comprehensive final exam objectives

What are the two fundamental cell types and how do they differ?

Prokaryotes lack a nucleus and membrane-bound organelles, have circular DNA, and 70S ribosomes; eukaryotes have a nucleus, membrane-bound organelles, linear DNA, and 80S ribosomes.

Which organisms are prokaryotic and which are eukaryotic?

Prokaryotes include bacteria and archaea; eukaryotes include fungi, protozoa, algae, and helminths.

What major groups of organisms are studied in microbiology?

Bacteria, archaea, fungi, protozoa, helminths, algae, viruses, and prions.

How do viruses and prions differ from living cells?

They are acellular, nonliving, and cannot reproduce independently or perform metabolism.

What roles do microbes serve on Earth?

They recycle nutrients, decompose matter, fix nitrogen, produce oxygen, and support ecosystems.

What is a biofilm and why is it significant?

A multicellular microbial community attached to a surface; clinically important because it increases antimicrobial resistance and causes persistent infections.

How do humans use microbes?

For biotechnology, fermentation, antibiotics, vaccines, industrial enzymes, and bioremediation.

What are phylogenetic trees used for?

To show evolutionary relationships between organisms.

What role does natural selection play in evolution?

It favors organisms with beneficial traits, leading to adaptation and evolutionary change.

Why is rRNA important in taxonomy?

It evolves slowly, is found in all organisms, and allows comparison across domains.

What are the three domains in the Woese system?

Bacteria, Archaea, and Eukarya.

What is a virulence factor?

A trait that helps a microbe infect, invade, or harm a host.

What bacterial shapes exist?

Cocci, bacilli, spirilla, spirochetes, vibrios.

What bacterial arrangements exist?

Singles, pairs (diplo-), chains (strepto-), clusters (staphylo-), tetrads, palisades.

What are major bacterial external structures and their functions?

Flagella (motility), fimbriae (attachment), pili (DNA transfer), glycocalyx (protection/adhesion).

What structures make up the bacterial cell envelope?

Cell membrane, cell wall, and in Gram-negatives, an outer membrane.

What is the difference between Gram-positive and Gram-negative bacteria?

Gram-positive have thick peptidoglycan and teichoic acids; Gram-negative have thin peptidoglycan, an outer membrane with LPS, and a periplasmic space.

Why is the Gram-negative outer membrane clinically important?

LPS is an endotoxin and outer membrane blocks many antibiotics.

What structures may be found in the bacterial cytoplasm?

Chromosome, plasmids, 70S ribosomes, inclusion bodies, microcompartments, cytoskeleton.

What are endospores and why are they medically relevant?

Dormant, resistant structures made by Bacillus and Clostridium; hard to kill and cause severe disease.

How do eukaryotic flagella and cilia compare to bacterial flagella?

Eukaryotic have a 9+2 microtubule structure and whip; bacterial rotate.

How do eukaryotic cell walls and membranes differ from bacterial ones?

Eukaryotic walls are cellulose or chitin; bacteria use peptidoglycan.

What are the major eukaryotic organelles and their functions?

Nucleus (genetic control), ER (protein/lipid synthesis), Golgi (processing/shipping), ribosomes (80S protein synthesis), mitochondria (ATP), chloroplasts (photosynthesis), lysosomes (digestion), peroxisomes (detox), vacuoles/vesicles (storage/transport).

How does the nucleus, ER, and Golgi work together for transport?

DNA → mRNA in nucleus → proteins made in ER → modified in Golgi → packaged into vesicles → shipped out.

Why is the difference between 70S and 80S ribosomes clinically relevant?

Many antibiotics target the 70S bacterial ribosome without harming eukaryotic cells.

What is the endosymbiotic theory?

Mitochondria and chloroplasts originated when ancestral cells engulfed bacteria.

What evidence supports the endosymbiotic theory?

They have circular DNA, 70S ribosomes, double membranes, and replicate independently.

What forms do microscopic fungi take and how do they feed?

Yeasts and molds; they are heterotrophs that act as saprobes or parasites.

How do fungi reproduce?

Asexually via conidia/sporangiospores; sexually via spores like basidiospores or ascospores.

What are key characteristics of protozoa?

Unicellular eukaryotes that lack cell walls and are mostly heterotrophic.

What are the life stages of protozoa?

Trophozoite (active) and cyst (dormant).

How are protozoa classified?

By motility: flagellates, ciliates, amoebas, apicomplexans.

What major groups of helminths exist?

Nematodes (roundworms), cestodes (tapeworms), trematodes (flukes).

What are metabolism, catabolism, and anabolism?

Metabolism is all chemical reactions; catabolism breaks molecules for energy; anabolism builds molecules.

What is ATP and how is it generated?

Cellular energy molecule; generated via substrate-level, oxidative, and photophosphorylation.

What are redox reactions and electron carriers?

Reactions that transfer electrons; carriers include NAD
⁺, FAD, NADP
⁺.

What are enzymes and how are they regulated?

Biological catalysts; may be constitutive or regulated by environment.

What are the main stages of aerobic respiration?

Glycolysis, intermediate step, Krebs cycle, and electron transport chain.

How many ATP are produced in aerobic respiration?

About 36–38 ATP (varies by organism).

How do aerobic respiration, anaerobic respiration, and fermentation compare?

Aerobic uses oxygen; anaerobic uses alternate electron acceptors; fermentation uses organic molecules and produces little ATP.

How are lipids and proteins catabolized?

Lipids via beta-oxidation; proteins via deamination; products enter central pathways.

What is amphibolism?

Pathways that can both break down and build molecules.

How is DNA structured?

