Virology Basics

Viruses and Prions

• Viruses and prions can cause disease.

Viruses

• Are obligate intracellular parasites, mandating living host cells for multiplication • Have very few to no enzymes and no ATP-generating mechanisms for metabolism in particular

Definitive Features of Viruses

• They can contain DNA or RNA, but never both
• Encapsulate their nucleic acid, with a protective protein coat
• Multiply intraceullarly using host cell machinery
• The multiplication of a virus inside living cells hinders antiviral drug development
• Are equipped with transferring structures of viral nucleic acid

Viruses: Host Spectrum

• Host range describes the spectrum of host cells a virus can infect.
• Host range may be very specific or broad, varying amongst different viruses.

Viruses: Specificity

• Many viruses infect only specific cell types within a specific species of host organisms.
• Viral specificity is determined by host attachment sites and cellular factors specific to host cells.
• Bacteriophages are an example of viruses that only infect bacteria .

Virion Structure

• Virion is the complete, fully developed viral particle, essential for causing an infection.
• Virions possess nucleic acid in the form of DNA or RNA, which can be single- or double-stranded, and either linear or circular
• Virions possess capsid, a protein coat made of capsomeres (subunits).
• Two structures compose the nucleocapsid: nucleic acid and capsid

Virion Structure

• All virions posses spikes, projections on the outer surface used for entry into the host cell
• Some virions have envelopes, these are lipid, protein, and carbohydrate coatings taken from the host membrane upon viral release

Virus Multiplication - Animal Viruses

• Adsorption: Viral attachment to receptors on the host cell membrane.
• Penetration and Uncoating: The virus enters the host cell via membrane fusion (enveloped viruses) or receptor-mediated endocytosis (naked viruses), followed by enzymes dissolving the vacuole membrane and the capsid to release DNA.
• Synthesis: Nucleic acid replication and protein production.
• Assembly: Nucleic acid and capsid proteins assemble to form the nucleocapsid.
• Release: Enveloped viruses are released through budding, while naked viruses induce rupture.

Virus Multiplication: Nucleic Acid Synthesis

• DNA Virus: DNA replication occurs in the nucleus and protein synthesis in the cytoplasm
• RNA Virus: RNA Replication and Protein synthesis both occur in the cytoplasm
• For specific features in the biosynthesis of DNA and RNA viruses, there is a table which indicates the viral nucleic acid, virus family, and special features of biosynthesis.

Virus Multiplication: Assembly and Release

• During the assembly stage of enveloped viruses portion of the host cell membrane. is acquired to form Viral matrix
• Nonenveloped viruses trigger escape through holes in membrane; host cell typically dies when breaking through causing Ruture

Pathogenic Properties of Viruses

• Viruses evade host defenses by growing inside host cells.
• Immune cells are unable to make contact inside of host cells

Pathogenic Properties of Viruses: Cytopathic Effects

• Visible infection effects: such cytocidal outcomes in cell death.
• In diagnosis; CPEs vary depending on the virus, specifically upon the point where they occur during infection

Cytopathic Effects of Viruses

• Stopping cell synthesis
• Causing cell lysosomes to release enzymes
• Creating inclusion bodies in the cell cytoplasm
  • These typically contain aggregated proteins and may represent sites of virus replication
  • These inclusions can be very diagnostic and help identify causative agents
• Fusing cells to create a syncytium

Pathogenic Properties of Viruses & Cytopathic Effects (CPE)

• Poliovirus (Enterovirus): cytocidal (cell death)
• Genital warts virus (Papillomavirus): acidophilic inclusion bodies in nucleus
• Adenovirus (Mastadenovirus): basophilic inclusion bodies in nucleus
• Lyssavirus: acidophilic inclusion bodies in cytoplasm
• CMV (Cytomegalovirus): acidophilic inclusion bodies in nucleus and cytoplasm
• Measles virus (Morbillivirus): cell fusion
• Polyomavirus: transformation
• HIV (Lentivirus): destruction of T cells

CPE and Cancer

• Changing host cell function or inducing chromosomal changes
  • Resulting in activated oncogenes
• Loss of contact inhibition in the cell
  • Leading to cancer

