Exam 3 Study Guide Flashcards
What cells do endospore formation produce?
Vegeative cells
All E. Coli have the same ___ genome but will exhibit different ___ genomes.
-pangenome
-core
What are paralogs?
-are similar genes with different functions in the same or different species.
What are orthologs?
-are the same gene in two different species.
Systems Biology
-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.
What is metabolomics?
-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
What does isoelectric focusing do?
-separates proteins based on their isoelectric points (pI).
-pI is the pH at which the protein carries no electric charge and remains stationary.
What is trancriptome?
-a set of genes that is transcribed under a particular set of growth conditions.
How is RNA sequencing used to define transcriptome?
-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.
How does genome size correspond to metabolic diversity?
-bigger genome, bigger metabolic diversity
-because more enzymes
___ are the second greatest means of transfer of antibiotic resistance genes, after ___.
-plasmids
-transposons
What ALWAYS destroys gene functions?
-when transposons insertion mutagenesis involves putting several kbp of foreign material into the middle of a gene.
What transposable elements can jump?
-insertion sequences
-transposons
What gene does tnp encode and what does it do?
-encodes transposase
-an enzyme that cuts at the ends of the transposons to allow movement to a new location
What is chromosome mobilization?
-F plasmids inserts into chromosome due to homology in multiple copies of IS sequence
What are Hfr strands?
-high frequency recombination
-plasmids that contain chromosome integrates into host chromosome
What are the 3 main steps of chromosome mobilization?
-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
In chromosome mobilization does the recipient get all the F plasmid?
-No
-the recipient can recombine
What are transposable elements?
-They jump from one site to another, inserting into other DNA molecules
-Found by McClintock (female)
-insertion sequence and transposons
Is conjugation DNase sensitive?
-No
What are the main features of conjugation?
-DNA transfer during direct cell-to-cell contact
-Process encoded on F(fertility) plasmid
-Replication of DNA during transfer
What are the main features of features of specialized transduction?
-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.
What are the main features of generalized transduction?
-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
During transduction, host cell DNA is ___ packaged inside bacteriophage virus particles.
-accidentally
What are the features of artificial transformation?
-No genes required
-not an active process of the cells
-chemical and electroporation
Features of chemical artificial transformation?
-treat in DNA
-disrupts cell wall
-uses chemicals
Features of electroporation artificial transformation?
-holes in the membrane
-uses voltage
-more species are effected by this
What are the features of natural transformation?
-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
Some bacteria are naturally ___, they posses genes that allow them to bind, uptake, and recombine DNA. This is called ___ transformation.
-competent
-natural
Describe the “transforming Principle” experiment by Griffith.
-used mouse and Streptococcus Pneumonia
-found that if you combine two strains ,that normally allow the mouse to live, it will die once combined.
Describe Avery and MacLeod’s experiment? What did they show and how?
-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
Donor cell/strain
the origin of the DNA that is entering a new cell
Recipient cell/strain
the cell that is receiving the new DNA
Recombinant cell/strain
-The result if the recipient can successfully integrate the new genetic information into its genome
-either into the chromosome or a stable plasmid
DNase
An enzyme that will degrade any DNA in a solution
___ is DNase sensitive. ___ involves a bacteriophage.
-Transformation
-Transduction
What type of genetic exchange requires cell-to-cell contact
-Conjugation
-(Horizontal gene exchange)
What is vertical gene transfer?
-One generation to the next
-new genetic material acquired via sexual reproduction
-within species
What is horizontal gene transfer?
-doesn’t come from parents, from siblings
-same generation
-not sexual reproduction
-across species
What are the steps involved in homologous recombination?
- DNA is nicked by endonuclease
- Binding of SSB protein
- Strand invasion of recipient DNA by Rec A protein
- Development of cross-strand exchange
-patches and splices
What molecules play a role in homologous recombination?
-Rec A protein
-ssDNA
-endonuclease and exonuclease
-DNA polymerase
-DNA ligase
In nature, homologous recombination creates ___. In lab, it allows ___.
-genetic diversity
-genetic mutation
What does homologous recombination require?
-two DNA molecules with extended regions of similar sequences
Are plasmids so mobile that they can move between members of different species?
-Yes
What are plasmids?
-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.
Why are plasmids important?
-Antibiotics resistance
-horizontal gene transfer
-evolution
What does Quorum sensing allow for?
-bacterial cells to determine population density and respond accordingly.
What is the order of sigma factors in sporulation?
-F-forespore
-E-mother cell
-G-forespore
-K mother cell
What two things does sporulation require and what do they do?
-The forespore makes internal spore components
-The mother call makes external spore wall and coat components
What is the process of sporulation process?
-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.
What is the difference between kinases and phosphatses?
The signal is transmitted by phosphorylation of the response regulator by the sensory kinase
What are the parts of the two-component regulatory system?
-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)
To which protein does the cAMP bind to? What do this cause?
-CRP protein
-this activates transcription
What is the signal that the cell “lacks” glucose?
-production of cAMP
What are the two conditions required for the production of lactose metabolites?
-Absence of glucose
-Presence of lactose
What is catabolite repression?
-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
Relative to the promoter, where is the activator binding site?
-can bind near or far upstream of the promoter
What does the DNA binding protein do?
-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
Presence of arginine within the cell results in arginine synthesis being ___ through the ___ of transcription
-repressed
-blockage
Genetic control is ___ with repression an ___ with activation.
-negative
-positive
What is genetic control?
-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
What does the Twin-Arginine System (TATA system) do?
-can export certain fully folded proteins through the membrane
Chaperone function requires hydrolysis of ___
ATP
What are folding chaperons?
-a protein that helps other proteins fold or refold from a partly denatured state
What are some examples of chaperons?
-Dna K/J
-Gro EL/ES
-they require ATP hydrolysis
Is the information for proper folding built into the primary amino acid sequence for most proteins?
-yes, this allows them to fold themselves
What are the benefits of coupling transcription and translation?
-rapid response to environment changes
-efficient use of resources and regulation of genes
-increase growth rate
What are the benefits of separating transcription and translation?
-precise regulation
-quality control
-greater complexity
-protection of genetic material
What are the first amino acids for bacteria, archaea, and Eukarya?
-Bacteria = N-formyl methionine
-Archaea and Eukarya = methionine
Who is coupled and who is not?
-Bacteria and archaea are coupled
-Eukarya are not coupled
What are the stop codons for mRNA?
-UAA
-UAG
-UGA
