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Bio5 Test 1 Study Guide Chapter 1 – Introduction A. Definitions a. Physiology – the study of function. b. Anatomy – the study of structure. c. Organization i. Levels – physiology can be studied on several levels (Fig. 1.1) ii. Systems – physiology can be studied based on systems and how they integrate (Tab. 1.1) B. Homeostasis – “staying the same” a. Health is often based on homeostasis (Fig. 1.3) b. Control systems contain an input controller output signal (Fig. 1.5) c. Most control systems use feedback mechanisms. (Fig. 1.10) i. Positive feedback – the product activates its maker. More rare. E.g. childbirth (Fig. 1.12) ii. Negative feedback – the product inhibits its maker. More common. E.g. temperature regulation. Similar to a thermostat/heater at home. (Fig. 1.11) d. Diabetes – an example of homeostatic imbalance i. Blood glucose is too high: greater than 100 mg/dL ii. Type 1 – insulin sensitive iii. Type 2 – insulin resistant C. Learning human physiology a. Use basic study skills: read assigned readings. Take notes. Review them with my study materials. Do problems. Repeat as needed. b. How to read maps (Fig. 1.2) c. How to read graphs (Fig. 1.14). Know x-axis is independent variable, y-axis is dependent variable. D. Ethics – many debatable situations a. Control groups in drug trials (withholding promising treatment for some patients) b. Taking biological tissue for research (the story of Henrietta Lacks) c. Privacy issues (collecting genome information) Chapter Problems: 1, 5, 7, 9, 10a-c, g, 13, 15, 16 Chapter 2 – Chemistry and Biological Molecules A. The atom (Fig. 2.5) a. Nucleus in center – made from protons (+) and neutrons (=). Both have an atomic weight of 1 b. Shell on outside. Made up of electrons (-) with close to zero weight. Electrons orbit the nucleus. c. Isotopes are atoms with a different number of neutrons. E.g. radioisotopes. B. Bonds a. Atoms form bonds with each other mostly because of electron stability. Atoms are happiest when outer shells have 2 or 8 electrons. If not, they try to share or give them to achieve this. b. Compound is a molecule made up of different types of atoms. c. Bonds (Fig. 2.6) i. Ionic – when electron is transferred. This results in charged atoms called ions. ii. Covalent – when electron is shared. This is how a molecule is formed. 1. Polar – asymmetrical, slight charge difference around molecule. 2. Non-polar – symmetrical, no charge differences. iii. Hydrogen – polar molecules form bonds from slight – and + charges. d. Chemical reactions i. Reactants Products, reversable ii. Exergonic releases energy while endergonic requires energy iii. Synthesis is a building reaction (anabolism) while decomposition is breaking down (catabolism). Exchange reactions involve both. C. Water – polarity and size give it unique properties a. Liquid vs. ice b. Cohesive and adhesive: surface tension. c. Solvent – solutes dissolve in it. (Fig. 2.8a) d. Heat sink – resists temperature change. Calorie is defined as energy required to raise 1 ml or g of water 1 oC. Heat is given off by evaporation, e.g. sweating. e. Acids and bases. Water dissociates into equal numbers of hydrogen ions and hydroxide ions. H2O H+ + OH- (Fig. 2.9) i. pH Scale. Defined as negative logarithm of the hydrogen ion concentration; pH = - log [H+]. Neutral water dissociates into 10-7 moles/liter of hydrogen ions. ii. Log is a ten-fold scale. iii. Buffers resist pH change. E.g. (bicarbonate) HCO3- + H+ H2CO3 (carbonic acid) in blood. D. Organic molecules contain carbon and hydrogen. a. Overview i. Functional groups give organic molecules different characteristics ii. Macromolecules are made from attaching monomers into polymers. b. Carbohydrates i. Chemical formula is usually (CH2O)n ii. Monosaccharide. Making disaccharide, polysaccharide (Fig. 2.2) iii. Examples 1. Starch – a storage polysaccharide in plants 2. Glycogen – storage in animals 3. Cellulose – cell wall structure c. Lipids – fats (Fig. 2.1) i. Hydrophobic – “water fearing”. Long hydrocarbon chains. ii. Triglyceride contains 3 fatty acid and 1 glycerol. Saturated vs. unsaturated fats. Unsaturated has double bonds and is not saturated with hydrogen. iii. Phospholipids have a polar head with a phosphate group and a non-polar tail. iv. Steroids – four ring groups. E.g. cholesterol (precursor to other steroids and membrane component), estradiol, testosterone d. Proteins (Fig. 2.3) i. Monomers are amino acids. Monomers are linked by peptide bonds. ii. 20 different amino acids based on R group differences. iii. Function related to final structure. 