Viruses and Cancer

• Integrated oncogenic viruses can activate oncogenes.
  • Which are involved in cell growth and proliferation/inhibition of apoptosis
• There are dozens of identified oncogenes
• Activated oncogenes allow designated apoptotic cells to survive and proliferation
• Normal cells transform into tumor cells: acquiring properties of cancer Altered from normally specified growth
• Cells may express tumor-specific antigens on the cell surface and in the nucleus

Virus and Cancer: Tumors

• Oncogenic viruses (oncoviruses) that are integrated into the host cell's DNA

  • This is a cause of ~10% of cancers that are virus-induced

• Oncoviruses often go undetected until cancer

  • Most virions dont induce cancer
  • Cancers may develop long after initial infection
  • Cancers caused by viruses are not contagious

Persistent Viral Infections

• Latent infections exhibit periods devoid of infectious virus, with reactivation potentially triggered by changes in immunity.
• Chronic infections are characterized by the continuous presence of infectious viruses, developing gradually over sustained durations.

Examples of Latent/Chronic Viral Human Infections

• Latent infections: exhibit no symptoms during latency; viruses not usually released, cold sores, leukemia
• Chronic infections: skin lesions, cervical cancer, HIV/AIDS, liver cancer

Virus Multiplication in Bacteriophage

• Lytic cycle (lysis): phage causes death as the host cell lyses
• Lysogenic cycle (latency): phage DNA is incorporated into the host DNA

Virus Multiplication in Bacteriophage: the Lysongenic Cycle

• Lysongeny is characterized by phages in dormancy or inactivity

• Phage DNA incorporates into host cell DNA

  • Is called prophage
  • When the host cell replicates, prophage replicates

• Lysogenic phages can reproduce using the lytic and lysogenic cycles

Virus Multiplication - Outcomes of Lysogeny

• Immunity to infection by same phage
• Specialized transduction
  • Here bacterial genes are transferred by the initiating of other bacteria by the phage
  • Changes the bacteria genetics and the phage

Virus Growth

• Requires growing in living cells
• Bacteriophages are grown in bacteria where they form plaques that can then be counted

Virus Growth: Cell Cultures

• Are detected when tissues are treated with enzymes to separate cells
• Virally infected cells then show the cytopathic effect

Prions: Proteinaceous Infectious Particle

• Is the cause of nine animal neurological diseases
  • Creating Spongiform encephalopathies; large vacuoles develop in the brain
• Through methods of inherited and transmissible
  • By way of ingestion, transplant, and surgical instruments
• Causing what can be the underdetermined means for cell damage
  • PrPC: normal cellular prion protein, on the cell surface
  • PrPSc: a scrapie protein that accumulates in brain cells and forming plagues

Microbial Nutrition

• Essential nutrients are required and cannot be made

  • Provided by the host

• Macronutrients

  • Are required in substantial amounts, playing principal roles in cell structure and metabolism
  • They provide carbon, hydrogen, and oxygen

• Micronutrients

  • Are present in much smaller amounts and support maintenance of protein structure
  • Also known as trace amounts
  • Some micronutreints are mananese, zinc, and nickel

Analysis of Microbial Cytoplasm

• Cytoplasm is 70% water
• 97% of dry cell weight is organic compounds
• 96% consists of elements from (C, H, N, O, P, S)

Chemical Composition of E. coli

• Chemical make up of E-coli
  • C 50%
  • O 20%
  • N 14%
  • H 8%
  • P 3%
  • S 1%
  • K 1%
  • Na 1%
  • Ca 0.5%
  • Mg 0.5%
  • Cl 0.5%
  • Fe 0.2%
  • Trace Metals 0.3%
  • Proteins 50%
  • Nucleic acids (RNA) 20%
  • Nucleic acids (DNA) 3%
  • Carbohydrates 10%
  • Lipids 10%
  • Water "none in dry weight"
  • All Others 3%

Organism and Carbon Source

• Heterotroph: These obtain carbon from sources (e.g. glucose)
• Autotroph: These use inorganic CO2, as its carbon source
  • Convert CO2 to organic compounds
  • Are not dependent

Microbial Nutrition: Obtaining Energy

• Chemotroph: obtains energy from chemical compounds.
• Phototroph: uses photosynthesis to gain energy

Heterotrophy and Their Energy

• Chemoheterotrophs derive carbon and energy from organic compounds
  • Which they process for cellular respiration or fermentation
• Saprobes
  • Decompose plant matter, animal matter, and other dead microbes
  • Recycling organic material this way
• Parasites
  • Derive from cells or tissues of a host
  • Causing damages of host cells by being a pathogen

