micro exam 2

fimbriae and pili

* short, thin hairlike protein appendages up to 1,000 per cell
* can mediate attachment to surfaces, motility, and DNA uptake
* is regulated by how many copies of the gene you have

sex pili

* longer, thicker, less numerous where there is 1-10 per cell
* genes for the formation on plasmids
* required for conjugation/ movement of DNA
* send to another cell to be able to send a plasmid and make genes from that same plasmid

structures similar to pili used by pathogens to secrete effector proteins in to or around the cells

what is a plasmid transfer?

flagella

* threadlike, locomotor appendage extending outward from the plasma membrane and cell wall
* helps with motility, attachment to surfaces, and may have virulence factors

monotrichous

one flagellum

polar flagellum

flagellum at end of cell

amphitrichous

one flagellum at each end of cell

lophotrichous

cluster of flagella at one or both ends

peritrichous

spread over entire surface of the cell

* thin, rigid protein structures that cannot be observed with bright-field microscope unless specially stained
* ultrastructure composed of three parts
* filament extends from cell surface to the tip
* hook links filament to basal body
* basal body is series of ring that drive flagellar motor

what is different about bacterial flagella?

flagellar synthesis

* complex process involving many genes/gene products
* new flagellin molecules transported through the hollow filament using Type III-like secretion system
* filament subunits self-assemble with help of filament cap at tip, not base

rotates like a propeller

how does the bacterial flagella move?

counterclockwise (CCW)

what is the general rotation for the flagella to have a run motion?

clockwise (CW)

what rotation disrupts run to cause the cell to stop and tumble?

help to avoid and move direction

what can tumbling of the flagella do?

2 part motor producing torque

how many parts is the flagellum made up of?

rotor and stator

what are the two parts that help with the motor of the flagellum?

Rotor

C (FliG protein) ring and MS ring turn and interact with stator

Mot A and Mot B proteins to help get through plasma membrane

what is the stator made up of?

stator

* form channel through the plasma membrane
* protons move through Mot A and Mot B channels using energy of proton motive force
* torque powers rotation of the basal body and filament

swarming

* move out from the center in a branched, defined pattern
* occurs on moist surfaces as a type of group behavior by bacteria
* have peritrichous flagella

spirochete motility

* multiple flagella form axial fibril to wind around the cell
* flagella remain in periplasmic space inside outer sheath
* corkscrew shape exhibits flexing and spinning movements

twitching and gliding motility

* occurs on solid media
* no flagella
* have Type IV pili and slime

twitching

* pili at ends of cell
* short, intermittent, jerky motions
* cells are in contact with each other and surface

gliding

smooth movement

chemotaxis

* movement toward a chemical attractant or away from chemical repellent
* changing concentration of chemical attractants and chemical repellents bind chemoreceptors of chemosensing system
* behavior of bacterium altered by temporal concentration of chemical
* presence of attractant/repellent, tumbling frequency is reduced’ runs toward/away from compound are longer

sessile cells

* bare minimum to survive
* hibernations to shut down everything not needed for survival in times of stress

spore formation

releasing small seed to make things again in a less stressful environment

endospore

* complex, dormant structure
* can form in various locations within the cell
* resistant to numerous environmental conditions

* calcium complexed with dipicolinic acid
* small, acid-soluble, DNA-binding proteins\\
* dehydrated core
* spore coat and exosporium protect

why are endospores resistant to numerous environmental conditions?

endospore structure

* spore surrounded by thin covering called exosporium
* thick layers of protein form the spore coat
* cortex, beneath the coat, thick peptidoglycan
* core has nucleoid and ribosomes

sporulation

* process sof endospore formation
* occurs in a few hours
* commences when growth ceases due to lack of nutrients
* complex multistage process

* activation
* germination
* outgrowth

types of formations of vegetative cell

activation

* prepares spores for germination
* results from treatments like heating

germination

* environmental nutrients are detected
* spore swelling and rupture of absorption of spore coat
* increased metabolic activity

outgrowth

emergence of vegetative cell to go back to normal cell size

* macleod and mccarthy showed that the transforming principle was DNA
* so there is a smooth strain of colony where the S strain has a capsule that killed the mouse
* there was an R strain that was rough with no capsule where the mouse was unharmed
* however, when they heat killed the S strain, there was no harm to the mouse
* finally, the thing is when they put the heat-killed S strain with the live R strain where they will both come together to form the S strain to kill the mouse, hence saw DNA as genetic material

how did scientists find out DNA is genetic material?

change of non-virulent organisms into virulent ones via transformation

what did Griffith discover in 1928?

transforming principle to prove that DNA is the genetic material

* type R cells with the type S DNA extract will make DNA through transformation
* when there is DNase with the Type R cell and the type S DNA extract, the DNA can be destroyed
* however, if protease or RNase is used, there will be DNA still transformed but either no protein or RNase

adenine, guanine, cytosine, and thymine

what are the nucleotide bases for DNA?

* bases
* deoxyribose sugar
* phosphate esterified to sugar carbon

what forms nucleotides for DNA?

covalent bonds between the 3’-hydroxyl of one sugar and a 5’-phosphate attached to an adjacent sugar

what bonds are formed for the sugar phosphate backbone?

major groove allows things to come through and to it easier

difference between minor groove and major groove?

