Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

BIO 315 > Module 5 - Bacterial Genetic Analysis > Flashcards

Module 5 - Bacterial Genetic Analysis Flashcards

You may prefer our related Brainscape-certified flashcards:
Biology 101 flashcards
1
Q

What types of bacteria has scientists focused on for science?

A

Pathogenic bacteria, or ones with practical importance

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What are some examples of bacteria that would be commonly studied?

A

E. coli found in the gut, salmonella species

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What are some applications of bacterial genetics?

A

Industrial applications, Streptomycin antibiotics, E. coli protein production, and Pseudomonas decontamination

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

How is Streptomycin used in bacterial genetics applications?

A

It can create antibiotics

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

How is E. coli used in bacterial genetics applications?

A

It can produce useful proteins

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

How is Pseudomonas used in bacterial genetics applications?

A

It can be used for decontamination by breaking down toluene

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

True or false: microbial genetics is important in the study of microbiology

A

True: it is important to understand the natural genetic tools for genetic research

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

What is growth?

A

Increasing the number of cells (not size)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

In which organisms is it easier to detect mutations: bacteria or eukaryotes?

A

Bacteria

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

How come it is easier to detect mutations in bacteria?

A

They have one copy of a gene, so a mutation can more easily be seen in the phenotype

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

How come it is harder to detect mutations in eukaryotes?

A

They have two copies of a gene, so a mutation can be masked by the other, functioning gene

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

In the first half of the 20th century, what was the belief about microbial genetics?

A

Microbes were too small to have genetic exchange

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Before bacteria, what organisms were shown to have genetic exchange?

A

Corn, peas, and paramecium protozoa

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

What did the study of genetic exchange in eukaryotic organisms show?

A

Inheritance followed a sexual event

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What do different strains of bacteria mean?

A

Genetically different cells (in the same species) with different phenotypes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What organism did Lederberg use for his experiments?

A

E. coli

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

What type of E. coli did Lederberg use in his experiments?

A

Different mutant nutrient strains, which had different metabolic requirements

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

What is an auxotroph?

A

A mutant strain having nutritional requirements additional to the wild type organism

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

What type of media would an auxotroph need?

A

Basic media, plus extra vitamins or amino acids

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

What is a prototroph?

A

A parent strain (to an auxotroph) that is able to grow just on basic media

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

What type of media would a prototroph need?

A

Basic media

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

What is found in basic media?

A

A source of carbon, nitrogen, and phosphorus (no additional vitamins or amino acids)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

How come auxotrophs cannot grow in basic media?

A

They have a mutation that prevents them from making a specific vitamin or amino acid

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

In Lederberg’s experiments, which organisms could grow in medium with both methionine and proline?

A

All of the strains

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

In Lederberg’s experiments, which organisms could grow in medium without methionine or proline?

A

Only the prototrophic strain (met+, pro+)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

In Lederberg’s experiments, which organisms could grow in medium with just methionine?

A

The prototrophic strain (met+, pro+), and the methionine auxotroph (met-, pro+)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

In Lederberg’s experiments, which organisms could grow in medium with just proline?

A

The protorophic strain (met+, pro+), and the proline auxotroph (met+, pro-)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

What is the makeup of a prototroph in Lederberg’s experiments?

A

Met+, pro+

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

What is the makeup of a methionine auxotroph in Lederberg’s experiments?

A

Met-, pro+

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

What is the makeup of a proline auxotroph in Lederberg’s experiments?

A

Met+, pro-

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

How can auxotrophs be used to see if bacteria can exchange genetic information?

A

If phylogeny of two auxotrophs can grow in general media, then there must be genetic exchange

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

True or false: if the phylogeny of two auxotrophs can grow in general media, there must be genetic exchange

A

False: reversion could have also occured

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

What is reversion?

A

A spontaneous mutation that corrected the metabolic deficiency

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

What are the chances of reversion for a single mutant?

A

10^-6 to 10^-7 for 10^8 cells

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

If 10^8 single mutants are plated, how many will rever?

A

10-100

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

What can be used to overcome the probability of reversion?

A

Double and triple mutant strains

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

What are the chances of reversion for a double mutant?

A

10^-12 to 10^-14 for 10^8 cells

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

What are the chances of reversion for a triple mutant?

A

10^-18 to 10^-21 for 10^8 cells

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
39
Q

What happened when Lederberg crossed two triple mutant auxotrophs?

A

There were still some phylogeny that could grow in simple media

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
40
Q

What was the conclusion of Lederberg’s experiment with triple mutant auxotrophs?

A

Genetic information must have been exchanged (reversion was very unlikely)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
41
Q

What did Lederberg show with cell extract?

A

Genes were not just taken up from dead cells

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
42
Q

What was the conclusion of Lederberg’s follow-up with cell extract?

A

Live cells must have transferred the genetic information

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
43
Q

Which is bigger: eukaryotic DNA or bacterial DNA?

A

Eukaryotic DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
44
Q

True or false: most of the eukaryotic DNA is transcribed

A

False: most of it does not encode for proteins

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
45
Q

True or false: most of the bacterial DNA is transcribed

A

True: most of it is transcribed

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
46
Q

What is the structure of DNA in most bacterial cells?

A

One circular chromosome

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
47
Q

How else can DNA be arranged in a bacteria (abnormally)?

A

As linear chromosomes, or having more than one chromosome

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
48
Q

Which bacterial species have linear chromosomes?

A

Streptomyces and Borrelia

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
49
Q

What is a plasmid?

A

A circular DNA molecule that can replicate independently of chromosomal DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
50
Q

What are genes on a plasmid usually used for?

A

Survival of bacteria

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
51
Q

What are some examples of genes found on plasmids?

A

Antibiotic resistance, toxic chemical degradation, or symbiosis

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
52
Q

What trait is found on the R1 plasmid?

A

Antibiotic resistance

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
53
Q

Where is R1 plasmid found?

A

Salmonella Paratyphi

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
54
Q

What trait is found on the pSym plasmid?

A

Nitrogen-fixing nodule formation on legume plant roots

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
55
Q

Where is pSym plasmid found?

A

Rhizobium

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
56
Q

What trait is found on the pTi plasmid?

A

Tumor formation on plants

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
57
Q

Where is pTi plasmid found?

A

Agrobacterium

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
58
Q

What trait is found on the pTol plasmid?

A

Toluene degradation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
59
Q

Where is pTol plasmid found?

A

Pseudomonas putida

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
60
Q

What trait is found on the pR773 plasmid?

A

Arsenic resistance

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
61
Q

Where is pR773 plasmid found?

