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240 Cards in this Set
- Front
- Back
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What are phylogenic relationships |
How genes are related |
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Where is horizontal gene transfer common among |
Common among even distantly related bacteria |
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What is horizontal gene transfer important for |
Important for genetic diversity and acquisition of new traits |
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Horizontal gene transfer can complicate interference of ______ relationships |
Phylogenic |
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Are entire chromosomes horizontally transferred? |
No |
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What is transformation gene transfer |
Free DNA taken up by competent cell |
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What is transduction |
Virus-mediated DNA transfer |
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What is conjugation |
DNA transfer via direct cell-to-cell contact |
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Might transformation burst out |
Yes it might And so DNA comes out a competent cell can bind and bring into the cell |
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What is transduction mediated by |
bacteriophages |
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Do you need an intact donor for transduction |
No |
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For conjugation, two cells need to _______ |
Make contact
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When two cells make contact during conjugation, what occurs between them |
DNA contact |
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What is the fate of incoming DNA |
Degraded by restriction enzymes Replicate seperate from chromosome (IE plasmids) Recombinate with chromosome |
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Nuclease do what to enzymes? |
Cut DNA in specific locations |
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Most of the time when DNA enters the cell will do what happens |
Be chewed up nuclease |
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What does recombining with chromosome |
Incoming piece of DNA has to come together with host chromosome and so the incoming DNA gets incorporated in the genome |
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What is the homologous recombination |
Sequence exchange between two similar DNA molecules |
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Homologous recombination can generate new ______ |
Genotypes |
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Homologous sequences must be ____ but _____ |
*Related *Genetically distinct |
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When does homologous recombination occur |
After transfer of DNA from donor to recipient |
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Deterction of homologous recombiantion depends on |
Conference of new phenotype |
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What do endonucleases do |
Nicks single DNA strands to start process And break the phosphodiesterase bonds |
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What do helicases do |
Untwist DNA |
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What are RecBCD |
Endonucleases Helicases |
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What do single-stranded binding proteins (SSBs) |
Unwound sDNA not happy so the SSBs keep it unwoumd |
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What are RecA for |
Nearly essential Binds to ssDNA Catalyzes branch migration |
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What are resolvases |
Resolve Holliday junction RecG, RuvC |
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How do donor DNA get into the cell (schematic) |
Endonuclease will nick 1 strand of DNa and ssBP will bind and keep stable and recA facilitates the strand invasion where it comes in and takes the single strand and links it to the double strand and creates cross-strand exchange and the holliday junction (donor DNa bound to other DNa strand) so genomes are twisted together and have resolvases come in) and break up junction and cut affects the later the DNA configurations |
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What are the two different types of DNA configurations |
Patches Splices |
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What are patches |
1 sequence in genome that wasn't there before (less new DNA) |
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What are splices |
1 piece of DNa that is half donor and half recipient (more new DNA) |
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For transformation _____ is taken up and incoporated into the recipient cell |
Free DNA |
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What are the fragments for transformation |
10 kbp (~10 genes) Tend to be small |
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What kind of cells perform transformation |
Naturally competant cells |
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Naturally competent cells are ______ determined |
Genetically |
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What types of cells do transformation |
Gram positive Gram negative Archaea |
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What does naturally competent cells includw |
*Membrane-associated DNA-binding proteins -Cell wall autolysin *Nucleases |
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What regulates natural competence |
Quorum sensing |
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What is rare of natural competence |
Gram positive (Bcillus, streptococcus) Gram negative (Acinetobacter, Haemophilus, neisseria, thermus) |
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When cells takes in other cells how many strands of DNA an they take in |
1 |
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What happens to the other strands on DNA left outside of the cell |
Chewed up |
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Can competence be induced |
Yes |
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How to induce competence |
*Treatment with clacium ions and cold shock (open up cell walls and membranes) *Electroporation (Works for bacteria as well as eyast and plant cells) --> Makes it easier for DNA to get in |
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Explain process of transformation |
Reversible binding of free DNA Irreversible binding of free DNA Complementary strand degraded upon uptake (sometimes dsDNA is taken up) SSB proteins bind Recombination (RecA) via heteroduplex formation [Rec A helps with recombination and helps with getting it together] |
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Frederick Griffith's and Oswald Avery's experiments with ________ |
S. Pneumoniae
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S. pneumoniae produces a ______ |
polysaccharide capsule |
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What does the polysaccharide capsule do to the body |
It invades the body |
