to tissue

How can telomeres protect organisms from developing cancer?

limiting the number of divisions that somatic cells can undergo

How does cancer persist in spite of telomeres?

Telomerase activity is abnormally high in cancerous somatic cells, suggesting that its ability to stabilize telomere length may allow these cancer cells to persist.

Define chromatin. What is the length of an average double helix chromosome in a human?

Chromatin is a complex of DNA and protein. The length of an average double helix chromosome would be about four cm long.

DNA is able to fit into the nucleus due to chromatin packing. Describe chromatin packing.

The chromatin condenses in order to fit into the nucleus.

Histones

responsible for the first level of DNA packing in chromatin

Nucleosomes

the basic units of DNA packing

Looped domains

attached to a chromosome scaffold composed of proteins.

What is the width of one chromatin fiber. What is the width of one looped domain. What is the width of one chromatin?

The width of one chromatin fiber is 10 nm, the width of one looped domain is 300 nm, and the width of one chromatid is 700 nm.

Heterochromatin

remains highly compacted during interphase and is generally not transcribed

Euchromatin

a less condensed form of eukaryotic chromatin that is available for transcription

What are the two chemical components of chromosomes?

DNA and protein

Why did researchers originally think that protein was the genetic material?

Until the 1940s, the case for proteins seemed stronger, especially since biochemists had identified them as a class of macromolecules with great heterogeneity and specificity of function, essential requirements for the hereditary material. Moreover, littl

Distinguish between the virulent and nonvirulent strains of Streptococcus pneumoniae studied by Frederick Griffith.

The virulent (S) strains are pathogenic (disease-causing), whereas the nonvirulent (R) strains are non- pathogenic (harmless).

What was the purpose of Griffith's studies?

Griffith was attempting to develop a vaccine against pneumonia.

Define transformation

A change in genotype and phenotype due to the assimilation of external DNA by a cell. When the external DNA is from a member of a different species, transformation results in horizontal gene transfer.

What did Avery, McCarty, and MacLeod determine to be the transforming factor?

DNA

How does a bacteriophage destroy a bacterial cell? Look ahead to Chapter 19, Figure 19.5, to explain this.

The T4 phage uses its tail fibers to bind to specific receptor sites on the outer surface of an E. coli cell. The sheath of the tail contracts, injecting the phage DNA into the cell and leaving an empty capsid outside. The cell's DNA is hydrolyzed. The ph

How did Hershey and Chase "label" viral DNA and viral protein so that they could be distinguished? Explain why they chose each radioactive tag in light of the chemical composition of DNA and protein.

used radioactive isotopes of sulfur to tag protein in one batch of T2 and a radioactive isotope of phosphorus to tag DNA in a second batch. Because proteins, but not DNA, contain sulfur, radioactive sulfur atoms were incorporated only into the protein of

Describe the means by which Hershey and Chase established that only the DNA of a phage enters an E. coli cell. What conclusions did these scientists draw based on these observations?

DNA injected by the phage must be the molecule carrying genetic information that makes the less produce new viral DNA and proteins.

What are Chargaff's rules?

1. The base composition varies between species.
2. Within a species, the number of A and T bases are equal and the number of G and C bases are
equal.

List the three components of a nucleotide.

Phosphate, Sugar (deoxyribose), Nitrogenous base

Who are the two men who built the first molecular model of DNA and shared the 1962 Nobel Prize for discovery of its structure?

James Watson and Francis Crick

What was the role of Rosalind Franklin in the discovery of the double helix?

Rosalind Franklin, a very accomplished X-ray crystallographer, conducted critical experiments resulting in the photograph that allowed Watson and Crick to deduce the double-helical structure of DNA.

How did Watson and Crick's model explain the basis for Chargaff's rules?

The adenine equals the amount of thymine and the guanine equals the amount of cytosine.

Given that the DNA of a certain fly species consists of 27.3% adenine and 22.5% guanine, use Chargaff's rules to deduce the percentages of thymine and cytosine.

T=27.6%
C=22.5%

distance across molecule

1 nm

distance between nucleotides

.34 nm

distance between turns

3.4 nm

components of the backbone

phosphates and pentose

components of the rungs

nitrogenous bases

Explain what is meant by 5' and 3' ends of the nucleotide.

The two free ends of the polymer are distinctly different from each other. One end has a phosphate attached to a 5' carbon, and the other has a hydroxyl group on the 3' carbon. We refer to these as the 5' end and the 3' end respectively.

What do we mean when we say the two strands of DNA are antiparallel?

Their subunits run in opposite directions

Who performed the experiments that elucidated the correct mechanism of DNA replication?

Matthew Messelson and Franklin Stahl

How did Meselson and Stahl create "heavy" DNA for their experiments?

They added a heavy isotope of nitrogen, 15N

Use Figure 16.11 to explain how Meselson and Stahl confirmed the semiconservative mechanism of DNA replication.

