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