Midterm 1

robert hooke

developed the microscope and drew the first descriptions of microorganisms

antoni van leeuwenhoek

amateur microscope builder known as a the father of microbiology

• called bacteria wee animalcules

spontaneous generation

the idea that life can emerge spontaneously from non-living materials

• was a prevailing concept for thousands of years

louis pasteur

disproved spontaneous generation

• created sterilization techniques

• understood that microbes did fermentation

• contributed to the advancement of vaccines

germ theory disease

the idea that microbes caused disease

koch’s postulates

1. the suspected pathogen must be present in all cases of disease and absent in healthy animals

2. the suspected pathogen must be grown in pure culture

3. cells from pure culture must cause disease in a healthy animal

4. the suspected pathogen must be re-isolated and shown toe be the same as the original

implications of Koch’s postulates

microbes are the cause of disease

limitations of koch’s postulates

• just because you can’t culture a pathogen doesnt mean it doesn’t cause disease

• some disease causing microbe can be present in healthy people but might only cause disease in certain people or conditions

three domains of life

• bacteria

• archaea

• eukaryotes

viruses

genetic elements that can only multiple within a living cell. fundamentally a different form of life.

LUCA

last universal common ancestor

RNA world hypothesis

Life on earth began with a self-replicating RNA world molecule

RNA world hypothesis evidence

• RNA can form intricate, stable structures that can carry out a wide range of chemical reactions and specifically bind many molecules

• proteins are still made today using RNA machinery such as tRNA and ribosomes

• many apparent relics from RNA world

main example of relics from RNA world

common biological molecules like ATP, NADP, FAD, and SAM are based on ribonucleotide components

RNA world → LUCA

1. RNA world

2. emergence of protein, DNA, and earliest cells (appearance of first life)

3. LUCA

presumed features of LUCA

• DNA replication, transcription, translation, cell division (central dogma)

• ATP served as energy intermediate

• had a lipid bilayer membrane

• anaerobic metabolism

• some other genes like ribosomal RNA which seem to have been conserved since LUCA (as well as genes that are now long lost)

chemotroph

derives energy from releasing bond energy from the chemical compounds

phototroph

absorbs light, and transforms it into chemical energy

the rise of oxygen on earth

the appearance of oxygen was likely due to the rise of photosynthetic bacteria that produced oxygen as a biproduct, therefore introducing it to the atmosphere

• first photosynthetic bacteria was cyanobacteria

why is the introduction of oxygen so important

oxygen is a great electron acceptor which gave rise to aerobic organisms that were able to produce energy more efficiently

• this efficiency is the cornerstone of complexity

evolution of eukarya

evolved from an archaea-like ancestor that engulfed an aerobic, respiring bacterium which became an endosymbiont and ultimately the mitochondria

plant emergence

A second event where an early eukarya engulfed a photosynthetic bacterium (cyanobacterium) which became the basis for the chloroplast

serial endosymbiosis hypothesis

complexity paved the way for endosymbiosis

• complex cell structure evolves early, facilitating endosymbiosis

symbiogenesis hypothesis

endosymbiosis caused complexity

• endosymbiosis occurs in an archael cell type, facilitating the evolution of cell complexity

evidence of endosymbiotic theory

DNA replication, transcription, and translation machinery of eukaryotes is more similar to archaea than bacteria

• mitochondria and chloroplasts have their own genomes, ribosomes, tRNA with similar sequences to proteobacteria and cyanobacteria

taxonomy

the science of classifying and naming biological organisms

phylogeny

the study of evolutionary relationships between different organisms

taxonomic hierarchy

• domain

• kingdom

• phylum

• class

• order

• family

• genus

• species

Carl Linnaeus

developed the system for classification using genus and species

three techniques of naming microbes

• descriptive characteristics

• honor a scientist

• physical properties and appearance

subspecies

a finer classification after species which is not always present

biotype

grouping based on physiological or biochemical difference from other members of the species

serotype

grouping based on specific surface antigens

strain

often used to refer to a specific isolate of a species

phylogenetic tree

visual means of showing predicted evolutionary relationships between different organisms