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Do mutants of s. pneumoniae produce capsules |
No |
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If the mutants of s. pneumoniae don't produce the capsule do they cause infection? |
No W |
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What are the two morphologies of the working strain of s. penumoniae |
*S strain = smooth colony which evades the immune system and could not attack those cells * R strain = no polysaccharide; could be attacked and animal did not dire |
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What did Griffith find with his experiment |
1) Mice exposed to live S strain die 2) Mice exposed to killed S strain live 3) Mice exposed to live R strain live 4) Mice exposed to killed R strain live 5) Mice exposed to live R strain and killed S strain die and S like strian is isolated from dead animal Therefore the presence of killed S strian transforms R strain into S like strain and the transofrming material is DNA |
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What did Avery's experiments show? |
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What is transduction |
DNA transfer mediated by bacteriophage |
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What is generalized transduction |
Random bacterial transferred in place of viral |
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What is specialized transduction |
Specific bacterial DNA transferred with viral genome |
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In both generalized and specialized transduction what happens to the virus? |
It is rendered non-infective |
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What does transduction occur in |
Lots of bacteria and archaea |
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What pathways can it go down |
Lytic Lysogenic |
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What pathways do temperate phages use |
Lytic Lysogenic |
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Virulent phages use what pathways |
Only use lytic pathway and kill host immediately |
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What pathway is the generalized transduction during |
Only during lytic pathway |
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Waht happens during the lytic infection for generalized transduction |
Host DNA is accidentally packaged into virus particles |
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Why is the genralized transduction non-infective |
Because there is no viral DNA |
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How much of the total phage is released during the generalized transduction |
Small portion |
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What does the transducing particle do |
Binds to new host cell and injects bacterial DNA |
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What type of viruses can generalized transduction occur in |
Occur in temperate and virulent viruses
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What is the process of generalized transduction |
Host cell makes lots of copies of viral DNA and starts to make that and packages up with new particles but on accidentally package some of the viral DNA with the normal phage and some are carrying the bacterial DNA (transducing particle) Transducing will bin to new cell and is similar to host genome and will have a transduced recipient cell that has genes from the first bacteria that got infected |
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What is specialized transduction |
Transfers only small portion of bacterial chromosome |
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Is specialized transduction or generalized transducton more efficient |
Specialized transduction |
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What first described specialized transduction |
Lambda phage with E coli |
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When does specialized transduction occur |
Only occurs with temeprate phage --> must be lysogenic |
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In specialized transduction cell is _____ by phage |
Lysogenized |
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What are the process of specialized transduction |
*Lytic cycle begins *Phage DNA is improperly excised from bacterial chromosome *Bacterial gene adjacent to prophage are packaged along with phage DNA into new virions (The genes have to be near the viral DNa) [Cell ifnected by bacteriphage and phage DNA becomes induced. Regions that are comp and becoems circular and these type becoems circular and can populate the DNA out of host chromosomes wihtout making error and phage gets replicated and lyses and all viral particles come out in normal even. But rarely incision gets messed up and pink genes are all included with viral chromosome so assumign that the gene making the viral particle that replicated of pacaking then lysis again except these phage now including bacterial DNa and accidentally brings back DNA) |
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Improperly excised phage genomes must still contain what for lysis and lysogeny in order to be viable |
Genes for protein coat and other genes |
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Are some phage DNA is left in bacterial genome during specialized transduction |
Yes
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What does specialized transduction typically result in |
Defective virons |
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What do plasmids carry |
Nonessential (but often very helpful_ genes |
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What shape are most plasmids |
Circular |
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Can the copy number of plasmids vary |
Yes (1 --> 100) |
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How are most plasmids mostly replicated |
Using bidirectional replication |
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What is plasmid replication similar to
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Chromosome |
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What is typically transfered during conjugation |
Plasmids |
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What is plasmid incombility |
Two different plasmids that are closely related will not be maintained--> incompatbile |
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What are episomes |
Plasmids that can integrate into the plasmid |
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What is curing |
Removal of plasmid by inhibiting replication |
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What do R plasmids do |
Confer resistance to growth inhibitors -Antibiotics -Mercury |
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Transfer of R plasmids can be _____ |
Group specific |
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R 100 can only be transferred among _____ bacteria |
Gram-negatic enteric |
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R plasmids contain ____ genes |
tra genes (Transfer genes) |
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What is virulence |
Disease-causing ability |
