Anatomy & Physiology Notes for Exam 1 PDF

A&P 1 - Notes/Study Guide for Exam 1 Lectures 1-4 Lecture One ​ Link to L1 Flashcards (Quizlet): ○​ (Not yet complete) 1.1 The Scope of Anatomy and Physiology (Slides 2-6) Introduction: Slide 3 ​ Anatomy: Study of the structure. ​ Physiology:...

A&P 1 - Notes/Study Guide for Exam 1 Lectures 1-4 Lecture One ​ Link to L1 Flashcards (Quizlet): ○​ (Not yet complete) 1.1 The Scope of Anatomy and Physiology (Slides 2-6) Introduction: Slide 3 ​ Anatomy: Study of the structure. ​ Physiology: Study of the function. ​ Anatomy and physiology are complementary and never entirely separable. ○​ Physiology provides meaning to anatomy. ○​ Anatomy is what makes physiology possible. Methods to Examine Structure of the Human Body: Slide 4 ​ Inspection: Visual examination. ​ Palpation: Feeling structures with hands. ​ Auscultation: Listening to sounds produced by the body. ​ Percussion: Tap on the body, feel for resistance, and listen to emitted sound for abnormalities. ​ Dissection: Cutting and separating human body tissues to reveal tissue relationships; use a cadaver. ​ Comparative Anatomy: Study (for example, dissection) of multiple species to learn about form, function, and evolution. ​ Exploratory Surgery: Opening the living body to see what is wrong; now replaced by medical imaging to view inside without surgery. ​ Medical Imaging: Non-invasive methods to visualize structures within the body. ​ Radiology: Branch of medicine specializing in imaging. Subdisciplines of Anatomy: Slide 5 ​ Gross Anatomy: Study of structures that can be seen with the naked eye. ​ Histology (microscopic anatomy): Examination of tissues with microscope. ​ Histopathology: Microscopic examination of trusses for signs of disease. ​ Cytology: Study of structure and function of cells; fine detail (ultrastructure) may be resolved using an electron microscope. Physiology Uses the Methods of Experimental Science: Slide 6 ​ Subdisciplines of physiology: ○​ Neurophysiology: Physiology of nervous system. ○​ Endocrinology: Physiology of hormones. ○​ Pathophysiology: Mechanisms of disease. ​ Comparative Physiology: Study of different species to learn about body functions. ○​ Basis for much of our understanding of human physiology and the development of new drugs and medical procedures. 1.2 The Origins of Biomedical Science (Slides 7-17) Greek and Roman Legacy: Slides 8 & 9 ​ Hippocrates (Greek Physician): ○​ “Father of Medicine” ○​ Established code of Ethics (Hippocratic Oath) ○​ Urged physicians to seek out natural causes of disease rather than attributing them to acts of the gods and demons. ​ Aristotle (Greek Philosopher/Scientist): ○​ Believed diseases had supernatural or physical causes. ○​ Called supernatural causes of disease theologi. ○​ Called natural causes of disease physiologi. ​ This gave rise to the terms physician and physiology. ○​ Believed complex structures were built from simpler parts. ​ Metrodora (Greek Physician): ○​ First woman to publish a medical textbook. ​ Claudius Galen (Greek Physician): ○​ Physician to Roman gladiators. ○​ Dissected animals because use of cadavers were banned. ○​ Saw science as a method of discovery. ○​ Teachings were adopted as dogma in Europe in the Middle Ages. The Birth of Modern Medicine: Slide 10 ​ Maimonides (Moses Ben Maimon): ○​ Jewish physician. ○​ Physician to Egyptian sultan, Saladin. ○​ Wrote 10 influential medical texts. ​ Avicenna (Ibn Sina):  ○​ From Muslim world. ○​ “The Galen of Islam”. ○​ Combined Galen and Aristotle’s findings with original discoveries. ○​ Wrote The Canon of Medicine. Used in medical schools for 500 years. Beginning of Modern Western Medicine: Slide 12-16 ​ Andreas Vesalius: ○​ Catholic Church relaxed restrictions on dissection of cadavers. ○​ Performed his own dissections rather than having the barber-surgeons dissect. ○​ Published first atlas of anatomy, De Humani Corporis Fabrica (On the Structure of the Human Body) in 1543. ​ William Harvey: ○​ Early physiologist - contributions represent the birth of experiment physiology. ○​ Published the book De Motu Cordis (On the Motion of the Heart) in 1628. ○​ Realized blood flows out from the heart and back to it again. ​ Credit also given to Michael Servetus. ​ Galileo: ○​ Patented the compound microscope as a by-product of his work with telescopes. ○​ Tube with lenses at each end: ocular lens and objective lens. ○​ Didn’t use it for studying biological material. ​ Marcello Malpighi: ○​ First to use compound microscope to study biological material. ○​ Observed blood cells, capillaries, and capillary blood flow. ​ Robert Hooke: ○​ Made many improvements to compound microscope. ○​ Invented specimen stage, illuminator, coarse, and fine focus controls. ○​ His microscopes magnified only 30x. ○​ First to see and name “cells”. ○​ Published first comprehensive book of microscopy (Micrographia) in 1665. ​ Antony van Leeuwenhoek: ○​ Invented simple (single-lens) microscope with great magnification (200x) looking at fabrics. ○​ Superior magnification compared to Hooke’s microscope due to Leeuwenhoek’s superior lens-making. ○​ Published his observations of blood, lake water, sperm, bacteria from tooth scrapings, and many other things. Beginning of the Cell Theory: Slide 17  ​ Matthias Schleiden and Theodor Schwann: ○​ Examined wide variety of specimens. ○​ Concluded that “all organisms were composed of cells”. ○​ First tenet of cell theory ​ Considered to be perhaps the most important breakthrough in biomedical history ​ All functions of the body are interpreted as effects of cellular activity. Living in a Revolution: Slide 18 ​ Modern Biomedical Science Advances: ○​ Germ theory of disease. ○​ Mechanisms of heredity. ○​ Structure of DNA. ○​ Advances in medical imaging. ○​ Disease imaging and treatment. ○​ Mapping of the human genome. 1.3 The Scientific Method (Slides 19-25) Introduction: Slide 20 ​ Scientific Method: The process of performing science, including careful observation, logical thinking, and proper analysis of observations and conclusions. ○​ Science and scientific methods set standards for truth. The Inductive Method: Slide 21 ​ Inductive Method: Process of making numerous observations until one becomes confident in drawing generalizations and predictions. ○​ Knowledge of anatomy obtained by this method. ​ What is Proof in Science?: ○​ Reliable observations, repeatedly confirmed. ○​ Not falsified by any credible observation. ​ In Science, All Truth is Tentative: ○​ Proof beyond a reasonable doubt. ○​ May abandon yesterday’s truth if tomorrow’s facts disprove it. The Hypothetico-Deductive Method: Slide 22  ​ Hypothetico-Deductive Method: Most physiological knowledge gained by this method. ​ Investigator formulates a hypothesis - an educated speculation or possible answer to the question. ○​ Good hypotheses are consistent with what is already known and are testable. ​ Falsifiability: If we claim something is scientifically true, we must be able to specify what evidence it would take to prove it wrong. Experimental Design: Slide 23 ​ Sample Size: Number of subjects in a study. ​ Controls: Control group resembles treatment group but does not receive treatment. ​ Psychosomatic Effects: Effects of subject’s state of mind on her or his physiology; tested by giving placebo to control group. ​ Experimenter Bias: Avoided with double-blind method. ○​ Neither the subject nor experimenter knows if the subject is a part of control or treatment group. ​ Statistical Testing: Use statistical tests to provides statement of probability that treatment was effective. Peer Review: Slide 24 ​ Peer Review: Critical evaluation by other experts in the field. ○​ Done prior to funding or publication. ○​ Done by using verification and repeatability of results. ○​ Ensures honesty, objectivity, and quality in science. Facts, Laws, and Theories: Slide 25 ​ Scientific Fact: Information that can be independently verified. ​ Law of Nature: ○​ Generalization about the way matter and energy behave. ○​ Results from inductive reasoning and repeated observations. ○​ Written as verbal statement or mathematical formula. ​ Theory: ○​ An explanatory statement or set of statements derived from facts, laws, and confirmed hypotheses. ○​ Summarizes what we know; suggests directions for further study. 