ch 11 & 12: mechanisms of microbial genetics Flashcards

Question

DNA replication: DNA polymerase I

Answer 1

exonuclease activity removes RNA primer and replaces it with newly synthesized DNA

Answer 2

main enzyme that adds nucleotide in the 5' to 3' direction

Answer 3

opens the DNA helix by breaking hydrogen bonds between the nitrogenous bases

Answer 4

seals the gaps between the Okazaki fragments on the lagging strand to create one continuous DNA strand

Answer 5

synthesizes RNA primers needed to start replication

Answer 6

bind to single-stranded DNA to prevent hydrogen bonding between DNA strands, reforming double-stranded DNA

Answer 7

helps hold DNA polymerase III in place when nucleotides are being added

Answer 8

relaxes supercoiled chromosome to make DNA more accessible for the initiation of replication - helps relieve the stress on DNA when unwinding, by causing breaks and then resealing the DNA

Answer 9

introduces single-stranded break into concatenated chromosomes to release them from each other - and then after will reseal DNA

Answer 10

short sections of DNA formed at the time of discontinuous synthesis of the lagging strand during replication of DNA - essential as it allows for the synthesis of both the daughter strands required for cell division

Answer 11

each daughter double helix obtains one old and one new strand - each strand of the double helix DNA serves as a template for synthesis of a new strand

Answer 12

where replication begins

Answer 13

when a single nucleotide is changed in a DNA sequence consist of: * silent mutation * missense mutation * nonsense mutation

Answer 14

change has no effect on protein structure

Answer 15

a base-pair substituion that results in a codon that codes for different amino acid

Answer 16

replaces an amino acid with a stop codon

Answer 17

involves the addition or subtraction of one or more nucleotides * frameshift mutation

Answer 18

occurs when a fragment of DNA is flipped in orientation in relation to the DNA on the other side

Answer 19

* a "mistake" by DNA polymerase that fails to be repaired * physical agents (i.e. cosmic rays, x-rays, UV radiation) * chemical agents

Answer 20

* base excision repair * methyl mismatch repair * SOS repair * DNA recombination

Answer 21

recognizes a specific damaged base and removes it from the DNA backbone

Answer 22

requires recognition of the methylation pattern in DNA bases

Answer 23

coordinated cellular response to damage that can introduce mutations in order to save the cell

Answer 24

the process of "crossing over" and exchange of two DNA helices

Answer 25

* changing the DNA sequence * control of transcription * translational control * post-translational control

Answer 26

some microbes change the DNA sequence to activate or disable a particular gene ex: phase variation

Answer 27

transcription can be regulated by protein repressors, activators, and alternative sigma factors

Answer 28

control of transcription initiation sequences that recognize specific repressor proteins

Answer 29

control of proteins that are already made

Answer 30

where structure proteins with related functions are usually encoded together includes: * promoter * operator * structural genes

Answer 31

prokaryotic operons are commonly controlled by the binding of repressors to operator regions, which _prevents the transcription of the structural genes_

Answer 32

tryptophan * typically contain genes encoding enzymes required for a biosynthetic pathway * as long as the product of the pathway (*trp*) continues to be required by the cell, a repressible operon will continue to be expressed * when the product begins to accumulate, the expression of the operon is repressed

Answer 33

*lac* operon * contain genes encoding enzymes in a pathway involved in the metabolism of a specific substrate like lactose * these enzymes are only required when that substrate is available, thus expression of the operons is typically induced only in the presence of the substrate

Answer 34

1. sensing the intracellular environment 2. global regulators 3. sensing the extracellular environment

Answer 35

different regulatory proteins bind to specific compounds to determine the compounds concentration ex: dtx, the diphtheria toxin gene iron binds to dtxR--> dtxR binds to regulatory region and no toxin expressed **OR** without iron, dtxR comes off DNA and toxin is expressed

Answer 36

proteins that affect the expression of many different genes ex: cAMP receptor protein (CRP) of E. *coli* and related species

Answer 37

a common mechanism used by bacteria to sense outside of the cell and transmit that information inside relies on a series of two-component protein phosphorylation relay systems ex: sensor kinase PhoQ in Salmonella

Answer 38

1. sensor kinase detects condition outside the cell 2. signal triggers (or prevents) autophosphorylation 3. phosphate is transferred to a response regulator in the cytoplasm. Regulator binds DNA and either stimulates or represses the target genes 4. a phosphatase removes the phosphate and down regulates the system

Answer 39

* _occurs during reproduction between generations of cells_ * exchange of genes between two DNA molecules * crossing over occurs when two chromosomes break and rejoin

Answer 40

the transfer of genes between cells of the same generation * also called lateral gene transfer - transformation, transduction and conjugation. * once the genetic information is transferred from the donor, it can enter the genome of the recipient by recombination

