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stupid orgo > bio 2200 > Flashcards

bio 2200 Flashcards

1
Q

hereditary molecule

A

molecular substance that carries and conveys the genetic information of a species

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2
Q

what are the 5 major characteristics of hereditary material

A
  1. localized in the nucleus and component of chromosomes
  2. present in stable form in cells
  3. sufficiently complex to contain information for structure, function, development, and reproduction of an organism
  4. able to accurately replicate itself so offspring can contain same information as parent cells
  5. mutable, low rate of mutation that introduces genetic variation and serves as a foundation for evolutionary change
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3
Q

what is the shape of bacterial and archaeal chromosomes

A

most cases, a single circular chromosome or less likely several chromosomes, or linear chromosomes

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4
Q

how is the chromosomes of bacteria and archaea organized

A

they are bound by small amounts of protein that localize bacterial chromosomes to a region of the cell known as the nucleoid.

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5
Q

how many copies of the genome do bacterial and archaea have

A

one set/ haploid

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6
Q

who identified the transforming principle

A

fred griffith

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7
Q

who identified that transforming principle is likely DNA

A

avery, mcarthy, and macleod

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8
Q

who definitively showed that DNA is the transforming principle

A

hershey and chase

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9
Q

what was the conclusion that frederick griffith came to with S and R bacteria and the rat experiment

A

hereditary molecule from the S3 bacteria transformed the R2 bacteria into S3 bacteria

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10
Q

what process did griffith discover that we now know to be true of bacteria to transfer DNA between cells

A

transformation

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11
Q

why is it unlikely that R2 bacteria mutated into the S3 bacteria (which were killed)?

A

because they are two different antigen strains (out of the four possible ones) and that means that a type 2 bacteria cannot be changed into a type 3 bacteria by a single mutation and it is unlikely for how often it was observed.

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12
Q

what year was DNA localized to chromosomes making it a candidate for hereditary material

A

1923`

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13
Q

what year was it discovered that nucleic acid is the genetic material

A

1944

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14
Q

what live bacteria were recovered from the dead mice

A

SIII

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15
Q

what were the options for the transformation factor?

A

DNA, RNA, protein, lipid, polysacharide

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16
Q

what was avery, macleod, and mccartys experiment

A

they used head killed SIII bacteria, live RII bacteria and mice with alliquots, each with either DNA, RNA, protein, lipid or polysaccharide

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17
Q

what was the result of avery, mcleod and mccartys experiement. why was this not conclusive

A

all the alliquots killed the mice except for the one which all the DNA was destroyed. this wasnt conclusive because what if there were still trace amounts of protiens, lipids, polysaccharides left in the alliquots

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18
Q

what did hershey and martha chase use to show that dna and not protein was responsible

A

bacteriophage infection of bacterial cells

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19
Q

what is the protein shell of bacteriophages called

A

capsid

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20
Q

where is the DNA of a bacteriophage

A

the head

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21
Q

what is the singular of bacteria

A

bacterium

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22
Q

what is the plural of bacteria

A

bacteria

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23
Q

do proteins have a lot of sulfur or phosphorus

A

large amounts of sulfur and almost no phosphorus

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24
Q

does DNA have lot of sulfur or phosphorus

A

large amounts of phosphorus and no sulfur

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25
Q

what were the phage proteins labelled with

A

S35

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26
Q

what were the phage DNA labelled with

A

P32

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27
Q

what was the process of hershey and chases experiment

A

they let the bacteriophages grow in the labelled chemicals, let the infection of the bacteria to begin, and they agitated the cell structures using a blender to seperate the empty phage particles from the infected bacteria

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28
Q

what were the results of hershey and chases experiment

A

the protein labelling (s35), the radioactivity was detected in empty phage particles
in the DNA lablelling (p32), the radioactivity was detected inside the infected bacteria

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29
Q

when was DNA identified to be the principle component of nuclein

A

in 1920

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30
Q

what are the four bases of DNA

A

cytosine, guanine, adenine, thymine

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31
Q

what is DNA

A

it is a polynucleotide consisting of non-identical repeating nucleotide units

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32
Q

how did watson and crick contribute to the structure of DNA

A

they figured out how the units that make up DNA are arranged in the bigger molecule

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33
Q

who was the forgotten scientist who paved the way for discovery of DNA’s structure

A

J. Michael Creeth

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34
Q

what did creeth show

A

that DNA had hydrogen bonds. he found that the viscosity in extreme temperatures and pH was lost and this was due to the loss of hydrogen bonds. he knew there was two chains in DNA and each had a sugar backbone on the outside and hydrogen bonded bases on the inside

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35
Q

who determined the percentages of the four nucleotide bases and found that adenine and thymine were close and cytosine and guanine were close?

