Gen Bio Finals 20XX PDF

Animal Systematics - Rana catesbeiana: bullfrog - Turdus migratorius: American robin Systematics - Homo sapiens: modern human The study of biological diversity and - Mucosa domestica: house fly classif...

Animal Systematics - Rana catesbeiana: bullfrog - Turdus migratorius: American robin Systematics - Homo sapiens: modern human The study of biological diversity and - Mucosa domestica: house fly classification Subspecies sometimes included classification of living organisms by - Gorilla gorilla beringei: mountain gorilla evolutionary relationship What is an Animal Classification Eucaryotic - cells divided into organelles Carolus Linnaeus (1707-1778) Multicellular - Swedish naturalist Heterotrophic- do not produce own Developed the modern taxonomic nutrients classification system Lack cell walls Tissues linked by proteins (e.g. collagen) Linnean System of Classification Cells often linked by cell junctions- gap, Kingdom Animalia adhesion, tight Phylum Chordata Possess electrogenic cells- nerve cells Class Mammalia and muscle cells Order Primates Reproduce sexually (diploid) Family Hominidae - sperm + egg → zygote → blastula → Genus Gorilla gastrula → larva → adult Species Gorilla gorilla Major Evolutionary Divergences Among Revised Linnean System Animals Development of Tissues Division Eukarya Development of Body Plans Kingdom Animalia Development of Body Cavities Phylum Chordata Developmental Origin of the Coelom Subphylum Vertebrata Superclass Tetrapoda Development of Tissues Class Mammalia Development of aggregations of similar Subclass Theria cells into patterns and layers Infraclass Eutheria Parazoa (sponges) - lack tissues Order Primates Eumetazoa - possess tissues Superfamily Anthropoidea Family Hominidae Development of Body Plans Subfamily Ponginae Central axis Genus Gorilla Pattern of body and structure Species Gorilla gorilla Number of embryonic cell layers Subspecies Gorilla gorilla beringei Radiata (e.g. jellyfish, hydra) - radial symmetry Binomial Nomenclature - diploblastic (2 germ cell layers) Genus + species Bilatera (everything else) Examples: - Bilateral symmetry - Triploblastic (3 germ cell layers) Parazoa: Phylum Porifera Development of Body Cavities sponges Acoelomates (flatworms) - no body little cell differentiation cavities sessile Pseudocoelomates (rotifers, roundworms) no nerve or muscle cells - body cavity not surrounded by mesoderm porous body (pseudocoelom) - enables water circulation through the Coelomates (everything else) body - body cavity enclosed by mesoderm - flow driven by choanocytes (coelom) - food collected and digested by amoebocytes Developmental Origin of the Coelom Coelomates are divided into two groups Radiata: based upon: Phylum Cnidaria 1. Pattern of cell cleavage during early Corals, jellyfish, anemones, corals development gastrovascular cavity - central 2. When cell developmental fate is compartment with single opening determined two basic body plans: 3. How the coelom is formed - polyp - usually sessile 4. How the digestive tract is formed - medusa - motile form during gastrulation tentacles arranged around opening to the gastrovascular cavity Protostomes lined with nematocysts - stinging cells Mollusks, earthworms, insects, etc. possess nerve cells forming nerve net Spiral cleavage - cell division diagonal to - no central nervous system vertical axis possess muscle-like cells Determinant cleavage - development into tissues determined very early in cleavage Radiata: Schizocoelous - coelom forms by splitting Comb jellies solid masses of mesoderm in Similar in appearance to jellyfish Blastopore forms mouth Possess comb-like plates of cilia used for locomotion Deuterostomes Collect food with tentacles covered with Starfish, vertebrates colloblasts (lasso cells) radial cleavage - cell division at right Phylum Ctenophora angles to vertical axis indeterminant cleavage- development Acoelomates: into tissues determined later in cleavage Phylum Platyhelminthes enterocoelous - coelom forms by Flatworms mesoderm layer budding from archenteron gastrovascular cavity with one opening blastopore forms anus Digestive tract true muscle tissue primitive excretory system (water balance)  sensory organs in head (photoreceptors, Protostome Coelomates: chemoreceptors) Lophophorate Phyla central nervous system (ganglia in head w/ possess