A

Escherichia coli

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
62
Q

What trait is found on the pWR100 plasmid?

A

Entry into host cells

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
63
Q

Where is pWR100 plasmid found?

A

Shingella flexneri

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
64
Q

What plasmid does Salmonella Paratyphi have?

A

R1

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
65
Q

What plasmid does Rhizobium have?

A

pSym

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
66
Q

What plasmid does Agrobacterium have?

A

pTi

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
67
Q

What plasmid does Pseudomonas putida have?

A

pTol

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
68
Q

What plasmid does Escherichia coli have?

A

pR773

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
69
Q

What plasmid does Shingella flexneri have?

A

pWR100

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
70
Q

Which plasmid gives antibiotic resistance?

A

R1

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
71
Q

Which plasmid gives nitrogen-fixing nodule formation on legume plant roots?

A

pSym

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
72
Q

Which plasmid gives tumor formation on plants?

A

pTi

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
73
Q

Which plasmid gives toluene degradation?

A

pTol

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
74
Q

Which plasmid gives arsenic resistance?

A

pR773

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
75
Q

Which plasmid gives entry into host cells?

A

pWR100

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
76
Q

What is a genome?

A

All the genetic material in a cell, including plasmid DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
77
Q

What is a replicon?

A

DNA, region of DNA, or bacterial plasmid/chromosome that can replicate from a single origin of replication

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
78
Q

What range can copy number take?

A

One to several hundred copies per cell

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
79
Q

What controls copy number?

A

The initiation of DNA replication

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
80
Q

What plays an important role in the evolution of bacterial chromosomes?

A

Bacteriophages and plasmid DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
81
Q

How come bacteriophages and plasmid DNA play an important role in the evolution of bacterial chromosomes?

A

They provide mechanisms of moving segments of the bacterial genome from one bacterial cell to another

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
82
Q

What is an example of phage DNA in bacteria?

A

Clostridium botulinum toxin

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
83
Q

What are incompatible plasmids?

A

Plasmids that cannot exist stably within a population

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
84
Q

How can two plasmids become incompatible?

A

If they have a similar origin of replication

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
85
Q

What happens if two plasmids in a cell have a similar origin of replication?

A

Replication will initiate randomly, so one of the plasmids will lose the count

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
86
Q

How will replication control treat two incompatible plasmids?

A

As a single plasmid

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
87
Q

What does random initiation of incompatible plasmids lead to?

A

Unequal numbers of the two plasmids

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
88
Q

True or false: incompatible plasmids is a competitive mechanism to prevent replication of the other plasmid

A

False: it is a random selection that prevents replication of the other plasmid

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
89
Q

What is a mutant?

A

A cell or strain possessing a mutation compared to a wild type strain

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
90
Q

What is a mutation?

A

A change in the DNA sequence

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
91
Q

What is an allele?

A

A different form of a gene (other)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
92
Q

What causes alleles?

A

Mutations

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
93
Q

What are the outcomes of a mutation?

A

Loss-of-function, or gain-of-function

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
94
Q

What is a genotype?

A

The collection of alleles of a given set of genes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
95
Q

How is a gene name written?

A

A 3 letter abbreviation in italics, followed by a capital letter

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
96
Q

What are some examples of proper gene names?

A

lacZ and lacY (should be in italics)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
97
Q

What is the purpose of the capital letter in a gene name?

A

To separate genes that are in a common pathway (eg: lacZ and lacY)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
98
Q

How is a protein name written?

A

Same 3 letter abbreviation as the gene name, with the first letter characterized and no italics

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
99
Q

What are some examples of proper protein names?

A

LacZ and LacY (no italics)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
100
Q

How can mutants be generated?

A

UV light or other chemicals

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
101
Q

How are mutants identified?

A

Through changes in phenotype of growth patterns

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
102
Q

What are some examples of phenotypes that can be used to identify mutants?

A
  1. Capsules –> mucoid / smooth colonies

2. Flagella / red pigmentation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
103
Q

What bacterial mutants can be identified by red pigmentation and flagella?

A

Serratia marcescens

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
104
Q

How can potentially rare mutants be detected?

A

Through phenotypic selection or phenotypic screening

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
105
Q

If 10^9 CFU are plated on media with proper growing requirements, how many cells are expected to grow?

A

10^9

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
106
Q

What happens if 10^9 CFU are plated on media with streptomycin?

A

A majority of the cells will not grow, but a few mutants resistant to streptomycin will grow

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
107
Q

What is commonly used for phenotypic selection?

A

A drug/antibiotic

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
108
Q

What are the steps of phenotypic selection?

A

Plate the bacteria on a plate with a drug or antibiotic, and see which ones grow

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
109
Q

What happens if mutants look different than wild type colonies?

A

They can be detected directly on a single plate

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
110
Q

What happens if mutants look like the wild type colonies?

A

2 different conditions are needed to distinguish between the two

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
111
Q

For phenotypic selection, what are the two conditions used?

A

All nutritional support, and lacking a particular nutrient

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
112
Q

For phenotypic selection, if condition 1 has all the nutritional support, what is the result?

A

All cells (wild type and mutant) will grow

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
113
Q

For phenotypic selection, if condition 2 lacks a particular nutrient, what is the result?

A

Only wild type cells will grow (the mutant cells will not grow)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
114
Q

For phenotypic selection, after having two conditions, which cells are the mutants?

A

Those that grow on the full support, but did not grow on the media lacking a nutrient

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
115
Q

What are the steps of phenotypic screening?

A

Plate the bacteria in two different conditions, and compare which ones didn’t grow in the condition lacking a particular nutrient

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
116
Q

Which is more efficient: screening or selection?

A

Screening

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
117
Q

How come screening is usually les efficient than selection?

A

Large amounts of colonies need to be screened to find a rare phenotype

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
118
Q

How can duplicate plates be created?

A

Through replica plating

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
119
Q

What process is replica plating useful for?

A

Phenotypic screening (when phenotypic selection can not work)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
120
Q

What is replica plating?

A

The process of duplicating the colonies onto multiple plates

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
121
Q

What is replica plating similar to?

A

Making a photocopy from a master copy

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
122
Q

What are the steps of replica plating?

A

Colonies are lifted from a master plate using a sterile velvet cloth, and then replicas are made on new plates

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
123
Q

True or false: all mutations are bad

A

False: while most can disrupt gene function, they can also be beneficial

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
124
Q

What provides the raw material for environmental pressures to act?

A

Changes in genetic material (mutations)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
125
Q

What happens if a mutation in a clone is disadvantageous?

