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BIOL 2604 > Exam 3 Study Guide > Flashcards

Exam 3 Study Guide Flashcards

1
Q

What cells do endospore formation produce?

A

Vegeative cells

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2
Q

All E. Coli have the same ___ genome but will exhibit different ___ genomes.

A

-pangenome
-core

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3
Q

What are paralogs?

A

-are similar genes with different functions in the same or different species.

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4
Q

What are orthologs?

A

-are the same gene in two different species.

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5
Q

Systems Biology

A

-understanding not just the full set of genes and molecules the cell expresses, but how those factors feedback to regulate the next steps in cell metabolism.

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6
Q

What is metabolomics?

A

-identifying and quantifying all of the small molecules in the cell under varying growth conditions
-measure/ID molecules using Gas C/MS or Liquid C/MS

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7
Q

What does isoelectric focusing do?

A

-separates proteins based on their isoelectric points (pI).
-pI is the pH at which the protein carries no electric charge and remains stationary.

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8
Q

What is trancriptome?

A

-a set of genes that is transcribed under a particular set of growth conditions.

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9
Q

How is RNA sequencing used to define transcriptome?

A

-by sequencing millions of short RNA fragments from the cell
-align to the DNA sequence of the genome
-Quantify relative expression of genes based on number of corresponding RNA sequences read.

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10
Q

How does genome size correspond to metabolic diversity?

A

-bigger genome, bigger metabolic diversity
-because more enzymes

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11
Q

___ are the second greatest means of transfer of antibiotic resistance genes, after ___.

A

-plasmids
-transposons

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12
Q

What ALWAYS destroys gene functions?

A

-when transposons insertion mutagenesis involves putting several kbp of foreign material into the middle of a gene.

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13
Q

What transposable elements can jump?

A

-insertion sequences
-transposons

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14
Q

What gene does tnp encode and what does it do?

A

-encodes transposase
-an enzyme that cuts at the ends of the transposons to allow movement to a new location

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15
Q

What is chromosome mobilization?

A

-F plasmids inserts into chromosome due to homology in multiple copies of IS sequence

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16
Q

What are Hfr strands?

A

-high frequency recombination
-plasmids that contain chromosome integrates into host chromosome

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17
Q

What are the 3 main steps of chromosome mobilization?

A

-Step 1: F plasmid is nicked in one strand
-Step 2: F is transferred, followed by chromosomal DNA.
-Step 3: Synthesis of the second strand in the recipient and donor cell

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18
Q

In chromosome mobilization does the recipient get all the F plasmid?

A

-No
-the recipient can recombine

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19
Q

What are transposable elements?

A

-They jump from one site to another, inserting into other DNA molecules
-Found by McClintock (female)
-insertion sequence and transposons

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20
Q

Is conjugation DNase sensitive?

A

-No

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21
Q

What are the main features of conjugation?

A

-DNA transfer during direct cell-to-cell contact
-Process encoded on F(fertility) plasmid
-Replication of DNA during transfer

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22
Q

What are the main features of features of specialized transduction?

A

-Phage lambda
-A lysogenic phage inserts its DNA in the host chromosome and lies dormant.
-Later on it can exit from the chromosome and reproduce.
-only genes right next to phage insertion site can be transferred.

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23
Q

What are the main features of generalized transduction?

A

-phage 22 or p1, e. coli
-“phage lysate” will contain many phage particles and some “transducing particles”
-Transduction particles still bind to another host cell and inject its DNA into the cell
-can potentially transfer any gene in the host genome!
-useful in labs strain construction

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24
Q

During transduction, host cell DNA is ___ packaged inside bacteriophage virus particles.

A

-accidentally

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25
Q

What are the features of artificial transformation?

A

-No genes required
-not an active process of the cells
-chemical and electroporation

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26
Q

Features of chemical artificial transformation?

A

-treat in DNA
-disrupts cell wall
-uses chemicals

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27
Q

Features of electroporation artificial transformation?

A

-holes in the membrane
-uses voltage
-more species are effected by this

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28
Q

What are the features of natural transformation?

A

-expressing genes each step, ds DNA (double stranded) is bound to a cell surface
-one strand is degraded and ONLY 1 ssDNA (single stranded) enters the cell competent cell.
-energy required

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29
Q

Some bacteria are naturally ___, they posses genes that allow them to bind, uptake, and recombine DNA. This is called ___ transformation.

A

-competent
-natural

30
Q

Describe the “transforming Principle” experiment by Griffith.

A

-used mouse and Streptococcus Pneumonia
-found that if you combine two strains ,that normally allow the mouse to live, it will die once combined.

31
Q

Describe Avery and MacLeod’s experiment? What did they show and how?

A

-They used the same method as Griffith with the mouse.
-Found that the heat killed capsuled transferred its DNA to the live Non capsuled
-Giving the noncapsuled a capsule and killing the mouse

32
Q

Donor cell/strain

A

the origin of the DNA that is entering a new cell

33
Q

Recipient cell/strain

A

the cell that is receiving the new DNA

34
Q

Recombinant cell/strain

A

-The result if the recipient can successfully integrate the new genetic information into its genome
-either into the chromosome or a stable plasmid

35
Q

DNase

A

An enzyme that will degrade any DNA in a solution

36
Q

___ is DNase sensitive. ___ involves a bacteriophage.

A

-Transformation
-Transduction

37
Q

What type of genetic exchange requires cell-to-cell contact

A

-Conjugation
-(Horizontal gene exchange)

38
Q

What is vertical gene transfer?

