Ch. 10 Bacterial Genetics Test 2

Front 1

How many base pairs are in the E. Coli chromosome? How long is this in minutes. What percentage of this is open reading frames?

Back 1

4.6mbp which is 100 minutes long with 88% accounting for open reading frames

Front 2

What are the top 3 gene functions of E. Coli?

Back 2

1) Unknown 38.1%

2) Metabolism 21%

3) Transport 10%

Front 3

What are the bottom 3 gene functions of E. Coli

Back 3

9) Transcription 1.3%

8) Replication 2.7%

7) Translation 4.5%

Front 4

Approximately how much of the E. Coli genome was attained from horizontal gene transfer?

Back 4

18%

Front 5

How do plasmids replicate? Describe their structure?

Back 5

They replicate independently of the host with the use of host enzymes. It is double stranded, supercoiled, and circular

Front 6

What is the function of the enzymes that plasmids encode?

Back 6

They function to direct initiation of replication and partitioning of replicated plasmids between daughter cells

Front 7

What do we call the number of a particular plasmid in a cell?

Back 7

Copy number

Front 8

How does the replication of gram-negative plasmids differ from that of gram-positive plasmids?

Back 8

Gram-negative: Bidirectional replication

Gram-positive: Rolling circle replication

Front 9

Incompatability groups are _______ encoded proteins that _____ the replication of other plasmids having the same Inc group. How does this effect the replication of unrelated Inc groups?

Back 9

chromosomally, prevent. This has no affect on the replication of unrelated Inc groups

Front 10

What is an episome? The removal of a plasmid and all copy numbers of the same plasmic sf said to cure the bacteria? Curing of plasmids is often accomplished how?

Back 10

Episomes are plasmids which integrate into host chromosome. Curing is accomplished by intercalation of acridine dyes and electroporation

Front 11

What kinds of functions do plasmids carry out in bacteria? What are the 3 categories of these functions?

Back 11

Usually specialized and non-essential functions.

1) Physiological functions

2) Resistance

3) Virulence

Front 12

What are 4 physiological functions of plasmids?

Back 12

1) Formation of chemical byproducts such as acetone

2) Utilization of specific compounds such as sucrose vs lactose

3) Degradation of refractory chemicals such as napthalene

4) Special functions such as nitrogen fixation

Front 13

What are 3 resistance functions of a plasmid?

Back 13

1) Antibiotic resistance

2) Resistance to heavy metals

3) Resistance to bacteriocins

Front 14

What is a bacteriocins?

Back 14

Proteins produced by bacteria to inhibit or kill closely related species

Front 15

What are the 3 virulence functions of a plasmid?

Back 15

1) Host cell invasion

2) Production of toxins, enzymes, surfactants

3) Tumorigenicity in plants

Front 16

Define genotype

Back 16

Precise genetic makeup of an organisms aka genetic make

Front 17

How can you differentiate a gene from a gene product using nomenclature rules? What do these rules have in common?

Back 17

Genes: First 3 letters are lowercase, Italicized

Products: First letter is uppercase, not Italicized

-In both sets of rules, the 4th letter is uppercase and represents order of discovery (e.g., A=1, B=2, etc)

Front 18

What is the gene nomenclature?

Back 18

3 lower case letters follow by a capital letter in all italics. First 3 letters represent the protein/enzyme encoded, product of a pathway associated with the gene, or activity of the gene products. The capital letter is determined by order of discovery.

Front 19

How do we designate a gene product with nomenclature?

Back 19

Gene products are written with a capital at the first letter, followed by 2 lower case letters, none in italics, followed by the gene number as a capital letter

Front 20

How do we designate particular mutations in a gene? How do we designate mutant phenotypes?

Back 20

Particular mutations are numbered (ex: hisC1 where all the letters are italicized since it's a gene)

Wild type = +

Mutant = -

Front 21

What is an auxotrophic organism?

Back 21

An organisms who's mutation results in a nutritional requirement being added to the medium to grow

Front 22

What is the wild-type organism called from which we derive auxotrophs via mutation?

Back 22

Prototroph

Front 23

What are the 3 ways to isolate a mutant?

