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BIOL 3421 - molecular biochem > nucleotides, genes, and chromosomes > Flashcards

nucleotides, genes, and chromosomes Flashcards

1
Q

list the basic structural components of a nucleotide

A

phosphate(s), base, sugar

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2
Q

list the basic structural components of a nucleoside

A

base, sugar

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3
Q

which has a phosphate: nucleotide or nucleoside

A

nucleotide has a phosphate

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4
Q

list the 2 types of nitrogenous bases

A

purine or pyrimidine

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5
Q

which type of sugar does a nucleotide/side have

A

pentose

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6
Q

T or F: a nucleotide can have one or more phosphates

A

true

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7
Q

how many rings do purines have

A

2

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8
Q

how many nitrogens do nitrogenous bases have PER RING

A

2 N per ring

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9
Q

how many rings do pyrimidines have

A

1

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10
Q

how many N do purines have

A

4 N

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11
Q

how many N do pyrimidines have

A

2 N

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12
Q

what type of bond links the nitrogenous base to the pentose sugar

A

covalently

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13
Q

in the covalent bonds between nitrogenous base and sugar, between which atoms does the covalent bond occur

A

nitrogen of the base with carbon of the sugar

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14
Q

which nitrogen in purines hold the covalent bond to the base

A

N 9

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15
Q

which nitrogen in pyrimidines hold the covalent bond to the base

A

N 1

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16
Q

T or F: thymine can occur in RNA

A

true, but this is rare

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17
Q

T or F: uracil can occur in DNA

A

true, but this is rare

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18
Q

by which bond does the phosphate join to the pentose sugar in a nucleotide

A

ester

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19
Q

by which bond is the base bound to the pentose sugar in a nucleotide/side

A

N-b-glycosyl bond

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20
Q

what sugars do RNA have

A

ribose

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21
Q

what sugars do DNA have

A

2’-deoxy-ribose

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22
Q

which atom in a nucleotide/side is denoted with primes (‘)

A

carbons

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23
Q

why do we denote sugar carbons in a nucleotide/side with primes (and not just the number on its own?)

A

bc it helps us distinguish between sugar carbons and base carbons

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24
Q

in a nucleotide/side, which carbon is denoted with primes: sugar carbons or base carbons

A

sugar carbons get primes

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25
Q

T or F: DNA and RNA also contain some additional nitrogenous bases in minor concentrations

A

true, but rare

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26
Q

describe 2 minor changes that can occur to RNA/DNA structure

A

methyl groups added to a ring carbon or an exocyclic group (methyl group modification)

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27
Q

T or F: methyl group modification on nucleotides is very common

A

false; it’s not super common

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28
Q

are RNA/DNA backbones hydrophilic or hydrophobic

A

hydrophilic

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29
Q

describe why the RNA/DNA backbone is hydrophilic

A

OH of sugars usually hydrogen bond with water. The fully ionized phosphate groups usually ionically interact with + charges on proteins or metal ions

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30
Q

linkages of nucleotides are formed by which type of reactions

A

dehydration

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31
Q

T or F: both purines and pyrimidines are aromatic

A

true

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32
Q

since purines/pyrimidines are aromatic, describe the types of bonds found within them

A

most of the bonds have a partial double bond character

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33
Q

since purines/pyrimidines are aromatic, describe what happens to the electrons

A

they delocalize

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34
Q

what is the UV absorption of purines/pyrimidines

A

260 nm

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35
Q

since purines/pyrimidines are aromatic, describe the general shape

A

pyrimidines = planar, purines = puckered (nearly planar)

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36
Q

T or F: purines/pyrimidines can exists as 2+ readily interconvertible isomers (tautomers)

A

true

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37
Q

list chargaff’s rules (4)

A
  1. base composition of DNA varies between species
  2. DNA from dif tissues of the same species have the same base composition
  3. base composition of DNA doesn’t change with organism’s age, nutritional state, or environment
  4. # A = # T, and # G = #C, and AG = purine, CT = pyrimidine
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38
Q

which bases are purines

A

adenosine and guanosine

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39
Q

which bases are pyrimidines

A

cytidine and thymidine

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40
Q

what are the two repeating periodicities of DNA

A

3.4 A and 34 A

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41
Q

why did watson and crick propose antiparallel strands for the DNA model

A

that’s the only way the hydrogen bonds line up

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42
Q

why do the antiparallel DNA strands become helical

A

the phosphodiester bonds that make up a stretch of nucleic acids make the molecule inherently diagonal. The only way to get hydrogen bonding is if the two strands twist around one another

