General Biology101 - 102 Lecture Topics Fall '09 and Spring '10       Fall Semester 2009 Part II  (Oct. 12 - Nov. 13) Biology 101 Lecture Outline         Chap. 24. The Immune System    This chapter describes how the human body protects itself from microbes in the environment.  It also describes how the body fights infections and disease. Lectures 1 and 2 Outline: Some terminology is defined below: antigen - Any molecule that is foreign to a white blood cell and triggers an immune response. An antigen is usually a protein or polysaccharide on the surface of a virus or foreign cell, etc. Each person has a specific set of self markers unique for that person (identical twins have the same markers). Self markers (also called self proteins)  introduced into another person are foreign to that person's white blood cells and are called antigens - their presence triggers an immune response.   Major histocompatibility complex (MHC) - a genetic term referring to the genes that code for the proteins that compose the self markers on the cell membrane. antibody - An antibody is a "Y" (or sometimes "T") shaped receptor molecule with a binding cite for a specific antigen so that it can be tagged for destruction. Antibodies are proteins that react against foreign substances, they attach to a portion of the antigen (epitope) and counter its effects. An antibody is composed of 4 polypeptide chains held together by disulfide bridges, 2 chains are long - called "heavy chains" and 2 are short - called "light chains". All 4 chains have constant (C) regions and variable (V) regions. The "V" recognizes and binds to the epitope while the "C" destroys the antigen.  The antigen-binding site is the region of the antibody that binds to the epitope of the antigen: see p.491 Fig.24.6. Note: The epitope (also referred to as the antigenic determinant) is the portion of an antigen recognized by the antibody. The epitope fits the antibody like a key fits a lock.  immunity - Resistance to a specific microbe (invader) obtained by having an infection or by vaccination (when the body receives a harmless form of the disease causing microbe as with the viral diseases polio, measles, smallpox and mumps). active immunity - When you make the antibodies yourself. Obtained when antigens enter the body naturally (ex. catching the flu) or artificially (getting a flu shot which contains a harmless form of the virus). The vaccine supplies the antigens and the body responds by making antibodies. Active immunity can last many years, perhaps a lifetime. passive immunity - When you receive the antibodies (your body does not synthesize the antibodies). Ex. Pregnant woman passes antibodies to her fetus. After birth, breast milk also provides antibodies. At best, passive immunity lasts no longer than a few months. complement proteins - involved in both non-specific and specific immunity. They are a group of over 20 proteins that circulate in an inactive form. When activated, they aid in the destruction of microbes in various ways. Among them, they can coat the surfaces of pathogens thereby making them more susceptible to capture by phagocytes. They can also rupture the cell membranes of bacteria causing their destruction.  lymphatic system  - The lymphatic system supplements the circulatory system by returning excess tissue fluid to the bloodstream. It is also the battlefield for fighting infections where B and T lymphocytes function. It filters out disease-causing organisms and removes old red blood cells from the blood. The lymphatic system is composed of lymphatic capillaries, larger vessels, lymph nodes, the spleen, tonsils and thymus. The fluid is "lymph" which is derived from blood plasma but is clearer and more watery. inflammatory response - A rapidly occurring chemical and cellular attack in response to an infection. It is triggered by damage to tissue caused by microbes or physical injury (ex. a scratch or insect bite). The tissue becomes swollen, red and warmer than the surrounding area. Can occur, for example, if a splinter enters the skin. Damaged cells release histamine and prostaglandins causing nearby blood vessels/capillaries to dilate (widen) permitting white blood cells to enter the damaged area and fight the infection. See page 628. septic shock - Septic shock refers to widespread inflammation (not localized) and is characterized by high fever and low blood pressure. Often induced by a bacterial infection - known to occur in critical care units of hospitals. autoimmune diseases - also known as autoimmune disorders - (ex. juvenile diabetes, rheumatoid arthritis, rheumatic fever) - lymphocytes produce antibodies that attack body cells. In multiple sclerosis, the T cells react against myelin (a protein that