A

The population of mutants will be low

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
126
Q

What happens if a mutation in a clone is advantageous?

A

It will compete with other cells, and the number of cells with that mutation will increase

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
127
Q

What did Richard Lenski do?

A

Proved that mutations can be advantageous experimentally

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
128
Q

What was Lenski’s experimental setup?

A

12 parallel cultures of E. coli were grown in a media, and frozen after every 75 days

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
129
Q

What was present in the media of Lenski’s experiments?

A

Glucose as a carbon source

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
130
Q

How were Lenski’s E. coli subcultured?

A

Once per day, into fresh glucose media

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
131
Q

How long did the Lenski experiment last?

A

10,000 generations (1500 days)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
132
Q

What did Lenski do after the 10,000 generations?

A

The new cells were compared to the frozen ancestors

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
133
Q

How come the ancestors were frozen in Lenski’s experiments?

A

To prevent them from evolving

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
134
Q

What was the conclusion of Lenski’s experiments?

A

The ability for E. coli to grow in culture was enhanced over time

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
135
Q

How did Lenski compare the new cells to the ancestral cells

A

He mixed them in equal ratio, and then plated them to see the proportion of each

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
136
Q

How were the two strains in Lenski’s experiments differentiated?

A

By color (through a neutral marker)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
137
Q

How was the relative fitness calculated?

A

The ratio of red (new) to white (ancestral) colonies

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
138
Q

What was the result of Lenski’s relative fitness calculations?

A

Both cell size and survivability increased in evolved cultures

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
139
Q

In Lenski’s experiments, how were fitness gains formed?

A

From mutations in genes involved in the cellular stress response

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
140
Q

What are fitness gains specific to?

A

Given environmental conditions

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
141
Q

What did Ester Lederberg do?

A

Studied whether mutations can arise in the absence of selective conditions

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
142
Q

What were the steps of Lederberg’s experiments on selection?

A
  1. E. coli were grown on a master plate without any drug
  2. Replica plates were made for plates with and without streptomycin
  3. Mutants from the antibiotic free plate were plated on streptomycin
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
143
Q

What was the purpose of the first two plates in the Lederberg experiment on selection?

A

To identify colonies that were streptomycin resistant

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
144
Q

What was the purpose of the third plate in the Lederberg experiment on selection?

A

To show that colonies were streptomycin resistant, even though they have not been subjected to streptomycin

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
145
Q

What was the conclusion of Lederberg’s experiments on selection?

A

Mutations can occur in the absence of selective pressure

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
146
Q

How did Lederberg’s results support her conclusion about selection?

A

Cells that were never exposed to streptomycin still developed resistance

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
147
Q

What role do restriction enzymes play?

A

Molecular scissors

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
148
Q

How do restriction enzymes work?

A

They recognize a specific DNA sequence, and make a double stranded cut

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
149
Q

What is a restriction site?

A

The DNA sequence recognized and cut by the restriction enzyme

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
150
Q

How many base pairs is a restriction site?

A

4, 6, or 8 bp

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
151
Q

What is another name for sticky ends?

A

Cohesive ends

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
152
Q

What is the result after restriction enzymes cut DNA?

A

Either sticky ends or blunt ends

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
153
Q

What do sticky ends look like?

A

Overhangs

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
154
Q

What do blunt ends look like?

A

Straight cuts

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
155
Q

What does the name of the restriction enzyme indicate?

A

The source (which bacterium it came from)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
156
Q

What does the first letter of a restriction enzyme indicate?

A

The genus of the source

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
157
Q

What do the second and third letters of a restriction enzyme indicate?

A

The species of the source

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
158
Q

What does the fourth letter of a restriction enzyme indicate?

A

The strain of the source

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
159
Q

What is the structure of restriction sites?

A

Palindromes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
160
Q

What is a palindrome?

A

A DNA sequence that is the same when read from both strands of DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
161
Q

How can DNA cut by restriction enzymes be joined together?

A

Through DNA ligase

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
162
Q

What does DNA ligase do?

A

Reforms the phosphodiester bonds between adjacent 5’ phosphate groups and 3’ hydroxyl groups

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
163
Q

What DNA can bind to blunt ends?

A

Any other DNA segment with blunt ends

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
164
Q

Where does EcoRI come from?

A

Escherichia coli

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
165
Q

Where does BamHI come from?

A

Bacillus amylolique faciens

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
166
Q

Where does HindIII come from?

A

Haemophilus influenzae

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
167
Q

Where does SmaI come from?

A

Serratia marcescens

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
168
Q

Which restriction enzyme produces blunt ends?

A

SmaI

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
169
Q

What is the restriction site for EcoRI?

A

5’ GAATTC 3’

3’ CTTAAG 5’

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
170
Q

What is the restriction site for BamHI?

A

5’ GGATCC 3’

3’ CCTAGG 5’

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
171
Q

What is the restriction site for HindIII?

A

5’ AAGCTT 3’

3’ TTCGAA 5’

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
172
Q

What is the restriction site for SmaI?

A

5’ CCCGGG 3’

3’ GGGCCC 5’

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
173
Q

How is the restriction site for EcoRI cut?

A

5’ G \ AATCC 3’

3’ CTTAA \ G 5’

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
174
Q

How is the restriction site for BamHI cut?

A

5’ G \ GATCC 3’

3’ CCTAG \ G 5’

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
175
Q

How is the restriction site for HindIII cut?

A

5’ A \ AGCTT 3’

3’ TTCGA \ A 5’

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
176
Q

How is the restriction site for SmaI cut?

A

5’ CCC \ GGG 3’

3’ GGG \ CCC

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
177
Q

What are the steps of generating recombinant DNA from restriction enzymes?

A
  1. Digest the DNA with the restriction enzyme
  2. Mix digested DNA and incubate
  3. Treat annealed DNA fragments with DNA liagse
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
178
Q

What can restriction enzymes be used to create?

A

Recombinant DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
179
Q

How do DNA molecules cut with EcoRI anneal?

A

Based on complementary base pairing on the sticky ends generated from EcoRI

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
180
Q

What is molecular (DNA) cloning?

A

The process of replicating recombinant DNA molecules

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
181
Q

What is used for DNA cloning?

A

Cloning vectors

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
182
Q

What is a cloning vector?

A

A DNA molecule that can be genetically manipulated or replicated within cells

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
183
Q

What are some examples of cloning vectors?

A

Plasmids, cosmids, and phages

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
184
Q

What does a vector do?

A

Inserts recombinant DNA molecule into a recipient host bacterial cell

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
185
Q

When were plasmid cloning vectors first used?

