Viruses: Nature, Structure, Hosts & Replication

Chapter 26: Viruses

• Chapter discussing Viruses

Nature of Viruses

• Viruses do not have cytoplasm, meaning that they are not cells.
• Viruses can be either DNA or RNA in structure and have either a circular or linear make up.
• Viruses are classified by their genomes, some classifications are RNA viruses, DNA viruses, and retroviruses.

Virus Structure

• Viruses have a protein sheath, or capsid, around their nucleic acid core.
• Some viruses store specialized enzymes within their nucleic acid core.
• Reverse transcriptase is often identified, not often found within the host cell.

Viral Hosts

• Viruses are obligate intracellular parasites.
• Each type of virus will have a limited host range.
• Tissue tropism means that a virus will only infect certain tissues inside a host.

Viral Replication

• Viruses infect a host cell through endocytosis, infecting virus contains a set of instructions.
• The viral genome is capable of tricking the host cell into making viruses.
• New viruses will then leave the host cell in order to infect further cells.

Viral Genomes

• Viral genomes vary both in their type of nucleic acid and number of strands.
• Most RNA viruses are single-stranded.
• Replication is error-prone in RNA viruses, which results in high rates of mutation.
• Retroviruses contain single-stranded RNA genome which is transcribed to double-stranded DNA.
• The majority of DNA viruses are double-stranded
• DNA viruses are replicated in the nucleus of a eukaryotic host cell.

Virus Classification

• Viruses can be classified based on taxonomy, genome, host, or the disease they cause.
• The International Committee on Taxonomy of Viruses, or ICTV, will use order, family, subfamily, and genus to classify the viruses.
• Baltimore classification is an example of genome classification.

Classification by Disease or Host

• Both methods of classifying are limited.
• Not all viruses cause disease.
• Viral infections will vary across conditions and different points of infection.
• Some viruses, for example, the common cold, can be caused by several viruses.
• Some viruses have the capacity to infect different types of organisms.

Classification by Genome Expression

• Genome classification based on expression is applicable more broadly than other classification types.
• Advances in metagenomics helps reveal important roles for viruses in ecology and evolution.

Bacteriophage

• Bacteriophages are classified by bacterial hosts.
• Bacteriophages called phages for short.

Reproductive Cycles of Bacteriophage: Lysogenic Cycle

• Viruses do not immediately kill infected cells.
• Viruses integrate viral nucleic acid into host cell genome/
• Integration allows viruses to replicate along with host cell's DNA as it divides.
• Integrated genome called a prophage.
• Cells containing a prophage is called a lysogen.

Phage Conversion

• During integrated portion of the lysogenic cycle, some viral genes may be expressed.
• Phenotype or characteristics are altered by the prophage.
• Vibrio cholerae phage conversion is an important occurrence in diseases.
• Lysogenic phage can introduce a gene coding for cholera toxin.
• This can be then incorporated into the host genome.

Viral Infections: Persistent vs. Acute

• Viral infections are categorized based on how rapidly and frequently that virus is produced.
• Viral infections also classified based on the appearance of associated/resultant symptoms.
• Persistent infections are latent or chronic.
• Acute infections show rapid replication of virus that leads to sudden symptom onset.

Types of Viral Infections

• Human Immunodeficiency Virus or HIV causes acquired immune deficiency syndrome, or AIDS.
• HIV infection is chronic.
• HIV infects and eliminates certain types of immune cells.

HIV Infection

• HIV infection compromises the host immune system.
• The lack of CD4+ cells and helper T cells means that there is no effective immune response.
• A host with HIV may die from a variety of opportunistic infections that do normally cause disease.

Latent Viral Infections

• Are viruses that "hide" in the host cell which allows for immune evasion, often found in viral infections.
• Viral reactivation and additional disease episodes are caused by physiological triggers.