* bases
* ribose sugar
* phosphodiester bonds

what are the parts to make nucleotides for RNA?

adenine, guanine, cytosine, and uracil

what are the bases of RNA?

* messenger RNA (mRNA)
* ribosomal RNA (rRNA)
* transfer RNA (tRNA)
* noncoding RNA ( ncRNA, snRNA, snoRNA, sRNA)

what are the four different types of RNA with different functions, site of synthesis, and structure?

it is read to make proteins

what is coding?

peptide bonds

what bonds do proteins have to link amino acids together?

* carboxy group (C-terminal)
* amino group (N-terminal)
* side chain (R)

what are the parts of amino acid?

polar, non-polar, or charged depending on the side chain, environment, and such

what can amino acids be?

synthesis is semi-conservative where each daughter cell obtains one old and one new strand

how is the DNA synthesis like?

you need to mutate it where it can’t start, so you have OR

how can you prove that the OR is where replication starts?

mainly circular

how is DNA like in bacteria?

bidirectionally from a single origin replication fork where the DNA is unwound and will wait until both sides are done to separate

how does DNA replication occur in bacteria?

replicon

origin and is replicated as a unit (entire genome in bacteria)

DNA gyrase

relieves supercoiling of DNA produced as DNA strand are separated by helicases; separate daugther molecules in final stages of replication

DnaA (initiator protein)

initiation of replication; binds origin of replication (or/C)

DnaB

helicases (5’ to 3’); breaks hydrogen bonds holding two strands of double helix together; promotes DNA primase activity; involved in primosome assembly

SSB proteins

bind single-stranded DNA after strands are separated by helicases

DnaC

helicase loader; working with DnaA, directs DnaB (helicase) to DNA template

DNA primase

synthesis of RNA primer; component of primosome

DNA polymerase III holoenzyme

catalyzes most of the DNA synthesis that occurs during DNA replication; has 3’ to 5’ exonuclease (proofreading) activity

DNA polymerase I

removes RNA primers; fills gaps in DNA formed by removal of RNA primer

removes RNA primers

ribonuclease H

DNA ligase

seals nicked DNA, joining DNA fragments together

Tus

termination replication

topoisomerase IV

separation of chromosomes upon completion of DNA replication

DNA polymerase

what catalyzes synthesis of complementary strand of DNA?

5’ to 3’ to form phosphodiester bonds

what direction does DNA synthesis go?

* a template to direct synthesis of complementary strand
* a primer from either DNA or RNA strand
* dNTPs (dATP, DTTP, DCTP, dGTP)- deoxynucleotide triphosphates

what do polymerases require?

5; polymerase III

how many DNA polymerases does E. coli have and what polymerase plays the major role in replication?

DNA polymerase holoenzyme

* complex of 10 proteins
* 3 proteins form core enzyme

2 core enzymes in each polymerase

* catalyze DNA synthesis
* proofreading for fidelity

topoisomerase

breaks one strand of DNA; relieves tension from rapid unwinding of double helix, prevents supercoiling

primase

synthesizes short complementary strands of RNA primers needed by DNA polymerase

DnaA proteins bind oriC (origin of replication ) causing bending and separation of strands

what is the first event at the replication fork in E. coli?

DnaB and other helicases

what helps separate the strands of DNA in E. coli to allow SSB attach?

primase

what will synthesize RNA primer for the E. coli?

DNA polymerase I

what removes the RNA primers and fills those gaps with DNA?

yes

can multiple codons code for the same amino acid?

Proofreading (making sure it is all good)

what is carried out by DNA polymerase III?

removal of mismatched base from 3’ end of growing strand by exonuclease activity of enzyme

what happens during proofreading?

* replisome reaches the termination site (ter) on DNA

how does DNA replication in E. coli stop?

catenanes

what forms when two circular daughter chromosomes do not seprate

* use topoisomerase and catanenes
* cross-over occurring at the ter site

ways to break apart daughter chromosomes in the bacteria

5’ to 3’

what does the mRNA read?

tRNA, mRNA, rRNA

what RNAs used to help with the translation of mRNA

template strand of DNA and read in 3’ to 5’ direction

what directs RNA synthesis and how is it read?

promoter

* located at the start of the gene
* recognition/binding site for RNA polymerase
* functions to orient polymerase

leader sequence

* transcribed into mRNA but not translated into amino acids
* shine-delgarno sequence is needed for initiation of translation

N-formylmethionine, a modified amino acid used to initiate protein synthesis in bacteria

what does AUG code for?

genes

DNA sequences that code for tRNA and rRNA

single, large precursor

genes coding for rRNA are transcribed as what?

spacers

what is removed between coding regions of transcription, either by special ribonucleases and ribozymes?

no

do prokaryotes have introns and exons?

polycistronic mRNA

* found in bacteria and archaea
* contains directions for >1 polypeptide catalyzed by a single RNA polymerase
* has a shine degarno sequence

initiation, elongation, termination

steps of transcription

5 chains and catalyzes RNA synthesis

what are core enzymes composed of in most bacterial RNA polymerases?

sigma factor

what has no catalytic activity but helps the core enzyme recognize the start of genes?

holoenzyme

core enzyme + sigma factor; only this can begin transcription