BIOS10501 Weeks 1-3 Review Sheet - Biology Review PDF

What makes up an organism? The Big Six Atoms: Hydrogen Carbon Nitrogen Oxygen Phosphorus Sulfur a. Atoms (i.e the big six) b. Molecules (water, proteins, fats, carbs, DNA, hormones, etc.) c. Cells (Neurons, Muscle Cells, Liver Cells, Blood Cells, etc.) d. Tissues...

What makes up an organism? The Big Six Atoms: Hydrogen Carbon Nitrogen Oxygen Phosphorus Sulfur a. Atoms (i.e the big six) b. Molecules (water, proteins, fats, carbs, DNA, hormones, etc.) c. Cells (Neurons, Muscle Cells, Liver Cells, Blood Cells, etc.) d. Tissues (Nerve, Muscle, Connective, Epithelial) e. Organs (Heart, Brain, Skin, Muscle, etc.) f. Systems (Nervous, Circulatory, Digestive, Muscular, Respiratory, Urinary, Skeletal, Integumentary, Immune, Endocrine, Reproductive) g. Organism (Human, Fruit Fly, Oak Tree, etc.) h. Population i. Ecosystem What is homeostasis: a. Homeo = similar b. Stasis = state Body systems maintain homeostasis, which is essential for the survival of cells, which make up body systems. Examples of Homeostasis: a. Regulation of Nutrient Molecules b. Regulation of Oxygen and Carbon Dioxide c. Regulation of Acidity (pH) d. Regulation of Water and Electrolytes (Ions) e. Regulation of Waste Products f. Regulation of Temperature g. Regulation of Volume and Pressure Homeostatic Control Systems a. Negative Feedback: The output of a process inhibits the process that created it. Ex. A house’s furnace  a. Signal: Cold Air b. Sensor: Thermometer c. Integrator: Thermostat d. Effector: Furnace e. Output: Hot Air Ex. Thermoregulation a. Signal: Cold Blood/Cold Skin b. Sensor: Cold Receptors c. Integrator: Brain d. Effector: Muscles e. Output: Heat Ex. Blood Sugar Regulation b. Positive Feedback: The output of a process stimulates the process that created it. Ex. Uterine Contractions a. Signal: Tension in Uterus b. Sensor: Stretch Receptors in Uterus c. Integrator: Brainstem d. Effector: Muscle in the Uterus e. Output: Uterus Contracts Ex. Blood Clotting c. Feed-Forward: A process is up-or down-regulated in anticipation of an event Ex. Food a. Signal: Food in mouth b. Sensor: Tastebuds c. Integrator: Brain d. Effector: Salivary Glands e. Output: Saliva No signal, sensor, or integrator in feed-forward Ex. Blood Flow in Trained Athletes Introduction to Proteins: Proteins are the workers of the cell, molecular machines, and perform functions. They can be found anywhere (ex. In cell membranes, cytoskeletons, viruses, etc.) Proteins do not work in isolation, they interact with other molecules These interactions are essential to control when and where certain processes occur in a cell. Amino Acids: a. Proteins are made of amino acids.  b. There are a total of 20 amino acids. c. There are 9 essential amino acids in humans. Phenylalanine, Valine, Threonine, Tryptophan, Isoleucine, Methionine, Leucine, Lysine, and Histidine d. Our bodies cannot synthesize these 9 essential amino acids, so they are ESSENTIAL. e. The pH of the solution around the amino acids is important. Dehydration Synthesis Reaction: a. Water is the byproduct of forming peptide bonds (between amino acid molecules) Important: a. It may be counterintuitive, but a dipeptide doesn’t mean two peptide bonds but is rather two amino acids connected by ONE peptide bond. Protein Structure a. Primary Structure Chain of individual amino acids connected by peptide bonds. 2-D, linear form of amino acids b. Secondary Structure Hydrogen bonds act in between different amino acids, which causes the spiral shapes (helix) or beta pleated sheets. c. Tertiary Structure Complete 3-D folding pattern, more hydrogen bonding and interactions, more folding than secondary structure, 1 individual subunit A single chain of proteins, forming into a glob d. Quarternary Structure Putting tertiary structures (multiple subunits) together Multiple polypeptides (protein chains) Ex. hemoglobin a. Structure = Function Phosphorylation Special Chemical Signals Proteins that function as enzymes (make the reaction faster) are a great example of structure = function Factors that can change the shape or function of a protein a. Change in the surrounding chemical environment b. Protein-protein interactions or other chemical-protein interactions result in a