Understanding the Immune System

Immune System

• Types of pathogens include bacteria, viruses, yeast, worms, and maggots.

Innate Immunity

• Innate immunity provides nonspecific and immediate defense and involves barriers in all animals.
• A small set of receptors recognizes traits shared by a broad range of pathogens.
• Lipopolysaccharide is commonly detected in bacterial cell walls.
• Barrier defenses include skin which has a low pH, mucus which is hostile to microbes, and secretions.
• Internal defenses involve phagocytes, antimicrobial proteins, inflammatory response, and natural killer cells.

Adaptive Immunity

• Adaptive immunity is specific and develops slower, occurring only in vertebrates.
• Traits specific to particular pathogens are recognized using a vast array of receptors, which can make millions.
• Humoral response involves B cells and antibodies, where antigens are caught and killed in the blood and lymph.
• Cell-mediated response involves T cells and cytotoxic cells, which mark and destroy host cells via apoptosis.

Innate Immunity Cells

• Types of cells in the blood all originate from bone marrow.
• Lymphoid progenitor cells make lymphocytes, including B lymphocytes, T lymphocytes, and natural killer cells.
• Myeloid progenitor cells produce neutrophils, monocytes, macrophages, and dendritic cells, all of which are professional phagocytes in innate immunity.
• Neutrophils stimulate inflammatory response in the blood.
• Monocytes make macrophages and dendritic cells.
• Macrophages activate T cells and digest microorganisms in tissues and organs.
• Dendritic cells present antigens to T cells.

Phagocytosis

• Pseudopodia surround the pathogen.
• A vacuole and lysosome fuse around the pathogen.
• The pathogen is engulfed by phagocytosis.
• The pathogen is destroyed from lysosomal enzymes, and debris is released.
• Main phagocytic cells are neutrophils, macrophages, and dendritic cells.
• Neutrophils circulate in the blood and are the most abundant white blood cells and first responders at the site of infection.
• Macrophages migrate through the body or reside permanently in organs and tissues.
• Dendritic cells are stationed under the skin and stimulate adaptive immunity.

Barrier Defenses

• These include skin and mucous membranes of the digestive, respiratory, urinary, and reproductive tracts.
• Many body fluids are hostile to microbes, and the low pH of skin prevents the growth of bacteria.
• In the respiratory tract, mucus traps pathogens in the air breathed in, and epithelial cells with cilia sweep the mucus out to keep the lungs clean.

Natural Killer Cells

• Undifferentiated T cells that never went to the thymus to mature.
• They detect and chemically kill abnormal cells in the body.
• They stop the spread of viral and cancerous cells.

Toll-Like Receptor Signaling

• Innate immune cells recognize pathogens via molecules called pathogen-associated molecular patterns (PAMPs).
• Some are found on the cell surface, and some are inside cells.
• They devour and destroy invading pathogens.

The Lymphatic System

• T cells develop in the thymus.
• B cells develop in bone marrow.

Lymph Nodes

• Contain packed immune cells
• Fluid is filtered through the nodes.
• Foreign cells activate immune cells.
• They resemble blood vessels but carry lymph.
• Blood flow causes pressure to send plasma out of capillaries into interstitial fluid (IF).
• Lymph carries the plasma back to the heart.

Antimicrobial Peptides and Proteins

• Attack and stop pathogen reproduction.
• Interferons interfere with viruses and activate macrophages.
• Thirty proteins make up a system that causes lysis and inflammation.

Inflammatory Response

• Histamine causes blood vessel dilation.
• Results in redness, swelling, and fever.
• Neutrophils and antimicrobials will enter the tissues to fight and ingest the pathogen.

Pathogen Evasion of Innate Immunity

• Some pathogens evade phagocytosis or recognition.
• Adaptive immunity will be the next line of defense.
• Examples include pneumonia and tuberculosis.

Adaptive Immunity

• Humoral Immune Response involves antibodies circulating in fluid, which neutralize or eliminate toxins and pathogens in blood and lymph.
• The cellular immune response involves specialized T cells that kill affected host cells and infected cells.

T Cells and B Cells

• Lymphocytes that mature in the thymus are T cells.
• Lymphocytes that mature in bone marrow are B cells.
• Both have antigen receptors.

Antigens

• Foreign substances that elicit immune responses, mostly proteins, lipoproteins, and polysaccharides.
• Both B and T cells are covered in thousands of antigen receptors that are specific to one antigen.

