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Biology 311C > DNA structure and replication (4) > Flashcards

DNA structure and replication (4) Flashcards

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1
Q

Why were proteins believed to be the genetic material?

A

diversity of their composition (20 amino acids) and their presence in chromosomes

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2
Q

Fredrik Griffith

A

used pneumonia causing bacteria on mice, concluded that a strain could transfer its genetic material to another strain

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3
Q

Oswald Avery, Colin McLeod, Maclyn McCarty

A

used DNase, RNase, and protase on strands in in vitro study. Found that the sample with DNase was the only one that did not transfer its genetic material to another

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4
Q

Bacteriophages

A

viruses infecting bacterial

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5
Q

Alfred Hershey and Martha Chase

A

used varuses and labeled dna and proteins. injected to bacterial.
centrifuged, found the pellet fraction contained most of the dna label.
concluded dna was the genetic material injected

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6
Q

Linus Pauling

A

proposed dna had a triple helix structure

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7
Q

dna

A

-nucleotide bases
-covalent bonds in a polymer

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8
Q

dna double helix 1

A
  1. dna consists of two strands that are h-boded together
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9
Q

dna double helix 2

A
  1. the two strands turn right to make a right-handed helix
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10
Q

dna double helix 3

A

the hydrophilic sugar phosphate is on the outside of the helix,
the negatively charged p groups make DNA souble in aqueous solutions

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11
Q

dna double helix 4

A

the hydrophobic nitrogenous bases are staked inside in a perpendicular manner to the strand. there are 10 bases per turn

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12
Q

dna double helix 5

A

-complimentary base pairing
- adenine pairs with thymine with 2 H-bonds and guanine pairs with cytosine with 3 H-bonds
- satisfices charagaff’s findings

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13
Q

dna double helix 6

A
  • the two strands run in oppositite directions (anti-parallel orientation)
  • The starting of dna has a phosphate group attached to the 5th C of ribose
  • The other end has a -OH group attached to the 3rd C of ribose
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14
Q

dna double helix 7

A

the helical turns make a major groove and a minor groove between the adjacent turns

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15
Q

dna double helix 8

A

dna stores information in its sequence of bases

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16
Q

dna double helix 9

A

based on the complimentary base pairing, dna replication was proposed to be semiconservative
- the new copy is made from a template dna with high specificity

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17
Q

Where does supercoiled dna occur?

A

in circular dna (plasmids, bacterial chromosomes, chloroplast, and mitochondrial dna) and linear eukaryotic chromosomes

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18
Q

Why is supercoiling important?

A

Important to keep dna compact in the cell and during dna replication

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19
Q

Where is single-stranded dna present?

A

viral genomes

20
Q

Why is the double strandedness of dna important?

A

important for stability and proofreading during replication

21
Q

How can double helix of dna be separated?

A

Since it is bonded with H-bonds and it can be separated by heating or exposure to alkaline conditions

22
Q

How does hybridization/renaturing of dna happen?

A

by gradual cooling or neutralizing the alkaline solution with a mild acid

23
Q

Semiconservative

A

Fact that half of a newly made DNA is the old template

DNA replication is semiconservative

24
Q

First in vitro DNA synthesis

A

-Arthur Kornberg
-used template DNA, DNA polymerase, 4 nucleotides
-if any of the nucleotides are missing DNA synthesis will stop

25
Q

Experiment that prove semiconservative mechanism

A
  • used isotopes to label old dna template and new dna made fromt that template
  • grew bacterial in a medium containing ¹⁵N and allowed it to create 17 generations
  • after took a sample from that and put them in a medium containg ¹⁴N allowed it to replicate thrice, collecting samples from all
  • proved that dna replication is a combination of old and new dna strands
26
Q

origin of replication

A

location on a dna molecule with a specific sequence that is recognized by enzymes involved in DNA replication

  • in eukaryotes the origin of replication is nor that well defined
27
Q

What is required for dna replication under in vitro conditions?

A
  • dna template
  • dna primer (short oligonucleotide)
  • Mg⁺⁺
  • dna polymerase
  • dNTPs in a suitable buffer
28
Q

dna replication in vivo

A
  • dna replication starts at the origin of replication and proceeds biderectionally
  • replication buble consists of two replication forks that grows wider as dna replication continues
29
Q

dna in vivo replication- initiation

A

starts with relaxation of supercoiling at origin of rep. by topoisomerase
- resulting single-straded dna is stabilized by ssb proteins
- rna primer starts new dna synthesis

30
Q

important enzymes and proteins

A
  • topoisomerase
  • ssb proteins
  • primase
  • dna polymerase iii (complex protein)
31
Q

Primase (def)

A

makes an rna primer that provides a 3-OH group and which is needed for dna polymerase to work, also starts new dna synthesis

32
Q

dna in vivo replication- elongation

A
  • dna polymerase iii binds to dna template + rna primer region and starts to add complementary nucleotides
  • dna synthesis always happen 5’ to 3’
    because dna polymerase links only to 3-OH group
  • a leading strand is synthesized continuously
  • dna is synthesized in okazaki fragments
33
Q

Okazaki fragments

A

because the opposite strand is not fully open to continue dna synthesis from the 5’ to 3’ direction, dna is synthesized in small fragments called okazaki fragments

34
Q

order in which dna enzymes work

A
  1. once dna strand is synthesized, dna polymeraze iii proofreads it makes sure errors are removed
  2. dna polymeraze i remove the dna primer and complete the dna strand
  3. once the small fragments are completed dna ligase joins the two ends of dna strands to complete dna replication
  4. dna gyrase facilitates the supercoiling of dna to compact the chromosomes into nucleosomes
35
Q

Topoisomerase function

A

relaxes the supercoiled dna

36
Q

Helicase

A

unwinds the double helix into a single-stranded dna

37
Q

SSB

A

single-stranded dna binding protein. stabilizes the ssDNA

38
Q

primase

A

synthesizes RNA primers

39
Q

DNA polymerase I

A

erases RNA primers and fills in the gaps

40
Q

DNA polymerase III Holoenzyme

A

DNA synthesis, proof reading, exonuclease activity and repair

41
Q

DNA ligase

A

covalently joins free 3’ and 5’ ends of two DNA fragments through phosphodiester linkage

42
Q

DNA gyrase

A

introduces supercoiling in DNA

43
Q

Mismatch repair

A
  • corrects error during dna replication
  • dna polymease III
  • these corrections use the mismatch repair mechanism by checking the complimentary bases pairing
44
Q

Excision repair

A
  • occurs after cell division, in the G1, S, G2 phase
  • damage caused by carcinogens and mutagenic radiations altering bases or making pyrimidine dimers
  • corrected by excising the damaged strands of DNA and making a new matching strand in its place
45
Q

Telomere repair

A
  • the enzyme telomerase extends the 3’ end of the telomere region and allows RNA primer to bind to its extended region protecting the telomere from being degraded
  • occurs in young and actively growing cells, but also in cancer cells

Biology 311C (10 decks)

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