Chapter 12-DNA: The Carrier of Genetic Information

Question 1

Griffeth’s transformation experiment

Answer 1

Frederick Griffeth conducted an experiment with mice where he injected them with smooth and rough cells of a virus. The smooth cells killed mice, the heat-killed smooth cells didn’t do anything and neither did the rough cells but when he injected rough cells AND heat killed smooth cells the mouse died which showed that cells can transform by transferring their genetic material which is contained within a substance.

Question 2

Avery and MacLeod

Answer 2

Oswald Avery and Colin MacLeod chemically identified Griffeth’s “transforming principle” as DNA

Question 3

the Hershey-Chase experiment

Answer 3

Alfred Hershey and Martha Chase conducted an experiment involving bacteriophages depositing their genetic material into bacterial cells, they ended up discovering that DNA, not proteins, is involved in viral reproduction and is the carrier of genetic material.

Question 4

Rosalind Franklin

Answer 4

produced the X-ray diffraction images of DNA that Watson and Crick used as a guide when completing their discoveries of the molecular structure of DNA which they received a Nobel Prize for after Franklin died (which is why she didn’t receive the prize as well), she produced the X-ray diffraction images by shining a beam of X-rays through a DNA sample onto a photographic plate which showed the atomic array of the DNA and produced the image, being exposed to these rays ultimately played a role in her early death

Question 5

Watson and Crick

Answer 5

proposed a model of the structure of DNA; this contribution is widely considered to be the start of a revolution in molecular biology that continues to the present, they were awarded a Nobel Prize in Medicine for their discoveries about the molecular structure of nucleic acids as well

Question 6

Meselson and Stahl

Answer 6

Matthew Meselson and Franklin Stahl demonstrated that DNA replication is semiconservative

Question 7

Chargaff

Answer 7

Erwin Chargaff discovered the relationships among DNA bases that provided a clue to the structure of DNA (he discovered that the ratio of purines/pyrimidines were equal as well as the ratio of guanine to cytosine)

Question 8

what is DNA made up of?

Answer 8

each DNA building block is a nucleotide consisting of deoxyribose, a phosphate, and one of four nitrogenous bases (A,T, C, G)

Question 9

Which nucleotides are pyrimidines? Which are purines?

Answer 9

pyrimidines: cytosine (C) and thymine (T); purines: guanine (G), adenine (A)

Question 10

what are Chargaff’s rules?

Answer 10

the number of adenines in a DNA strand equals the number of thymines, and the number of guanines equals the number of cytosines

Question 11

If DNA is like a ladder, what would be considered the rungs? The rails?

Answer 11

the rungs of the ladder would be the nucleotide bases and the sugar-phosphate backbone would be the “rails”

Question 12

What does it mean that the DNA strands run antiparallel?

Answer 12

it means that they run in opposite directions; 5’ to 3’ on one strand and 3’ to 5’ on the other

Question 13

how many hydrogen bonds form between adenine and thymine? cytosine and guanine?

Answer 13

A&T: 2 hydrogen bonds, C&G: 3 hydrogen bonds

Question 14

Why do adenine and thymine only pair with each other and cytosine and guanine stick together?

Answer 14

because 1) a purine and pyrimidine have to be paired with each other rather than two purines or two pyrimidines because if two purines were paired the width of the helix would be too wide and if two pyrimidines paired with each other the width would be too narrow; 2) adenine can pair with thymine (and guanine with cytosine) in such a way that hydrogen bonds form between them, in opposite combinations, cytosine with adenine and guanine with thymine, do not lead to favorably hydrogen bonding

Question 15

Describe how the two strands of DNA are oriented with respect to each other.

Answer 15

Each DNA molecule consists of two polynucleotide chains that associate as a double helix. The two chains are antiparallel (running in opposite directions); at each end of the DNA molecule, one chain has a phosphate attached to a 5’ deoxyribose carbon, the 5’ end, and the other has a hydroxyl group attached to a 3’ deoxyribose carbon, the 3’ end.

Question 16

State the base pairing rules for DNA and describe how complementary bases bind to each other.

Answer 16

Hydrogen bonding between specific base pairs holds together the two chains of the helix. Adenine (A) forms two hydrogen bonds with thymine (T); guanine (G) forms three hydrogen bonds with cytosine (C). Complementary base pairing between A and T and between G and C is the bases of Chargaff’s rules, which state that A equals T and that G equals C. Because complementary base pairing holds together the two strands of DNA, it is possible to predict the base sequence of one strand if you know the base sequence of the other strand.

Question 17

What is the central dogma?

Answer 17

the central dogma is the flow of information: DNA is transcribed into RNA which is translated into a protein

Question 18

What did T.H. Morgan’s work show?

Answer 18

that chromosomes are key in passing information and that chromosomes are made of DNA and protein

Question 19

DNA Replication

Answer 19

the process by which DNA is duplicated; ordinaily a semiconservative process in which a double helix gives rise to two double helices, each with an “old” strand and a newly synthesized strand

Question 20

semiconservative replication

Answer 20

when each daughter double helix consists of an original strand from the parent molecule and a newly synthesized complementary strand

Question 21

Discuss evidence from Meselson and Stahl’s experiment that enabled scientists to differentiate between semiconservative replication of DNA and alternative models.

Answer 21

When E. Coli cells are grown for many generations in a medium containing heavy nitrogen (15N), they incorporate the 15N into their DNA. When researchers transfer cells from a 15N medium to a 14N medium and isolate them after either one or two generations, the density of the DNA in each group is what would be expected if DNA replication were semiconservative.