A

1970

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
186
Q

Who performed the first plasmid cloning experiments?

A

Stanley Cohen

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
187
Q

What plasmids were used in the first plasmid cloning experiments?

A

pSC101 and pSC102

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
188
Q

What does pSC101 contain?

A

A tetracycline resistance gene

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
189
Q

What does pSC102 contain?

A

A kanamycin resistance gene

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
190
Q

What does Cohen do with pSC101 and pSC102?

A

He digested them with EcoRI, and combined the fragments to create pSC105

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
191
Q

What is pSC105?

A

A plasmid created from pSC101 and pSC102

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
192
Q

What does pSC105 contain?

A

A tetracycline resistance gene, and a kanamycin resistance gene

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
193
Q

What does blue-white screening allow for?

A

Visual differentiation of colonies that carry the insert or do not

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
194
Q

What is the advantage of blue-white screening?

A

Screening is done all on one medium

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
195
Q

What plasmid is commonly used for blue-white screening?

A

pUC18

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
196
Q

What is pUC18 used for?

A

Blue-white screening

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
197
Q

What does pUC18 contain?

A

An ori, an antibiotic resistance gene, and a lacZ gene

198
Q

What does the lacZ gene of pUC18 code for?

A

The amino terminal fragment of the enzyme beta-galactosidase

199
Q

What part of beta-galatosidase does E. coli produce (without the plasmid)?

A

The carboxyl terminal fragment

200
Q

What happens if pUC18 is inserted into E. coli (unchanged)?

A

Functional beta-galactosidase is formed, which can break down X-gal

201
Q

What does beta-galactosidase do?

A

Breaks down X-gal, which gives colonies a blue color

202
Q

What color are cells with unedited pUC18?

A

Blue

203
Q

What happens when a gene of interest is inserted into pUC18?

A

It disrupts the lacZ gene, so beta-galactosidase cannot be formed

204
Q

What happens if pUC18 with a gene of interest is inserted into E. coli?

A

Beta-galactosidase cannot be formed, so they cannot break down X-gal

205
Q

What color are cells with pUC18 with the gene of interest?

A

White

206
Q

What does white cells mean in blue-white screening?

A

The bacteria took up the plasmid with the gene of interest

207
Q

What does blue cells mean in blue-white screening?

A

The bacteria took up the plasmid, but not with the gene of interest

208
Q

Where is a gene of interest inserted in pUC18?

A

In the middle of the lacZ gene

209
Q

What traits (5) are desirable on plasmids for easier gene cloning?

A

Origin of replication, selectable marker gene, multiple cloning site, small size, and high copy number

210
Q

True or false: any ori will work on a plasmid

A

False: the ori needs to work in the specific host cell

211
Q

What types of genes are commonly found as selectable markers?

A

Antibiotic resistance

212
Q

Why would researchers want a plasmid with small size?

A

It maximizes transfer

213
Q

Why would researchers want a plasmid with high copy number?

A

Many DNA fragments can be made in a small number of cells

214
Q

Why would researchers want a plasmid with a multiple cloning site?

A

It helps in cloning and screening of cells containing clone DNA

215
Q

What is the most common vector used?

A

Plasmids

216
Q

What is the reasoning behind phage vectors?

A

They take advantage of the ability of viruses to infect and deliver genomes into cells

217
Q

How is a phage vector developed?

A

The DNA fragments that need to be cloned and phage DNA are mixed and ligated together

218
Q

How big is the entire lambda phage genome?

A

~50 kb

219
Q

What is done after the phage vector is developed?

A

It is added to E. coli on solid media to form plaques

220
Q

What happens if a phage vector is integrated?

A

The phylogeny phages are not produced, so clone fragments will not be amplified

221
Q

How is the problem of phage vectors being incorporated overcome?

A

By removing the genes for integration and excision (not essential for viral replication)

222
Q

True or false: the integration and excision genes in phage vectors are necessary for viral replication

A

False: they can be removed from the genome

223
Q

How big are the integration and excision genes?

A

~20 kb

224
Q

Where is the DNA inserted in the phage vector?

A

Where the integration and excision genes used to be in the phage genome

225
Q

What is a cosmid?

A

A hybrid plasmid that contains phage cos sequences

226
Q

What is a cosmid a combination of?

A

A cos site and a plasmid

227
Q

What does a cos site do?

A

It is required for packing into phage particles

228
Q

Where are cosmid DNA sequences originally from?

A

The lambda phage

229
Q

Once the DNA is in the host cell, how is the cosmid maintained?

A

As a plasmid

230
Q

How big of an insert can most plasmids handle?

A

Up to 15 kb

231
Q

How big of an insert can phages handle?

A

Up to 24 kb

232
Q

How big of an insert can cosmids handle?

A

Up to 45 kb

233
Q

What is the composition of a cosmid?

A

A cos site, a multiple cloning site, and an antibiotic selection marker (plus the gene of interest)

234
Q

How come a cosmid has a lot of room for insert DNA?

A

Nearly all of the phage DNA is omitted

235
Q

What is horizontal gene transfer?

A

The movement of DNA between microbes

236
Q

True or false: horizontal gene transfer is a major contributor to evolution

A

True: it can facilitate the movement of DNA

237
Q

When DNA enters a cell, what are its two options?

A

Either replicate on its own (plasmid), or join the host cell’s DNA

238
Q

What is recombination?

A

The incorporation of foreign DNA into host cell’s chromosomes

239
Q

What does recombination involve?

A

The breaking and joining of two DNA strands

240
Q

What are the two forms of recombination?

A

Homologous and non-homologous recombination

241
Q

What is homologous recombination?

A

When 2 identical (or nearly identical) fragments of DNA line up and exchange pieces

242
Q

What is another name for homologous recombination?

A

Crossover

243
Q

In what organism is homologous recombination best understood?

A

E. coli

244
Q

Which enzymes are present in homologous recombination?

A

The RecBCD complex and the protein RecA

245
Q

What structure is produced during homologous recombination?

A

The Holliday junction

246
Q

What is the structure of the Holliday junction?

A

An X shape, where the 2 DNA molecules are linked together

247
Q

What happens when the Holliday junction is cleaved?

A

The DNA is separated such that recombined DNA molecules are formed

248
Q

What does RecBCD do?

A

Unwinds and nicks the DNA fragment

249
Q

What does RecA do?

A

Bind single stranded DNA to scan for homology. It then produces a nick, and joins the strands together

250
Q

What is strand exchange?

A

When the two DNA strands are swapped by RecA in homologous recombination

251
Q

What happens if there is a single crossover between two circular molecules?