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What are virulence traits |
Ability of pathogen to attach and colonize speicifc tissues Production of toxin, enzymes and other molecules and damage host |
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Some virulence traits are _____ |
Plasmid-encoded |
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What are f plasmids |
Circular piece of DNA has tra genes for transfer and has gene coding for pilli and see are pretty improtant for linking two cells together Mostly between realte taxa and most important process genes genes get in between |
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Does transduction happen for F plasmids very often |
No |
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What are bacteriocins |
Proteins produced by bacteria to inhibit growth of their competitors |
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For bacteriocins genes usually carried on _____ |
Plasmids |
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For the genes usually carried on plasmids what do they do |
Processing Transport Immunity |
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What do the Col plasmids of E coli do |
Disrupt cell membrane Nucleases that degrade DNA or RNA (especially rRNA) |
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Is transformation too important in nature |
No |
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Plasmids are transferred via ____ |
Conjugation |
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______ plasmids are capable of transferred themselves |
Conjugative |
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What type of genes are transferred |
Tra |
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What types of taxa does conjugation occur |
Mostly between related taxa |
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What is conjugation |
Direct transfer of DNA from cell-to-cell |
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Conjugation-related genes are encoded on ____ plasmids |
F |
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Does the donor cell contain a F plasmid |
Yes |
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Does the recipient cell contain the F plasmid |
No |
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Does plasmids for conjugation contain genes coding for pili? |
Yes |
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How does conjugation occur? |
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What direction is rolling cell replication in |
Unidirectional |
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How quick is rolling circle |
Rapid |
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For rolling circle replication use as a template |
Un-nicked starnd |
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What does the DNA polymerase complex do during the rollign circle replication |
Displaces nicked strand as it proceeds around the circle |
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Is rolling circle replication used by some viruses |
Yes |
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What is the complimentary straind in the recipient cell made by during the rolling circle replication |
Normal lagging strand synthesis |
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What is complementation |
Functional copy of a gene on a plasmid can complement mutated version of gene on a chromosome to preserve wild-type phenotype |
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What are merodiploids |
Cells that are diploid for any chromosomal segment (One copy of chromosome; other copy on plasmid or phage) |
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What is complementation tests used for |
Can be used to determine if mutations conferring mutatnt phenotype are in different regions of one gene or in different genes in the same pathway |
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Where does the RNA pol attah |
Promotor |
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Explain process of transcription |
RNA polymerase sits down on sigma factor and that helps it direct to the right spot Can get transcription of RNA and then end up with mRNA transcript |
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Can transcription and translation happen simulataneously? |
Yes |
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What are polysomes |
All mRNA with ribosomes |
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What do DNA binding do |
Serve to regulate gene transcription |
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Where do DNA binding proteins interact and bind |
With the major groove of DNA |
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DNA binding proteins generally recognize what |
Specific inverted repeat sequences in the DNA |
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What are the types of gene regulation |
Negative (repression and induction) Positive |
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Blocks transcription |
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What does positive gene regulation |
Promotes transcription |
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What does negative regulation via reperession like? |
Cell downregulates production of arginine biosynthesis enymes if there is a surplus of arginine |
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Have the image of the binding sites |
RNA polymerase normally in the promotor area and so transcription proceeds of all of the arginine biosythesis If have the arginine then binds to the rep4ressor and becoems a corepressor to work with operator to create the other biosynthetic gene |
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What is the negative regulation via induction |
Cell will only make enzymes to process lactose if lactose is present |
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What is the gene of negative regulation via the induction |
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What is the gene schematic for positive regulation via activators |
Presence of an inducer allow for activator protein and RNa polymerase to bind to DNA and initiate transcription |
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What do activators do for positive regulation |
RNAP only has weak affinity for promotor so the activators help RNAP recognize promotor W |
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What is an operator |
Set of genes controlled under a single promotor |
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What is a regulator |
Set of operons controlled under a single regulatory proteins |
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What is global gene expression |
Can regulate many unrelated genes simulatneously in response to changes in environment |
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What is catabolite repression? |
Is a type of global control that decides between available carbon soures |
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Catabolite repression can lead to ______ |
Diauxic growth |
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What does betal gal do |
Breaks down lactose to glucose and galactose |
