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Microbiology > L7 > Flashcards

L7 Flashcards

1
Q

define genome

A

entire genetic component

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2
Q

define genetics

A

study of inheritance/inheritable traits

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3
Q

define gene

A

sequence that codes for a specific polypedtide or RNA

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4
Q

What are nucleotides?

A

building blocks of nucleic acids

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5
Q

What are base pairs, and how do they pair up?

A

(bp), the specific pairs of nitrogenous bases, G:C, A:T, A:U

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6
Q

What is the 5’ end?

A

terminates in a phosphate group attached to the 5’ carbon

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7
Q

What is the 3’ end?

A

terminates with a hydroxyl group bound to the 3’ carbon, strands run antiparallel (one runs 5’ to 3’, the other 3’ to 5’)

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8
Q

define genotype

A

genetic makeup, potential properties

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9
Q

What is the term for properties of appearance that is expressed genetically?

A

phenotypes

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10
Q

define Central Dogma of Molecular Biology and who discovered/invented it

A

DNA > RNA > protein, by Francis

Crick in 1956

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11
Q

localized region of bacterial chromosome

A

nucleoid

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12
Q

organized molecule of DNA associated with proteins, typically circular in bacteria, usually 1-2 of them, cells are haploid, not back to back genes - there are non-coding STRs (short tandem repeats) occur in most repeating sequences of 2-5 bases

A

chromosomes

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13
Q

small, circular DNA molecules that replicate independently of chromosomes

A

plasmids

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14
Q

carry genes for enzymes or toxins to make the bacteria pathogenic

A

virulence plasmids

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15
Q

carry genes for bacteriocins (toxins) to kill competitor bacteria, can kill same or similar species without the facter

A

bacteriocin plasmids

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16
Q

double membrane surrounds genetic material

A

nuclear envelope

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17
Q

10 nm beads of DNA wrapped around histones

A

nucleosomes

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18
Q

nucleosomes clumped with proteins to form 30nm diameter fibers dispersed throughout nucleus

A

chromatin

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19
Q

globular proteins used in packing DNA into chromosomes, DNA has a negative charge, histones have positive charge

A

histones

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20
Q

Which genome is often diploid with more than 1 chromosome and linear?

A

eukaryotic genome

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21
Q

This term describes the single leg of chromosome.

A

chromatid

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22
Q

With semiconservative replication, the replicated DNA is composed of what two parts?

A

original daughter strand and one new strand

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23
Q

Initial Process: begins at sequence called “__,” DNA __ unzip DNA and exposed nucleotides in __, DNA __ binds strand and adds nucleotides from __’ to __’

A

origin; helicases; polymerase; 3; 5

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24
Q

Synthesis of lagging strand: synthesized in __ segments that are later __

A

short; joined

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25
Q

Synthesis of leading strand: synthesized __ as a single long chain of nucleotides from __’ to __’

A

continuously; 5; 3

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26
Q

__ synthesis usually proceeds in both directions from its origin, involves sets of enzymes and replication forks

A

bidirectional synthesis

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27
Q

removes coils from unwinding by cutting, rotating, and rejoining ends

A

gyrase and topoisomerase

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28
Q

Replication of eukaryotic DNA uses different DNA polymerases, __ initiates and synthesizes primer, __ elongates leading strand, __ elongates lagging strand, __ replicates mitchondrial DNA

A

1st; 2nd; 3rd; 4th

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29
Q

Due to long, linear chromosome, how many origins of replication might you see eukaryotic DNA?

A

1000s

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30
Q

Approximately how many nucleotides long are Okazaki fragments in eukaryotic DNA?

