slide set 2 - prokaryotic structure and function: bacteria and archaea

classification schemes + basis

3 domains based on ribosomal RNA comparison

main domains

bacteria (true bacteria)

archaea

eukarya (eukaryotes)

prokaryotes (examples, differences from eukaryotes)

lacks internal membrane

different in size + simplicity

text uses bacteria and archaea

bacterial arrangements

size, shape, arrangement

shape

round or rod shaped

arrangement

clusters

size

varies

common shapes

coccus, bacillus, vibrio, spirillum

coccus

spherical

bacillus

rod

vibrio

curved rod

spirillum

spiral

spriochete

thin, coiled, corkscrew

budding and appendaged

stalks and hyphae

filamentous

long, forms filaments

haloarchaea

archaea salty: flat, square shapes

stella

star-shaped

many prokaryotes shapes are

pleomorphic - many shapes

arrangements

diplo

strepto

staphylo

tetrads

sarcina

diplo

pairs

strepto

chain

staphylo

clusters

tetrads

4

sarcina

8, cube

bacterial cell common features

cell envelope (3 layers), cytoplasm, external structures

inclusions

not organelles, they are storage granules

inclusion body membranes (layers, composition and names)

single layered membrane

made of protein or lipids

called microcompartments

what do inclusion bodies store (5)

carbon, glycogen, amino acids, phosphate, sulfur, others

carbon storage in inclusions

PHB - poly-B-hydroxybutyrate

carbon and energy storage (bioplastics)

amino acid storage in inclusions

cyanophycin granulaes

phosphate storage in inclusions + function

polyphosphate (volitin granules)

ATP synthesis, DNA, RNA, plasma membrane

sulfur globules in inclusion functions

sulfur + energy storage (photosynthesis)

microcompartments function + composition + membranes

not membrane bound

have compartments for certain functions

carboxysomes

what are carboxysomes and what do they contain

CO2 fixing bacteria

contain rubisco enzyme to do this

gas vesicles (composition + function)

protein, filled with gas

used by microbes positioning themselves in a water column

what is the purpose of microbes positioning themselves in a water column

photosynthetic microbes, different O2 concentrations

magnetosome (what type of domain are they in, function)

found in aquatic bacteria, act as a compass

what helps magnetosomes function as a compass

magnetite (Fe3O4) particles help orientation in Earth’s magnetic field

ribosome composition

protein/RNA structures which are complex

bacterial ribosomal RNA

complex protein/RNA structures

sites of protein syntehsis

what does S in microbio stand for

Svedburg unit

svedburg in bacterial and archaea ribosome

50+30 = 70S

svedburg in eukaryote

60+40 = 80S

small rRNA subunit

16S = 30S

large rRNA subunit

23S + 5S = 50S

nucleoid (membrane, contents, DNA, and proteins)

not membrane bound

1 circular, double-stranded DNA

supercoiled + nucleoid-associated proteins - help with folding

where chromosome associated proteins are

plasmids (what are they, typical locations)

extrachromosomal DNA, small closed DNA molecules

Found in: bacteria, archaea, fungi

what do plasmids carry

antibiotic resistance, virulence factors, metabolic genes

bacterial cell envelope

1. plasma membrane

2. cell wall

3. layers outside the cell wall

plasma membrane location and functions

encompasses the cytoplasm, selectively permeable barrier, interacts with external environment

plasma membrane composition + requirement

absolute requirement for all living organisms

phospholipid bilayer, proteins, hopanoids

how does the plasma membrane interact with the external environment

receptors for detection of and response to chemicals in surroundings, transport systems, metabolic processes

lipid composition and function

phospholipids composed of fatty acid esters of glycerol

amphipathic

glycerol linkage in lipids

third OH of glycerol is linked to a phosphate linked to a phosphate forming a phosphoester bond

lipid saturation

saturation levels of membrane lipids reflect environmental conditions such as temperature

membrane structure

proteins, lipid bilayer + floating proteins, hopanoids (not sterols)

lipid bilayers with floating proteins features

amphipathic lipids

• polar ends (hydrophilic - interact with water)

