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Microbiology > (Exam 2)- Chapter 8 > Flashcards

(Exam 2)- Chapter 8 Flashcards

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1
Q

How would this procedure be modified to identify temperature sensitive mutant?

A

slide 74

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2
Q

Describe the process of Genetic transfer in E.coli

A

slide 106

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3
Q

occurs when two chromosomes break and rejoin

A

crossing over

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4
Q

Catabolite repression

A

A mechanism by which the cell ensures that if glucose is present, all the other catabolic genes that would be necessary are turned off. Glucose is the preferred carbon source. Why make the enzymes for other carbon source catabolism if they are not needed.

However, when glucose has run out some of the other genes are turned on (there is a lag period so that the lactose enzymes can be made), and then lactose is utilized

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5
Q

inhibition of the synthesis of
alternative catabolic enzymes by a preferred carbon
source (i.e. glucose).

A

catabolite repression

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6
Q

Encode resistance to antibiotics or heavy

metals and often

A

r factors/ plasmids

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7
Q

Direct uptake of DNA by recipient cells

A

transformation

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8
Q

a random fragment of bacterial DNA is accidentally encapsulated in a phage protein coat in place of the phage DNA

A

generalized transduction

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9
Q

Describe the process of replica plating

A
  1. sterile velvet is pressed on the grown colonies on the master plate
  2. cells from each colony are transferred from the velvet to new plats
  3. Plates are incubated
  4. growth on plates is compared. A colony that grows on teh medium with histidine but could not grown on the medium without histidine is auxotrophic (histidine-requiring mutant)
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10
Q

thymidine analog used to treat AIDS

A

azidothymidine (AZT)

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11
Q

Each different mutant is assigned a

unique _______ number

A

allele

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12
Q

In bacteria the start codon encodes for ____________

A

N-formylmethionine

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13
Q

Self mobilizable genetic elements or jumping genes” that can be transferred from
place to place on the chromosome and into and out of plasmids

A

transposable elements

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14
Q

would leave the two original template DNA strands together in a double helix and would produce a copy composed of two new strands containing all of the new DNA base pairs.

A

conservative replication

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15
Q

separate thymine dimers

A

photolyases

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16
Q

a base substitution
results in the replacement of one amino
acid for another

A

missense mutations

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17
Q

Classes of mutagenic agents

A
  • Base modifiers
  • Base analogs
  • Radiation
  • Frame shift mutagens
  • Mobile genetic elements
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18
Q

Can nucleotide excision repair deletions?

A

slide 67

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19
Q

alter bases that are already incorporated into the DNA, once altered the binding property changes

A

Base modifiers

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20
Q

Transcription begins when RNA polymerase binds to the __________ sequence

A

promoter

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21
Q

DNA is transcribed to make what?

A

RNA (mRNA, tRNA, rRNA etc.)

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22
Q

Describe positive regulation (induction) of the lac operon

A 
The lac operon is composed of: 
- regulatory gene
- promoter
- operator
- structural genes
allolactose is the inducer that is made by the regulatory gene. Allolactose binds to the repressor protein and inactivates it. Now transcription of the lac operon can occur and B-galactosides, permease, and transacetylase can be made via translation of the lac operon mRNA
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23
Q 
X-rays and
gamma rays can physically
break one or both of the
sugar phosphate
backbones, break the
hydrogen bonds or damage
the bases of DNA
A

direct action of ionizing radiation

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24
Q

___ sense codons on mRNA encode the 20 amino acids

A

61 (64 minus the three stop codons)

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25
Q

In gram negative bacteria, how are incorrect
bases that are undamaged distinguished
from correct bases?

A

slide 67

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26
Q

How is the energy for DNA synthesis supplied?

A

energy is supplied from dNTPs

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27
Q

_________ _______ occurs concomitantly with DNA replication, so
that the donor cell does not lose genetic information.

A

conjugative transfer

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28
Q

What direction does transcription work in?

A

5’ to 3’

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29
Q

Following conjugation between Hfr and F- cells, does the F- cell
become Hfr?

A

slide 89

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30
Q

What are ORFs?

A

In molecular genetics, an open reading frame (ORF) is the part of a reading frame that has the ability to be translated. An ORF is a continuous stretch of codons that contain a start codon (usually AUG) and a stop codon (usually UAA, UAG or UGA).

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31
Q

What are temperature sensitive mutants

and how are they related to conditional lethal mutants?

A

temperature sensitive mutants are a class of conditional lethal mutants (they can work at a certain temperature but not at another)

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32
Q

requires biotin added as a supplement to minimal medium

A

bio-

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33
Q

not limited to thymine dimers

A

nucleotide excision repair

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34
Q

How do you positively (direct) select a mutant?

