Prokaryotic Cells, Bacteria & Viruses

• These study notes cover prokaryotic cell structure and function, bacterial culture growth and development, and viruses.

Prokaryotic Cell Structure & Function

• Prokaryotic cells have structures, key components common to all cells, with differences between prokaryotes and eukaryotes.
• Cell membrane has phospholipids, proteins, hopanoids, and unique structures in mycobacteria and archaea.
• Cell membrane proteins perform various functions.
• Transport across the membrane is passive (simple and facilitated diffusion), active (group translocation, ABC transporters), and via osmosis and aquaporins.
• Cytoplasm contains the nucleoid, plasmids, and is where transcription, translation (polysome formation), and DNA replication (replisomes) occur bidirectionally, followed by septation.
• Cell division involves divisome and polar aging.

Bacterial Cell Wall Structure

• Peptidoglycan layer structure and synthesis are very important.
• Gram-positive cell envelopes have teichoic acids and an S layer.
• Mycoplasma species lack cell walls.
• Mycobacterial cell envelope contains mycolic acids.
• Archaea cell walls contain pseudomurein and ether-linked membrane lipids (terpenoids).
• Gram-negative cell envelopes contain murein lipoprotein with diaminopimelic acid.
• Lipopolysaccharide (LPS) layer structure includes O polysaccharide, Lipid A (endotoxin).
• Outer membrane proteins are present in the periplasmic space.
• Bacterial cytoskeleton provides structure with proteins like FtsZ, MreB, and CreS.

Specialized Structures and External Components

• Specialized structures include thylakoids, carboxysomes, and gas vacuoles.
• Storage granules include metachromatic granules, starch, glycogen, PHB, and sulfur granules.
• Magnetosomes, Pili/fimbriae enable twitching motility.
• Stalks, nanotubules, flagella aid chemotaxis.
• External components: slime layer, capsule, biofilm.

Bacterial Culture, Growth, & Development

• Microbial growth study is important to understand requirements like macro- and micro-nutrients, growth factors, and essential nutrients.
• Compare Prototrophs, which do not require growth factors, to auxotrophs.
• Complex media versus defined (minimal) media differ in composition that affects growth rates and enrichment culture for fastidious microbes.

Classifying Microbes and Growth Phases

• Microbes are classified by carbon & energy sources: heterotroph, autotroph, chemotroph, phototroph, chemoheterotroph (chemoorganotroph), photoheterotroph, chemoautotroph (chemolithotroph), and photoautotroph.
• Each classification is defined by carbon, energy, and electron source.
• Growth phases: exponential/logarithmic growth which includes the lag, log, stationary, and death phases.
• Growth is graphically represented and generation (doubling) time measured in minutes.

Growth Rate and Biofilm Formation

• Important growth calculations: 2n; No x 2n = Nt; n = log10(Nt/No)/0.301.
• Mean growth rate (k) = n/t = log10 (Nt/No)/0.301(t) indicates generations per unit time.
• Batch cultures are closed systems, whereas fed-batch cultures allow for continuous feeding.
• Biofilm formation is a complex process.

Cellular Differentiation

• Differentiation includes spore formation in Bacillus & Clostridium.
• Spore formation differs from vegetative growth and involves stages like forespore, mother cell, septum, spore cortex, and dipicolinic acid/Ca2+.

Viruses: Structure & Function

• Viruses are acellular, defined by a virion structure.
• Viruses benefit ecosystems in marine environments through the viral shunt.
• Viral infectivity is determined by host range and specificity, recognizing host cells via viral capsid proteins, glycoproteins, or other surface molecules.
• Viral tropism is the ability to infect a particular tissue.
• Viral genomes vary.

Viral Structure and Classification

• Viruses have a capsid, can be symmetrical (icosahedral, filamentous) or asymmetrical, and have an envelope with glycoprotein spikes (e.g., influenza viruses).
• Viroids and prions exist.
• Classification by ICTV & Baltimore categorizes viruses by genome type and route to express mRNA (Groups I-VII).
• RNA viruses: (+) ss RNA, (-) ssRNA, dsRNA require RNA-dependent RNA polymerase.
• Retroviruses [(+) ss RNA] use reverse transcriptase.

Viral Life Cycles & Host Defenses

• Viral life cycles share common steps.
• Bacteriophage cycles are lytic (virulent) and lysogenic (temperate).
• Phage exits host cells via lysis or slow release (M13 - filamentous phages).
• Bacterial host defenses: genetic resistance, CRISPR, and restriction enzymes.

Animal Virus Cycles & Examples

• Animal virus cycles includes tropism and uncoating mechanisms.
• DNA viruses, RNA viruses, and retroviruses differ in their multiplication.
• RNA-dependent RNA polymerase and reverse transcriptase used.
• (+) RNA is sense RNA; (-) RNA is antisense.
• Release of progeny occurs via lysis or budding.
• Examples: HPV (DNA virus) causes cancer; Picornavirus (+RNA); HIV retrovirus (RNA; reverse transcriptase).
• Animal/Plant host defenses: RNAi, mutation, and interferon.