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microbio unit 2 > week 7 lecture 1 > Flashcards

week 7 lecture 1 Flashcards

1
Q

What is the difference between spontaneous mutations and induced mutations?

A
  • Induced mutations - result to an exposure of a mutagen or a physical or chemical agent that damages DNA
  • Spontaneous (random, usually happens during replication)
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2
Q

why do spontaneous mutations happen?

A
  • Errors in DNA replication
  • Head-on collisions between the replisome and RNA polymerase
  • Spontaneously occurring lesions in DNA
  • The action of mobile genetic elements
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3
Q

Tautomerization? spontaneous or induced?

A
  • nitrogenous base of nucleotide shifts to turmeric form, allowing for unique base pairing to occur
  • Turmeric form is where there are two or more interconvertible structures that are different in terms of the relative position of one atomic nucleus
  • spontaneous
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4
Q

transition muation ? induced or spontaneous?

A
  • stable alteration of teh nucleotide sequence
  • Purine is replaced by another purine, or a pyrimidine is replaced by another pyrimidine
  • s
  • Purine A and g
    Pyrimidine T/G/U
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5
Q

trasnversion mutation? spontaneous or induced?

A

when a purine is substituted for a pyrimidine = steric problem
Purine A and g
Pyrimidine T/c/U
- s

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6
Q

insertion and deletions? spontaneous or induced?

A
  • Occurs at short stretches of repeated nucleotide sequences
  • The pairing of the template and new strands can be displaced
  • S
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7
Q

base analogs ? s or I ?

A
  • structurally similar to regular bases, but mistakes will happen when they are incorporated into the DNA (molecules that mimic DNA bases)
  • I
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8
Q

DNA-modifying agents? I or S?

A
  • alter a base, causing it to mispair
  • It could be a mutagen-causing like chemicals or UV
  • I
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9
Q

Intercalating agents? induced or spontaneous ? (example)

A
  • distort DNA to induce single nt pair insertions and deletions
  • Example: thymine-thymine dimer formation because of UV radiation
  • They form a double bond between the two nucleotides, making them become one nucleotide, and eventually, every single dimer will bind to only one nucleotide
  • i
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10
Q

lessions? I or S? created by? without correction then?

A
  • Forms apurinic site (a site in DNA where a base is missing) that cannot base pair and may cause mutation in the subsequent replication round
  • A gap is created in teh DNA sequence when the glycosidic bond between a base and sugar backbone is broken. This leads to AP sites, which distorts the DNA like a transversion mutation.
  • Without a proper template, an incorrect nucleotide will be inserted during DNA replication—there is only a fourth of a chance of it being fixed.
  • I
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11
Q

wild type?

A
  • most prevalent form of a gene and is associated with phenotype
    Leads to no change in teh phenotype
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12
Q

foward muatation

A

going from wild type to mutant

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13
Q

reversible mutation

A

mutant phenotype back to wild-type phenotype

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14
Q

supressor mutation

A
  • wildtype phenotype is restored by a second mutation at a different site than the original mutation
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15
Q

silent mutation

A

change in the third nucleotide in the codon that will code for the same protein

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16
Q

nonsense muation

A
  • change in a nucleotide that will make a stop codon
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17
Q

missense mutation

A
  • converts into a different protein
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18
Q

How does DNA replication make base-paining problems permanent in the genome?

A

When DNA replication is performed on a strand containing a mutation before it can be repaired, the mutation becomes a part of the new strand that will serve as a template and further perpetuate the error

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19
Q

point mutation

A

when a single base pair in the genome is altered, added, or deleted, and DNA repair mechanisms can repair these mutations

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20
Q

genetic mutation

A

are permanent changes in DNA sequence and have already been replicated.

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21
Q

frameshift mutation

A

inserts or loses a nucleotide that will create a large-scale change that will mess it up (nucleotide should not be divisible by three)

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22
Q

What are the potential effects of a mutation in the regulatory region?

A
  • Promoters: disrupt the binding of transcription factors
  • enhancers /silencers: misregulation of gene
  • Reduce transcription and changes the level of gene expression
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23
Q

What experimental technique can we use to detect and isolate mutants? Explain what it can tell you?

A
  • replica plating, which can screen for auxotrophic or prototrophic parents
  • Distinguishes mutants from wild type based on their ability to grow in the absence of a particular biosynthetic end product
  • Growth under different conditions
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24
Q

What is the process for replica plating?

A
  1. start with a master plate where bacteria grow on a perfect nutrient-rich plate
  2. use a velvet-covered tool to stamp the surface
  3. stamp the velvet on another plate (one that is a complete medium and another plate with a missing specific nutrient)
  4. compare the plates, If a colony grows on the complete plate but doesn’t grow on the incomplete plate, the bacteria in that colony need the missing nutrient to survive.
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25
Q

conditional mutations

A
  • having a different phenotype under certain environmental conditions
26
Q

auxotrophic mutants

A
  • unable to make an essential macromolecule such as an amino acid or nucleotide
27
Q

what is metagenomics? used to learn? where does each DNA come from?

