bacterial genetic

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1

auxotroph antonym prototroph means early form of

auxo : increase

troph: nourishment

is a mutant that require an organic growth factor

2

Natural selection

favors those best adapted to their
environment

3

mutation

Change in organism’s DNA

can change an organism phenotype

4

phenotype

the observed characteristic of a cell

5

genotype

(the sequence of nucleotides in DNA)

6

wild type

wild type E coli

the typical phenotype of strains isolated from
nature

is an prototroph

7

vertical gene transfer

when mutation change the existing nucleotide sequence of a cell DNA which is then passed on to the progeny( daughter cells )

8

horizontal gene transfer

is the movement of DNA from one organism to another

9

a stain that cannot make tryptophan is design

STREPTOMYCIN RESISTANT is design

TRP-

StrR

10

SPONTANEOUS MUTATIONS

are genetic changes that result form normal cell process

11

the mutation rate

is defined as the probability that a mutation will occur in a given gene per cell division/ it varies between 10-4 to 10-12 per cell division

12

reversion

when a mutation change back to to its original non mutated state

13

base substitution

the common type of mutation occurs during DNA synthesis when an incorrect nucleotide is incorporate

14

point mutation

is if only one base pair is changed

15

base substitution has three type of mutation

silent, nonsense and missense

16

silent mutation

a base substitution has occurred ,the resulting codon still code for the same amino acid as the wild type codon

the amino acid sequence of protein remains unchanged

17

a missense mutation or leaky mutation

when the altered codon codes for a different amino acid

cells grow slowly because of the encoded protein functions only partially

18

Nonsense mutation

Specifies stop codon in the middle
of the protein
Gives a shorter protein which is nonfunctional

19

spontaneous mutation

deletion or addition of nucleotide during DNA replication

Impact depends on number of nucleotide

Impact depends on location of amino acid within
protein

One or two nucleotide changes causes shift in
reading frame. Sometimes causes a stop codon

20

frameshit mutation

add or subtracting one or two pair of nucleotide.

results in a shortened ,non functional protein, a knock out mutation

21

transposons or jumping genes

are pieces of DNA that can move from one location to another in cell's genome

that process is called transposition

Gene with new piece of DNA may be insertionally
inactivated

22

study of transposition

observation color variation on corn kernels moving into and out of genes controlling pigment synthesis

23

Induced mutations

mutagen

genetic changes that occurs due to an influence outside of a cell such as exposure to a chemical or radiation

Agent that induces change

24

chemical agent

alkylating agents add alkyl group onto nucleobase

25

radiation:

ultra violet and X ray

26

ultra violet

Forms thymine dimers
– Covalent bonds between adjacent thymines
– Cannot fit into double helix; distorts molecule
– Replication and transcription stall at distortion
– Cell will die if damage not repaired

27

X ray

cause single and double bond strand to break in DNA

Often produce lethal deletions

28

Base analogs

Resemble nucleobases
(nitrogen bases in DNA)
but have different
bonding properties

Can be mistakenly
incorporated by DNA
polymerase in replication

29

Intercalating agents

increase frameshift mutations because they are Flat molecules that intercalate (insert) between adjacent base pairs in DNA strand which Pushes nucleotides apart, and produces space that allow errors during replication

30

ethiduim broomide

a chemical to stain dna in the lab as an intercalating agent

31

chloriquine

is an intercalating agent to treat malaria

32

two type of radiation

Ultraviolet irradiation and X ray

33

Spontaneous and mutagen-induced damage to
DNA

Can lead to cell death or cancer in animals
• Mutations are actually rare; changes in DNA are
generally repaired before being passed to progeny
• Several different DNA repair mechanisms

34

Repair of Errors in Nucleotide Incorporation

During replication, DNA polymerase sometimes
incorporates wrong nucleotide

Mutation is prevented by correcting the wrong
nucleotide in the DNA before replication

35

Two mechanisms for repair

proofreading and mismatch
repair

36

proofreading by dna polymerase

Confirms accuracy
The enzyme can back up and cut out the bad nucleotide
It then incorporates the correct nucleotide
Very efficient but not perfect

37

mismatch repair

fixes error missed by the proofreading of dna polymerase

Enzyme cuts sugar phosphate
backbone of the new dna strand

Another enzyme degrades short region of DNA strand
DNA polymerase and DNA ligase make repairs

38

how does the cell know which strand is the new one

because of methylation of the dna nucleobases

it allows the repair enzyme to distinguish between the two strand

39

Repair of Thymine Dimers (UV Damage)

Photoreactivation , Excision repair and SOS repair

40

Photoreactivation

light
repair (only in bacteria)
• Enzyme uses energy
from light (hence name)
• Breaks covalent bonds of
thymine dimer, restoring
DNA to original state