lophophore ventral nerve cords) - ciliated fold around mouth Major Classes no head - Turbellaria U-shaped digestive tract planarians (free living) - Monogenea and Tremotoda Protostome Coelomates: flukes (parasites) Lophophorate Phyla - Cestoidea Bryozoans - sessile, resemble moss, hard tapeworms (parasites) exoskeletons Phoronids - horseshoe worms Pseudocoelomates: Brachiopods - resemble bivalves Phylum Rotifera Rotifers Protostome Coelomates: complete digestive tract Phylum Mollusca - separate mouth and anus Mollusks pseudocoelomic fluid acts as circulatory Major Classes: system - Class Polyplacophora chitons cilia lining crown draw water into the - Class Gastropoda snails and slugs mouth - Class Bivalvia clams, oysters, mussels, etc. Pseudocoelomates: - Class Cephalopoda octopus, squid, Nematoda nautiluses Nematodes (roundworms) Muscular foot Coelom complete digestive tract visceral mass- contains organs pseudocoelomic fluid acts as circulatory gills (respiration) system complete digestive tract w/ specialized longitudinal muscle orientation organs aquatic habitats, soils, plant and animal open circulatory system (blood not parasites confined to vessels) mantle- covers visceral mass, secretes Protostome Coelomates: shell Phylum Nemertea Proboscis worms Protostome Coelomates: acoelomous body, except for fluid-filled Phylum Annelida sac used to extend proboscis Annelids (segmented worms) similar excretory, sensory and nervous hydrostatic skeleton systems to flatworms coelom in repeating segments with complete digestive tract alternating longitudinal and circular closed circulatory system (blood confined muscles, setae, and metanephridia to vessels) (excretion) closed circulatory system  several specialized regions in digestive - three body segments (head, thorax, tract abdomen) cerebral ganglia with ventral nerve cord - many possess wings - specialized digestive system Protostome Coelomates: - Malpighian tubules (excretion) Phylum Annelida - tracheal system (respiration) Major Classes - Class Oligochaeta (earthworms) Arthropods: - Class Polychaeta (polychaetes) Crustaceans - Class Hirudinea (leeches) mandibles, 2 pair of antennae, branched appendages Protostome Coelomates: Class Crustacea- possess gills Phylum Arthropoda - salt glands (hemolymph salt balance) specialization of body segments Groups - specialized limbs, etc. - Isopods (e.g. pill bugs) hard exoskeleton- protein and chitin - Copepods (e.g. Cyclops) high cephalization of sensory organs - Decapods (crabs, lobsters, etc.) open circulatory systems - blood (hemolymph) not confined to vessels Deuterostome Coelomates : Phylum Echinodermata Arthropods: sea stars, sea urchins, sea cucumbers Chelicerates adults have radial symmetry claw-like feeding appendages (chelicerae), bilateral larvae lack antennae endoskeleton of hard plates Class Arachnida (spiders, scorpions, water vascular system- used to ticks, mites) manipulate tube feet 2 body segments (cephalothorax and abdomen) Deuterostome Coelomates : - 6 pairs of appendages Phylum Chordata chelicerae, pedipalps, 4 pr walking legs Lancelets tunicates, vertebrates extend from cephalothorax Characteristics of embryos: - book lungs 1. possess notochord longitudinal, enhances gas exchange between flexible rod between digestive tract and hemolymph and air nerve cord 2. possess dorsal hollow nerve cord Arthropods: 3. have pharyngeal slits modified for gas Uniramians exchanges, jaw support, hearing, etc. jaw-like feeding appendages (mandibles), 4. have muscular postanal tail 1 pair of antennae, unbranched appendages Invertebrate Chordates Class Diplopoda - millipedes Subphylum Urochordata Class Chilopoda - centipedes - tunicates Class Insecta - insects - sessile marine animals - chordate characters seen only in larvae  Subphylum Cephalochordata Superclass Tetrapoda: - lancelets Class Reptilia Reptiles Subphylum Vertebrata Scaly, impermeable skin Characteristics Amniotes- Lay shelled amniotic eggs - neural crest formation during embryonic Chelonians (Testudines)- Turtles development Lepidosaurians- Tuatara, snakes, lizards - vertebral column + skull Archosaurs- Crocodilians, dinosaurs, - pronounced cephalization of sensory and birds neural apparati - closed circulatory system Superclass Tetrapoda: Agnathans- lack hinged jaws, notochord Class Aves present throughout life Birds Gnathostomes- possess