insulates axons of neurons). Juvenile diabetes occurs when the immune system attacks the insulin secreting cells of the pancreas. immunodeficiency diseases - disorders in the body's defenses, for example: AIDS  ( acquired immune deficiency syndrome) -  T4 lymphocytes and macrophages are attacked. SCID (severe combined immune deficiency) the T and B cells do not function. allergic reactions - Ex. peanut allergies are responsible for approximately 15,000 emergency room treatments and about 100 yearly deaths. Like other allergies, it is caused by an immune overreaction. Exposure to the proteins in peanuts stimulates the immune system to carry out a series of defense mechanisms used to fight infections. As a result, histamine is released resulting in a variety of symptoms such as hives, itching, nasal congestion, shortness of breath and swelling of the tongue and eyes. An epinephrine pen (an injector) is prescribed by physicians in emergencies while waiting for medical help. Some people (about 20%) outgrow allergies to peanuts. .................................... .................................................................................................. There are 3 lines of defense to combat microbial invasion: I. First line of defense: Innate Immunity - A. External Barriers - Always ready to fight infections. Nonspecific, generalized and not directed against a specific invader. Serves for protection: examples are the skin, digestive, respiratory systems to block entrance, lysozyme (in sweat glands, tears, lungs).   When the first line of defense is not adequate: II. Second line of defense: Innate Immunity - B. Internal Defenses - Cellular and Chemical Counterattack. Occurs when the first line of defense has failed. Involves nonspecific white blood cells: macrophages, neutrophils and natural killer cells as well as chemical defenses (complement system and interferons) that quickly respond to the invading microbe.  Natural Killer Cells - destroy virus-infected cells, cancerous cells, cells containing bacteria, fungi, etc.  Inflammation - an immediate response to infection or injury. What causes inflammation?  Phagocytes - neutrophils arrive first and produce secretions that destroy microbes and attract macrophages.  Antimicrobial chemicals:  Examples: histamine,  complement proteins,  interferons   Fever: interleukin proteins raise the body temperature which is controlled by the hypothalamus portion of the brain. A low-grade fever (below 103 degrees) stimulates phagocytosis and decreases the growth rate of many microorganisms. It also fights viral infections by increasing the production of interferon.  However, a fever of 103 degrees and above is detrimental and can be fatal. If the above defenses are not adequate: III. Third line of defense: Acquired Immunity also known as the Specific Immune  Response. Develops after exposure to the pathogen and functions when the invader is not destroyed during the second line of defense.  Consists of humoral immunity and cellular immunity:     A. Humoral Immunity: Fights invaders outside the cell and involves macrophages and various B lymphocytes. Important for antibody production to attack microbes outside the body cells and provides protection if in the future the microbe reinfects the body.       Kinds of B lymphocytes: virgin B cells - membrane bound antibodies,  plasma cells also referred to as effector B cells produce antibodies, and B memory cells remember a specific antigen. Clonal selection theory, monoclonal antibodies.     B. Cellular Immunity: Fights invaders inside the cell. Involves a group of T lymphocytes.  Results in the destruction of body cells containing the microbe.  APC macrophages (initiate immune responses).       Types of T lymphocytes: helper T cells - activates B cells to produce antibodies, activates cytotoxic T cells to attack infected cells by destroying cells with non-self antigens, (HIV attacks by attaching to CD4 markers of helper T cells).   T memory cell (remembers a specific antigen), suppressor T cells (diminishes both B and T immune responses). Cyclosporine inhibits interleukin-2. Why is this drug administered to patients receiving organ transplants? SOME WAYS TO PROTECT YOUR IMMUNE SYSTEM: Exercise on a regular basis Maintain a normal weight Receive adequate sleep Control blood pressure Eat a well balanced diet include fruits, whole grains, vegetables, select food items low in saturated fat  and thoroughly cook meat. Wash your hands regularly - especially when preparing food and before meals. Regular medical checkups (including the dentist along with good brushing and flossing habits). Chronic inflammation  It is currently believed that chronic inflammation is associated with the formation