Virus Structure and Characteristics

Viral Characteristics

• Viruses lack metabolic processes, preventing them from using nutrients to extract energy.
• Viruses cannot independently produce cell components like nucleic acids or proteins and depend on a host.
• Viruses are obligate intracellular pathogens, meaning they need a host for replication.
• Viruses are acellular, not cells.
• Viruses can infect bacteria, algae, fungi, protozoa, plants, and animals.
• Viruses are not alive.

Viral Structure

• Capsids are protein shells protecting the genome, accounting for most of the virion mass, composed of capsomere subunits.
• Virions are single, infectious virus particles with a protective protein capsid and genetic material (DNA or RNA).
• Naked viruses consist only of a nucleocapsid; bacteriophages are examples of naked viruses.
• Enveloped viruses have an envelope surrounding the nucleocapsid, common in animal viruses.
• Viral shapes include tetrahedral (4 faces), icosahedral (20 faces), helical (spiral/rod/tube), cube (6 faces), octahedron (8 faces), and dodecahedron (12 faces).

Virome vs. Microbiome

• A virome is the collection of all viruses in an organism or ecosystem.
• A microbiome is the collection of bacteria in the gastrointestinal tract.

Viral Genomes and Enzymes

• Viral genomes can be RNA or DNA, single or double-stranded, single or segmented, circular or linear.
• Viral genomes aim to make a host cell produce viral proteins, creating more virions.
• Every virus uses its genome to make mRNA, subsequently used by the host's machinery to create viral proteins.
• Retroviruses are single-stranded RNA viruses with an mRNA-like genome that needs to be converted to DNA.
• Polymerases synthesize DNA and RNA.
• Replicases copy RNA.
• Reverse transcriptase synthesizes DNA from RNA.
• DNases break down/destroy host DNA.
• Arenaviruses pack along host ribosomes.
• Retroviruses borrow the host’s tRNA molecules.

Viral Classification

• Informal classification includes animal, plant, or bacterial viruses, enveloped or naked viruses, DNA and RNA viruses, and helical or icosahedral viruses.
• Formal classification criteria include structure, chemical composition, and genetic makeup similarities.
• Virus orders end in "-virales."
• Virus families end in "-viridae."
• Virus genera end in "-virus."

Multiplication Cycle of Animal Viruses

• Adsorption occurs when the virus attaches to receptor sites on a susceptible host cell membrane.
• Penetration follows adsorption.
• Uncoating involves enzymes dissolving the envelope and capsid, releasing the virus into the cytoplasm.
• Synthesis is when viral nucleic acid controls the host's machinery to transcribe and translate viral genes, varying between DNA and RNA viruses.
• Assembly is the process of putting together the virus particles.
• Release occurs when the virus exits the host cell by budding or exocytosis.

Proviruses

• A provirus is a virus integrated into the host cell's DNA.
• They are usually inactive and can be passed to future cell generations.
• HIV is an example of a provirus.

Oncogenic Viruses

• Viruses cause 13% of human cancers.
• The virus carries cancer-causing genes.
• The virus produces proteins that cause a loss of growth regulation in the cell.

Bacteriophages

• Bacteriophages are relatively easy to grow in a laboratory.
• In plaque assays, phages infect cells, leading to cell lysis.
• Lysed cells create clear zones (plaques).

Lytic and Lysogenic Cycles

• The lytic cycle includes adsorption, penetration, replication, assembly, and release.
• The lysogenic cycle includes attachment, penetration, phage genome integration into the host genome (forming a prophage), prophage copying during cell division, and potential excision from the host genome under stress, leading to the lytic replication pathway.

Prions

• Prions are infectious proteins without genetic material.
• Prions are acellular.
• Prions do not replicate.
• Prions cause transmissible spongiform encephalopathies.
• Normally found in the brain, prions become infectious upon misfolding.
• Infectious prions convert normal prions, causing a chain reaction of misfolding.
• The brain degenerates, resulting in spongiform encephalopathy.
• Prion diseases can be inherited or acquired, like "mad cow disease."

Genome Locations and Forms

• Eukaryotes have a genome of DNA in the nucleus, mitochondria, chloroplast, and plasmids.
• Prokaryotes have a genome of DNA in the nucleoid region and plasmids.
• Viruses have either DNA or RNA, but never both.
• Transcription and translation are physically separated in eukaryotes by the nuclear membrane.
• Eukaryotic genes contain introns that are transcribed into RNA and later removed from the transcript.
• Eukaryotic genes are not arranged in operons.
• Bacterial genes are arranged in operons.

Genotype vs. Phenotype

• Genotype is the sum of all genes constituting a distinctive genetic makeup.
• Phenotype is the expression of the genotype that creates certain traits.
• A phenotype can change depending on which genes are expressed.

