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MBB 222 > final > Flashcards

final Flashcards

1
Q

what is chromatin a mixture of

A

dna and proteins that form chromosomes

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2
Q

what do the proteins in chromatin do, what is the main one

A

they pack dna into a compact form, especially histones

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3
Q

what phase of the cell cycle is dna especially compact

A

metaphase

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4
Q

what is chromosome structure during each phase of cell cycle

A

interphase : chromosomes are present as chromatin (uncondensed)

s phase (DNA synthesis): each chromosome is replicated, resulting in 2 sister chromatids

prophase: chromosome becomes more condensed

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5
Q

what happens to chromosome once cell division is complete

A

becomes less condensed

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6
Q

what is euchromatin

A

less condensed form of chromatin, in non-dividing cells

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7
Q

what is heterochromatin

A

more condensed form, in diving cells

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8
Q

what do histones do

A

protect and package the dna and regulate replication and transcription by controlling access to the machinery

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9
Q

what is a nucleosome

A

dna wrapped around histones

fundamental unit of chromatin (beads on a string)

histones packages and orders dna into them

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10
Q

what does a core histone comprise of

A

2 copies of each, form an octet (8 subunits)

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11
Q

what chromatin is 11 nm and what one is 30nm

A

11 - beads on a string - heterochromatin

30- solenoid - euchromatin

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12
Q

what holds dna on histone core

A

H1 histone

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13
Q

how much h1 is there on genes being actively transcribed (being used as templates)

A

little to none

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14
Q

what is higher order chromatin structure attached to

A

nuclear/chromosome scaffold

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15
Q

what do histones mainly react with , what does this explain

A

phosphate backbone on dna

explains their lack of specificity

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16
Q

what mediates assembly of 30nm fiber

A

N terminal histone tail

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17
Q

what is 30nm finer held together by

A

h1 proteins - pull nucleosomes together

N terminal tails - bind dna on existing nucleosomes

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18
Q

does gene transcription occur in solenoid

A

no

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19
Q

what is chromatin remolded by

A

enzymes that covalently modify histones (ex HATs)

chromatin remolding complexes (increase decrease accessibility to dna

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20
Q

what 3 dna sequences control separation and copying of chromosomes

A

replication of origins

centromere

telomere

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21
Q

what is the replication origin

A

where dna duplication begins

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22
Q

why do eukaryotic chromosomes contain may replication origins

A

to ensure they can be duplicated rapidly

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23
Q

what is a centromere

A

attachment site for biotic spindle via protein complex called kinetochore

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24
Q

what is a telomere

A

formed at end of chromosomes

like aglet on shoelaces

protects end of chromosomes from shortening with each cell division

highly repetitive - so not recognized as dna

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25
Q

what do telomerases have as part of their active site and why

A

RNA molecule

acts as template for extension of telomere, which allows their degradation

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26
Q

why are telomerases a reverse transcriptase

A

since they use ran template to make dna

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27
Q

why are the 3’ ends of chromosome ssDNA

A

degradation of rna primer

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28
Q

what happens to 3’ ssDNA

A

dsDNA is synthesized from extended 3’ ends using ran primer, dna pol

remaining ss 3’ oh ends are protected by looping and dna binding proteins
telomeres

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29
Q

what is primary structure

A

nucleotide sequence

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30
Q

what is secondary structure

A

stable structure adopted by a segment of dna

typically a base paired double helix

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31
Q

what is a tertiary structure

A

3d fold

complex folding into super coils and chromatins

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32
Q

what are the purines

A

adenine

guanine

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33
Q

what are the pyridines

A

thymine, uracil, cytosine

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34
Q

what does base + sugar =

A

nucleoside

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35
Q

what is base + sugar + phosphate =

A

nucleotide

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36
Q

what is pentose in rna and dna

A

ribose in rna

deoxyribose in dna

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37
Q

what does rna have on 2’ carbon

A

2’-OH

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38
Q

what does dna have in 2’

A

2’-H (acid)

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39
Q

is the 2’-oh of rna or 2’-h of dna less stable

A

rna is less stable and more reactive

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40
Q

where is ribose attached to base on nucleoside

A

attached to base via its 1’ carbon

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41
Q

what attacks phosphate

A

5’ c of pentose

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42
Q

what is 3’-oh of one nucleotide is linked to 5’ phosphate on adjacent nucleotide forming ?

