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Micro 265 Fall 2023 > 3.2 - Prokaryotic Genetics > Flashcards

3.2 - Prokaryotic Genetics Flashcards

1
Q

how often do humans generate new genetic diversity?

A
  • every generation using sexual replication.
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2
Q

How do prokaryotes reproduce?

A
  • they do not reproduce sexually.
  • they reproduce simple binary fission produce genetically identical offspring.
  • prokaryotes are not genetically stagnant! (They mutate, exchange genes)
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3
Q

Naming Gene Names

A
  • Gene names are 4 letters
  • the first 3 letters –> describe function
  • the 4th letter –> designates a specific gene.
  • Genes names are ALWAYS italicized.
  • the first three letters are lower case.
  • the 4th letter is uppercase

ex. btuC –>
btu = B Twelve Uptake , C = gene c

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4
Q

Naming Protein names

A
  • they start with the and uppercase letter and are NOT ITALICIZED.

-Gene names are 4 letters

  • the first 3 letters –> describe function
  • the 4th letter –> designates a specific gene.
  • ex. BtuC

**begins with a capital letter - protein name

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5
Q

what is a mutation?

A
  • A heritable change in the DNA sequence of a genome.
    Includes substitution mutations, insertions, deletions – any change.
  • does not have to be a swam in DNA sequence it can be insertion or deletion
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6
Q

what is a mutant?

A
  • it is a mutant strain.
  • It is an organism whose genome carries a mutation.
  • organism that has mutataion
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7
Q

what is a wild type strain?

A
  • strain isolated from nature and/or one being used as
    the parental strain in a genetic study. The term “wild-type” can also be
    applied to a single gene
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8
Q

what is a genotype?

A
  • the complete genetic makeup of an organism
  • all genomes in an organism.
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9
Q

what is a phenotype?

A
  • an observable characteristic of an organism

-There can be
many different sorts of phenotypes: metabolic, virulence, morphology

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10
Q

what is a genomic locus?

A
  • a specific position on the chromosome

-it can have two mutations, which lead to the loss of maltose fermentation.

  • The indicator plates that detect maltose fermentation in purple show this loss of function phenotype in these mutant strains
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11
Q

How are mapped mutations described?

A
  • using nucleotide or amino numbers.
  • you write it like: Wildtype base or A.A, number, then mutant base or amino acid.

ex. HisC (A77K) –> residue 77 mutated form an Alanine (A) to a Lysine (k)

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12
Q

what symbol is used for deletion mutations?

A
  • shown by a delta symbol
  • like deltabtuC
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12
Q

How to name phenotype names?

A
  • they have three letters.
  • the first letter is capitalized.
  • designations and strain are shown by a + or a + sign for that phenotype.

ex. His+ strain can make histidine. His- strain is a histidine auxotroph
– can’t make histidine.

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13
Q

what is a auxotroph?

A

-requiring a specific growth substance beyond the minimum required for normal metabolism and reproduction by the parental or wild-type strain.

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14
Q

What types of mutations can there be?

A
  • spontaneous –> naturally occurring mistakes.
  • nonspontaneous –> mistake cause by mutagenic chemicals or by DNA damage from UV
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15
Q

what is a point mutation?

A
  • mutations to a single base pair
  • they are within protein coding sequence.
  • there are three types:
    a. silent
    b. missense
    c. nonsense
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16
Q

what is a silent mutation?

A
  • do not change amino
    acid sequence, different codon, but same amino acid.
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17
Q

what is a missense mutation?

A
  • lead to a change in that amino acid to a different amino acid
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18
Q

what is a nonsense mutation?

A
  • lead to a change in that amino acid to a stop codon, leading to a premature end to the protein sequence. (truncation)
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19
Q

what is truncation?

A
  • the process of shortening a molecule or sequence by removing a portion of it.
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20
Q

Deletion and Insertion mutations?