change of shape. c. Phosphorylation: adding phosphate (strong negative charge) group to R (side chain) The Central Dogma a. Cells can make proteins. Start with DNA (double helix structure), which contains the information inside all cells. (DNA is complimentary and there are 3.2 billion pairs that make up the human genome) DNA gets transformed into RNA. - transcription RNA turns into proteins. - translation Mutations: a. Change in the DNA sequence of a cell b. Caused by: Radiation: UV radiation, X-rays Chemicals: Cigarettes, Nitrate, Barbecuing, Benzoyl Peroxide Infectious Agents: Human Papillomavirus (HPV), Helicobacter Pylori c. Types of Mutations: Normal Silent Mutation: when a change in DNA sequence doesn't affect the amino acid sequence of the protein Missense Mutation: results in a different amino acid than the wild-type protein Nonsense Mutation: occurs when two different amino acids are placed in the produced protein Frameshift Mutation: occurs when an insertion or deletion that is not a multiple of three happens within the protein-coding region of a gene Cell Physiology: Our bodies consist of around 30 trillion cells. These cells all work in harmony to carry out all the basic functions necessary for humans to survive. Our bodies also consist of around 38 trillion bacterial cells. Many important functions, from nutrient metabolism, drug and toxins metabolism, development of the immune system, protection against pathogens, and regulation of brain chemistry. Common Features of ALL Living Cells: a. Cytoplasm b. Plasma Membrane c. Ribosomes d. DNA Cellular Membranes: Phospholipid Bilayer and Proteins a. Phospholipids are amphipathic. b. One end of the molecule is hydrophobic (tail) and the other is hydrophilic (head). c. Membrane Proteins: Integral and Peripheral d. Functions: Receptors, Enzymes, Transport (Channels, Carriers, Pumps), Structural (junctional) - communication, adhesion, scaffolding, docking The Cytosol: Liquid part of the cytoplasm a. Water, ions, and other solutes (in all cells) b. Enzymes: Glycolysis, protein, nucleic acids and lipid metabolism, signaling enzymes c. Storage: Fat: excess food is stored in lipid droplets. Glycogen: excess carbohydrates are stored as glycogen inclusion bodies (mostly in the liver and muscle) Secretory Vesicles: packaged by the Golgi complex (remain in the cytosol until signaled to be released) d. Location of the Cytoskeleton and Proteins of Mobility Eukaryotes: Cellular Organelles a. About 50% of the total cell volume is occupied by organelles. Nucleus (always one) Endoplasmic Reticulum Golgi Complex Lysosomes Mitochondria Nucleus a. Genes are in the nucleus. b. Signals outside the cell control gene expression. c. These signals have to reach the nucleus. Important Questions: a. Do all cells have the same shape? No. (Red blood cells, nerve cells) b. Do cells change shape? Yes. (White blood cells) c. Do cells move? Yes. (WBC, sperm cells) Cytoskeleton: The Bone and Muscle of the Cell a. Provides shape, scaffolding, movement, and stress relief. b. Made up of microfilaments, intermediate filaments (not discussed), microtubules Microfilaments: a. Made up of a protein called actin. b. Actin exists as monomers of globular shape. c. Many actin monomers come together to form filamentous actin fibers (microfilaments). d. They consist of two chains of filamentous actin fibers coiled as a helix. e. Actin is an ATPase (enzyme) that can bind to ATP and hydrolyze it to the ADP and phosphate group. f. ATPase activity is important in the formation of filaments. g. It helps with stress resistance, holding organelles in place, cytokinesis, and ameboid movement (some organisms). It maintains and changes shape to allow movement, movement of skeletal, cardiac, and smooth muscle, cell extensions, and cell junctions. Microtubules: a. Made of monomers of a protein called tubulin (alfa and beta). b. The monomers assemble as a hollow tube. c. Grow longer and shorter by the addition of or removal of dimers at the ends. d. Tubulin is a GTPase activity. Important in the formation of microtubules. e. Microtubules are dynamic, constantly assembling and disassembling. f. They are essential for maintaining shape (asymmetrical shape ex. Nerve cell with a long slender axon), tracking motor