A

erwin chargaff

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36
Q

what did watson and crick use to find the structure of DNA

A

fibre diffraction patterns

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37
Q

what are the two forms of the 4 bases

A

the enol and the keto form. they are in equilibrium and the normal form is the keto form

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38
Q

what happens when the alternate tautomeric forms happen

A

they cause mispairing and mutation

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39
Q

who obtained the x-ray diffraction patterns of DNA fibres that suggested a helical structure

A

maurice wilkins and rosalind franklin

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40
Q

which from of the DNA pattern A or B was the one that wilkins showed to watson which is of “wetter” DNA fibres

A

the B pattern

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41
Q

what are the characteristics of the DNA strands

A

they are complimentary and antiparallel.

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42
Q

what are the bonds holding the nucleotides together in DNA

A

covalent phosphodiester bonds

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43
Q

what comprises the backbone of DNA

A

sugar-phosphate in alternating sugar and phosphate groups

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44
Q

what makes up a nucleotide

A

a base, a sugar, and a phosphate group

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45
Q

what are the two purines

A

adenine and guanine

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46
Q

what are the two pyrimidines

A

cytosine and thymine

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47
Q

what differentiates RNA from DNA

A

it has a ribose (2’OH) in place of deoxyribose

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48
Q

what are the numbers of the phosphate and the hydroxy groups on the sugar

A

5’ phosphate and 3’ hydroxy

49
Q

which are numbered with primes, the sugar of the base carbons

A

the sugar carbons

50
Q

what is the bond that holds the sugar and the base together called

A

glycosidic bond

51
Q

what are the bonds that connect to the phosphates called. how many bonds can they make

A

phosphodiester bonds. they make two bonds with adjacent sugars

52
Q

what are the three types of phosphates

A

alpha (closest to sugar)
beta(second closest)
gamma(third closest)

53
Q

which of the three types of phosphates are incorporated into polynucleotides

A

the alpha phosphate

54
Q

what is the base plus the sugar called

A

nucleoside

55
Q

what is the nucleoside plus the phosphate called

A

nucleotide

56
Q

what is the nucleoside for adenine

A

adenosine

57
Q

what is the nucleoside for cytosine

A

cytidine

58
Q

what is the nucleoside for guanine

A

guanosine

59
Q

what is the nucleoside for thymine

A

thymidine

60
Q

what is the nucleoside for uracil

A

uridine

61
Q

which: purines or pyrimidines have a double ring structure

A

purines

62
Q

is uracil a purine or pyrimidine

A

a pyrimidine

63
Q

true or false: both purines and pyrimidines have anti and syn conformations

A

true

64
Q

what are the two rules for DNA

A
  1. the bases of one strand are complementary to the bases in the other strands forming hydrogen bonds
  2. the two chains are antiparallel with respect to their 5’ and 3’ ends
65
Q

how many bonds are between Adenine and thymine

A

two

66
Q

how many bonds are between cytosine and guanine

A

three

67
Q

how long is a helical repeat

A

34 angstroms

68
Q

how many base pairs does it take to make one repeating unit

A

10.5

69
Q

how wide is a dna strand

A

20 angstroms

70
Q

what stabilizes the base pairs

A

vertical van der waals interactions

71
Q

how wide is a complementary base pair

A

11 angstroms or 1.1 nanometer

72
Q

what does tight packing of bases lead to

A

base stacking

73
Q

what is base stacking

A

the offset of adjacent base pairs so that the base pairs are essentially parallel to one another

74
Q

what does base stacking lead to

A

the double helix

75
Q

how wide is the major and minor groove

A

12 and 6 angstroms

76
Q

what occurs at the major and minor grooves

A

DNA binding proteins can make direct and specific contact/hydrogen bonds with nucleotides or with electrostatic interactions with the charged phosphates