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What is beta-gal part of |
Lac operon |
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If glucose is present there is _____ amount of cAMP |
Low |
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If glucose is present, the levels of cAMP in the cell _____ |
Increase |
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What happens if glucose is present |
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If glucose is not present what happens |
All lactose binds with LacI so can't go and interact with DNa anymore. Take away the repression mechanism |
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Waht does the stringent response |
Control changes in gene expression in response to drastic decreases in nutrient availability (amino acids) |
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Explain the stringent response |
Alarm response ppGpp//pppGpp are regulatory nucleotides in the stringent response made by ReIA |
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What does the stringent response serve to down regulate |
ribosome tRNA protein DNA synthesis Cell divison |
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What does the stringent response serve to up regulate genes for? |
amino acid biosyntheiss |
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How do cells move in liquids |
Swimming |
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How do cell move on solids |
*Gliding *Swarming *Twitching |
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What is twitching |
Pili mediated mobility |
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Swimming is mediated by what |
Flagella |
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How large is flagella |
15-20 nm in diameter |
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What are the types of flagella |
Petrichious (all over) Monotrichous (polar) (one flagella) Lophotrichou (tuft on one end) Amphitrichious (bipolar, one on each pole) |
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Do different flagella give the same or different swimming behavior |
Different |
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How does petrichious change swimming |
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What is reversible vs unidirectional flagella |
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What is the flagellin |
Protein that makes up the flagellar tail |
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What is the hook |
Anchors flagellin filament to motor |
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What does th ebasal body contain |
Central rod Rings Mot and Fil proteinsW |
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What side is the L ring for |
LPS side
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What side is the P ring with |
Periplasm |
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What side is the C ring with |
CytoplasmQ |
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Where is the Mot protein found |
Transverse rod protein
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Where is the Fil protein |
In the middle |
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What are the Mot and Fil proteins for |
They are switch proteins that trun the rod (in opp directions of each other |
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The motor uses _____ |
Proton motive force to rotate the flagelum
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What do Fli proteins control |
Direction of rotation |
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Is flagella biosynthesis a highly regulated process |
Yes |
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Is flagella biosynthesis an energetically costly process |
Yes
It is costly to build and maintain flagella |
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What is the flagella biosynthesis like |
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What is the non-flagellar based gliding motility |
*Secrete polysaccharide slime pulls cells along solid surface like a slug *Protein "legs" propel cells |
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What is the pili based gliding motility |
*Extension/retration of type IV pili |
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What are variant of gliding behavior |
Twitching Swarming |
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What is taxes |
Directed movement in response to environmental signal |
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What is chemotaxis |
Directed movement in response to chemical cues
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What is phototaxis for |
Light
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What is aerotaxis for |
Oxygen |
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What is osmotaxis |
Ionic strength
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What is hydrotaxis |
Hydration |
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What are the mot common taxis |
Chemotaxis Phototaxis Aerotaxis |
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Bacteria use what to influence motility |
Environmental cues W |
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What type of movement does ttractant present |
Random |
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What type of movement when there is an attractant |
Directed movement |
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How do we assay for chemotaxis in the lab |
Capillary assay Swarm plate assay |
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What is capillary assay |
Have liquid culture with bacterial cells in it Have cpaillary and bacterial cells will be primed for chemotaxis More cells in tube for attractant Less cells in tube for repellentW |
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What is a swarm plate assay |
Instead of very solid agar is more jello like Bac on swim on top and through agar Spot bac cell and grow and swarm outward and form ring can see differnece in sizes of rings |
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What is motility assay |
Phototaxis
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What is air bubble assay for |
Aerotaxis |
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Chemotaxis is a _____ system |
Phospho-relay |
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Phospho-relay system does what |
Rapdily respond to changes in extracellular environments |
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What is the mechanisms of chemotaxis |
1) Response to signal MCPs receive singal by binding directly or indirectly to signaling molecules CheA=sensor kinase, gets phosphorylated by itself 2) Controlling flagellar rotation -CheA transfers phosphate to CheY -CheY-P can itneract with the flagellar motor and change the direction of flagella turn -CheZ removes P form CheY 3) Adaptation -CheR adds methyl groups onto McPs -CheB-P removes methyl groups from MCPs |
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Methylated MCPs are mroe sensitive to ____ |
Repellats |
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What are unmehtylated MCPs are more sensitive to what |
