Viral Structure and Replication

Viral Structure

• A protein capsid, composed of capsomeres, encloses viral genetic material
• Capsid symmetry varies among viruses like adenovirus, tobacco mosaic virus, coronavirus, influenza virus, and bacteriophage T4
• Some viruses possess a viral envelope derived from the host cell membrane
• Viral nucleic acid can be either RNA or DNA, and single or double-stranded
• Host range is typically narrow, preventing cross-species infections, but exceptions exist

Viral Replication

• Viruses, lacking metabolic enzymes, are obligate intracellular parasites
• Entry into host cells involves specific mechanisms, seen in the COVID-19 spike protein
• Bacteriophages replicate through two cycles: lytic and lysogenic
• Lytic cycle: Involves virulent or temperate phages, leading to host cell lysis
• Lysogenic cycle: Involves only temperate phages, incorporating viral genetic material as a prophage
• Viruses can remain latent during the lysogenic cycle, becoming lytic under environmental stress

Viral Diseases

• HIV causes AIDS
• Measles virus causes measles
• Influenza viruses cause the flu

Retroviruses

• Retroviruses, like HIV, use reverse transcriptase to convert their RNA genome into DNA
• The DNA integrates into the host genome as a provirus, allowing for latency

Viral Evolution

• Viruses may have evolved from fragments of prokaryotic or eukaryotic genomes
• They might also have originated from assembled pieces of DNA or RNA

Emerging Viruses

• Emerging viruses such as H5N1, the 1918 "Spanish flu," Ebola, and SARS (the origin of COVID-19) pose significant threats

Other Acellular Entities

• Virions are individual viral particles outside a host cell
• Viroids, found in plants, are simple strands of RNA without a capsid
• Prions are misfolded proteins implicated in slow-acting, hard-to-destroy brain diseases like Mad cow and Kuru's disease

Bacterial Characteristics

• Bacteria lack a membranous nucleus, having only a nucleoid region
• Genetic material is circular DNA that follows base pairing rules
• They lack membrane-bound organelles, but have ribosomes that differ in size from eukaryotic ribosomes
• Capsules protect bacteria in harsh conditions

Bacterial History

• Anton van Leeuwenhoek was the first to observe prokaryotes with a microscope
• Louis Pasteur and Robert Koch developed methods for isolating bacteria and identifying causative agents of diseases
• Koch's postulates are used to establish a causative link between a microorganism and a disease

Archaea

• Bacteria and Archaea are distinct lineages with differing biochemistries
• Some archaeans share genetic similarities with eukaryotes

Prokaryote Shape and Structure

• Common prokaryotic shapes include coccus, bacillus, and spirillum
• Prokaryotes often form biofilms
• Cell wall composition differs between bacteria and archaea, affecting Gram stain results
• Gram-positive bacteria stain violet, while Gram-negative bacteria stain red

Internal Prokaryotic Structures

• Prokaryotes lack a nucleus around their circular DNA
• Bacterial endospores provide resistance to harsh conditions
• Flagella differ significantly from eukaryotic flagella
• Pili are present

Prokaryotic Evolution

• Rapid reproduction, mutation, and genetic recombination contribute to prokaryotic evolution
• Transformation and transduction are mechanisms of genetic recombination
• Plasmids, including the F factor and R plasmids, can confer antibiotic resistance

Prokaryotic Metabolism

• Nutritional and metabolic diversity enables prokaryotes to inhabit diverse environments
• Metabolic strategies include obligation aerobes, obligate anaerobes, anaerobic respiration, and nitrogen fixation
• Metabolic cooperation occurs in biofilms and through specialized cells like heterocysts in Anabaena