A

sugar-phosphate backbone of DNA

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43
Q

how does phosphate group link pentoses

A

phosphodiester bond

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44
Q

what happens to phosphate group of every nucleotide at physiological pH

A

its deprotonated so they carry a negative charge

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45
Q

how many h bonds are between G and C

A

3

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46
Q

how many h bonds are between A and T/U

A

2

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47
Q

what type of linkage is the bond between pentose and base

A

beta linkage

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48
Q

what does a b linkage mean

A

base lies in plain above the sugar

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49
Q

what does an alpha linkage mean

A

base lies below the plane of sugar

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50
Q

how do ribonucleotides differ from deoxyribonucleotides

A

have hydroxyl at the ribose 2’ (not deoxy)
uracil

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51
Q

what holds two dna strands together

A

h bonds

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52
Q

do dna strands run in same direction

A

no, they’re anti parallel

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53
Q

in addition to h - bonds what else holds double helix together

A

base stacking between aromatic hydrophobic bases

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54
Q

what does base stacking do

A

minimizes contact with h2o, stabilizing it

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55
Q

what force is base stacking a form of

A

van der waals

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56
Q

what does base stacking result in

A

minor / major grooves

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57
Q

what are the difference in depth of major and minor grooves

A

major = deep

minor = shallow

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58
Q

what type of groove are base pairs more exposed to solvent

A

major

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59
Q

where are functional groups in base pairs that aren’t involved in bp more exposed, and what is the purpose of this

A

in grooves, especially major

these exocyclic groups serve as contact points for proteins

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60
Q

what is a b form (b-helix/bDNA)

A

form normally found in cells

right handed

most stable under physiological conditions

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61
Q

what is a-form of dna

A

when dna is dehydrated it assesses the a form

right handed double helix

wider shorter, bp are more tilted, deeper major grooves, shallower minor grooves

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62
Q

where is a form frequently found

A

dna-rna hydrids

ds RNA (tRNA)

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63
Q

what is z-form dna

A

left handed and stretched

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64
Q

what frequency do nucleotide bases absorb light at

A

260 nm

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65
Q

what is TM

A

melting point

temperature at which half of dna is ss and other half is ds

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66
Q

do stacked bases absorb more or less UV light

A

less

hypochromism

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67
Q

what determines what temperature TM occurs at

A

nucleotide sequence length

[salt]

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68
Q

what does high [salt] and longer sequences result in, why

A

stablize sequence, increase TM

salt ions shield negatively charged phosphates on DNA backbone, which repel each other when unshielded

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69
Q

under what circumstances can supercoiling only occur

A

in a molecule where both strands are closed circles or fixed at one end

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70
Q

what a LK

A

of times one strand crosses over the other

LK for closed circular DNA is always an integer

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71
Q

what level of wound is most cellular dna

A

umderwound (fewer helical turns than expected for B form)

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72
Q

what does unwinding induce and what does it do to accommodate

A

structural strain

can accommodate by supercoiling or break H bonds (usually super coiling)

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73
Q

what does cells underwinding their dna using topoisomerases to result in a strained state result in

A

form of stored energy

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74
Q

what does underwound supercoiled state allow

A

compact packaging of DNA

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75
Q

what is the only way LK can change

A

unless one or both of the strands is broken

can be changed by means of topoisomerases

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76
Q

does super coiled dna more slower/fatser

A

faster

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77
Q

what is a topoisomerases

A

enzymes that catalyze interconversion of topoisomers (change supercoiling by cutting / splicing DNA)

chang LK

78
Q

how do topoisomerases change the LK

A
  1. cleavage of one/both strands of DNA
  2. passage of segments of DNA through this break
  3. resealing of DNA breaks
79
Q

what are the two types pf topoisomerases

A

TOPO I : change LK by increments of 1

TOPO II : removing 2 turns at a time

80
Q

what is protein synthesis

A

translation

nucleotide sequence in mRNA is translated by tRNAs into amino acid sequence in polypeptides

81
Q

what is link between DNA and protein

A

RNA

82
Q

where do steps of protein synthesis take place in eukaryotes

A

DNA is confined to the nucleus, RNA is made in nucleus (transcriptions) but is exported to cytoplasm

protein is synthesized in cytoplasm

83
Q

what is protein synthesis proportional to

A

amount of RNA in cell

84
Q

what is mRNA

A

intermediary between gene and protein

provides transcript that is read by tRNA

85
Q

what is tRNA

A

reads genetic code, brings amino acids to the growing polypeptide chain

86
Q

what is rRNA

A

in ribosome

provide scaffold for protein synthesis, catalyze peptide bond formation

87
Q

do amino acids bind directly to mRNA

A

no

88
Q

what is a frameshift

A

insertion or deletion of one of two bases result in frameshift

89
Q

how is nucleotide sequence in mRNA translated into an amino acid sequence in proteins

