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BIOL 239 > Week 6 > Flashcards

Week 6 Flashcards

DNA and the Genetic Code

1
Q

where is DNA located

A

almost exclusively within the chromosomes

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2
Q

what does the Schiff reagent do

A

stains DNA red

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3
Q

what are the 4 bases of DNA

A
  • cytosine
  • adenine
  • guanine
  • thymine
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4
Q

what species did Frederick Griffith perform studies on (1923)

A

Streptococcus pneumoniae and its 2 forms
- smooth (S) : wild-type
- rough (R) : mutant

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5
Q

what did Griffith find

A

when injecting Streptococcus pneumoniae into mice:
- S form = lethal
- R or heat-killed S = not lethal
- mixture of R and heat-killed S = lethal

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6
Q

define: transformation

A

the ability of a substance to change the genetic characteristics of a cell

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7
Q

what Oswald Avery discover

A

DNA was the only that could cause transformation, suggesting genes were made up of DNA

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8
Q

what experiments did Avery perform

A

they prepared various purified and semi-purified components from the mixture and tested to see if they could transform R form bacteria and subjected it to various chemicals
e.g. live R + DNA from heat-killed S
- + protease => live S
- + ribonuclease => live S
- + deoxyribonuclease => none

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9
Q

what experiment did Hershey and Chase perform

A

the waring blender experiment, determined which substance directed the production of new phage particles, DNA or protein

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10
Q

what are T2 bacteriophages composed of

A

approximately equal weights of protein and DNA

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11
Q

what is the bacteriophage life cycle

A
  1. phage attaches and injects genes into host bacterium
  2. phage DNA replicates and new phage proteins are made
  3. phage particles assemble
  4. cell bursts releasing new phage
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12
Q

what do phages leave on the surface of the cell when they infect bacteria

A

viral shell (ghost)

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13
Q

how did Hershey and Chase label DNA

A

with 32P

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14
Q

how did Hershey and Chase label protein

A

with 35S

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15
Q

how did Hershey and Chase separate the bacteria from the phage ghosts

A

with a blender

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16
Q

what did Hershey and Chase discover

A

bacteria only contained the viral DNA, phage ghosts only contained the viral protein

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17
Q

what are the 3 parts of a nucleotide

A
  1. phosphate group
  2. five carbon sugar (pentose)
  3. cyclic nitrogenous base
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18
Q

which nitrogenous bases are pyrimidines

A
  • cytosine
  • thymine
  • uracil
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19
Q

which nitrogenous bases are purines

A
  • guanine
  • adenine
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20
Q

how are nucleotides linked

A

through phosphodiester bonds

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21
Q

in which direction are nucleotides added

A

5’ to 3’

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22
Q

who proposed the double helix

A

Watson and Crick

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23
Q

who collected X-ray diffraction data which helped in proving the double helix

A

Rosalind Franklin

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24
Q

what did Watson and Crick find out about the ratio of nucleotides in DNA

A

A:T and G:C both exist in ratios of 1:1

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25
Q

what is the structure of the double-strand of DNA

A
  • anti-parallel strands
  • strands are held together by hydrogen bonding
  • one complete turn every 34Å (3.4 nm)
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26
Q

what is the backbone of DNA

A

sugar-phosphate

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27
Q

which form of DNA is hydrated

A

B-form

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28
Q

which form of DNA is dehydrated

A

A-form

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29
Q

which way do A-form and B-form DNA spiral

A

to the right

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30
Q

which form of DNA spirals to the left

A

Z-form

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31
Q

where is circular DNA molecules found

A

chromosomes of prokaryotic bacteria, mitochondria, chloroplasts, and some viruses

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32
Q

where is single-stranded DNA found

A

in some viruses - serve as the template for synthesis of a second strand once inside the host cell

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33
Q

what is an alternative to DNA in some viruses (e.g. retroviruses)

A

RNA, DNA is made using viral reverse transcriptase

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34
Q

what is the Watson-Crick model of DNA replication

A
  1. original double helix
  2. strands separate
  3. complementary bases align opposite templates
  4. enzymes link sugar-phosphate elements of aligned nucleotides into a continuous strand
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35
Q

what did Meselson and Stahl prove

A

DNA was semiconservative

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36
Q

what are the three possible models for DNA replication

A
  1. semiconservative
  2. conservative
  3. dispersive
37
Q

what did the Meselson-Stahl experiment use

A

incubated bacteria with media containing 14N and 15N, and extracted DNA using CsCl density gradient technique

38
Q

what does centrifuging DNA in a CsCl solution at 50,000 rpm for 72 hours do

A

causes 14N and 15N to separate into bands according to difference in weight

39
Q

what was found for F1 DNA in the Meselson-Stahl experiment

A

1 hybrid band

40
Q

what was found for F2 DNA in the Meselson-Stahl experiment

A

2 bands, F1 and hybrid

41
Q

what is the model organism for DNA replication

42
Q

what are the two steps of DNA replication

A

initiation and elongation

43
Q

how many origins of replication does E. coli have

44
Q

how many origins of replication do eukaryotes have

45
Q

what is the origin or replication of E. coli known as

46
Q

what is ori C rich in

47
Q

what are the steps of initiation

A
  1. DNA-A protein binds to the four 9 base-pair repeats in oriC
  2. more DNA-A binds forming a complex with ori C
  3. DNA-B (DNA helicase) and DNA-C protein join the initiation complex and produce a replication bubble
  4. DNA helicase catalyzes the unwinding of the parental double helix
  5. single-stranded binding (SSB) proteins keep the strands apart
48
Q

