micro exam 2

Chemotaxis

-response to gradients via comparisons via receptors

MCP

methyl accepting chemotaxis protein

Are the chemotaxis receptors spread through out or concentrated in one spot?

one spot- kinda like a nose

what happens if there is no gradient

random movement of runs and tumbles

CCW results in what

run

CW results in what

tumbles

What type of pathway is used for chemotaxis

signal transduction pathway

What is the default rotation of the flagella? is CheY phosphorylated in this state or not?

runs (ccw)
-not phosphorylated

does phosphorylation cause runs or tumbles?

tumbles

How are less tumbles produced when attractants are near by?

-the attracted substance binds
-this causes a change in conformation of CheW and CheA decreasing the rate of autophosphorylation
-This decreases the rate that CheY is phoshorylated
-since phosphorlation leads to tumbles, this decreases the number of tumble (cw) and increases the run (ccw)

What happens when attractants are not bound?

-CheW and CheA autophosphorylation and are dephosphorylated when they phosphorylate CheY
-CheW and CheA phosphorylate CheY
-When CheY is phosphorylated it causes tumbles (cw)
(the opposite of the default rotation ccw, runs)

CheW and CheA

autophosphorylate and phosphorylate CheY
+ decreased non-p CheW and CheA are caused by attractant bound, leading to runs
+p CheW and CheA are caused by no attractant bound, leading to tumbles

CheZ

desphosphorylates CheY

CheY-P

causes the flagella to rotate cw, tumbles

non p CheY causes the flagella to rotate

ccw, runs (its default roatation)

CheB

phosphorylates CheY

Without attractant:

series of runs and tumbles

With attractant

fewer tumbles due to decreased CheY phosphorylation

Chemotaxis Assay

to test if they are attracted or repelled
-open capillary tube

Aerotaxis example

algae that produces o2 in the center
-microbes that want to get near o2 are drawn to the algae

Phototaxis

movement in response to light

Gas Vesicles: a means of locomotion

-bac, archaea, cyanobacteria/ not Euk
-vesicles that expand or contract depending on where they need to orient themselves in the water column

microbial growth

increase in number of cells, not cell size

exponential growth

all cells doubling, becomes logarithmic

extremophiles

Archaea that live in extreme environments.

binary fission

A form of asexual reproduction in single-celled organisms by which one cell divides into two cells of the same size

oriC

origin of replication in binary fission

DnaA

Initiator, binds oriC
-binds and opens up double helix

Z ring formation

role in septation

Divisome

cell division apparatus
series of proteins in all bacteria essential for cell division

Fts proteins

filamentous Temperature Senstitive

FtsZ

forms Z ring

Zip proteins

ZipA anchors FtsZ ring to CM

Min protiens

help guide FtsZ ring to the midpoint of the cell

Proteins involved in FtsZ ring and cell division

FtsZ- form ring
FtsA- help anchor Z ring/ homologous to actin
ZipA- help anchor Z ring/actually anchors to CM

FtsZ mutant

mutant under high enough temps (other things can also cause this)
mutant form causes long filaments to form

Cell wall synthesis: PDG

process of adding CM and PDG to the new areas that were cleaved from seperation
-as the cell is growing osmotic pressure can cause a problem

pentapeptide
Lipid II
flippase
autolysin activity
Transglycosylase activity
Transpeptidation

pentapeptide

(NAG and NAM made in pieces in the cytoplasm)
5 amino acids
-the AA that are attached to NAM which is attached to NAG

Lipid II

Carrier molecule
-attaches to subunits attached to NAG and NAMs

Flippase

-allows piece to get transported across membrane

Autolysin

hydrolyzes bonds--\> makes hole in cell wall so you can put a new piece in

transglycosylase

-glues NAG and NAMs together
-can be inhibited by penicillin antibiotics

Transpeptidation

final step in cell wall synthesis
-Forms the peptide cross-links between NAMs residues in adjacent glycan chains

Transglycosylase vs transpeptidase

Transglycosylase: Connects NAGs and NAMs together (forms line of NAG and NAMs) (forms glyosidic bonds)

Transpeptidase: connects the AA side chains of NAMs together\= forms the cross links (forms peptide bonds)

Environmental factors effecting growth

Temp
pH
Osmolarity: halophile
Oxygen

Psychrophiles

what would be able to grow in the fridge

Mesophiles

moderate temperature loving microbes
15-45 c

Thermophiles

heat loving microbes
40-80

Hyperthermophiles

65-121 c
hot water springs
only archaea

3 cardinal temperatures

minimum, maximum, optimum
actual temps vary greatly for different environments/ microbes

growth rate vs temp

Minimum temp

membrane gelling; transport processes so slow that growth cannot occur
-if too cold proteins can not function: not flexible
-membrane less fluid
-microbes frozen\= don't have anything going across membrane