Answer 41

in transformation, the cell takes up DNA directly from the environment. the DNA may remain separate as a plasmid or be incorporated into the host genome

Answer 42

a bacteriophage injects DNA that is a hybrid of viral DNA and DNA from a previously infected bacterial cell

Answer 43

DNA is transferred between cells through a cytoplasmic bridge after a conjugation plus draws the two cells close together

Answer 44

* mostly circular, double-stranded, extrachromosomal DNA * self replicating by the same mechanisms as any other DNA * most of the plasmids have been identified due to having some function they allow the bacterium to survive

Answer 45

direct synthesis of proteins towards the pili

Answer 46

carry genes that provide resistance to antimicrobials (chloramphenicol, arsenic etc)

Answer 47

(neurotoxin) cause disease signs and symptoms

Answer 48

cause tumor formation in plants

Answer 49

not essential for cell growth

Answer 50

direct synthesis of bacteriocins (bacteria killing)

Answer 51

* genes that can move from one chromosome to another * exist in virtually all life forms * unlike plasmids, transposable elements cannot replicate outside a larger DNA molecule * all transposable elements include a _transposase_ gene whose enzyme product moves the element from one DNA molecule into another

Answer 52

* importing free DNA from the environment into bacterial cells * natural transformation is a property inherent to many bacterial species and is carried out by specific protein complexes - **transformasome** * *Streptococcus, Bacillus, Haemophilus, Neisseria* = naturally competent * E. *coli, Salmonella* = can be manipulated to be made artificially competent * **Electroporation**: a brief electrical pulse shoots DNA across the membrane

Answer 53

1. competence factor (CF) is synthesized and exported 2. as cell numbers rise, external CF level increases and activates sensor kinase 3. the sensor kinase transfers a signal (phosphate) to a transcriptional activator that stimulates transcription of the transformasome gene 4. transformasome binds extracellular DNA. One strand is transported; one strand is degraded

Answer 54

gene transfer is mediated by a bacteriophage vector Trans "across" ductio " to pull" * originally discovered in *Salmonella* in 1952

Answer 55

1. phage DNA integrates into host DNA 2. copies of phage DNA include adjacent host DNA (gene D) 3. Lysis releases progeny phage whose genome includes gene D 4. phage including gene D infects recipient cell 5. phage genome integrates with host genome including gene D from donor cell

Answer 56

1. transfer genetic material from one bacterial cell to another and alters the genetic characteristics of the recipient cell 2. incorporation of phage DNA into a bacterial chromosome demonstrates a close evolutionary relationship between the prophage and host bacterial cell 3. the fact that a prophage can remain for long periods of time in a cell suggests a similar mechanism for the viral origin of cancer 4. the viruses bring alone genes from their previous host, thus, if this type of virus infects us, the type of DNA incorporated into us might belong to another animal, AKA we might consider ourselves transgenic 5. it provides a way to study gene linkage to do chromosome mapping

Answer 57

1. pilus of donor cell attaches to recipient cell. pilus contracts, drawing the cells close together 2. one strand of F plasmid DNA transfers from donor cell to recipient cell 3. donor synthesizes complementary strand to restore plasmid. recipient synthesizes complementary strand to become F+ cell with pilus

Answer 58

"Hfr" refers to the high frequency of recombination seen when the recipient F- cells receive genetic information from Hfr cells through conjugation form when F plasmid integrates into the bacterial chromosome through recombination Imprecise excision of the F plasmid from the chromosome of an Hfr cell may lead to the production of an F' plasmid that carries chromosomal DNA adjacent to the integration site

Answer 59

1. contributes to genetic diversity - larger amounts of DNA are transferred 2. may represent an evolutionary stage between asexual processes and the actual fusion of whole cells (the gametes) 3. plasmids are self transmissible and can sometimes be promiscuous 4. some gram + bacteria have self mating plasmids that do not form a F pili, instead they secrete peptide compounds which simulate nearby bacteria that do not contain the plasmid to mate with them

Answer 60

DNA plasmids have certain DNA sequences that can be cut by a specific enzyme called a restriction endonuclease * usually the restriction sequence is a "palindrome", in which the sequence of the base pairs reads the same forward and back

Answer 61

technique commonly used to separate biological molecules based on size and biochemical characteristics, such as charge and polarity * DNA has a negative charge and will be drawn to the positive electrode * smaller molecules travel faster

Answer 62

* transposition of genes from one location of the chromosome to another - fusion of two genes together * depending on the design - a function may be inactivated or a function may be placed under the control of a different regulatory sequence

ch 11 & 12: mechanisms of microbial genetics Flashcards

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