• evolutionary time goes from root to modern lineages

how to determine phylogenetic relationships by comparing DNA sequences

compare DNA sequences that are conserved amongst all organisms being compared

• the more differences in DNA, the more evolutionary distance

  • it is usually better to pick conserved genes with conserved functions that accumulate mutations slowly and randomly overtime

comparing DNA sequences of closely related organisms

they have more genes in common so you need to look for a difference

• need to compare multiple genes or a whole genome

comparing DNA sequences of distantly related organisms

have fewer genes in common with more sequence drift, so you look for a similarity

• use one or few very highly conserved genes

SSU rRNA sequencing

sequencing of the small subunit ribosomal RNA which is commonly a highly conserved gene that is useful for comparing things that are distantly related

• used often to infer phylogenetic relationship

woese tree of life

universal tree of life based on nucleotide sequence similarity in ribosomal RNA

16S rDNA

used to identify and quantify microbes in a complex sample

• gives you genus level, but not enough differences to distinguish between species

events that mess with analyses and phylogenetic tree creation

• horizontal gene transfer

• gene duplication/gene loss

• selective pressure

horizontal gene transfer

microbes acquiring foreign DNA mixed into genome alongside ancestral DNA or replaces native DNA sequences

gene duplication

random duplication of DNA that might lead to losses in one copy

selective pressure

DNA comparing mutating at different rates in different species due to selective pressure

two major differences between prokaryotes and eukaryotes

• prokaryotes are generally much smaller in size: roughly equivalent to a mitochondrion

• eukaryotes contain numerous membrane bound compartments and prokaryotes generally lack organelles entirely

surface area to volume ratio

affects how quickly cells exchange nutrients and waste in their environment

• therefore small cells generally grow more quickly

cocci

spherical bacteria

staphylococci

clusters of cocci

staphylococcus aureus

opportunistic pathogen often in cuts and a common example of antibiotic resistance

diplococci

pairs of cocci

neisseria gonorrhoeae

example of diplococci which causes gonorrhea

streptococci

chains of cocci

streptococcus pyogenes

example of streptococcus which causes a range of diseases including strep throat

bacilli

rod shaped bacteria

salmonella enterica

example of a rod shaped bacteria that is a common cause of food poisoning and typhoid fever

vibrio

comma shaped bacteria

• bent rod caused by one side growing faster than the other

vibrio cholerae

example of a vibrio bacteria which is the cause of cholera

helical bacteria

bacteria shape of tight helices (corkscrew) which helps with movement

helicobacter pylori

example of helical bacteria which is common found in the human stomach but might cause stomach ulcers and cancers

spirochetes

long spiral bacteria

• seem helical but are longer and more drawn out (looser spirals)

borrelia burgdorferi

example of spirochete bacteria which is the pathogen that causes lyme disease

appendage

stalk sticking out of cell

caulobacter crescentus

example of an appendaged bacteria used as a model system to study bacterial cell cylce, and asymmetric cell division

filamentous bacteria

elongated and thread like bacteria

chloroflexus aurantiacus

an example of filamentous bacteria which is photosynthetic but does not produce oxygen

• studied to understand the evolutionary origins of photosynthesis

monomorphic

The bacteria always has the same shape

• observed in most pure cultures of bacteria

pleomorphic

the same bacterium has multiple different morphologies

arthrobacter crystallopoietes

example of pleomorphic bacteria

• grows as rod during logarithmic grown

• becomes a coccus in stationary phase

why is the cell envelope important

it is the most common way to differentiate bacteria into two major categories

cell envelope

generic term used to describe the structures surrounding the cytoplasm

• can include cytoplasmic membrane, cell wall, outer membrane, S-layers, and other layers

roles of cell envelope

• maintains barrier with environment

• protects cell from stress

• allows transport of nutrients into cell and waste out of cell

• energy conservation and production

cytoplasmic cell membrane

primary barrier between the inner working of the cell and its environment

• acts as a permeability barrier, protein anchor, and site for energy conservation using proton motive force

phosphatidylethanolamine

common phospholipid in the cell membrane bilayer with an ethanolamine side chain and unsaturated fatty acid tails

peripheral membrane proteins

loosely associated from the membrane, often with the ability to detach but is never physically inside the membrane

integral membrane proteins

non-trans proteins that embed inside the membrane but don’t reach fully across to both sides

transmembrane protein

type of integral proteins that pass all the way through the membrane

diffusion

the net movement of a chemical down its concentration gradient in an entropically favorable manner

facilitated diffusion

diffusion of molecules across the membrane through a membrane protein that acts as a channel