hinged jaws, Amniotes notochord replaced by vertebrae, paired Possess feathers appendages Possess wings (flight) Tetrapods- Possess two pairs of Endothermic- most body heat generated appendages internally Two-circuit circulatory system Superclass Agnatha lack hinged jaws, Superclass Tetrapoda: notochord present throughout life Class Mammalia no paired appendages Mammals lampreys and hagfish Possess hair Possess mammary glands Superclass Gnathostoma: Endothermic Jawed Fish Two-circuit circulatory system Class Chondrichthyes- Sharks, rays Most give birth to young (amniotic) - cartilaginous skeletons Diaphragm for active ventilation of lungs Class Osteichthyes- bony fish (bone Groups- Monotremes skeletons) lay eggs - Subclass Actinopterygii Ray-finned fish platypuses, echidnas - Subclass Sarcopterygii Lobe-finned fish - Marsupials embryo completes development in pouch kangaroos and Superclass Tetrapoda: opossums Class Amphibia - Eutherians form placenta cats, humans, Characteristics squirrels - tetrapods (4 limbs) - terrestrial movement - aquatic larval stage MEMBRANE PHYSIOLOGY AND - moist, permeable skin ELECTROCHEMICAL Anurans- frogs and toads GRADIENT Urodeles- salamanders and newts Caecilians- legless, fossorial amphibians PLASMA MEMBRANE Selective transport of molecules into and out of the cell. A function carried out by membrane transport proteins. Cell recognition through the use of cell surface antigens. Cell communication through neurotransmitter and hormone receptors and through signal transduction pathways. Tissue organization, such as temporary and permanent cell junctions, and interaction with the extracellular matrix, with PLASMA MEMBRANE LIPIDS the use of a variety of cell adhesion molecules. Membrane-dependent enzymatic activity. Determination of cell shape by linkage of the cytoskeleton (is the skeletal system of the cell that gives shape) to the plasma membrane. Primary Location in Membrane Outer leaflet Outer leaflet Inner leaflet Inner leaflet Inner leaflet MODELS OF THE MAJOR CLASSES OF Phospholipid PLASMA MEMBRANE LIPIDS Phosphatidylcholine The phospholipid composition of the Sphingomyelin membrane varies among different cell types Phosphatidylethanolamine and even between the bilayer leaflets. Phosphatidylserine For example, in the erythrocyte plasma Phosphatidylinositol membrane, phosphatidylcholine and *Involved in signal transduction.* sphingomyelin are found predominantly in the outer leaflet of the membrane, whereas CHOLESTEROL AND GLYCOLIPIDS phosphatidylethanolamine, The sterol molecule cholesterol is also a phosphatidylserine, and phosphatidylinositol critical component of the plasma are found in the inner leaflet. membrane. It is found in both leaflets and serves to stabilize the membrane at normal body temperature (37°C). As much as 50% of the lipids found in the membrane can be cholesterol. As temperature increases, the fluidity of the membrane increases. The presence of unsaturated fatty acyl chains in the phospholipids and glycolipids also increases membrane fluidity. If a fatty acyl chain is unsaturated, the presence of a CHOLESTEROL AND GLYCOLIPIDS double bond introduces a "kink" in the A minor lipid component of the plasma molecule. membrane is glycolipids. These lipids, as This kink prevents the molecule from their name indicates, consist of two fatty associating closely with surrounding lipids, acyl chains linked to polar head groups that and, as a result, membrane fluidity is consist of carbohydrates. increased. One glycolipid, Although the lipid bilayer is "fluid," glycosy|phosphatidylinositol (GPI), plays movement of proteins in the membrane can an important role in anchoring proteins to be constrained or limited. the outer leaflet of the membrane. Both cholesterol and glycolipids, like MEMBRANE PROTEINS the phospholipids, are amphipathic, and As much as 50% of the plasma membrane they are oriented with their polar groups on is composed of proteins. These membrane the outer surface of the leaflet in which they proteins are classified as integral, are located. lipid-anchored, or peripheral. INTEGRAL MEMBRANE PROTEINS Integral membrane proteins are embedded in the lipid bilayer, where hydrophobic amino acid residues are associated with the hydrophobic fatty acyl chains of the membrane lipids. LIPID BILAYER Many integral membrane proteins span the The lipid bilayer is not a static structure. bilayer; such proteins are termed The lipids and associated proteins can transmembrane proteins. diffuse within the plane of the membrane. Transmembrane proteins have both The fluidity of the membrane is determined hydrophobic and hydrophilic regions. The by temperature and by its lipid composition a hydrophobic region, often in the form of a helix, spans the membrane.  