Viruses: Structure, Replication, and Bacteriophages

Viruses

• Viruses are parasitic, non-living entities storing hereditary data as either DNA or RNA.
• The hereditary data is encased in a capsid.
• Capsids can have 3 to 2,000 genes which manifest as either circular or linear.
• Some viruses are nonenveloped, others are enveloped.
• Viral envelopes that surround virus capsids give further protection, especially in influenza.
• They are simpler in structure to prokaryotic cells, and classified as obligate intracellular parasites.
• Parasites can only infect a specific number of cells.
• Bacteriophages are viruses that specifically infect bacteria; more than 10^30 exist on Earth.
• Bacteria coevolve with bacteriophages.
• Bacteria deploy CRISPR-Cas9 systems and restriction enzymes to combat viral DNA.
• Viruses infect cells by releasing their genome once inside.
• This causes the virus's genetic information to be replicated alongside the host cell's DNA.
• Replication causes more viruses to form through spontaneous self-assembly.
• Viruses disperse through lysis, exocytosis, or budding.
• Lysis involves the cell bursting.
• Exocytosis involves the cell secreting viruses using cellular machinery.
• Budding, occurring mainly with enveloped viruses, involves the cell secreting viruses with the membrane.
• SARS-CoV2 is a parasitic virus using four proteins for infection.
• The viral Spike, membrane, nucleocapsid, and envelope proteins infect a host.
• Spike proteins from SARS-CoV2 bind to ACE2 proteins on host cells.
• ACE2 proteins typically regulate the aldosterone system in the body.
• Airborne SARS-CoV2 easily infects people because of ACE2 receptor presence in noses.
• Vaccines help the immune system fight infections.
• Vaccines are created by exposing a body to a small derivative of a virus.
• Exposing the body to a derivative of a virus trains antigens to fight the live virus.
• Antibiotics are ineffective against viruses.

Prions

• Prions are misfolded proteins behaving similarly to viruses.
• Animals infected by prions can develop brain diseases.
• Symptoms take many years to manifest.
• They cause proteins of the same type to become misfolded, quickly transmitting the disease.
• They are mainly transmitted by the consumption of contaminated food.

Discovery of Evolution

• Darwin first proposed evolution: the accumulation of species changes over time.
• Linnaeus created his Binomial Nomenclature.
• Cuvier founded Paleontology via fossil study.
• Lamarck wrongly theorized species willing themselves to change.
• Darwin's understanding of life was influenced by these theories.
• Darwin read Lyell and Hutton's geological texts while on the Beagle.
• Darwin observed changes in Galapagos finches based on the island they inhabited.
• Darwin noticed adaptation.
• Adaptation is an individual characteristic change to improve survival.

Parts of Evolution

• Natural selection is the process by which favorable traits reproduce for species viability.
• Natural selection increases the abundance of traits that adapt a population to the environment.
• Artificial selection allows humans to selectively breed traits they desire in a population.

Evolution Evidence

• Homology is one form of evidence of evolution.
• Homologous structures are structures with similar construction, but different functions.
• Analogous structures with different structures but similar functions from convergent evolution also evidence evolution.
• Vestigial structures, which have no function, also evidence evolution.
• Evolutionary trees and clades can visually represent evolutionary history.
• Fossils demonstrate evolutionary descent and relationships.
• Introductions such as viruses or predators can trigger evolution.

Genetics Behind Evolution

• Genotype (genetic makeup) determines phenotype (physical appearance).
• Populations can have different genotypes, and thus different phenotypes.
• Environmental factors indicate the fitness of a phenotype.
• Mutations randomly affect DNA bases in genes, causing the creation of a new phenotype.
• Mutations can increase species fitness, leading to natural selection.
• Changes culminating from selective mutations often take thousands of years.
• Not every mutation is beneficial: some can make organisms less fit, in which case they won't pass down the mutation.

Genetics Influences Evolution

• Genetics makes evolution feasible through genetic variation.
• Genetic variation can result from mutations, chromosomal change, rapid or sexual reproduction, and create favorable or unfavorable genes.