A

One circular molecule is produced (integration)

252
Q

What happens if there is a double crossover between two circular molecules?

A

There is reciprocal exchange of the region between the 2 crossover events (DNA swap)

253
Q

What happens if there is a double crossover between a circular molecule and a linear molecule?

A

Reciprocal exchange of the DNA from first molecule into the second molecule (integration) between the 2 crossover events

254
Q

Where does non-homologous recombination take place?

A

In all forms of life

255
Q

Where is non-homologous recombination most common?

A

Viruses and transposable elements

256
Q

What is non-homologous recombination?

A

Recombination of DNA pieces with little or no sequence similarity

257
Q

How do viruses use non-homologous recombination?

A

They can integrate their genome into the host chromosome

258
Q

Where does integration of the viral genome into the host chromosome occur?

A

At specific, but non-homologous, sites

259
Q

What enzyme allows for the viral genome to be integrated into the host chromosome?

A

Integrase

260
Q

What does integrase do?

A

Allows the viral genome to be integrated into the host chromosome

261
Q

What is transformation?

A

The introduction of extracellular DNA (plasmid/DNA fragment) directly into an organism

262
Q

True or false: transformation requires cell/cell contact

A

False: transformation does not require cell/cell contact for DNA uptake

263
Q

What bacteria are naturally competent to take up DNA from their surroundings?

A

Bacillus, Streptococcus, Haemophilus, and Neisseria

264
Q

How come Bacillus and Streptococcus are naturally competent to take up DNA from their surroundings?

A

They have specialized machinery for the uptake of DNA

265
Q

Which bacteria are not naturally competent to take up DNA from their surroundings?

A

E. coli

266
Q

How can cells like E. coli be made competent for transformation?

A

Through adding calcium ions or through electroporation

267
Q

How does a solution of cations like calcium aid in transformation?

A

It makes the membrane more permeable to large molecules, such as DNA

268
Q

What is electroporation?

A

Applying an electric current that generates holes in the cellular membrane for DNA to enter

269
Q

What is the advantage of electroporation?

A

It can be applied to a broad range of bacteria

270
Q

What is the first step of transformation for naturally competent cells?

A

DNA binds to a DNA binding receptor on the cell surface

271
Q

What happens once DNA binds to a DNA binding receptor?

A

One strand is degraded, and the other strand transported through a specialized channel pore

272
Q

What happens once DNA enters a cell through the DNA binding receptor?

A

It can either be used as nutrients, or integrated into the host chromosome through recombination

273
Q

What enzyme pulls DNA into the cell?

A

DNA translocase

274
Q

What does DNA translocase do?

A

Pulls DNA into the cell

275
Q

What happens to the single stranded DNA once it enters the cell?

A

It binds to single stranded DNA binding proteins and RecA

276
Q

What is conjugation?

A

Transfer of DNA from cell/cell via direct contact/sex pilus formation

277
Q

True or false: conjugation can only occur within one domain

A

False: conjugation can occur between domains

278
Q

True of false: conjugation can lead to human pathogens

A

True: conjugation can result in the conversion of non-pathogenic organisms into human pathogens

279
Q

What does conjugation in E. coli require?

A

The fertility factor F

280
Q

What is the fertility factor?

A

A circular double stranded DNA plasmid called the F plasmid

281
Q

What are F+ strains?

A

Stains that have the F plasmid

282
Q

What can F+ strains do?

A

Can donate DNA to F- strains

283
Q

What happens when an F+ strain donates DNA to an F- strain?

A

The F- strain becomes an F+ strain

284
Q

What does the F plasmid contain?

A

All genes needed for conjugation and plasmid maitenance

285
Q

What does tra region stand for?

A

Transfer region

286
Q

What is found in the tra regions?

A

Genes for proteins needed for production of conjugational structures that link cells together and transport DNA

287
Q

How can the F plasmid be copied?

A

Using the rolling circle method, and then sent across the bridge into the recipient cell

288
Q

What mediates conjugation?

A

A special sex pili

289
Q

What encodes the sex pili?

A

Some of the tra genes

290
Q

What happens after a donor and recipient contact (in conjugation)?

A

A mating bridge forms

291
Q

What is a mating bridge?

A

A complex of tra encoded proteins that facilitates transfer of DNA in conjugation

292
Q

What happens in the donor cell once a mating bridge is formed?

A

An endonuclease makes a single stranded nick at the origin of transfer of the F plasmid

293
Q

What happens once there is a nick in the F plasmid at the origin of transfer?

A

One strand of the F plasmid gets donated to the recipient cell through the mating bridge

294
Q

What happens once each cell in conjugation has one strand of DNA?

A

DNA polymerase synthesizes the complementary strand

295
Q

After the mating bridge, how many strands of DNA are found in each cell?

A

Each cell has one strand

296
Q

What happens once DNA polymerase synthesizes the complementary strands of the plasmids in conjugation?

A

The ends of the plasmid release from the mating bridge, and attach to the plasmid to regain the circular form

297
Q

Besides conjugation, what can the F plasmid do?

A

Integrate with the host chromosome

298
Q

What type of recombination can occur between the F plasmid and the host chromosome?

A

Homologous DNA recombination

299
Q

What type of crossover produces an HFR strain?

A

A single crossover event (incorporation)

300
Q

What is an HFR strain?

A

A strain where the entire F plasmid incorporates into the chromosome

301
Q

What does HFR stand for?

A

High frequency of recombination

302
Q

What happens when the F plasmid in an HFR strain initiates transfer?

A

Attached chromosomal genes can also be transferred to the recipient cell

303
Q

What is the significance of HFR strains?

A

They allow new opportunities to pass genetic information from one cell to another

304
Q

How can researchers use HFR strains?

A

They can be used to map locations of genes in the host chromosome

305
Q

How can HFR strains be used to map locations of genes on the host chromosome?

A

Multiple auxotrophic mutants can be monitored for regained function over time of conjugation

306
Q

True or false: HFR strains convert F- strains into F+ cells

A

False: the recipient cell remains an F- cell

307
Q

How come HFR strains do not convert F- strains into F+ strains?

A

Only a part of the host chromosome (F plasmid) is transferred into recipient cells

308
Q

What happens when a mating bridge is formed in HFR strains?

A

The origin of transfer is nicked, and only part of the F plasmid is transferred

309
Q

For the entire F plasmid to be transferred in an HFR strain, what would need to happen?

A

The entire chromosome would need to move into the recipient cell

310
Q

How come it is rare for an HFR strain to transfer the entire F plasmid?