1.4 Human Origins and Adaptations (Slides 27-32) Introduction: Slide 27  ​ Theory of Natural Selection: Explanation of how species originate and change through time; help understand the human body. ​ Charles Darwin: ○​ Influential biologist. ○​ Presented first well-supported theory of how evolution works. ​ On the Origin of Species by Means of Natural Selection (1859) -“the book that shook the world”. ​ The Descent of Man (1871) - Human evolution and relationship to other animals. Evolution, Selection, and Adaptation: Slide 28 ​ Evolution: ○​ Change in genetic composition of population of organisms. ​ Example: Development of bacterial resistance to antibiotics. ​ Natural Selection: ○​ How evolution works. ○​ Selection Pressures: Forces that promote reproductive success of some individuals more than others. ​ Example: Predators ○​ Adaptations: Inherited features of anatomy and physiology that evolved in response to pressures and that enable organisms to succeed. ​ Example: Better camouflage. Our Basic Primate Adaptations: Slide 29 ​ Some human anatomical and physiological features can be traced back to ancestral primates. ​ Early primates were arboreal (tree-dwelling) ○​ Mobile shoulders - better movement among branches. ○​ Opposable thumbs and prehensile hands - grasps branches and manipulate objects. ○​ Forward-facing eyes with stereoscopic vision - depth perception. ○​ Color vision - find ripe fruit. ○​ Large brain - memory allowing efficient food finding. Walking Upright: Slides 31 & 32 ​ Bipedalism: Standing and walking on two legs. ○​ Helps spot predators, carry food, tools, infants. ○​ Adaptation to living on savanna (grassland) as Africa became hotter and drier.  ​ Skeletal and muscular modifications. ​ Changes to family structure. ○​ Australopithecus: A bipedal primate genus that lived more than 3 million yrs ago. ○​ Homo genus appeared 2.5 million yrs ago. ​ Taller, larger brain volume, tool-making. ○​ Homo erectus appeared 1.8 million yrs ago. ​ Migrated from Africa to parts of Asia. ○​ Homo sapiens originated in Africa 200,000 yrs ago. ○​ Evolutionary medicine traces some of our diseases to difference between modern and prehistoric environments. 1.5 Human Structure (Slides 34-40) The Hierarchy of Complexity: Slides 34 & 35 ​ Human organization based on successive levels of hierarchy. Organism composed of organ systems. Organ systems composed of organs. Organs composed of tissues. Tissues composed of cells. Cells composed partly of organelles. Organelles composed of molecules. ↑Molecules composed of atoms. Hierarchy of Human Complexity: Slides 36 & 37 ​ Organism: Single, complete individual. ​ Organ System: Group of organs with a unique collective function. ○​ Example: Circulation, respiration, digestion. ​ Organ: Structure composed of two or more tissue types that work together to carry out a function. ○​ An organ has defined anatomical boundaries; can have organs within organs. ​ Tissue: Similar cells and cell products forming a discrete region of an organ and performs a specific function. ​ Cell: Smallest unit to carry out all basic functions of life. ​ Organelle: Structure within a cell that carries out a function. ​ Molecule: Particle composed of two or more atoms. ○​ Largest molecules (Proteins, fats, DNA) called macromolecules. ​ Atom: Smallest particle with unique chemical identity. Approaches to Studying and Understanding Human Life: Slide 38 ​ Reductionism: Theory that large, complex systems can be understood by studying their simple components. ○​ Essential to scientific thinking, but some properties cannot be predicted from individual parts. ​ Holism: “Emergent properties” occur as we ascend the levels of organization; these cannot be predicted from the properties of individual parts alone. ○​ Humans are more than the sum of their parts. Anatomical Variation: Slide 39 ​ No two humans are exactly alike; even identical twins have differences. ○​ Some individuals… ​ Lack certain muscles. ​ Have atypical number of vertebrae. ​ Have atypical number of certain organs (Example, kidneys). ​ Show situs inversus - left-right reversal of organ placement. 1.6 Human Function (Slides 41-58) Characteristics of Life: Slides 43 & 44 ​ Life is a collection of properties that distinguish living from nonliving things. ​ Organization: Living things exhibit a higher level of organization than non-living things. ​ Cellular Composition: Living matter is always compartmentalized into one or more cells. ​ Metabolism: The sum of internal chemical change. ​ Responsiveness (Excitability): Ability to sense and react to changes in environment (stimuli). ​ Movement: Movement of entire organism or of substances within the organism. ​ Homeostasis: Maintaining relatively stable internal conditions. ​ Development: Change in form or function over time. ○​ Differentiation: Transformation of unspecified cells into cells with a committed task. ○​ Growth: Increase in size; occurs through chemical change. ​ Reproduction: Organisms produce copies of themselves; pass genes to offspring. ​ Evolution: Genetic change from generation to generation; occurs due to mutations (change in DNA structure).  ○​ Observe evolution in population as a whole; a single organism does not evolve over the course of its life. Physiological Variation: Slide 45 ​ Physiology more variable than anatomy: ○​ Variations in sex, age, diet, weight, physical activity, genetics, and environment. ○​ Typical physiological values: ​ Reference man: 22 yr old, 154 lbs, light physical activity, consumes 2,800 kcal/day. ​ Reference woman: Same as man except 128 lbs and 2,000 kcal/day. ○​ Failure to consider variation can lead to overmedication of elderly or medicating women on the basis of research done on men. Negative Feedback and Homeostasis: Slides 46-52 ​ Homeostasis: The ability to detect change, activate mechanisms that oppose it, and thereby maintain relatively stable internal conditions. ○​ Claude Bernard (1813 to 1878): Noted fairly constant internal conditions despite changing external conditions. ​ Example: Temperature. ○​ Walter Cannon (1871 to 1945): Coined the term homeostasis. ○​ Negative Feedback allows for dynamic equilibrium within a limited range around a set point. ​ The body senses a change and “negates” or reverses it. ○​ Loss of homeostatic control causes illness or death. ○​ Internal conditions fluctuate within a limited range. ​ Dynamic Equilibrium: Around a set point. ​ Negative Feedback: Mechanism that keeps a variable close to set point; the body senses a change and reverses it. ○​ Because feedback mechanisms alter original changes that trigger them, they are called feedback loops. ○​ Example: Homeostasis in body temperature. ​ If too warm, skin blood vessels dilate (vasodilation) and sweating begins (heat-losing mechanism). ​ If too cold, skin blood vessels constrict (vasoconstriction) and shivering begins (heat-gaining mechanism). ​ Homeostasis Example: Slide 50 ○​ Homeostasis of blood pressure (baroreflex).  ​ Rise from bed, blood drains from head and blood pressure falls in this region. ​ Detected by baroreceptors that transmit signals to cardiac center of the brainstem. ​ Cardiac center transmits signals to heart to increase heart rate, raising blood pressure and restoring homeostasis. ○​ Baroreflex illustrates the common components of a feedback loop. ​ Receptor: Structure that senses change in the body. ​ Example: The baroreceptors above heart that monitor blood pressure. ​ Integrating (control) center: Control center that processes the sensory information “makes a decision”, and directs the response. ​ Example: Cardiac center of brainstem. ​ Effector: Cell or organ that carries out the final corrective action to restore homeostasis. ​ Example: The heart. Positive Feedback and Rapid Change: Slides 53 & 54 ​ Positive Feedback: Self-amplifying cycle. ○​ Leads to greater change in same direction, as opposed to the corrective action of negative feedback. ○​ Normal way of producing rapid changes. ​ Example: Childbirth, blood clotting, protein digestion, and generation of nerve signals. ○​ Can sometimes be dangerous. ​ Example: Vicious circle of runaway fever. Gradients and Flow: Slides 55-58 ​ Matter and energy tend to flow down gradients. ​ Gradient: Difference in chemical concentration, charge, temperature, or pressure between two points. ○​ Blood flows down a pressure gradient, from a place of higher pressure to lower pressure. ​ Chemicals flow down a concentration gradient. ​ Charged particles flow down an electrical gradient. ​ Electrochemical Gradient: Combination of concentration, electrical gradients. ​ Heat flows down a thermal gradient.  ​ Movement in the opposite direction is up the gradient and requires spending metabolic energy. 1.7 The Language of Medicine (Slides 59-64) The History of Anatomical Terminology: Slide 60 ​ About 90% of current medical terms come from 1,200 Greek and Latin roots reflecting ancient past. ​ The Renaissance brought progress but confusion. ○​ Some structures are named differently in varied countries, and some are named after people (eponyms). ​ In 1895, anatomists established worldwide naming conventions. ○​ Rejected eponyms; used unique Latin names. ​ Terminologia Anatomica (TA) provided standard international anatomical terms. ○​ Provided Latin names and English equivalents. ○​ In 1998, approved by anatomists in over 50 countries. Analyzing Medical Terms: Slide 61 ​ Anatomical terminology based on word elements such as roots, prefixes, suffixes. ○​ Scientific terms: ​ One root (stem) with core meaning ​ Combining vowels join roots into a word ​ Prefix and/or suffix may modify meaning of root word. ​ Acronyms: Pronounceable words formed from first letter, or first few letters, of series of words. ○​ Example: PET scans. Plurals, Adjectives, and Possessive Forms: Slide 62 ​ Plural forms of anatomical terms vary. ○​ Examples: Cortex vs cortices, corpus vs corpora. ​ Adjective often follows noun it modifies ○​ Example: Biceps brachii. ​ Adjectival form of a term can appear different than noun form. ○​ Example: Brachium (n.) referring to the arm, vs. brachii (adj.) referring to “of the arm”. 1.8 Review of Major Themes (Slides 65-75) Key Unifying Principles of Anatomy and Physiology: Slide 65 ​ Unity of Form and Function: Anatomy and physiology complement each other and cannot be divorced from one another. ​ Cell Theory: All structure and functions result from the activity of cells. ​ Evolution: The human body is a product of evolution. ​ Hierarchy of Complexity: Human structure can be viewed as a series of levels of complexity. ​ Homeostasis: The Purpose of most normal physiology is to maintain stable conditions within the body. ​ Gradients and Flow: Matter and Energy tend to flow down gradients. Medical Imaging: Slides 66-75 ​ Radiography (X-rays): ○​ Over half of all medical imaging. ○​ Penetrate tissues to darken photographic film beneath the body; dense tissue appears white. ○​ Radiopaque substances can be injected or swallowed to fill hollow structures. ​ Example: Blood vessels, intestinal tract. ○​ Digital Subtraction Angiography (DSA): Useful for showing blockages and blood flow. ​ Computed Tomography (CT Scan): ○​ Formerly called a CAT scan. ○​ Low-intensity X-rays and computer analysis. ○​ Slice-type image. ○​ Increased sharpness of image. ​ Magnetic Resonance Imaging (MRI): ○​ Superior quality to CT scan and no X-ray exposure. ○​ Best for soft tissue. ○​ Functional MRI (fMRI): Real time changes in brain. ​ Positron Emission Tomography (PET): ○​ Assesses metabolic state of tissue. ○​ Inject radioactively labeled glucose. ○​ Image color shows tissues using the most glucose at the moment. ○​ Damaged tissues appear dark. ​ Sonography: ○​ Second oldest and second most widely used.  ○​ High-frequency sound waves echo back from internal organs. ○​ Avoids harmful X-rays so good for obstetrics. ○​ Image not very sharp. Lecture Two 2.1 The Chemical Elements (Slides 4-27) Chemical Elements: Slide 4 ​ A chemical element is the simplest form of matter to have unique chemical properties. ○​ Identified by an atomic number - number of protons in nucleus. ​ Periodic table arranges elements by atomic number. ○​ 91 naturally occurring elements: ​ 24 play roles in humans; 6 are most abundant (98.5% body weight). ​ Oxygen, carbon, hydrogen, nitrogen, calcium, and phosphorus. ○​ Trace Elements: Present in minute amounts, play vital roles. ​ Some are minerals: Inorganic elements extracted from soil by plant, passed up food chain to humans ○​ 4% of body weight, mostly calcium and phosphorus. ○​ Body structure (bones, teeth), enzyme function, nerve/muscle cell functions. Atomic Structure: Slide5-7 ​ Greek philosopher coined term “atom” (“indivisible”) as the smallest unit of matter. ​ Neils Bohr proposed planetary model of atomic structure in 1913; useful as a schematic, but not accurate structure. ○​ Nucleus: Center of atom, composed of protons and neutrons. ​ Protons: Single (+) charge; mass = 1 atomic mass unit (amu). ​ Neutrons: No charge; mass = 1 amu. ○​ Electrons: Concentric clouds (electron shells or energy levels) surrounding nucleus. ​ Have single (-) charge; very low mass. ​ An atom is electrically neutral, as number of electrons = number of protons. ○​ Valence Electrons: In outermost sell and determine chemical bonding properties of an atom. Isotopes and Radioactivity: Slides 8-11  ​ Isotopes: Varieties of an element that differ only in number of neutrons and therefore in atomic mass. ○​ Extra neutrons increase atomic weight. ○​ Isotopes of an element are chemically similar because they have same number of valence electrons. ○​ Atomic weight (relative atomic mass) of an element accounts for the fact that an element is a mixture of isotopes. ​ Isotopes of an element have identical chemical behavior, but can differ in physical behavior. ○​ Radioisotopes: Unstable isotopes that decay and give off radiation in process called radioactivity. ​ Every element has at least one radioisotope. ​ Incense radiation can be ionizing (ionizing radiation) - ejects electrons, destroys molecules, creates free radicals - and can cause genetic mutations and cancer. ​ Example: UV radiation, X-rays, alpha particles, beta particles, gamma rays. ○​ Physical half-life