Genetic Regulation of Protein Synthesis

• The lac operon is normally "off" and does not initiate transcription when the substrate is absent.
• Repressible operons remain "on" when nutrient products are highly demanded because the repressor cannot bind to the operator at low nutrient levels.
• Repressible operons often encode genes involved in biosynthetic pathways.
• Phase variation is when bacteria turn genes on or off, resulting in phenotype changes.
• This is heritable and passed down to subsequent generations.
• Allows microbes to adapt and attach to different environments.
• Also allows microbes to evade the immune system.
• Inducible operons encode enzymes required for catabolic processes and are "off" when the substrate is absent.

DNA Recombination and Horizontal Gene Transfer

• Recombination is when one bacterium donates DNA to another, resulting in a different strain.
• Plasmids are extrachromosomal DNA adept at moving between cells.
• Horizontal gene transfer is DNA transfer resulting in organisms acquiring new genes that did not come from parent organisms.
• Conjugation is genetic transmission through direct contact between two cells.
• Transformation is the acceptance of solvable DNA fragments from the surrounding environment by a bacterial cell (indirect)
• Transduction is a virus transferring genetic material from one bacterium to another (indirect)
• Transposons, or "jumping genes," are DNA segments that can move around the cell’s genome.
• Griffith's experiment with Streptococcus pneumoniae led to the discovery of genetic transformation in bacteria.
• Plasmids exist outside the chromosome and can replicate independently.
• Plasmids confer a survival advantage as they carry specific genes related to antibiotic resistance.

Mutation Types

• Point mutations are small mutations that affect a single base on a gene, involving addition, deletion, or substitution.
• Lethal mutations lead to cell dysfunction or death.
• Neutral mutations produce neither adverse nor helpful changes.
• Missense mutations lead to the placement of a different amino acid.
• Nonsense mutations change a normal codon into a stop codon.
• Frameshift mutations involve base insertion or deletion, altering the reading frame.
• Silent mutations alter a base, but do not change the amino acid.
• Back mutation is when a mutated gene reverses to its original base composition.
• Repair mutation is the process of fixing damaged DNA.

Ames Test

• The Ames test is a rapid method to detect chemicals with carcinogenic potential.
• Uses bacteria rather than experimental animals.
• Uses Salmonella Typhimurium bacteria that has lost its ability to synthesize the amino acid histidine.
• Allows easy observation and monitoring of gene expression and mutation rate.
• Chemicals capable of mutating bacterial DNA could similarly mutate mammalian DNA and are potentially hazardous.

Enzymes

• Restriction endonucleases clip DNA crosswise at selected positions, recognizing and acting upon foreign DNA.
• Ligases seal sticky ends together by rejoining phosphate-sugar bonds cut by endonucleases.
• Reverse transcriptase replicates HIV and some other retroviruses, converting RNA into DNA.

CRISPR Technology

• CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats.
• The Cas9 enzyme in CRISPR recognizes and cuts out foreign DNA left by bacteriophages or plasmids.
• Scientists exploit this system to cut DNA in any organism exactly where they want to.

Polymerase Chain Reaction (PCR)

• Denaturation: heat target DNA to 94°C to separate strands, and then cool to 50-65°C to keep the strands separate.
• Priming: primers bind to the complementary strand of DNA.
• Extension: Increase temperature to 72°C, and add DNA polymerase and nucleotides to produce two complete strands of DNA.
• PCR uses opening of the double helix, using exposed strands as templates addition of primers, and the action of DNA polymerase
• Primers are synthetic oligonucleotides (15-30 bases) that indicate the start of DNA amplification.
• DNA polymerases are enzymes responsible for replicating DNA; those from thermophilic bacteria are needed due to high temperatures.
• Taq polymerase comes from Thermus aquaticus.
• Vent polymerase comes from Thermococcus litoralis.
• Template DNA is the copied DNA sequence during PCR.
• dNTPs are building blocks consisting of the four nucleotides (A, C, G, and T)

Recombinant DNA Technology

• Step 1: isolate the desired gene.
• Step 2: insert the gene into an expression vector.
• Step 3: transform host cells with the expression vector.
• Step 4: grow the transformed cells into suitable quantities.
• Step 5: purify the expressed protein.

Gene Therapy

• Gene therapy is the method of repairing or correcting faulty genes.
• Traditional treatments use medicine. Genetic engineering methods repair or replace faulty genes.
• Somatic gene therapy makes changes to the patient’s genes but cannot pass them to offspring.
• Germline gene therapy makes changes to the egg, sperm, or early embryo and the gene is expressed in all cells of the individual and can pass to the offspring.

