Chapter 9

Question 1

Transformation

Answer 1

-process of importing DNA from the environment into bacterial cells

Question 2

competence

Answer 2

• ability it take up new DNA

- done by perturbing the membrane by chemical (CaCl2) or electrical (electroporation) methods

Question 3

Transformation in some Gram-positive species

Answer 3

-use a transformasometo become competent and acquire DNA

Question 4

Transformation in some Gram-negative species

Answer 4

• don’t use competence factors (CF).

- Either they are always competent, or they become competent when starved

Question 5

Conjugation

Answer 5

• transfer of DNA from one bacterium to another via cell-to-cell contact.
• Often called “bacterial sex.”
• initiated by a special sex pilus protruding from the donor cell
• requires the presence of special (conjugal) plasmids-contain the genes needed for pilus formation

Question 6

fertility factor (F factor) plasmid

Answer 6

• well-studied example of conjugal plasmid in E. coli
• Contains two replication origins:
  1. oriV: used for normal replication
  2. oriT: used during DNA transfer

-begins with contact between the donor cell, called the F+ cell, and a recipient F– cell

Question 7

conjugation process

Answer 7

1. The sex pilus draws cells together
2. The plasmid is nicked at oriT
3. Rolling circle replication in donor cell
4. Transferred ssDNA is replicated in recipient cell
5. F- recipient cell is converted to F+

Question 8

Agrobacterium tumefaciens

Answer 8

• bacteria that can transfer genes across phylogenetic domains
• causes crown gall disease
• Contains a tumor-inducing plasmid (Ti) that can be transferred via conjugation to plant cells
• transferred T-DNA “engineers” plant cells to proliferate and feed the Agrobacterium cells in the plant gall (tumor)
• Can be used to transfer cloned genes into plant genomes

Question 9

Transduction

Answer 9

• process in which bacteriophages carry host DNA from one cell to another
• occurs accidentally as an offshoot of the phage life cycle

Question 10

Generalized transduction

Answer 10

-can transfer any gene from a donor to a recipient cell

Question 11

protection system, restriction and modification, involves

Answer 11

• Enzymatic cleavage of alien DNA, by restriction endonucleases that recognize specific short sequences
• Protective methylation of those sequences in the host’s own DNA

Question 12

Generalized recombination

Answer 12

requires a considerable stretch of homologous DNA sequences, which are very similar in sequence

Question 13

Site-specific recombination

Answer 13

• requires short specific sequences that are the same between the recombining DNA molecules.
• specific short sequences are recognized by specific recombination enzymes

Question 14

RecA protein

Answer 14

• required by Generalized recombination
• molecules are also called synaptases
• They scan DNA molecules for homology and align the homologous regions, forming a triplex DNA molecule, or synapse

Question 15

site-specific recombinase enzyme

Answer 15

-involves very short specific homology sequences between donor and target DNA molecules

Question 16

Point mutation

Answer 16

change in a single base

Question 17

Insertion and deletion

Answer 17

addition or subtraction of one or more bases

Question 18

Inversion

Answer 18

• DNA segment is flipped in orientation

- Mutations are reversible

Question 19

Reversion

Answer 19

DNA mutates back to original sequence

Question 20

Silent mutation

Answer 20

does not change the amino acid sequence

Question 21

Missense mutation

Answer 21

-changes an amino acid

Question 22

Nonsense mutation

Answer 22

-changes a codon to a stop codon

Question 23

Frame-shift mutation

Answer 23

changes the reading frame of the ORF so that all following codons are all wrong

Question 24

mutations arise naturally for 2 reasons

Answer 24

1. Chemical shifts in DNA bases that alter base-pairing properties
2. Oxidative deamination of bases and formation of apurinic sites

Question 25

Chemical mutagens

Answer 25

- Base analogs - Base modifiers: alkylating and deaminating agents - Chemical intercalators that bind to and distort DNA

Question 26

Electromagnetic radiation as mutagens

Answer 26

- X-rays and gamma rays: break the DNA | - Ultraviolet rays (from sunlight): form pyrimidine dimers

Question 27

Ames test

Answer 27

- relies on a mutant bacterial strain that is defective in the hisG gene - Cannot grow on a medium lacking histidine - mutagen-containing disk is placed on an agar plate with a thin lawn of the mutant strain - mutagen causes reversion mutations, and colonies start to appear around the disk

Question 28

Error-proof repair pathways

Answer 28

- which prevent mutations - Methyl mismatch repair - Photoreactivation - Nucleotide excision repair - Base excision repair - Recombinational repair

Question 29

Error-prone repair pathways

Answer 29

- which risk introducing mutations | - Operate only when damage is so severe that the cell has no other choice but to die

Question 30

Error-Prone DNA Repair -SOS (“Save Our Ship”) repair

Answer 30

- Induced by extensive DNA damage - causes increase in ssDNA - causes expression of many DNA repair enzymes - two “sloppy” DNA polymerases that lack proofreading activity - cell has no other option but to “mutate or die”

Question 31

Nucleotide excision repair

Answer 31

- Thymine dimer - DNA is cut - DNA Polymerase and DNA ligase repair the damage

Question 32

Transposable elements

Answer 32

- move from one position in DNA to another - Exist in virtually all life-forms - Can move within and between chromosomes

Question 33

Insertion sequence (IS)

Answer 33

- Simple transposable elements containing a transposase gene, flanked by short inverted repeat sequences - are targets for the transposase enzyme two mechanisms: 1. Nonreplicative (cut and paste) 2. Replicative transposition

Question 34

Transposons

Answer 34

carry additional genes

Question 35

Horizontal Gene Transfer

Answer 35

-Sometimes multiple genes are acquired -Genomic islands move by horizontal gene transfer -DNA region that contains many genes -Provide acquisition of new complex phenotypes including: Pathogenicity islands Symbiosis islands Fitness islands

Question 36

Genome reduction

Answer 36

- the loss of genes through evolution - Genes no longer needed in ecological niche - Over half of the Mycobacterium leprae genome is composed of nonfunctional pseudogenes, which are not expressed

Question 37

Duplications and Divergence

Answer 37

- Duplication frees a gene from its previous functional constraints and allows divergent evolution through mutation. - Families of related proteins arise by divergent evolution and share structural and functional features, but may catalyze different reactions