-microbes may not be growing at all--\> actually being persevered from falling apart

Minimum to optimum temp

enzymatic reactions occurring at increasingly rapid rates
-can still functions at these temps just not as fast as at its optimum temp

optimum temperature

enzymatic reactions occurring at maximal possible rate
-everything functioning at correct temp

maximum temperature

temperature above which bacterial growth will not take place
-protein denaturation
-collapse of the cytoplasmic membrane
-thermal lysis\= membrane so fluid it starts to come apart and stuff is leaking out

Example of psychrophile

Listeria monocytogenes

example of a mesophile and optimal temp

E.coil
39 c

Pasteurization

-exposure to a burst of heat: enough to bring down mirco org. number to an acceptable level

Staphyloccus aureus

Present on skin lesions
-some people have it as a commensal bacteria but can become dangerous if gets in cut or transferred to others

Refrigerator temps

may allow slow growth of spoilage bacteria; very few pathogens
-fungi grow first, have more tolerance than bac

Example of psychrotolerant

Listeria monocytogenes

psychrophiles proteins

flexible at lower temps
-more alpha helices and less B-sheets
-more polar & fewer hydrophobic AA's
-Fewer weak bonds & interactions b/w protein domains (do not need as much bonding)
-Antifreeze proteins

Does freezing kill microbes?

Ice often has microscopic pockets of liquid water
Freezing prevents microbial growth (does necessarily kill microbes tho)
-some liquid is still available

Thermophiles and Hyperthermophiles

greater than 65 c\= only pro survive

thermophiles: primarily pro
-optima\= greater than 45 c
-hot springs, compost, hot water lines, surface soils in full sunlight

Hyperthermophiles: mainly archaea
-optima- greater than 80 c
-only pro: mainly archaea
-no bac above 95 c
-up to 122 c
-volcanic &thermal vents, hot springs

What temps do you find euk and prokaryotes microog chart

Euk: protozoa, algae, fungi: 56-62 c
Pro:
Bacteria-
cyanobacteria 73 c
anoxygenic phototrophs 70-73
Chemoorgantrophs/ chemoliothrophs 95 c

Archaea: (extremeophiles)
chemoorganothrophs/ chemoliothrophs 122

Thermophiles: molecular adaptions in the cell

Proteins: stable at higher temps
-increased number of charged amino acids (increased bonding) & highly hydrophobic interiors
-proteins tethered to other parts of the cell
-chaperone proteins & protective solutes (various phosphates) help stabilize proteins

Genomes packed w/ numerous DNA-binding proteins
-stabilize DNA
-DNA more tightly coiled

What species is used for PCR? What is it used for?

Thermus aquaticus
Taq polymerase

most bacteria pH

6.5 to 7.5

fungi pH

5 or lower

cytoplasmic pH

around 7

cytoplasmic pH regulation

import/export of ions and acid shock proteins

acidophiles require \____ for membrane stability

protons

water activity

measure of how much water is available for use

osmolarity

measure of the number of solute molecules in solution and is inversely related to asubw

high/low concentration of solutes is osmotically stressful for microorganisms

high

halophiles

high NaCl concentrations

extreme halophiles

15-30%

osmophiles

higher sugar concentrations

halotolerant

tolerate wide ranges of osmotic pressure

halotolerant examples

staphylococcus aureus

halophile example

aliivibrio fischeri

extreme halophile

halobacterium salinarum

aerotolerant anaerobes

grow in oxygen while retaining a fermentation-based metabolism

macronutrients for growth

carbon, hydrogen, nitrogen, oxygen, phosphorus, sulfur

lithotrophs

electrons from inorganic materials

organotrophs

electrons from organic materials

autotrophs

carbon from CO2

heterotrophs

carbon from organic chemicals

photolithoautotrophs

light for energy, inorganic electrons, CO2 for carbon

fastidious organisms

needs something else besides normal carbon source

aerobic respiration

oxygen serves as the terminal electron acceptor

respiration

glycolysis, CAC, ETC

citric acid cycle

substrate-level phosphorylation

electron transport chain

oxidative phosphorylation

glycolysis products

atp and nadh

CAC products

produce atp, nadh, fadh2

ETC

produce atp via pmf

embden-meyerhoff parnas pathway

cytoplasm of cell, functions with or without oxygen

glycolysis stage 1

glucose converted to phosphorylated form that yields energy

glycolysis stage 2

make pyruvate and atp

ether-dourdorof pathway

alternate to glycolysis