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bio 2200 Flashcards

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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
what were the phage proteins labelled with
S35
26
what were the phage DNA labelled with
P32
27
what was the process of hershey and chases experiment
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
28
what were the results of hershey and chases experiment
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
29
when was DNA identified to be the principle component of nuclein
in 1920
30
what are the four bases of DNA
cytosine, guanine, adenine, thymine
31
what is DNA
it is a polynucleotide consisting of non-identical repeating nucleotide units
32
how did watson and crick contribute to the structure of DNA
they figured out how the units that make up DNA are arranged in the bigger molecule
33
who was the forgotten scientist who paved the way for discovery of DNA's structure
J. Michael Creeth
34
what did creeth show
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
35
who determined the percentages of the four nucleotide bases and found that adenine and thymine were close and cytosine and guanine were close?
erwin chargaff
36
what did watson and crick use to find the structure of DNA
fibre diffraction patterns
37
what are the two forms of the 4 bases
the enol and the keto form. they are in equilibrium and the normal form is the keto form
38
what happens when the alternate tautomeric forms happen
they cause mispairing and mutation
39
who obtained the x-ray diffraction patterns of DNA fibres that suggested a helical structure
maurice wilkins and rosalind franklin
40
which from of the DNA pattern A or B was the one that wilkins showed to watson which is of "wetter" DNA fibres
the B pattern
41
what are the characteristics of the DNA strands
they are complimentary and antiparallel.
42
what are the bonds holding the nucleotides together in DNA
covalent phosphodiester bonds
43
what comprises the backbone of DNA
sugar-phosphate in alternating sugar and phosphate groups
44
what makes up a nucleotide
a base, a sugar, and a phosphate group
45
what are the two purines
adenine and guanine
46
what are the two pyrimidines
cytosine and thymine
47
what differentiates RNA from DNA
it has a ribose (2'OH) in place of deoxyribose
48
what are the numbers of the phosphate and the hydroxy groups on the sugar
5' phosphate and 3' hydroxy
49
which are numbered with primes, the sugar of the base carbons
the sugar carbons
50
what is the bond that holds the sugar and the base together called
glycosidic bond
51
what are the bonds that connect to the phosphates called. how many bonds can they make
phosphodiester bonds. they make two bonds with adjacent sugars
52
what are the three types of phosphates
alpha (closest to sugar) beta(second closest) gamma(third closest)
53
which of the three types of phosphates are incorporated into polynucleotides
the alpha phosphate
54
what is the base plus the sugar called
nucleoside
55
what is the nucleoside plus the phosphate called
nucleotide
56
what is the nucleoside for adenine
adenosine
57
what is the nucleoside for cytosine
cytidine
58
what is the nucleoside for guanine
guanosine
59
what is the nucleoside for thymine
thymidine
60
what is the nucleoside for uracil
uridine
61
which: purines or pyrimidines have a double ring structure
purines
62
is uracil a purine or pyrimidine
a pyrimidine
63
true or false: both purines and pyrimidines have anti and syn conformations
true
64
what are the two rules for DNA
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
how many bonds are between Adenine and thymine
two
66
how many bonds are between cytosine and guanine
three
67
how long is a helical repeat
34 angstroms
68
how many base pairs does it take to make one repeating unit
10.5
69
how wide is a dna strand
20 angstroms
70
what stabilizes the base pairs
vertical van der waals interactions
71
how wide is a complementary base pair
11 angstroms or 1.1 nanometer
72
what does tight packing of bases lead to
base stacking
73
what is base stacking
the offset of adjacent base pairs so that the base pairs are essentially parallel to one another
74
what does base stacking lead to
the double helix
75
how wide is the major and minor groove
12 and 6 angstroms
76
what occurs at the major and minor grooves
DNA binding proteins can make direct and specific contact/hydrogen bonds with nucleotides or with electrostatic interactions with the charged phosphates
77
is B DNA the real structure
no there are small differences of where atoms are located
78
what is x ray crystalography used for
to determine the precise position of atoms in a molecule
79
what is the difference between fibre diffracted rounds and crystal diffracted rounds
the starting matterial. fibre rounds are ordered but not purified like crystals are
80
what is the space filling diagram based off of
crystal structure
81
what is the same between the ball and stick diagram and the ribbon diagram (B dna and the actual one)
dimensions, complementarity and handedness
82
what is the difference between B DNA and the actual one
base pairs are not actually flat but slightly twisted and they are at an angle of 4 degrees
83
what does melting DNA mean
Separating the strands
84
what word describes the two strands of DNA going back together
reanneal
85
what does the over or under winding of DNA lead to
tortional stress which results in supervoiling
86
what does tortional stress in DNA lead to
potential energy for strand seperation
87
when is supercoiling evident
when the dna molecule is covalently closed
88
what can be used as an advantage when DNA strands need to be seperated
supercoiling
89
topological equivalent
undercoiled dna and supercoiled dna are topologically equivalent
90
how many supercoils need to form to fix a DNA strand that used to have 20 but now has 18turns
2 supercoils
91
positive supercoiling
twists the DNA so that it is over roated
92
negative supercoiling
twists the DNA so that it is under roated
93
what is the benifit of negative supercoiling
allows DNA to melt so that it is the first step of replication and transcription
94
what enzyme regulates supercoiling
topiosomerases
95
what are the two ways that the state of DNA can be changed
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
type I enzyme
make transient single stranded breaks in DNA. change L by one turn
97
type II enzyme
make transient double stranded breaks in DNA therefore change L by two turns
98
DNA gyrase
found in bacteria: is able to introduce supercoils in DNA
99
what type of enzyme is DNA gyrase
type I
100
scleroderma
autoimune disease, hardening of skin and organs
101
what attacks topoisomerases in scleroderma
auto antibodies (anti-scl-70)
102
treatability of scleroderma
systemic form is untretable and fatal
103
lupus
autoimmune disease where topoisomerase I is a target in some patients
104
what causes cancer in colorectal tumors and hodgkins disease
over expression of topoisomerase II alpha
105
examples of antibiotics
ciprofloxacin | novobiocin
106
how do antibiotics function
by inhibiting DNA gyrase
107
how do chemotheraputic agnets work
inhibiting eukaryotic type II topoisomerases selectively killing rapidly dividing cells
108
5-methyl-C
gene expression control (repressive)
109
5-hydroxymethyl-C
thought to override 5-methyl-C therefore activating in brain
110
5-formyl-c | 5-carboxyl-c
may reduce the rate of substrate specifically of RNA polymerase II transcription (repressive)
111
what can cause localized rigidity in DNA
run of adenines in one strand leading to significant ring stacking overlap
112
how can you make sure DNA is flexible
have alternating purines and pyrimidines
113
what is the significant role of A DNA
has a significant role when RNA strands form double helixes
114
how many degrees off the plane is A DNA
20
115
how is A DNA different from B DNA
Sugar conformation is ifferent and b is more hydrated
116
why is B DNA more hydrated
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
what was the handedness of the first crystal structure of DNA molecule Z DNA GCGCGC
LEFT HANDED
118
why was Z DNA left handed
because the crystal bases GCGCGC were flipped from anti to syn possibly important in control of some gene expression

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