A
  • Study of microbial genomes based on DNA extracted directly from the environment and Identification of mutants in microbial community
  • Used to learn more about the diversity and metabolic potential of microbial communities
  • Each DNA fragment comes from a collection of genomes found in a microbial community, not a single organism.
28
Q

what is bioinformatics? two types?

A

This gives you the genome annotation we will use to predict and confirm what is there through experiments.
ID/characterizes
- genome annotation and BLAST

29
Q

what is genome annotation?

A
  • Process that locates genes in the genome map
  • Identifies open reading frame - predictions based on architecture, repeating units, consensus sequences
30
Q

what is BLAST? how does it work?

A
  • Base by base comparison 2+ gene sequences and Compares gene sequence and assigns gene function
  • Database of characterized proteins from specific organisms to what their function is going to be
31
Q

what is excision repair? two types?

A
  • This corrects damage that distorts the DNA double helix and use the intact strand as a template to synthesize new DNA
  • nucleotide excision repair and Base excision repair
32
Q

what is nucleotide excision repair? uses what? removes?

A
  • remove thymine dimers or other injury produced by distorting DNA
  • It uses intact strands as a template and synthesizes new DNA
  • Removes lesions and prevents mutations caused by thymidine dimers
33
Q

how does nucleotide excision repair work?

A

UvrA scans for damage in teh DNA and will bind, UvrB will be recruited to he site (to shield the bottom strands), uvrC will cut both sides of the damaged site, urvD (helicase) that will remove teh damaged regions and DNAP 1 and DNA ligase seal the gap

34
Q

what is base excision repair? removed by?

A
  • removes damaged or unnatural bases yielding apurinic or apyrimidinic AP sites.
  • These are cleaved by AP endonuclease and DNAP/ DNA ligase
  • Removing minor damage before replication
35
Q

how is DNA repaired?

A
  • Proofreadings -Correction of errors in base pairing made during DNA replication but will be fixed by DNA polymerase.
  • Mismatch repair - The enzymes will scan newly synthesized DNA for mismatched pairs, which DNA polymerase will remove and replace.
36
Q

what is high-fidelity repair?

A
  • 3’ to 5; exonuclease activity
  • Correct mismatch during DNA replication
  • Accurately reduce replication errors
37
Q

what is error-prone repair? increased what?

A
  • When severe DNA damage occurs, there is specialized DNAP replicates over the lesions
  • There is an increased mutation rate but may allow for surviva
38
Q

what is an sos repair response? what responsibility does RecA have?

A
  • An inducible repair system (global control network - -regulator or TF can respond to specific environmental signals that will regulate a dozen or so genes in response)
  • Used when the damage is so significant that normal repair mechanism will not work
  • recA protein acts as a protease, destroying lexA, to increase the production of excision repair enzymes
  • recA protein initiates recombination repair - >50 genes
  • Increased mutation rate but survival of massive DNA damage
39
Q

what is recombination repair?

A
  • Corrects DNA that has both bases of a pair missing or damaged (only within a certain window of opportunity)
  • Involves recombination with an undamaged chromosomal copy
  • recA aligns damaged DNA with teh second copy of the genome that is undamaged
  • Corrects double-stranded breaks
40
Q

how does recombination repair work (explain process) ?

A

Through recombination, the region with the gap will be switched with the above region through RecA, and the gap will be filled in by DNA pol one and ligase using strand B as a template. Once the gap has been repaired, thymine dimers will remain and be removed by another system
(switch A with bad C, and recA will fill in the gaps)

41
Q

what is the difference between HGT and VGT?

A
  • Vertical gene transfer = transfer of genes from parent to offspring
  • in eukaryotes, sexual reproduction involves genetic recombination - meiosis and Bacteria use binary fission
  • Horizontal gene transfer: moving genes from one organism to another to increase diversity (bacteria and archea use because they do not reproduce sexually and need a mechanism to increase diversity )
42
Q

what are the three mechanisms of HGT?

A
  1. transformation - DNA acquired directly from the environment
  2. conjugation - DNA transferred from a donor cell
  3. transduction - DNA transported in a bacteriophage
43
Q

what is natural trasnformation?

A
  • Bacteria lyse and release DNA into the environment
  • These large fragments contain multiple genes
  • DNA that comes in contact with a competent cell is imported
  • Plasmids can be transferred between bacteria
44
Q

why is the F plasmid used during conjugation? genes are used for?

A
  • F plasmid - sexual gene transfer through a direct cell-to-cell contact
  • has genes responsible for cell attachment and plasmid transfer between E. Coli cells and Encodes proteins to build the sex pilus, anchoring to donor
45
Q

what are the two main steps from F+ x F- mating ?

A
  • F+ donor creates the sex pilus, making contact with F- recipient cell
  • Replication of the F factor occurs via rolling-circle replication
46
Q

what role does rolling circle have in the F mating? which two portein used? what is it?

A
  • Unidirectional nucleic acid replication that can rapidly synthesize multiple copies of circular molecules of DNA/RNA
  • Requires only two proteins, polymerase and recombinase, for replication
  • As F plasmid is transferred, it is also copied
47
Q

what is High-frequency recombination (Hfr) conjugation ? what is it associated with the F stuff?