1. Many types of bonds are involved (Fig. 2-10). 2. Temperature, pH and salt can affect final shape. Denaturation like boiled eggs. (Fig. 2-21) 3. Proteins have specific binding partners iv. Levels of structure 1. Primary – basic amino acid sequence 2. Secondary – local folding motifs within protein, e.g. helix, sheet 3. Tertiary – whole protein structure 4. Quaternary – if more than 1 peptide is involved in final structure e. Nucleic Acids (Fig. 2.4) i. Monomer is nucleotide (phosphate-sugar-base) ii. DNA is string of deoxynucleotides. Has four bases ATGC. Genetic material. iii. RNA is less stable. Has AUGC. Genetic messenger. iv. ATP is a unit of energy. High energy phosphate bond. Chapter Problems: 1-3, 5-7, 9, 10, 17, 18, 21, 22, 26 Chapters 5 (and parts of 3) – Cellular Membranes A. Structure – Fluid Mosaic Model (Fig. 3.2b) a. Phospholipid bilayer (Fig. 3.2a) i. Phospholipids have polar head and nonpolar tail ii. Tails inside, heads face out. b. Proteins and other components i. Peripheral – on outside of bilayer. Can be involved in signaling, support, enzymes. ii. Integral – embedded in membrane. Can be involved in transport across membrane and signaling. B. Transport Across Membranes (Fig. 5.5) a. Passive transport – diffusion (Fig. Fig. 5.6) i. Down a concentration gradient (high low) ii. When across a membrane, need to apply Fick’s Law (Fig. 5.7) 1. Rate of diffusion is positively affected by surface area, concentration gradient, and permeability. 2. Rate of diffusion is negatively affected by membrane thickness. iii. Osmosis – diffusion of water across a membrane. (Fig. 5.2) 1. If there is a non-permeable solute, water will move down its concentration gradient if it exists. 2. Tonicity – relationship of solute concentrations across a membrane (Tab. 5.3) a. Isotonic: = (solution = cell). No net movement b. Hypotonic < (solution is less than cell). Water moves in. c. Hypertonic > (solution is greater than cell). Water moves out. iv. Facilitated diffusion – uses a protein (Fig. 5.10) 1. Channel proteins form a passageway. Can be gated or just a pore. Cystic fibrosis is due to a nonfunctional Cl- channel. (Fig. 5.11) 2. Carrier proteins bind to substance. This changes shape of protein. (Fig. 5.12b) b. Active transport i. Against concentration gradient, requires energy. ii. Primary – uses ATP as an energy source. Example: Na-K pump – an antiport (Fig. 5.14) 1. Pumps Na out and K in. 2. Mechanism (Fig. 5.15) a. 3 Na bind b. ATP attaches P and shape changes c. 3 Na are released d. 2 K bind e. P released and shape changes back to original conformation. 2 K are released. iii. Secondary – uses the diffusion of one substance to bring another against its concentration gradient. Example: Na-glucose pump – a symport. (Fig. 5.16) 1. Na binds 2. Glucose binds, shape changes 3. Both are released, shape resets. iv. Phagocytosis – large particles are taken in by membrane invagination. Uses lots of ATP (Fig. 5.18) v. Endocytosis – smaller particles taken into a vesicle. (Fig. 5.19) 1. Receptor mediated endocytosis. Meant for specific molecules (ligands). Receptors are organized on surface by clathrin. Once receptors are filled by ligand, invagination occurs. Uses many ATP. vi. Exocytosis – follows the opposite process of endocytosis. C. Electrical Potential a. An electrical potential is an electrical gradient due to the different types of solutes across a membrane. This creates potential for work, like a battery. b. The resting membrane potential is the charge at rest before an action occurs (Fig. 5.23) c. Potential can be measured. d. Changes in potential are an indication of work or signaling. These are due to movement of ions through channels, carriers, or pumps (Fig. 