Microbial Nutrition: Transport Mechanisms

• Transport of necessary nutrients occurs across the cytoplasmic membrane
  • Even for organisms with cell membranes
• Driving force: atomic and molecular movement
• Diffusion
  • Molecular movement of concentration
  • Atoms move in a gradient

Diffusion

• Membrane pores allow free diffusion of water
  • Blocks other molecules from dissolving (solutes)
• Water moves in relation to the solute concentration
• The relationship between cells and the environment
  • Is determined by the concetration on the sides of plasma

Osmosis: Isotonic Solutions

• Solute concentrations are isotonically equal when inside and outside the cell
  • Water is at equilibrium

Osmosis: Hypertonic Solutions

• Contain a greater solute concentration than the cell does - with preserved foods for preservation (salmon, honey)
  • Creates plasmolysis and high osmotic pressure

Osmosis: Hypotonic Solutions

• Solute concentration is lower outside than the cell
  • The cell wall prevents osmotic Lysis
  • Membrane rupture occurs with excess water

Microbial Nutrition : Transport Mechanisms

• Moving materials depends on passive processes

  • Because they don't use energy
    • Substances move from high to low

• Active processes move nutrients

  • Faster than diffusion
    • Using membrane protients and requiring more energy

• These processes occur in Eukaryotes and Prokaryotes

Transport: Simple Diffusion

• From more to less concentrated areas until equilibrium occurs

Transport: Facilitated Diffusion

• Transport proteins move molecules from areas of high concentration to lesser

Transport: Water

• Osmosis involves lipid layering

Transport: Carrier Processes

• Atoms or molecules are pumped in and out
• This is achieved by receptors through the need of energy

Transport: Endocytosis

• The ell encloses substances within its membrane
• Accomplishing vesicle and Vacuole formation

Transport: Movement

• Phagocytosis is for amoebas/white blood cells while pinocytosis ingests liquids

Microbial Factors: Environmental

• Specific chemicals and physical demands meet relevant microbes
  • Physical factors:Temperature, pH, Osmotic pressure
  • Chemical factors: Nutrients and Oxygen

Extremophiles

• Thrive in normally lethal physical/chemical conditions
• Extreme Acidophiles have -pH
• Halophiles: are 2-5 NaCL
• Barlophiles >100mpa
• Temperature:
  • Psychrophiles: <15 celcius
  • Mesophiles are: 15-60 C
  • Thermophiles: 60-80C
    • Hyperthermophiles: >80C

Temperature for Microbes

• Growth Temperatures
  • Minimum : lowest temperature that's supports growth
  • Optimum is best for fastest growth
  • Maximum is highest

Temperature Groups and Classifications

• Psychrophiles: are cold microbes living, Psychrotrophs are 20-30C but can grow at 0C
  • Thermophiles – loving (50-60°C/122-140°F)

Factors: pH

• Most bacteria grow in neutral pH
• Produces acids during fermentation
• Molds and yeasts grow between pH 5 and 6

Factors: Osmotic Pressure

• Can cause lysis plasmolysis when not at equilibrium

Microbial Factors: Oxygen

• Yields more nutrients than non users and is commonly toxic
• Radicals steal electrons to disrupt process
  • Superoxide radicals: O2-
  • Peroxide anion: O22-
    • Destroy pathogens

Oxygen and Bacteria

• Bacteria that grow produce O2 to make super dismutase
  • The enzyme converts superoxide radicals into O2 and hydrogen peroxide H2O2 O2- + O2- + 2H+ -> H2O2 + O2

Oxygen: Catalase reactions

• The hydrogen in proxide is toxic, and also a key component of treatment catalase produces : 2H2) --->2H2O + O2 , peroxidase reaction produces : . H2O2 + 2H = 2h2O

Oxygen Effects

• Obligate aerobes, require oxygen
  • Facultative anaerobes fermentation with or without oxygen
    • Anaerobes are the inability to use oxygen
      • Aerotolerant anaerobes tolerate and are not microaerophiles requirers for low

Microbes with Oxygen (Table 6.1)