A

100-400 nucleotides

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31
Q

sets of genes in genome of organism

A

genotype

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32
Q

physical features/traits of organism

A

phenotype

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33
Q

DNA > RNA, make an RNA copy of a gene from DNA

A

transcription

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34
Q

synthesis of polypeptide (proteins) from the RNA copy

A

translation

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35
Q

RNA molecules that act as enzymes

A

ribozymes

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36
Q

carry genetic information from chromosomes to ribsomes

A

mRNA

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37
Q

delivers amino acids to ribosomes

A

tRNA

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38
Q

used by DNA polymerase during DNA replication

A

RNA primer

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39
Q

combine with ribosomal polypeptides to form ribosomes

A

rRNA

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40
Q

interacts with DNA to control gene expression

A

regulatory RNA

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41
Q

(initiation) bacteria, unzips and unwinds DNA, binds promotor, sigma factor is necessary to recognize the promotor in

A

RNA polymerase

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42
Q

(initiation) near the beginning of the gene, initiates transcription, not all RNA polymerase binds to all promotos equally strong, affects amount/type of protein transcribed

A

promotor

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43
Q

(initiation) in bactera, this portion of RNA polymerase is needed for recognition

A

sigma factor

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44
Q

(initiation) protein used in eukaryotes to help bind RNA polymerase to primer

A

transcription factors

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45
Q

(elongation) Begins __ nucleotides away from promotor.

A

10

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46
Q

(elongation) Transcribes 1st __ ribonucleotides.

A

10

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47
Q

(elongation) RNA polymerase releases its __ to allow it to __ to the DNA tightly

A

sigma factor; adhere

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48
Q

(elongation) Many RNA polymerases can __ transcibe the same gene.

A

concurrently

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49
Q

(elongate) Links nucleotides in __ direction.

A

5’ to 3’ direction

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50
Q

self termination: RNA __ transcribes a terminator sequence rich in __ and __ bases followed by a region rich in __ and __

A

polymerase; G; C; A; U

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51
Q

(self-termination) It slows down in __ region, because of 3 __ bonds between them.

A

GC; H

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52
Q

(self-termination) Forms __ and __ structure to put __ on structure and then pulls off in __ rich area.

A

stem; loop; tension; adenine

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53
Q

(enzyme dependent termination) = __ dependent: depends on termination __ that binds to specific sequence near the __ of RNA __ moves towards __ end and forces RNA __ and DNA apart

A

Rho; protein; end; transcript; 3’ end; polymerase

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54
Q

RNA unwinds DNA itself, DNA requires __.

A

helicase

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55
Q

RNA, regarding speed is __ compared to DNA.

A

slower

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56
Q

RNA incorporates __ instead of DNA’s __.

A

ribonucleotides; deoxyribonucleotides

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57
Q

RNA uses “U” instead of DNA’s __.

A

T

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58
Q

RNA is __ efficient proofreading compared to DNA, errors that occur every __ nucleotides.

A

less; 10,000

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59
Q

RNA polymerase copies only __ of the DNA strands

A

1

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60
Q

Transcription occurs in the __ of eukaryotics cell, and in the __ of a prokaryotic cell.

A

nucleus; cytoplasm

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61
Q

Transcription factors assist in binding __ to __.

A

RNA polymerase; promotor

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62
Q

Eukaryotes must process __ before translation.

A

mRNA

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63
Q

Name three events of eukaryotic DNA processing.

A

1) add 5’ cap
2) add poly A tail
3) splicing to remove introns

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64
Q

introns

A

intervening sequences

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65
Q

exons

A

expressed/coding sequences

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66
Q

define translation

A

ribosomes read genetic info to synthesize polypeptide

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67
Q

What are the stop sequence codes?

A

UAA, UAG, UGA

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68
Q

What are the start codons in eukaryotes and prokaryotes?

A

AUG: methionine in eukaryotes; n-formyl methionine in prokaryotes

69
Q

define genetic code

A

nearly universal with few exceptions, is redundant, more than 1 codon associated with each amino acid

70
Q

Codons are triplets of mRNA nucleotides associated with what?

A

amino acids

71
Q

What does mRNA carry?