what must DNA polymerase have to add nucleotides

A

a free 3’ OH, orientation of strands is very important

49
Q

what are the steps of elongation

A
  • a DNA primase (RNA polymerase) makes an RNA primer with a free 3’ OH for DNA polymerase to elongate
  • DNA polymerase III extends DNA using RNA primers
  • RNA primers are added as the replication bubble opens up
  • RNA primers are removed by DNA polymerase I, which simultaneously replaces them with DNA (still 5’ to 3’)
  • DNA ligase seals 3’ OH and 5’ PO4 nicks by catalyzing the formation of phosphodiester bonds
50
Q

what is the trombone model of DNA replication

A
  • DNA polymerase III does not actually travel along the DNA strands, instead the DNA is spooled through the polymerase
  • DNA polymerase III has a sliding clamp function to hold the DNA in place and allow it to slide through
51
Q

what is the complex of DNA polymerases working on leading and lagging strands called

52
Q

in which direction does DNA polymerase add nucleotides

A

only in the 5’ to 3’ direction

53
Q

how does DNA polymerase know which nucleotides to add

A

complementarity to template

54
Q

what are the two types of DNA polymerase in E. coli

55
Q

what is DNA polymerase III responsible for

A

synthesis of new strands

56
Q

what is DNA polymerase I responsible for

A

gap-filling after removal of the RNA primer

57
Q

how does DNA polymerase proof read in E. coli

A
  • DNA polymerase I “proof reads” the synthesize strands in the 3’ to 5’ direction, removing any incorrect base pairs (has exonuclease activity)
  • DNA polymerase III replaces the error with the correct nucleotide
58
Q

what does topoisomerase do

A

makes transient nicks to relieve torsion and nick both DNA strands to separate the two daughter molecules

59
Q

what is a problem with circular chromosomes

A

as replication forks move in both direction, supercoiling occurs in front of the replication forks

60
Q

why do eukaryotes have multiple origins or replication

A

must replicate all DNA in S phase, speeds up the process

61
Q

what are telomeres

A

repeat units of TTAGGG x 250-1500 (in humans)

62
Q

what is the problem with linear DNA

A

RNA primers can’t be replaced with DNA at the ends of the chromosome since a free 3’ OH is needed

63
Q

what is the purpose of telomeres

A

they “absorb” the lose of RNA primers so the critical information is not immediately affected

64
Q

what is the action of telomerase

A
  1. telomerase (containing RNA template) binds to parent strand and extends the 3’ end of the parent strand
  2. translocates along the parent strand (in 3’ direction) allowing further extension
  3. telomerase releases, and primase adds an RNA primer
  4. DNA polymerase III fills the gap
  5. DNA polymerase I replaces RNA primer
65
Q

when does senescence of telomerase usually occur

A

after < 50 generations in culture

66
Q

define: progeria

A

genetic disease causing rapid aging

67
Q

define: codon

A

nucleotide triplet

68
Q

what is substituted for thymine in mRNA

69
Q

what type of relationship is there between the nucleotide sequence in a gene and the order or amino acids in the polypeptide chain

A

linear relationship

70
Q

what did Crick and Brenner conclude

A

a codon is composed of three nucleotides and the designated starting point for each gene establishes the reading frame

71
Q

what gene did Crick and Brenner study

A

T4 rIIB gene

72
Q

define: intragenic suppression

A

the restoration of gene function when one mutation cancels another

73
Q

what is the evidence of a triplet code

A

if a gene sustains 3 or multiples of 3 nucleotide mutations of the same sign (insertions or deletions), the protein can still function [if they’re near each other!]

74
Q

define: frameshift mutation

A

changes that alter the grouping of nucleotides into codons

75
Q

what happens when there are mutations between genes

A

no effect, DNA region between genes does not code from proteins

76
Q

what is the start codon

77
Q

what are the stop codons

78
Q

does each amino acid have a unique codon

A

no, most amino acids are specified by more than one codon

79
Q

how did researchers discover protein synthesis takes place in the cytoplasm (1950s)

A

using radioactively labeled amino acids

80
Q

what transports DNA sequence information to the cytoplasm

81
Q

how did researchers find out which codons corresponded to which amino acids

A

synthetic mRNA of known sequence

82
Q

what mixture was used in experiments for cracking the genetic code

A
  • synthetically created mini-mRNA
  • ribosomal subunits
  • specific tRNA carrying its 14C-labelled amino acid
83
Q

suppose the mRNA is CUCUCUCUCU, and both Ser and Leu are included in the polypeptide chain, how do you know which amino acid corresponds to which codon

A

1) synthesize trinucleotide
2) label only one amino acid out of 20
3) attach to corresponding tRNA
4) add ribosomes
5) pour mixture through filter
only those tRNAs carrying the radiolabeled amino acid corresponding to the triplet will bind to the ribosome and stick to the filter

84
Q

what is the start of the polypeptide chain called

A

N-terminus

85
Q

what is the end of the polypeptide chain called

A

C-terminus

86
Q

what are the 2 newly discovered amino acids

A
  • selenocysteine (has selenium atom instead of sulphur atom) [UGA]
  • L-pyrrolysine (only prokaryotes so far) [UAG]
87
Q

what does interpretation as stop or amino acid appears to be depend on

A

surrounding context of the codons

88
Q

is the genetic code universal

A

no, there are some exceptions
e.g. mitochondria of yeast specify threonine with CUA instead of leucine

BIOL 239 (12 decks)

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