A
  • Hfr cell = bacterium with a conjugative plasmid integrated into its chromosome
  • F factor tends to transfer itself during conjugation, so it can attempt (unsuccessfully) to drag the rest of the genome with it
  • The F factor can also leave the bacterial chromosome and continue its status as an autosomal plasmid.
48
Q

how does transduction work? two types?

A
  • DNA transported in a bacteriophage
  • Transfer of bacterial genes by viruses
  • Lysogens - insertion of the viral genome into bacterial chromosomes (temperant phages that are introduced into the genome)
  • generalized and specialized trasnductoin
49
Q

what is generalized transduction? what happens to the DNA?

A
  • During virion assembly, a fragment of the host that is the same length as the phage genome may be mistakenly packaged and then transferred during the next infection.
  • Once DNA is in the recipient cell, it is incorporated into the host chromosome.
50
Q

what is specialized transduction?

A
  • The phage lambda integrates at a special attachment site in bacterial and phage genomes, called att lambda.
    -only specific, limited regions of bacterial DNA are transferred by a virus
51
Q

what is recombination? what effect does it have? two types?

A
  • a process where nucleic acids are rearranged or combined to produce a new nucleotide sequence
  • Shifts in environmental pressures lead to changes in the population and the evolution of a new species.
  • homologus recombination and site-specific recombination
52
Q

what is the difference between homologous and site-specific recombination?

A
  • it happens between long regions of DNA and recA carries this process out
  • there is a double-stranded break occurs, and reunion leads to crossing over (1 mom and 1 dad crossover and exchange lil part)
  • in site: It does not require long sequence homology, Recombination occurs at specific target sites in DNA molecules
    Recombinase - catalyst - enzyme
53
Q

what are transposable elements? what are the two types?

A
  • , “jumping genes” are a type pf mobile genetic element (MGE)
    1. Simple transposition - cut and past mechanics
    2. Replicative transposition - copy and paste mechanisms
54
Q

what are core genomes and pan-genomes? effects on survival? type of?

A
  • core genome - sets of genes found in all members of a species (minimal amount of genes needed to sruvive)
  • pan-genome - genes vary in a strain of species (More recently, these genes have been acquired to enable the microbial colonization of new niches. )
  • HGT
55
Q

what are three examples of HGT with the aqusition of drug resistance?

A
  • Immunity genes - typically protect microbes from teh antibiotics they synthesize
  • Horizontal gene transfer- transfers immunity.
  • Resistance genes can be found on - chromosomes, transposons, R plasmids, and pathogenicity islands.
56
Q

what are the two ways to guage the genome and and protein expression profiles?

A
  • DNA microarray analysis -
  • RNA-sequencing - Quantifying mRNA levels by measuring the “reads” matching each genome
57
Q

what is DNA microarray analysis? how does it work?

A
  • determines which genes are expressed at a certain time
  • Arrays are solid supports to which DNA is attached and organized as a grid
  • Each DNA spot (probe - a PCR product made from the gene of intrest) represents a single gene
  • Set up a control vs experiment where you extract an mRNA and generate cDNA that is labeled with a fluorescence tag and compare the two
    It will tell you how much of a signal there is for a given mRNA transcript. ‘
    If a gene is highly regulated, then there will be no signal
58
Q

how does RNA-sequencing work?

A
  • Quantifying mRNA levels by measuring the “reads” matching each genome
  • Cellular mRNA is converted into cDNA by reverse transcriptase
  • cDNA is sequenced using next-generation sequencing\
59
Q

what is technique is used for probing DNA-protein interactions?

A
  • CHIP - Survey protein DNA interactions in living cells
  • DNA is extracted and cut
  • Antibodies bind to proteins, and antibody-protein-DNA complexes are precipitated
  • Proteins were removed, and DNA sequenced
  • technique used to identify where specific proteins, like transcription factors, bind to DNA within a cell, essentially allowing researchers to see which parts of the genome are associated with a particular protein of interest
60
Q

what are bacterial plasmids? 5 types?

A
  • small circular DNA

F plasmid
R plasmid - confer resistance to antimicrobials
Col plasmids - allow expression of bacteriocins
Metabolic plasmids - necessary for certain metabolic reactions
Virulence plasmids - make organisms more pathogenic

61
Q

how are plasmids transfered?

A
  • through conjugation or transformation
  • Intasepecies transfer
  • Interspecies transfer
62
Q

what are the four pathways that foreign particles will take in a HGT?

A
  1. Integration - donor DNA pairs with the recipient DNA and recombines and reproduces to make a population of stable recombinants
  2. Separates existence of DNA - if donor DNA can replicate it will have a plasmid in the cell - that reproduces and makes a population of stable recombinants.
  3. Remains in cytoplasm - when donor DNA is unable to replicate when the recipient reproduces
  4. Degradation led by CRISPR/Cas - prevents the formation of recombinant cells.

microbio unit 2 (6 decks)

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