Prions

• Described as "Proteinaceous infectious particles" that results in transmissible spongiform encephalopathies, or TSEs.
• Prions cause "Mad cow" disease, or BSE.
• They also cause Creutzfeldt-Jacob disease in humans, or CJD.
• A host will have normal prion proteins, identified as, PrPc.
• Misfolded proteins are identified as, PrPsc, and they cause normal PrP to misfold. The combination causes these diseases.

Viroids

• Are tiny naked molecules of circular RNA that uses host protein to replicate.
• Small interfering RNAs, or siRNAs, interfere with plant growth and development.

Chapter 27: Prokaryotes

• Chapter dedicated to the make up of Prokaryotes

Prokaryotic DIversity

• Prokaryotes are the oldest, structurally simplest, and most abundant forms of life, predating eukaryotes.
• Divided into two domains; Bacteria and Archaea.

Characteristics of Prokaryotes

• Prokaryotes are unicellular.
• Most are single-celled.
• Associations and biofilms can form when prokaryotes exist near to each other.
• Cell size of prokaryotes varies tremendously.
• Prokaryotes have a nucleoid with a chromosome that is often linear double-stranded DNA.
• Plasmids are common in prokaryotes.
• Most prokaryotes will divide by binary fission.
• Prokaryotes exchange genetic material through horizontal gene transfer, this is not reproduction.
• Prokaryotes do not have membrane-bounded organelles.
• Plasma membrane is extensively in-folded.
• Prokaryotic flagella described as simple in structure and different than eukaryotic flagella.

Bacteria vs. Archaea

• All prokaryotes have a plasma membrane.
• Archaean membranes are formed of linked glycerol to hydrocarbon chains by ether linkages, while bacteria membranes are formed of ester linkages.
• Typically archaea will then form a monolayer instead of a bilayer; allows extremophiles to withstand high temperatures.

Prokaryotic Cell Characteristics: Cell Wall

• Bacteria cell walls contains Peptidoglycan which is a rigid network that will maintain its shape.
• Peptidoglycan also aids bacteria cell walls to withstands hypotonic environments.
• Archaea will possess a similar molecule, called pseudomurein.

Prokaryotic Cell Walls

• Gram positive bacteria displays a thick, complex network of peptidoglycan within the cell wall. Gram negative bacteria exhibits a thin layer of peptidoglycan.
• Gram negative bacteria displays a second outer membrane with lipopolysaccharide.
• Gram negative bacteria is resistant to many antibiotics due to its thicker cell walls.
• S-layer consist outer membrane layers, it's found pili and it's diverse.
• Capsule is gelatinous helps attach to each other and protects the cell from immune response.

Molecular Classification

• Prokaryotes can be classified by looking at: amino acid sequences of key proteins, percent guanine-cytosine content and sequencing gene and RNA, especially rRNA and whole-genome.

Prokaryotic Cell Structure

• 3 basic shapes exist.
• Bacillus.
• Coccus.
• Spirillum.
• Bacteria cell structures consist of slender, rigid, helical structures that enables locomotion
• Flagella contains flagellin.
• Pili which are hair-like structures found in gram-negative bacteria enables to attach to other cells and is used for transfer of genetic information.

Prokaryotic Cell Organization

• Cells contains a nucleoid region with a single, circular chromosome, may contain plasmids.
• Ribosomes Smaller than those of eukaryotes differs in protein and RNA content.
• Some antibiotics target prokaryotes, attacking their RNA content.

Prokaryotic Genetics

• Prokaryotes do not reproduce sexually.
• There are 3 types of horizontal gene transfer that occur within prokaryotes:
• Conjugation.
• Transformation.
• Transduction.
• All 3 processes have been observed in archaea.

Conjugation

• Conjugation begins genetic exchange between donor and recipient cell by forming a plus that exchange genetic material through chromosome and plasmids

Antibiotic Resistance via Conjugation

• Antibiotic resistance results from R, or resistance, plasmids, which encode antibiotic resistance genes. Plasmids are acquired through transposable elements.
• Genes from pathogenic species transferred by plasmids or transduction.

