Micro Exam 3 and Practical 2

Energy source

Fuels metabolism (light or chemical compounds)

Carbon source

Backbone of biomolecules (CO₂ or organic compounds)

Nitrogen

Used in amino acids, nucleic acids, and enzymes

Sulfur

Used in amino acids and enzymes

Phosphorus

Used in nucleic acids, ATP, and phospholipids

Trace elements & Water

Essential for various cellular functions, growth, and reproduction

Source of energy

Drives cellular reactions and ATP generation

Source of carbon

Provides carbon skeletons for biosynthesis of macromolecules

Water

Essential solvent for cellular processes and reactions

Essential nutrients

N, P, S, trace metals needed for building macromolecules and enzymes

Proper environmental conditions

Temperature, pH, oxygen, etc., crucial for enzyme activity and cell survival

Light

CO₂

Photoautotroph

Energy from light, carbon from CO₂

Light

Organic

Photoheterotroph

Energy from light, carbon from organic compounds

Chemicals

CO₂

Chemoautotroph

Energy from chemical compounds, carbon from CO₂

Chemicals

Organic

Chemoheterotroph

Energy from chemical compounds, carbon from organic compounds

Morphology

Shape and structure (e.g., coccus, bacillus)

Staining characteristics

Reactivity to stains (e.g., Gram positive/negative, acid-fast)

Metabolism

Energy and nutrient sources utilized

Genetics

DNA/RNA sequencing, GC content, ribosomal RNA analysis

Ecology

Habitat, temperature, oxygen needs, and other environmental preferences

Energy source

Drives cellular reactions; primarily for ATP generation

Building material source

Provides carbon skeletons; used to build macromolecules (e.g., proteins, nucleic acids)

Coccus

Spherical shape

Staphylococcus

Bacillus

Rod-shaped

Bacillus subtilis

Spirillum

Rigid spiral shape

Spirillum volutans

Spirochete

Flexible spiral shape

Treponema

Vibrio

Comma-shaped

Vibrio cholerae

Coccobacillus

Oval shape

Haemophilus influenzae

Binary fission

Main method: cell grows, duplicates DNA, then divides into two identical cells

Budding/spore formation

Occurs in some species (e.g., Streptomyces, Actinomyces), involving an outgrowth or specialized spore

Peptidoglycan

Thick layer

Thin layer

Outer membrane

Absent

Present (contains LPS)

Teichoic acids

Present

Absent

LPS (Lipopolysaccharide)

Absent

Present (endotoxin)

Periplasmic space

Small or absent

Prominent

Stain color

Retains crystal violet; appears purple after Gram stain

Crystal violet washes out; appears pink/red after safranin counterstain

Cell wall composition

No peptidoglycan

Membrane lipids

Unique ether-linked lipids (branched hydrocarbons)

Habitat

Often extremophiles (e.g., thermophiles, halophiles, methanogens)

rRNA sequences

Differ significantly from bacteria and eukaryotes, a basis for classification

Biochemical tests

Assess metabolic capabilities (e.g., sugar fermentation, enzyme activity)

Molecular tests

Analyze genetic material (e.g., PCR for specific genes, rRNA sequencing)

Staining and microscopy

Observe morphology, size, arrangement, and staining characteristics

Serological tests

Detect specific antigens or antibodies using immunological reactions

Growth pattern observation

Observe growth on different media, colony characteristics, oxygen requirements

Extremophiles

Microorganisms that thrive in extreme environments (e.g., high temperature, salinity, pH)

GC ratio

The percentage of guanine and cytosine bases in an organism's DNA, used for classification ($(\frac{G+C}{A+T+G+C}) \times 100$%)

Bacterial groups

Broad categories of bacteria based on characteristics like Gram stain, morphology, metabolism, and phylogeny (e.g., Proteobacteria, Firmicutes, Actinobacteria)

Parabasala

Flagellated, no mitochondria

Trichomonas vaginalis

Alveolates

Contain alveoli sacs; diverse motility

Plasmodium (non-motile parasites), Ciliates (motile)

Euglenozoa

Have flagella and eyespots

Euglena

Amoebozoa

Move by pseudopodia

Amoeba, Naegleria

Flatworms (Platyhelminths)

Dorsoventrally flattened, often hermaphroditic

Flukes (Schistosoma), Tapeworms (Taenia)

Roundworms (Nematodes)

Cylindrical, unsegmented, separate sexes

Ascaris, Enterobius

Annelids/Arthropods

Segmented worms, or vectors; complex life cycles

Annelids (Leeches), Arthropods (Ticks, Mosquitoes)

Fungi

Heterotrophs; chitin cell walls

Reproduce via spores

Yeasts (unicellular), Molds (multicellular, hyphae)

Lichens

Symbiotic partnership between a fungus and alga/cyanobacterium

Mutualistic relationship

Crustose, Foliose, Fruticose lichens

Genome type

DNA/RNA, ss/ds (single-stranded/double-stranded), sense/antisense

Capsid morphology

Helical, icosahedral, complex shapes

Host range

Bacteriophage (bacteria), animal viruses, plant viruses

Lytic

Virus immediately replicates, produces progeny viruses

Host cell lysis and destruction

Lysogenic

Viral DNA integrates into host genome (prophage)

Viral genome persists, host cell survives and replicates with prophage; may later enter lytic cycle

Latency

Animal cells

Viral genome persists in host cells without immediate replication

Herpes simplex virus

Lysogeny

Bacterial cells

Viral genome integrates into bacterial DNA (prophage) and replicates with host genome

Lambda ($\lambda$$) phage

Viral Oncogenesis

Some viruses insert oncogenes or disrupt tumor-suppressor genes, leading to uncontrolled cellular growth

HPV (Human Papillomavirus) causing cervical cancer

In vivo

Using whole living animals or embryonated eggs for viral replication

Influenza virus in eggs

In vitro

Utilizing cell cultures (e.g., tissue culture)

Poliovirus in cell lines

Bacteriophage assays

Growing bacteriophages on bacterial lawns to observe plaques (clear zones)

T4 phage on E. coli

Viroids

Infectious circular RNA

Plants

Potato spindle tuber viroid

Cause diseases in plants; lack protein coat

Prions

Infectious proteins (misfolded)

Animals

PrPSc (scrapie prion protein)

Cause transmissible spongiform encephalopathies (e.g., mad cow disease, CJD); lack nucleic acid

Classification

Descriptive categorization based on observable traits

Taxonomy

Biological ranking and naming based on evolutionary relationships

Identification Goal

Recognize by appearance, motility, and life cycle stage

Flatworm

Class Trematoda (flukes)

Schistosoma species

Tick

Phylum Arthropoda

Ixodes scapularis

Protozoan cyst

Phylum Amoebozoa

Entamoeba histolytica

Living/Minimum Requirements

Microbial Classification Forms

Protozoa

Viral Classification

Nutrient Classification (Chemo/Photo)

Energy vs. Building Material

Non-Microbial Parasites

Lytic vs. Lysogenic Cycles

Bacterial Morphology

Fungi & Lichens

Latency vs. Lysogeny

Prokaryotic Reproduction Methods

Viral Oncogenesis

Bacterial Cell Wall Comparison

Culturing Viruses

Archaea Features

Subviral Particles

Microbiological Identification Tests

Extremophiles, GC Ratio, & Bacterial Groups