A

Mating pairs often separate before the entire chromosome can be transferred

311
Q

Which genes in an HFR strain are donated at the highest rate?

A

Those near the site of F insertion

312
Q

Which genes in an HFR strain are donated at the lowest rate?

A

Those further from the site of F insertion

313
Q

How is an F’ plasmid formed?

A

Recombination occurs between either side of F insertion, resulting in looping out of a segment of the chromosome

314
Q

What is an F’ plasmid?

A

An F plasmid that also contains large amounts of chromosomal DNA

315
Q

What is an F’ strain?

A

A strain that contains an F’ plasmid

316
Q

What genes (generally) do F’ strains donate, and how frequently?

A

They transfer only a limited number of genes, but do so at extremely high frequency

317
Q

What happens when F’ strains mate with F- strains?

A

They transfer the modified F’ plasmid into the recipient cell

318
Q

What happens to the transferred chromosomal DNA in F’ strains after conjugation?

A

It remains part of the F plasmid in the recipient cell

319
Q

What happens to the host chromosome after an F’ plasmid is created?

A

There is a deletion of the the genes (they are not found on the F’ plasmid)

320
Q

What is transposition?

A

Movement of DNA via mobile genetic elements (transposable elements)

321
Q

What do transposable elements do?

A

Mediate gene arrangements by moving within and between genomes

322
Q

Where were transposable elements first discovered?

A

In corn by Barbara McClintock

323
Q

What did Barbara McClintock do?

A

First discovered transposable elements in corn

324
Q

True or false: transposable elements are limited to a few species

A

False: they are found in virtually all genomes

325
Q

What are simple transposable elements?

A

Sequences that only encode for proteins necessary for transposition

326
Q

What is another name for simple transposable elements?

A

Insertion sequences, or IS elements

327
Q

What does IS elements stand for?

A

Insertion sequences

328
Q

What are complex transposons?

A

Sequences that encode for proteins necessary for transposition as well as other genes (such as antibiotic resistance)

329
Q

What does Tn stand for?

A

Transposon

330
Q

Where do transposable elements insert themselves?

A

Randomly into the genome

331
Q

How do many researchers use transposable elemtns?

A

By using them to generate mutations to disrupt the function

332
Q

How to transposable elements disrupt gene function?

A

By inserting themselves within a gene, thus disrupting the sequence and consequently the function

333
Q

What is needed for transposon mutagenesis?

A

A suicide vector plasmid

334
Q

What is a suicide vector?

A

A transposon carrying plasmid that is unable to replicate inside the cell

335
Q

How are transposon insertion mutants isolated?

A

By using an antibiotic resistance transposon on a suicide vector

336
Q

What is selected for in transposon insertion mutants?

A

The antibiotic resistance transposon to move from the suicide plasmid (lost from the cell) to the host chromosome

337
Q

What is transduction?

A

The transfer of bacterial DNA from one cell to another by a bacteriophage

338
Q

How do phages work?

A

They infect bacteria, and use cellular machinery to copy themselves

339
Q

What can happen during viral packaging in a host cell?

A

Segments of genomic DNA from the infected bacterial cell can become packaged into the virus capsid

340
Q

What are transducing particles?

A

Phages that carry bacterial DNA

341
Q

True or false: transducing particles are effective in infection

A

False: they are usually not effective in infection

342
Q

How come transducing particles are not effective in infection?

A

They usually lack phage genes needed to form infectious viral particles

343
Q

True or false: transducing particles cannot transmit their DNA

A

False: they can attach to recipient cells and inject the DNA

344
Q

What happens to DNA injected from a transducing particle?

A

It can undergo homologous recombination to insert into the recipient genome

345
Q

What is a transductant?

A

Bacteria that receive DNA through transduction

346
Q

What is the host range of phages?

A

Very narrow

347
Q

In what circumstance is transduction particularly efficient?

A

Transferring DNA between strains in the same species

348
Q

What is needed for incorporation in transduction?

A

Homologous recombination

349
Q

True or false: transducing particles can replicate

A

False: they cannot replicate

350
Q

How come transducing particles cannot replicate?

A

They lack the viral genome

351
Q

Why are Bacillus commonly studied?

A

They create endospores

352
Q

When did microbial genetics first start?

A

The mid 20th century

353
Q

Before microbes, what were the model organisms for genetics?

A

Fruit flies, corn, and peas

354
Q

What are some advantages of bacteria as a genetic organism of study?

A
  1. Each cell is a complete organism (growth = more cells)
  2. Simple cellular differentiation
  3. Simpler chromosome organization
355
Q

If 10^8 double mutants are plated, how many will revert?

A

0.0001-0.00001 colonies per plate

356
Q

If 10^8 triple mutants are plated, how many will revert?

A

Virtually no colonies

357
Q

What does it mean if a genome is “genetically compact”?

A

Most of the DNA encodes functional proteins

358
Q

What genes are found in the host chromosome of bacteria?

A

Genes for basic metabolic processes of the organism

359
Q

Which species of bacteria have more than one chromosome?

A

Agrobacterium, Vibrio cholerae, and Burkholderia

360
Q

What chromosomes does Agrobacterium have?

A

One linear, one circular

361
Q

What chromosomes does Vibrio cholerae have?

A

Two circular

362
Q

What chromosomes does Burkholderia have?

A

Three circular

363
Q

What is copy number?

A

The controlled number of plasmid molecules in a cell

364
Q

What controls the copy number?

A

Initiation of DNA replication

365
Q

True or false: DNA polymerase acts at a constant rate

A

True: it is not responsible for copy number since it replicates at a constant rate

366
Q

How come DNA polymerase does not affect copy number?

A

It replicates at a constant rate

367
Q

For two or more plasmids to exist inside a cell, what needs to happen?

A

They need to be in different incompatibility groups

368
Q

What is a wild-type strain?

A

A strain that possesses the typical or representative characteristics of the species

369
Q

How can a wild-type strain be first isolated?

A

Either in nature, or the common lab strain that mutants are derived from

370
Q

What is the wild-type strain for E. coli?

A

E. coli K12

371
Q

Where and when was the wild-type strain of E. coli isoalted?

A

From human feces in 1922

372
Q

Where was the wild-type strain of Sinorhizobium meliloti isolated from?

A

An antibiotic-resistant derivative of an isolate from an alfalfa root nodule

373
Q

What happens if a new strain is identified?

A

It is archived and cataloged in freezers in central strain locations

374
Q

What is the common name for HisC?

A

Histidinol phosphate aminotransferase

375
Q

What does HisC do?

A

It is involved in the biosynthesis of histidine

376
Q

What types of phenotypes are selection used for?

