MicroBio Midterm

scary!!

Ways microbes affect our lives

Decompose waste and recycle nutrients;

produce oxygen (photosynthesis);

make food and drink (bread, cheese, yogurt);

biotech and medicine (insulin, antibiotics);

normal microbiota (digestion, vitamins, protection);

cause disease

Scientific nomenclature

Binomial system: Genus species. Genus capitalized, species lowercase, both italicized or underlined (Escherichia coli, abbreviated E. coli)

Archaea

Prokaryotes, no peptidoglycan, often extreme environments, no known human pathogens

Fungi

Eukaryotes, chitin cell walls, heterotrophs that absorb nutrients (yeasts and molds)

Protozoa

Single-celled eukaryotes, no cell wall, heterotrophic, usually motile

Algae

Photosynthetic eukaryotes, cellulose cell walls

Viruses

Acellular; DNA or RNA genome in a protein coat; obligate intracellular parasites

Helminths

Multicellular parasitic worms (flatworms and roundworms)

Hooke

1665, observed cork and coined the word "cells"; early compound microscope; saw molds

Leeuwenhoek

1670s, first to see live microorganisms ("animalcules") using single-lens microscopes

Spontaneous generation

life arises from nonliving matter.

Biogenesis

life arises only from preexisting life

How was biogenesis proven?

Redi (flies and meat), then Pasteur's swan-neck flask (1861): broth stayed sterile until microbes could enter

Fermentation

Pasteur showed microbes convert sugars to alcohol or acids, usually without oxygen

Pasteurization

Mild heat to kill spoilage microbes and pathogens without ruining the product

Germ theory

Specific microorganisms cause specific diseases

Koch

Koch's postulates; linked specific bacteria to anthrax and TB

Jenner

First vaccine (1796): used cowpox to protect against smallpox

Lister

Introduced antisepsis in surgery using phenol (carbolic acid)

EID

Emerging infectious diseases: new, changing, or reappearing diseases with rising incidence (COVID-19, Ebola, antibiotic-resistant bacteria)

Prokaryote

no nucleus (nucleoid), no membrane-bound organelles, small (1-10 um), 70S ribosomes, circular chromosome, peptidoglycan walls.

Eukaryote

true nucleus, organelles, larger, 80S ribosomes, linear chromosomes

Three basic bacterial shapes

Coccus (sphere)

bacillus (rod)

spiral (vibrio, spirillum, spirochete)

Coccus arrangements

Diplococci (pairs)

streptococci (chains)

tetrads (4)

sarcinae (cube of 8)

staphylococci (clusters)

Bacillus arrangements

Diplobacilli (pairs)

streptobacilli (chains)

coccobacilli (short ovals)

Main prokaryotic structures

Cell wall, plasma membrane, cytoplasm, ribosomes, nucleoid, plasmids, capsule/glycocalyx, flagella, fimbriae, pili, inclusions, endospores

Flagella function

Motility (movement toward or away from stimuli); made of flagellin; parts: filament, hook, basal body

Flagella arrangements

Monotrichous (one)

amphitrichous (one at each end),

lophotrichous (tuft),

peritrichous (all around);

atrichous = none

Fimbriae

Short, numerous hairlike projections for attachment to surfaces and host cells

Pili

Longer, fewer; conjugation pili transfer DNA between cells; also some twitching motility

Cell wall function

Maintains shape, protects against osmotic lysis, provides structure

Peptidoglycan

Chains of NAG and NAM cross-linked by peptides; makes up bacterial cell walls

Teichoic acid

Found only in Gram-positive walls; aids rigidity and ion movement; lipoteichoic acid anchors wall to membrane

LPS (lipopolysaccharide)

In outer membrane of Gram-negative bacteria; lipid A is the endotoxin, O polysaccharide is an antigen

Gram-positive wall

Thick peptidoglycan, teichoic acids, no outer membrane

Gram-negative wall

Thin peptidoglycan, outer membrane with LPS, periplasmic space

Gram stain outcomes

Gram-positive: purple (keeps crystal violet).

Gram-negative: pink/red (loses crystal violet, takes up safranin)

Gram stain steps

Crystal violet, iodine (mordant), alcohol decolorizer, safranin counterstain

Archaea cell wall

Pseudomurein or other polymers; no true peptidoglycan

Mycobacterium cell wall

Waxy mycolic acids; acid-fast

Mycoplasma cell wall

None; sterols in membrane for stability

Nocardia cell wall

Contains mycolic acids; weakly acid-fast

Plasmid

Small circular extra-chromosomal DNA; not essential but can give advantages (resistance, toxins)

Nucleoid

Region of a prokaryotic cell holding the chromosome

Endospore

Dormant, highly resistant structure formed by Bacillus and Clostridium when nutrients run out