A

AUG start

72
Q

Prokaryotic ribosomes can start translation before transcription is done, T or F?

A

true

73
Q

Eukaryotic mRNA contains __ called __.

A

noncoding regions; pre-RNA

74
Q

Introns: __ removed to make a functional mRNA “__”

A

noncoding regions; intervening sequences

75
Q

Exons: __, aka “__”

A

coding regions; expressed

76
Q

Eukaryotic mRNA carry instructions for only __ polypeptide, where there may be more than __ in prokaryotes.

A

1; 1

77
Q

Eukaryotic __ not __ until fully transcribed and move __ of nucleus.

A

mRNA; translated

78
Q

enRPS: small nuclear __, remove __ and __ exons together, in some __ act as a __ to __ own __

A

ribonucleoproteins; introns; splice; introns; ribozyme; catalyze; removal

79
Q

How many ribonucleotides long is tRNA? What structure does it form? Where are its receptor sites located, and what do they accept?

A

about 75; 3 main haripin loops; acceptor site for a specific amino acid at 3’ end and anticodon in the bottom loop

80
Q

Where are anticodons located? How many anticodons?

A

at the bottm of tRNA; 64

81
Q

What benefit comes from most amino acids having signals from multiple alternative codons?

A

degeneracy

82
Q

Ribosome: __ in prokaryotes, __ in eukaryotes, each has 2 subunits, the smaller subunit shaped to accomodate 3 __ a __ time

A

70s; 80s; codons; 1

83
Q

the A site

A

accomodates tRNA delivering an amino acid

84
Q

the P site

A

holds a tRNA and growing polypeptides

85
Q

the E site

A

tRNA exits from this site

86
Q

During initiation, what components form the initiation complex?

A

nRNA, 2 ribosomal subunits, tRNA, and several protein factors

87
Q

During the first step of elongation the tRNA matching the next codon attaches to a __ site.

A

A

88
Q

What happens in step 2 of elongation?

A

larger subunits ribozyme forms peptide bond between the terminal amino acid, the newly introduced amino acid, polypeptide attached to tRNA on A site

89
Q

In step 3 of elongation, using GTP energy, the ribosome moves down 1 codon and transfers tRNA to what?

A

adjacent site

90
Q

In step 4 of elongation, ribosomes release what?

A

“empty” tRNA from E site to be recharged

91
Q

In step 5 of elongation, the cycle repeats, at about what rate of amino acid per second?

A

15 amino acids/second

92
Q

after one ribosome exposes the start, additional ribosomes may attach behind the first one

A

polyribosome

93
Q

release factor halt elongation, recognize stop codons and modify large subunit to activate ribosome to sever polypeptide from final tRNA and dissociates subunits

A

termination

94
Q

about 75% of genes are expressed all of the time, others are regulated to polypeptides are only synthesized when needed

A

control of transcription

95
Q

This type of transmission is similar to eukaryotes, but lacks ER.

A

archae translation

96
Q

What components make up operon?

A

promotor, adjacent operator, and series of genes which code for enzymes and structures

97
Q

Where does the repressor protein bond to stop transciption?

A

operator

98
Q

This must be activated by inducers and its not usually transcribed.

A

inducible operon

99
Q

What deactivates a repressible operon?

A

repressors

100
Q

What controls a lactose operon?

A

regulator gene

101
Q

What are two events that can activate a lac operon?

A

1) positive regulation by the CAP (catabolite activator protein)
2) deactivation of repressor

102
Q

What does allolactose do to the lac operon?

A

induces lac operon by inactivating repressor so RNA polymerase can bind and translate lac genes

103
Q

When tryptophan is not present, the operon is __.

A

tryptophan (operon)

104
Q

There are used to regulate translation of polypeptides.