• Obligate aerobes: Require oxygen. Facultative anaerobes: Grow with or without oxygen (fermentation)
• Obligate anaerobes: Only grow without oxygen
• Lack enzymes to neutralize harmful oxygen forms and cannot tolerate oxygen.
• Aerotolerant anaerobes: With or without oxygen but oxygen has no effect, Microaerophiles: Only grow with the need of oxygen.
  • Produces lethal amounts of toxic oxygen forms if a low concentration

Study - Bacterial Growth

• By Binary fission
  • Which = increase in cell
  • Cell divides into new

Growth: Exponential

• Occurs most in bacterial cells
• Is calculated at 20 minutes

Growth in Bacteria as Numbers

• Logarithmic scale is useful for exponential growth

Bacterial Phases

• Display a logarithmic growth over an amount of time with 4 main phases.
  • The most relevant being that both stationary and death phases may be affected by limiting and damaging factors for optimal growth

Measuring Bacterial Growth

Directly: plate accounts, serial dilution, filtration Indirectly: turbidity

Microbial Metabolism: Anabolism and Catabolism

• Cellular chemical reactions occur that buildup and breakdown nutrients giving energy for cells to sustaining substances
• Anabolism: synthesis cell molecules and structures
• Catabolism: breaks bonds of molecules with the release of smaller molecules

Enzymes: Metabolism

• Simplified model of metabolism indicates precursors to macromolecules, proteins, and cellular functions through ATP

Bacterial Effects: Metabolism

• Bacterial metabolism has opposing influences that are positive such as nutrients and negative such as food and chemical
  • The bacteria's ability to survive related to the metabolism
  • metabolism depends on type and amount of bacteria which are expressed

Enzymes

• Are biological catalysts that have active sites to change substances
  • The catalyze rate increases chemical functions but won't consume in the structure

Enzymes: Acceleration

• Rapid acceleration can be described by its lower action

Enzyme: Formation

• A simple enzyme consists of protein
• Conjugated Enzymes consist of Protein and non
  • Holoenzyme (Protein, enzyme and metal ions) or cofactors

Factors: Influencing Enzymes

• temporary substrate union = active site union
• this helps to make designated reaction
• Product is formed where union occurs
• Enzymes unchanged with the ability to repeat

Cofactors: Catalysis

• Can be a trace element, Coenzymes, Organic compounds, and Apoenzymes

Enzyme Activity: Influencers

• Activity relies on cell environment
• natural temperature ,pH, and osmotic pressure
• Denaturation
• weak bonds that maintain shap
• enzyme distortion

Enzyme Action: Types

• Constitutive enzymes always remain present with specific substrate levels
  • A regulated enzyme is only present when the substrate is around

Enzyme Activity: Regulatory

• Competitive inhibition requires resembled enzyme substance
  • Noncompetitive inhibition is slowing enzyme concentration

Enzyme Synthesis: Conrtol

• This can be achieved through product binding

Metabolic Rate of Nutrient

• Is a pathway and many sites - May be branches and cycles where it can initiate anther cycle

Enzymes

• Series of interactions - Oxidation - Reduction
• Coupled

Production: Energy

• Adenosine triphosphate
• energy carrier of cells
• it has a few unstable bonds
• can take lipids/proteins

Carbohydrate Catabolism

• Production depends on breaking down molecules from glycolysis
• This process yields 38 ATP to the cells

Production: cellular respiration

• Consist of the
• Krebs cycle
• Electron transport chain (process) chemiosmosis
  • All producing ATP and electrons

Metabolism: cellular pathways

• Multienzyme and its systems include diversion and convergence.
• All are linear, cyclic ,branched for alternate methods

Genetics: Introduction

• Study of inheritance in genetics

• biological traits from parents are expressed and passed down with its functions for changes

Genetics: Nature - Eukaryotes

• Cells (some fungi to protonzoa) with plasm, mitochondrion, and chromosomes
• DNA from some bacteria forms chromosomes or plasm

Genetics: Cellular Components - Nature

Genome most exist as DNA with enzymes for replication Cells contain DNA, Virus has wither - Virus only contains either DNA/RNA

Genetics: Chromosmes

• distinct cellular structure composed of DNA

eukaryotic vs Bacterial:

• Euka -

  • Histone

• Bacteria

  • Histone like protien

• Genotype/Phenotype

• geno = genetic

• pheno is expressed trait from functions

The DNA Code: Nucleotides

• Is the single or basic unit of a structure contains phosphate, deoxyribose, and nitrogen
• The chain covalenty bonds and is shaped

DNA Code Cont.