A

-One generation to the next
-new genetic material acquired via sexual reproduction
-within species

39
Q

What is horizontal gene transfer?

A

-doesn’t come from parents, from siblings
-same generation
-not sexual reproduction
-across species

40
Q

What are the steps involved in homologous recombination?

A
  1. DNA is nicked by endonuclease
  2. Binding of SSB protein
  3. Strand invasion of recipient DNA by Rec A protein
  4. Development of cross-strand exchange
    -patches and splices
41
Q

What molecules play a role in homologous recombination?

A

-Rec A protein
-ssDNA
-endonuclease and exonuclease
-DNA polymerase
-DNA ligase

42
Q

In nature, homologous recombination creates ___. In lab, it allows ___.

A

-genetic diversity
-genetic mutation

43
Q

What does homologous recombination require?

A

-two DNA molecules with extended regions of similar sequences

44
Q

Are plasmids so mobile that they can move between members of different species?

A

-Yes

45
Q

What are plasmids?

A

-major mediators of genetic exchange
-have extra chromosomal genetic elements
-circular
-smaller than chromosome
-posses their own origin of replication, but use the cells normal DNA replication machinery to make multiple copies.

46
Q

Why are plasmids important?

A

-Antibiotics resistance
-horizontal gene transfer
-evolution

47
Q

What does Quorum sensing allow for?

A

-bacterial cells to determine population density and respond accordingly.

48
Q

What is the order of sigma factors in sporulation?

A

-F-forespore
-E-mother cell
-G-forespore
-K mother cell

49
Q

What two things does sporulation require and what do they do?

A

-The forespore makes internal spore components
-The mother call makes external spore wall and coat components

50
Q

What is the process of sporulation process?

A

-each cell must change its pattern of gene expression several times during sporulation and it must happen in the proper order
-the two cells communicate to active new sigma factors to direct transcription at the proper time and in the proper cell type.

51
Q

What is the difference between kinases and phosphatses?

A

The signal is transmitted by phosphorylation of the response regulator by the sensory kinase

52
Q

What are the parts of the two-component regulatory system?

A

-Component #1 Sensory Kinases: protein that receives a signal, often extracellular and transmits that signal to component #2
-Component #2 Response Regulator: a transcription regulator (a repressor or activator)

53
Q

To which protein does the cAMP bind to? What do this cause?

A

-CRP protein
-this activates transcription

54
Q

What is the signal that the cell “lacks” glucose?

A

-production of cAMP

55
Q

What are the two conditions required for the production of lactose metabolites?

A

-Absence of glucose
-Presence of lactose

56
Q

What is catabolite repression?

A

-a regulatory mechanism used to contain gene expression
-makes sure that glucose is used a primary carbon source
-makes sure resources are not wasted by producing enzymes that aren’t needed

57
Q

Relative to the promoter, where is the activator binding site?

A

-can bind near or far upstream of the promoter

58
Q

What does the DNA binding protein do?

A

-does the regulating
-bind to specific sequences either in major or minor grooves of DNA helix
-for transcription they interact with enhancers and promoters
-dimer, 2 subunits

59
Q

Presence of arginine within the cell results in arginine synthesis being ___ through the ___ of transcription

A

-repressed
-blockage

60
Q

Genetic control is ___ with repression an ___ with activation.

A

-negative
-positive

61
Q

What is genetic control?

A

-the process when genes regulate the expression of other genes or themselves.
-Critical to the normal function of cells so genes are expressed at the right amount and time

62
Q

What does the Twin-Arginine System (TATA system) do?

A

-can export certain fully folded proteins through the membrane

63
Q

Chaperone function requires hydrolysis of ___

A

ATP

64
Q

What are folding chaperons?

A

-a protein that helps other proteins fold or refold from a partly denatured state

65
Q

What are some examples of chaperons?

A

-Dna K/J
-Gro EL/ES
-they require ATP hydrolysis

66
Q

Is the information for proper folding built into the primary amino acid sequence for most proteins?

A

-yes, this allows them to fold themselves

67
Q

What are the benefits of coupling transcription and translation?

A

-rapid response to environment changes
-efficient use of resources and regulation of genes
-increase growth rate

68
Q

What are the benefits of separating transcription and translation?

A

-precise regulation
-quality control
-greater complexity
-protection of genetic material

69
Q

What are the first amino acids for bacteria, archaea, and Eukarya?

A

-Bacteria = N-formyl methionine
-Archaea and Eukarya = methionine

70
Q

Who is coupled and who is not?

A

-Bacteria and archaea are coupled
-Eukarya are not coupled

71
Q

What are the stop codons for mRNA?

A

-UAA
-UAG
-UGA

BIOL 2604 (17 decks)

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