of radioisotopes - time required for 50% to decay to a stable state. ○​ Biological half-life of radioisotopes - time required for 50% to disappear from the body. ​ Standard measure of radiation dosage is Sievert (Sv). ○​ 5 Sv or more is usually fatal. ○​ Standard acceptable exposure = 50 mSv per yr. ​ Background radiation: ○​ Natural sources such as radon gas and cosmic rays. ○​ Average = 2.4 mSv per yr. ​ Artificial sources of radiation: ○​ X-rays, color Tvs. ○​ Average = 0.6 mSv per yr. Radiation and Madame Curie: Slide 12 ​ First woman to receive Nobel Prize (1903). ​ First woman to receive a PhD. ​ Coined term “radioactivity”. ​ Discovered radioactivity of polonium and radium. ​ Trained physicians in use of X-rays and pioneered radiation therapy as cancer treatment. ​ Died of radiation poisoning at age 67. Ions, Electrons, and Free Radicals: Slides 13-17 ​ Ion: Charged particle (atom or molecule) with unequal number of protons and electrons. ○​ Ionization: Transfer of electrons from one atom to another. ○​ Anion: Particle that has net negative charge due to gain of electrons. ○​ Cation: Particle that has net positive charge due to loss of electrons. ○​ Ions with opposite charges are attracted to each other. ​ Slats: Electrically neutral compounds of cations and anions; readily dissociate in water into ions and act as electrolytes. ○​ Example: Sodium chloride (table salt), calcium chloride. ​ Electrolytes: Substances that ionize in water and form solutions capable of conducting electric current. ​ Functions of electrolytes: ○​ Chemical reactivity, osmotic effects, electrical excitability of nerve and muscle. ○​ Electrolyte balance is one of the most important considerations in patient care (imbalances can lead to coma or cardiac arrest). ​ Free Radicals: Unstable, highly reactive particles with unusual number of electrons. ○​ Produced by normal metabolic reactions, radiation, certain chemicals. ○​ Trigger reactions that destroy molecules, and can cause cancer, death of heart tissue, and aging. ​ Example: Superoxide anion. ​ Antioxidants: Chemicals that neutralize free radicals. ○​ Example: Superoxide Dismutase (SOD) is an antioxidant enzyme that converts superoxide anion into oxygen and hydrogen peroxide. ○​ Selenium, vitamin E, vitamin C, and carotenoids are antioxidants obtained through diet. Molecules and Chemical Bonds: Slides 18-27 ​ Atoms can combine to form molecules. ○​ Molecule: Particle composed of two or more atoms united by a chemical bond. ​ Compound: Molecule composed of two or more different elements. ​ Can be represented by a molecular formula, which identifies constituent elements and how many atoms of each are present. ​ Also can be represented by a structural formula, which identifies the location of each atom. ○​ Isomers: Molecules with identical molecular formula but different arrangements of their atoms. ​ Molecular Weight (MW): Sum of the atomic weight of atoms. ○​ Example: To calculate MW of glucose (C6H12O6).  ​ 66 C atoms x 12 amu each = 72 amu. ​ 12 H atoms x 1 amu each = 12 amu. ​ 6 O atoms x 16 amu each = 96 amu. ​ MW = 180 amu. ​ Chemical bonds hold atoms together within a molecule, or attract one molecular to another. ○​ Ionic Bonds: Attraction of a cation to an anion. ​ Example: Sodium and chlorine ions bond to form sodium chloride. ​ Relatively easily broken by something more attractive, such as water. ○​ Covalent Bonds: Atoms share one or more pairs of electrons. ​ Single covalent bond: Nuclei share 1 pair of electrons ​ Double covalent bond: Nuclei share 2 pairs of electrons ​ If electrons are shared equally, it’s a nonpolar covalent bond; example: carbon atoms bonding together. ​ If electrons are shared unequally, it’s a polar covalent bond; example: hydrogen bonding with oxygen, electrons spend more time by oxygen. ​ A hydrogen bond is a weak attraction between a slight positive hydrogen atom in one molecule and a slightly negative oxygen or nitrogen atom in another atom. ○​ Relatively weak bonds. Very important to physiology. ​ Water molecules are attracted to each by hydrogen bonds. ​ Large molecules (DNA and proteins) are shaped in part by the formation of hydrogen bonds within them. ​ Van der Waals forces are weak, brief attractions between neutral atoms. ○​ Fluctuations in electron density within an atom creates polarity for a moment, and attracts adjacent atom for a very short time. ○​ Only 1% as strong as covalent bond. Play important role in physiology (for example, protein folding). 2.2 Water and Mixtures (Slides 28-45) Body Fluids are Complex Mixtures of Chemicals: Slide 29 ​ Mixtures: Consists of substances that are physically blended but not chemically combined; each substance retains its own chemical properties. Water: Slides 31-34 ​ Most mixtures in our bodies consist of chemicals dissolved or suspended in water. ​ Water is 50-75% of body weight.  ​ Polar covalent bonds and a V-shape give water a set of properties that account for its ability to support life. ○​ Solvency ○​ Cohesion ○​ Adhesion ○​ Chemical reactivity ○​ Thermal stability ​ Properties of Water: ○​ Solvency: Ability to dissolve other chemicals ​ Water is the universal solvent because it dissolves more substances than any other solvent. ​ Metabolic reactions depend on solvency of water. ​ Hydrophilic substances dissolve in water; are polarized or charged.. ​ Hydrophobic substances do not dissolve in water; are nonpolar or neutral. ○​ To be soluble in water, molecule must be polarized or charged. ​ Example: Attractions to water overpower ionic bonds in NaCl. ​ Water forms hydration spheres around each ion and the salt dissolves; water’s negative pole faces, it’s positive pole faces. ○​ Adhesion: Tendency of one substance to cling to another. ​ Water adheres to membranes reducing friction around organ. ○​ Cohesion: Tendency of molecules of the same substance to cling to each other. ​ Water is very cohesive due to its hydrogen bonds. ​ Surface film on surface of water is due to molecules being held together by surface tension. ○​ Chemical Reactivity: Ability to participate in chemical reactions. ​ Water ionized into; ionizes other chemicals (acids, salts), involved in hydrolysis and dehydration synthesis reactions. ○​ Thermal stability due to high heat capacity - amount of heat needed to raise the temperature of 1g of a substance by 1°C. ​ Calorie (cal) is the base unit of heat; 1 cal is the amount of heat to raise the temperature of 1g of water by 1°C. ​ Water stabilizes internal temperature; hydrogen bonds resist temperature increases by inhibiting molecular motion. Solutions, Colloids, and Suspensions: Slides 35-38 ​ Mixtures of other substances in water classified as solutions, colloids, and suspensions. ○​ Solution: Consists of particles called the solute mixed with a more abundant substance (usually water) called the solvent. ​ Solute can be gas, solid, or liquid.  ​ Solutions are defined by the following properties: ​ Solute particles under 1nm. ​ Solute particles do not scatter light. ​ Will pass through most membranes. ​ Will not separate on standing. ○​ Colloids: ​ Colloids in the body are often mixture of protein and water. ​ Many can change from liquid to gel state within and between cells. ​ Colloids are defined by the following physical propertie: ​ Particles range from 1-100 nm in size. ​ Scatter light and are usually cloudy. ​ Particles too large to pass through semipermeable membrane. ​ Particles remain permanently mixed with the solvent when mixture stands. ○​ Suspension: ​ Defined by the following physical properties: ​ Particles exceed 100 nm. ​ Too large to penetrate selectively permeable membranes. ​ Cloudy or opaque. ​ Separates on standing. ​ Example: Blood cells in blood plasma. ○​ Emulsion: Suspension of one liquid to another. ​ Example: Oil-and-vinegar salad dressing; fat in breast milk. Acids, Bases, and pH: Slides 39-42 ​ Substances can be acids or bases depending on their tendency to release or bind ions. ○​ An acid is a proton donor, releases ions in water. ○​ A base is a proton acceptor, accepts ions in water. ​ Acidity is measured by pH scale. ○​ Derived from the molarity of: ​ pH of 7.0 is neutral. ​ pH of less than 7 is acidic. ​ pH of greater than 7 is basic. ○​ Maintaining normal (slightly basic) pH of blood is crucial for physiological functions. ​ Buffers are chemical solutions that resist changes in pH. ​ pH is the negative logarithm of hydrogen ion molarity. ○​ pH = XXXXX ○​ Example: If XXXX  ​ A change of one number on the pH scale represents a tenfold change in concentration. ○​ pH 4.0 is 10x as acidic as pH of 5.0. Other Measures of Concentration: Slides 43-45 ​ Solutions measured in terms of their concentration of solute: Several different expressions of concentration. ○​ Weight per volume: ​ Weight of solute in a given volume of solution ​ Example: IV saline contains 8.5g NaCl per liter of solution. ​ Common biology units: milligrams per deciliter (mg/dl). ​ Example: Serum cholesterol may be 200 mg/dl. ○​ Percentage: ​ Might be weight of solute (solid) per volume. ​ Example: 5% dextrose solution has 5g solute in 100ml solution, ​ Might be volume of solute (liquid) per volume of solution. ​ Example: 70% ethanol has 70ml of ethanol in 100ml solution. ​ Expressions of concentration: ○​ Molarity: ​ Number of moles of solute per liter of solution. ​ One mole is the number of grams equal to its molecular weight. ​ Often the most physiological meaningful measure of concentration. ​ Body fluids usually quantified in millimolar (mM) concentrations. ○​ Milliequivalents per liter (mEq/L) ​ Expression of electrolyte concentration. ​ Accounts for millimolar concentration of solute and electrical charge of its particles. ​ Important for nerve firing, the heartbeat, muscle contractions, and delivery of intravenous fluids. 2.3 Energy and Chemical Reactions (Slides 46-56) Energy and Work: Slide 47 ​ Energy is the capacity to do work. ○​ To do work means to move something, such as a muscle or molecule. ○​ Potential Energy: Energy stored in an object, but not currently doing work. ​ Example: Water behind a dam. ​ Chemical Energy: Potential energy in molecular bonds. ​ Free Energy: Potential energy available in a system to do work.  ○​ Kinetic Energy: Energy in motion, energy doing work. ​ Examples: Muscle movements, flow of ions, vibration of eardrum. ​ Heat - Kinetic energy of molecular motion. ​ Electromagnetic energy - kinetic energy of photons. ​ Electrical energy has both potential and kinetic forms. Classes of Chemical Reactions: Slides 48-53 ​ A chemical reaction is a process in which a covalent or ionic bond is formed or broken. ○​ A chemical equation symbolizes the course of a chemical reaction. ​ Reactants (on left) → Products (on right) ○​ Classes of chemical reactions include: ​ Decomposition reactions ​ Synthesis reactions ​ Exchange reactions ​ Decomposition Reactions: ○​ Large molecule breaks down into two or more smaller ones. ○​ AB → A+B. ​ Synthesis Reactions: ○​ For more small molecules combine to form a larger one. ○​ A+B → AB ​ Exchange Reactions: ○​ Two molecules exchange atoms or groups of atoms. ○​ AB + CD → AC + BD. ○​ Example: Stomach acid (HCI) and sodium bicarbonate (NaHCO3) from the pancreas combine to form NaCL and H2CO3. ​ Reversible Reactions: ○​ Can proceed in either direction under different circumstances. ​ Symbolized with double-headed arrow. ​ Example: XXXXX ​ An important reaction in respiratory, urinary, and digestive physiology. ○​ Reversible reactions follow the law of mass action. ​ Direction of reaction determined by relevant abundance of substances on either side of equation. ​ Equilibrium is reached when ratio of products to reactants is stable. Reaction Rates: Slide 54 ​ Reactions occur when molecules collide with enough force and create orientation. ○​ Reaction rates increase when:  ​ Concentration of reactants increases. ​ Temperature rises ​ A catalyst is present ​ Enzyme catalysts bind to reactants and hold them in orientations that facilitate the reaction. ​ Catalysts are not charged by the reaction and can repeat the process frequently. Metabolism, Oxidation, and Reduction: Slides 55 & 56 ​ Metabolism: All chemical reactions of the body; two divisions: ○​ Catabolism: ​ Energy-releasing (exergonic) decomposition reactions ​ Breaks covalent bonds ​ Produces small molecules. ○​ Anabolism: ​ Energy-storing (endergonic) synthesis reactions. ​ Requires energy input. ​ Example: Production of protein or fat. ​ Catabolism and anabolism are inseparably linked. ○​ Anabolism is driven by energy released by catabolism. ​ Oxidation: ○​ A chemical reaction in which a molecule gives up electrons and releases energy. ​ Molecule is oxidized when it loses electrons. ​ The oxidizing agent is the electron acceptor (often oxygen). ​ Reduction: ○​ Any chemical reaction in which a molecule gains electrons in energy. ​ Molecule is reduced when it accepts electrons. ​ The reducing agent is the molecule that donates electrons. ​ Oxidation of one molecule is always accompanied by reduction of another; called oxidation-reduction (redox) reactions. 2.4 Organic Compounds (Slides 57-120) Carbon Compounds and Functional Groups: Slides 59-62 ​ Organic chemistry is the study of compounds containing carbon. ○​ Four categories: ​ Carbohydrates. ​ Lipids.  ​ Proteins. ​ Nucleic acids. ​ Carbon Uniquely suited to form a variety of structures. ○​ Carbon: ​ Has four valence electrons; can form four covalent bonds with other atoms. ​ Can bind readily with other carbon atoms to form carbon backbones - long chains, branched molecules, rings. ​ Readily bonds with hydrogen, oxygen, nitrogen, so far, and other elements. ○​ Carbon backbones carry a variety of functional groups. ​ Small clusters of atoms attached to carbon backbone. ​ Determine many of the properties of organic molecules. ​ Examples: hydroxyl, methyl, carboxyl, amino, phosphate. Monomers and Polymers: Slides 63-65 ​ Macromolecules are large organic molecules with high molecular weights. ○​ Most macromolecules are polymers. ​ Molecules made of a repetitive series of identical or similar subunits called monomers. ​ Monomers may be identical or similar. ​ Examples: Starch is a polymer of about 3,000 identical glucose monomers; DNA is a polymer of 4 different nucleotide monomers. ○​ Polymers formed by polymerization - the joining of monomers. ​ Polymerization: ○​ Monomers covalently linked together by dehydration synthesis (condensation) reactions. ​ A hydroxyl (-OH) group is removed from one monomer, and a hydrogen (-H) from another; water produced as a by-product. ○​ Hydrolysis is the opposite of dehydration synthesis. ​ Splitting a polymer and monomers by the addition of water. ​ Enzyme helps break the covalent bond that links two monomers together. ​ A water molecule ionized into ​ XXXXX is added to one monomer. ​ XXXXX is added to the other monomer. Carbohydrates: Slides 66-74 ​ Carbohydrates are hydrophilic organic molecules.  ○​ General formula: n = number of carbon atoms ​ Glucose, n = 6, so formula is XXXXX ○​ 2:1 ratio of hydrogen to oxygen ○​ Names of carbohydrates often built from the root “sacchar-” and the suffix “-ose” both meaning sugar, sweet. ​ Examples: Sugars and starches. ​ Monosaccharides are the simplest carbohydrate. ○​ Monomers of larger carbohydrates. ○​ Three important monomers are glucose, galactose, and fructose. ​ Produced by digestion of more complex carbohydrates. ​ Glucose is blood sugar. ​ All three have the same molecular formula: C6H12O6. ​ Isomers of each other. ​ Ribose and deoxyribose are also monomers. ​ Part of RNA and DNA, respectively. ​ Disaccharides are sugars made two covalently bonded monosaccharides. ○​ Three important disaccharides: ​ Sucrose (table sugar) - glucose + fructose. ​ Lactose (milk sugar) - glucose + galactose. ​ Maltose (sugar in grain products) - glucose + glucose. ​ Oligosaccharides are short chains of 3 or more monosaccharides ​ Polysaccharides are long chains of monosaccharide (~50 or more, up to thousands). ○​ Three important polysaccharides: ​ Glycogen - Energy storage in cells of liver, muscle, brain, uterus, vagina. ​ Starch - Energy storage in plants that is digestible by humans. ​ Cellulose - Structural molecule in plants that is important for human dietary fiber (but indigestible to us). ​ Functions of carbohydrates: ○​ Quickly mobilized source of energy ​ All digested carbohydrates converted to glucose. ​ Oxidized to make ATP. ○​ Often conjugated (bound) to lipids and proteins. ​ Example: Lipids, proteins of cell membrane have chairs of up to 12 sugars attached to form glycolipids and glycoproteins, respectively. ​ Glycoproteins are a major component of mucus. ○​ Proteoglycans - Macromolecules that are more carbohydrate than protein. ​ From gels that hold cells and tissues together, fill umbilical cord and eye. ​ Joint lubrication; responsible for the rubbery texture of cartilage. ○​ Moiety: Each component of a conjugated macromolecule. Lipids: Slides 75-85 ​ Lipids are hydrophobic organic molecules with a high ratio of hydrogen to oxygen. ○​ More calories per gram than carbohydrates. ○​ Five primary types of lipids in the human body: ​ Fatty acids. ​ Triglycerides. ​ Phospholipids. ​ Eicosanoids. ​ Steroids. ​ Fatty acids - chains of 4-24 carbon atoms with carboxyl group on one end and methyl group on the other. ○​ Essential fatty acids must be obtained from food. ​ Fatty acids are classified as saturated or unsaturated. ○​ Saturated fatty acid - Carbon atoms linked by single covalent bonds. ​ Molecule contains as much hydrogen as possible (“saturated” with hydrogen). ○​ Unsaturated fatty acid - Contains some double bonds between carbons. ​ Molecule has potential to add hydrogen. ○​ Polyunsaturated fatty acids have multiple double bonds between carbons. ​ Triglycerides - three fatty acids linked to glycerol. ○​ Formed by dehydration synthesis; broken down by hydrolysis. ○​ Primary function is energy storage; also help with insulation and shock absorption (adipose tissue). ○​ Also called neutral fats because once formed, fatty acid is no longer acidic. ​ Dietary oils and fats are triglycerides. ○​ Oils are usually liquid at room or body temperature. ​ Example: Plant-derived polyunsaturated triglycerides (polyunsaturated fats) such as corn and olive oils. ○​ Saturated fats are solid at room or body temperature. ​ Example: Animal-derived saturated triglycerides (for example, animal fat). ​ A trans fat is a triglyceride with one or more trans-fatty acids. ○​ Trans-fatty acids - Two covalent single C-C bonds angle in opposite directions (trans means “across from”) on each side of the C=C double bonds. ​ Carbon chains are straighter than cis-fatty acids; pack more densely and are solid at room temp. ○​ Abundant in partially hydrogenated oil (PHO), sold as vegetable shortening; popular for baked goods.  ○​ Resists enzymatic breakdown in the human body, remain in circulation longer, deposits in the arteries; thus, raises the risk of heart disease. ​ Phospholipids - Similar to triglycerides, but one fatty acid is replaced by a phosphate group. ○​ Phospholipids are amphipathic. ​ Fatty acids “tails” are hydrophobic. ​ Phosphate “head” is hydrophilic. ○​ Phosphate group linked to other functional groups. ○​ Structural foundation of cell membrane. ​ Eicosanoids - 20 carbon compounds derived from a fatty acid called arachidonic acid. ○​ Hormone-like chemical signals between cells. ​ Includes prostaglandins ​ Function in inflammation, blood clotting, hormone action, labor contraction, blood vessel diameter. ​ Steroids - Lipid with 17 carbon atoms in four rings. ○​ Cholesterol is the “parent” steroid from which other steroids are synthesized. ​ Important for nervous system function and structural integrity for all cell membranes. ​ 15% of our cholesterol comes from the diet. ​ 85% is internally synthesized (mostly in liver). ○​ Other steroids include cortisol, progesterone, estrogens, testosterone, and bile acids. Cholesterol: Slides 86 & 87 ​ “Good” and “Bad” Cholesterol: ○​ There is only one kind of cholesterol. ○​ “Good” and “bad” cholesterol refer to droplets of lipoprotein in the blood that are complexes of cholesterol, fat, phospholipids, and protein. ​ HDL (High-Density Lipoprotein) = “Good cholesterol”). ​ Lower ratio of lipid to protein. ​ May help to prevent cardiovascular disease. ​ LDL (Low-Density Lipoprotein) = “Bad cholesterol”). ​ High ratio of lipid to protein. ​ Contributes to cardiovascular disease. Proteins: Slides 88-91 ​ A protein is a polymer of amino acids. ○​ Amino acids have a central carbon with three attachments.  ​ Amino group (-NH2). ​ Carboxyl group (-COOH). ​ R (Radical) group. ​ 20 amino acids used to make the protein are identical except for the radical R group. ​ Properties of each amino acid determined by R group. ​ A peptide is composed of two or more amino acids joined by peptide bonds. ○​ Peptide bond: ​ Joins amino group of one amino acid to carboxyl group of the next. ​ Formed by dehydration synthesis. ○​ Peptides are named for the number of amino acids they contain. ​ Dipeptides (2 amino acids). ​ Tripeptides (3 amino acids). ​ Oligopeptides (fewer than 10-15 amino acids). ​ Polypeptides (larger than 15 amino acids). Protein Structure: Slides 92-98 ​ Proteins have a complex three-dimensional shape referred to as their confirmation. ○​ Unique; crucial to function. ​ Proteins can reversibly change conformation to affect function. ​ Important examples seen in muscle contraction, enzyme catalysis, membrane channel opening, and so on. ​ Denaturation - Extreme conformational change that destroys function. ○​ Extreme heat or pH may cause permanent (irreversible) denaturation. ​ Example: Cooked egg white becomes opaque and stiff. ​ Proteins have three to four levels of complexity: ○​ Primary structure: ​ Sequence of amino acids within protein molecule. ​ Primary structure is encoded by genes. ○​ Secondary structure: ​ Coiled or folded shape held together by hydrogen bonds. ​ Hydrogen bonds between slight negative C=O and slightly positive -NH groups. ​ Most common secondary structures: ​ Alpha helix - springlike shape. ​ Beta sheet (beta-pleated sheet) - folded, ribbonlike shape. ○​ Tertiary structure: ​ Further bending and folding of proteins into globular and fibrous shapes due to hydrophobic-hydrophilic interactions and van der Waals forces.  ​ Disulfide bridges between cysteine amino acids stabilize tertiary structure. ​ Globular proteins: ​ Compact tertiary structure for proteins within cell membrane and proteins that move freely in body fluids. ​ Fibrous proteins: ​ Slender filaments suited for roles in muscle contraction and strengthening of skin and hair. ○​ Quaternary structure: ​ Associations of two or more polypeptide chains due to ionic bonds and hydrophobic-hydrophilic interactions. ​ Occurs only in some proteins. ​ Example: Hemoglobin has four peptide subunits. ​ Conjugated proteins contain a non-amino acid moiety called a prosthetic group covalently bound to them. ○​ Example: Hemoglobin contains four complex iron-containing rings called a heme moiety (see previous slide). Protein Functions: Slides 99-101 ​ Proteins have more diverse functions than other macromolecules. ○​ Structure: ​ Keratin - Tough structural protein of hair, nails, skin surface. ​ Collagen - Contained in deeper layers of skin, bones, cartilage, and teeth. ○​ Communication: ​ Neurotransmitters, some hormones, and other signaling molecules are proteins. ​ Signaling molecules that exert their effects by reversibly binding to a receptor molecule are called ligands. ​ The receptors to which the signaling molecules bind are also proteins. ​ Membrane Transport: ○​ Channels allow hydrophilic substances to diffuse across cell membranes. ○​ Carries help solute cross cell membranes via active or passive transport. ​ Catalysis: ○​ The enzymes that catalyze physiological reactions are usually globular proteins. ​ Recognition and Protection: ○​ Glycoproteins are important for immune recognition. ○​ Antibodies are proteins. ​ Movement:  ○​ Molecular motors (motor proteins) are molecules with the ability to change shape repeatedly. ​ Cell Adhesion: ○​ Proteins bind cells together. Enzyme and Metabolism: Slides 102 & 103 ​ Enzymes are proteins that function as biological catalysts. ○​ Some are ribozymes, composed of RNA found in ribosomes. ○​ Enzymes act on one or more substrates. ○​ Speed up chemical reaction by lowering the activation energy–the energy needed to get a reaction started. ○​ Permit reactions to occur rapidly at body temperature. ○​ Enzyme naming convention: ​ Named for substrate with -ase as the suffix. ​ Examples: Amylase catalyzes the hydrolysis of amylose (starch); lactase catalyzes the hydrolysis of lactose (milk sugar). Enzyme Structure and Action: Slides 104-106 ​ Enzyme action: ○​ Substrate binds to pocket on enzyme called the active site. ○​ Formation of enzyme-substrate complex. ○​ Enzyme-substrate specificity is like a lock and key. ○​ Enzyme releases reaction products. ○​ Enzyme uncharged and can repeat process. ○​ Example: The substrate sucrose is hydrolyzed by sucrase into the reaction products glucose and fructose. ​ Temperature, pH and other factors can change enzyme shape and function. ○​ Can alter ability of enzyme to bind to substrate. ○​ Enzymes vary in optimum pH. ​ Salivary amylase works best at pH 7.0. ​ Pepsin in stomach works best at pH 2.0. ○​ Temperature optimum for human enzymes is usually near body temperature (37°C). Cofactors: Slides 107 & 108 ​ Many human enzymes require a nonprotein partner called a cofactor. ○​ Cofactors may be inorganic or organic.  ​ Inorganic cofactors include the ions iron, copper, zinc, magnesium, and calcium. ​ Some of these work by binding to the enzyme, triggering a conformational change that activates the active site. ​ Organic cofactors are called coenzymes. ​ Often derived from vitamins. ​ Example: XXXXX derived from niacin; acts as an electron shuttle between the metabolic pathways glycolysis and aerobic respiration. Metabolic Pathways: Slides 109 & 110 ​ A metabolic pathway is a chain of reactions, each catalyzed by a different enzyme. ○​ A simple metabolic pathway may be symbolized as follows: XXXXX ​ A is the initial reactant, B and C are intermediates, and D is the end product. ​ The Greek letters (α, β, and γ) above the reaction arrows represent the enzymes that catalyze each step. ​ A is the enzyme substrate for enzyme α. ​ B is the enzyme substrate for enzyme β. ​ C is the enzyme substrate for enzyme γ. ​ Metabolic pathways are turned on or off by altering enzyme activity. ○​ This may be achieved many ways including: ​ Binding or dissociation of cofactors. ​ The end product inhibits an enzyme at an earlier step (for example. product D binds to enzyme A and shuts down production of intermediate product B). ​ Pathway is turned on when end product is in demand (low concentration) and turned off once concentration increases. ATP, Other Nucleotides, and Nucleic Acids: Slides 111 & 112 ​ Nucleotides - Organic compounds with three components: ○​ Nitrogenous base (single or double carbon-nitrogen ring). ○​ Sugar (monosaccharide). ○​ One or more phosphate groups. ​ Example: ATP (Adenosine triphosphate) - has adenine nitrogenous base, a ribose sugar, and three phosphate group. Adenosine Triphosphate: Slides 113-117 ​ Adenosine Triphosphate (ATP) is the body’s most important energy-transfer molecule. ○​ Stores energy gained from exergonic reactions. ○​ Releases it within seconds for physiological work. ○​ Holds energy in covalent bonds between phosphates. ​ Second and third phosphate groups have high energy bonds. ​ Most energy transfers to and from ATP involve adding and removing the third phosphate group. ​ Hydrolysis of ATP is catalyzed by adenosine Triphosphate (ATPases) ○​ Breaks the third high-energy phosphate bond of ATP to produce adenosine diphosphate (ADP), inorganic phosphate XXXXX and energy. ○​ XXXXX ○​ Releases 7.3kcal of energy per mole (505g) of ATP. ​ Phosphorylation - Addition of free phosphate group (released from ATP hydrolysis) to another molecule to activate it. ○​ Carried out by enzymes called kinases. ​ Energy for ATP synthesis comes primarily from glucose oxidation. ○​ First stage is glycolysis - splitting glucose into two pyruvate molecules. ​ A little ATP made in this process; most chemical energy remains in the pyruvate. ○​ Fate of pyruvate depends on oxygen supply. ​ If ATP demand outpaces oxygen supply, pyruvate undergoes anaerobic fermentation to lactate. ​ If enough oxygen is available, aerobic respiration occurs in mitochondria. Other Nucleotides: Slides 118 & 119 ​ Guanosine Triphosphate (GTP): ○​ Another nucleotide involved in energy transfer. ○​ In some reactions, donates a phosphate group. ​ Cyclic Adenosine Monophosphate (cAMP): ○​ Formed by removal of second and third phosphate groups from ATP. ○​ In many cases, its formation is triggered by a chemical signal (example: hormone) binding to cell surface. ○​ cAMP becomes “second messenger” within cell. Nucleic Acids: Slide 120  ​ Nucleic acids are polymers of nucleotides: ○​ DNA (Deoxyribonucleic acid): ​ Contains millions of nucleotides. ​ Constitutes genes, the instructions for synthesizing proteins. ○​ RNA (Ribonucleic acid): ​ 70 to 10,000 nucleotides long. ​ Carries out genetic instruction (encoded in DNA) for synthesizing proteins. ​ Assembles amino acids in right order to produce proteins. Lecture Three 3.1 Development of the Cell Theory (Slides 3-11) Cytology and Cell Theory: Slide 3 ​ Cytology: Scientific study of cells. ​ Generalizations of cells are described by the cell theory: ○​ All organisms composed of cells and cell products. ○​ Cell is the simplest structural and functional unit of life. ○​ An organism’s structure and functions are due to activities of cells. ○​ Cells come only from preexisting cells. Cell Shapes and Sizes: Slides 4-7 ​ There are about 200 types of cells in human body, with varied shapes, sizes, functions. ○​ Organs, tissues often refer to the shapes of their cells: ​ Squamous - Thin, flat, scaly. ​ Cuboidal - Squarish looking. ​ Columnar - Taller than wide. ​ Polygonal - Irregularly angular shapes, multiple sizes. ​ Stellate - Starlike shape. ​ Spheroid to Ovoid - Round to oval. ​ Disodial - Disc shaped. ​ Fusiform - Thick in middle, tapered towards end. ​ Fibrous - Threadlike. ○​ A cell’s shape can appear different if viewed in a different type of section (longitudinal versus cross section). ​ Most human cells are about 10-15µm in diameter.  ○​ 1 micrometer (µm), or micron = one-millionth of a meter or one-thousandth of a millimeter. ○​ Egg cells (very large) = 100µm diameter. ○​ Some nerve cells over 1m long. ○​ There is a limit on cell size. ​ An overly large cell cannot support itself; may rupture. ​ For a given increase in diameter, volume increases more than surface area. ​ Volume proportional to cube of diameter. ​ Surface area proportional to square of diameter. Basic Components of a Cell: Slides 8-11 ​ Improvements in microscopy allied cell ultrastructure to be visualized. ○​ Light microscope (LM) revealed plasma membrane, nucleus, and cytoplasm (fluid between nucleus and surface). ○​ Transmission Electron Microscope (TEM) improved resolution - the ability to reveal detail. ​ Uses beam of electrons rather than light. ○​ Scanning Electron Microscope (SEM) produces dramatic 3-D images at high magnification and resolution, but only for surface features. ​ Vascular corrosion cast is an SEM application for visualizing blood vessels. ​ Major components of a cell: ○​ Cell is surrounded by a plasma (cell) membrane. ​ Defines cell boundaries. ​ Made of proteins and lipids. ​ Composition can vary between regions of the cell. ○​ Cytoplasm is within the cell. ​ Contains organelles, cytoskeleton, inclusions (stored or foreign particles), and clear gel called the cytosol or intracellular fluid (ICF). ○​ Extracellular Fluid (ECF) is located outside of cells. ​ ECF includes any fluid outside of cells, including tissue (interstitial) fluid, blood plasma, lymph, and cerebrospinal fluid. 3.2 The Cell Surface (Slides 12-35) The Plasma Membrane: Slides 13 & 16 ​ Plasma membrane defines the boundaries of the cell. ○​ Appears as pair of dark parallel lines when viewed with electron microscope.  ○​ Has intracellular face and extracellular face. Membrane Lipids: Slides 14 & 15 ​ Most of membrane (~98% is composed of lipids, mostly phospholipids. ○​ Phospholipids ​ 75% of membrane lipids. ​ Amphipathic molecules arranged in a bilayer. ​ Hydrophilic phosphate heads face water on each side of membrane. ​ Hydrophobic tails are directed toward the center, avoiding water. ​ Drift laterally, keeping membrane fluid. ○​ Cholesterol ​ 20% of the membrane lipids. ​ Holds phospholipids still and can stiffen membrane. ○​ Glycolipids ​ 5% of the membrane lipids. ​ Phospholipids with short carbohydrate chains on extracelular face. ​ Contribute to glycocalyx - carbohydrate coating on cell surface. Membrane Proteins: Slides 17-20 ​ Membrane proteins constitute 2% of the molecules by 50% of the weight of membrane. ○​ Transmembrane proteins pass completely through membrane. ​ Hydrophilic regions contact the watery cytoplasm, extracellular fluid. ​ Hydrophobic regions pass through lipid of the membrane. ​ Most are glycoproteins. ​ Some drift in membrane, others anchored to cytoskeleton. ○​ Peripheral proteins adhere to one face of the membrane. ​ Those on inner face are usually tethered to a transmembrane protein and the cytoskeleton. ​ Functions of membrane proteins: ○​ Receptors - Bind chemical signals to trigger internal changes. ​ May cause production of a second messenger within cell receiving the chemical message. ○​ Enzymes - Catalyze reactions including digestion of molecules, production of second messengers. ○​ Channel proteins - Allow hydrophilic solutes and water to pass through membrane. ​ Some are always open, called leak channels, and some are gates (gated channels) that open only when triggered.  ○​ Carriers - Bind solutes and transfer them across membrane. ​ Pumps - Carriers that consume ATP. ○​ Cell-identity markers - Glycoproteins acting as identification tags. ○​ Cell-adhesion molecules (CAMs) - Mechanically link cell to another cell and to extracellular material. Second Messengers: Slides 23 & 24 ​ Example of second messenger system: Stimulation of a cell by epinephrine. ​ “First messenger” (epinephrine) binds to a surface receptor. ​ Receptor activates as a G protein. ○​ G protein is an intracellular peripheral protein that gets energy from guanosine triphosphate (GTP). ○​ G protein relays signal to adenylate cyclase which converts ATP to cyclic AMP (cAMP), the second messenger. ​ cAMP activates cytoplasmic kinases. ○​ Kinases add phosphate groups to other enzymes, turning some on and others off. ​ Up to 60% of drugs work through G proteins and second messengers. The Glycocalyx: Slide 29 ​ Glycocalyx - Carbohydrate moieties of glycoproteins and glycolipids external to plasma membrane, ​ Unique in everyone but identical twins. ​ Functions: ○​ Protection. ○​ Immunity to infection. ○​ Defense against cancer. ○​ Transplant compatibility. ○​ Cell adhesion. ○​ Fertilization. ○​ Embryonic development. Extensions of the Cell Surface: Slides 30-32, 34-35 ​ Microvilli - Extensions (1-2µm) of the membrane that serve to increase surface area. ○​ Provide 15-40 times more surface area to cells that have them. ○​ Best developed in cells specialized in absorption. ○​ Some absorptive cells they are very dense and appear as a fringe called the brush border.  ○​ Some microvilli contain actin filaments that are tugged toward center of cell to milk absorbed contents into cell. ​ Cilia - Hair-like processes 7-10µm long. ○​ Single, nonmotile primary cilium found on nearly every cell; serves as “antenna” for monitoring nearby conditions. ​ Helps with balance in inner ear; light detection in retina. ○​ Multiple nonmotile cilia found on sensory cells of nose. ○​ Motile cilia less widespread. ​ Found in respiratory tract, uterine tubes, ventricles of brain, ducts of testes. ​ 50-200 on each cell. ​ Beat in waves sweeping material across a surface in one direction. ​ Power stroke followed by recovery stroke. ○​ Cilia move within saline layer at cell surface; mucus “floats” atop this layer. ○​ Structure cilium: ​ Axoneme - Core of motile cilium consisting of microtubules. ​ 9+2 structure - Two central microtubules surrounded by ring of nine pairs. ​ Ring of nine pairs anchors cilium to cell as part of basal body. ​ Dynein arms “crawl” up adjacent microtubule, bending the cilium; uses energy from ATP. ​ Flagellum - Whiplike structure. ○​ Tail of a sperm is only functional flagellum in humans. ○​ Whip-like structure with axoneme identical to cilium. ​ Much longer than cilium. ​ Stiffened by coarse fibers that support the tail. ○​ Movement is undulating, snake-like, corkscrew. ​ No power stroke and recovery strokes. ​ Pseudopods - Continually changing extensions of the cell that vary in shape and size. ○​ Can be used for cellular locomotion, capturing foreign particles. Cystic Fibrosis: Slide 33 ​ Cystic fibrosis - Hereditary disease in which cells make chloride pumps, but fail to install them in the plasma membrane. ○​ Chloride pumps fail to create adequate saline layer on cell surface. ○​ Thick mucus plugs pancreatic ducts and respiratory tract. ○​ Inadequate digestion of nutrients and absorption of oxygen. ○​ Chronic respiratory infections. ○​ Mean life expectancy of 44. 3.3 Membrane Transport (Slides 36-X)