Mathematical Measurement of Genetic Variation

• Hardy-Weinberg Equilibrium mathematically describes relations between phenotype frequencies and gene frequencies.
• It comes in two formulas: p + q = 1, and p² + 2pq + q² = 1.
• p = frequency of dominant allele.
• q = frequency of the recessive allele.
• p² = frequency of homozygous dominant members.
• 2pq = frequency of heterozygous members.
• q² = frequency of homozygous recessive members.
• Hardy-Weinberg's equilibrium is only valid if there are no mutations, natural selection, or gene flow, mating is random, and a large population.
• If all conditions are met, the equations accurately predict gene dispersion in a population.

Factors That Alter Allele Frequencies

• Natural Selection, namely adaptive evolution, increases favorable genes over time which can alter allele frequency.
• Gene flow, the flow of genes in and out of a population, can also affect frequencies.
• Genetic drift, or totally random events that affect allele frequencies across small populations, can also alter allele frequencies.
• The founder effect and genetic bottlenecks appear in genetic drift.
• A small subset of a population generates a new one in the founder effect.
• Genetic bottlenecks occur when random events kill off random population members.

Adaptive Evolution

• Natural selection consistently causes adaptive evolution given drive by relative fitness.
• Changes over time can favor members with previously unfavored traits.
• Directional selection favors one side of a bell curve.
• Stabilizing selection favors a narrow region of the middle.
• Disruptive Selection favors both bell curve ends.
• Sexual selection can lead to sexual dimorphism, or secondary sex characteristic differences between male and female members of a population.
• Intrasexual selection determines a member is willing to mate with anyone, often leading to intense competition.
• Intersexual Selection determines members are picky about mating with others.

Balancing Selection

• Balancing Selection is a process in which population gene and phenotype frequencies are maintained thanks to fitness.
• Frequency-dependent selection determines rare genotypes have an advantage.
• Heterozygote advantage selection is when heterozygous members have an advantage.
• Natural selection is imperfect as it acts on existing variations, is historically limited, adaptations compromise, plus environmental roles.
• Natural selection can still give rise to fitter individuals.

Speciation

• Speciation is the process by which new species come from old ones, bridging macro and microevolution.
• Species are members of a population that can breed with one another, defined by morphological or ecological differences.

Isolation Types

• Reproductive isolation means two members of a population can't breed with each other for any reason.
• Prezygotic and postzygotic isolation comprise reproductive isolation.
• Prezygotic Isolation affects isolation before zygote formation, including habitat, temporal, mechanical, and gametic isolation.
• Postzygotic isolation affects isolation after zygote formation, including hybrid viability via failed development, sterile fertility, and sterile Presence.
• Reproductive isolation can occur for several reasons.
• Geographic isolation occurs because two species can't breed given geographic isolation, forming new species away from each other
• Sympatric speciation, the formation of new species in the same geographic location, is rarer.
• Sympatric Speciation can occur through polyploidy or sexual selection.
• Polyploidy increases chromosomes in an organism.
• Autopolyploid plants' polyploidism derives from themselves.
• Allopolyploid plants' polyploidism derives from interbreeding with other plants.

Hybridization

• Two slightly different species meeting in a hybrid zone form a zone bearing species that share traits from species ancestries
• Hybrid zones form due to time or environmental factors.
• They can strengthen species barriers, fuse two species through weakening, or remain unchanged.

Speciation Genetics

• Speciation can occur via punctuated equilibrium.
• Punctuated equilibrium affects short immediate changes.
• Gradual Equilibrium causes slow steady changes
• Genetically, speciation begins from single gene changes, leading to cascade changes.

Nervous System

• Neurons are cells within the nervous system that transmit signals.
• Sensory neurons pick up input and integrate it into the central processing center, the brain for humans, and ganglia for others.
• Motor neurons conduct a task.
• The central nervous system consists of the brain and spinal cord.
• The peripheral nervous system consists of all other neurons in the body.
• Glial cells support and accelerate neurons.