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43
Q

what is the distance between each base in DNA

A

3.4 A

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44
Q

what is the width of the DNA helix

A

20 A

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45
Q

what is the width of the DNA helix when only the backbone is considered

A

11 A

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46
Q

how many stacked bases are there per turn

A

10.5 bases

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47
Q

what is the length of the 10.5 stacked bases in a turn

A

36 A

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48
Q

which is stronger: AT bonds or GC bonds

A

GC

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49
Q

why are GC bonds stronger than AT

A

GC have 3 hydrogen bonds whereas AT have only two

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50
Q

what are the two types of helical grooves

A

major and minor

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51
Q

what do the major and minor grooves dictate?

A

how easily proteins can bind to the molecule

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52
Q

T or F: a nucleotide is flexible around its bonds

A

true

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53
Q

why is a nucleotide flexible

A

it rotates around 7 different bonds

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54
Q

how many bonds does a nucleotide rotate around

A

7

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55
Q

which has two forms due to steric hindrance: purines or pyrimidines

A

purines

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56
Q

which two forms do purines have due to steric hindrance

A

anti and syn

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57
Q

which form do pyrimidines have: anti or syn

A

anti

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58
Q

which has less steric hindrance: anti or syn

A

anti

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59
Q

what is the name of the most stable watson-crick DNA structure

A

B form

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60
Q

other than B form, what are the two other forms

A

A and Z

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61
Q

when is A form common

A

in low-water conditions

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62
Q

when is Z form common

A

can occur when there’s alternating G/C residues

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63
Q

how does the major groove change in A form vs B

A

in A, the major groove is more pronounced

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64
Q

how does the major groove change in Z form vs B

A

in Z, the major groove is less pronounced

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65
Q

which has a wider helix w/ more base pairs per helical turn than B form: A or Z

A

A

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66
Q

which has a skinnier helix with more bp per helical turn than B: A or Z

A

Z

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67
Q

rank the DNA forms from widest to skinniest: A B and Z

A

A, B, Z

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68
Q

what is the handedness of B form

A

right

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69
Q

what is the handedness of A form

A

right

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70
Q

what is the handedness of Z form

A

left!!!!

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71
Q

rank the DNA forms from least to most bp per helical turn: A, B, Z

A

B, A, Z

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72
Q

what is the primary structure of nucleic acids

A

nucleotide sequence

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73
Q

what is the secondary structure of nucleic acids

A

regular, stable structures of some/all nucleotides

74
Q

what is the tertiary structure of nucleic acids

A

complex folding of chromosomes, tRNA, and rRNA molecules

75
Q

what is a palindrome

A

repeated section on a dif strand (complementary across a vertical axis on the other strand)

76
Q

what is a mirror repeat

A

repeated section on the same strand (identical across a vertical axis)

77
Q

which two structures can palindromes form

A

single-strand hairpins, double-strand cruciform

78
Q

what causes RNA to fold weird

A

G-U pairings (unusual)

79
Q

in the unusual G-U pairings that can occur in RNA, when does it occur: during folding or synthesis

A

folding

80
Q

T or F: DNA molecules are much larger than the structures that house them

A

true

81
Q

only about __% of human DNA codes for exons

A

1.5%

82
Q

how much of our DNA is made up of introns

A

almost a quarter

83
Q

considering both exons and introns, how much of the human genome consists of protein-coding genes

A

30%

84
Q

what does SSR stand for

A

simple sequence repeat

85
Q

what are SSRs (structure) + give 2 examples of DNA regions that contain lots of SSRs

A

short sequences less than 10 bp long, examples = telomeres and centromere

86
Q

what is the centromere

A

DNA that serves as an attachment point for proteins during cell division

87
Q

T or F: the telomere DNA sequence is different in everyone

A

false! it’s the same in everyone

88
Q

T or F: the number of SSR repeats in telomeres is the same in everyone

A

false; it’s different in everyone

89
Q

describe how telomeres are unique and similar amongst humans

A

everyone has the same SSR sequence in telomeres, but the number of SSRs is what differs

90
Q

what does CODIS stand for

A

combined DNA index system

91
Q

what does CODIS do

A

analyzes SSRs in two samples and shows you if there’s a match (ie in paternity tests, crime, etc)

92
Q

using SSRs, how do you determine a parental match (ie is he the father?)

