Chapter 9

Question 1

Genomic analysis shows that microbes undergo extensive gene loss and gain

result of?

Answer 1

20% of E. coli genome may have originated in other microbes

horizontal gene transfer, recombinations, and a variety of mutagenic and DNA repair strategies

Question 2

Horizontal gene transfer

Answer 2

movement of genes between species or genera

Question 3

vertical gene transfer

Answer 3

generational passing of genes from parent to offspring (cell division)

Question 4

transformation

Answer 4

importing DNA into cells
• At least 82 known naturally competent (capable of importing DNA) species
• Gram-positive (Streptococcus, Bacillus)
• Gram-negative (Haemophilus, Nisseria)
Requires specific protein complexes called transformasomes

Question 5

• Why is natural transformation useful?

Answer 5

• Use as ”food”
• DNA repair
• Influence evolution – species adjust to new envir. by new genes.

Question 6

Gram-positive – growth phase dependent competence

Answer 6

• Triggered by quorum sensing
• Each cell secretes a small peptide called competence factor (CF) – unique to each species
• CF increases as population increases
• Above a certain concentration CF activates a phosphorylation cascade that activates transcription of transformasome

Question 7

Gram-negative

Answer 7

•no CF-always competent (Nisseria) or become comp. when starved (Haemophilus)
•Have a similar transformasome
•Outer membrane barrier
-Neisseria use pilus assembly-when pilus disassembles it drags DNA into cell
-Pilus naturally assembles and disassembles during growth

Question 8

Transformation is species and sequence specific

Answer 8

limits exchange between genera

Question 9

conjugation

Answer 9

cell-cell contact w sex pilus sticking out from a donor cell

Question 10

Hfr strain

Answer 10

high-frequency recombination strain – F-

factor integrated into chromosome

Question 11

Generalized transduction

Answer 11

take gene from donor cell to recipient
• Uses rolling circle-makes long copy of dna (concatemers)
• pac site to cut them into indiv. pieces

Question 12

Specialized transduction

Answer 12

transfer only a few closely linked genes b/w cells
• Example (E. coli)
• integrates into host chromosome(lysogenic)
• Improper excision by host recombination enzymes – take host genes adjacent to attachment site

Question 13

What is the fate of new DNA that has entered the cell?

Answer 13

• Plasmid capable of autonomous replication
• May be incorporated into chromosome
• Degraded by nucleases –seen as foreign DNA bc lack of methylation or by CRISPR

Question 14

Generalized recombination

Answer 14

two recombining molecules w significant homology (crossing over in sections of dna)

Question 15

Site specific recombination

Answer 15

little sequence homology – requires short (10-20 bp) sequence recognized by recombination enzyme

Question 16

Why is recombination advantageous?

Answer 16

• DNA repair mechanism
• Cells w/ damaged chromosomes use DNA donated by others from same species to repair damaged genes
• “Self-improvement” program – samples genes from other organisms to enhance fitness of cell

Question 17

Mutation

Answer 17

• change in base sequence and failure for cell to repair the change

Question 18

point mutation

Answer 18

change in a single nucleotide

Question 19

silent mutation

Answer 19

does not change AA sequence. lys–>lys (degenerate codon)

Question 20

Missense mutation

Answer 20

changes aa sequence

Question 21

Loss-of-function mutation

Answer 21

decreases or eliminates protein activity

Question 22

gain-of-function mutation

Answer 22

increases or gain new activity

Question 23

knockout mutation

Answer 23

eliminates function

Question 24

Frameshift mutation

Answer 24

insertion or deletion of 1-2 bp (not multiple of 3). ribosome reads wrong triplets. sometimes stop codon.

Question 25

mutagens

ex. uv light

Answer 25

chemical agents that can damage DNA

for pyrimidine-creates pyrimidine dimer that blocks replication/transcription

Question 26

spontaneous mutations

Answer 26

• Rare bc DNA repair/proofreading is efficient
• Tautomeric shifts- C binds to A
• Deamination reactions – C change to U
• Damage by reactive oxygen species (H2O2, superoxide/hydroxyl radicals)
-interfere w/ polymerases and stops replication/transcription

Question 27

Methyl mismatch repair

Answer 27

deoxyadenosine methylase (Dam) –methylates GATC
• Only parent strand methylated
• Mut proteins-cut out incorrect base, DNA Pol I fills in correct base

Question 28

DNA repair – Error proof repair

• Photoreactivation

Answer 28

Photolyase binds pyrimidine dimer and cleaves cyclobutane ring linking damaged nucleotides

Question 29

DNA repair – Error proof repair

• Nucleotide excision repair

Answer 29

• removes 12-13 nucleotides

* DNA Pol I repairs gap

Question 30

DNA repair – Error proof repair

• Base excision repair

Answer 30

• Glycosylase clip damaged bases
-U fromC deamination 
-Deamination of A to hypoxanthine
• Cuts out single base
• Endonuclease cleaves the backbone
• DNA Pol I repairs strand

Question 31

• E. coli’s genome is rife with

Answer 31

genomic islands, inversions, deletions, paralogs and orthologs

Question 32

Transposable elements

Answer 32

enzyme that copies sequence from one dna into anther (tranasposase enzyme makes this happen)
• Not autonomous – cant exist outside of larger DNA molecule

Question 33

insertion sequences (FOR TRANSPOSABLE ELEMENTS)

Answer 33

simple transposable element (700- 1500 bp)

Question 34

Transposons

Answer 34

carry other genes plus those required for transposition

Question 35

transposition

Answer 35

moving a transposable element b/w DNA

Question 36

stop codons

Answer 36

uaa, uga, uag

Question 37

F’ factor

Answer 37

takes some chromosomal dna

Question 38

DNA repair – Error proof repair

Recombinational repair

Answer 38

•both strand/one strand is damaged
-DNA Pol III skips over damaged regions
• RecA binds gap and w/ piece of undamaged DNA
• Damage can be repaired by other mechanisms

Question 39

DNA repair – Error proof repair

• SOS (“save our ship”) repair

Answer 39

extensive damage
• RecA binds ssDNA (stimulates autodig. of LexA repressor)
“sloppy ”polymerases w/ NO proofreading- insert whatever is available

Question 40

DNA repair – Error proof repair

Nonhomologous end joining

Answer 40

Double stranded breaks are

dangerous. Ku and LigD recombine them. can be errors.