Transformation

• Transformation process is a natural process that results with live cell uptake of dead cell DNA where DNA fragments are incorporated with live cells.

Transduction

• Generalized transduction gene transfers via accidents in the lytic cycle while Specialized transduction occurs through accident in lysogenic cycle.

Beneficial Prokaryotes

• Decomposers release a dead organism's atoms to the environment
• Photosynthesizers involved with carbon sugars fixation and nitrogen is reduced in Nitrogen fixation that's reduced from N₂ to NH3 (ammonia).
• Ancient cyanobacteria resulted in oxygen presence in the air.

Chapter 28: Protists

• Chapter discussing aspects of protists

Overview of Protists

• Most diverse of the four eukaryotic kingdoms
• Variety of forms exhibited.
• Unicellular, colonial, and multicellular groups.
• Most are microscopic but some are huge.
• All symmetries.
• All types of nutrition.
• Protists are found across all six eukaryotic supergroups
• Present in Excavata, Chromalveolata, Archaeplastida, Rhizaria, Amoebozoa and Ophisthokonta.
• Exhibits Cell surface that include extracellular matrix in plasma membrane and dormant cysts cells that may contain resistant outer protection.

Locomotion in Protists

• Protists have varied array of cell surfaces
• Plasma membrane is often identified.
• Extracellular matrix, or ECM, maybe present in some.
• Cysts are also present.
• Cysts are dormant cells with a resistant outer covering.

Protists are Bridge to Multicellularity

• Protists exhibits a locomotion of single cells, colonies and multicellularity that all arisen multiple times.
• Protists utilizes Flagellum/a to occur more then once during this process while utilizing more but shorter cilia.
• Pseudopodia ("false feet") is the chief means of locomotion for amoebas that's used by other protists as well.

SG Excavata- Euglenozoa

• Protists is identified as cells that change shape when swimming
• Alternate is exhibited between being stretched out and rounded up
• This cell is noted to possess the earliest mitochondria in eukaryotes to ever exist

SG SAR

• SAR Supergroup consists of three branches: the stramenopiles, alveolates and rhizaria

SG SAR: Alveolates

• In SAR: Alveolates structure flattened vesicles are described as alveoli cells with some of the components that are identified as Dinoflagellates, Apicomplexans and Ciliates

SG SAR: Alveolates: Dinoflagellates

• Dinoflagellates are Photosynthetic, unicellular with flagella that are sometimes are luminescent

SG SAR: Stramenopiles

• Stramenopiles are Brown algae, diatoms, and oomycetes with Fine hairs that covers is flagella

SG SAR: Stramenopiles- Brown Algae

• Brown Algae are often Seaweeds of northern region commonly made of Macrocystis
• Contains a single pore-studded shell that's typically a marine protist

SG SAR: Stramenopiles- Diatoms

• Stramenopiles also includes Diatoms and Rhizaria - Radiolarians or Foraminferans.
• Diatoms includes Phylum Chrysophyta, they also included in Radiolarians and Foraminiferans.
• Has Pphylum Retaria are unique double shells made of silica. Has an heterotrophic make up that can photosynthesize in most

SG SAR: Phylum Retaria: Foraminifera

• Retaria consist of Heterotrophic marine protists that are often formed through shells connected that allows for thin podia merging.
• Podia is essential in swimming and feeding process while Limestone is know to have rich foraminifera deposits in areas they are found

SG Archaeplastida

Thys group consist of Rhodophyta, Chlorophyta, Charophytes, and land plants as well as photosythetic organisms

Rhodophyta

• Contains an variety of reed algae that's ranges from microscopic to larger with not flagellum that contains red accesory pigment in some Coralline algae.