Nucleus

Eukaryotic organelle that houses DNA and controls cell activity

Nucleolus

Inside nucleus; makes rRNA and assembles ribosomes

Catabolic reaction

Breaks molecules down, releases energy (glycolysis, hydrolysis)

Anabolic reaction

Builds molecules, requires energy (protein synthesis, dehydration synthesis)

Enzyme

Protein catalyst that lowers activation energy

Active site

Region of enzyme where the substrate binds

Cofactor

Inorganic helper (ions like Mg2+, Zn2+) needed for enzyme activity

Coenzyme

Organic helper (NAD+, FAD, vitamin derivatives)

Effect of changing enzyme or active site

Heat, pH, or mutation can denature the enzyme or alter the active site shape, so substrate no longer fits and function drops. Missing cofactor or coenzyme also stops activity

Competitive inhibition

Inhibitor mimics substrate and blocks the active site

Noncompetitive inhibition

Inhibitor binds an allosteric site and changes the enzyme's shape

Feedback inhibition

End product of a pathway inhibits an early enzyme in that pathway

Cellular respiration

uses electron transport chain and an external final electron acceptor, high ATP.

Fermentation

no ETC, organic final acceptor, low ATP

Cellular respiration pathway and products

Glycolysis, Krebs cycle, electron transport chain; produces ATP, CO2, H2O

Photosynthesis pathway and products

Light reactions (light to ATP, NADPH, O2) and Calvin cycle (CO2 to sugar)

ATP yield of fermentation

2 ATP net (from glycolysis only)

Fermentation pathways and end products

Alcohol fermentation: ethanol + CO2. Lactic acid fermentation: lactic acid. Others: mixed acid, butanediol. All regenerate NAD+

Chemoheterotroph

Energy from chemicals, carbon from organic compounds

Chemoautotroph

Energy from chemicals, carbon from CO2

Photoheterotroph

Energy from light, carbon from organic compounds

Photoautotroph

Energy from light, carbon from CO2

Aerobic respiration

O2 is final electron acceptor (most ATP).

Anaerobic respiration

other inorganic acceptor (nitrate, sulfate, carbonate), less ATP

Microbial growth

Increase in number of cells (binary fission), not cell size

Temperature requirements

Each microbe has a minimum, optimum, and maximum; too cold slows enzymes, too hot denatures them

Psychrophile

Cold-loving; grows near 0 C or below; optimum about 15 C

Psychrotroph

microorganisms that grow at low temperatures (7°C and below) and have a maximum growth temperature above 20°C. They are widespread in natural environments and foods, where they can outgrow mesophilic organisms and cause spoilage of refrigerated foods.

Mesophile

Moderate temps, optimum about 37 C; most human pathogens

Thermophile

Heat-loving; optimum roughly 50-60 C

Hyperthermophile

Extreme heat, optimum 80 C or higher; usually Archaea

Acidophile

Grows best at acidic pH (below about 5.5)

Neutrophile

Grows best near neutral pH (about 5.5-8); most bacteria

Alkaliphile

Grows best at alkaline pH (above about 8)

Osmotic pressure

Pressure needed to stop net water movement across a membrane; water moves toward higher solute

Isotonic solution

Equal solute inside and out: no net water movement

Hypotonic solution

Less solute outside: water enters, cell swells and may lyse (wall protects bacteria)

Hypertonic solution

More solute outside: water leaves, cell shrinks (plasmolysis); basis of salt and sugar preservation

Obligate aerobe

Requires oxygen

Obligate anaerobe

Killed by oxygen

Facultative anaerobe

Grows with or without oxygen, better with it

Aerotolerant anaerobe

Does not use oxygen but is not harmed by it

Microaerophile

Needs low oxygen levels

Growth location in thioglycolate tube

Obligate aerobe: top.

Obligate anaerobe: bottom.

Facultative: throughout, densest at top.

Aerotolerant: evenly throughout.

Microaerophile: just below the surface

Biofilm

Community of microbes attached to a surface in a slimy extracellular matrix

Biofilm significance in environment

Nutrient cycling, bioremediation, wastewater treatment; also clogs pipes and causes corrosion

Biofilm significance in health and clinical settings

Dental plaque, catheters, implants, cystic fibrosis lungs; highly resistant to antibiotics and immune defenses; contributes to HAIs

Sepsis

Presence of pathogens or toxins in blood or tissue

Asepsis

Absence of significant contamination

Sterilization

Removal or destruction of all life, including endospores

Disinfection

Removing pathogens from inanimate objects

Antisepsis

Removing pathogens from living tissue

Degerming

Mechanically removing microbes from a limited area of skin (scrubbing, alcohol wipe)

-cide

kills (bactericide).

-static

inhibits growth; reversible (bacteriostatic)