Structure of Antigens

• Epitopes are the small portions of antigens that interact with antigen receptors.

Structure of Antigen Receptors

• In B cells, antigen receptors are Y-shaped molecules with two identical heavy chains and two identical light chains bonded by disulfide bridges.
• Heavy chains are long, and light chains are short.
• The constant C regions of the chains vary little among B cells and are conserved between amino acids of the same class.
• Variable (V) regions differ greatly and determine antigen specificity.
• In T cells, antigen receptors consist of two polypeptide chains (α and β).
• Tips of the chains form a variable (V) region, and the rest is a constant C region.

Antigen Recognition by T Cells and B Cells

• In B cells, binding of a B cell to a target activates it and proliferates into plasma cells with the same specificity that secrete antibodies.
• In T cells, binding occurs with antigen fragments presented on MHC molecules, and cells proliferate after activation.

Class 1 and 2 MHC Proteins

• MHC are plasma membrane glycoproteins that stick out on the surface of the cell.
• Initially discovered when bodies would reject donor organs after a transplant, MHC proteins recognize anything foreign.
• Class 1 MHC proteins are present on the surface of every cell in vertebrates, except red blood cells.
• Class 2 MHC proteins are found mostly on the surface of B cells, dendritic cells, and macrophages, also referred to as antigen-presenting cells.
• In a process called antigen presentation, MHC molecules bind and transport antigen fragments to the cell surface.

Origin of Self Tolerance

• As lymphocytes mature in the lymphatic system, they are tested for self-reactivity.
• B and T cells with receptors specific for the body's own molecules are destroyed by apoptosis.
• This leaves only those that react against foreign molecules.

Proliferation of B and T cells

• In the lymph nodes, an antigen is exposed to a steady stream of lymphocytes until a match is made.
• Most activated B/T cells become effector cells (plasma cells) that act against antigens and are short-lived.
• Others become memory cells that are long-lived and immediately activated when they encounter the antigen again.

Immunological Memory

• Long-term protection against diseases.
• Primary immune response occurs on first exposure to a specific antigen (slow and weak).
• Secondary immune response is fast and strong (the reason for vaccines).

Helper T Cells

• These are a type of T cell that activates both humoral and cell-mediated immunity.
• Antigen receptors on the surface of helper T cells bind to the antigen and MHC II molecule.
• Cytokine signals are exchanged through autocrine signaling between the two cells.
• The helper T cell is activated, proliferates, and forms a clone of helper T cells, which then activates appropriate B cells.

B Cell Activation

• All occurs in lymph nodes:
  1. Helper T cell is first activated.
  2. Double binding of CD4 and antigen receptor to MHC II.
  3. Releasing of cytokines activates B cell.
• B cell proliferates into memory B cells and plasma cells, which secrete antibodies to lymph fluid and then travel to the bloodstream.

Antibody Function

• Mark pathogens for inactivation or destruction.
• Neutralization involves antibodies binding to viral surface proteins, preventing infection of a host cell, allowing phagocytes to come and consume it.
• Opsonization involves antibodies binding to antigens on bacteria, triggering phagocytosis, where antibodies can bind to two bacterial cells simultaneously.
• Binding of antibodies activates the complement system and triggers lysis.
• Agglutination aggregates large cells.
• Precipitation aggresses small cells.

Types of Antibodies

• IgG is a monomer.
• IgM is a pentamer.
• IgD is a monomer.
• IgA is a dimer.
• IgE is a monomer and is considered "bad."
• IdD is always found on the surface of cells, while the other four are soluble.

Cytotoxic T cells

• Use toxic proteins to kill cells infected by viruses or other intracellular pathogens.
• Recognize fragments of foreign proteins produced by infected cells.
• Activated cytotoxic T cells secrete proteins that disrupt the membranes of infected cells and trigger apoptosis.
• CD8 is an accessory protein that ensures binding to the correct cell.

Excretory System

• A system with the main function of:
• Blood carries nutrients and waste and requires filtration to remove garbage.
• Maintains osmotic balance of cells to prevent extreme volume changes.
• Osmoconformers live in the ocean and have to equilibrate osmolarity with the ocean.
• Osmoregulators conserve water and excrete salt.
• Waste products of metabolism are ammonia.
• Land animals have to excrete less toxic forms, ureotelic and uric acid.