Back 23

Positive selection

Negative selection

Screening

Front 24

What can be easily detected via positive selection isolation of mutants by culturing only the mutant on a particular medium or under specific growth conditions?

Back 24

Antibiotic resistance

Front 25

What is a common technique used in negative selection. How does this technique work?

Back 25

Replica plating is a common technique by which we take a copy of a master plate to incubate 2 petri dishes who have different conditions to find the target colonies

Front 26

What is the basis of negative selection?

Back 26

We can screen for a mutant by identifying a specific condition under which the mutant cannot grow but the wild-type can.

Front 27

When do we do genetic screening to identify mutants?

Back 27

We do this when a mutation does not result in a selectable train

Front 28

What are the 3 major sources of mutation?

Back 28

1) Damage

2) Replication errors

3) Repair errors

Front 29

What is the difference between a spontaneous and an induced mutation?

Back 29

Spontaneous: The natural occurance of mutation during the life of an organism

Induced: As a result of some mutagen

Front 30

What is a readthrough mutation?

Back 30

When a stop codon is mutated to an amino acid and the RNA Pol keeps transcribing

Front 31

How do non-frameshift mutation occur? These mutations produce effects similar to what other kind of mutation?

Back 31

This occurs when 3 NT's are added or deleted forming a codon and adding or subtracting 1 extra amino acid. The effects are similar to a missense mutation

Front 32

What is a conditionally lethal mutation. Give an example.

Back 32

A mutation that is lethal under one condition but not lethal under another condition such as a temperature-sensitivity mutation

Front 33

Where do insertion mutations usually originate from?

Back 33

Transposable elements

Front 34

What is a translocation mutation?

Back 34

Movement of a large section of chromosomal DNA to a new location

Front 35

What is the average frequency of errors in spontaneous DNA replication?

Back 35

10^-6 per generation

Front 36

What is a inversion mutation?

Back 36

The reversal of the orientation of a specific sequence

Front 37

Order spontaneous, nonsense, reversion, and transposition mutation rates

Back 37

Transposition > Spontaneous = Reversion > Nonsense

Front 38

What is a reversion mutation?

Back 38

A point mutation that reverses another point mutation, in which the nucleotide is changed back to its original state or protein functionality is regained via some other way due to the mutation

Front 39

What are base analogs?

Back 39

Mutagenic chemicals that can substitute for a normal nucleobase in nucleic acids such as purine or pyrimidine analogs

Front 40

What are the 4 types of chemical mutagens?

Back 40

1) Base analogs

2) Chemicals that react with and change DNA

3) Alkylating agents

4) Intercalating agents

Front 41

Crossing over is an example of genetic _______. This can occur between DNA elements from the same chromosome or between donor and recipient DNA. In E. Coli, at least ___ genes are involved in homologous recombination. What is homologous recombination?

Back 41

recombination, 25. Homologousrecombination is the geneticexchange between homologous DNA sequences from two different sources

Front 42

Recombination involves the participation of recombination genes. The first step in recombination is to ____ one strand of DNA from the donor. What is the next step?

Back 42

Nick one strand. The next step is to partially separate the ssDNA from it's complement by activity of helicase at which point ssBP stabilize the single strand.

Front 43

What happens in recombination after the ssDNA is separated from it's complementary sequence?

Back 43

RecA protein binds to the separated strand. This results in a complex thatpromotes base pairing with the complementary sequence in therecipient DNA molecule. This base pairing in turn displaces theother strand of the recipient DNA molecule andis appropriately called strand invasion.

Front 44

What is the last step after RecA facilitated strand invasion?

Back 44

Endonucleases cut the combined strands, ligases splices the cut ends closed, and a heteroduplex DNA is formed

Front 45

What are the 4 principal mechanisms of horizontal gene transfer used by bacteria?

Back 45

1) Transformation

2) Electroporation

3) Transduction

4) Conjugation

Front 46

Define a transformation

Back 46

Transfer of bare DNA into a recipient cell without the participation of a donor cell/virus

Front 47

What genetic trait is the measure of how well a cell take up bare DNA? Where does this bare DNA usually originate?