A

you get one SSR allele from each parent, so if one SSR is different then the suspected person is not the father

93
Q

contrast a coil with a supercoil

A

coil = DNA double helix
supercoil = double helix coiling around itself

94
Q

what do we call DNA that is not supercoiled

A

relaxed

95
Q

T or F: relaxed DNA has no coils

A

false; it is coiled (double helix), but the coil does not coil around itself

96
Q

T or F: supercoiling is an intrinsic property of DNA

A

true

97
Q

in which DNA form are closed circular plasmids

A

B form

98
Q

in closed circular plasmids (B form), how many bp are there per helical turn

A

10.5 bp

99
Q

supercoiling often results from DNA that is (overwound/underwound) relative to B form

A

underwound

100
Q

since supercoiling results from underwound DNA relative to the B form, describe how the bp per helical turn + number of helical turns change

A

bp per helical turn increases, number of helical turns overall decreases

101
Q

T or F: so little as 1 extra/less helical turn from the relaxed # of helical turns can cause DNA to supercoil

A

true

102
Q

what are two possible ways a DNA molecule will accommodate strain

A

supercoiling, strand separation

103
Q

which is more likely: supercoiling or strand separation? why

A

supercoiling = more common. Strand separation requires the breaking of hydrogen bonds

104
Q

describe supercoiling during DNA transcription

A

DNA transcription requires strand separation = strain. DNA is overwound ahead of DNA pol, and underwound behind it

105
Q

is DNA typically overwound or underwound

A

underwound

106
Q

what happens if there is a nick in a supercoiled DNA

A

converts it to the relaxed state (circular)

107
Q

what is the linking number a measure of

A

the number of times a strand pierces the surface of a second strand

108
Q

T or F: as long as the strands are intact, the linking number is the same regardless of DNA bending or deformation

A

true

109
Q

T or F: linking number is always an integer

A

true

110
Q

T or F: linking number is almost always positive

A

true

111
Q

what letters represent linking number in an equation

A

Lk

112
Q

formula for determining linking number?

A

Lk = total # bp/number of bp per turn

113
Q

for relaxed DNA, how is Lk referred to as

A

Lk0

114
Q

formula for Lk0?

A

Lk0 = total # bp/10.5 bp per turn

115
Q

formula for delta Lk?

A

delta Lk = Lk - Lk0

116
Q

what does it mean to have a negative delta Lk

A

underwinding by n turns = n negative supercoils have been introduced

117
Q

what does it mean to have a positive delta Lk

A

overwinding by n turns = n positive supercoils have been introduced

118
Q

what is the handedness of a positive supercoil

A

left

119
Q

what is the handedness of a negative supercoil

A

right

120
Q

what is the Lk when the closed circular DNA has a nick? why?

A

no defined Lk because it could theoretically completely separate

121
Q

define superhelical density

A

a percentage of unwound or overwound turns

122
Q

formula for superhelical density?

A

σ = delta Lk/Lk0

123
Q

underwinding DNA leads to a (+/-) σ

A

negative

124
Q

overwinding DNA leads to a (+/-) σ

A

positive

125
Q

what is the name for enzymes that increase or decrease the extent of DNA underwinding

A

topoisomerases

126
Q

what do topoisomerases do to DNA

A

they change the Lk

127
Q

when do topoisomerases manage strain in the DNA

A

during replication

128
Q

how many types of topoisomerases are there

A

2

129
Q

describe the role of type I topoisomerase

A

transiently breaks one of the two DNA strands, then passes the unbroken strand through the break and then rejoins the break

130
Q

by how much do type I topoisomerases change the Lk (and is it adding or reducing)

A

reduces it by 1

131
Q

describe the role of type II topoisomerase

A

transiently breaks both strands and passes another part of the helix through the gap

132
Q

by how much do type II topoisomerases change the Lk (and is it adding or reducing)

A

reduces it by 2

133
Q

describe the full mechanism of topoisomerases (type 1)

A

open conformation: active site Tyr attacks a phosphodiester bond in one strand = cleaving it. Unbroken DNA passes through the break.
closed conformation: cleaved DNA is re-ligated

134
Q

in solution, what is the structure of supercoiled DNA

A

plectonemic

135
Q

describe plectonemic structure

A

simple, intertwined structure

136
Q

does plectonemic structure provide sufficient compaction?

