chapter 12

Question 1

What is replication?

Answer 1

Cells can make exact copies of their DNA

Question 2

what’s the name given to errors that are caused during replication?

Answer 2

mutations

Question 3

How does replication happen? Explain

Answer 3

• two strands of parental DNA separate
• each serves as the template for
  synthesis of a daughter strand
• Replication occurs from 5’ to 3’

Question 4

What are the different hypothetical models
for replication

Answer 4

semiconservative

conservative

Question 5

what’s a semiconservative mode of replication?

Answer 5

New DNA duplex consists of one old
strand (parental) and one new strand
(daughter)

Question 6

what’s a conservative mode of replication?

Answer 6

New DNA complex consists of two newly
synthesized daughter strands leaving the
parental duplex intact

Question 7

who discovered that DNA replication is
semiconservative?

Answer 7

Matthew Meselson & Franklin Stahl

Question 8

How did they discover the semi-conservative model of replication?

Answer 8

Nonradioactive “heavy” nitrogen isotope (15N) to tag
parental DNA strands

DNA molecules with different densities were separated
by a special type of centrifugation

Question 9

what’s the Meselson & Stahl
Experiment

Answer 9

Question 10

How are proteins involved in replication?

Answer 10

• DNA polymerase - main molecule synthesizing DNA strands
• Helicase - responsible for unwinding DNA
  *

Question 11

The function of sliding DNA clamp

Answer 11

•Protein that encircles DNA and attaches to the rear of DNA polymerase (relative to
forward movement)
•Tethers DNA polymerase to the template strand and increases the rate of DNA
synthesis

Question 12

DNA polymerase structure

Answer 12

thumb structure

Question 13

where does replication starts?

Answer 13

origin of replication (ori)

Question 14

function of topisomerase

Answer 14

prevents twisting as DNA unwinds

Question 15

function of single stranded binding proteins SSBs

Answer 15

coat and stabilize single stranded DNA, preventing two strands from re-forming double stranded DNA

Question 16

what’s okazaki fragments?

Answer 16

DNA polymerase copies the other strand in short lengths

synthesis of lagging strand occurs in small discontinous stretches

Question 17

what is discontinuous replication?

Answer 17

The synthesis of a new strand of a replicating DNA molecule as a series of short fragments that are subsequently joined together.

Question 18

what’s leading strand ?

Answer 18

• In DNA replication, the new DNA strand synthesized in the direction of DNA unwinding
• Synthesized on the leading strand template
• One primer is required
  •Replication continues to the end.
  •The strand is replaced by DNA when the last fragment
  catches up to it.

Question 19

what’s lagging strand?

Answer 19

•New DNA strand synthesized discontinuously, in the direction opposite DNA
unwinding
•Synthesized on the lagging strand template

• Multiple RNA primers are required.
• The final primer is added 100 nucleotides from the 3’ end of
  the template leaving the new daughter strand shortened by
  about 100 nucleotides.

Question 20

DNA polymerase ass nucleotides only to an existing strand

T/F

Answer 20

T

Question 21

How does a new strand beings and what enzyme is used?

Answer 21

• new strand begins with a short chain of RNA primer synthesized by enzyme primase
• Primase leaves the template, and DNA polymerase takes over, extending the RNA
  primer with DNA nucleotides as it synthesizes the new DNA chain
• RNA primers are replaced with DNA later in replication

Question 22

How does DNA plymerase correct its own errors?

Answer 22

• proofreading, detects the mispairing of improper hydrogen bonds
• when the error is detected DNA polymerase activates cleavage function removes and replace

Question 23

what is origin of replication?

Answer 23

• each point where DNA replication is initiated
• The opening of the double helix at each
  origin of replication forms a replication
  bubble with a replication fork on each side.

Question 24

large linear chromosomes have one origin of replication

T/F

Answer 24

F many origins of replication

Question 25

examples of circular DNA

Answer 25

mitochondria, chloroplasts

Question 26

how do circular DNA replicate?

Answer 26

* there is a single origin of replication * Replication proceeds in both directions until the replication forks meet and fuse on the opposite side, completing one round of replication.

Question 27

what is telomere?

Answer 27

End of a eukaryotic chromosome is capped by a repeating sequence called the telomere

Question 28

How many telomeres do humans have?