Meselson and Stahl transferred their "heavy" DNA to a medium with a lighter isotope, 14N. A sample was taken after DNA replicated one; another sample was taken after DNA replicated again. They extracted DNA from the bacteria in the samples and then centri

Define origins of replication

Where the replication of a chromosome begins, consists of a specific sequence of nucleotides

What is the direction of synthesis of the new strand?

5' to 3'

What are Okazaki fragments? How are they welded together?

short segments of DNA synthesized away from the replication fork on a template strand during DNA replication. Many such segments are joined together by the enzyme DNA ligase to make up the lagging strand of newly synthesized DNA.

untwists and separates strands

helicases

holds DNA strands apart

single-strand binding proteins

synthesizes RNA primer

primase

adds DNA nucleotides to new strands

DNA polymerases

relieves strain caused by unwinding

topoisomerase

joins DNA fragments together

DNA ligase

removes RNA primer and replaces with DNA

DNA polymerases

Make a detailed list of the steps that occur in the synthesis of a new strand.

1. Helicase unwinds the parental double helix.
2. Molecules of single-stranded binding protein stabilize the unwound template strands.
3. The leading strand is synthesized continuously in the 5'3' direction by DNA polymerase III after being primed by prim

DNA polymerase

Fills the gap left after nuclease excises damaged segments of the DNA strand

Nuclease

DNA-cutting enzyme

Ligase

Joins the sugar-phosphate backbones of all the Okazaki fragments into a continuous DNA strand

DNA polymerase

Proofread and repair DNA

What is a thymine dimer?

A thymine dimmer is the covalent linking of thymine bases that are adjacent on a DNA strand, causing the DNA to buckle and interfere with DNA replication.

How is a thymine dimer repaired?

a nuclease enzyme cuts the damaged DNA strand, and the damaged section is removed. DNA polymerase fills in the missing nucleotides, and DNA ligase seals the free end of the new DNA to the old DNA, making the strand complete.

What did the specific base pairing suggest?

a possible copying mechanism for genetic material

Result of DNA replication

two identical daughter cells

How did Meselson and Stahl label the DNA?

The old strands-heavy isotopes of nitrogen
The new strands-lighter isotope of nitrogen

How many enzymes and proteins participate in DNA replication?

more than a dozen enzymes as well as other proteins

A replication bubble exposes

the bases on each side of the DNA

How long does it take E. coli to copy each of the 4.6 million nucleotide pairs in its single chromosome to form two identical daughter cells?

less than an hour

How long does it take for a human cell to copy its 6 billion nucleotide pairs and divide into daughter cells?

few hours

How many bubbles will eukaryotes typically have?

100's or even thousands

In which direction does replication proceed?

in both directions from each origin until the entire molecule is copied

Bacterial DNA in a single circular plasmid will only have

one replication bubble

What is the function of a primase?

can start an RNA chain from scratch and adds RNA nucleotides one at a time using the parental DNA as a template and synthesizes and adds the RNA primer to the DNA template

How long is an RNA primer

5-10 nucleotides long, 3' end is the start

Each nucleotide that is added to a growing DNA strand is a _____ _______.

nucleoside triphosphate

A nucleoside is a

base, sugar, and three phosphate groups

dATP supplies adenine to DNA and is similar to the ATP of energy metabolism. How does dATP differ from ATP?

dATP has deoxyribose while ATP has ribose.

Describe the process of replication along the leading strand

1. Only one sequence of RNA primer is needed
2. Then, DNA polymerase will add the nucleotides in a continuous manner.
3. A sliding clamp encircles the DNA and moves the polymerase along the template.

The lagging strand is synthesized as a series of short segments called Okazaki fragments, which are joined together by

DNA ligase

List the steps of replication along the lagging strand.

1. Primase brings in an RNA primer and joins the DNA template.
2. DNA polymerase adds DNA nucleotides to the primer at the DNA template, forming Okazaki fragment #1.
3. The process repeats itself many times. There are gaps between the fragments.
4.RNA pri

Mutations are the source of the ______ _______ upon which natural selection operates.

genetic variation

In his work with pneumonia-causing bacteria and mice, Griffith found that

some substance from pathogenic cells was transferred to nonpathogenic cells, making them pathogenic

What is the basis for the difference in how the leading and lagging strands of DNA molecules are synthesized?

DNA polymerase can join new nucleotides only to the 3' end of a pre-existing strand

The elongation of the leading stand during DNA synthesis

depends on the action of DNA polymerase

In a nucleosome, the DNA is wrapped around

histones

E. coli cells grown on 15N medium are transferred to 14N medium and allowed to grow for two more generations. DNA extracted from these cells are centrifuged. What density distribution would u expect in this experiment?

one low-density and one intermediate-density band

When she adds some of the DNA to the mixture, replication occurs, but each DNA molecule consists of a normal strand paired with numerous segments of DNA a few hundred nucleotides long. What has she probably left out of the mixture?

DNA ligase

The spontaneous loss of amino groups from adenine in DNA results in hypoxanthine, an uncommon base, opposite thymine. What combination of proteins could repair such damage.

nuclease, DNA polymerase, DNA ligase