Neuron Function

• Neurons transmit charge via a cell membrane gradient.
• A cell membrane gradient is composed of positive and negative ions that contribute to the membrane's overall charge.
• Neuron resting potential about -70mV, and happens when neurons aren't firing.
• Sodium-potassium pumps use ATP to bring two potassium ions into the cell and three sodium ions outside of the cell.
• This creates a positive charge outside on the extracellular side and a negative charge on the inside.
• Potassium leak channels always allow potassium to leave the cell.
• Hyperpolarization is where the surface gets more polar, causing a more negative charge internally.
• Depolarization is where the surface is less polar, causing a less negative charge internally as sodium enters.
• Graded potentials are changes where the magnitude of the change varies with the strength of the stimulus.
• Once an action potential voltage reaches threshold, an all-or-nothing action potential fires.
• As it depolarizes, the neuron repolarizes a bit by releasing potassium ions before overshooting, forming a hyperpolarization that eventually levels out.
• Neurons lined by myelin sheaths cannot back propagate.
• Myelin sheaths help neurons propagate signals faster.
• Electrical signals are caused by charge differences.
• Chemical signals are caused by neurotransmitters moving from dendrites to axons within synaptic clefts.
• Neurotransmitters propagate signals across a neuron.
• Postsynaptic potentials caused by chemicals can either be excitatory or inhibitory.
• Excitatory postsynaptic potentials cases depolarization.
• Inhibitory postsynaptic potentials causes hyperpolarization.
• A single EPSP is ineffective at activating an action potential, but hundreds can.
• Firing an action potential takes at least two major excitatory signals.
• Enzymatic digestion or reuse clears chemical messengers for later signals.
• Clearing the signals is necessary, as the neurotransmitters will block the space if not cleared.

Immune System

• The immune system is two parts: innate and adaptive.
• Innate immunity recognizes foreign molecules immediately and is often general.
• Adaptive immunity develops over time and responds to specific pathogens.
• Most pathogens in the body are killed by innate recognition.

Innate Immunity

• Bearing physical, cellular, and chemical defenses are forms of innate immunity for all animals.
• Physical defenses include outer skin/wall, mucous membranes, or cilia.
• Cellular defenses include cells engulfing pathogens, or cells killing themselves.
• Chemical defenses include dissolving enzymes, antibodies, pH, or temperature.
• Invertebrates have chitin exoskeletons and produce lysozyme to dissolve bacterial cell walls.
• Invertebrates use phagocytosis where cell membranes fuse pathogens to make them meet lysosomes and be destroyed and ejected .
• Hemocytes, immune cells in insects, excrete antimicrobial peptides after binding infectious fungi or bacteria.
• Some animals broken down infectious RNA.
• When bodies are infected, cells release chemical signals to alert other cells and call upon the immune system.
• The immune system first releases macrophages to swallow anything not dangerous.
• Macrophages also clean up old cells and let other cells know of infection.
• Neutrophils release toxic chemicals to kill pathogens if macrophages become overpowered.
• Neutrophils will commit apoptosis before they can kill beneficial cells.
• This is the first defense line.

Specific Innate Cells

• Macrophage cells eat and kill pathogens while cleaning up old cells and infections.
• Neutrophil cells act as phagocytes, release toxic chemicals, and sometime deploy neutrophil nets of DNA to trap pathogens.
• Blood samples on average contain 1560-6450 neutrophil cells per microliter.
• Dendritic cells collect information rather than killing, and display information from infectious materials and send out warning signals.
• These dendritic cells effectively serve as the generals of the immune system.
• Natural killer cells kill host cells with infections to prevent further development.
• This prevents the damage of nearby cells.

