Lecture 1: Microbiology Basics

microorganisms (microbes)

microscopic living organisms (with the exception of viruses)

prion

infectious protein particle (no DNA/RNA) that can infect the nervous system in humans and animals

CJD

example of a prion that infects humans

virus

infectious nucleoprotein particle (contains DNA and RNA with a capsid protein coat) that can infect all organisms

archaea

unicellular prokaryotes that live in extreme environments and are more similar to eukaryotes (not known to be pathogenic)

bacteria (eubacteria)

unicellular prokaryotes that can be pathogenic or symbiotic (most well known microbes)

eukaryotic cells

have a nucleus and organelles; includes protists and fungi (may be unicellular or multicellular)

protozoa

animal-like protists

algae

plant-like protists

yeast

unicellular fungi

mold

multicellular fungi

1 um

size of prokaryotes (archaea and bacteria)

10-100 um

size of eukaryotic cells

viroids

RNA particles that only infect plants

nucleus

structure of eukaryotic cells that houses the DNA and is the site of transcription

ribosomes

structure of eukaryotic cells that is the site of protein synthesis

mitochondria

structure of eukaryotic cells that is the site of energy production (ATP synthesis)

lysosome

structure of eukaryotic cells that is the site of cellular digestion

endoplasmic reticulum (ER)

structure of eukaryotic cells that is an extension of the outer membrane of the nucleus (the site of protein synthesis, modification, and packaging)

nucleoid

structure of prokaryotic cells that is the region that contains DNA with proteins (chromosome)

plasmid

structure of prokaryotic cells that is extrachromosomal DNA (circular)

cell envelope

structure of prokaryotic cells that includes the cell membrane, cell wall, and another layer

cell membrane, ribosomes, cytoplasm

What cellular components are common between prokaryotic and eukaryotic cells?

cell wall

layer outside of the plasma membrane in bacterial cells; composed of peptidoglycans

peptidoglycans

sugar chains connected by peptides; makes up the cell wall in bacterial cells

gram positive

bacteria with a thick cell wall (stains purple)

gram negative

bacteria with a thin cell wall sandwiched between 2 membranes (stains pink)

lipopolysaccharide (LPS)

found in the outer membrane of gram negative bacteria; can function as an antigen recognized by the immune system to trigger an immune response

beta-lactam antibiotics

antibiotics that inhibit cell wall biosynthesis by inhibiting the enzymes that connect sugar chains (ex: penicillin)

mycoplasma

bacterial species that lacks peptidoglycan cells walls, making it pleomorphic (irregular/varied shape); not responsive to beta-lactam antibiotics

(atypical) pneumonia

some pathogenic species of mycoplasma can cause...

glycocalyx

network of polysaccharides and proteins outside the cell wall (can be a capsule or slime layer); contributes to the invasiveness of pathogenic bacteria

capsule

glycocalyx that is compact, mainly polysaccharides, and a major virulence factor of bacteria (protects bacteria by impeding recognition and phagocytosis)

Streptococcus pneumoniae, Klebsiella pneumoniae

examples of bacteria with capsules

slime layer

glycocalyx made of loose, unorganized sugar-protein material that absorbs and retains water (protects the bacteria from antibiotics/desiccation and enhances cell adherence)

Streptococcus mutans (plaque formation/cavities)

example of bacteria with a slime layer

flagella (flagellum)

thread-like appendage that functions in motility and attachment; virulence factor and is highly antigenic (activates the immune system)

E. coli (used as a virulence factor in the urinary tract)

example of a bacteria with a flagellum

pili (pilus)

small, fine, hair-like appendages that function in attachment to the host cell (and motility at times); virulence factor that allows pathogenic bacteria to attach to cells

sex pili

appendages that facilitate the exchange of DNA in bacterial reproduction

Neisseria gonorrheae (allows it to attach to cervical cells and cause gonorrhea)

example of a bacteria with pili

- blood

- throat

- sputum

- spinal fluid

- stool

- urine

- genital tract

- wound/abscess

examples of samples that can be collected

Staphylococcus

example of a gram positive bacteria

E. coli

example of a gram negative bacteria

acid fast stain

detect bacteria with large amounts of waxy lipids (mycolic acid) that do not stain with Gram staining

mycobacterium (TB)

example of a bacteria that requires acid fast staining

cocci (single or strips)

shape of Streptococcus

bacilli (rods)

shape of Bacillus

spiral

shape of Borrelia (Lyme disease)

comma

shape of Vibrio (cholera)

S-shaped

shape of Campylobacter (food poisoning)

pleomorphic

shape of mycoplasma

clusters (of cocci)

shape of Staphylococcus

diplococci (pairs of cocci)

shape of Neisseria (gonorrhea/meningitis)