A

Positive (direct) selection detects mutant cells that

grow under conditions their unmutated parents won’t

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35
Q

Makes covalent bonds to join DNA strands; joins Okazaki fragments and new segments in excision repair

A

DNA Ligase

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36
Q

What are the three ways to define a mutation rate?

A

1) mutations per base pair per generation/cell division*
2) mutations per gene per generation/cell division*
3) mutations per genome per generation/cell division* (less common)

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37
Q

requires methionine added as a supplement to minimal medium

A

met-

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38
Q

Why is the operon off if there is no glucose and no lactose?

A

because the lac repressor is bound

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39
Q

A change in the base sequence of DNA

A

mutations

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40
Q

The molecular study of genomes

A

genomics

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41
Q

Occur in the absence of a mutagen

A

spontaneous mutations

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42
Q

After duplication, each copy of the chromosome origin binds to the membrane at ________ ______

A

opposite poles

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43
Q

The external manifestations of an organisms

genotype

A

phenotype

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44
Q

Degeneracy enables ________ mutations

A

silent

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45
Q

Staphylcoccus epidermis produces ____________
(Escherichia coli produces ___________)
(Lactococccus lactis produces ________)

A

staphylcoccin
colicin
nisin

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46
Q

increase the mutation rate 10 to 1000 times

A

mutagens

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47
Q

How would your modify a double stranded DNA to represent dsRNA?

A
  • ribose sugar

- replace Thymine with Uracil

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48
Q

look like nucleotides, and polymerase places them into the DNA and change what is being bound

A

base analogs

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49
Q

This experiment demonstrated genetic transformation

A

Frederick Griffith’s experiment (1928)

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50
Q

What compounds are used in a phenotypic screening?

A

– pH indicators
– Differential breakdown of materials in media
• e.g. sugars
• e.g. blood

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51
Q

insertion or deletion
of one or a few bases which alters the
reading frame

A

frameshift mutations

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52
Q

What is meant by cell “competence”?

A

slide 83

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53
Q

phage mediated genetic recombination in bacteria

A

transduction

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54
Q

a deletion and reassertion

in the opposite orientation

A

inversion

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55
Q

a base substitution does
not alter the amino acid composition of
the protein

A

silent mutations

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56
Q

What is the best studied conjugative plasmid?

A

The F-plasmid

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57
Q

Bacterial chromosomal DNA is compacted into what percentage of the cell’s volume (E.coli)?

A

10%

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58
Q

mutations may be ________, ________, or _________

A

neutral, beneficial, or harmful

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59
Q

In prokaryotes ______ is the predominant
methylation and is important for restriction
modification and replication fidelity. May also influence gene expression (i.e. Biofilm behavior and
pilus phase variation)

A

GA*TC

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60
Q

How are genes written?

A

written in lower case and italicized

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61
Q

Cuts DNA backbone, leaving single-stranded “sticky ends’

A

Transposase

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62
Q

The genetic makeup of an

organism/ an organisms collection of genes

A

genotype

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63
Q

a base substitution

creates an in frame stop codon

A

nonsense mutations

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64
Q

approx. 22 nucleotide single-stranded RNAs that are incorporated
into a RISC and serve to target specific mRNAs in eukaryotic cells to alter translation or stability.

A

microRNAs

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65
Q

E. coli DNA replication is ____________

A

bidirectional

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66
Q

2-AP binds with thymine in its _______ form, when does it bind with cytosine?

A

Normal; When it is protonated. Now a Cytosine has replaced what was supposed to be a thymine. An AT pair becomes a CG pair

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67
Q

The base analog ______________ is

used as an antiretroviral drug?

A

azidothymidine (AZT); Yes this thymidine analog is used to treat AIDS

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68
Q

What is codon bias?

A

Codon usage bias refers to differences in the frequency of occurrence of synonymous codons in coding DNA. The overabundance in the number of codons allows many amino acids to be encoded by more than one codon. The genetic codes of different organisms are often biased towards using one of the several codons that encode the same amino acid over the others—that is, a greater frequency of one will be found than expected by chance.

It is the probability that a given codon will be used to code for an amino acid over a different codon which codes for the same amino acid

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69
Q

What happens when lactose is present, but not glucose?

A

cAMP binds to the inactive CAP and activates it. The lac repressor is still inactive. Now the active CAP can bind to the promoter region and transcribe the lacZ gene

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70
Q

When is the trp operon off? Under what conditions?

A

In the presence of tryptophan, the trp operon is off. Tryptophan can bind to the repressor protein and act as a co-repressor. and bind to the operator region.

