bio prelim 1

lecture 1-22

whyis a. large surface to voume ratio facorable for bacteria

bc bacteria rely on diffusion for many nutrients/oxygen and want to maximize their surface area in relaton to their volume. if the surface area to volume is high then the nutrients can be spread to the entire cell more efficently

what is the basis for fluoresence microscopy

some chemical substances and proteins will emit light of a certain color when energized via lght with a certain wavelength

what are soe advantges of cryo-EM

• can visualize small cellualr structures like ribosomes

• sampples are flash frozen and thus providea perfect snapshot of a natural cell

what would u use to see corona virus

either an electron microscope or cryo-EM

what would u use to see ribosomes in their natural state

cryo-EM

what would u use to see large eukaryotic cells 

laser scanning confocal microscope

what would u use to see small bacterial cells

phase contrast microscope

what is likely the most important factor limiting bacterial size

nutrient diffusion limits the internal volume (if volume is too big, nutrients cannot diffuse efficiently)

two differecne between eukaryotic and prokaryotic cells

• prokaryotes do not have a special compartment for their DNA but eukaryotes do (nucleus)

• prokaryotic cells are typically smaller than eukaryotic celsl

what is the most useful way to assess micobial diversity in a gram of soil

• use metagenomics to assemble all bacterial genomes or their 16s gene that are in the soil

what are the three domains of life

archaea, eukarya, bacteria

proteobacteria

alpha= rhizobium, agrobacterium

gram negative

beta= meningitis (Neissera), thunderclap

gamma= ecoli, cholera, pseudomonas

actinbacteria

gram positive

antibiotics producer

• streptomyces

cyanobacteria

-gram negative

toxic bloom 

anacentor oof chloroplast

firmicutes

gram positive

• staphyloccocus

• bacilli subtillus forms endospore

• anaerobes important for GI tract

bacteriodetes

gram negative

breaks down complex foods like carbons, imporatatn in gut microbiota 

why has it been traditional diffcult to define species in bacteria

morphology amongst cells is not that diverse to classify bacteria by just looking at the cells

• convergent evolutionis rampant

how did molecular genetics and biology hep “define species of bacteria 

comparing the universal phylogentic maker, 16s rRNA, revealed relationships between groups of microbes

what was Woese’s revolutionary realization?

he thought he was working with bacteria but he was working with archaea even though they look alike they are comletely different lineages

by current understadning, where did eukaryotic ells come about

Aphaproteobacteria and an archaea formed together to form cells containing mitochondria

which pair from the five phyla are the most closely related according to phylogenetic tree

firmicutes adn proteobacteria

what do hopanoids do

they regualte membrane fluidity and stability in some bacteria

what are the names of the three phospholipid head groups

1. cardiolipin

2. phosphatidylglycerol

3. phosphatidylethanolamine 

uniporters

transport one molecule down one way

antiporters

one moleule in one way and anotehr moleule out another way

symporters

two types of molecules going in the same way

lac permease of e.coli

lac permease is a symporter protein that transports lactose into E. coli. this is part of active transport as it rewuires the enrgy from a proton motor force. this is an example of simple transport because t requires just the PMF

simple transport (include example)

powered by PMF example inludes LAc permease which sues a symporter to get lactose into e coli

example of group translocation

The phosphotransferase system (PTS) in E.coli is actively driven by the phosphate bond in phosphoenolpyruvate. a substance is chemically modified as it goes throught the channel protein. substnace that use the PTS system included Glucose, fructose , an mannose

ABC transporter

highly substrate selective, iver 200 different systems, reguires 3 htings, periplasmic binding protein, membrane spanning transporter and atp hydrolyzing protein

gram stain porcedure

1. stain with crystal violet= all cells turn purple

2. flood with iodine= cells still purple

3. decolorize wth alcohol= only positive are still purplle

4. counterstain with safranin= only gram negative are pink 

whats in peptidoglycan (murein in bacteria)

polysachardie back bine containe N-acetylglucoseamine, N-acetylmuramic acid

has peptide side chains that can crosslink such as Dap and D-ala, or D-ala and L-lys

osmosis

creates turgor pressure on the cell membrane and the cell wall prevents rupture

cell wall assembly

transpeptidation, glycosyltransferase 3, penicillin binding protein

transpeptidation occurs in gram negative directly binding amino acids to form peptides. in gram positive they are sometimes binded by an interbridge 

lysozome

enzyme that cleaves bonds at the beta-1,4 bonds of peptidoglycanbackbone

beta lactam antibiotics

binds to and inhbitis transpeptidation (penicllin binding proteins)

whats in the gram positive cell envelope

-up to 90% is peptidoglycan

• often have teichoic (lipoteichoic acid) which increase cell wall stability have cell wall reggualtory functions like lysozome regulation 

autolysinss

cut peptidoglcan bonds so that penicillin binding proteins can add new cell wall material 

gram negative cell envelope

• about 10% peptidoglycan 

• the outer membrane has lps that makes up most of the envelope

• bottom to top= cytoplasmic membrane, periplasm (that holds te cell wall made of peptidoglycan), then outer membrane

periplasm 

between the cytoplasmic membrane and the outer membrane 

houses the cell wall that is made of peptidogluycan 

outer membrane 

has LPS, Porins, proteins, 

Lipopolysacharide

made of three parts

Opolysachradie (0157), core polysacharide and Lipid A

LPS provokes a stong immune repsonse in humans

Lipid A

endotoxin for pathogens

porins:

allows for the passive diffsuin of small, hydrophillic molcuels such as amino acids, sugar, and ions thorugh the OM