Nephron Structure

• Nephron structure has 3 major parts :
• Renal corpuscle is the site of filtration.
• Renal tubule is the site of processing.
• Collecting duct is the site of urine processing.
• Renal corpuscle, proximal and distal tubules in the cortex (outside).
• Loop of Henle descends into the medulla, goes up and down, and then the collecting duct.
• Urine formed drains into the ureter, stored in the bladder, exits out the urethra.
• Afferent arteriole brings blood into the glomerulus.
• Efferent arteriole takes blood away from the glomerulus.
• One collecting duct can accept filtrate from several nephrons.
• A key for making concentrated urine is the Loop of Henle.
• A longer Loop of Henle results in more concentrated urine.

Renal Tubule

• Is a site of processing whose structure / function all 4 must know :
• Glomeruli are highly permeable capillary beds.
• Bowman's capsule cells surround the glomeruli; as blood pressure increases, fluid flows into Bowman's space and through the renal corpuscle.
• Podocytes are surface cells of Bowman's capsule; act as a sieve to filter liquids and small molecules.
• Proximal convoluted tubule:
  • As filtrate moves through proximal tubule, more than 70% is reabsorbed back into the body.
  • 75% of NaCl, almost all glucose and amino acids.
  • Highly active cells, active transport.
  • Full of mitochondria.
  • Surface has microvilli to increase surface area.
  • Inner surface has invaginations to increase surface area.
  • Regulates pH by secreting H+ and absorbing HCO3- (bicarbonate buffer system).
  • Materials removed from tubules returned to venous blood via uptake in peritubular capillaries.
• Loop of Henle: Ascending + Descending limb. Important to create concentration gradient in the medulla. Osmolarity of Interstitial Fluid increases going down Loop of Henle. Blood osmolarity is 300 mosm/L, goes up to 1200 in Loop of Henle. Humans can only make urine 4x more concentrated than our blood. Thin portion has no active transport. Counter current exchange allows fluid to be 100% saturated with O2.
• Concentration gradient arises from different permeabilities in different areas.
• Descending limb is highly permeable to water but not ions.
• Thin ascending limb is permeable to NaCl.
• Thick ascending limb actively secretes NaCl, with low water permeability.
• Water that leaves descending limb enters vasa recta.
• Distal convoluted tubule
• This controls more water and salt reabsorption.
• Cells have mitochondria and invaginations.
• Peritubular capillaries collect whatever renal tubules are absorbing back into filtrate.
• Vasa recta are blood capillaries that surround Loop of Henle.
• Collecting duct
• Has cells with few mitochondria.
• Permeable to water but not ions.
• Water leaves by osmosis > urine concentration increases, depending on body needs.
• Mechanism of massive water flux (How we reabsorb large volumes of water):
  • Aquaporins are a family of water channels with high water permeabilities that only allow water through and nothing else. Some hormone regulated, some not. Humans have 13.
  • Abundant in structures with high water permeability (proximal convoluted tubule, descending limb of henle, collecting duct).
  • Diabetes insipidus results from aquaporin mutation which produces lots of dilute urine (danger of dehydration).

Mechanisms to Maintain Renal Blood Pressure

• If systemic pressure decreases, afferent (incoming) renal arterioles dilate to maintain flow through capillaries.
• Systemic regulation of blood pressure:
  • Angiotensin increases local and systemic BP by effects on vessels and fluid intake; produced by the liver and always circulating in the body in an inactive form.
  • Efferent renal arteriole constricts; pressure in glomerulus increases leading to more filtrate.
  • Peripheral blood vessels constrict, raising central BP.
  • Stimulates thirst: drink more water, reabsorb to increase BP.
  • Stimulates an increase of aldosterone, a steroid hormone that works on kidneys to stimulate Sodium reabsorption.
• Renin Secretion.
  1. Blood pressure/volume drops.
  2. Sensors in Juxtaglomerular apparatus (JGA) detect decrease and produce renin (an enzyme that acts on angiotensinogen).
  3. Renin releases angiotensin I which releases angiotensin II, the more active form of the hormone.
  4. Angiotensin II stimulates adrenal gland to release aldosterone so Na+ and H2O are reabsorbed.
  5. Arterioles constrict which stimulates the brain to feel thirsty.
• ADH system:
  • Response to increased osmolarity.
  • Increase water reabsorption to concentrate urine.
  • Increases the water permeability of the collecting duct via effects on aquaporin content. ANP System releases in response to atrial stretch reduces salt and water uptake in the kidneys inhibits synthesis and the release of aldosterone, inhibits renin production and ADH release, increases water and salts excreted.