A
  • DNA being added or lost.
  • Deletion Mutations (DNA lost) and insertion mutations ( DNA added to a specific location) can be small as. single bp or can be as large as thousand of bp
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21
Q

what does deletions or insertions within a protein-coding regions often result in?

A
  • frameshift mutation

-the insertion or deletion of nucleotide bases in numbers that are not multiples of three.

-codon not grouped in three

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22
Q

what is a genetic reversion?

A
  • mutant strain has a specific mutation.
  • it acquires. mutations that change it back to the original wild-type sequence, so the strain is now WT again.

-genetic alterations that reverse the effect of mutations

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23
Q

what is a phenotypic reversion?

A
  • Mutant strain has a certain phenotype. It
    then acquires another mutation to “revert” back to the wild-type
    phenotype. Might be a genetic reversion, might be some other
    mutation
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24
Q

what is a supressor mutataions?

A
  • Cause phenotypic reversions.

-Mutations
that compensate for the effects of a prior mutation – return the
phenotype of the strain partially or fully back to WT.

  • IT IS NOT A GENETIC REVERSIONS - different genetic change “suppresses”
    phenotype of original mutation. Mutation often (but not always) to a
    different gene – “fixes problem” that was created by initial mutation.
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25
Q

what does selection do?

A
  • selection can induce mutations in different ways (ex. mutagens, transposons)
  • many times mutant are isolate via selection
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26
Q

what is selection?

A
  • the selection is when the mutant grows but the parent does not (or grows significantly worse)
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27
Q

is selection efficient?

A
  • it is highly efficient and can identify a single mutant with a desired phenotype out of millions of cells.
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28
Q

Is it easier to identify mutants that grow better than parent by selection?

A
  • yes it is
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29
Q

what do we use to identify the absence of growth?

A
  • we use replica plating (plating the same colony on two different plates –
    under two different conditions), you can identify mutants that grow
    worse than parent (or not at all)
  • if missing spots then mutants did not grow.
  • no missing spots all colonies grew.
30
Q

what is an indicator plate?

A
  • when you can link a phenotype to a change in colony
    appearance or to a detectable signal (colour, fluorescence, luminescence)

-Mutants with a desired phenotype can then be isolated by detecting
single colonies the do (or do not) produce that signal

31
Q

which enzyme is commonly used in identifying colonies?

A
  • enzyme B-galactosidase (lac z gene) is commonly used as a tool to identify colonies with
    altered gene expression in bacteria.

-B-galactosidase substrates such as X-gal can be added to plates that produce a signal (blue)

  • by placing the lac Z under the control of the promoter you want to study, you seek a mutant that can turn on and turn off this promoter.
32
Q

what is natural mutataion?

A
  • rate is from 10^-6 and 10^-7 per 1000 bp per round of replication for prokaryotes.
  • DNA polymerase errors when copying genomic DNA.
33
Q

if you have large enough numbers of bacteria in population….

A

will likely have some genetic diversity in each gene (even though genomes are identical or almost identical)

34
Q

what is horizontal gene transfer?

A
  • acquiring new genetic material from
    (foreign DNA) from the environment plays an even bigger role

-a process in which an organism transfers genetic material to another organism that is not its offspring

35
Q

What are the three ways foreign DNA can enter a prokaryotic cell?

A
  1. transformation
  2. transduction
  3. conjugation
36
Q

What happens once the foreign DNA is inside the cell, what can the DNA do?

A
  1. Be degraded/ lost
  2. replicate as a separate entity (Plasmids, phage)
  3. Be integrated into the chromosome (recombination, transposition )
37
Q

How is foreign DNA can be integrated into a host genome?

A
  1. Genetic recombination
  2. Transposition
38
Q

what is genetic recombination?

A
  • a physical exchange of DNA between genetic elements. (IMPORTANT TYPE IS HOMOLOGOUS RECOMBINATION (HR))
  • In genetic recombination, Foreign DNA with homology to a region of the host chromosome can be
    inserted into the genome in place of - or in addition to - the native DNA
    sequence.
39
Q

What is HR?