proteins, organelles, and vesicles, forming the mitotic spindle, acting as the core of cilia and flagella, signal transduction (interacts with signaling molecules). Why would a cell want to secrete a protein? a. Defense (antibodies and cytokines) b. Hormones (insulin) c. Neurotransmitters (acetylcholine) d. Enzymes (digestive enzymes) e. Structural (collagen) Relationship between Endoplasmic Reticulum and The Golgi Complex: Exocytosis a. The rough ER, in association with its ribosomes, synthesizes and releases new proteins into the ER lumen. b. Within the ER lumen, a newly synthesized protein is folded into a final conformation and may be modified. c. A new protein is not able to traverse the ER membrane. d. Transport vesicles that fuse with the Golgi complex are formed.  e. As the vesicles travel through the ER and Golgi complex they are modified to their final form by post-translational modifications. Contents are sorted, packaged, and directed to final destinations. f. Secretory vesicles receive signals that initiate their fusion and release of vesicle contents by exocytosis. g. The smooth ER does not contain ribosomes but packages the new protein into transport vesicles. Endocytosis: a. Recycling of Content b. Fusion with Lysosome for Degradation c. Reuse and Redistribution Endoplasmic Reticulum in Different Cell Types: a. Muscle Cell: Sarcoplasmic Reticulum stores calcium b. Plasma Cell: Secretes huge amounts of antibodies. ER is very developed and occupies the whole cytoplasm. c. Mature Red Blood Cell: It has no nucleus and no ER. After maturation, it becomes a packet of circulating hemoglobin. Mitochondria: a. The site of MOST ATP production. b. Source of energy of the cell and recharges an ADP with phosphate. The ATP Cycle: a. When a cell needs energy, ATP is broken down, or hydrolyzed, into ADP and phosphate, which releases energy. b. The ADP produced is recycled back into ATP by adding a phosphate group. Specialized Cell Junctions: a. Desmosomes: Specialized cell structures that anchor adjacent cells together, providing mechanical stability and strength to tissues. Cytoskeletal components and other proteins. b. Tight Junctions: Creates a barrier to prevent the passage of molecules and ions between cells. c. Intestinal Epithelium: Tight junctions prevent the leakage of nutrients and pathogens from the gut lumen into the bloodstream. d. Blood-Brain Barrier: Restricts the movement of harmful substances. e. Gap Junctions: Intercellular connections that allow direct communication between adjacent cells. They contain protein channels called connexons, which enable the transfer of ions, small molecules, and signaling compounds.  f. Cardiac Muscle: Gap junctions allow for synchronized contraction of heart cells by enabling the rapid spread of electrical impulses. Diffusion: a. Movement of molecules from high concentration to low concentration. Both the solute and solvent move. Osmosis: a. Movement of solvent (water) across a semipermeable membrane from high to low solvent concentration. Only the solvent moves. Transport Across a Plasma Membrane: a. One main function of the plasma membrane is to serve as a permeability barrier. b. It is a selective membrane. c. Those substances that are lipid soluble are free to diffuse, others must be transported across the membrane. Fick’s Equation for Diffusion across a Lipid Membrane a. Q = the speed at which particles or molecules move from areas of high concentration to areas of low concentration. b. Triangle C: Concentration Gradient of that Substance c. P = Permeability of that substance (P = lipid partition coefficient) d. A = Surface Area of the barrier (membrane) e. MW = molecular weight of the substance (square root of MW approx. molecular radius) f. Triangle X: Membrane Thickness What is the lipid bilayer permeable to? a. Hydrophobic Molecules (oxygen, carbon dioxide, nitrogen, steroids) b. Small Uncharged Polar Molecules (water, glycerol, urea, ethanol) c. These molecules move by diffusion. What is the lipid bilayer not permeable to? a. Large uncharged polar molecules (glucose and sucrose) b. Ions (sodium, potassium, calcium, hydrogen, chloride) Passive Transport: a. Movement of molecules across the cell membrane from an area of high concentration to