Green Algae

• Commonly have Chlorine in there make up and possess diversity
• Chlorophytes - Have and unsuual diversity
• Charophytes - that can rize to the land plants

Opisthokonta

• Chapter discussing Opisthokonta make up

Opisthokonts

• Contains Choanoflagellates
• Unicellular organisms that has funnel single emergent flagellum surrounded contractile collar that can be the ancestors to some fungi and animals species

Chapter 29: Seedless Plants

• Chapter dedicated to aspects of Seedless Plants, including but not limited to:
  • Origin, adaption, life cycle and different types of seedless plants

Origin Of Land Plants

• All green algae and land plants shared a common ancestor a little over 1 BYA
• Collectivity Green Plants are not always photoautotrophs. The cell wall of these are made of a Cellulose cell wall and starch for carbohydrates.

Life On Land

• Some concerns that plants need to overcome a life on land are water loss, sun radiation, and gravity
• Plant overcome these problems with desiccation.

Green Algae and Land Plants

• Green algae split into two major clades
• Chlorophytes never made it to land
• Charophytes are known as sisters to all land plants

Adaptations to Terrestrial Life

• In arid climates plants require Protection from desiccation which includes cuticle and stomata and as a transport medium for water and nutrient transport
• Moving water occurs Tracheophytes via tracheids that creates a loop that conducts the food
• Plants have seen a Shift to a dominant diploid generation to better reproduce and more diversity
• Plants have adapted to haplodiplontic life cycle and have reached Multi cellular haploid and diploid life stages.

Haplodiplontic Life Cycle

• Multi cellular diploid stage – sporophyte often produces haploid cells to allow spores for Myosis reproduction
• Diploid spore mother cells , or sporocytes, that's form during meiosis in the plant is called sporangia and it produces four haploid spores.
• First cells are then translated to gametophyte generation which exhibits Multi cellular haploid stage.
• This is caused as the spores divide through Mitosis where they then Produce gametes which fuse to form diploid or zygote in order to move on to the sporophyte phase.

Bryophytes

• Bryophytes can be closest living descendants of the first land plants
• This means they are often classified as non-tracheophytes that utilizes other conducting cells to better adhere to there climate.
• Mycorrhizal is seen to be important as can enhances water uptake for Bryophytes

Mosses

• Gametophytes consist of small structures like a stem where true leave are absent due to not being real vascular material like the structure is.
• Mosses form substrate by rhizoids
• Moss often form gametangia forms at the tips of gametophytes.
• Archegonia – Female gametangia. Antheridia – Male gametangia. Flagellated sperm allows for movement of water.

Tracheophyte Plants

• Cooksonia, is considered to be one of the first primitive forms of vascular land plant
• Plants Appeared about 420 MYA and are part of Phylum Rhyniophyta
• Often these plant forms only a few centimeters tall and have almost non existent roots and are completely homosporous

Vascular Tissues

• Xylem is essential to conduct water and dissolved minerals from the roots, up to the rest of the plant.
• Phloem essential to conduct sucrose and hormones throughout the plant.

Tracheophytes: Stems, Roots, and Leaves

• Fossil records show the evolutionary relationship and adaptation from primitive forms where stems but no roots or leaves evolved.
• Leaves exhibit great adaption where as they can increase surface area for photosynthesis. and evolved twice.
• This has translated to the evolution of Euphylls , or true leaves, found in ferns and seed plants as well Lycophylls found in seed plants.
• Roots Provide transport and support while Lack of roots limited early tracheophytes.

Seeds

• Display properties of High resistance to decay in the right climate
• Contain is known to be the source of of food supply for young plant with the aide of Fruits in the flowering plant and flowers (angiosperms)

Pterophytes

• Phylogenetic are commonly sorted out through ferns that have been shown to have an ancestors with whisk forms and horsetails.

Ferns

• Most abundant group of seedless vascular plants, where Most abundant group of seedless vascular plants and the most abundant that we have observed.
• About 11,000 species are known as the best types of material needed to produced materials like coal for the forest and the smaller gametophyte are known to be photosythetic.