A

regulatory RNA molecules

105
Q

small interfering RNAs, ds, may be complementary to mRNA, tRNA, or DNA, join RISC proteins to form siRISC, binds and cuts target nucleic acids to silence genes

A

siRNAs

106
Q

RNA molecules that change shape in response to environmental conditions, some mRNAs can act as riboswitches to either favor or block translation depending on conditions and cells’ needs

A

riboswitch

107
Q

microRNAs, eukaryotic cells transcribe as miRNAs, not translated but join with regulatory proteins to form miRNA-induced silencing complex (miRISC), binds complementary mRNA and can cut mRNA to disable it or hide it from ribosomes to block translation, used to regulate embryogenesis, apoptosis, cell division, blood cell formation, and cancer among other things

A

miRNAs

108
Q

How does epigenetic control turn genes off?

A

by methylating certain nucleotides

109
Q

define mutations

A

a heritable change in the nucleotide base sequence of genome - particularly a gene

110
Q

insert extra nucleotides

A

insertions

111
Q

insert wrong nucleotides

A

substitutions

112
Q

insertions or deletions

A

frameshift mutations

113
Q

just 1 or a few nucleotide base pairs affected

A

point mutations

114
Q

loss of a nucleotide

A

deletions

115
Q

What causes frameshift mutation?

A

both insertions and deletions

116
Q

What causes silent mutations?

A

when a substitution does not change the amino acid sequence

117
Q

Which mutation has the worse consequences, missense mutation or nosense mutation?

A

nonsense

118
Q

What is the term for physical/chemical agents that induce mutations?

A

mutagens

119
Q

define spontaneous mutations

A

result from errors in replications and repair, in the absence of any mutation causing agents

120
Q

define recombination mutation

A

relatively long stretches of DNA move along the chromosome (introduce frameshift)

121
Q

This type of radiation can include z-rays and gamma rays. How does it affect DNA?

A

can cause mutations or break the DNA backbone and chromosomes

122
Q

This type of radiation can include UV light. How does it affect DNA?

A

causes adjacent T bases to covalently bond to a make thymine (pyrimidine) dimmers –> prevent H bonding with A –> distorts sugar phosphate backbone

123
Q

structurally similar to normal nucleotides, incorporate into DNA, inhibit polymerase/mismatch pairing, EX: 5 bromouracil, 5FU, antiviral and anticancer drugs

A

nucleotide/nucleoside analogs

124
Q

alter structure of nucleotide: ex: nitrous acid removes amine off adenine and converts it to guanine analog, AT pair changed to GC pair, aflatoxin converts gaunine into T, so GC converted to TA base pair, aflatoxin can cause cancer

A

nucleotide altering chemicals

125
Q

Give an example of a frameshift mutation. What do they do?

A

benopyrine in smoke, ethidium bromide used to stain DNA, acridine

insert or delete nucleotide base pairs, or slip between adjoining nucleotides

126
Q

What is the mutation frequency?

A

seen in 1 out of 1 million genes, mutagens increase the rate 10-1000X, induce error in 1/1000 - 1/100,000 genes

127
Q

What is the mutation rate?

A

probability that a gene will mutate when a cell divides, usually stated as a power of 10

128
Q

What happens during Base-Excision repair?

A

enzymes cuts out erroneous base and DNA polymerase fills in gap

129
Q

In prokaryotes, what activates DNA photolyase and what does it do?

A

activated by visible light; breaks bond between thymines

130
Q

What happens in light repair?

A

enzyme photolyase activated by light, reverses mutation and restores original sequence

131
Q

What happens in dark repair?

A

in prokaryotes, occurs in dark or light, cuts damaged section from DNA and is repaired by DNA polymerase ! and DNA ligase = nucleotide excision repair

132
Q

What happens to old strands of DNA during mismatch repair?

A

they are methylated

133
Q

What repair system is considered the last resort?

A

error-prone repair

134
Q

What occurs when damage is too extreme to repair?

A

SOS repair = a new DNA polymerase capable of copying sequences with mistakes is used, introduces mutations but allows offspring to survive, involves novel DNA polymerase IV and V capable of copying less than perfect DNA

135
Q

What are mutant cells?