low concentration (down the concentration gradient). b. This kind of movement does not require the use of energy. c. Ex. diffusion, osmosis, and facilitated diffusion. Passive Transport Ex. a. Non-lipid-soluble substances cross cell membranes via intrinsic membrane proteins. Passive transport, they are channels and carriers. b. Channels select what gets through based on size and charge. c. In gated channels, there is actually a “gate” that opens static pores. d. There are temperature-gated, pH-gated, phosphorylation, and mechanically-gated channels. e. Carriers select what gets through based on binding specificity. f. Facilitated diffusion via carriers relies on specific recognition of the transported substance by the carrier protein AND a concentration gradient. g. Ionic transport via channels relies on specific recognition of the transported ion and a concentration and/or electrical gradient. Active Transport: a. Movement of molecules against the concentration gradient (from low to high concentration). b. This requires energy (ATP) and involves transport proteins called pumps. c. Ex. sodium-potassium pump Cellular Communication: a. Two major regulatory systems of the body ensure the survival of the body: The Endocrine System: Hormonal communication accomplished by hormones. The Nervous System: Communication requires the presence of membrane potentials, which can be modulated by various signals. These shifts in membrane potential enable cells to transmit electrical impulses, playing a crucial role in cell communication and responses to stimuli. Primary Active Transport: a. The energy of ATP is directly used to move sodium and potassium. b. Ex. sodium-potassium pumps (in all cells) Secondary Active Transport: a. The energy of ATP is used indirectly to transport substances. b. Ex. Sodium/Hydrogen Antiporter (in kidney cells) and Sodium/Glucose Symporter (in small intestine and kidney cells) Tertiary Active Transport: a. Ex. Hydrogen/Peptide Symporter (in small intestine) Membrane Potential: a. The plasma membrane of all living cells has a membrane potential (polarized electrically). b. This potential is the separation of opposite charges across the plasma membrane. c. Positive and negative attract each other and a lot of work is needed to separate them. If, after separation, they are allowed to go back together, the force of their attraction can be used to do work. d. The separation of charges across the membrane is called “potential” because it has the potential to do work. e. The work can be used for communication. Membrane Potential Continued: a. Sodium and Potassium ATPases maintain the sodium and potassium gradients across the cell membrane. b. A large population of potassium leak channels allows a lot of potassium to leak out of the cell. c. A small population of sodium leak channels allows some sodium to leak into the cell. d. Net Effect: At steady state, a typical cell maintains a membrane potential of about -70mV, relative to the extracellular space. Potassium: a. The concentration gradient for potassium tends to move this ion out of the cell. b. The outside of the cell becomes more positive as potassium ions move to the outside down their concentration gradient. c. The membrane is impermeable to the large intracellular protein anion. The inside of the cell becomes more negative as potassium ions move out, leaving behind anion. d. The resulting electrical gradient tends to move potassium into the cell. e. No further net movement of potassium occurs when the inward electrical gradient exactly counterbalances the outward concentration gradient. The membrane potential at this equilibrium point is the equilibrium potential for potassium at -90 mV. Sodium: a. The concentration gradient for sodium tends to move ions into the cell. b. The inside of the cell becomes more positive as sodium ions move to the inside down their concentration gradient. c. The outside becomes more negative as sodium ions move in, leaving behind in the ECF unbalanced negatively charged ions, mostly chloride. d. The resulting electrical gradient tends to move sodium out of the cell.  e. No further net movement of sodium occurs when the outward electrical gradient exactly counterbalances the inward concentration gradient. The