Plant Architecture

• Cell Wall Cell wall, chloroplast, and central vacuole differentiate plant cells from animal cells.
• The central vacuole is required for growing plant cells.

Formation of a new cell wall

• When plant cells divide, a new cell wall synthesizes in between the cells.
• Both daughter cells send vesicles toward the cell plate.
• Vesicles fuse to form middle lamella (with some gaps).
• Vesicles contain pectin, which is the glue that holds plant cells together.
  • Allows adjacent cells' cytoplasms to be continuous for communication.
• Resukts in a gradient within the wall (oldest = middle lamella, primary cell wall, secondary cell wall, youngest = PM).
• If a plant grows to its desired size, it will develop a secondary cell wall, internal to the primary cell wall which makes it extremely rigid and the plant cells will no longer be able to grow. Not all cells secrete this

Constraints imposed by the cell wall

• Cell position is fixed glued together by the middle lamella, though growth depends on turgor pressure to stretch walls.

Plasmodesmata

• Permanent connections that allow the transport and communication of fluids and small molecules between adjacent cells.
• Gating refers to a plant's ability to change pore sizes within the plasmodesmata.
  • Plant viruses can increase pore size so they don't have to go through the cell wall.
• Even when plants lay down 2º cell walls, plasmodes are maintained in pit fields.

Composition of a cell wall

• Cell walls are comprised of 25-30% cellulose (main structural component), 40-50% other polysaccharides, 1-15% protein, and fully hydrated
  • Hemicellulose are cross-linked with microfibrils.

Cellulose

• Linear glucose polymer, joined by 1,4 glycosidic bonds, lots of H-bonding potential and extremely stable and a singular cellulose microfibril contains 30-250 cellulose molecules H-bonded.
  • Length varies from 200-25000 residues per molecule, 1º cell walls shorter than 2º cell walls.
• Cellulose is synthesized on the cell surface by cellulose synthase
  • Cellulose secretes cellulose microfibrils outside the plasma membrane
  • It binds to microtubules and use it like railroad tracks to move along them As they move, it synthesizes cellulose chains
• These chains H bond into microtubules.
• Elongation
  • Plant cells can elongate up to 200x requires turgor pressure and wall loosening. Loosening cell walls requires increasing osmolarity in vacuoles, which causes water to enter by osmosis.
  • A major increase in cell volume occurs in the vacuole, not cytoplasm
  • The direction of expansion is always perpendicular to cellulose microfibrils and cell expansion is accompanied by new cell wall synthesis
• Old microfibrils shift to more vertical orientation as cell elongates
  • Secondary walls are impregnated by a variety of specialized polymers that give rise to distinct characteristics of different plant cells
    • Lignin is found in woods and what makes wood so strong.

Apoplast Pathway

• Transports molecules through cell walls

Symplastic Pathway

• Transports molecules through the cytoplasm
• Basic plant body with basic plant body plan indeterminate and repetitive.
  • Repeat units of Nodes (where the leaf comes out) and internodes (space between nodes)

Tissues

• Tissues are classified into Dermal (outermost), vascular (xylem + phloem), and ground (3 types)
• Presented in all organs of plants
• Ground acts as a "filler" of plant tissues
• Stele is the vascular core of the root

Source of tissues:

• Meristems plant-stem cells located in tips (apices) of leaves/roots and assorted patches and can divide indefinitely.
• Primary vs. secondary growth,
  • Apical meristems are responsible for 1º plant body (vertical height), while lateral meristem is responsible for 2º growth (horizontal thickening).
    • Not all plants have 2º growth: important for thickening of stem and root.
      • Vascular cambium: gives rise to vascular tissue: xylem and phloem cells.
      • Cork cambium: gives rise to the outer layer of the plant.
• Primary growth:
  • Apical meristems can divide into two cells in which one will remain undifferentiated, the other will differentiate into either dermal, ground, or vascular tissue.
• Secondary growth:
  • As vascular cambium cells differentiate, they will differentiate into xylem cells towards the inside of the plant, then they will differentiate into phloem cells towards to outside of the plant
  • As cork cambium cells differentiate they will make up the outside of plants, in order to make plants waterproof which prevents dehydration