DNA Profiling and Microarray

• DNA profiling (fingerprinting) is a forensic tool that relies on the fact that DNA in individuals contains differences.
• Restriction enzymes cut DNA in different places, resulting in fragments of different lengths in digested samples.
• DNA microarray analysis allows viewing the expression of genes in any given cell and tracks thousands of genes at once.
• Uses include developing sensitive diagnostic tests that search for a pattern of gene expression.
• Can identify cancer subtypes, allowing doctors and pharmacologists to treat each cancer with the most effective drug.

Nutrients

• Nutrients are acquired from the environment and used for cellular activities.
• Essential nutrients must be provided to an organism (CHONPS).
• Macronutrients are required in relatively large quantities and play roles in cell structure and metabolism.
• Micronutrients (trace elements) are present in smaller amounts and involved in enzyme function and protein structure.
• Inorganic nutrients are atoms or simple molecules that contain a combination of atoms other than carbon and hydrogen.
• Organic nutrients contain carbon and hydrogen atoms and are usually products of living things.
• Trace elements like iron, copper, arsenic, or lead, are chemical elements that are present in small amounts in substances such as rocks, plants, and living organisms.

Categories of Carbon Sources

• Heterotrophs obtain carbon in organic form and depend on other life forms; larger molecules must be digested before absorption.
• Photoheterotrophs: sunlight (photosynthetic organisms: purple/green photosynthetic bacteria)
• Chemoheterotroph - Saprobe: metabolizing the organic matter of dead organisms (fungi and bacteria decomposers)
• Chemoheterotroph - Parasite: utilizing the tissues and fluids of a live host : (bacteria, fungi, protozoa and animals)
• Autotrophs use inorganic CO2 as the carbon source and convert it into organic compounds, not nutritionally dependent on other living things.
• Photoautotrophs: sunlight: (photosynthetic organisms: algae, plants and most cyanobacteria)
• Chemoautotroph: chemoorganic autotroph= organic compounds like (methanogens)
• Chemoautotroph: chemolithoautotrophs= inorganic compounds like (thiobacillus, rock eating bacteria)

Nutrient Absorption

• Necessary nutrients must be taken into the cell and waste materials transported out across the cell membrane.
• Diffusion is the movement of molecules from higher to lower density/concentration, determined by the concentration gradient and the permeability of the substance.
• Osmosis is the movement of water across a selectively permeable membrane.
• Isotonic solutions have equal solute concentration in the external environment and the cell, generally the most stable environment for cells.
• Hypotonic conditions are when the solute concentration of the external environment is lower than that of the cell’s internal environment; cells without walls swell and can burst.
• Hypertonic environments have a higher concentration of solutes outside the cell, limiting growth; used in concentrated salt/sugar solutions to preserve food.

Active Transport

• Nutrients are transported against the diffusion gradient or faster by diffusion alone.
• Specific membrane proteins (permeates and pumps) act as carriers.
• Energy is required.
• Specialized pumps carry ions such as K+, Na+, and H+ across the membrane.

Cardinal Temperatures

• Cardinal temperatures are the range of temperatures for microbial growth.
• Psychrophiles have an optimum temperature below 15°C, can grow at 0°C, and cannot grow above 20°C; found in lakes, rivers, snowfields, polar ice, and the deep ocean.
• Psychrotolerant: grow slowly in the cold, but have an optimum temperature between 15°C and 30°C
• Mesophiles are the majority of medically significant organisms, grow from 10-50°C, with an optimum of 20-40°C; most human pathogens have optima between 30-40°C.
• Thermoduric microbes survive short exposure to high temperatures; common contaminants of heated or pasteurized foods.
• Thermophiles grow optimally above 45°C, in soil and water associated with volcanic activity, compost piles, habitat directly exposed to the sun, general range of growth 45°C to 80°C
• Extreme thermophiles grow between 80-121°C.

Microbes and Gases

• Aerobes use gaseous oxygen in metabolism and possess enzymes to process toxic oxygen products.
• Obligate aerobes cannot grow without oxygen.
• Facultative anaerobes do not require oxygen for metabolism but can grow in its absence, metabolizing by aerobic respiration when oxygen is present and adopting anaerobic metabolism when it is absent.
• Anaerobes lack metabolic enzyme systems for using oxygen, strict or obligate anaerobes cannot tolerate free oxygen and will die in its presence
• Aerotolerant anaerobes do not use oxygen but can survive and grow to a limited extent in its presence, not harmed by oxygen.

Osmophiles

• Osmophiles live in habitats with high solute concentrations.
• Halophiles prefer high salt concentrations for growth.
• Barophiles are deep-sea microbes that exist in pressures up to 1000 times atmospheric pressure and rupture when exposed to normal pressure.