membrane potential at this equilibrium point is the equilibrium potential for sodium at +60 mV. How do we calculate the membrane potential? a. Nernst Equation: EzF = RT ln (C left side over C right side) b. E= membrane potential (voltage) c. z= electrical charge of the permeable ion d. F= Faraday’s constant e. R= the ideal gas constant f. T= temperature g. C= concentration of the permeable ion The Equation for the Equilibrium Potential: a. The equilibrium potential for a given ion is the voltage required to oppose a given concentration gradient for that ion. Membrane Potential: a. The sodium-potassium pump actively transports sodium out and potassium into the cell, keeping the concentration of sodium high in the ECF and the concentration of potassium high in the ICF. b. Given the concentration gradients that exist across the plasma membrane, potassium tends to drive membrane potential to the equilibrium potential for potassium (-90 mV), whereas sodium tends to drive membrane potential to the equilibrium potential for sodium (+60 mV). c. However, potassium exerts the dominant effect on resting membrane potential because the membrane is more permeable to potassium. As a result, resting potential (-70mV) is much closer to potassium than to sodium. d. During the establishment of resting potential, the relatively large net diffusion of potassium outward does not produce a potential of -90 mV because the resting membrane is slightly permeable to sodium and the relatively small net diffusion of sodium inward neutralizes some of the potential that would be created by potassium alone, brining resting potential to -70mV, slightly less than potassium. Important: The potential is influenced not just by the concentration but also the permeability. Altering the Membrane Potential: a. Many cells can transiently alter their Vm by opening and closing specific ion channels like this - we call these gated ion channels.  b. There are 4 classes of gated ion channels: Chemically Gated Channels: A specific chemical binds to a channel and makes the channel open (or close) Mechanically Gated Channels: A specific mechanical event such as touch or stretch makes the channel open (or close). Voltage-Gated Channels: A raising or lowering of the membrane potential (Vm) makes the channel open (or close) Thermally Gated Channels: A raising or lowering of the temperature makes the channel open (or close) Types of Cellular Communication: a. Direct Cell-Cell Signaling (Gap Junctions and Transient Linkage) b. Chemical Messengers (Paracrines, Hormones, Neurotransmitters, Neurohormones) Chemical Messengers can open ion channels or induce the formation of a second messenger. Chemical Messengers: a. Function by binding to specific receptors: Chemical Messenger + Receptor (inside target cell or on cell surface) Binds and creates the Activated Receptor This leads to a biological effect Ex. Change membrane permeability, activate protein synthesis, stimulate the release of some cell product, up-or-down regulate a cellular process Remembering Membrane Potentials: a. What Vm would result if potassium were the only permeable ion? Vm = -95.5 mV b. What Vm would result if sodium were the only permeable ion? Vm = +71.4 mV c. Many cells can alter their membrane potentials by transiently opening and closing specific ion channels. d. These transiently openable/closable channels are what we call gated ion channels. Anatomy of a Neuron: a. Dendrites - input zone, contains lots of gated channels b. Nucleus c. Cell Body d. Axon Hillock - trigger zone, particularly high density of V-gated sodium channels and V-gated potassium channels. e. Axon - conducting zone, membranes of axons contain V-gated sodium and potassium channels. f. Axon Terminals - output zone The opening of gated ion channels leads to a graded potential. a. The magnitude of the stimulus determines the magnitude of the response. b. Graded potentials decrease over space and time. c. Think of graded potentials as dropping a pebble in a pool of water - the height of the resulting ripple depends on the force of the pebble, and the ripple gets smaller as it moves further away in both space and time. d. In the case of sensory neurons, the resulting graded potential is referred to as a receptor