A

Ones where the mutant can grow and the wild type can not

377
Q

What types of phenotypes are screening used for?

A

Ones where the wild type can grow and the mutant can not

378
Q

What is an alternative to the velvet cloth method for replica plating?

A

Using a toothpick and a grid to transfer colonies

379
Q

What are the advantages of using a toothpick and grid over a sterile velvet cloth?

A

It has greater precision and reproducibility

380
Q

What are bacterial colonies composed of?

A

Millions of genetically identical organisms (clones)

381
Q

When did Lenski first start his experiments?

A

February 15th, 1988

382
Q

What does LTEE stand for?

A

Long Term Evolution Experiment

383
Q

What was the purpose of Lederberg removing cells distant from the antibiotic resistant plate in the selection experiments?

A

It served as a control that not all the bacteria were resistant to streptomycin

384
Q

What did Salvador Luria and Max Delbruck do?

A

Investigated whether mutations occurred randomly and spontaneously

385
Q

Who continued Lederberg’s idea about mutations occuring randomly?

A

Salvador Luria and Max Delbruck

386
Q

What was the rationale behind Luria’s and Delbruck experiment?

A

E. coli resistant to T1 phage would pass it on to their offspring. If they developed it earlier, more phylogeny would have the resistance

387
Q

What experiment did Luria and Delbruck run?

A

The fluctuation test

388
Q

What are the steps of the fluctuation test?

A
  1. Inoculate a large flask with E. coli, and plate onto plates with T1
  2. At the same time, inoculate independent cultures, and plate each onto plates with T1
389
Q

What were the results of the large flask from the fluctuation test?

A

Similar numbers of resistant colonies were seen in the plates

390
Q

What were the results of the independent cultures from the fluctuation test?

A

Each plate had a variable amount of resistant colonies

391
Q

How come independent cultures led to variable amounts of resistant colonies in the fluctuation test?

A

Each colony developed resistance at a different point, and thus more or less bacteria would gain resistance

392
Q

How come the large flask led to similar amounts of resistant colonies in the fluctuation test?

A

The mutants were evenly distributed in the large culture

393
Q

What was the conclusion of the fluctuation test?

A

Mutations occur spontaneously and randomly in the absence of selective pressure

394
Q

What were the sequence of advancements towards recombinant DNA?

A
  1. 1944 - DNA was shown to be the heritable material
  2. 1960s - DNA could be extracted from cells
  3. DNA ligase was extracted
  4. 1970 - restriction enzymes were discovered
  5. 1973 - first recombinant DNA was made
395
Q

When was the first recombinant DNA molecule made?

A

1973

396
Q

Who showed the DNA was the first heritable material?

A

Avery, MacLeod, and McCarthy

397
Q

What does a Roman numeral refer to in the name of a restriction enzyme?

A

Its order of isolation from that strain

398
Q

What was one of the first cloning vectors used?

A

pBR322

399
Q

What is contained in pBR322?

A

Ampicillin resistance, tetracycline resistance, unique restriction sites, and a small size (4.36 kb)

400
Q

How are linear and circular DNA molecules selected against in transformation?

A

DNA without an ori will be degraded and lost from the cell

401
Q

If an alpha-amylase gene is inserted into pBR322, what steps are done to screen for it?

A
  1. Do a general transformation on ampicillin for ampicillin resistance
  2. Do a screening on tetracycline for tetracycline sensitivity
  3. Do a functional analysis on starch breakdown for amylase activity
402
Q

What is a multiple cloning site?

A

Short segments on the vector that contain a cluster of different restriction enzyme sites that only appear once in the plasmid

403
Q

What is the advantage of a multiple cloning site?

A

It makes it easier to clone the vector by only having one place to cleave

404
Q

What does blue-white screening combine?

A

Antibiotic resistance screening with visual differentiation screening

405
Q

What are most of the plasmids used in molecular biology derived from?

A

ColE1 from E. coli

406
Q

What ori does ColE1 have?

A

OriV

407
Q

What does oriV do?

A

It is an origin of replication only for E. coli and closely related species

408
Q

What are shuttle vectors?

A

Vectors that can replicate in a more diverse range of hosts

409
Q

How do shuttle vectors work?

A

They have multiple oris so they can replicate in multiple hosts

410
Q

What is one use for shuttle vectors?

A

The in vivo assembly of synthesized overlapping oligonucleotide fragments in yeast

411
Q

How do yeast function in synthesizing DNA fragments?

A

In yeast, DNA fragments can form one, continuous fragment, which can be ligated into the shuttle vector and inserted into E. coli

412
Q

What is the advantage of using yeast to synthesize DNA fragments?

A

It can produce very large fragments of DNA with minimal in vitro steps

413
Q

What is needed for DNA to be packages correctly in a phage vector?

A

A phage cos site at both ends of the linear fragment

414
Q

What happens once the DNA fragment enters the capsid head?

A

A viral endonuclease cleaves the DNA at each cos site, leaving single strand overhangs that can recircularize the DNA once in the cell

415
Q

What is vertical gene transfer?

A

The inheritance of a gene from a direct ancestor

416
Q

What is recombination a spin-off of?

A

The DNA repair mechanism

417
Q

What happens once the Holliday junction is formed?

A

Two nicks are made to produce two recombinant DNA molecules

418
Q

What is the result of a single crossover between a circular chromosome and a linear DNA fragment?

A

A single linear molecule, which is not stable and thus degraded

419
Q

What is lytic replication?

A

New copies of the virus are produced within the cell

420
Q

What is lysogenic replication?

A

The phage genome becomes integrated into the host chromosome

421
Q

What is site-specific recombination?

A

Non-homologous recombination at specific sites (usually seen in viral replication)

422
Q

What is a knockout mutant?

A

A mutant where the function of a gene is disrupted

423
Q

True or false: a suicide vector has no ori

A

False: it usually has an ori for the cloning cell, but not the host cell

424
Q

What is a cointegrate?

A

The joining of a plasmid and the chromosome as one unit

425
Q

What are the advantages and disadvantages of using a double crossover gene knockout?

A

They lead to more stable insertions, but they are harder to make

426
Q

What does sacB do?

A

It leads to sensitivity to sucrose by producing levansucrase

427
Q

What does levansucrase do?

A

Hydrolyzes sucrose

428
Q

What happens if a sacB gene is active in a cell?

A

The cell will die in the presence of sucrose

429
Q

How can sacB be used in a double crossover gene knockout?

A

It can be used to ensure proper crossover (kanamycin and sucrose resistant mutants have the gene of interest)

430
Q

In a double crosover gene knockout, where would the sacB gene be found?