A
  1. enzyme called tRNA synthase attaches an amino acid onto one end of tRNA
  2. tRNA brings that amino acid to growing polypeptide chain in the ribosome, selected by base pairing between 3’ nucleotide and anticodon on the tRNA and the 3 nucleotide codon on mRNA
90
Q

are tRNA and mRNA parallel

A

no

91
Q

what is a start codon

A

at start of gene - signals start of protein synthesis

92
Q

what is a stop codon

A

signal the end of gene

terminate protein synthesis

93
Q

do stop codons encode an amino acid

A

no

94
Q

what direction does tRNA read mRNA

A

5’ to 3’

95
Q

what are the 4 steps of polypeptide synthesis

A
  1. initiation
  2. elongation
  3. termination
  4. ribosome recycling
96
Q

what are ribosomes

A

ribonucleoproteins that catalyze protein translation

97
Q

what are the 3 sites on a ribosome

A

a site : for aminoacyl tRNA

P site : for peptidyl tRNA

E site: for exit

98
Q

what direction do ribosomes tracks along the mRNA

A

5’ to 3’

N to C

99
Q

what are the steps of initiation

A
  1. GTP and initiation factors bind to 30S ribosomal subunit
  2. complex tracks along mRNA until it finds the ribosomal binding site (RBS) (In banteria its the shine-dalgarno sequence SDS), positioning the the start codon in the P site. then a special initiation tRNA charged with a modified methionine (fmet) binds to that start codon
  3. the 50S ribosomla subunit binds, GTP is hydrolyzed and initiation factors are released, forming a functional 70s subunit initiation complex , with modified methionine (fmet) in P site, with A and E site empty
100
Q

what are the steps of prokaryotic initiation

A
  1. initiation factors bind to 30s subunit. some bind to/hydrolyze GTP to facilitate steps in translation
  2. since SDS is upstream of start codon on the mRNA, it positions the start codon on the P-site. 30s subunit recognizes SDS via bp and rRNA
  3. Initiation factor is released and the 50S subunit binds to the 30S

GTP is hydrolyzed, facilitating release of ignition factors, resulting in 70s ignition complex

101
Q

what is the only thing that can bind to P site

A

Initiating tRNA (fmet - tRNA ) can bind to p site

all other amino acids bind to a site

102
Q

why is GTP like ATP

A

has high energy phosphodiester bonds

hydrolysis of these bonds provide energy

103
Q

what are the steps of elongation

A
  1. elongation factor binds to GTP and then to an amino acid - tRNA
  2. GTP binds to 70s initiation complex at the a site via base pairing with mRNA
  3. GTP is hydolyzed and GTP is released and recycled
  4. the rna in the 50s subunit catalyzes the transfer of amino acid #1 (fmet tRNA) to the new amino acid, forming new peptide bond
  5. for the ribosome to translocate one codon along the mRNA to next site of amino acid addition, a second elongation factor binds to GTP and associates with the A site
  6. GTP is hydrolyzed and ribosome is translocated along mRNA in 5’ to 3’ direction. new initiating tRNA is in P site, and discharged tRNA is now in e site where its released, opening a site
104
Q

what catalyzes the transfer of growing polypeptide to from tRNA in p site to the amino acid on the rna in the a site

A

ribozyme activity of rRNA within the p site of 50s subunit

105
Q

during peptidyl transfer what acts as nucleophile

A

amino n of incoming A site amino acid , attacking C electrophile in 3’ terminus of p site

106
Q

what is an termination/release factor (RF)

A

protein that mimics tRNA transfer and can bind to a site when a stop codon is present

107
Q

what happens in bacteria when a codon occupies a site

A

a GTP bound RF binds to a site, which causes dissociation of 70s subunit

108
Q

what initiates protein synthesis of eukaryotes

A

mRNA binds to ribosomes at 3’ poly A tail by poly A binding protein (PABP)

109
Q

what is the only thing that can bind to the small subunit at p site without complete ribosome present