potential. Voltage-Gated Sodium Channels: Voltage-Gated Potassium Channels: Myelin Speeds Conduction: a. Myelin insulates the axon with blobs of fat. Myelin-producing cells wrap around axons many times, producing thick layers of cell membranes. b. This insulation leads to saltatory conduction. Action potentials jump from node to node very quickly. c. This results in a very fast transmission of action potentials. Conduction velocities up to 120m/sec (300 mi/hr) How do neurons communicate with other cells? a. Some synapses in the body are electrical connections (so far only found in particular neurons in the brain, very rare) b. Nearly all synapses in the body (including those in muscles) are chemical connections. Second Messenger Systems: a. They are widely used by cells of the body. b. First Messenger: An extracellular chemical messenger (could be a neurotransmitter, a hormone, or some other chemical) Steps: a. 1 first messenger molecule binds to 1 receptor protein. b. Several G-proteins are activated c. Many cAMP’s are produced d. A lot of protein kinase e. ATP and ADP are activated  f. A whole lot of proteins are activated g. A very big cellular response Important: Two advantages of having such a crazy-complicated process: a. Amplification of response b. It gives the cell a chance to regulate the magnitude of the response. Hormones: a. Hormones are produced by endocrine tissues: Produced by an endocrine gland Secreted into the blood Transported by the blood to its target cells Binds to specific receptors on (or within) the target cells to exert its effect b. Types of Hormones: Peptide Hormones (hydrophilic - water loving) Amine Hormones (hydrophilic except for thyroid hormone) Steroid Hormones (hydrophobic - water-hating) c. A hormone’s bioavailability influences its effect: How quickly is the hormone secreted into the blood? How is the hormone transported in the blood? Does the hormone need to be activated? How quickly is the hormone cleared from the circulation? Does the hormone interact with other hormones? Peptide Hormones: a. Most hormones are peptide hormones. b. String of amino acids. c. Synthesized in specific endocrine cells, stored in secretory vesicles prior to release d. Hydrophilic in structure (they dissolve right into blood plasma) e. Binds to receptors on the surface of target cells, activate intracellular response f. A peptide hormone might bind to a specific GPCR (G-protein Coupled Receptor) to open ion channels or to activate a 2nd messenger pathway within a target cell. g. A peptide hormone might bind to a specific enzyme that then phosphorylates proteins within a target cell. h. Examples: Human Growth Hormone and Insulin Insulin: a. Produced in beta cells of the pancreas, the release is stimulated by elevated blood glucose b. The pancreas contains a whole lot of different cell types.  c. Insulin circulates the bloodstream, and exerts tissue-specific effects: d. Insulin allows skeletal, muscle, heart, and fat cells to uptake glucose from blood. e. Insulin also tells the liver to store glucose. f. Insulin can be thought of as the “feasting” hormone since its job is to lower blood glucose. g. Exercise also causes these glucose channels to insert into the cell membranes, no insulin or insulin receptors are required. The mechanism of how this works is still being studied. h. Insulin molecules and all molecules are broken down as they circulate through the liver and kidneys. Steroid Hormones: a. Produced primarily in gonads and adrenal glands. b. All steroids are derivatives of cholesterol. c. Steroids are hydrophobic d. They are produced primarily in 3 endocrine tissues (adrenal glands, testes, ovaries) e. Steroids circulate through the blood bound to carrier proteins. f. When a steroid molecule falls off of its carrier protein, it can diffuse right through cell membranes and bind to a specific receptor within a target cell. g. The steroid bound to its receptor then moves into the nucleus docks onto DNA and activates transcription of specific genes within the target tissue. Amine Hormones: a. Derivatives of the amino acids Tyrosine and Tryptophan Tyrosine: a. Thyroid Hormone - Hydrophobic b. Epinephrine and Dopamine - Hydrophilic Tryptophan: a. Serotonin - Hydrophilic b. Melatonin - Hydrophilic