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71
Q 
cause the
formation of ions that can
oxidize bases resulting in
errors in replication and
repair that causes
mutations
A

indirect action of ionizing radiation

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72
Q

Genes not listed in the genotype are assumed _______

A

wildtype

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73
Q

Do all bacterial proteins in the cell contain N-formylmethionine as the first amino acid?

A

It is placed first, but after protein synthesis is completed. N-formylmethionine is cleaved off by an enzyme. Once the protein is fully synthesized, most bacterial proteins do no have N-formylmethionine.

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74
Q

Relaxes supercoiling ahead of the replication fork; separates DNA circles at the end of DNA replication

A

Topoisomerase

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75
Q

Target site preferences are rarely very ________ or very ______. Thus, suitable insertion locations
for many ISs occur thousands of times in each genome. However, insertion is NOT _______.

A

stringent; long; random

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76
Q

A ________ identifies mutant cells that appear different

A

screen

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77
Q

What are the two versions of positive regulation in bacteria? Provide examples

A

Positive regulation: an inducer/ activator protein

  1. when the inducer is bound and the small molecule activates it
  2. when the inducer is not bound and the small molecule turns the gene off (if cAMP binds CAP, then CAP is activated and binds to the DNA and turns transcription of the lac operon on)
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78
Q

Approximately ____ min is required to replicate the E. coli chromosome. Yet the doubling time of the organism can be as fast as ___ minutes. How is this possible?

A

40; 20; It is 40 . min the first time but each subsequent division has a 1/2 the original time

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79
Q

In __________ transcription & translation are coupled

A

prokaryotes

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80
Q

Relaxes supercoiling ahead of the replication fork

A

DNA Gyrase

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81
Q

cannot utilize lactose as a carbon source

A

lac-

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82
Q

a __________ transposon leaves a copy of itself at
the original location whereas a _________ transposon does not leave a copy of itself.
(most transposons are ____________)

A

replicative; nonreplicative; replicative

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83
Q

What is the difference between bacteriocin and antibiotic?

A

The antibiotics are secondary metabolites with broad spectrum of anti-microbial activity. While the bacteriocins (antimicrobial peptides) are synthesized on ribosomes by translation process as they are polymer of amino acids and have a narrow spectrum of anti-microbial activity mainly against closely related species.

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84
Q

Although, __________ likely has only a minor effect on gene flow in natural _________
populations, it is extremely useful experimentally for introducing DNA into
_______ cells.

A

transformation; bacteria; bacterial

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85
Q

Encode enzymes for catabolism of
unusual compounds
-prevalent in some species of Pseudomonas
(toluene, camphor and petroleum hydrocarbons)

A

dissimilation plasmid

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86
Q

production of hydroxyl radicals, breaks DNA

A

radiation

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87
Q

The transfer of genes between cells of the same

generation.

A

horizontal gene transfer

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88
Q

the probability that a gene will mutate when a cell divides

A

mutation rate

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89
Q

DNA polymerases only add new dNTPs to the ___-end

A

3’

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90
Q

How did E.coli O157:H7 acquire this toxin gene?

A

slide 107

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91
Q

Since the transferred DNA usually does not contain an _______ ____ _________ these genes will be passed on to succeeding _________ only if the transferred DNA becomes _________ into the recipient chromosome

A

origin of replication; generations; incorporated

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92
Q

50-500 nucleotide non-coding RNAs that can either bind to proteins
targets and modify function or bind to mRNA targets and
regulate translation or stabilit

A

Bacterial small regulatory

RNAs (sRNAs)

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93
Q

DNA methylation turns genes _____

A

off (silences them)

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94
Q

Why do frame shift mutations generally lead to premature termination?

A

if you scramble the sequence, because stop codons are so infrequent normally, a frameshift would increase their frequency

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95
Q

___ ________ causes thymine dimers: repair mechanisms

A

UV radiation

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96
Q

What advantage does direct selection have over indirect selection?

A

slide 75

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97
Q

present in smoke and soot

A

benzopyrene

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98
Q

Describe the Homologous Recombination pathway

A
  1. DNA from one cell aligns with DNA in the recipient cell. Notice that there is a nick in the donor DNA
  2. DNA from the donor aligns with complementary base pairs in the recipient’s chromosome. This can involve thousands of base pairs.
  3. RecA protein catalyzes the joining of the two strands
  4. The result is that the recipient’s chromosome contains new DNA. Complementary base pairs between the two strands will be resolved by DNA polymerase and ligase. The donor DNA will be destroyed. The recipient may now have one or more new genes
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99
Q

What are the genes where the transcription rate increased by a regulatory protein called a ___________. Default
position is off.