A

cell that does not successfully repair its mutation and its descendants

136
Q

What cells are found normally in nature?

A

wild type cells

137
Q

What is positive selection?

A

selecting a mutation by eliminating wild type phenotypes

138
Q

What is negative selection?

A

selects for auxotrophic mutants

139
Q

What term describes organisms with different nutritional requirements than its wild-type phenotype?

A

auxotroph

140
Q

What is the Ames test used for?

A

screens for mutants

141
Q

What term describes something that causes cancer causing mutations?

A

carcinogenic/carcinogens

142
Q

Genetic recombination: exchange between __ DNA molecules that are composed of __ sequences

A

2; homologous

143
Q

Homologous sequences: DNA segments composed of __ sequences

A

identical/nearly identical

144
Q

Crossing over: in __, homologous chromosomes __ while forming gametes

A

eukaryotes; recombine

145
Q

Vertical gene transfer: passing copy of __ from 1 generation to the next

A

genome

146
Q

Horizontal gene transfer: in less than __ % of population, in prokaryotes, can acquire genes from another microbe in the same generation

A

1

147
Q

Donor cell: contributes part of __ to recipient

A

genome

148
Q

Recipient cell: may be different __ or genus

A

species

149
Q

Transformation: recipient cell takes up DNA from the __ such as dead organisms, cells have ability to take up __ are said to be “competent,” results from __ in cell wall making it __ to large DNA molecules

A

environment; DNA; alterations; permeable

150
Q

Transduction: transfer of DNA from 1 __ to another via __ viruses, both in pro and eukaryotes, __ method of horizontal gene transfer

A

cell; replicating; 2nd

151
Q

Phage (bacteriophage): virus that infects __

A

bacteria

152
Q

phage proteins incorporate bacteria DNA long with phage DNA when assembling new phase particles

A

transducing phage

153
Q

generalized transduction: phage carriers __ DNA segment from donor and host cell to recipient, all __ equally likely to be packaged in a phage __ and transferred

A

random; genes; coat

154
Q

specialized transduction: only certain host __ are transferred along with phage DNA

A

sequences

155
Q

What happens in bacterial conjugation?

A

donor remains alive

156
Q

define conjugation pili

A

(sex pili) protein rods extending from surface of cell to transfer genetic materials

157
Q

What is F plasmid?

A

contains gene coding for sex pili, conjugative plasmid contains F factors

158
Q

In Hfr, plasmid does not remain __ in but rather integrates into __.

A

cytosol; chromosome

159
Q

dissimilation plasmids

A

code for enzyme that triggers catabolism of unusual sugars or hydrocarbons

160
Q

transposons

A

segments of DNA 700-40,000 bp that can move from 1 location to another in DNA

161
Q

transposition

A

action of transposon, acts like a frameshift insertion, in pro, eukary, and viruses

162
Q

palinodrome

A

a sequence that reads the same forwards or backwards, usually on both ends of transposons, in genetics the region of DNA in which the sequence of nucleotides is identical to an inverted sequence in the complementary strand

163
Q

IR = inverted repeat

A

sequence of nucleotides identical to inverted sequence in complementary strand

GAATTC
CTTAAG

164
Q

transposase

A

recongizes own inverted repeat at a target site and cuts DNA at that location, and inserts transposon (or copy) into DNA at that site

165
Q

insertion sequences

A

simplest transposons, consist of no more than 2 inverted repeats and a gene encoding transposas

166
Q

complex transposons

A

contain 1 or more genes not connected with the transposition such as genes for AB resistance

167
Q

R plasmids

A

often contain transposons

168
Q

R factors

A

resistance factors, give resistance to heavy metals or toxins, many have 2 groups of genes, r-determinants have the resistance genes and the RTF (resistance transfer factor) includes genes for plasmid replications and conjugation

Microbiology (10 decks)

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