41

Excision repair or dark repair

Enzyme removes
damaged DNA

DNA polymerase and
DNA ligase repair

42

SOS repair

last effort repair mechanism
• Induced following extensive DNA damage that cannot be
repaired by photoreactivation or excision repair

DNA and RNA polymerases stall at unrepaired sites so that the cell cannot replicate or transcribe their DNA

43

Several dozen genes in SOS system activated( SOS REPAIR)

Includes a DNA polymerase that synthesizes even in
extensively damaged regions it Has no proofreading ability, so errors made result is SOS mutagenesis

44

two type of mutant selection

direct and indirect selection

45

direct selection:

cells inoculated onto medium that supports growth of
mutant but not parent

46

indirect selection

isolates auxotroph (nutrient-requiring
mutant) from prototrophic parent strain
• Replica plating allows for selection

47

Penicillin enrichment of mutants

Increases number of auxotrophs in broth culture

Penicillin is added to medium lacking a particular nutrient.
It kills growing cells (prototrophs) but not auxotrophs, as these are not dividing
• Penicillinase then added to destroy the penicillin and the Cells plated on complete medium in which auxotrophs
can grow

48

Screening for Possible Carcinogens

Carcinogens cause many cancers
• Historically carcinogens are identified using animal tests.
These are expensive, time-consuming and cruel

49

Ames test

measures effect of chemical on reversion rate
of histidine-requiring Salmonella auxotroph. Any
chemicals causing reversion then used in animal tests

50

Ames test

Test uses direct selection
• If the chemical is mutagenic, reversion rate increases
relative to control
• Rat liver extract added since non-carcinogenic chemicals
often converted to carcinogens by animal enzymes

51

Genes naturally transferred by three mechanisms

Transformation: naked DNA
uptake by bacteria
• Transduction: bacterial DNA
transfer by viruses
• Conjugation: DNA transfer
between bacterial cells

52

DNA-Mediated Transformation

Naked DNA is not within cell or virus. It has been released into the environment whencells lysed
• Demonstration of transformation in pneumococci by Frederick Griffith
• Only encapsulated cells pathogenic
• Unencapsulated bacteria gain capsule gene

53

Transformation

Recipient cell must be competent (able to take up
foreign DNA)
• Most competent bacteria take up DNA regardless of origin
• Some accept only from closely related bacteria
• Process tightly regulated

54

Transduction

transfer of genes by bacteriophage

55

bacteriophage

are viruses that infect bacteria

56

conjugation

DNA transfer between bacterial
cells
• Requires contact between a donor cell and a recipient cells
• Contact provided by sex pilus

57

conjugation plasmid

direct their own transfer

58

conjugation of F plasmid

F plasmid of E. coli
• F+ cells have this plasmid, F– do not
• F plasmid encodes F pilus
• F pilus is a sex pilus
• Brings cells into contact
• Enzyme cuts plasmid
• Single DNA strand of plasmid
is transferred from F+ to F- cell
• Complementary strands synthesized in each cell
• Both cells are now F

59

Chromosomal DNA
transfer

Involves Hfr cells (high
frequency of recombination)
• F plasmid is integrated into chromosome via homologous recombination
• Process is reversible – F plasmid may leave chromosome
• F′ cell results when small piece of chromosome is removed with F plasmid
DNA when F plasmid leaves the chromosome

Hfr cell produces F pilus
• Transfer begins with genes on one side of origin of transfer of plasmid
(in chromosome)
• Part of chromosome transferred to
recipient cell
• Chromosome usually breaks before
complete transfer (full transfer
would take ~100 minutes)
• Recipient cell remains F– since incomplete F plasmid transferred

60

The Mobile Gene Pool

75% of E. coli genes found in all strains of the species
• Termed core genome of species

The remaining genes make up the mobile gene pool
and are composed of plasmids, transposons, genomic
islands, phage DNA

61

Plasmids found in most Bacteria and Archaea
and even some Eucarya

are dsDNA with an origin of replication
• Plasmids contain a few genes to thousands of genes
• Genes on plasmids are generally nonessential

Most have narrow host range
• Single species
• Some broad host range
• Includes Gram– and Gram+

62

Resistance plasmids

Confer resistance to antimicrobial medications, heavy
metals (mercury, arsenic)
• These are compounds found in hospital environments
• Often broad host range
• Normal microbiota can transfer these plasmids to
pathogens

63

insertion sequence

Simplest type of transposon
• Has only transposase enzyme and inverted repeats for
insertion

64

Composite transposons

include one or more genes
• Integrate via non-homologous recombination

65

common plant disease

crown gall is a bacterium - agrobacterium tumefaciens