GLYCOCALYX In many cells, some of the outer leaflet lipids, as well as many of the proteins exposed on the outer surface of the membrane, are glycosylated (i.e., have short chains of sugars, called oligosaccharides, attached to them). Collectively, these glycolipids and glycoproteins form what is called the glycocalyx. Depending on the cell these glycolipids and glycoproteins may be involved in cell Hydrophilic amino acid residues are then recognition (e.g., cell surface antigens) and exposed to the aqueous environment on formation of cell-cell interactions (e.g., either side of the membrane. attachment of neutrophils to vascular Transmembrane proteins may pass endothelial cells). through the membrane multiple times. LIPID ANCHORED PROTEIN protein can also be attached to the membrane via lipid anchors. The protein is covalently attached to a lipid molecule, which is then embedded in one leaflet of the bilayer. MEMBRANE TRANSPORT Glycosy|phosphatidylinositol (GPI) It has been estimated that anchors proteins to the outer leaflet of the approximately 10% of human genes membrane. (~2000) code for transporters. They are also Proteins can be attached to the inner leaflet targets for numerous drugs. via their amino-terminus by fatty acids (e.g., The intracellular and extracellular fluids are myristate or palmitate) or via their composed primarily of carboxyl-terminus by prenyl anchors (e.g., H2O, in which solutes (e.g., ions, glucose, farnesyl or geranyl-geranyl) amino acids) are dissolved. It also restricts the movement of water PERIPHERAL PROTEINS across the membrane. Lipid-anchored protein The presence of specific membrane Peripheral proteins may be associated with transporters in the membrane is responsible the polar head groups of the membrane for the movement of these solutes and lipids, but they more commonly bind to water across the membrane. integral or lipid-anchored proteins MEMBRANE TRANSPORT CHANNEL CONDUCTANCE PROTEINS The conductance varies, depending on the direction in which the ion is moving. WATER CHANNELS For example, if the channel has a larger Water channels, or aquaporins(AQPs), are conductance when ions are moving into the the main routes for water movement into cell than when they are moving out of the and out of the cell. cell, the channel is said to be an inward They are widely distributed throughout the rectifier. body (e.g., the brain, lungs, kidneys, Moreover, ion channels fluctuate between salivary glands, gastrointestinal tract, and an open state or a closed state, a process liver). called gating Cells in the collecting ducts of the kidneys express AQP3 and AQP4 in their SOLUTE CARRIERS basolateral membrane and AQP2 in their - Solute carriers (denoted SLCs by the apical membrane. HUGO Gene Nomenclature Committee) Moreover, the abundance of AQP2 in the represent a large group of membrane apical membrane is regulated by antidiuretic transporters categorized into more than 50 hormone (also called arginine families; almost 400 specific transporters vasopressin), which is crucial for the ability have been identified to date. of the kidneys to concentrate the urine. - These carriers can be divided into three Although all AQP isoforms allow the groups according to their mode of transport. passive movement of H20 across the membrane, some isoforms also provide a SOLUTE CARRIERS pathway for other molecules such as 1.Uniporters (or facilitated transporters), glycerol, urea, mannitol, purines, -transports a single molecule across the pyrimidines, CO2, and NH3 to cross the membrane. membrane. - The transporter that brings glucose into Because glycerol was one of the first the cell (glucose transporter 1 [GLUT-11, molecules identified as crossing the or SLC2A1) is an important member of this membrane via some AQPs, this group of group. AQPs is collectively called aquaglyceroporins. 