5.26) i. Depolarization – membrane potential goes down and causes a spike (more positive reading) ii. Repolarization – membrane potential is restored. iii. Hyperpolarization – overshooting resting membrane potential. Chapter 3 Problems: 1-3, Chapter 5 Problems: 2, 3, 5-7, 11, 14, 19, 21-24, 26, 28, 30, 34 Chapter 4 (and parts of 2) – Metabolism A. Energy – ability to do work a. Metabolism – the sum of all reactions in a cell i. Catabolism – breakdown molecules ii. Anabolism – build iii. Energy transfer summary in the body (Fig. 4.1) b. Kinetic (motion) vs. potential (stored). Chemical is potential energy (Fig. 4.2) c. Thermodynamics – study of energy transformations (Fig. 4.4) i. 1st Law: conservation (energy neither created nor destroyed) ii. 2nd Law: conversion (entropy always increases). Entropy is a measure of randomness (higher=more randomness) d. Free energy – available energy in a system to do work (Fig. 4.5) e. Types of reactions i. Endergonic – requires energy ii. Exergonic – releases energy iii. Coupled – use energy from an exergonic to drive an endergonic f. ATP i. ATP ADP + Pi + energy ii. Releases 7.3kcal/mol, enough for most reactions iii. ATP can be restored in a coupling cycle iv. Type of work ATP drives: mechanical, transport, chemical B. Enzymes a. Are catalysts that lower energy of activation (Fig. 4.3, 4.7) b. Enzyme characteristics i. Specific for certain substrates ii. Reaction must be spontaneous iii. Reusable c. Substrate Product d. Catalytic cycle: E + S ES EP E + P i. Substrate binding: uses “induced fit” instead of “lock-n-key” (Fig. 2.10) e. Regulation i. Environmental factors 1. Optimal pH, temperature, salt produce bell curves (Fig. 4.6) ii. Activators (Fig 2.12) 1. Cofactors (non-organic) 2. Coenzymes (organic) iii. Inhibitors 1. Competitive – binds active site (Fig. 2.12) 2. Noncompetitive – binds allosteric site C. Respiration a. C6H12O6 + 6 O2 6 CO2 + 6 H2O yielding a maximum of 38 ATP i. Two important coenzymes: NAD and FAD. These pick up electrons and transfer them later to make ATP. NAD can yield 3 ATP, FAD can yield 2 ATP. 1. NAD+ + H2 NADH + H+ 2. FAD + H2 FADH2 b. Occurs in 4 sets of reactions: Glycolysis Acetyl-CoA Formation Citric Acid Cycle Oxidative Phosphorylation (Fig. 4.11) c. Glycolysis (Fig. 4.12) i. Glucose Pyruvate ii. Yields 2 ATP and 2 NADH iii. Glucose activation steps 1. 2 ATPs used in 3 steps. 2. C6 2C3 (G3P) in 1½ steps. iv. Energy harvesting steps 1. 4 ATPs and 2 NADHs produced in 5 steps. Remember, these totals reflect doubling of reactions because of 2C3 molecules. 2. These ATPs are made by direct transfer of phosphate by enzymes. d. Acetyl-CoA formation i. Yields 2 NADH (1 per pyruvate) ii. Pyruvate + CoA CO2 + Acetyl-CoA e. Citric Acid Cycle (Fig. 4.13) i. Yields 2 ATP, 6 NADH, and 2 FADH2 (2 turns for 2 acetyl-CoA) ii. C4 (oxaloacetate) + Acetyl-CoA citrate (C6) + CoA iii. C6 C5 C4 yielding 2 CO2 + energy. f. Oxidative Phosphorylation (Fig. 4.14) i. Occurs on a membrane. ii. Converts energy carried by NADH and FADH2 to ATP (3/NAD, 2/FAD) iii. Chemiosmosis – production of ATP by a proton (H+) gradient. 1. Electrons are donated by NAD and FAD to the electron transport chain. 2. This triggers protons to be pumped into intermembrane space. High concentration creates a concentration gradient. 3. ATP synthase: proton movement through this protein back into matrix powers ATP synthesis. 4. Electrons accepted by oxygen g. Balance sheet: 38 ATP (34 from 10 NAD and 2 FAD) (Fig. 4.15) b. Fermentation – a “shortcut” respiration process. It just regenerates NAD+ to run glycolysis. Pyruvate is converted to lactate. This produces ATP by glycolysis only. Inefficient but very fast and no oxygen required. (Fig. 4.16). c. Lipid and Protein Catabolism i. Fats and proteins enter in different places of respiration ii. Proteins are broken down to amino acids and deaminated. iii. Triglycerides are broken down to fatty acid and glycerol iv. Both these pathways can be reversed to produce lipids and proteins (anabolism) D. Gene Expression a. Central Dogma: DNA RNA Protein. Transcription makes RNA by reading DNA and translation makes protein by reading RNA. (Fig. 4.18) i. DNA – uses ATGC bases ii. RNA 1. Uses AUGC bases 2. mRNA, rRNA, tRNA are a few important forms iii. Genetic Code (Fig. 4.17) 1. Each triplet codes for one amino acid (or stop codon) 2. 