L6+7: bacteria structure + function

what are 4 ways bacteria are phenotypically different

morphology, size, colour, smell

describe the most common bacteria morphologies

cocci

rods

curved

spiral

exotic

explain the advantages of the small bacteria size

large SA:V ratio- nutrient exchange + growth rate, higher IC nutrient concentration

what are 4 pigments produced by bacteria + their roles

prodigiosin: immunosuppressant

staphylocanthin: antioxidant + detoxifies ROS

violacein: antioxidant + detoxifies ROS

pyocyanin: cytotoxicity, neutrophil apoptosis, ciliary dysmotility, proinflammatory

what are 2 examples of odors resulting from bacterial metabolism

degradation of human apocrine secretory products (leucine → isovaleric acid by staph; production of propionic acid by propionibacteria)

decarboxylation of amino acids to produce polyamines (putrescine, spermidine, cadaverine; role in bacterial physiology)

describe the principle of the gram stain

crystal violet penetrates bacterial surface

iodine complexes with crystal violet to fix it

washed with alcohol

counter stain with safranin

what is a gram +ve bacteria

no outer membrane + thick cell wall

what is a gram -ve bacteria

outer membrane + thin cell wall

what is an exception to the gram stain

mycobacteria

what are 3 structures that can be bound to the outer membrane or cell wall

s-layers

capsules

exopolysaccharides

what are s-layers

facultative structures (don’t exist in most model organisms)

non covalently bound to cell surface.

self assembling proteinaceous crystalline arrays

what are capsules

most made of polysaccharides

some made of aa(poly-g-D-glutamate),

covalently bound to cell wall/outer membrane

confer resistance to host phagocyte/bacteriophage + keep environment hydrated

what are exopolysaccharides

homo or heteropolysaccharides

non covalently attached to the cell surface

important for biofilm formation

some are economically important (xanthan gum in ice cream, toothpaste, salad dressing, hydrogels)

what are the key components of the outer membrane

phospholipids

proteins inc. porins (trimeric assembly for solute transport)

lipoproteins (Braun lipoprotein/Lpos) covalently linked to peptidoglycan (others like ompA bind non covalently)

LPS (endotoxin): potent activator of the immune system (septic shock)

what is peptidoglycan

elastic 3D network, subcellular compartment

dynamic regulation of exchanges with the environment

what are the roles of peptidoglycan

cell shape

scaffold for display of polymers + proteins

exoskeleton- resistance to osmotic stress

what is the composition of peptidoglycan

glycan chains alternating N-acetylglucosamine (GlcNAc) + N-acetylmuramic acid (MurNAc) substituted via short peptides (L- and D- amino acids)

structure conserved but composition differs between bacteria

what are the key components of the cytoplasmic membrane

phospholipids- unsaturated FA that modulate membrane fluidity + permeability

hopanoids (equivalent to sterols in eukaryotes)- modulate membrane fluidity + permeability

proteins (transporters, sensors, etc)- ion, protein, nutrient transport

what are features of bacterial chromosomes

always dsDNA

always circular chromosome in the vast majority of bacteria

variable size: 0.5 - 14.8 Mbp

organised as a nucleoid

supercoiled around histone-like proteins

what are features of plasmids

always dsDNA, usually circular

variable copy number 1-several hundreds

size between 2 - 600 kbp

can be (self)-transferable (horizontal transfer)

carry resistant genes

how does bacterial gene structure differ to eukaryotes

no introns- instead continuous coding sequence (open reading frame/ORF)

relitively small

what are operons

one promotor with several ORFs

how transcription initiated in bacteria

1. RNA polymerase (α₂ββ’σω) scans DNA forming a loose complex

2. the σ factor binds to a two specific sequence upstream of the start codon (closed complex)

3. DNA is unwinded allowing the formation of the open complex. transcription starts + the σ factor is released

how is transcription terminated in bacteria (rho independent)

topology of DNA triggers polymerase release:

1. requires palindromic GC-rich region upstream of an AT-rich sequence.

2. once the GC-rich region has been transcribed, it forms a hairpin structure that makes RNA pol fall apart; helped by AT-rich sequence (few H bonds)

how is transcription terminated in bacteria (rho dependent)

1. rho proteins (275kDa hexamer) recognises + binds to 72 residues GC-rich

2. thanks to RNA-dependent ATPase activity, wraps downstream RNA around itself. once it reaches polymerase Rho unwinds RNA-DNA duplex + releases RNA polymerase

how does transcription differ in pro+eukaryotes

transcription site (nucleus vs cytoplasm)

1 RNA pol in pro, 3 in euk

termination involves AAUAAA seq in euk (mRNA cleavage)

mRNA modified in euk (polyA, splicing, cap)

how is translation different in prokaryotes and eukaryotes

coupled with transcription in prokaryotes

ribosomes in prokaryotes are 70S with a 50S large subunit and a 30S small subunit

ribosomes in eukaryotes are 80S with a 60S large subunit and a 40S small subunit

the 40S subunit is guided by the 5’ cap on mRNA

30S subunit recognises the shine-Dalgarno sequence

eukaryotic translation is inhibited by cycloheximide

explain the concept of metabolic diversity in bacteria

extremely diverse energy, carbon, and electron source