Climate Impact

• Why do trees in temperate climates have rings within their trunks? Due to the periderm (cork cambium and cork cells) and it changes in Differing water levels during the seasons one ring = one year of growth
• During spring, xylem vessels are larger because more rain = more water transport = thicker ring
• During summer, xylem vessels are smaller because less water = thinner ring.
• There are differences between Eudicot and Monocot plants:
• Eudicot Stems have vascular tissue in a ring while Monocot stems have vascular tissue scattered containing both xylem and phloem.
• Eudicot Roots have vascular tissue in the center (+) while Monocot roots have vascular tissue in a ring.

Transport

Vascular system

• Xylem is the site of mineral and water movement, where it drives force for movement (water potential gradient) and the path of water movement flow through plant (root > stem > leaf)

Xylem structures have two major cell types:

• Tracheids are long narrow cells found in all vascular plant cells that have thick 2º walls containing lignin
• Vessel elements are shorter, thicker cells evolved later in flowering plants

Common traits

• Are cells dead by apoptosis by the time they mature, water must travel apoplastic pathway through the plant cell wal and the xylem vessel is always located in a bunch
• Ends of cells are partially broken down so one cell connected to other cell can form continuous pipeline for water conduction (from root > stem > veins in leaves)
• Water movement:
  • Water potential gradient (Y) = driving force for water movement. Passive, requires no energy
• Water cohesive due to H-bonds allows column of H2O to move .
  • Stoma: pores on the surface of leaves .When open, allows water on leaves to evaporate, pulls water in plant to go up like a straw
  • Water always moves to regions of lower Ψ, Pure water has Y=0, dissolved solutes Y <0
• Evaporation, Cohesion, and Tension of Water happens due xylem connects water in soil and to air surrounding eaves therefore Evaporation draws water out of leaves and Transpiration Stream: continuous column of water in plants maintained by water cohesion in which water moves under tension.
  • Neg press gets sucked up.
• Water piston example What happens if you take a piston and push it on a column of water ? Forces H2O molecules out of column into beaker, it is possible for returns to original gradient before Equilibrium Xylem sap can be under tension If xylem sap were to be under (+) pressure, no transpiration stream will occur but Why should you cut flower stems under water because xylem sap can get sucked in Once you it in water, any air bubbles stay in water will not travel if under pressure so that plants can heal under pressure that plant water not be pulled out but be pushed.

Guttation

• Water appearing on leaf veins from root pressure in high humidity conditions and only haves at night when water is not evaporating, only short plants, not trees
• Water moves column of leaf is the amount tension created on water or to high the water can vaporize and air renders useless or water would need to get to the the air bubble.

Rate of water regulation Controlled via temperature, evaporation rate, vessel width water travels

Mineral Water Management

• Membrane channels, which contain pectin, can be altered by the salt in the mineral water and rate of hydration.
• K+ regulation or water management
• Moves water through cortex, requiring symplastic movement across endodermis

Why water does symplastic

• Allows for selects water that moves or does not across pathway of root water More roots surface = More surface movement for water transport

Transport

• every endodermal cell surrounded by strip impregnated by waxy polymers. casparian strip waxy prevents apoplastic movement by repelling water creates opportunities for selective uptake in minerals (often agaisnt gradient); requires atp

• the ATP allows gradient which also generates pH which allows water to move and transport. After most % Water and Solute goes down the gradient of the cell which generates membrane volume

Water Management:Stomata

• During day it needs CO2 is needed as sugar
• Open allows
• Stream
• Guard pairs with specialized cells a set of pore levels need H20 high to open cell, closes if water loses to be used for photo.
• Light intensity is low cell are deflated
• opening/closing depends cell for H20 usage and how Light/low conc regulate h20.
  • light regulates hormones to regulate. Cells are short action of h20.
• the cell.

In plants and cells, light = long

Photosynthesis

Photosynath

chemical what creates more sucrose and amino. More life with h20.

Lumen cells must come to come 2h0

Primary: is in meso cell, they are green/ yellow in chlorophyll b Spongy: in meso where water is contained Chloroplast : water from the outside Light = outside to to Glum = start or phiooid Light for heat and to move.

Pigments or absorbable which is how is made up. Each system is set for all the cells to keep what is needed. When cells collect energy of how to give each electrons.