Specific Organs

• The lymphatic system works to transport lymph fluid that permeates the body.
• Bone marrow develops necessary blood and cells to fight infections, and generates lymphoid/myeloid progenitor cells.
• Lymphoid progenitor cells generate T, B, and natural killer cells.
• Myeloid progenitor cells generate red blood cells, and basophil/dendritic/neutrophil/mast cells respectively.
• The thymus makes T cells after the bone marrow first develops them.
• The thymus also tests their ability to recognize themselves or non-self cells.
• T cells forced to commit apoptosis if they recognize themselves.
• 2% of T cells survive the thymus.
• T cells genes also undergo Somatic Cell Recombination; this alters the genetic makeup of T cells.
• Lymph nodes act as nodes for B and T cells to meet and exchange infection information.
• The spleen recycles old cells and generates phagocytes and B/T cells; these are not needed to survive.

Adaptive Immunity

• Only vertebrates have adaptive immunity via lymphocytes composed of T and B cells.
• Diversity, lymphocyte proliferation and memory, and self-tolerance are the unique traits of adaptive Immunity.
• Dendritic cells pick up information about invading pathogens and call on helper T cells.
• This activates the second line of defense, which consists of activated helper T cells (helper and cytotoxic T cells).
• Activated helper T cells clone each other, giving necessary information to macrophages to kill pathogens.
• B cells activated and cloned with helper T cells, and pump out antibodies to kill pathogens.
• Memory B cells retain information of invading pathogens and activate correct responses for reinfection.
• T and B cells posses unique receptors, enabling them to distinguish between different antigens.
• 10-20% of 10 billion circulating cells in the body are B cells.
• B cells produce the same receptors while pathogens can have multiple receptors.
• T cells can only bind to surface antigen fragments tethered to a host cell bound to MHC molecules.
• MHC molecules tolerate and bind to many things.
• B cells instigate the humoral response.
• T cells instigate the cell-mediated response.
• Initially, adaptive immunity can take 2 weeks to activate.
• With vaccines, the adaptive immune response is quickly activated.
• Autoimmune diseases are exaggerated immune system responses stemming from autoimmune or immunodeficiency diseases.
• Deactivated adaptive immunity can cause cancers.
• Six viruses can cause cancers.
• Three examples include Kaposi's sarcoma herpesvirus, hepatitis B, and human papillomavirus (HPV).

Blood Circulation

• Diffusion facilitates gas exchange effectively over only short ranges.
• Circulatory systems deliver oxygen internally to animals that cannot exchange gas with direct environment.
• Diffusion time is proportional to the square of the diffusion distance.
• Circulatory systems each contain a set of vessels, circulatory fluid, and a heart.
• Open circulatory systems have hemolymph, which is pumped in vessels before flowing back into the heart.
• Closed circulatory systems contain all the blood that is pumped throughout the body through vessels.

Cardiac Flow

• Human blood picks up oxygen from lungs in heart, flows via arteries, and enters capillaries to exchange gas.
• Blood returns through the heart via veins.
• Most arteries carry oxygenated blood save for the pulmonary artery; pulmonary artery takes deoxygenated blood to lungs.
• The heart pumps 5 quarts of blood each minute using coordinated electrical stimuli.
• The left coronary artery transports 55% of the blood.
• Ventricles pump and contract during systole.
• Ventricles relax and take in blood during diastole.
• The atrium contracts for .1 seconds.
• The ventricle contracts for 0.3 seconds, and then both relax for .4 seconds.
• Heart murmurs are turbulent in blood flow, causing irregular heartbeats.
• S1 is when blood enters the ventricles during diastole.
• S2 is when blood enters the atrium during systole.
• A valve defect causes backflows that cause heart murmurs.
• Heart failure occurs when the heart weakens and can't sufficiently fill or pump blood.
• Over time, a heart with heart failure will weaken and beat faster before failing and killing an individual.

Cardiac Electrical Contractions

• The Sinoatrial node (SA node) in the heart triggers the signal, which travels to the atrioventricular node (AV node) before passing through the bundle branches, and finally the purkinje fibers that contracts ventricles.
• Brachycardia occurs when the heart rate is too slow.
• Tachycardia occurs when the heart rate is too fast.

Blood Vessels and Pressure

• The aorta leads into arteries that lead into arterioles then capillaries.
• Blood passes out from venules to lead into the veins and then vena cavas.
• Blood velocity decreases with vasodilation, opening up vessels.
• Blood velocity increases with vasoconstriction, closing vessels.
• Veins must use skeletal muscles and valves to draw blood back to the heart, as the aorta is strong enough to push blood through body.
• Blood can only flow through the whole capillary network if the precapillary sphincters are relaxed.
• Blood can only flow forwards without branching if precapillary sphincters are constricted.
• Blood pressure equals cardiac output (CO) multiplied by peripheral resistance.
• CO relies on heart rate and stroke volume. SV is influenced by blood volume.
• Hypertension, or high blood pressure, can cause heart failure, aneurysms, renal failure, retinopathy, strokes, or myocardial infarction.

Lymphatic System

• The lymphatic system regulates blood flow and wastes and also constitutes a large component of the immune system.
• Blood is regulated and made of plasma, leukocytes, erythrocytes, and platelets.
• Erythrocytes comprise 45% of the blood, plasma comprises 55%.
• Hemoglobin is a protein in blood that carries oxygen.
• Stem cells transform to lymphoid progenitor cells, and myeloid progenitor cells.
• Lymphoid progenitor cells become lymphocytes, myeloid cells creates everything else.
• Anemia is a red blood cell deficiency, which is why females are more prone due to menstruation.
• Blood clots, caused by plaque, reduce blood flow.
• Heart attacks are the cause of blocked LCAs.
• Strokes result from prevented oxygen from entering the brain.
• Stents widen arteries.
• Pulmonary embolism is a blood clot in the lungs
• Deep vein thrombosis from lower legs cause blood clots in veins, traveling to the lungs and causing pulmonary embolism.

Respiratory System

• The respiratory system inhales gas and facilitates gas exchange.
• Oxygen enters through the pharynx.
• After passing the esophagus, oxygen enters the larynx.
• From the larynx, oxygen travels down the trachea into the lungs.
• Oxygen proceeds down bronchi, into bronchioles, finally reaching alveoli to meet blood in capillaries.
• Blood then exchanges carbon dioxide within capillaries.
• The diaphragm contraction and expansion breathes in and out, creating respectively negative and positive pressure in the lungs.
• Medulla oblongata controls breathing, increasing or decreasing breath rate based on blood pH stemming from carbon dioxide buildup.
• Asthma is a swelling in the bronchial tubes trapping air in alveoli and complicating breathing.
• Alleviating asthma involves inhalers.
• Chronic Obstructive Pulmonary Disease damages the alveoli by blocking them, worsening asthma over time.

Animal Physiology

• Animals must obtain nutrients/O2, fight infections, and reproduce.
• Anatomy studies biological structure.
• Physiology studies biological function.
• Behavior studies how animals act.
• Convergent evolution adapts similar A&P given similar environments.
• Thicker skeletons suit larger animals.
• Muscles represent a larger fraction of body mass.
• A high Rate of Exchange demands a high surface area ratio.
• A high Amount of Exchange demands a lower surface area ratio (volume).

Tissues

• Organs rely on organized tissues, which in turn comprise organ systems.
• Epithelial tissue, such as skin, covers organs and the body.
• Lumen lines the digestive tract by connecting to the apical surface.
• Organs lined by basal surface.
• Connective tissues have extracellular matrices that hold tissues together.
• Fibrous connective tissues include tendons and ligaments.
• Blood contains cells and fragments in plasma.
• Muscles are tissues that affect movement.
• Skeletal muscles are voluntary muscles found on the skeleton.
• Cardiac muscles are involuntary and contract the heart.
• Smooth muscles are involuntary and move other things.
• Nervous tissues have neurons, which transmit electrical signals.
• Glia support nervous cells.
• The endocrine system is free range, releasing hormones that differ from nerves, which release signals for short periods to specific areas.
• Endocrine signals have less of an immediate effect.