A

only the met charged with initiating tRNA met can bind to it

110
Q

what is initiation powered by

A

ATP and GTP hydrolysis

111
Q

what do chaperons do

A

prevent proteins from aggregating via exposed hydrophobic regions

shield hydrophobic regions

also help fold misfolded proteins correctly

112
Q

what destroys misfolded proteins

A

atp- dependent protease complex called proteasome

113
Q

what does ubiquitin do

A

marks proteins with exposed hydrophobic regions for destruction

allows them to be recognized by proteasome

114
Q

what is a mobile genetic element

A

nucleic acid segments (DNA/RNA) that can move in/out of cells or between different regions of of cell genome

115
Q

what is recombination

A

when some mobile genetic elements get integrated into host genome

116
Q

what are the types of mobile genetic elements

A

plasmids

viruses

transposable elements (transposons)

free dna

117
Q

what is a plasmid

A

extra chromosomal circular ds dna found in bacteria, yeast, fungi

replicates with host machinery

lack protein coat and cant more independently from cell to cell, can through conjugation

118
Q

what is a virus

A

infectious dna or rna containing elements that possess a protein coat that allows them to move from cell to cell

replicate using host proteins, use some of their own which are synthesized into host

119
Q

what are transposable elements

A

lack a protein coat and can be excised from one part of host genome and can insert into another part via recombination

120
Q

what is free dna

A

from lysed bacteria, can be taken up by other related bacteria

121
Q

what do plasmids often encode

A

functions that can give an advantage to host such as abiotic resistance

122
Q

do plasmids tend to incorporate into host genome

A

no

123
Q

what are virulence factors

A

may contribute to virulence (severity) of pathogen

124
Q

what are plasmids related to

A

bacteriophage genomes

125
Q

what happens to lytic phage genome

A

doesn’t integrate into the host chromosome, replicated extra-chromosally

assembled phage often lyse their host cell when they’re released

126
Q

what is lysogenic phage genome

A

becomes integrated into host genome via recombination , forms a prophage that is replicated along with host dna, passed onto daughter cells

127
Q

how can plasmids, phage, and free dna can be passed from one cell to another

A

horizontal gene transfer :

  1. transformation: uptake of naked DNA
  2. transduction: injection of foreign dna by a bacteriophage
  3. conjugation: compatible strains join via a conjugative pilus - conjugation bridge forms
128
Q

what do restriction endonucleases do

A

degrade viral genome
recognize a short DNA sequence (a restriction site) and cut the strands

129
Q

what produces restriction endonucleases (RE)

A

by bacteria to protect from viral infection

130
Q

what does a polymerase chain reaction (PCR) do

A

amplifies specific DNA sequence

so you don’t need to cut gene of interest out

131
Q

when must rna bp with dna

A

transcription

132
Q

is rRNA coding

A

no

133
Q

in prokaryotes what are all RNAs transcribed by

A

a single RNA polymerase

134
Q

where does bacterial transcription take place

A

all in cytoplasm (no nucleus)

135
Q

what processes are coupled in bacteria

A

transcription + translation

both occur in same direction (5’ to 3”) and everything is synthesized in cytoplasm so protein synthesis can occur as mRNA is being synthesized

136
Q

what regulates protein expression in bacteria

A

mRNA production

137
Q

what does [mRNA] depend on

A

rate of synthesis/degradation of mRNA

138
Q

what are three elements of gene control in prokaryotes in order of importance

A
  1. transcription initiation
  2. rna turnover (by nuclease degradation)
  3. transcription termination
139
Q

what does dna transcription produce

A

ss rna

140
Q

what does prokaryotic transcription require

A

rna polymerase

ds dna template

ribonuclease (NTP)

Mg 2+

no primer !

141
Q

what do Mg ions do

A

coordinate the phosphates of incoming NTPs, position P alpha for nuc attack

142
Q

what do ribonucleases (NTP) do

A

breaks down the RNA by cleaving the phosphorus-oxygen bonds.May 20, 2022

143
Q

what does RNA pol do to initiate rna syntheis

A

bind to promoter sequences,

recognizes promoter via sigma factor

144
Q

what does RNA pol + sigma subunit =

A

rna polymerase holoenzyme

145
Q

what is the bacterial transcription cycle

A
  1. initatition: rna polymerase holoenzyme forms, binds non-specifically to DNA
  2. polymerase partially unwinds DNA (has helices like activity), opens complex and begins transcribing
  3. after about ten ribosucleitides are polymerized, polymerase undergoes conformation change, releasing sigma factor , enabling it to move forward rapidly
  4. elongation
  5. termination
146
Q

what stage in prokaryote transcription relies on a sigma factor

A

initiation

147
Q

where does prokaryotic transcription have to start

A

at promoter

148
Q

what is rho

A

a termination factor

prokaryotes are either rho dependent or independent

149
Q

what are activators

A

increase expression levels

150
Q

what are repressors

A

decrease expression levels

151
Q

how do repressors work

A

bind near promoter and block RNA polymerase transcription

152
Q

how do activators work

A

bind near promoter and enhance ability of RNA polymerase

often near weak promoter

153
Q

what are inducers:

A

ligand that decrease affinity of the repressor

154
Q

what are co-repressors

A

ligands that increase the affinity of repressor

155
Q

where is transcription machinery in eukaryotes

A

nucleus

156
Q

are eukaryotes cells organized into operons

how are they organized

A

no

transcribed as monocistronic messages with a promoter for every gene

157
Q

what does rna polymerase I (RNAPI) synthesize

A

synthesis of rRNA

158
Q

what does rna polymerase II (RNAPII) synthesize

A

mRNA

159
Q

what does rna polymerase I (RNAPIII) synthesize

A

tRNA

160
Q

what do eukaryotic polymerases require to bind DNA

A

transcriptions factors

161
Q

in eukaryotes what provides transcription for a given promoter

A

TF

162
Q

what does RNAP I transcribe

A

transcends 1 gene
4ss precursor rna for rRNA

163
Q

how much stuff does RNAP II transcribe

A

tens of thousands

164
Q

how much stuff does RNAP III transcribe

A

hundreds

165
Q

what does binding of RNAP II factors to promoter do

A

imitates polymerization

166
Q

do eukaryotes use positive or negative regulation more

A

positive

167
Q

where do activators bind in eukaryotes

A

specifically to enhancer sequences near promoter

168
Q

how do activators help assemble polymerase initiation complex

A

by recruiting RNAP II

169
Q

what mediates splicing

A

spliceosome complex that associates with RNAP II

170
Q

what are introns

A

non coding regions

171
Q

what is the difference between group 1 and 2 introns

A

The key difference between group I and group II introns is that in group I introns, the splicing reaction is initiated by a guanosine cofactor, while in group II introns, the splicing reaction is initiated by internal adenosine

172
Q

what is dna replication

A

duplication of chromosomes

173
Q

what are the dna building blocks

A

deoxynucleoside monophosphate (dNMP or NMP)

174
Q

what does replication occur by

A

addition of NMPs to 3’-OH of a nascent (new) strand

175
Q

what direction does dna synthesis occur in

A

5’ to 3’

176
Q

what are the raw materials of dna replication

A

dna template
deoxynucleoside triphosphate (dNTPs)
Mg2+ ions (cofactor for polymerase)
DNA/RNA primer to provide first 3’-oh
dna polymerase

177
Q

what is DNA polymerase

A

large protein complex that includes the enzyme that catalyzes the addition on NMPs to DNA polymer

178
Q

what do DNA polymerase reactions add to the 3’ end of growing strand

A

deoxynucleotide

179
Q

what does Mg2+ do

A

stabilize negative charges on incoming dNTP and assists in deprotonation of 3’-OH

180
Q

what does DNA pol III do

A

main polymerizing enzyme

181
Q

what does DNA pol I do

A

completes Okazaki fragment synthesis (replace RNA with DNA)

182
Q

what direction is polymerization always in

A

5’ to 3’

183
Q

what is exonuclease

A

an enzyme that catalyzes the hydrolysis of phosphodiester bonds at the end of nucleic acid molecules (cuts DNA strand)

184
Q

where does dna replication occur

A

replication forks

185
Q

what are the pimosomes and what do they do

A

primase: generates rna primer

helicase: unwinds dna

186
Q

why does lagging stand loop around

A

allows both dna pol III subunits to move together in same direction

187
Q

what is processivity

A

the ability of an enzyme to repetitively continue in catalytic function without dissociating from substrate

188
Q

what dna pol is less processive, why

A

dna pol I

doesn’t have clamp

189
Q

what does the beta clamp allow for and not allow for

A

allows for processivity of leading but not lagging strand

190
Q

what is nick translation

A

process of simultaneously adding NMPs to the 3’ end of Okazaki fragment and removing NMPs from the adjacent from the adjacent 5’ end of the rna primers

completes synthesis of lagging strand

191
Q

what do incorrect bases result in

A

steric clashes

MBB 222 (3 decks)

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