Bacterial Lineages

• Proteobacteria: Gram-negative bacteria including alpha, beta, gamma, delta, and epsilon subgroups
• Alpha: rhizobium (N2 fixation in legumes)
• Beta: Nitrosomas (NH4 to NO2 conversion)
• Gamma: Legionella, Salmonella, Vibrio, and Escherichia coli
• Delta: Myxobacteria (fruiting body production)
• Epsilon: Campylobacter, Helicobacter
• Chlamydia: (Gram negative) trachomatis can cause blindness/urethritis, most common STD in the US
• Spirochetes: (Gram negative)
  • Treponema pallidum (syphilis)
  • Borrelia burgdorferi (Lyme disease)
• Cyanobacteria: (Gram negative) photosynthetic, may be solitary or filamentous
• Gram-positive bacteria:
  • Actinomycetes: Important in soils
  • Clostridium botulinum
  • Bacillius antracis
  • Staphylococcus aureus
  • Streptococcus pneumonia

Archaeal Lineages

• Extreme halophiles thrive in high salt concentrations
• Extreme thermophiles thrive in high temperatures

Protists

• Protists are a diverse group of eukaryotes
• Early eukaryotes developed nuclei and organelles
• Multicellularity originated multiple times

Endosymbiotic Theory

• Early protists acquired bacteria that became mitochondria
• Later, additional structures were acquired, leading to plastids (e.g., chloroplasts)
• Serial endosymbiosis explains multiple acquisitions of endosymbionts

Characteristics of Protists

• Eukaryotic: Includes nuclei
• Protists are neither plants, fungi, nor animals
• Can be single-celled, colonial, or multicellular, such as seaweed-like kelps

Protist Structures

• Blade Resembles leaves
• Stipe Resembles stems
• Holdfast Resembles roots

Protist Reproduction

• Most are freeliving, but some are parasitic
• Primarily reproduce asexually, but can reproduce sexually
• Nutrition
  • Photoautotrophic (producers): Responsible for photosynthesis
• Symbionts: Live with fungal partners
  • General term for protists that carry out photosynthesis is Algae

Green Algae

• Phylum Chlorophyta: Green algae, many varations
• Includes Chlamydomonas and Chlorophyta
• Sea lettuce looks plant like
• Volvox are colonial

Red Algae

• Seaweed
• Used in agar, cosmetics and sushi wrap

Brown Algae

• Seaweed
• Contains Fucoxanthin

Yellow-Green Algae

• Diatoms-silica outer shell, diatomaceous earth: sand
• Major phytoplankton component

Protists Locomotion

• Cilia, Pseudopodia, Flagella

Protist Supergroups

• Excavata: diplomonads, parabaslids, and euglenozoans
  • Diplomonads have mitosomes (Giardia)
  • Parabaslids have hydrogenosomes (Trichomonas vaginalis)
  • Euglenozoans have a crystalline rod in their flagellum and a kinetoplast (Trypanosomes-sleeping sickness)
• Archaeplastida: red algae, green algae, and plants
• SAR (Stramenopiles (like diatoms), alveolates (Plasmodium- malaria), Rhizarians are amoeba)
  • Brown algae are multicellular strameophiles and have a holdfast, stipe and blades = seaweed
• Unikonta: amoebas, fungi and animals

Protist Diseases

• Dinoflagellates= red tides also bioluminescence
  • Cell walls have cellulose
  • Will often bloom and use up all the oxygen while absorbing nutrients from runoff killing fish and shrimp
• Parasites are spread by insect vectors:
  • Giardia lamblia: diarrhea
  • Trypanosoma bruci: Sleeping sickness with Tsetse flies
  • Trypanosoma cruzi: Chaga’s disease spread by “kissing bug”
  • Trichomomas vaginalis: STD
  • Entamoeba histolytica: Amoebic dysentery--fecal water contamination

Protist Reproduction

• Ciliates (Paramecium):
  • micronucleus (heredity)
  • macronucleus (metabolism)
  • Significance: Beta Sexual reproduction "beta testing"

Protist slime molds

• Plasmodial slime- giant multinucleate mass
• Cellular slime molds are autonomous amoeba
• Reproduce by spores