Attractants |
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Is chemotaxis only for bacteria |
No |
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What is archael chemotaxis |
Proteins are related but not strictly the same as bacterial proteinsW
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hat is eukaryotic chemotaxis |
*Very divergent proteins *Development, immune response |
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How does the two compoenent system work in bacteria |
Sensor kinase portien (similar to CheA) Response regulator protein (simialr to CheY) |
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What is the quorum sensing a mechnaism to do |
Assess population density |
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What is an autoinducer |
Specific singaling molecule |
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Many human pathogens regulate virulence factors via _____ |
Quorum sensing
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QS also influences _______ |
Biofilm formation |
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What does H pylori cause |
Ulcers and gastric caner |
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H pylori recieves the quorum sening molecule _____ as a repellent
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A1-2 |
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What was the Earth like 4.57 billion years ago |
*Thick CO2 amosphere *No life *Very hot *bombarded with comets and asteroids |
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What was the Earth like 4.4-3.8 bya |
*First H2O (gaseous) *Rock formation *(Still) no life *Temperature cooled off *Liquid H2O |
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When did life first appear |
~3.5 bya |
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What was the evidence of life first appearing |
Fossil record of filamentous phototrophic bacteria |
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What were these filamentous phototrophic bacteria called |
Stromatolites
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What is the surface origin hypotehsis |
"Primordial soup" Proposed in darwin "Soup" in organic and inorganic compouds |
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Waht was the evidence of surface origin hypothesis |
In vitro stimulation of early earth (methane, ammonia) can result in the synthesis of amino soup |
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What were the caveats |
*Experimental design did not take into account concentrations of starting molecuels (hydrogen( *Earth's surface was hostileW |
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hat was the surface origin hypothesis |
-(more) constant conditions *Lots of H2, H2S *Phosphate present *Metals/mineralsW |
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What did probiotic world say |
Prebiotic synthesia Assembly of nucleic acids |
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What was RNA world |
DNA as gentic storage with RNA catalyzed metabolic machinery |
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What was the RNa world hypothesis |
Self-replicating RNA molecules were precursors to all current life on Earth
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What is the DNA/Proten world |
DNA is genetic storage with protein catalyste |
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Life needs a membrane for ____ |
Energy conservation
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Membrane encloses what |
Genetic material and biochemical machinery |
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______ are important for life |
Replication and divison |
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What was said to be the origin ~4.3 bya |
LUCA (Last universal common ancestor) |
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What was the evidence for early metabolsim and diversification
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From geological recod and ancient, extant lineages suggests -Anaerobic -CO2 -Heat-stable -H2 as energy source |
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What did cyanobacteria do |
Developed photosytem in which water replaces H2S in redox reaction Results in O2 as wast product instead of sulfur |
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When/what was the great oxidation event
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~2.5 bya Oxygen! |
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Was there an increase or decrease in metabolic diversity after the presence of oxygen in the atmosphere |
Increase |
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Why was the presence of oxygen a good thing for life? |
Good electron acceptor and is beneficial for redox reaction Faster growing and more natural selection Lead to evolution of eukaryotes |
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Why was oxygen a bad thing |
Toxic to orgnaisms who can't tolerate it Extinction event |
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What was the first hypothesis of endosymbiotic theory |
*Nucleus came first *Mitochondrion second *Chloroplast third Mitochondrion was bacterial cell that was efficent at using oxygen for energy use *Chloroplast was bacteria cell that was capable of carrying out photosynthesis |
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What was the second hypothesis for the endosymbiotic theory |
*mitochondrion first *Nucleus second *Chloroplast third |
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How do we measure evolutionary relationships for microorganisms |
Compare small subunit rRNA gene sequences |
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Why are SSU rRNA genes useful for inferring phylogenci relationships |
*All organisms have them *They all perform the same function *Sequences change slwoly over time *Adequate length for determining deep phylogentic relaitonships |
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What is a species |
A group of living orgnaisms consisting of similar individuals capable of exchanging genes or interbreading |
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When are prokaryotic species considered the same |
If *70% similarity in genomic DNA sequence *97% similarity in 165 ribosomal RNA |
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What are the ways we've improvedo n our way to classify microorganisms as technology advances |
*Phylogenic probes *Microbial community analysis *Ribotyping |
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What is an ecotype |
Cells in a population that share a particular resource
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How does microbial diversification happen early and often |
Rapid division allows for faster mutation rate
More mutation allows for selective adaption |
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What are the small genotypic differences that can result in large phenotypic differneces |
Difficult to assign species
Make even more difficult through horizontal gene transfer |
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The tree of life is more like a _____ |
Web |