of atherosclerotic plaque (hardening of the arteries). Chronic inflammation is low-grade inflammation that occurs when the triggering cause is not fully eliminated or when suppressor T cells do not completely turn off the immune system. This ongoing condition wages war on body tissues which wear away. It should be noted that when under control, inflammation is a normal  and an essential part of the immune response. However, when not controlled it can lead to pain and disease. Coronary heart disease, rheumatoid arthritis, Crohn's disease, diabetes, cancer (lymphoma) and Alzheimer's disease among others are currently linked to chronic inflammation. High levels of C reactive protein (CRP) (a marker for inflammation) are associated with the above diseases. It is believed that nonsteroidal anti-inflammatory drugs (NSAIDS) like aspirin, ibuprofen and naproxen reduce inflammation and are thought to put off these diseases. High calory diets, obesity, refined carbohydrates, saturated fats and trans fats as well as smoking and poor dental hygiene increase inflammation. Omega-3 fatty acids and monounsaturated oils (like olive and canola) reduce inflammation. Nonsteroidal anti-inflammatory drugs (NSAIDS) for pain or arthritis like aspirin, ibuprofen, and naproxen reduce inflammation and are believed to put off diseases linked to chronic inflammation.   Lectures 3-7: Chapter 31 Plant Structure Chapter 32 Plant Nutrition/Transport, Chapter 17 Plant Diversity. Terms: autotrophic vs. heterotrophic, photosynthesis, vascular tissue (conducting tissue), sexual vs. asexual reproduction, plant cell walls, angiosperms, alternation of generations. Some general terms: diploid - The normal number of chromosomes in the cells of most organisms. In humans, the number is 46 which exists as 23 pairs of homologous chromosomes. Homologous chromosomes are identical in size and shape and have a set of genes that govern the same traits. Diploid is usually expressed as 2N or 2n. For example, in man 2N = 46. in corn plants 2N = 20. haploid - The normal number of chromosomes an organism carries in its reproductive cells. It is 1/2 the diploid number and is referred to as a chromosome complement (unpaired set of chromosomes). Haploid is usually expressed as 1N or N. In man, N = 23. In corn, N = 10.  gamete - Any cell capable of fusing with another cell to form a new individual is a gamete. Examples include egg and sperm. zygote - The cell formed by the fusion of gametes through fertilization. Ex. sperm fertilizes an egg to produce the zygote.  meiosis (also called reduction division) - The process by which the chromosomes in a cell are reduced from the diploid to the haploid condition. It usually consists of two successive divisions resulting in four haploid nuclei. The actual reduction occurs during the first division. In humans meiosis converts diploid cells into haploid cells (egg and sperm). Fertilization restores the diploid condition. Lecture 3: The Plant Kingdom     Vascular Plants - plants that produce conducting tissues in the form of xylem and phloem. The sporophyte generation (2N)  is larger in size than the gametophyte generation (1N).          Angiosperms: seeds, flowers, monocots vs. dicots          Gymnosperms: seeds, no flowers          Ferns: spores (seedless vascular plants)     Non-vascular Plants - plants without vascular tissues (lack xylem and phloem). The gametophyte generation is larger in size than the sporophyte generation.          Bryophytes. Ex. mosses - form spores  (seedless non-vascular plants)   Lecture 4: Angiosperms  Sexual Reproduction -  The Flower - Four flower parts: 1) carpel (stigma, style, ovary, ovule)  2) stamen (anther, filament, pollen, pollination) 3) corolla 4) calyx. Sexual reproduction, microspore mother cell, microspores, megaspore mother cell, megaspores, double fertilization, endosperm, seed, fruit. Asexual Reproduction - any method of reproduction that does not involve seeds. Also known as vegetative reproduction and produces plant clones: by roots, stems, leaves.   Lecture 5: Alternation of Generations, Plant cells and Tissues    Plant cells and tissues, primary and secondary plant growth Types of plant cells & tissues.  Terms: alternation of generations (gametophyte generation, sporophyte generation); cell walls, 9 cell types: meristematic (apical, lateral), epidermal, parenchyma, collenchyma, sclerenchyma (fiber, sclereid), vessel element, tracheid, sieve tube member, companion cell.   