2. Symporters (or cotransporters), -couples the movement of two or more ION CHANNELS molecules/ions across the membrane. As Ion channels are found in all cells, and are the name implies, the molecules/ions especially important for the function of are transported in the same direction. excitable cells (e.g., neurons and muscle - The Nat, K+,2CI-(NKCC) symporter cells). found in the kidney (NKCC2, or lon channels are classified by their SLC12A1), which is crucial for diluting and selectivity, conductance and mechanism of concentrating the urine is a member of this channel gating (i.e., opening and closing). group. Selectivity is defined as the nature of the ions that pass through the channel. 3. Antiporters (or exchange organelles (e.g., endosomes, lysosomes); transporters), also couples the movement as a result, they are also referred to as of two or more molecules/ions across the vacuolar H+-ATPases. membrane; in this case, however, the - H+-ATPase in the plasma membrane molecules/ions are transported in opposite plays an important role in urinary directions. acidification - The Na+- H+ antiporter is a member of this group of solute carriers. ADENOSINE - The Na+,K+,2CI-(NKCC) symporter found TRIPHOSPHATE-DEPENDENT in the kidney (NKCC2, or SLC12A1), which TRANSPORTERS is crucial for diluting and concentrating the - ABC transporters in humans and more urine is a member of this group. than 40 specific transporters have been identified to date. ADENOSINE. -They transport a diverse group of TRIPHOSPHATE-DEPENDENT molecules/ions, including CI-, cholesterol, TRANSPORTERS bile acids, drugs, iron, and organic anions. Use the energy in ATP to drive the -ATP-binding cassette (ABC) movement of molecules/ ions across the transporters. The ATPase ion transporters membrane. are subdivided into P-type ATPases and 2 groups of ATP-dependent V-type ATPases. transporters: 1. ATPase ion transporters (P-type ATPases and V-type ATPases) MEMBRANE TRANSPORT 2. ATP-binding cassette (ABC) The amount of a molecule being transporters. The ATPase ion transporters transported across the membrane can be are subdivided into P-type ATPases and regulated. V-type ATPases. Such regulation can take place through altering the number of transporters in the ATPASE ION TRANSPORTERS membrane or altering the rate or kinetics of The P-type ATPases are phosphorylated individual transporters (e.g., the time an ion during the transport cycle. channel stays in the open versus closed - Na+,K+-ATPase is an important example state), or both. of a P-type ATPase. - With the hydrolysis of each ATP molecule, VESICULAR TRANSPORT it transports three Nations out of the cell and ENDOCYTOSIS two K+ions into the cell. Na+,K+-ATPase is - A process wherein solute and water can present in all cells and plays a critical role in be brought into the cell. establishing cellular ion and electrical - The process whereby a piece of the gradients, as well as maintaining cell plasma membrane pinches off and is volume. internalized into the cell interior, and exocytosis is the process whereby vesicles ATPASE ION TRANSPORTERS inside the cell fuse with the plasma - V-type H+-ATPases are found in the membrane. membranes of several intracellular EXOCYTOSIS Allows the uptake of specific molecules - A process wherein solute and water can into the cell. In this form of endocytosis, be released from the cell molecules bind to receptors on the surface of the cell. VESICULAR TRANSPORT Endocytosis involves a number of In some cells (e.g., the epithelial cells lining accessory proteins, including adaptin, the gastro-intestinal tract), endocytosis clathrin, and the GPase dynamin across one membrane of the cell is followed by exocytosis across the opposite RECEPTOR-MEDIATED membrane. ENDOCYTOSIS This allows the transport of substances MECHANISMS OF ENDOCYTOSIS inside the vesicles across the epithelium, a A clathrin-coated pit is formed with adaptin process termed transcytosis linking the receptor molecules to clathrin. Dynamin, a guanosine triphosphatase MECHANISMS OF ENDOCYTOSIS (GTPase), assists in separation of the Consists of the nonspecific uptake of small endocytic vesicle from the membrane. molecules and water into the cell. Once inside the cell, the clathrin and Prominent feature of the endothelial cells adaptin molecules dissociate and are that line capillaries and is recycled. responsible for a portion of the fluid The uncoated vesicle is then ready to fuse