what determine diffusion efficiency in the OM

both size and hydrophobicity

what is a good antibiotic for gram negatives and 2 poor ones

one good one is ampicillin

2 bad ones are penicllin and vancomycin 

Archaeal cell envelope

• archea dont have peptidoglycan, instead they have pseudomurein 

• they tyoucally lack an outer membrane 

• instead of the cell wall they have an S layer

S layer

pretty tough crystalline structure made of glycoproteins

pseudomurein

similar to peptidoglycan but lacks D-amino acids, has beta 1,3 bonds, not N-acetylmuramicacid but N-acetyltalosaminornic acid

examples of storage polymers

1. sulfur granule: energy storage for certain sulfur bacteria

2. glycogen: sotres carbon and energy, glucose polymer

3. phosphates: phosphates and enrgy storage

4. poly B- hydroxyalkanoate (PHA): polyester, carbon and energy storage (food storage)

ribosome

site of protein synthesis in all cells

carboxysome

protein shell that makes sure Co2 i near fixing enzyme, protects rubisco from coming in contact with oxygen

endospores

A vegetative cell that differentiates into a mother cell and an endospore

have dipicolinic acid, which promotes dessication

endospores are highly resistant to heat, dessicaiton, and radiation and harsh chemcials

when conditions are good they can germinate back into vegetiave cells 

what is dipicolinic acid

accounts for ten percent of spore mass

and it increases heat resistant by by binding to water molecuels

Glycocalyx: capusules and slime layers

• polysacharide layers

• helps with attachemnt (helps biofilms attach)

• protects against phagocytosis

• resists drying

• the slime layer is loosely attached whereas the capsule is tightly attacehd

Fimbria

they are short, filamentous protein structues and they assist in attachment

Pili

long filamenotus dynamic protein strucutes

assist in attachmetn

facilitate conjugation

type 5 pilli involved in twitiching motility (pili=long twitchers)

flagella

-long helical protein structure

enables swimming motility (think sperm)

able to rotate

describe three types of flagella

1. peritrichous= flagella coming from every which way

2. polar= one long strand coming from one end

3. lophotrichous= alot of strands from only one end

swimming motiltiy

flagellar-dependent motility in bacteria and archaea

can be either reversible or unidirectional 

examples of bacteria with non-motile and motile 

klebsiella pneumonia has no flagella so it oes not psread wheras enterobacter cloacae has swimming motiltiy so it spreads

examples of chemotaxis

osmotaxis: response to ionic strength

hydrotaxis= response to water

what can chemoreceptors sense

they can sense changes in chemical concentrtion over time

peritrichous flagella movement

run and tumble that leads to the random biased walk

polar flagella movent

think polar, they can go go bidirectional or unidirectional, stops thenreorients 

bacterial flagella

uses PMF to rotate

-swimming motility

helical filament composed of fagellin protein

archeal flagella

-swimming motilty

-helical filament composed of archaealin protein 

-uses atp to rotate

twitching motility

-requires surface attachment by type 4 pilus

• atp dependent pilus retraction 

• very slow

gliding motility 

• requres surface attachment 

• complex molecualr mechanism

• -requires Proton motor force for energy 

how is DNA replicated in the bacterial cell

helicase splits helix, rna primer binds and makes short complementary strand then DNA pol 3 comes and syntehsizes in the 3 to 5 prime direction. dna pol 1 replaces all the rna primers with DNA and then ligase comes and fills in the gaps with DNA

how do bacteria fit a 1.6 mm long chromosome into a 3 micrometer cell

dna is comapcted by supercoiling and sturcutural proteins

why is gyrase needed for replciaiton

DNa unwinding y helicase creates pressure on DNA downstream of the leading stradn replcation fork: gyrase “ounter unwinds” DNA to relieve this pressure

which enzyme synthesizes RNA during transcription 

RNA polymerase

true or false: bacterial RNA polymerase has few subunits and is distinct from archaeal and eukaryotic polymerases.

true

bacterial transcription

• the sequence of the newlymade RNA transcript is identical to the coding strand except swaps U for Ts

• rNTPS are incorpratedinstead of DNTPS

• no primer is required

where d sigma factors bind

-10 and -25 region of the promoter

whyy does E. coli have so many alternative sigma factors

to initiate transcription of different genes under different enviormental conditions

what is polycistronic RNA

multiple RNAs made in a single primary transcript

difference between primary and secondary RNA structure

• primary structure include covalent bonds while seoncary includes hydrogenbonds

whats the difference between rho-dependent and rho-independent terminaton of transcription

rho independent requires a stem-loop structure followed by a string of U’s, wherae Rho dependent requires a helicase and pasue site

what are the 5 ways bacteria can become resistant to antibiotics

1. modify the LPS and make it positive to colistin (polymyxin) cannot bind

2. decrease presence of porins so that antibacteria cannot attack the outer membrane(beta-lactams enter through porins so that blocks them from getting to the peptidoglycan)

3. Changing the target site for the antibiotic. methicillin-resistant S. aueres (MRSA) replace the protein transpeptidase with a resistant version so that penicillin cannot bind

4. destroy the antibiotic. betalactamses hydrolyze beta lacatams. another way to inactivate antibiotics is by adding a funcional group

5. remove the antibiotic using efflux pumps which use ATP r a proton gradient

rank the target of antibiotics

1. cell wall synthesis

2. transcription

3. translation

4. dna replication

5. outer membrane (gram negative)

who disovered the antibiotic penicllin

alexander fleming

how do beta lactamases work

they hydrolyze the beta-lactam ring of the beta-lactam antibiotic

most antiobiotics are isolated from where

soil microorganisms