Double helix, antiparallel strands, 5’→3’ directionality.

How is genetic material organized in prokaryotes vs. eukaryotes?

Prokaryotes have circular DNA and plasmids; eukaryotes have linear chromosomes packaged with histones.

What is DNA replication?

Semiconservative synthesis of DNA using polymerases and other enzymes.

What is the central dogma?

DNA → RNA → Protein.

What happens in transcription and translation?

Transcription makes RNA from DNA; translation uses codons, anticodons, tRNA, and ribosomes to make proteins.

What is an operon?

A group of genes controlled together; example: lac operon.

What is the difference between genotype and phenotype?

Genotype is genetic makeup; phenotype is expressed traits.

What are vertical and horizontal gene transfer?

Vertical is parent → offspring; horizontal includes conjugation, transformation, transduction.

What are transposons?

“Jumping genes” that move within genomes.

What kinds of mutations exist?

Missense, nonsense, frameshift, SNPs.

What are the effects of mutations?

Can be beneficial, harmful, or neutral.

What are common genetic technologies?

Restriction enzymes, plasmids, PCR, sequencing, gene therapy, CRISPR.

What nutrients do microbes need?

Macronutrients (C, H, O, N, P, S) and micronutrients (trace metals), plus growth factors.

What are microbial nutritional types?

Photoautotrophs, chemoautotrophs, photoheterotrophs, chemoheterotrophs.

What transport mechanisms move nutrients?

Passive (diffusion, facilitated), active (pumps, group translocation).

How do osmotic conditions affect microbes?

Hypotonic swells, hypertonic shrivels; halophiles tolerate high salt.

How do microbes respond to temperature and pH?

Psychrophiles prefer cold, mesophiles moderate, thermophiles hot; pH preferences vary.

What is microbial growth?

Increase in population via binary fission.

What are planktonic cells vs. biofilms?

Planktonic are free-floating; biofilms are surface-associated communities.

What are the bacterial growth curve phases?

Lag, log, stationary, death.

How is microbial growth measured?

Plate count, MPN, flow cytometry, turbidity, dry weight, genetic methods.

What kinds of microbial relationships exist?

Mutualism, commensalism, parasitism.

What is normal microbiota?

Beneficial microorganisms living on the body; can become opportunistic pathogens.

What are viruses and virions?

Viruses are infectious particles; a virion is a complete virus particle.

What are viral genome types?

dsDNA, ssDNA, +RNA, –RNA, dsRNA, retroviral RNA.

What is the viral envelope and what do spikes do?

Lipid membrane around some viruses; spikes are attachment proteins.

What are the stages of viral replication?

Adsorption, penetration, synthesis, assembly, release.

What is the difference between the lytic and lysogenic cycles?

Lytic destroys cell; lysogenic integrates into genome.

What is viral latency?

Dormant infection that can reactivate.

How are viruses grown in labs?

Plaque assays, cell cultures, embryonated eggs.

Why are antiviral drugs difficult to develop?

Viruses use host machinery.

What are prions and how are they deactivated?

Misfolded proteins; very resistant, require harsh treatments.

How do pathogens cause disease?

Entry, adhesion, invasion, evasion, damage.

What are exotoxins vs. endotoxins?

Exotoxins: secreted proteins; endotoxin: LPS released from Gram-negatives.

What is infectious dose?

Minimum number of microbes needed to cause infection.

What are the stages of disease progression?

Incubation, prodromal, illness, decline, convalescence.

What are modes of transmission?

Contact, vehicle, vector; direct or indirect.

What is incidence vs. prevalence?

Incidence: new cases; prevalence: total cases.

What types of epidemics exist?

Point-source, common-source, propagated.

What are notifiable diseases?

Diseases required by law to be reported.

What are Koch’s postulates and limitations?

Criteria for identifying pathogens; limitations include viruses and asymptomatic carriers.

What is herd immunity?

When enough people are immune that disease spread is limited.

What are healthcare-associated infections (HAIs)?

Infections acquired in healthcare settings.

What are the three lines of defense?

Physical/chemical barriers, innate immunity, adaptive immunity.

How does innate immunity differ from adaptive immunity?

Innate is nonspecific and fast; adaptive is specific and has memory.

What are major innate immune processes?

Inflammation, phagocytosis, complement, interferons, fever.

What are the steps of phagocytosis?

Chemotaxis, adhesion, ingestion, phagolysosome formation, killing, exocytosis.

What are NK cells and eosinophils?

NK cells kill infected/cancer cells; eosinophils attack parasites.

What is adaptive immunity?

Specific responses involving B and T cells with memory.

What are BCRs, TCRs, and antibodies?

Receptors on B and T cells; antibodies are proteins produced by B cells.

What is antigen presentation via MHC I and MHC II?

MHC I presents to CD8 T cells; MHC II presents to CD4 T cells.

What do helper, cytotoxic, and regulatory T cells do?

Helper activate responses; cytotoxic kill cells via perforin/granzymes; regulatory suppress responses.

What is the difference between T-dependent and T-independent B cell activation?

T-dependent requires T cell help; T-independent does not.

What are the antibody classes?

IgM, IgG, IgA, IgE, IgD.

What is the difference between primary and secondary immune responses?

Secondary is faster and stronger due to memory.

What are natural vs artificial and active vs passive immunity?

Natural active = infection; natural passive = maternal antibodies; artificial active = vaccines; artificial passive = antibody injections.

What is selective toxicity?

Drugs harming microbes but not host cells.

What are major classes of antimicrobial drugs?

Cell wall inhibitors, protein synthesis inhibitors, nucleic acid inhibitors, metabolic pathway inhibitors, membrane disruptors.