• DNA has interacting bases:
• Purines (A/G)
• Interactions based on bases' weak
• A is 5 , G is 3 - Helps for information encoding

Antiparallel and strands

• the opposite ends run from 5' to 3'
• this is essential for DNA synthesis and protein production

Duplication

• Enzymes that seperate are for creating two molecules
• composition from origin
• semi
• *each mole has strand

DNA replication

• Helicase unzips the DNA, single stranded binding protein and keeps it apart, & the binding of DNA topoisomerases (initiates protein and begins coding with new primer and direction

Central Dogma: Process

• DNA encodes RNA, RNA encodes Protein (Replication and transcription)
  1. Transcription of DNA: tRNA, MRNA, rRNA

Regulation of Protein.

• Can be accomplished with inhibitory enzyme production and regulatory proteins.
• In bacteria and archaea
• *Operons (gene groups regulate units)
• Inducible (enzymatic and on)
• repressible (turn off and repressed)
• • can result in new proteins being activated from product or enzyme

Events: Recombination

• When new cells exchange to resist
• DNA can come from bacterium through plasmids for genetics changes

Transfer: genes in bacteria

• is vertical and horizantal. and flows from cell to replication Transfer in Bacteria can rely on - Transduction, transformation (DNA uptakes)

• Plasmids Small DNA Carry origin Not necessary but replicate on their own

Must integrate for bacterial replicating R = Share through conjugation

Horizontal Gene Transfer: Conjugation

– With direct contact such as Gram-negative cells creating pilus as well as their fertility.

• Positive cells pass through with their envelope. (R) plasmid resistance :Share for a few genes to transfer , such to bacterial , virulence , toxins

Horizontal Gene Transfer: Transformation

• Recipient has an easy DNA uptake which may or may not special appendages or direct contact

Transdcution : Horizontal DNA

• bacterial transfer by bacteriophage
• host dna
• recombine
  • some infections in bacterial dna
• which enters B for recombinant

horizontal is for transposition

• dna pieces switch between traits and resistance
  1. Small with small dna 2 . DNA pieces switch between genome

Infectious Affecting the Eyes

• Eyes defense systems conjunctivitis and tears provide the surface of defense
• Immune response are light and inflammation restricted

Microbial Systems: Eyes

• Normal biota of conjunctiva is protective as defenses produce mucus

Infections: Conjunctivitis also referred to as PINK EYE symptoms include: glued eyes with secretions or milky discharge

• cause = allergies or multiple microbes -- Newborn, may cause Herpes simplex
• ** BACTERIAL AND VIRAL CAN BE CONTRACTED

Keratisis: infectious deeper eye tissues.

• results in corneal destruction a can be caused by
• Acanthamoeba/ Herpes simplex
• -- Acanth livein fresh water, results in inflammation by having previous injury

Infectious Affecting the Nevisous System

• CNS: Brain cord are protected by vertebrae column that contain fluid to be the main defenders of
  1. the control system that interperets outside world + impulses
• • 2: a. communication for actions**
• Nerves and Ganglia

Structure or Nevisous System Cont

.The system relies on blood brain to form a membrane

• the low cells in CSF act as immuno and help body

Defenses of Body

• Bacteria is not natural only and are a sign of disease

Meningtis

• inflammation of the brain or membranes
• ** most common to impact system, can be altered by bad blood flow

Meninges

• Symptoms include triad for headache, and a stiff area
• can get worse with convulsions or trauma with bacteria,viruses
• may be oppotunisitics for people with +Nesseria ,strep
• • • travel blood with neurological issue
    • Treatement through antibiotics such

Mengitis from Zika

Results from a caused infection transmitted from mother

Zika leads to

• Microcephaly- Small heads
• Vision problems
• Seizures

Poliomyelitis

• Can be caused by poliovirus or ingestion
• Leads throat infection, damage in some.

Treatable

• through - vaccines Leads paralysis /death with respiratory

Brain: infections (rare)

• Caused by amobeas or parasites
• In a form of meningo-en

Brain injuries

• Can happen from the vector from bugs in
• Mosquitoes vector with multiple variations that are preventable

Explore the fundamental aspects of virology, including viral structure, replication, and effects on host cells. This quiz covers key topics such as virus composition, host range, and viral multiplication. Learn about bacteriophages, nucleocapsids, and the impact of viral infections.