UV Damage and Repair Mechanisms

UV damage

Caused by short-wavelength radiation, forming thymine dimers inhibiting DNA replication/transcription.

Thymine dimers

Covalent bond between adjacent thymines caused by UV radiation.

Photoreactivation

Repair mechanism using blue light to break thymine dimers.

Nucleotide Excision

Repair mechanism involving UvrABC breaking sugar-phosphate backbone near dimers.

Kirby-Bauer setup

Antibiotic zones measured on agar with paper disks to determine effectiveness.

Antibiotic resistance

Selected for by antibiotics, not caused by them.

Phenotypic characteristics

Classical approach: staining, colony morphology, biochemical testing.

Genotypic characteristics

Molecular techniques like nucleotide sequencing for detailed identification.

Gram-Positive Catalase

Breaks down H2O2 into H2O and O2, indicating Staph over Strep species.

α-hemolysis

Partial hemolysis on BAP, green/brown zone around bacteria.

β-hemolysis

Complete hemolysis on BAP, transparent zone around bacteria.

γ-hemolysis

No hemolysis on BAP.

Streptolysin-O

Beta hemolysis around stab on BAP, indicates Streptococcus pyogenes.

Taxos A

Bacitracin sensitivity test for S. pyogenes and S. agalactiae.

Taxos P

Optochin sensitivity test for S. pneumoniae and S. mitis.

Motility test

Indicates organism's ability to diffuse in agar.

Nitrate Test

Detects nitrate reduction by bacteria.

Starch test

Detects organism's ability to use starch as a carbon source.

Spirit Blue test

Detects organism's ability to hydrolyze olive oil.

MSA test

Differentiates S. aureus based on halotolerance and fermentation.

Coagulase test

Indicates ability to clot plasma, definitive for S. aureus.

Bile Esculin test

Detects esculin hydrolysis, definitive for Enterococcus faecalis.

CAMP test

Identifies S. agalactiae with arrow-head shaped beta hemolysis.

Rapid KOH test

Gram-negative bacteria lysis with KOH, producing slimy string.

MacConkey Agar

Differentiates Gram-negative bacteria based on lactose fermentation.

Glucose/Lactose/Mannitol Fermentation

Detects fermentation and gas production in broth.

Oxidase test

Detects Cytochrome C Oxidase production, definitive for P. aeruginosa.

Methyl-Red test

Detects mixed-acid fermentation pathway.

Voges-Proskauer test

Detects 2,3-butanediol fermentation pathway.

Urease test

Detects urea conversion to NH3 and CO2, indicative of Proteus species.

SIM test

Indole, H2S, and motility test for bacterial characteristics.

Sulfur

Forms black precipitate

Citrate

Utilized as a carbon source, agar turns blue

Bacteriophage

Virus infecting bacteria, lytic life cycle stages

Phage Adsorption

Tail fibers attach to receptor sites

Phage Penetration

Sheath unwraps, DNA enters cytoplasm

Phage Biosynthesis

Phage hijacks host machinery

Phage Maturation

New phages assembled

Phage Lysis

Host cell bursts, releasing phages

Phage Head/Capsid

Stores genetic information

Phage Core and Sheath

Passage for nucleic acid

Phage Baseplate

Structural component of bacteriophage

Phage Titer Calculation

Multiply dilutions, adjust for plate factor

Plaque Forming Units (pfu)

Number of viral particles per mL

Colilert Test

Rapid water test for E. coli presence

Potable Water

Safe for drinking and consumption

Coliforms

Indicator of fecal contamination in water

MTFM

Determines coliform presence using lactose broth

PCR Uses

Detect target sequences quickly

PCR Steps

Denaturation, Annealing, Extension temperatures

Real-Time PCR

Quantitative PCR measuring fluorescence

Gel Electrophoresis

Separates molecules by size

Food Intoxication

Results from ingesting pathogen-produced toxins

Food Infection

Requires ingestion and growth of pathogenic bacteria

Ames Test Purpose

Screens compounds for carcinogenic properties

Auxotroph

Organism needing additional nutrients

Reversion Mutation

Restores normal phenotype

Transformation Heat Shock

Makes cells competent for DNA uptake

pGLO Plasmid Regions

Includes bla, gfp, araC genes

araC gene

Encodes regulatory C protein, controls arabinose operon

Transformation

Uptake of naked DNA by competent cell

Transduction

Horizontal gene transfer via bacteriophage

Conjugation

Transfer of genetic material through sex pilus

Disinfectants

Remove microbes on objects, do not sterilize

Antiseptics

Applied to bodily surfaces, less harsh than disinfectants

Sterilization

Complete removal of all living microorganisms

Phenolic compounds

Denature proteins and disrupt cell membranes

Detergents

Disrupt microbial membranes and denature proteins

Alcohols

Denature proteins and extract membrane lipids

Hydrogen peroxide

Causes oxidative damage to cellular materials

Halogens

Oxidize cellular materials

Probiotics

Live cultures in fermented milk products

Prebiotics

Non-digestible food ingredients stimulating bacterial growth

Yogurt production

Fermentation of milk sugar to lactic acid

SCOBY

Symbiotic Culture of Bacteria and Yeast

Fungi vs. Bacteria

Fungi are eukaryotic, secrete enzymes for energy

Saprophyte

Organism decomposing dead organic matter

Thallus

Body of a fungus

Hyphae

Long, branched filaments forming mycelium

Soil Microbes

Important in biogeochemical cycles, decomposition

Nitrogen Cycle

Conversion of N2 to NH3, nitrification, denitrification

Jensen's Medium

Used to isolate Streptomyces

Martin's Medium

Enrichment medium favoring mold growth

TSA

Medium for isolating Gram-negative bacteria

Antigen

Perceived foreign substance by the immune system

Antibody

Y-shaped protein neutralizing antigens

Innate Immunity

Built-in immediate immune responses

Adaptive Immunity

Delayed immune response with memory

White Blood Cells

Neutrophils, lymphocytes, monocytes, eosinophils, basophils

ELISA

Detects antigens or antibodies in serum samples