A
  • HR is an important DNA repair mechanism used to repair double
    strand breaks.
  • HR also important for horizontal gene transfer
  • HR is basically DNA with
    similar sequences can get “shuffled around” using this machinery.
  • is HR important for genome rearrangements.
40
Q

What is Transposable Elements?

A
  • they are mobile genetic elements found in almost all species.
  • it contains transposes gene bounded by inverted species.
41
Q

What are transposase enzymes able to do?

A
  • Recognize inverted repeats of DNA sequences
  • Cleave that DNA to free “transposable element”

-Cleave another DNA (e.g. chromosomal DNA)

  • Insert the transposable element into that DNA
  • This process is called “transposition”.
42
Q

what do insertion sequence elements have?

A
  • they have only transposition machinery
43
Q

what are transposons?

A
  • contains extra genes as well, such as antibiotic-resistance genes

-they are used in lab and generate mutant strains.

  • Can insert randomly into genome,
    inactivating genes

-

44
Q

Are many transposable elements are conservative (cut and paste)?

A

-yes they have conservative mechanisms where they can move form one place to another.

45
Q

Are many transposable elements are replicative mechanisms?

A
  • yes they have replicative mechanisms where transposons remain at its locus and copy is produced and inserted everywhere.
46
Q

How foreign DNA can make its way into a prokaryotic cell?

A
  1. Transformation
  2. Transduction
  3. Conjugation

(happen in archaea)

47
Q

what is transformation?

A
  • in which free DNA is incorporated into a recipient cell and brings about genetic change.
  • the DNA can come form a variety of sources, usually from dead prokaryotes in the environment
48
Q

Does DNA freely cross the membrane?

A

no it cannot, therefore it is competent (capable of taking up free DNA)

  • many bacteria and archaea are naturally competent (helps DNA get in the cell)
49
Q

what do we do if a bacteria is not competent?

A
  • we transfer DNA into cells in an artificial manner in the lab
50
Q

In transformation how is DNA captured form the environment?

A
  • captured by pili.
  • this retracts the DNA through OM and the cell wall.
  • one strand of DNA typically degraded and the other strand passes through the cytoplasmic membrane and into the cell via a multi-proton competence system.
51
Q

steps to transformation:

A
  1. pilus useful for moving, it binds to an extracellular DNA.
  2. it retracts the DNA inside the cell membrane.
  3. you have 2 strands:
    a. 1 strand = chewed up and used in some productive wayb. 2 strand = brought into the cell
    i. no guarantee that it ends up in gene.
    ii. though recombination.
52
Q

what is a bacteriophage?

A
  • is a virus that infects a bacterium.
53
Q

what are the viruses DNA packaged in?

A
  • it is packaged in virions, which feature protein coats that protect the DNA.
  • the viron will bind the cell and will inject DNA.
54
Q

what are the two ways used by bacteriophages?

A
  1. lytic pathway - phage DNA replicated and new particles produced using host cell, released to infect new cell.
  2. lysogenic pathway - viral DNA integrated into host DNA (prophage). can be induced by triggering the lytic cycle.

(bacteriophages can produce in a mixture of lytic and lysogenic pathaway)

55
Q

steps of how bacteriophages are infected:

A
  1. attachment of the viruses to the host cell
  2. injection of viral DNA
  3. This then splits into Lytic Pathway and then the Lysogenic pathway.
  4. Lytic Pathway:
    a. lytic events are initiatedb. phage components are synthesized and virons are assembled.c. lysis of host cell and release of new phage virons.d. once DNA made, them many copies are made.
  5. Lysogenic Pathway:
    a. viral DNA is integrated into host DNA.b. the lysogenized cell is made, it has a prophage.c. the viral DNA is replicated with host DNA at cell division.

d. at this point in time the cell can go into the lytic pathway via induction.

56
Q

what is transduction?

A
  • process in which a virus transfers of DNA from one to another
  • There are two types of transduction
57
Q

What is Generalized Transduction?