Associations Between Organisms

• Biofilms are mixed communities of different kinds of bacteria and other microbes:
• cells are stimulated to release chemicals as the population grows to monitor its size

Binary Fission

• Parent cell enlarges, chromosomes duplicate, cell envelope pulls together to form a septum, and the cell divides into two daughter cells.

Generation Time

• Generation time or doubling time is the time required for a complete fission cycle; each new fission cycle doubles the population.
• The length of the generation time is a measure of the growth rate of an organism

Normal Growth Curve Stages

• Lag Phase: Newly inoculated cells require adjustment, cells are not multiplying, population is so sparse that sampling misses them.
• Log Phases or exponential growth: period during which the curve increases dramatically phase will continue as long as cells have adequate nutrients, and the environment is favorable
• Stationary growth and death phases: population enters, survival mode,cells stop growing or grow slowly
• Death phase: limiting factors intensify and cells begin to die at an exponential rate, curve dips downward

Enzymes & Catalysts

• Enzymes overcome the activation energy allowing the reaction to proceed by increasing thermal energy (heating) increasing the concentration of reactants adding a catalyst
• Enzymes hold reactants in their proper orientation and lower the energy required for starting the reaction (lower activation energy)
• Most composed of protein and may require cofactors, act as a organic catalyst to speed up the rate of cellular reactions, lower the activation energy required for a chemical reaction and have unique characteristics such as shape, specificity, and function
• Activity is affected by temperature, PH and regulatory mechanisms
• Associate closely with substrates but do not become integrated into the reaction products
• Not used up or permanently changed by the reaction and can be recycled, thus function in extremely low concentrations
• Active site is for target molecules (substrates) and molecules are much larger in size than their substrates that is affected by temperature and pH but, can be regulated by feedback and genetic mechanisms
• Substrates: reactant molecules upon which enzymes act
• Enzymes bind to substrates and participate directly in changes to the substrate, does not become part of the products, is not used up by the reaction, can function over and over again
• Simple enzymes: consist of protein alone
• conjugated enzymes: contain protein and some other nonprotein molecule
• Catalysts: speed up the rate of a chemical reaction without becoming part of the products or being consumed in the reaction
• 3 basic catabolic pathway are aerobic respiration, anaerobic respiration and fermentation
• The electron transport system transforms the energy of electrons into the potential energy of an electrochemical gradient (proton gradient) across the cell membrane (bacteria) or inner mitochondrial membrane (eukaryotes). This proton gradient provides the energy used by ATP synthase to phosphorylate ADP, producing ATP.
• Holoenzymes: when enzymes are whole
• Apoenzymes: protein portion of the holoenzyme
• Cofactor: nonprotein portion of the holoenzyme: organic molecule, also called coenzyme inorganic (metal ions)
• Coenzymes: organic compounds that work with the apoenzyme to alter the substrate; remove a chemical group from one substrate and add it to another; carry and transfer hydrogen atoms, electrons, carbon dioxide and amino groups
• Common coenzymes that serve as electron carriers include: NAD+, NADP+, FMN, FAD
• Enzymes are named using a suffix “-ase” and a prefix that describes the substrate/reaction they act on, name usually comes from the chemical change the enzymes catalyzes
• Exoenzymes - transported extracellularly to breakdown large food molecules or harmful chemicals
• Endoenzymes: retained intracellularly and function there, the most enzymes of metabolic pathways
• Constitutive enzymes: always present in relatively constant amounts, regardless of the cellular environments
• Regulated enzymes: productions is turned on (induced) or turned off (repressed) in response to changes in concentration of substrate/present ONLY when substrate is present
• Microbes secrete unique exoenzymes that help them avoid host defenses or promote multiplication in tissues (considered virulence factors/toxins)
• Sensitivity of enzymes to their environment: Cofactors, temperature, pH, amount of substrate present, phosphorylation state, the presence of inhibitors
• Acidic fermentation: pathways extremely varied, lactic acid bacteria reduce pyruvate to lactic acid mainly. Homolactic (yogurt examples) and Heterolactic fermentation: glucose is fermented to a mixture of lactic acid, acetic acid, and carbon dioxide
• Mixed fermentation: members of the family enterobacteriaceae posses enzyme systems for converting peruvian acid to several acids simultaneously acetic, lactic, succinc, formic acids, as well as CO2 (example swiss cheese) the intestines where this fermentative activity occurs in gas accumulates
• Alcoholic fermentation: pyruvic acid to ethanol in yeast or bacterial species that have metabolic pathways for converting pyruvic acid to ethanol; Decarboxylation of pyyruvic acid to acetaldehyde and reduction of acetaldehyde to ethanol; NADH formed during glycolysis is oxidized, regenerating NAD and allowing glycolysis to continue