Equilibrium and Heat

• Regulators manage their body temperature regardless of external conditions.
• Conformers cannot control internal conditions and conform to outside influences as a result; in other words, they are endothermic.
• Regulators are called ectothermic, and are energy efficient.
• Homeostasis governs internal conditions in animals using sets, sensors, and stimuli.
• Stimuli elicit a response from sensors.
• Control centers release responses to stimuli to match a set point.
• Positive feedback increases intensity of a thing, negative feedback either stops or slows it.
• The hypothalamus monitors heat and triggers blood dilation, shivering to control homeostasis.
• Heat exchange occurs through evaporation, conduction, convection and electromagnetic waves.
• An integumentary system requires hair, skin, and nails to thermoregulate the body.
• Circulation, evaporation, thermogenesis, and insulation all contribute to thermoregulation.
• Countercurrent heat exchangers use blood to transport heat.
• Acclimatization modifies insulation in response to seasonal change with help from lipid modification.
• Adaption differs from lipid molecule alteration due to temporary nature of acclimatization.
• Bioenergetics determines survival through energy requirements.
• Energy-containing food maintains homeostasis where the excess becomes heat.
• Metabolic rate measures energy an organism gains, loses, and uses.
• Basal metabolic rate measure rate of endotherms at rest.
• Standard metabolic rate measures rate of ectotherms at rest.

Plant Responses

• Plants are innately passive and responsive to their locale.
• Plants alter development/growth via signaling and responses.
• Cellular changes and stimuli cause proteins to change, second messengers send messages via phytochrome.
• Rhizoids grow in many directions until they hit light, then utilize light and gravity.
• Plasmodesmata facilitate communication between cells to relay messages via cytoplasm.
• The amounts of plant hormones have a big effect on a response, a quasi-nervous system.
• Calcium is the common, quick signaling molecule.
• Opium poppies secrete protect structure protein, pectin, in response to an attack.

Hormones

• A hormone is auxin, causing a plant to bend based on incident light.
• Auxin stimulates cell building apart from incident light, promoting growth and curvature.
• Auxin supports meristem, primary, and later root growth as found in most fruits, vascular differentiation, axial dominance, some tropisms, and leaf abscission .
• It travels through xylem; however, high concentration can inhibit instead of grow.
• Auxin molecules are for elongation.
• IBA can create adventitious roots, with auxins supporting production in seed development, synthetic fertilizers, and enzyme cuts that lead to stretches.
• Production of fruit and promotion of the plant defense are functions of the hormone, ethylene.
• As related to flowering, ethylene can encourage senescence, a horizontal expansion, and a stop to stem elongation.
• By mutating mutants which can form a triple response, some Arabidopsis can make Arabidopsis ethylene-insensitive or ethylene-overproducing.

Tropisms

• Plants grow using tropisms.
• Phototropism occurs due to light, spurring growth in that direction
• Gravity results in gravitropism, with plants that grow against gravity as triggered by statoliths.
• Water leads to hydrotropism; thus, plants will grow in search of it, or away from its absence.
• Anoxia plants will wilt in dryness or the reverse can create knee growth.
• Disturbance triggers thigmomorphogenesis.
• Contact leads to thigmotropism, creating touch sensors that coil around triggers from actions.
• Salinity instigates halotropism as triggered by salt, with salt stress growing away from the stimulant.
• Temperature also acts as a stimulant due to heat, that kills as a thermotropism.
• Too hot or cold can pose a bad situation but this can be regulated with heat shock protein and antifreeze.

Defenses

• Herbivores can cause thigmotropism, triggering defensive immunity on cells or within the cell like trichomes, irritants, or deterrents for defenses.
• Plants, such as opium plants, can produce chemicals to deter animals or tough sclerenchyma.
• Disgusting Organs change according to the light as defensive adaptations deter animals.
• Masting yields lots of seeds, ensuring survival with protection against animals.