• often very specific

sodium proton antiporter

exchanges H+ for Na+ by using the energy of H+ flow into cell to power Na+ efflux out of the cell

ABC transporters

also called ATP binding cassettes. Use ATP to power the transport of substances across the cytoplasmic membrane

• also one of the largest/oldest gene families in all phyla on earth

structure of ABC transporters

• 2 ATPase domains to provide energy

• transmembrane domains which form the selective channel

• substrate binding protein binds molecules with high affinity and delivers it to the channel (not usually directly connected to transporter)

common example of ABC transporter

BtuC for vitamin B12 uptake in E. coli

structure of vitamin B12 ABC transporter

• BtuF - substrate binding protein that binds to vitamin B12 and brings it to BtuC

• BtuC - transmembrane channel protein which allows B12 through

• BtuD - ATPase protein which generates the power used to allow vitamin B12 in

cell wall

present in the majority of bacterial cells to provide strength in order to prevent cells from bursting due to osmotic pressure

• also provides cell shape and rigidity

• made of peptidoglycan

Gram-positive bacteria

• thick cell wall

• no outer membrane

Gram-negative bacteria

• thin cell wall

• LPS outer membrane

peptidoglycan

a lattice like structure formed from chains of glycans linked together by peptide bridges

• sugar backbone contains alternating N-acetylglucosamine (NAG or GlcNAc) and N-Acetylmuramic (NAM or MurNAc) acid groups connected by beta(1,4) glycosidic bonds

• peptide crosslinks are short peptide chains from NAM which covalently link to the peptide from an adjacent chain by peptide bond

peptide section of peptidoglycan

• sequence can vary between species, but is conserved within a single organism

• D-isomer or amino acids are used (we only see L isomers in proteins)

• crosslinks are peptide bonds between position 3 and position 4

lysozyme

antibacterial enzyme widespread in nature and produced by the human immune system and many other species

• cleaves the peptidoglycan layer by breaking the beta-1,4 bond between MurNAc and GlcNAc in the backbone

cell wall of gram negative bacteria

• 1-2 peptidoglycan layers

• flexible and porous but still very strong

cell wall of gram positive bacteria

• thicker peptidoglycan layer, usually more than 15 layers

• contain interbridges which help connect different layers by helping create extra peptide crosslinks

• contain teichoic acids

teichoic acids

long polymers of glycerol phosphate or ribitol phosphate with attached D-glucose or D-alanine

• covalently attached to peptidoglycan or cytoplasmic membranes of Gram-positive bacteria to provide strength

• have a negative charge which helps trap divalent metal ions

characteristics of the cell wall

• porous and not generally a permeability barrier except to large molecules like protein and protein complexes

• dynamic; constantly being synthesized, degraded and remodeled

Steps of Gram staining

1. cells are stained uniformly with insoluble crystal violet-iodine complex which stains both Gram + and - cells purple

2. cells are decolorized with alcohol which gets rid of the purple in the Gram negative

3. cells are counterstained with pink safranin which stains both but is only visible in the Gram negative (purple of gram positive overrides)

mycoplasma pneumoniae

example of a bacteria that lacks a cell wall

• human pathogen that is an intracellular parasite

• doesn’t need a cell wall because their is minimal osmotic pressure within the host cell so it is unlikely to burst

• has a strong cell membrane to make up for the wall absence

Outer membrane

characteristic of Gram negative bacteria

• outer leaflet outside of cell wall that is made of LPS

outer membrane structure

asymmetrical lipid bilayer

• inner leaflet is comprised of phospholipid

• outer leaflet os exclusively LPS