BIOS 3220 Exam 1

Prokaryotes

lack a true membrane delimited nucleus

Eukaryotes

have membrane-enclosed nucleus, more morphologically complex, larger

Three domain system

Based on comparison of ribosomal RNA genes- Bacteria, Archaea, Eukarya

Domain bacteria

Usually single celled, cell wall with peptidoglycan, ubiquitous

Domain archaea

lack peptidoglycan, unique membrane lipids and metabolic characteristics, extreme environments, highly diverse, features in common with eukarya and bacteria, non pathogenic

Eukara microorganisms

Protists and fungi

Protists

catch all for Eukarya, generally larger than prokaryotes

Fungi

Yeast and mold

Acellular infectious agents

viruses, viroids and satellites, prions

viruses

smallest microbe, requires host cell to replicate, causes disease

Viroids and satellites

infectious agent composed of RNA

prions

infectious proteins

Swartkoppie chert

3.5 billion year old microbial fossil

Early molecules

RNA surrounded by liposomes, protein and hereditary functions

Ribozymes

RNA molecules that perform cellular work, functional as RNA

Endosymbiotic hypothesis

mitochondria and chloroplasts originated from endosymbiont- bacteria engulfed, have own prokaryotic DNA

RNA

associated with ribosome, catalytic in protein synthesis, may be precursor to double stranded DNA, regulate gene expression, very fragile

16 S RNA

1,500 nucleotide molecule, structural role in ribosome, scaffolds position of ribosomal proteins, highly conserved and variable regions

Evolutionary distance

calculated using aligned small subunit ribosomal RNA sequences, can’t measure time of divergence

LUCA

root of modern life, archaea and eukarya developed independently of bacteria

Horizontal gene transfer

increases gene pool within same generation in bacteria and archaea, donor to recipient

van Leeuwenhoek

first person to observe and describe microorganisms accuratelu

spontaneous generation

false idea that living organisms can develop from nonliving matter

Pasteur

Disproved spontaneous generation theory by blocking entrance to non-living material, showed that microorganisms did fermentation, developed pasteurization, showed that microorganisms cause disease

Miasma theory

theory that disease is caused by foul air and bad smells

Lister

Provided evidence that microorganisms were agents of disease by developing surgery hygiene practices to prevent microorganisms from entering wounds

Koch

established relationship between anthrax poisoning and Bacillus anthracis

Koch’s postulates

Microorganism must be present in every case of disease and absent in health, grown in pure culture, same disease must result from microorganism grown in pure culture, same microorganisms must be isolated from diseased host

Koch’s postulates limitations

Some organisms can’t grow in pure culture, ethical issues, asymptomatic carriage, co-infections, microbe imbalance diseases

Taxonomy

Science of biological classification- classification, nomenclature, identification

Gene formatting

abcD

Protein formatting

AbcD

Common bacterial shapes

cocci and rods

diplococci

pairs of cocci

streptococci

chains of cocci

staphylococci

grape-like clusters of cocci

tetrads

four cocci in a square

sarcina

cubic formation of eight cocci

bacilli

rods

coccobacilli

very short rods

streptobacilli

chains of rods

Vibrios

comma shaped bacterial structure

Spirilla

bacterial structure, rigid helicies

Spirochetes

bacterial structure, flexible helicies

Mycelium

bacterial structure, long filaments

Pleomorphic

bacterial organisms that are variable in shape

Average rod size

1.5-1.1 X 2-6 um

bacterial genome size

500,000 bp to 10,000,000 bp

Surface to volume ratio

bacterial cells are small, metabolic and nutrient uptake processes occur on surface

Bacterial cell common features

Cell envelope, cytoplasm, external structures

Bacterial plasma membrane

Semi-permeable, metabolic processes, interaction with external environment- lipid bilayer with floating proteins

phospholipids

polar hydrophilic heads, non polar hydrophobic tails, form bilayers

Peripheral membrane proteins

20-30%, loosely connected, easily removed

Integral membrane proteins

70-80%, embedded within membrane, amphipathic, carry out important functions

Amphipathic

possessing both hydrophobic and hydrophilic qualities

Saturated phospholipids

no double carbon bonds, less fluid

unsaturated phospholipids

double carbon bonds, more fluid

Hopaniods

stabilize membrane in bacteria

Organic macronutrients

C, O, H, N, S, P

Cationic macronutrients

K, Ca, Mg, Fe, serve as enzymes and biosynthesizers

Macronutrients

Required in large amounts

Micronutrients

Mn, Zn, Mo, Ni, Cu, required in trace amounts, serve as enzymes and cofactors

Growth factors

organic compounds, cell components or precursors that cell cannot synthesize, must be supplied by environment

Common growth factors

Amino acids, purines and pyrimidines, vitamins, heme

Uptake of nutrients

Passive diffusion, active transport, group translocation, endocytosis

Passive diffusion

Molecules move from higher to lower concentration without energy

Facilitated diffusion

Carrier proteins move molecules from higher to lower concentration without energy, smaller concentration gradient required, glycerol, sugars, AAs

Active transport

Energy dependent, ATP or PMF used, against concentration gradient, concentrate molecules inside cell

Primary active transport

utilizes ABC transporters and ATP to move molecules against concentration gradient

ABC transporter

2 hydrophobic membrane spanning domains, 2 cytoplasmic associated ATP binding domains, substrate binding domains

Secondary active transport

Uses ion gradients to co-transport substances

Symporter

Moves two molecules in same direction

Antiporter

Moves two molecules in different directions

Group translocation

Energy dependent, chemically modifies molecules entering cell

PTS group translocation

transports sugars, Enzyme 1 and HPr always same, enzyme 2 varies depending on substrate

Iron uptake in microorganisms

Ferric iron transported into cell in complex with siderophores

Ferric iron

very insoluble, uptake difficult

Bacterial cell wall functions

shape, prevent osmotic lysis, protection, pathogenicity

Gram positive

Stains purple, peptidoglycan 20-80 nm

Gram negative

Stains pink, contains outer membrane, peptidoglycan 2-7 nm thick

Periplasm

Area between peptidoglycan and plasma membrane

Peptidoglycan monomer

NAM glycocydically bonded to NAG, alternating D and L AA peptide strand

Peptidoglydican crosslinking

direct or through peptide bridges

Transpeptidation

formation of cross-links between peptidoglycan monomers that build bacterial cell walls

Peptidoglycan variation

Composition of linkage, linkage, AA at 3

Composition of linkage variation peptidoglycan

direct or bridge

3 AA variation peptidoglycan

DAP, L-Lys, L-Hsr

Linkage variation peptidoglycan

3-4 or 2-4

enantiomers

forms of amino acids, L or D

L amino acids

utilized by ribosomes in protein translation

D amino acids

rare outside of cell walls

Glycosidic bond

bond between NAM and NAG sugars

Beta glycosidic bond

Bonded hydrogen and hydroxyl

Alpha glycosidic bond

bonded hydrogen and hydrogen or hydroxyl and hydroxyl

Gram positive cell walls

Primarily peptidoglycan, may contain covalently connected teichoic acids

teichoic acids

polymer of alternating phosphate/sugar groups, maintain cell envelope, protection, bind to host cells, covalently connect to peptidoglycan and lipoteichoic acids

Periplasmic space gram positive

between plasma membrane and cell wall, smaller, few proteins, sortase

Gram positive cell wall proteins

important for virulence, covalently connect to peptidoglycan through T residue by sortase enzyme, have sequence LPXTG

Gram negative cell walls

Outer membrane composed of lipids, lipoproteins, lipopolysaccherides, no teichoic acids, inner/plasma membrane

Gram negative peptidoglycan

2-7 nm, 5-10% of cell wall weight