Answer 28

In humans, the telomere consists of the sequence 5’-TTAGGG-3’ repeated approximately 1500-3000 times.

Question 29

how many base pairs are lost by chromosomes after replication?

Answer 29

50–200 base pairs

Question 30

when does the cell die?

Answer 30

after 20-30 divisions

Question 31

what is telomerase?

Answer 31

enzyme that adds nucleotides to telomeres, especially in cancer cells.

Question 32

what is PCR?

Answer 32

Polymerase chain reaction - Cyclical process that makes millions of copies of a section of DNA

Question 33

what are the steps of PCR

Answer 33

Each cycle of amplification includes three steps 1. Denaturation 2. Annealing 3. Extension

Question 34

what contains in the PCR mix?

Answer 34

Genomic DNA (contains target) Primer A Primer B Buffer dATP dGTP dCTP dTTP DNA polymerase

Question 35

Define denaturation in PCR

Answer 35

A solution containing double-stranded DNA (the template duplex) is heated to separate the DNA into two individual strands.

Question 36

Define annealing in PCR

Answer 36

When the solution is cooled, the two primers anneal to their complementary sequence on the strands of the template duplex.

Question 37

Define extension in PCR

Answer 37

DNA polymerase synthesizes new DNA strands (complementary to the template duplex strands) by extending primers in a 5’ to 3’ direction.

Question 38

At what temperature is DNA polymerase optimal?

Answer 38

37 C

Question 39

whose DNA polymerase does not denature at high temperature?

Answer 39

``` Thermus aquaticus (bacterium) – lives in hot springs at extremely hot temperatures ```

Question 40

what is PCR used for?

Answer 40

* Author Ricki Lewis (Human Genetics), lists some very interesting applications: * A preserved quagga (a relative of the zebra) and a marsupial wolf, both extinct. * Poached moose meat in hamburger. * The brain of a 7,000-year-old human mummy. * The digestive tracts of carnivores, to reveal food web interactions. * Roadkill and carcasses washed ashore, to identify locally threatened species. * Products illegally made from endangered species. * Genetically modified bacteria released in field tests, to follow their dispersion. * One cell of an 8-celled human embryo to detect a disease-causing mutation. * Remains in Jesse James’s grave, to make a positive identification. * The intestines of genital crab lice on a rape victim, which matched the DNA of the suspect. * Fur from Snowball, a cat that linked a murder suspect to a crime.

Question 41

what is gel electrophoresis ?

Answer 41

In electrophoresis, DNA molecules separate by size. Larger molecules move more slowly because they take longer to work their way through the pores in the gel.

Question 42

In addition to amplifying DNA, it can be useful to “cut” DNA at specific sites. T/F

Answer 42

T

Question 43

what ahppens when you cut pieces of DNA?

Answer 43

allows pieces from the same or different organisms to be brought together in recombinant DNA technology.

Question 44

where are restriction enzymes sourced from?

Answer 44

bacteria

Question 45

what is restriction enzyme ?

Answer 45

A restriction enzyme is a protein isolated from bacteria that cleaves DNA sequences at sequence-specific sites, producing DNA fragments with a known sequence at each end

Question 46

what is southern blot?

Answer 46

a procedure for identifying specific sequences of DNA, in which fragments separated on a gel are transferred directly to a second medium on which detection by hybridization may be carried out.

Question 47

what goes in the sequencing PCR mix?

Answer 47

Genomic DNA (contains target) Primer A Primer B Buffer dATP dGTP dCTP dTTP DNA polymerase ddATP\* ddGTP\* ddCTP\* ddTTP\*

Question 48

what is dna sequencing ?

Answer 48

DNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA.

Question 49

what is recombinant DNA

Answer 49

* Recombines DNA from two or more sources into a single molecule * The donor fragment may be a protein coding gene, a regulatory part of a gene, or any DNA segment of interest. * Vector carries the donor fragment (often a bacterial plasmid.

Question 50

what is transformation of DNA ?

Answer 50

* The recombinant DNA is introduced into a bacterial cell by means of transformation, in which bacteria are chemically induced into a state in which they take up DNA from outside the cell. * As the bacterial cell replicates and divides, it also replicates the recombinant DNA.

Question 51

what is DNA editing

Answer 51

DNA is inserted, deleted, modified or replaced in the genome of a living organism.