Fungi

• Heterotrophs: They utilize external digestion and absorb materials in their hyphae.
• Cell walls with chitin
• Coenocytic fungi lack septa; septate have septae
• Reproduce sexually or asexually
• Plasmogamy: union of plasma membrane
• Karogamy: union of haploid nuclei
• Deuteromycete: known sexual reproductive stage
• Microsporidia: primitive fungi
• Roles: decomposition, mutualists, and pathogens

Examples of Fungi

• Cryptomycetes: parasites of other fungi
• Microsporidians: parasites with harpoon spores
• Chytrids: fungus attacking frogs and salamanders
• Zoopagomycetes: parasites/symbionts of animals
• Mucuromycetes: molds implicated in food storage
• Ascomycetes: sac fungi which produce ascocarps
• Basidiomycetes: club fungi; decomposers and mushrooms

Plants

• Adapted to life on land
• Had to evolve methods for Structural support and protection from drying out
• Alternation of generations
  • Diploid Sporophyte(2n) -> haploid spores
  • Haploid Gametophyte (n) -> haploid gametes
• Charophytes share key traits

Plant Structures

• Apical meristem: shoots and roots
• Waxy cuticle: leaf protection

Derived Plant Traits

• multicellular dependent embryos
• walled spores produced in sporangia
• multicellular gametangia
• apical meristems
• Vascular structures
• Suffix phyll: derived from leaves

Extant Plants

• Gymnosperms: No flowers, fruits
• Angiosperms: Flowers, fruits
• Sporophytes are 2n and gametophytes are n

Examples of Plants

• Moss life cycle: gametophyte form
• Fern life cycle: sporophyte
  • NO seeds but spores on frond
  • Flagellated sperm
  • Heart shaped gametophyte (n)
  • Fronds are sporophyte (2n)

Lycophytes

• microphylls (club mosses, quillworts, spike mosses)

Symbiotic Fungi

• Allows for transfer to land

seed plants

• sporophyte
• Monocots: ONE cotyledon or seed leaf
• Dicots: EUDICOT means
• Two Spores
  • megasporangia: megaspores (female gametophytes)
  • microsporangia: microspores (male gametophytes)

Pollen

• Pollen works around the problem that Sperm are no longer flagellated, Need water
• Pollination may be by wind, animals, insects or water

Gymnosperms

• Naked seeds on scales on cones
• Ovule BUT NO OVARIES
• Usually male and female cones

Types of Gymnosperms

• Conifers (cone bearing)
• Cycads
• Ginkgophytes
• Gnetophytes

Angiosperms

• Characteristics include fruits, flowers and double fertilization to give endosperm
• Male = Stamen
  • filament
  • anther
• Female= Carpel
  • Stigma
  • Style
  • Ovary
  • ovule

Complete angiosperm

• Both male and female parts

Plant organs

• roots, stems and leaves

Root Types

• Includes:
  • Prop or brace roots
  • Aerial roots
  • Storage roots
  • Pneumatophores
  • Buttress roots

Stem Anatomy

• Nodes
• Internodes
• Axillary buds
• Apical bud

Stem Adaptations

• Rhizomes
• Bulbs
• Stolons
• Tubers

Leaf Anatomy

• Monocots have parellel veins
• Edicots are Branchlike
• simple vs compound

Leaf Adaptations

• Storage leaves - onion
• Tendrils
• Reproductive leaves
• Cactus spines

Plant Tissues

• Dermal: epidermis
• Vascular: xylem and phloem
• Ground: all others

Plant Cells

• Parenchyma: flexible primary walls
• Collenchyma: uneven cell walls
• Sclerenchyma: secondary cell walls made of lignin

Water vs Sugar Conduction

• Water conduction cells are lignified and are dead allowing water to passively move
• Sugar conducting cells are alive

Plant type growth

• determinate
• indeterminate
• Primary: apical meristems
• Secondary: lateral meristems

Structures

• Cork cambium: waxy suberin
• Bark: all tissues outside of vascular cambium
• Leaves: spongy mesophyll, palisade mesophyll, upper and lower epidermis