Question 22

conservative replication

Answer 22

a theory that when DNA was replicated, both parent (or old) strands would remain together, and the two newly synthesized strands would form a second double helix

Question 23

dispersive replication

Answer 23

a hypothesis where the parental and newly synthesized strands might become randomly mixed during the replication process of DNA

Question 24

origins of replication

Answer 24

specific sites on the DNA molecule where DNA replication begins, small sections of the double helix unwind here

Question 25

DNA helicases

Answer 25

helix-destabilizing enzymes that bind to DNA at the origin of replication and break hydrogen bonds, thereby separating the two strands

Question 26

replication fork

Answer 26

Y-shaped structure produced during the semiconservative replication of DNA

Question 27

single-strand binding (SSB) proteins

Answer 27

bind to the single DNA strands after they have been separated for replication and stabilize them which prevents the double helix from re-forming until the strands are replicated; they also prevent the hydrolysis of the single-strand regions by other enzymes

Question 28

topoisomerases

Answer 28

enzymes that produce breaks in the DNA molecules and then rejoin the strands, relieveing strain and preventing supercoiling and knot formation during replication (ex. like a rope); there are two ways that topoisomerases reduce supercoiling: by producing a temporary break in the polynucleotide backbone of a single strand of DNA, passing that strand through the excessively twisted part, and resealing the break, or by breaking both DNA strands, passing some of the helix between the cut ends, and the resealing the break

Question 29

When does DNA replication occur?

Answer 29

during the S phase of Interphase

Question 30

Summarize how DNA replicates

Answer 30

During DNA replication, the two strands of the double helix unwind. Each strand serves as a template for forming a new, complementary strand. Replication is initiated as DNA primase sythesizes a short RNA primer. DNA polymerase then adds new nucleotide subunits to the growing DNA strand. Additional enzymes and other proteins are required to unwind and stabilize the separated DNA helix. DNA helicases open the double helix, and topoisomerases prevent tangling and knotting.

Question 31

Explain the complexities of DNA replication that make it (a) bidirectional and (b) continuous in one strand and discontinuous in the other.

Answer 31

DNA replication is bidirectional, starting at the origin of replication and proceeding in both directions from that point. A eukaryotic chromosome may have multiple origins of replication and may be replicating at many points along its length at any one time.
DNA synthesis always proceeds in a 5’->3’ direction. This requires that one DNA strand, the lagging strand, be synthesized discontinuously, as short Okazaki fragments. DNA primase sythesizes short RNA primers on the lagging strand, and DNA ligase links Okazaki fragments of newly synthesized DNA. The opposite strand, the leading strand, is synthesized continuously.

Question 32

What is the immediate source of energy for DNA replication?

Answer 32

the hydrolysis of nucleotides with three phosphate groups

Question 33

DNA polymerase

Answer 33

links nucleotide subunits to form a new DNA strand from a DNA template

Question 34

DNA primase

Answer 34

sythesizes short RNA primers on the lagging strand; begins replication of the leading strand

Question 35

DNA ligase

Answer 35

links Okazaki fragments by joining the 3’ end of the new DNA fragment to the 5’ end of the adjoining DNA

Question 36

plasmid

Answer 36

small, circular DNA molecules that carry genes separate from those on a bacterial chromosome

Question 37

mismatch repair

Answer 37

when there is an error in DNA replication, special enzymes recognize the incorrectly paired nucleotides and remove them, DNA polymerases then fill in the missing nucleotides

Question 38

nucleotide excision repair

Answer 38

a type of DNA repair involving three enzymes: a nuclease to cut out the damaged DNA, a DNA polymerase to add the correct nucleotides, and a DNA ligase to close the breaks in the sugar-phosphate backbone

Question 39

telomeres

Answer 39

the protective end caps of chromosomes that consist of short, simple, noncoding DNA sequences that repeat many times

Question 40

telomerase

Answer 40

a special DNA replication enzyme that can lengthen telomeric DNA by adding repetitive nucleotide sequences to the ends of eukaryotic chromosomes; typically present in cells that divide an unlimited number of times

Question 41

Discuss how enzymes proofread and repair errors in DNA.

Answer 41

During replication, DNA polymerases proofred each newly added nucleotide against its template nucleotide. When an error in base pairing is found, DNA polymerase immediately removes the incorrect nucleotide and inserts the correct one. In mismatch repair, enzymes recognize incorrectly paired nucleotides and remove them; DNA polymerases then fill in the missing nucleotides. Nucleotide excision repair is commonly used to repair DNA lesions caused by the sun’s ultraviolet radiation or by harmful chemicals. Three enzymes are involved in it: a nuclease to cut out the damaged DNA, a DNA polymerase to add the correct nucleotides, and DNA ligase to close the breaks in the sugar-phosphate backbone.

Question 42

Define telomere, and describe the possible connections between telomerase and cell aging and between telomerase and cancer.

Answer 42

Eukaryotic chromosome ends, called telomeres, are short, noncoding, repetitive DNA sequences. Telomeres shorten slightly with each cell cycle but can be extended by the enzyme telomerase. The absence of telomerase activity in certain cells may be a cause of cell aging, in which cells lose their ability to divide after a limited number of cell divisions. Most cancer cells have telomerase to maintain telomere length and possibly to resist apoptosis which is programmed cell death.

Question 43

What are the steps in DNA replication?

Answer 43

1) Helicase breaks hydrogen bonds and opens up the double strand, 2) Binding proteins stabilize the strands and prevent them from rejoining, 3) DNA primase makes a RNA primer, 4) Free nucleotides move in and hydrogen bond; DNA polymerase links nucleotides to each other starting at the primer and working in the 5’ to 3’ direction, 5) DNA polymerase “proofreads” the new strand and replace incorrect bases if needed, 6) DNA replication is continuous on the leading strand, 7) DNA replication is discontinuous on the lagging strand, producing Okazaki fragments that are eventually put together by DNA ligase