A

no

137
Q

when stabilized by proteins, what structure does DNA take the form of

A

solenoid

138
Q

describe solenoidal structure

A

like a garden hose

139
Q

which is more compact: solenoidal or plectonemic

A

solenoidal is more compact

140
Q

T or F: DNA can easily interchange between plectonemic and solenoidal supercoiling

A

true

141
Q

in what form is DNA in non-dividing cells, G1, G2, and S

A

an anamorphous + randomly dispersed blob

142
Q

in which phase of the cell cycle do chromosomes condense and take the form of well-defined pairs of sister chromatids

A

prophase

143
Q

what is chromatin

A

the material within a chromosome

144
Q

chromatin is __% protein and __% DNA

A

50/50

145
Q

which proteins are the main component of chromatin

A

histone proteins

146
Q

how many monomers makes up a histone

A

8

147
Q

how many bp of DNA wrap around the histone octamer

A

200 bp

148
Q

list the classes of histones

A

H1, H2A, H2B, H3, H4

149
Q

how many times does the histone octamer wrap around the DNA

A

1.67 x

150
Q

how many bp serve as linker DNA between histones

A

50 bp

151
Q

which histones/how many histones do nucleosomes have

A

contains two copies of H2A, H2B, H3, and H4

152
Q

in which type of supercoil does DNA wrap around a histone

A

solendoial supercoil

153
Q

how is contact formed between nucleosomes

A

histones have disordered N-terminal tails that extend outwords

154
Q

T or F: histone tails can be modified

A

true

155
Q

give 2 examples of histone tail modification

A

methylation, ubiquitinylation

156
Q

how many nm are the beads on a string structure

A

10 nm

157
Q

in the compaction hierarchy, what comes after the 10 nm beads on a string

A

30 nm fiber

158
Q

how is formation of the 30 nm fiber initiated

A

initiated by histone H1 binding to the linker DNA between histone octamers

159
Q

in the compaction hierarchy, which two forms come after the 30 nm fiber

A

use of scaffolding proteins and rosette coiling

160
Q

what does SMC stand for

A

structural maintenance of chromosomes

161
Q

how many domains do SMC proteins have

A

5

162
Q

list the 5 domains of SMC proteins

A

N term globular head, N term a-helical connector, hinge domain, C term a-helical connector, C term globular head

163
Q

in regards to SMC protein structure, when can ATP hydrolysis occur? explain

A

N and C globular heads each contain part of an ATP hydrolysis site, so when they’re folded then these sites can interact and ATP hydrolysis can occur

164
Q

describe the structure when SMC proteins fold

A

V-shaped dimer where monomers are connected at the hinge site

165
Q

T or F: SMC proteins are found in all organisms

A

true

166
Q

list the two major eukaryotic SMC families

A

cohesin and condensin

167
Q

role of cohesins?

A

help link together sister chromatids immediately after replication and keep them together until metaphase

168
Q

how do cohesins keep sister chromatids together

A

they form a ring around them that ties DNA together

169
Q

role of condensins?

A

help chromosomes condense for the entirety of mitosis

170
Q

how do condensins keep chromosomes condensed

A

they induce overwinding/positive supercoiling

171
Q

briefly describe the condensin mechanism

A

initially DNA is bound at the hinge region inside a ring formed by the condensin dimer. ATP binding and hydrolysis changes the condensin conformation and the protein then induces positive supercoiling (supercoiling can happen two ways)

172
Q

describe the two ways of supercoiling that can occur via condensin

A

DNA can coil between hinge regions (=fibers), or around the hinge regions (=rings)

173
Q

SMC mechanism: describe the steps

A

cohesins are loaded onto the chromosomes during S phase and tie the sister chromatids together during replication. At the onset of mitosis, condensins bind and maintain the chromosomes in the condensed state. Right before anaphase, the enzyme separase degrades the cogesisn and the chromatids can separate. At the end of mitosis, condensins begin to unload and the daughter chromosomes return to the uncondensed state

174
Q

T or F: The entire eukaryotic chromosome, once condensed, is limited to a particular subnuclear domain or chromosome territory

A

true

175
Q

T or F: there is little interaction between DNA in different territories

A

true

176
Q

where is euchromatin located in a cell? why

A

near the center of the nucleus because they have many actively expressed genes

177
Q

where is heterochromatin located in a cell

A

in the peripheral territories

178
Q

bacterial DNA is compacted in a structure called the _________

A

nucleoid

179
Q

describe the organization of bacterial DNA in the cell

A

circular DNA is looped into domains of 10,000 bp by scaffolds. There’s 500 of these looped domains

180
Q

why doesn’t bacterial DNA condense or form DNA-protein interactions

A

because it needs to be accessible for replication more often

BIOL 3421 - molecular biochem (20 decks)

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