Xylem tissue, phloem tissue. alternation of generations - There are 2 generations in the life cycle of a plant that reproduces sexually (in other words, from the time of fertilization and zygote formation to the development of gametes in the life cycle). There is a distinct diploid (or 2N) generation referred to as the sporophyte as well a haploid (or 1N) generation known as the gametophyte. The diploid sporophyte generation produces spores which are the products of meiosis. These are the haploid spores that begin the gametophyte generation. The gametophyte generation functions to produce gametes. Fertilization produces the zygote which is diploid and marks the first cell of the sporophyte generation. Therefore, in the life cycle from zygote through fertilization there are 2 generations: the sporophyte generation and the gametophyte generation: this is known as the alternation of generations. Q. Can you identify the spores produced by angiosperms that begin the gametophyte generation? Q. Among angiosperms, which generation is more conspicuous (larger in size) - the gametophyte generation or the sporophyte generation? State a reason for your answer. Q. Where is the zygote produced in angiosperms? Q. Identify "pericarp" and its parts in relation to fruit formation as in the peach and tomato. Q. Why is a cucumber referred to as a fruit? Q. Identify the one angiosperm structure where both meiosis and fertilization occur. Q. What is vegetative reproduction? Provide some examples. Lecture 6: Primary and Secondary Growth in Angiosperms  dicot stem cross-sections, vascular cambium for secondary xylem & secondary phloem, springwood vs. summerwood, heartwood vs. sapwood, cork cambium, tree bark. Angiosperms - continued. The angiosperms are a large group of vascular plants. They are subdivided into two major groups: the monocots and the dicots.  The monocots have a single cotyledon (or seed leaf) in their seeds and have a parallel leaf vein pattern. Their flower parts tend to occur in 3's (for ex. 3, 6, 9 or 12 stamens) and in addition they lack a vascular pattern. Ex. corn, orchids and lawn grass. The dicots have two cotyledons in their seeds and exhibit a "net" leaf vein pattern (their veins branch and are not parallel). Flower parts are generally in 4's and 5's and a vascular cambium is produced. Ex. rose, tomato, maple tree. Q. If an angiosperm has a flower with 12 stamens and 24 petals how would you go about determining if it is a monocot or dicot? ----------------------------------------------------------------------------------------   Lecture 7: The Gymnosperms, Ferns and Mosses Text Chap. 17 p. 346 - 349  Chap. 33 Control Systems in Plants. Ferns: frond, rhizome, root, sorus, sporangia, spores, antheridium, archegonium, rhizoids. Mosses: characteristics of the gametophyte & sporophyte.  Plant control systems: There are five major kinds of hormones that regulate plant development and growth. Table 33.2 p. 664. Lecture 8: The Fungi Chap. 17 p.341, 355-363. Fungi: mycology, chitin (a common component of fungal cell walls), heterotrophic, no vascular tissue, no embryo.     Importance: decomposers, source of food, antibiotics, cyclosporine, allergies (by inhaling spores), toxic fungi (poisonous mushrooms, etc.).  mycoses: fungal infections of man and animals. Ex. ringworm, athlete's foot, candidosis. mycorrhiza: the close association of fungi with the roots of plants. Describe why mycorrhizal relationships are important. How do fungi influence life on earth?  Why were fungi once classified as plants?      Structures: hypha, mycelium, coenocytic vs. septate, asexual vs. sexual spores Examples of asexually produced spores are sporangiospores and conidia (singular: conidium). Examples of spores that are produced through sexual reproduction are zygospores in the class Zygomycetes, ascospores in the class Ascomycetes and basidiospores in the class Basidiomycetes.     Some mycologists separate the fungi into five groups: Chytrids, Zygomycetes, Glomeromycetes, Ascomycetes and Basidiomycetes Note: The chytrids are the only fungi that produce flagellated spores and are capable of swimming.  Members of all five groups are capable of asexual and sexual reproduction. However, some fungi do not reproduce sexually or the sexual stage is uncertain and are referred to informally as the "Fungi Imperfecti" and have a great impact on human affairs. Of particular importance is the genus Alternaria solani which is responsible for some plant diseases as well as certain allergies in man.   Why are fungi not classified as members of the plant kingdom since both fungi and plants have cell walls?     What are mycoses and why are they difficult to treat?                          Lecture 9: Review for exam.             General Biology 102 Spring Semester 2010 Lecture Outline   READ THE CHAPTER ASSIGNMENTS BEFORE  CLASS      Weeks 1 & 2:    Chapter 2. The Chemical Basis of Life and Chapter 3 The Molecules of Cells Matter, chemical elements, molecules- organic vs. inorganic molecules Matter: Anything that occupies space and has mass. Matter can exist in three forms - gas, liquid or solid. All life is composed of matter. Matter can be broken down into pure substances called chemical elements.  