64 possibilites with 20 a.a., therefore redundancy b. Transcription (Fig. 4.19) i. Occurs in the nucleus. ii. Occurs whenever a gene product needs to be made. iii. RNA polymerase links together ribonucleotides iv. mRNA will be processed and exit the nucleus c. Translation(Fig. 4.21) i. tRNA: one for each amino acid. Has anticodon that is complementary to mRNA and site to add the right amino acid. ii. Ribosome is enzyme (organelle) that attaches amino acids together. iii. aa-tRNA comes into empty site in ribosome. Polymerization occurs then shift of ribosome. Used tRNA exits. iv. Stop codon will end the process. Chapter 4 Problems: 2-7, 9, 13-17, 20-28 Chapter 6 – Cellular Communication A. Cell to Cell Communication a. Mating types of yeast (a and ) lead to early cell communication studies. Mating factors are specific for mating receptors of opposite mating types. Binding causes shmoos (mating projections) b. Types of signaling depends on range/speed (Fig. 6.1) i. Gap junctions – molecules pass between cells. ii. Contact – cells must touch. Membrane molecules make contact. iii. Paracrine – short distance with neighboring cells using chemical signals. iv. Neuronal – long/short distances using electrical/chemical signals. v. Endocrine – long distance, uses hormones vi. Cytokine – long/short distances, uses cytokines (small proteins) B. Signaling Mechanisms a. Stages of cell signaling (Fig. 6.2) i. Signal Production – a cell produces and sends out a signal ii. Reception – signal is received. Binding of signal to receptor and information transmitted to inside of cell. iii. Signal Transduction – relays and amplifies the message iv. Targeting – target proteins receive the signal v. Response – a cellular response. The target protein performs its function. b. Reception i. Lipophilic (hormonal) – intracellular. The signal enters the cell and binds to receptor (Fig. 6.3a) ii. Lipophobic – extracellular. The signal binds a receptor that must be membranebound. Information has to be relayed into the cell (Fig. 6.3b,c) c. Signal Transduction i. Goal is to amplify the signal to give a strong response. (Fig. 6.4, 5) ii. Mechanisms 1. Phosphorylation cascades. One protein phosphorylates the next which activates more and more (Fig. 6.6) 2. Second messengers. Small ions or molecules that get released in bursts. They start new signaling cascades. a. Calcium as an example (Fig. 6.11) i. Calcium is stored in many compartments. Signals open gated channels and release it. ii. Release of calcium can trigger cellular response or bind other target proteins b. Cyclooxygenase (COX) produces prostoglandins. Many pain relievers block this enzyme. (Fig. 6.12) d. Modulation i. Signaling depends on the mechanism present for each cell. Some signals can give opposite responses (Fig. 6.13) ii. Competitive binding of receptors (Fig. 6.14) 1. Agonist – activates the receptor 2. Antagonist – blocks the receptor iii. Change number of receptors present 1. Up-regulation – low ligand numbers can be compensated by increasing receptor number 2. Down-regulation – high ligand numbers can lead to desensitization by lowering receptor amount C. Control Pathways a. Cannon’s Postulates, 1929 i. The nervous system can sense and control internal environment ii. There are systems under tonic control (one control element with volume knob) (Fig. 6.15a) iii. There are systems under antagonistic control (two competing control elements) (Fig. 6.15b) iv. A signal can have different response in different tissues b. Local control is short distance, reflex control covers long distances c. Response loops (Fig. 6.16) i. Negative feedback – the stimulus turns off pathway ii. Positive feedback – the stimulus accelerates pathway d. Comparing reflexes (Fig. 6.19, Tab. 6-4) i. Neural – highly specific, electrical, rapid, short duration, equal intensity ii. Endocrine – not very specific, chemical, slow, long duration, varying intensity Chapter 6 Problems: 1, 3, 4, 6, 8-11, 12b-d, 14, 16, 17, 21a, 22