exchange that occurs across these vessels. with other organelles in the cell 2. PHAGOCYTOSIS Allows for the cellular internalization of large particles (e.g., bacteria, cell debris). This process is an important characteristic of cells in the immune system (e.g., neutrophils and macrophages). Often, but not always, phagocytosis is a receptor-mediated process. Macrophages have receptors When bacteria invade the body on their surface that bind the Fc portion of h they are often coated with immunoglobulins. antibody, a process called opsonization. These bacteria then attach to the MECHANISMS OF EXOCYTOSIS membrane of macrophages via the fragment crystallizable (Fc) portion of the CONSTITUTIVE immunoglobulin, undergo phagocytosis, and Occurs in plasma cells that are secreting are destroyed inside the cell. immunoglobulin or in fibroblasts secreting collagen. 3. RECEPTOR-MEDIATED ENDOCYTOSIS  difference) is used to quantitate the driving force acting on a molecule to cause it to move across a membrane. A measure of the free energy available to carry out the useful work of transporting the molecule across the membrane. TWO COMPONENTS 1)​ Chemical Potential Difference REGULATED represents the energy in the Occurs in endocrine cells, neurons, and concentration gradient for X across exocrine glandular cells (e.g., pancreatic the membrane acinar cells). 2)​ Electrical Potential Difference In these cells the secretory product( e.g., represents the energy associated hormones, neurotransmitter, or digestive with moving charged molecules enzyme) after synthesis and (e.g., ions) across the membrane processing in the rough endoplasmic when a membrane potential exits reticulum and Golgi apparatus, is stored in the cytoplasm in secretory granules until an ELECTROCHEMICAL GRADIENT approval signal for secretion is received. Thus for the movement of glucose across a These signals may be hormonal or neural. membrane, only the concentrations of Once the cell receives the appropriate glucose inside and outside of the cell need stimulus, the secretory vesicle fuses with to be considered. However, the movement the plasma membrane and releases its of K+ across the membrane, for example, contents into the extracellular fluid. would be determined both from the K+ concentrations inside and outside of the cell BASIC PRINCIPLES OF SOLUTE AND and from the membrane voltage. WATER TRANSPORT ACTIVE AND PASSIVE TRANSPORT DIFFUSION When the net movement of a molecule Diffusion is the process by which molecules across a membrane occurs in the direction move spontaneously from an area of high predicted by the electrochemical gradient, concentration to one of low concentration. that movement is termed passive Thus wherever a concentration gradient transport. exists, diffusion of molecules from the Transport that is passive is sometimes region of high concentration to the region of referred to as either "downhill transport" low concentration dissipates the gradient. or "transport with the electrochemical Diffusion is a random process driven by the gradient." thermal motion of the molecules. ELECTROCHEMICAL GRADIENT The electrochemical gradient (also called the electrochemical potential  Measurements of osmolarity are temperature dependent because the volume of the solvent varies is larger at higher temperatures. OSMOLALITY Refers to the number of molecules dissolved in 1 kg of solvent. In contrast, osmolality, which is based on the mass of the solvent, is temperature OSMOSIS AND OSMOTIC PRESSURE independent. The movement of water across cell For this reason, osmolality is the preferred membranes occurs by the process of term for biologic systems osmosis. The movement of water is passive, with the OSMOLALITY driving force for this movement being the Because the solvent in biological solutions osmotic pressure difference across the cell and bodily fluids is water, and because of membrane. the dilute nature of biological solutions and bodily solutions, osmolalities are OSMOSIS AND OSMOTIC PRESSURE expressed as milliosmoles per kilogram of water (mOsm/kg H20). OSMOSIS AND OSMOTIC PRESSURE п = nCRT where n = number of dissociable particles per molecule C = total solute concentration R = gas constant T = temperature in degrees Kelvin OSMOLARITY Refers to the osmotic pressure generated by the dissolved solute molecules in 1 L of solvent.