MacConkey agar

used as a selective and differential medium

- selective as it only allows bacteria that can withstand bile salts to grow

- differential as it can show which bacteria have the enzyme to break down lactose (appear pink/red)

biochemical testing

detects a bacteria's ability to break down sugars, amino acids, etc. and ferment substrates to produce acids (ex: enterotube)

oxidase

enzyme used in cellular respiration; sample turns purple/blue when tested for

catalase

enzyme that breaks down hydrogen peroxide to form oxygen (bubbles when tested for)

1) DNA PCR amplification

2) DNA probes

3) DNA sequence analysis

types of genetic testing

DNA probe

genetic testing in which a 96 well plate has single stranded DNA from known pathogens (the sample will bind to its pair and appear bright when double stranded DNA is formed)

immunological tests

involve detection of antibodies or antigens

antigen

any substance that causes your immune system to produce antibodies against it

antibody

produced by the immune system to detect specific antigens

shape

What determines antigen-antibody binding?

capsular swelling reaction

test in which the capsule swells in the presence of a corresponding antibody (can identify serotypes of Streptococcus pneumoniae)

slide agglutination test

test in which antibodies cause bacterial cells to agglutinate (clump); directed against cell wall O antigens of LPS

ELISA (enzyme linked immunosorbent assay)

technique in which an enzyme breaks down the substrate to produce light (specific antibody is linked to an enzyme)

serologic test

detection of antibody in a patient's serum (used to test for syphilis); also often an agglutination (clumping) test

phage typing

classifies bacteria according to the susceptibility of the bacteria to lysis by bacteriophages (allows for intra-species differentiation of some bacteria); useful in epidemiological roles for S. aureus & S. enterica serotype Typhi

1) viable cell count (dilution series)

2) turbidity (absorbance)

3) dry weight

3 ways cell concentration is measured

1) lag

2) log (experimental)

3) stationary

4) death

4 stages of bacterial growth in a closed system (finite resources)

lag phase

stage of growth in a closed system in which:

- cells adapt to the new environment (prepare to divide)

- enzymes and chemical intermediates accumulate

log phase (exponential growth phase)

stage of growth in a closed system with exponential (logarithmic) cell division

stationary phase

stage of growth in a closed system in which:

- growth ceases

- resources are running out

death phase

stage of growth in a closed system in which:

- cells start to die or go dormant

- toxic compounds are released

open system

system for bacteria with a constant supply of nutrients and removal of dead cells; allows for constant growth (ex: chemostat, bioreactor)

antibiotics, insulin, alcohol

What is bacterial growth in an open system used for?

bactericidal

antibiotics that inhibit cell wall formation, killing bacteria (ex: penicillin)

bacteriostatic

antibiotics that inhibit protein synthesis, suppressing bacterial growth without killing (ex: tetracycline)

heat

denatures proteins

radiation

causes DNA damage

alcohol

dissolves bacterial membranes

aldehydes

antimicrobial agents found in essential oils

phenols

inhibit fatty acid synthesis and the formation of bacterial cell membranes (ex: triclosan in health care products)

bleach (sodium hypochlorite)

oxidizes proteins and lipids

heavy metals (ex: silver)

inhibit enzymes and DNA replication (used in wound dressings)

catabolism

the set of metabolic pathways that breaks down molecules into smaller units that are either oxidized to release energy or used in other anabolic reactions (as building blocks)

anabolism

the set of metabolic pathways that construct molecules from smaller units (require energy/endergonic)

assimilatory pathways

incorporate inorganic molecules into organic molecules in cells (ex: nitrogen assimilation); can facilitate biosynthesis of macromolecules (ex: proteins, nucleotides)

nitrogen assimilation

nitrogen is reduced to ammonium, which is assimilated into organic molecules to produce glutamine (precursor for amino acids and nucleotides)

soil uptake -> nitrate (NO3) -> nitrite (NO2) -> NH4 -> glutamate -> amino acids (proteins, nucleotides)

nitrogen assimilation pathway

glycolysis

oxidation of glucose into pyruvate; releases a small amount of ATP

citric acid cycle

completes the breakdown of glucose using oxidation and electron carriers (NADH, FADH2); releases a small amount of ATP and CO2

oxidative phosphorylation

process through which NADH & FADH2 produced in glycolysis and the citric acid cycle enter electron transport for ATP production (produces a large amount of ATP)

proton gradient

difference in concentration of H+ (protons) created when electrons from NADH are passed to oxygen (via electron transport); powers most ATP synthesis through ATP synthase

tryptophan

metabolite that can directly inhibit the production of biosynthetic enzymes and enzyme activity (example of metabolic regulation)

genome

sequenced genetic information of an organism

2%

percentage of the human genome that is protein coding

45%

percentage of the human genome that is mobile transposable elements (transposons/jumping genes)

introns

interrupt genes in the human genome