A

On the suicide vector

431
Q

What is an example of transformation being used by researchers?

A

The studies by Fredrick Griffith in the 1920s

432
Q

What did Fredrick Griffith do?

A

Studied how Streptococcus could become pathogenic through transformation

433
Q

Who demonstrated that gene transfer in conjugation occurred in only a single direction?

A

William Hayes

434
Q

What did William Hayes do?

A

Showed that gene transfer in conjugation occurred in only a single direction

435
Q

What happens if there is a loss-of-function of the tra genes?

A

There is a loss of F plasmid transfer function

436
Q

What did Bernard Davis do?

A

Used immersed filters that prevented cellular contact to study conjugation

437
Q

Who studied if conjugation required cellular contact?

A

Bernard Davis

438
Q

What does oriT stand for?

A

Origin of transfer

439
Q

How does the F plasmid integrate into the host chromosome?

A

Through a single-crossover event

440
Q

What is a transductant?

A

A cell that has incorporated DNA from another cell via conjugation

441
Q

How does a transductant incorporate DNA?

A

Through homologous recombination

442
Q

How can a gradient of transfer for HFR strains be tested?

A

Through purposeful interruption of mating during conjugation

443
Q

Before DNA sequencing was available, how were genes mapped in E. coli?

A

Through a gradient of transfer of HFR strains

444
Q

How long does it take for an entire chromosome to be transferred during conjugation

A

A constant rate of 100 minutes for the entire chromosome to be transferred

445
Q

For the E. coli K12 genome, what is the rate of transfer?

A

46 kbp per min

446
Q

How were F’ plasmids used in research?

A

Strains can be constructed that carry two different gene alleles or copies of a chromosomal region

447
Q

How would an F’ plasmid be used to make two alleles?

A

One allele would be in the host chromosome, and the other would be on the F’ plasmid

448
Q

What is a merodiploid?

A

A partial diploid that has two copies of some of its DNA

449
Q

Why did triparental conjugation need to be derived?

A

Conjugation requires oriT and tra genes, but this would make the plasmid too large

450
Q

How does triparental conjugation work?

A

The tra genes are provided by a helper plasmid, while the donor strain has the recombinant plasmid to be donated to the recipient cell through conjugation

451
Q

What is the first step of triparental conjugation?

A

The helper strain transmits the helper plasmid into the donor strain

452
Q

What is the second step of triparental conjugation?

A

The helper plasmid expresses the tra genes to allow the recombinant plasmid to move from the host to the recipient through conjugation

453
Q

How can the recipient cell be isolated in triparental conjugation?

A

By using media where none of the three original strains can grow

454
Q

What is needed for transposition to occur?

A

Transposase and terminal inverted repeat sequences

455
Q

What does the transposase enzyme do?

A

Recognizes terminal inverted repeat sequences and performs single-stranded cleavage

456
Q

What is non-replicative transposition referred to as?

A

Cut-and-paste

457
Q

What is the result of non-replicative transposition?

A

Transposable elements re excised from one location and inserted into another

458
Q

What is replicative transposition referred to as?

A

Copy-and-paste

459
Q

What is the result of replicative transposition?

A

It requires a replication step to leave the transposable element at the original site

460
Q

What do res sites do?

A

Site for resolvase to separate joined DNA molecules

461
Q

What does resolvase do?

A

Separates joined DNA molecules in replicative transposition

462
Q

What happens in non-replicative transposition?

A

There is repair of single-stranded gaps by DNA polymerase and DNA ligase

463
Q

What happens in replicative transposition?

A

Replication of the transposon by DNA polymerase results in joining of two DNA molecules, which is separated by resolvase

464
Q

What happens once transposase recognizes the sequences?

A

There is a joining of the cleaved strands to form an intermediate

465
Q

What is the significance of terminal inverted repeat sequences?

A

Site that transposase recognizes

466
Q

What sites does transposase recognize?

A

Terminal inverted repeat sequences

467
Q

What is the composition of IS elements?

A

A transposase gene flanked by two terminal inverted repeat sequences

468
Q

What are terminal inverted repeat sequences?

A

Short sequences of DNA that exist in an inverted orientation relative to each other

469
Q

What type of transposition can IS elements undergo?

A

Non-replicative transposition

470
Q

What is needed in the transposon to undergo replicative transposition?

A

A resolvase gene and a res site

471
Q

Which genes have often been associated with transposons?

A

Antibiotic resistance genes

472
Q

True or false: transposons have target site specificity

A

False: transposable elements can insert anywhere in the genome

473
Q

What does homologous recombination of transposons lead do?

A

Deletions, inversions, and translocations

474
Q

How do most researchers use transposons?

A

To generate mutations in a bacterial cell

475
Q

How were transposons used in the 2008 study in Alabama?

A

The transposon was used to create mutations, and the places that the transposon inserted at the cell survived were deemed not necessary for survival

476
Q

Which transposon was used in the 2008 study in Alabama?

A

Tn4001T

477
Q

What organism was studied in the 208 study in Alabama?

A

Mycoplasma pulmonis

478
Q

How are transposition mutants isolated?

A

Through a suicide vector and antibiotic screening

479
Q

Who first discovered transduction?

A

Norton Zinder

480
Q

What did Norton Zinder do?

A

First discovered transduction

481
Q

What was the first organism used to discover transduction?

A

Salmonella typhimurium

482
Q

What bacteriophage was used to discover transduction?

A

P22

483
Q

What experiment did Zinder do?

A

He observed prototrophic recombinants resulting from mixing two auxotrophic strains, even when a filter was applied

484
Q

What are the steps for using transduction in a lab?

A
  1. Culture bacteria with a small amount of lysate
  2. Collecting the resulting viral particles
  3. Use these particles for the recipient strains
485
Q

How does DNA in transduction integrate into the host cell genome?

A

Through double crossover recombination

486
Q

What is cotransduction frequency?

A

The frequency with which an unselectable marker gene is transduced along with a given selectable marker gene

487
Q

What is cotransduction used for?

A

Mapping genes

488
Q

What does cotransduction frequency depend on?

A

The distance between marker genes

489
Q

How was transduction used to combat HIV?

A

CCL3 and CCL5 genes were transduced into Latobacillus gasseria bacteria

490
Q

What bacteria was targeted for HIV treatment?

A

Latobacillus gasseria

491
Q

Where is Latobacillus gasseria found?

A

In the vagina

492
Q

What do CCL3 and CCL5 do?

A

Potentially combat against HIV

BIO 315 (12 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions