Chapter 8 Flashcards

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1
Q

what is the central dogma

A

the overall flow of genetic information within the cell

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2
Q

3 steps of the overall flow of information (central dogma)

A

DNA –> RNA –> Protein

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3
Q

mutations can be caused by

A

base substitutions or frameshift mutations

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4
Q

genetics

A

the study of genes, how they carry information, how information is expressed, and ow genes are replicated

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5
Q

chromosome

A

structures containing DNA that physically carry hereditary information; the chromosome contain genes

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6
Q

Genes

A

segments of DNA that encode functional products, usually proteins

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7
Q

Genome

A

all the genetic information in a cell

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8
Q

genetic code

A

set of rules that determines how a nucleotide sequence is converted to an amino acid sequence of a protein

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9
Q

genotype

A

the genetic make up of an organism

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10
Q

genotype represents _______ expression

A

potential

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11
Q

phenotype represents ________ expression

A

actual

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12
Q

bacteria usually have a _______ circular chromosome made of ____ and associated _________

A

single, DNA, protein

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13
Q

the chromosome is _______ and ________ and attached at one or several points to the _________ ________

A

looped, folded, plasma membrane

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14
Q

how much volume does the chromosome take up

A

10%

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15
Q

why does a chromosome only take up 10% volume

A

decays the DNA is supercoiled

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16
Q

the entire genome does not consist of __________

A

back-to-back genes

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17
Q

short tandem repeats

A

repeating sequences of noncoding DNA

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18
Q

short tandem repeats can be used in

A

DNA fingerprinting

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19
Q

Genomics

A

the sequencing and molecular characterization of genomes

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20
Q

computers are used to search for opening reading frames

A

regions of DNA likely to encode a protein

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21
Q

vertical gene transfer

A

flow of genetic information from one generation to the next

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22
Q

DNA is _________ into mRNA and then __________ into protein

A

transcribed, translated

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23
Q

DNA is the blueprint for a cells _______

A

proteins

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24
Q

DNA is obtained

A

from another cell in the same generation
or
from a parent cell during cell division

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25
Q

DNA can be expressed within a cell or transferred to another cell through __________ and ___________

A

recombination and replication

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26
Q

expression

A

genetic information is used within a cell to produce the proteins needed for the cell to function

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27
Q

recombination

A

genetic information can be transferred horizontally between cells of the same generation

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28
Q

replication

A

genetic information can be transferred vertically to the next generation of cells

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29
Q

DNA backbone consists of

A

deoxyribose-phosphate

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30
Q

DNA strands are

A

antiparallel

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31
Q

in DNA order of nitrogen containing bases forms the

A

genetic instructions of the organism

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32
Q

DNA replication one strand serves as a template for _________ of a second strand

A

production

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33
Q

in DNA replication one parental double stranded DNA molecule is converted to

A

two identical offspring moleules

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34
Q

in DNA replication _______ and ________ relax the strand

A

topoisomerase, gyrase

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35
Q

in DNA replication _________ separated the strands

A

helicase

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36
Q

in DNA replication a __________ ____ is created

A

replication fork

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37
Q

in DNA replication DNA _________ adds _________ to the growing DNA strand

A

polymerase, nucleotides

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38
Q

DNA replication works in the __ to __ direction

A

5’, 3’

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39
Q

DNA replication adding nucleotides is initiated by

A

RNA primer

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40
Q

DNA replication leading strand is synthesized

A

continuously

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41
Q

DNA replication lagging strand is synthesized discontinuously creating a

A

Okazaki fragment

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42
Q

DNA replication DNA polymerase removes ___________; Okazaki fragments are joined by the DNA polymerase and _________

A

RNA primers, DNa ligase

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43
Q

Events at the DNA replication fork step 1:
enzyme unwind the parental _______ _____

A

double helix

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44
Q

Events at the DNA replication fork step 2:
proteins ______ the unwound parental DNA

A

stabilize

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45
Q

Events at the DNA replication fork step 3:
the leading strand is synthesized _________ by ___ ________

A

continuously, DNA polymerase

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46
Q

Events at the DNA replication fork step 4:
the lagging strand is synthesized ___________. ______, an RNA polymerase, synthesizes a short ____ ________ which is then extended by ____ ________

A

discontinuously, Primase, RNA primer, DNA polymerase

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47
Q

Events at the DNA replication fork step 5:
DNA polymerase digests ____ _______ and replaces it with ___

A

RNA primer, DNA

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48
Q

Events at the DNA replication fork step 6:
____ _______ joins the discontinuous fragments of the lagoon strand

A

DNA ligase

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49
Q

most bacterial DNA replication is

A

bidirectional

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50
Q

replication is highly accurate due to the proofreading capability of

A

DNA polymerase

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51
Q

DNA replication is the process of

A

copying DNA

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52
Q

rRNA

A

integral part of ribosomes

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53
Q

tRNA

A

transports amino acids during protein synthesis

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54
Q

mRNA

A

carriers coded information from DNA to ribosomes

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55
Q

Prokaryote Transcription begins when

A

RNA polymerase binds to the promoter sequence on DNA

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56
Q

prokaryote transcription proceeds in the ______ direction

A

5’–>3’

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57
Q

prokaryotes are both DNA strands or just one transcribed

A

only one

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58
Q

prokaryotes transcription stops when it reaches the

A

terminator sequence

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59
Q

transcription step 1:
RNA polymerase binds to the _____, and DNA unwinds at the beginning of the ______

A

promoter, gene

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60
Q

transcription step 2:
RNA is synthesized by complementary base paring of free ________ with the nucleotide bases on the template strand of DNA

A

nucelotides

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61
Q

transcription step 3:
the site of synthesis moves along ____; DNA that has been transcribed ______

A

DNA, rewinds

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62
Q

transcription step 4:
transcription reaches the ________

A

terminator

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63
Q

transcription step 5:
RNA and RNA polymerase are _____ and the DNA helix ______

A

released, reforms

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64
Q

3 phases of transcription

A

Initiation, elongation, termination

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65
Q

initiation step 1:
RNA polymerase binds to the DNA and recognizes a site called a ________ at the end of ___

A

promoter, 3’

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66
Q

initiation step 2:
when RNA polymerase finds a promoter it breaks the ________ _____ holding the DNA strands together at the site of the _________

A

hydrogen bonds, promoter

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67
Q

RNA polymerase does not bind to all promoters with

A

equal affinity

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68
Q

the difference in promoter strength is one way that cells can control

A

gene expression

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69
Q

the more strongly RNA polymerase binds to a particular promoter the more likely the gene is to be

A

transcribed

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70
Q

increase levels of transcription leads to increase levels of _________ leads to increased concentrations of that ___________

A

translation, polypeptide

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71
Q

elongation step 1:
one strand of DNA serves as a template strand. The RNA transcript is copied from this strand of the gene and therfor has an _____________ complementary to this strand

A

RNA sequence

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72
Q

elongation step 2:
RNA polymerase moves along the ___, opening up a bubble in the DNA

A

DNA

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73
Q

elongation step 3:
as it moves RNA polymerase adds bases to the __ end of the growing RNA transcript

A

3’

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74
Q

elongation step 4:
this continues until RNA polymerase reaches a site on the DNA called the ________

A

terminator

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75
Q

termination step 1:
at this side RNA polymerase and the newly synthesized RNA transcript are _______ from the DNA

A

released

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76
Q

termination can occur in 2 ways

A

self terminator and enzyme dependent termination

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77
Q

self termination:
the RNA sequence transcribed at the terminator causes the RNA to ________ ____ with it self forming a ____ ____ ______ which essentially pulls the RNA polymerase off the DNA

A

hydrogen bond, stem loop structure

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78
Q

enzyme dependent termination:
a termination _____ binds to the terminator and pushes RNA polymerase off the DNA

A

protein

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79
Q

codons

A

groups of three mRNA nucelotides that code for a particular amino acid

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80
Q

61 sense codons encode the

A

20 amino acids

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81
Q

degeneracy

A

each amino acids is coded by several codons

82
Q

AUG stands for

A

start

83
Q

UAA stands for

A

stop

84
Q

UAG stands for

A

stop

85
Q

UGA stands for

A

stop

86
Q

_______ molecules transport the required amino acid to the ribosomes

A

tRNA

87
Q

amino acids are joined by

A

peptide bonds

88
Q

translation step 1:
on the assembled ribosomes, a tRNA carrying the first ______ ____ is paired with the start codon on the ______. the place where this first tRNA sits is called the ______.

A

amino acid, mRNA, P site

89
Q

translation step 2:
the second codon of the mRNA pairs with a tRNA carrying the second amino acid at the ______. the first amino acid joins to the second by a ______ bond, this attaches the polypeptide to the tRNA in the _______

A

A site, peptide, P site

90
Q

translation step 3:
the ribosome moves along the mRNA until the second tRNA is in the _______. the next codon to be translated is brought to the A site, the first tRNA now occupies the _______

A

P site, E site

91
Q

translation step 4:
the second amino acid joins to the third by another peptide bond, and the first tRNA is ________ from the _____

A

released, E site

92
Q

translation step 5:
the ribosome continues to move along the _____ and new amino acids are added to the polypeptide

A

mRNA

93
Q

translation step 6:
when the ribosome reaches a stop codon the ________ is ________

A

polypeptide, released

94
Q

translation step 7: the last tRNA is released and the ribosome comes apart. The released polypeptide forms a new

A

protein

95
Q

in eukaryotes where does transcription occur

A

nucleus

96
Q

exons (transcription in eukaryotes)

A

regions of the DNA that code for proteins

97
Q

introns (transcription in eukaryotes)

A

are regions of DNA that do not code for proteins

98
Q

small nuclear ribonucleoproteins AKA snRNPs (transcription in eukaryotes)

A

removed introns and splice exons together

99
Q

repression inhibits ____ ______ and decreases _______ ________

A

gene expression, enzyme synthesis

100
Q

repression is always on until repressor protein binds and then is able to block

A

transcription

101
Q

repression is mediated by _______, proteins that block transcription

A

repressors

102
Q

default position of a repressible gene is

A

on

103
Q

induction

A

turns on gene expression

104
Q

induction is initiated by an

A

inducer

105
Q

default position of an inducible gene is

A

off

106
Q

when a inducer binds to a repressor protein it

A

inactivates it

107
Q

repression and induction are 2 genetic __ _________ control mechanisms that regulate the transcription of mRNA, and this regulates the synthesis of enzymes

A

pre transcription

108
Q

promoter

A

segment of DNA where DNA polymerase imitates transcription of structural genes

109
Q

operator

A

segment of DNA that controls transcription of structural genes

110
Q

operon

A

set of operator and promoter sites and the structural genes they control

111
Q

inducible operon

A

structural genes are not transcribed unless an inducer is present

112
Q

example of inducible operon:
in the absences of lactose, the repressor binds to the operator preventing

A

transcription

113
Q

example of inducible operon:
in the presence of lactose, metabolite of lactose (allolactose) binds to the repressor; the repressor cannot bind to the operator and

A

transcription occurs

114
Q

operon consists of ______ (P) site and _______ (operator) site

A

promoter, operator

115
Q

operon is regulated by the product of the

A

regulatory gene (I)

116
Q

in repressible operons structural genes are transcribed until they are

A

turned off

117
Q

catabolite repression inhibits cells from using _____ sources other than glucose

A

carbon

118
Q

cAMP is

A

cyclic AMP

119
Q

cAMP builds up in the cell when glucose is

A

not avaliable

120
Q

cAMP binds to the _________ _______ ______ (CAP) that in turn binds the lac promoter, imitating transcription and allowing the cell to use ________

A

catabolic activator protein (CAP)

121
Q

methylating nucleotides turns genes

A

off

122
Q

can methylated genes be passed to offspring cells

A

yes

123
Q

is methylated nucleotides permeant

A

no, can be turned back on

124
Q

how can you methylate a nucelotide

A

add a methyl group, CH3

125
Q

riboswitch

A

part of an mRNA molecule that binds to a substrate and changes the mRNA structure

126
Q

post transcriptional control stops protein synthesis after

A

transcription has occured

127
Q

both eukaryotes and prokaryotes use riboswitches to control expression of certain

A

proteins

128
Q

microRNAs (miRNAs)

A

base pair with mRNA to make it double stranded

129
Q

miRNAs affect protein _____ and play many regulatory roles

A

expression

130
Q

mutation

A

permanent change in the base sequence of DNA

131
Q

mutations may be

A

neutral, beneficial or harmful

132
Q

mutagens

A

agents that cause mutations

133
Q

spontaneous mutations

A

occur in the absence of a mutagen

134
Q

base substation (point mutation)

A

change in one base in DNA

135
Q

frameshift mutation

A

insertion or deletion of one of more nucleotide pairs

136
Q

frameshift is called frameshift because

A

shifts the reading frame so the correct nucleotides do not line up

137
Q

missence mutation

A

base substitutions result in change in amino acid

138
Q

nonsense mutation

A

base substitution results in nonsense (stop) codon

139
Q

silent base substitution affects the phenotype or genotype?

A

genotype

140
Q

frameshift leads to non functioning

A

protein

141
Q

two types of radiation

A

ionizing and nonionizing

142
Q

ionizing consists of what rays

A

gamma and x

143
Q

ionizing with X and gamma rays cause cells to lose electrons leading to

A

free radicals

144
Q

non ionizing radiation is caused by

A

UV light

145
Q

non ionizing radiation causes thymine dimers, what are those?

A

when 2 thymines next to each other get covalently bonded to one another

146
Q

thymine dimers prevent

A

replication and transcription

147
Q

ionizing radiation causes the formation of ions that can _________ nucleotides and break the deoxyribose phosphate backbone

A

oxidize

148
Q

2 types that can fix thymine dimers

A

photolyases and nucleotide excision repair

149
Q

photolyases separate the thymine dimers by using ________ _____

A

visible light

150
Q

nucleotide excision repair

A

enzymes cut out incorrect bases and fill in correct bases

151
Q

excision repair enzymes is called ______ ____, it can occur with or without light

A

dark repair

152
Q

mismatch repair enzymes scan newly synthesized DNA for mismatches and if they find one they repair it. The lack of ___________ to identify newly synthesized DNA and removed the new mutation before it can become _______

A

methylation, methylated

153
Q

in mismatch repair enzymes if the mutation is already methylated can the repair enzyme fix it or not?

A

no it cannot fix it once it is methylated

154
Q

positive (direct) selection

A

detects mutant cells because they grow or appear different than unmated cells

155
Q

negative (indirect) selection

A

detects mutant cells that cannot grow or preform a certain function

156
Q

auxtotroph

A

mutant that has a nutritional requirement absent in the parent

157
Q

what is the technique to identify auxtotroph

A

use of replica plating

158
Q

replica plating:
1. sterile velvet is pressed on the grown colonies on the master plate
2. cells from each colony are transferred from the velvet to the new plates (containing histidine, lacking histamine)
3. plates are incubated
4. a colony that grows on the medium _____ __________ but could not grow on the medium _____ ________ is auxotrophic

A

with histidine, without histidine

159
Q

Ames test exposed mutant bacteria to mutagenic substances to measure

A

the rate of reversal of the mutation

160
Q

Ames test indicates the degree to which a substance is

A

mutagenic

161
Q

genetic recombination

A

exchange of genes between two DNA molecules; creates diversity

162
Q

crossing over

A

two chromosomes break and rejoin, resulting in the insertion of foreign DNA into the chromosome

163
Q

crossing over:
1. DNA from one cell aligns with DNA in the recipient cell
2. DNA from the donor aligns with complementary base pair in the recipient chromosome
3. RecA protein catalyzes the joining of the two strands
4. the results is that the recipients chromosome contains new DNA. Complementary base pairs between the two strands will be resolved by ___ _________ and ________. The donor DNA will be _________. The recipient may now have one or more new genes

A

DNA polymerase, ligase, destroyed

164
Q

vertical gene transfer

A

transfer of gene from an organism to its offspring

165
Q

horizontal gene transfer

A

transfer of gene between cells of the same generation

166
Q

3 types of horizontal

A

transformation
transduction
conjucation

167
Q

plasmids and transposons are mobile genetic elements

A

move from one chromosome to another or from one cell to another

168
Q

plasmids

A

self replicating circular pieces of DNA

169
Q

plasmids take up __-__% of a bacterial chromosome

A

1,5

170
Q

plasmids often code for proteins that enhance the

A

pathogenicity of a bacterium

171
Q

plasmids can confer ability to resist

A

antibiotics

172
Q

3 types of plasmid

A

conjugative plasmid
dissimilation plasmids
resistance factors (R factor)

173
Q

conjugative plasmid

A

carriers genes for sex pili and transfer of the plasmid

174
Q

dissimilation plasmid

A

encode enzymes for the catabolism of unusual componds

175
Q

resistance factors (R factor)

A

encode antibiotic resistance

176
Q

2 things that make up R factor

A

RTF and R-determinant

177
Q

transposons

A

segments of DNA that can move from one region of DNA to another

178
Q

transposons contain insertion sequences (IS) that code for ___________ that cut and reseals DNA

A

transposase

179
Q

complex transposons carry other _____

A

genes

180
Q

simple transposons

A

only contain the essential elements needed for transportation

181
Q

inverted repeat

A

region of DNA in which the sequence of nucleotides is identical to an inverted sequence in the complementary strand

182
Q

transposons move through 1 of 2 mechanisms
1. cut and paste:
2. replicative:

A

cut and paste: the entire transposon moves to another location
Replicative: transposons is copied to a new location

183
Q

complex transposons consist of 2 simple transposons with another sequence of DNA between them, other DNA is often a gene that gives some selective

A

advantage to the organism for containing the transposons

184
Q

transformation in bacteria

A

gene transferred from one bacterium to another as “naked” DNA

185
Q

transformation bacteria are capable of

A

taking up fragments of DNA from their surroundings and integrating the fragments into their own chromosome by recombination

186
Q

competent

A

cells capable of taking up DNA from their environment

187
Q

what is a competent bacteria

A

streptococcus pneumoniae

188
Q

conjugation

A

plasmids transferred from one bacterium to another

189
Q

conjugation requires

A

cell to cell contact via sex pili

190
Q

donor cells carry the plasmid (F factor) and are called

A

F+ cells

191
Q

Her (high frequency of recombination) cells contain the F factor on the

A

chromosome

192
Q

cells lacking the F factor are called

A

F- cells

193
Q

F- cells serve as

A

DNA recipients

194
Q

start of conjugation F factor: conjugation pills extends from __ cell to the __ cell, and pulls the cells together. The cells come together and stabilize. Transfer of DNA begins. Single stranded copy of the F factor is transferred from F+ to F-. each cell synthesizes a __________ strand of plasmid resulting in a complete copy of the plasmid in each cell. After conjugation, both cells contain _____________

A

F+, F-, complementary, a copy of the F factor

195
Q

start of conjugation Hfr: cells come together and stabilize. Transfer of DNA begins. DNA transfer begins in the middle of the F factor with in the Hfr cells chromosome. The result is the

A

F- cell does not receive a full copy of the F factor. Since the recipient cell does not receive a complete copy of the F factor, it remains F-. The DNA from the donor can recombine with recipient chromosome, giving the recipient new chromosomal genes

196
Q

conjugation can be used to map the location of

A

gene on a chromosome

197
Q

DNA is transferred from a donor cell to a recipient via a

A

bacteriophage

198
Q

generalized transduction

A

random bacterial DNA is packaged inside a phage and transferred to a recipient cell

199
Q

specialized transduction

A

specific bacterial gene are packaged inside a phage and transferred to a recipient cell

200
Q

mutations are recombination create

A

diversity

201
Q

natural selection acts on populations of organisms to ensure the

A

survival of organisms within a particular environment