A
  • during the lytic cycle some host cell DNA is accidentally packaged into a viral particle.
  • This DNA is injected into new cell in place of phage DNA.
58
Q

what is specialized Transduction?

A
  • when a prophage is induced, its DNA is excised from genome and packaged into phage particles.
  • in many cases some neighbouring DNA is also packaged.
  • this DNA can be injected into a new cell by that phage particle
59
Q

steps of general transduction:

A
  1. a phage infects the donor bacterial cell.
  2. phage DNA and proteins are made and the bacterial chromosome is broken down into pieces.
  3. pieces of bacterial DNA are packaged in a phage capsid. Then the donor cell lyses and releases phage particles containing bacterial DNA.
  4. A phage carrying bacterial DNA infects a new host cell, the recipient cell.
  5. Recombination can occur producing a recombinant cell with a genotype from both the donor an recipient cells.
60
Q

steps of Specialized transduction:

A
  1. page DNA integrates into the chromosome
  2. prophage integrates and picks up pieces of the bacterial chromosome.
  3. replication of viral DNA and destruction of bacterial DNA.
  4. Virus capsid synthesis as assembly.
  5. Lysis of bacterial cell, phage release, infection of new bacterial cell.
  6. crossover and stable gene transfer into recipient cell chromosome.
61
Q

What is conjugation?

A
  • Horizontal gene transfer that requires cell-cell contact
62
Q

what is conjugative plasmids?

A
  • Typically conjugation is mediated by plasmids
    a.the F-plasmids
63
Q

What are F-plasmids?

A
  • it is large
  • f = fertility
  • Strains with an F plasmid are
    called F+ and are donor cells
64
Q

what can F-plasmids be transferred to?

A

cells that
lack the plasmid (F-), recipient cells

65
Q

How is the DNA transferred in conjugation ( F-plasmids) ?

A
  • DNA transfer only from donor to
    recipient (unidirectional). Only between
    F+ and F- cells (two F+ cells won’t mates)
66
Q

what do F-plasmids encode?

A
  • many tra (transfer) genes that are involved in the
    conjugative transfer process
67
Q

what is a conjugative pilus and who encodes it?

A
  • tra genes encode it
  • it is produced by F+ cells,
    attach to F- cells only (F plasmid encodes genes that prevent attachment)
68
Q

what are the steps of conjugation?

A
  1. Pilus attaches
  2. brings two cells together
  3. Conjugative bridge forms (pilus gets strengthen by bridge)
  4. Beginning at oriT, DNA is nicked and single strand is copied
  5. Copied strand passed to type IV
    secretion system
  6. This then transfers F
    plasmid DNA from F+ cell to F- cell
    through the bridge
  7. F- cell now F+, can act as donor. F+ cell
    remains F+
69
Q

what happens in the conjugative transfer of Hfr strains?

A
  • F plasmid has insertion sequences & can
    integrate into chromosome producing an Hfr
    cell

-Conjugative transfer machinery still intact and
active – oriT now on chromosome

  • Transfer to F- cell via a synonymous
    mechanism, but can also transfer part of
    donor’s chromosomal DNA
  • Transferred DNA can be incorporated into
    recipient strain’s genome
  • Doesn’t transfer full F plasmid, so recipient
    strain remains F-
70
Q

is all DNA evolutionary useful?

A
  • it may get lost
  • even if in genome, it doesn’t means it always gets changed.
71
Q

what is selective advantage?

A
  • this gene is more selectively preferable than the other one.
72
Q

what do microbial genes contain?

A
  • great deal of horizontally acquired DNA
  • ex GC% –> G pairs with C VS A pairs with T (easy way to tell where DNA came from)
73
Q

what is horizontal gene transfer?

A
  • huge impacts in all aspects of
    microbiology.
  • the movement of genetic information between organisms, a process that includes the spread of antibiotic resistance genes among bacteria

Micro 265 Fall 2023 (9 decks)

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