• non-polar tails (hydrophobic - insoluble in water)

membrane protein types

peripheral, integral

peripheral proteins

loosely connected to membrane, easily removed

integral proteins

embedded within membrane, carry out important functions

hopanoids (exception, function, location)

not sterols

stabilize membrane

found in petroleum

bacterial lipids (exceptions, what do they contain)

no sterols

have sterol-like molecules + hopanoids

fluid mosaic model (what is is and what is happening)

lipid bilayers with floating proteins

individual lipids and proteins form a mosaic which is free to change constantly

archaeal membrane similarities + differences

chemistry varies between organisms, function and properties are related

archaea linkage in phospholipids

ether

bacteria and eukarya linkage in phospholipids

ester

archaeal lipids features

no fatty acids, some have isoprenes

archaeal membrane layers

monolayers or lipid bilayer

bacteria vs eukaryotes membrane stabilizer

bacteria → hopanoids

eukaryotes → sterols

functions of the plasma membrane

permeability barrier, protein anchor, energy conservation

plasma membrane permeability barrier functions + exceptions

• polar and charged molecueles must be transported

• transport protein accumulate solutes against the concentration gradient

• prevents leakage

plasma membrane protein anchor function

holds transport and sensor proteins in place

energy conservation of plasma membrane

charge separation by pumping H+ across the membrane (proton motive force aka PMF)

permeability from high to low

water, glycerol, tryptophan, glucose, chloride ion, potassium ion, sodium ion

facilitated diffusion (carrier, concentration gradient, transporters, most prominent in which domain)

• membrane-bound carrier molecules (aka permeases)

• requires smaller concentration gradient for significant uptake

• effectively transports glycerol, sugars, and amino acids

• more prominent in eukaryotic cells than bacteria or archaea

active transport systems and energy requirements

a. simple transport

b. group translocation

c. ABC system

require energy in some form

what kind of energy is used in active transport systems

proton motive force (h+) or ATP

simple transport (buddies and protein)

single protein needed

transport with co-transport (H+)

group translocation (buddies and protein, transport + system)

series of proteins needed

transport by conversion of energy rich compound (phosphotransferase system)

ABC system (protein requirements)

requires 3 proteins: substrate-binding, transporter, ATP hydrolase

simple transport (facilitation, ions)

• major facilitator superfamily

• use ion gradients to cotransport substance

ion gradients in simple transport

protons

symport - two substances both move in the same direction

antiport - two substances move in opposite direction

simple transport driver

symport or antiport driven by a proton gradient

ABC transporter acronym

atp binding cassette transporter

ABC transporters are observed in which domains

bacteria, archaea, and eukaryotes

ABC transport composition (in specific domains)

2 hydrophobic membrane spanning domains

2 cytoplasmic associated ATP binding domains

substrate (solute) binding domains

ABC transporter process

1. after binding solute, solute-binded protein approaches ABC transport

2. solute-binding protein attaches to transporter and releases solute energy from ATP hydrolysis from membrane

group translocation (most common system, movement source, what happens to the molecule)

-energy dependent transport

-chemically modifies molecule during entrance into the cell

-most common system: phosphoenolpyruvate: sugar phosphotransferase system (PTS)

type iii secretion system (what kind of bacteria is it found in, what does it do, where are proteins found)

• gram neg bacteria

• transports proteins out of the cell

• proteins are found in plasma and outer membranes

why is iron uptake needed, and what are some barriers to it

microorganisms require iron

ferric iron is insoluble, making uptake difficult

what aids in iron uptake

microorganisms secrete siderophores which complexes with ferric ion, transporting it into the cell

cell wall function

maintain cell shape and protect from osmotic pressure

bacteria cell wall component

peptidoglycan

archaeal cell wall component

pseudomurien

peptidoglycan (other name, uniqueness, composition)

• murien

• unique to bacteria

• made of glycan chains, cross-linked by short peptide

peptidoglycan shape

meshlike polymer of identical subunits forming long helical strands

peptidoglycan composition

two alternating sugars

alternating D- and L- amino acids

3 of 4 amino acids are non protein AA

alternating sugars

N-acetylglucosamine (NAG)

N-acetylmuramic acid (NAM)

peptidoglycan strands unique features

can form interbridges

peptidoglycan sacs- interconnected networks
various structures occur

gram positive cell wall composition

mainly made of peptidoglycan, some have protein layer on surface

has teichoic acids