Back 47

Competence is the ability to take up bare DNA that is usually taken from fragments of chromosomes from lysed cells

Front 48

How do gram positive and gram negative bacteria differ when it comes to genetic transformation?

Back 48

Gram-negative: Uses dsDNA

Gram-positive: Uses ssDNA

Front 49

What does a gram positive cell do when it encounters a dsDNA that it will be taking in?

Back 49

The cell incorporates the ssDNA and degrades the remaining strand while it is still outside the cell

Front 50

What is the effect of a short duration high energy pulse of electricity on the bacterial envelope of a bacteria? What's the purpose of this? What is this method called?

Back 50

We generate small pores allowing for entry and exit of plasmids. This is DNA transfer by Electroporation

Front 51

What 2 types of gene transfer are a result of viral infection? How do they differ? What do they have in common

Back 51

These are both packaging and transfer of DNA

Generalized Transduction: From random sites on the donor genome

Specialized Transduction: From specific sites on the donor chromosome into which a prophage is integrated and can only be carried out by a temperate phage

Front 52

What is a transducing phage?

Back 52

Any bacteriophage that can package DNA from a bacterium

Front 53

What do transducing phage's generally lack?

Back 53

They generally lack an ability to lyse the cell to infect a new host

Front 54

What is the probability of a transducing phage in generalized transduction to carry a particular gene per infected bacterium? How does this differ for specialized transduction?

Back 54

Generalized: 10^-7

Specialized: Much higher

Front 55

What about the way that prophages incorporate makes the specialized transduction target gene rates so high?

Back 55

Prophage's integrate to an adjacent site of the target genetic information

Front 56

Sex Pilus generally mediate what form of genetic transfer? Where is this process encoded? What is the name for this plasmid?

Back 56

Conjugation is plasmid encoded and requires a plasmid in the donor cell. The conjugation plasmid is called the F plasmid.

Front 57

What constitutes a male bacteria? What kind of cells utilize this mechanism? What constitutes a female?

Back 57

Gram-negative bacteria can be males if they use an F pilus. The female is the recipient bacteria

Front 58

When does replication occur in conjugation? Describe this DNA replication.

Back 58

During the transfer the donor DNA is replicated as a rolling circle with a single stand being injected into the recipient

Front 59

What are F+ bacteria? What are Hfr bacteria?

Back 59

F+ bacteria are cells which contain a free F plasmid in their cytoplasm. Hfr bacteria are cells in which the F plasmid is inegrated into the chromosome.

Front 60

Following the transfer of the F plasmid into the recipient. Both the donor and recipient can be considered ____. Prior to the transfer recipient cells are referred to as ___

Back 60

F+, F-

Front 61

After transfer of genetic material from Hfr (High frequency recombination) bacteria, a recipient does not usually become Hfr. Why?

Back 61

Following transfer of DNA, usually only part of the donor chromosome is transferred and the integrated plasmid is generally lost

Front 62

Insertion sequences, transposons, and transposable viruses such as mu are considered ____ ____ elements. What are they capable of?

Back 62

These are mobile genetic elements capable of moving from one site on the chromosome to another

Front 63

What do all mobile genetic elements share in common?

Back 63

Regions of inverted repeat DNA at the end of the element aka inverted terminal repeats

Front 64

What are the similarities and differences between insertion sequences and transposons?

Back 64

Transposons = Insertional sequences + an additional gene for function other than transposition, often for antibiotic resistance

Insertional Sequences = short DNA sequence that acts as a simple transposable element

Front 65

What is transposase? Where would I find this enzyme?

Back 65

Transposase directs the transposition of genes. Transposase is found in insertion sequences and transposons.

Front 66

What is the difference between RecA recombination and transposition? What do they both have in common.

Back 66

Transposition: Site specific recombination event, does not requirehomologous DNA.

Rex A Recombination: Requires homologous DNA

They both direct insertional events

Front 67

What is the difference between transduction and transformation?

Back 67

In transformation, the recipient bacterium takes up extracellular donor DNA. In transduction, donor DNA packaged in a bacteriophage infects the recipient bacterium. The difference is how the DNA is presented to the recipient.