A

inducible genes; inducer

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100
Q

A segment of DNA or RNA that encodes for
a polypeptide or RNA chain that has a
function in the organism

A

gene

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101
Q

Translation of mRNA begins at the start codon: _____

A

AUG methionine

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102
Q

What are the Different types of sequence changes

(mutations) in DNA?

A
  1. base substitutions
  2. additions and deletions
  3. inversions
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103
Q

R factor/ plasmids that are conjugative

A

resistance transfer factor, RTF

104
Q

Although we have discussed the __________ as an example, keep in mind that analogous events occur with other conjugative plasmids.

A

F plasmid

105
Q 
F- cells that
are \_\_\_\_\_ are
crossed with
Hfr cells that
are \_\_\_\_
A

strr; strs

106
Q

Mos resistance gene transfer is _______ mediated, but ________ mediated traits can interchange with chromosomal elements

A

plasmid

107
Q

what type of rays are used in ionizing radiation

A

x rays and gamma ray

108
Q

cannot ulitize galactose as a carbon source

A

gal-

109
Q

produced by a variety of

molds that grow on peanuts and grain

A

alfatoxin

110
Q

What is cotransduction frequency?

A

slide 99

111
Q

process of converting DNA to RNA

A

transcription

112
Q
  • hair-like projections termed _____ _______ are required to make contact with specific receptor sites on the surface of the recipient cell
  • the ____ _______ is a hollow tube but DNA does not appear to pass through the tube. It serves to bring the cells in close proximity
A

sex pillus

113
Q

The linear order of transfer is dependent on the ____ strain

A

Hfr

114
Q

The genetic code is ____________

A

degenerate

115
Q

How is the correct AUG start codon recognized in prokaryotes vs. in eukaryotes?

A

In the eukaryotic cell, ribosomes are located in the cytoplasm or associated with the ER, in the prokaryotic cells, such as bacteria, ribosomes float freely in the cytoplasm.

116
Q

RNA protein complex that removes introns and splices exons together

A

snRNP

117
Q

change within a gene in
which one base pair in the DNA sequence is
altered

A

point mutations

118
Q

Why isn’t transcription and translation coupled in eukaryotes?

A

Because they two processes occur in separate regions of the cell.

119
Q

What sequences do F plasmids and bacterial chromosomes have in
common that permit integration via homologous recombination?

A

slide 89

120
Q

What does conjugation differ between?

A

Gram-negative and

Gram-positive species

121
Q

Describe the process of repairing thymine dimers

A
  1. exposure to UV light causes adjacent thymines to become cross-linked forming a thymine dimer and disrupting their normal base pairing
  2. an endonuclease cuts the DNA, and an exonuclease removes the damaged DNA
  3. DNA polymerase fills the gap by synthesizing new DNA, using the intact strand as a template and DNA ligase seals the gap
122
Q

Occurs during reproduction between generations of cells.

A

vertical gene transfer

123
Q

What are the two versions of negative regulation in bacteria? Provide examples

A

Negative regulation: a repressor protein

  1. When the repressor is bound, and a small molecule activates it
    (Example: trp operon- when tryptophan is present, transcription of the gene is off)
  2. When the repressor is not bound, and a small molecule inactivates it
    (Example: lac operon- when allolactose is present the repressor does not bind to the operon)
124
Q

is the main recombination pathway used in many bacteria.

A

RecBCD pathway

125
Q

Describe the process of conjugation

A

slide 85, 86, 87

126
Q

Describe the process of translation

A

Once in the cytoplasm, the mRNA strand complexes with a ribosomal complex. While the mRNA-ribosome complex is assembling, many other important activites are occurring in the cytoplasm. For example, tRNA subunits are connected to particular AAs in energy-requiring processes. This is done by a family of enzymes called aminoacyl-tRNA synthetases.

  1. Activation: Once bound to their amino acids, the tRNA molecules travel to the ribosome where the mRNA molecule is anchored. The starting tRNA binds to the start codon.
  2. Initiation: The critical step is matching of the codon on the mRNA molecule with the anticodon on the tRNA molecule. A certain amino acid is brought into position. At the A site.
  3. Elongation: The ribosome moves along the mRNA ensuring that each codon and anticodon matches. Enzyme aminoacyl tRNA synthetase create peptide bonds between the amino acids to forma polypeptide of increasing length. The tRNA with the newly formed peptide bond moves into the P site. The old tRNA without the amino acid now, moves to the E site and is ejected. This process continues as a new tRNA with attached amino acid moves into the A site. The ribosome moves along the mRNA in a 5’ to 3’ fashion.
  4. Termination: stop codons on the mRNA molecule signal to halt. At this point the polypeptide is released from the ribosome and is further processed to yield a functional protein.
127
Q

What is the major difference between conjugation in gram positive and gram negative bacteria?

A

positive: does not require a sex pili

128
Q

Are mutagens also carcinogens?

A

slide 78

129
Q

What is an example of generalized transduction?

A

The P1 bacteriophage

130
Q

Exchange of genes between two DNA molecules. A complex process involving many different enzymes, with redundant functions.

A

homologous recombination

131
Q

What is phenotypic screening?

A

Recognizable differences in colony morphology – not selection, just screening

132
Q

How do you negatively (indirect) select a mutant?

A

Negative (indirect) selection detects mutant cells because they do not grow.
- Replica plating

133
Q

deaminates adenines and cytosines so they base pair with C and A thus changing the base binding properties

A

nitrous acid

134
Q

encode for proteins that enhance the
pathogenicity of the bacteria
- host attachment
- toxins (exfoliative, neurotoxins, shiga toxin)

A

virulence plasmids

135
Q

Characteristics of the bacterial plasmid

A
  1. automatic, self-replicating extrachromosomal DNA
  2. 1.5-300 Kb
  3. Contain genes that are conditional. Not necessary
    for day-to-day survival but required under certain
    conditions. Ex. Resistance, virulence, metabolic
    pathways, bacteriocins and plasmid transfer genes.
    Also can carry transposons.
136
Q

The structure that carries

essential hereditary information

A

chromosome

137
Q

Type of mutation in an Ames test?

A

slide 77

138
Q

Cut DNA backbone in a strand of DNA; facilitate repair and insertions

A

Endonucleases

139
Q

fluorescent cationic dye

A

acridine orange

140
Q

some are named after the species it is produced by adding “____” to the species or genus of the bacteria

A

cin

141
Q

a specialized transducing particle contains a _______ phage and
________ DNA molecule which integrates into the ________ genome as the ________ DNA would do process of becoming a
normal prophage.

A

hybrid; bacterial; phage; phage

142
Q

would produce two copies of the DNA, both containing distinct regions of DNA composed of either both original strands or both new strands.

A

dispersive model of replication

143
Q

Carries genes necessary for transfer of

the plasmid to another cell

A

conjugative plasmid

144
Q

Why is it useful to generate mutants?

A

slide 71

145
Q

Do nucleotide changes outside ORFs impact gene expression?

A

Yes, you could have a mutation in a promoter, inducer, repressor regions

146
Q

What is unique about the genetic map of a bacterial chromosome?

A

The entire genome
does not consist of
back-to-back genes

147
Q

Why is the frequency of transducting a specific gene from a donor cell to a recipient cell low? (4 reasons)

A

1) The encapsulation of bacterial DNA is low (1/1000)
2) The probability that the transducing particle carries the gene of
interest is low. (depends on genome size and capacity of the
virus particle)
3) Successful infection of the P1 transducing particle is required
4) The transduced gene must recombine with the homologous
portion of the chromosome.

148
Q

(composite and Tn3)
- carry antibiotic resistance
genes.

A

transposons

149
Q

Resistance plasmid R100 (a __________ plasmid): Can be transferred between a number of _______ species

A

conjugative; enteric

150
Q

During translation, what are the necessary components for initiation?

A

large subunit (70) and the small subunit (30), tRNA with anticodon and amino acid, and the mRNA

151
Q

Cell division and generation are equivalent for _______-cell organisms

A

single

152
Q

Describe the process of Transcription in Prokaryotes

A
  1. RNA polymerase binds to the promoter, and DNA unwinds at the beginning of a gene
  2. RNA is synthesized by complementary base pairing of free nucleotides with the nucleotide bases on the template strand of DNA
  3. The site of synthesis moves along DNA; DNA that has been transcribed rewinds
  4. Transcription reaches the terminator
  5. RNA and RNA polymerase are released and the DNA helix reforms
153
Q

What are three major kinds of transposable elements?

A
  1. insertion sequence (IS) elements
  2. transposons
  3. certain phages (such as Mu)
154
Q

The ______________ is incorporated into DNA in place of adenine

A

2-aminopurine nucleoside

155
Q

Why is the operon off if there is glucose, but no lactose?

A
  1. because lac repressor is bound

2. there is no CAP bound

156
Q

The natural occurrence of this property is
unusual among ________ (1% in laboratory
conditions) and _______ specific (about 15
species of ________)

A

bacteria; species; bacteria

157
Q

Characteristics of the bacterial chromosome (4)

A
  1. circular, singular, and double stranded
  2. 500-6k kb
  3. Looped, folded and attached at one or several
    points on plasma membrane
  4. carries all the essential genes
158
Q

Some bacterial transcriptional regulator
proteins recognize the same sequence
but _______ one gene and _______ another. How is this possible?

A

activate; repress

They recognize the same sequence, but some can bind upstream of the promoter and block DNA polymerase from binding.

159
Q

Describe the process of DNA synthesis

A
  1. Enzymes unwind the parental double helix
  2. Proteins stabilize the unwound parental DNA
  3. The leading strand is synthesized continuously by DNA polymerase
  4. The lagging strand is synethisized discountinously. RNA polymerase synthesizes a short RNA primer, which is then extended by DNA polymerase
  5. DNA polymerase digests RNA primer and replaces it with DNA
  6. DNA ligase joins the discontinuous fragments of the lagging strand
160
Q

The __________ can integrate into the E. coli genome via
homologous recombination, thereby allowing the chromosome the
ability to transfer itself to another cell.

A

F plasmid

161
Q

homologous recombination requires which protein?

A

RecA

162
Q

When is the lac operon on? Under what conditions

A

when glucose is not present (CAP is bound) and when lactose is present (lac repressor is not bound)

163
Q 
have a number of
mutations that
prevent them
from carrying out
certain metabolic
steps
A

F- cells

164
Q

Describe the process of mRNA transcription and processing in eukaryotes

A
  1. in the nucleus, a gene composed of exons and introns is transcribed to RNA by RNA polymerase
  2. Processing involves snRNPs in the nucleus to remove the intron-derived RNA and splice together the exon-derived RNA into mRNA
  3. After further modification, the mature mRNA travels to the cytoplasm, where it directs protein synthesis
  4. These modification steps include a 5’ cap and a poly A tail
165
Q

Translation ends at _________ codons: UAA, UAG, UGA

A

nonsense

166
Q

The ____________ is incorporated into DNA in place of thymine (used as an anticancer drug)

A

5-bromouracil nucleoside

167
Q

(60-80%) of genes are expressed at a fixed rate

A

constitutive genes

168
Q

Why is the retrovirus impaired more than

the host?

A

slide 69

169
Q

Which of the different types of mutations is most easily reverted?

A

either of the base substitutions:

  1. transitions
  2. transversions
170
Q

5-BrU binds with adenine in its ______ form, when does it bind with guanine?

A

Keto; When it is in its enol form. Now an guanine has replaced what was supposed to be an adenine. An AT pair becomes a GC pair.

171
Q

When does transcription stop?

A

when it reaches the terminator sequence

172
Q

tRNA carries the complementary _________

A

anticodon

173
Q

What are the genes where the transcription rate decreased by a regulatory protein called a _________. Default
position is on.

A

repressible genes; repressor

174
Q

how large is a gene in terms of base pairs?

A

1 gene= 1000 base pairs

175
Q

What is the toxin-producing strain of E.coli that was first seen in 1982?

A

Escherichia coli O157:H7

176
Q

Why is the operon off if there is both glucose and lactose?

A

because CAP is not bound

177
Q

DNA is copied by _____ __________
– In the 5’ to 3’ direction
– Initiated by an ____ ______
– _______ ________ is synthesized continuously
– ________ ________ is synthesized discontinuously
(Okazaki fragments)
– RNA primers are removed and Okazaki fragments
joined by a _____ _________ and ____ _________
– Overall error rate of E. coli DNA polymerase is low
(10^-5) then reduced to 10^-9 bases due by
_______

A

DNA polymerase; RNA primer; leading strand; lagging strand; DNA polymerase; DNA ligase; proofreading

178
Q

All the genetic information in a cell

A

genome

179
Q

What test is used to detect chemical carcinogens?

A

ames test

180
Q

Describe the process of forming an Hfr strain

A

slide 90, 91, and 92

181
Q

Who showed that DNA was responsible

for converting the harmless S. pneumoniae into virulent strains

A

(1944) Avery, MacLeod and McCarty

182
Q

• Grow on media supporting mutant but not wild-type
• Only rare mutants will
survive
• e.g., antibiotic resistance

A

direct selection

183
Q

Give an example of gram-positive bacteria that undergoes conjugation

A

Enterococcus faecalis; pCF10

184
Q

Is bacterial chromosome the same thing as bacterial genome?

A

No, the genome consists of either the chromosome or a plasmid or both

185
Q

When is the trp operon on? Under what conditions?

A

When the repressor is inactive, and polypeptides are made that make up the enzymes that are used for tryptophan synthesis

186
Q

encode for __________ (ribosome synthesized

peptides that kill closely related bacterial species or even different strains of the same species )

A

bacteriocin plasmids; bacteriocin

187
Q

Uses visible light energy to separate UV induced pyrimidine dimers

A

Photolyase

188
Q

How are genes assigned to organisms?

A

Genes are assigned a 3-letter designation

pathway, cell structure, function or mutant phenotype

189
Q

What are short tandem repeats?

A

A Short Tandem Repeat (STR) analysis is one of the most useful methods in molecular biology which is used to compare specific loci on DNA from two or more samples. A short tandem repeat is a microsatellite, consisting of a unit of two to thirteen nucleotides repeated hundreds of times in a row on the DNA strand.

190
Q

What is semiconservative replication?

A

Semiconservative replication describes the mechanism by which DNA is replicated in all known cells. A double stranded DNA molecule separate, and each strand is used as a template for the synthesis of a new strand. This results in the formation of two identical copies of the original double stranded molecule.

191
Q

substitution of one

single nucleotide base for another

A

Base substitutions

192
Q

The science of heredity and gene function

A

genetics

193
Q

Why are bacteria useful for generating mutants?

A

slide 71

194
Q

Describe the process of insertion of transposon Tn5 into R100

A
  1. transposase cuts DNA, leaving sticky ends

2. sticky ends of transposon and target DNA anneal

195
Q

Chromosomal genes are transferred from an ____ cell to an _____ cell with higher frequency than from an ____ cell

A

Hfr; F-; F+

196
Q

typically mutation rates are expressed as power of _____

A

10

197
Q

What is an operon?

A

a unit made up of linked genes that is thought to regulate other genes responsible for protein synthesis.

198
Q

What is the toxin produced by this strain?

A

slide 107

199
Q

Different genes affecting the same pathway

are distinguished by ________________

A

capital letters

200
Q

how long is E.coli chromosomal DNA?

A

~1 mm long

201
Q

Single base deletion resulting in a

______ ______ mutation

A

frame shift

202
Q

Describe the F’ generation process

A

slide 97

203
Q

how many kb is the human genome?

A

humans 3.3 million kb—-600 fold increase

204
Q

a chromosomal segment that can undergo transposition, especially a segment of bacterial DNA that can be translocated as a whole between chromosomal, phage, and plasmid DNA in the absence of a complementary sequence in the host DNA.

A

transposon

205
Q

a transducing particle might be regarded as

____________ (or phage-____________ hybrid) in a phage coat

A

bacterial DNA; phage-bacterial DNA hybrid

206
Q

what type of genetic transfer can bacteria do?

A

Bacteria can do both vertical and horizontal gene transfer

207
Q

What is the difference between the processes of generalized transduction and specialized transduction?

A

slide 101

208
Q

How are DNA gyrase and topoisomerase similar/ different?

A

DNA gyrase, or simply gyrase, is an enzyme within the class of topoisomerase (Type II topoisomerase) that relieves strain while double-stranded DNA is being unwound by helicase. The enzyme causes negative supercoiling of the DNA or relaxes positive supercoils.

209
Q

Describe Frederick Griffith’s experiment.

A

1a. living encapsulated bacteria injected into mouse
2a. mouse dies
3a. colonies of encapsulated bacteria were isolated from dead mouse

1b. living nonencapsulated bacteria injected into mouse
2b. mouse remained healthy
3b. A few colonies of nonencapsulated bacteria were isolated from mouse; phagocytes destroyed nonencapsulated bacteria

1c. heat-killed encapsulated bacteria injected into mouse
2c. mouse remained healthy
3c. no colonies were isolated from mouse

1d. living nonencapsulated and heat-killed encapsulated bacteria injected into mouse
2d. mouse died
3d. colonies of encapsulated bacteria were isolated from dead mouse

210
Q

an active process
demanding specific enzymes produced by the
recipient cell.

A

natural transformation

211
Q

Describe the structure of DNA

A 
- Polymer of nucleotides:
Adenine, thymine,
cytosine, and guanine
• Double helix
• "Backbone" is
deoxyribose-phosphate
• Strands are held together
by hydrogen bonds
between AT and CG
• Strands are antiparallel
212
Q

Is integration of the F plasmid into the bacterial chromosome
random?

A

slide 89

213
Q

Tn3 (type) transposon

A

slide 103

214
Q

mRNA is translated in _______ (three nucleotides)

A

codons

215
Q

What are the two major kinds of transduction?

A
  1. generalized transduction

2. specialized transduction

216
Q

Synthesizes DNA; proofreads and repairs DNA

A

DNA polymerase

217
Q

requires arginine added as a supplement to minimal medium

A

arg-

218
Q

Adds methyl group to selected bases in newly made DNA

A

Methylase

219
Q

What does Hfr stand for?

A

high frequency recombination

220
Q

What is the E.coli spontaneous mutation rate?

A 
1 in 10^9
replicated base pairs (10-9) or 
1 in 10^6 replicated
genes (10^-6) or
 1 in 1000 genomes (10^-3)
221
Q

Agent that causes mutations

A

mutagen

222
Q

Is the mitochondrial RNA polymerase sensitive to AZT?

A

slide 69

223
Q

What are the 3 mechanisms of gene transfer in bacteria?

A

I. Transformation
II. Conjugation
III. Transduction

224
Q

What are bacterial gene expression traits that can be regulated?

A

mRNA stability
translation
protein stability

225
Q

resistant to the antibiotic streptomycin

A

str^r

226
Q

Unwinds double-stranded DNA

A

Helicase

227
Q

The F plasmid can be correctly excised from ____ _____
to yield an F+ cell containing the original bacterial
chromosome and an independent F factor.

A

Hfr DNA

228
Q

What nucleotides in eukaryotes are methylated?

A

C*G

229
Q

two types of base substitutions

A
  1. Transitions

2. Transversions

230
Q

sensitive to the antibiotic streptomycin

A

str^s

231
Q

copies RNA from a DNA template

A

RNA polymerase

232
Q

how many genes are in bacteria vs humans?

A

5,000 genes vs. 21,000

233
Q

Describe negative regulation (repression) of the lac operon

A

The lac operon is composed of:

  • regulatory gene
  • promoter
  • operator
  • structural genes

The regulatory gene makes the repressor mRNA and the repressor protein. The operon is off because the repressor protein binds to the operator region and inhibits RNA polymerase from transcribing the DNA.

234
Q

How could you distinguish whether a cell is F+, Hfr, or F’?

A

slide 96

235
Q

A cell with an integrated F

A

Hfr cell

236
Q

Cut DNA from an exposed end of DNA; facilitate repair

A

Exonucleases

237
Q

What happens when lactose and glucose are present to the lac operon?

A

There is an inactive lac repressor and an inactive CAP

238
Q

Describe the Ames test

A

slide 77

239
Q

Leading cause of diarrhea world wide?

A

Escherichia coli O157:H7

240
Q

DNA replication, expression and repair enzymes that are specific to prokaryotes or eukaryotes?

A

snRNP- is only used in eukaryotes because only eukaryotes have introns

241
Q

6 different RNA products

A

mRNA - Messenger RNA: Encodes amino acid sequence of a polypeptide.
tRNA - Transfer RNA: Brings amino acids to ribosomes during translation.
rRNA - Ribosomal RNA: With ribosomal proteins, makes up the ribosomes, the organelles that translate the mRNA.
snRNA - Small nuclear RNA: With proteins, forms complexes that are used in RNA processing in eukaryotes. (Not found in prokaryotes.)

242
Q

Mutations are rare even in the presence of a ________

A

mutagen

243
Q

Can methylation traits be inherited?

A

Yes, but can be reversed later

244
Q

Virtually all resistance determinant genes on R plasmids are present
as what?

A

transposons

245
Q

Use when there is no medium on which the mutant can grow and the parent cell cannot
- mutants that require a growth factor not normally present (i.e. auxotrophic mutants)
- conditional lethal mutants (i.e. Ts)
• Procedure requires:
– Replica plating

A

indirect selection

246
Q

What is an example of a gram negative bacteria in which conjugation takes place?

A

E.coli

247
Q

Only those genes located on the bacterial genome in close proximity to the prophage insertion
site can be transduced.

A

specialized transduction

248
Q

phenotypic screening for E.coli

A

MacConkey agar (lactose positive shows up)

249
Q

Are mutations generally beneficial, neutral or

detrimental to the cell?

A

neutral or detrimental

250
Q

An RNA polymerase that makes RNA primers from a DNA template

A

RNA Primase

251
Q

R factor/ plasmids that carry multiple resistance genes

A

r-determinants

252
Q

However, should the excision involve a different
bacterial IS element than was originally used for
integration, the excised F factor will contain a segment
of bacterial DNA. What is this called?

A

F’

253
Q

Define epigenetic control

A

heritable changes in gene expression that occur

without changes in the DNA sequence — a change in phenotype without a change in genotype

254
Q

transfer of a plasmid from one cell to another by means of cell to cell contact

A

bacterial conjucation

255
Q

Normally, E.coli benefits the body by suppressing the growth of harmful bacterial species and synthesizing appreciable amounds of _________.

A

vitamins

256
Q

Which organisms have RNA genes?

A

viruses

257
Q

Describe the process of conjugation in gram-positive bacteria

A

slide 88

Microbiology (15 decks)

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