77
Q

is B DNA the real structure

A

no there are small differences of where atoms are located

78
Q

what is x ray crystalography used for

A

to determine the precise position of atoms in a molecule

79
Q

what is the difference between fibre diffracted rounds and crystal diffracted rounds

A

the starting matterial. fibre rounds are ordered but not purified like crystals are

80
Q

what is the space filling diagram based off of

A

crystal structure

81
Q

what is the same between the ball and stick diagram and the ribbon diagram (B dna and the actual one)

A

dimensions, complementarity and handedness

82
Q

what is the difference between B DNA and the actual one

A

base pairs are not actually flat but slightly twisted and they are at an angle of 4 degrees

83
Q

what does melting DNA mean

A

Separating the strands

84
Q

what word describes the two strands of DNA going back together

A

reanneal

85
Q

what does the over or under winding of DNA lead to

A

tortional stress which results in supervoiling

86
Q

what does tortional stress in DNA lead to

A

potential energy for strand seperation

87
Q

when is supercoiling evident

A

when the dna molecule is covalently closed

88
Q

what can be used as an advantage when DNA strands need to be seperated

A

supercoiling

89
Q

topological equivalent

A

undercoiled dna and supercoiled dna are topologically equivalent

90
Q

how many supercoils need to form to fix a DNA strand that used to have 20 but now has 18turns

A

2 supercoils

91
Q

positive supercoiling

A

twists the DNA so that it is over roated

92
Q

negative supercoiling

A

twists the DNA so that it is under roated

93
Q

what is the benifit of negative supercoiling

A

allows DNA to melt so that it is the first step of replication and transcription

94
Q

what enzyme regulates supercoiling

A

topiosomerases

95
Q

what are the two ways that the state of DNA can be changed

A

cut one of the strands and rotate it around the other strand so cutting one strand takes out one supercoil
cut both strands and reattatch with respect to the 5’-3’ so cutting both takes out 2 supercoils

96
Q

type I enzyme

A

make transient single stranded breaks in DNA. change L by one turn

97
Q

type II enzyme

A

make transient double stranded breaks in DNA therefore change L by two turns

98
Q

DNA gyrase

A

found in bacteria: is able to introduce supercoils in DNA

99
Q

what type of enzyme is DNA gyrase

A

type I

100
Q

scleroderma

A

autoimune disease, hardening of skin and organs

101
Q

what attacks topoisomerases in scleroderma

A

auto antibodies (anti-scl-70)

102
Q

treatability of scleroderma

A

systemic form is untretable and fatal

103
Q

lupus

A

autoimmune disease where topoisomerase I is a target in some patients

104
Q

what causes cancer in colorectal tumors and hodgkins disease

A

over expression of topoisomerase II alpha

105
Q

examples of antibiotics

A

ciprofloxacin

novobiocin

106
Q

how do antibiotics function

A

by inhibiting DNA gyrase

107
Q

how do chemotheraputic agnets work

A

inhibiting eukaryotic type II topoisomerases selectively killing rapidly dividing cells

108
Q

5-methyl-C

A

gene expression control (repressive)

109
Q

5-hydroxymethyl-C

A

thought to override 5-methyl-C therefore activating in brain

110
Q

5-formyl-c

5-carboxyl-c

A

may reduce the rate of substrate specifically of RNA polymerase II transcription (repressive)

111
Q

what can cause localized rigidity in DNA

A

run of adenines in one strand leading to significant ring stacking overlap

112
Q

how can you make sure DNA is flexible

A

have alternating purines and pyrimidines

113
Q

what is the significant role of A DNA

A

has a significant role when RNA strands form double helixes

114
Q

how many degrees off the plane is A DNA

A

20

115
Q

how is A DNA different from B DNA

A

Sugar conformation is ifferent and b is more hydrated

116
Q

why is B DNA more hydrated

A

because there is the presence of a spine of hydrogen bonded water molecules in the minor groove leading to a stiffer more stable molecule

117
Q

what was the handedness of the first crystal structure of DNA molecule Z DNA GCGCGC

A

LEFT HANDED

118
Q

why was Z DNA left handed

A

because the crystal bases GCGCGC were flipped from anti to syn possibly important in control of some gene expression

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