Element: A substance that cannot be broken down to other substances by ordinary chemical means. There are 92 naturally occurring elements. About 25 of the naturally occurring elements are essential for life. The chemical elements most abundant in organisms are 0 (oxygen),  C (carbon),  H (hydrogen) and N  (nitrogen). Atom: The smallest unit of an element that retains the characteristics of the element. The atom is composed of subatomic particles: protons (+ electrical charge) and neutrons (no charge, neutral) which make up the nucleus of the atom and electrons (negative electrical charge) that surround the nucleus and travel in an orbit.  Molecules: Atoms combine to form molecules by bonding together. Ex. Atmospheric oxygen is composed of two atoms of oxygen and forms one molecule. A compound is a substance containing two or more different elements in a fixed ratio as for example the element Na (sodium) combines with Cl (chlorine) to form the compound: NaCl (table salt). An organic molecule always contains, as a minimum, both carbon (C) and hydrogen (H). An inorganic molecule may contain carbon or hydrogen (not both) or lack carbon and hydrogen as in NaCl. Chemical bonds: Atoms in a molecule are held together in chemical bonds. Types: ionic bonds ex. NaCl where sodium has one electron in its outer shell while chlorine has seven. When they collide, Cl takes Na's outer electron and fills its outer shell with electrons (so sodium is now positively charged while chlorine is negatively charged. Both atoms are "ions" (an atom or molecule with an electrical charge resulting from the gain or loss of electrons. The opposite charges hold them together to form NaCl which is electrically neutral.  Covalent bonds: When two atoms share one or more pairs of electrons. Referred to as a double covalent bond when two atoms share two pairs of electrons (or four electrons) are shared. Note: Atoms in a covalently bonded molecule are in a constant tug for the shared electrons. In molecules made of one element it's an equal pull and the molecule is "nonpolar", but water (2 hydrogens and 1 oxygen) it is "polar" because oxygen pulls the electrons closer to itself making oxygen partially negative and hydrogen partially positive, so water has a slight negative and positive charge but as a whole is neutral. carbonyl groups: aldehyde vs. ketone hydroxyl group, carboxyl group Metabolism - anabolic vs. catabolic reactions, hydrolysis vs. dehydration synthesis, monomer vs. polymer.    ORGANIC  MOLECULES  OF  MAJOR  BIOLOGICAL  IMPORTANCE: 1. CARBOHYDRATES -  Importance, types and functions     4 calories/gram - one teaspoon of sugar is 16 calories. One tablespoon of sugar (3 teaspoons) is equivalent to 48 calories.      A. Monosaccharides - Serve as energy sources - ex. glucose, fructose and ribose. Glucose and fructose are isomers.         Describe "high-fructose" corn syrup. Where is it found? It it associated with obesity? P. 38.      B. Disaccharides - Serve as energy sources - ex. sucrose and lactose which are isomers. The glycosidic bond joins monosaccharides.     C. Polysaccharides - Serve as energy sources (starch, glycogen) while others are structural compounds (cellulose and chitin). Sugar is sometimes hidden in prepared foods and may be listed as corn syrup, high-fructose corn syrup, turbinado, mannitol, sorghum,fruit juice, maltodextrin and sorbitol (among others). Artifical sweeteners: Aspartame (Equal, Nutra-sweet) is 180 times sweeter than sugar but cases of nervous symptom problems have been reported. 2. LIPIDS - Importance, kinds and functions    A. Lipids with fatty acids:     1. Fats and oils - 9 calories/gram, one tablespoon of oil or lard has approximately 120 calories. Butter has 100 calories per tablespoon (butter contains fewer calories because it contains a small amount of water).           triglycerides, glycerol, fatty acids (saturated, monounsaturated, polyunsaturated). Ester bonds unite fatty acids to glycerol to make a triglyceride.          omega-3 vs. omega-6 fatty acids, trans fats          Sources of saturated fats include red meat, whole milk, butter, cheese, ice cream, chocolate, poultry skin, coconut oil and palm oil. These fats are associated with an increase in heart disease and perhaps prostate cancer. They prevent the body from eliminating cholesterol and raise the "bad" LDL in the blood. LDL cholesterol increases the chances of heart attack and stroke while HDL cholesterol decreases the chances of heart attack and stroke.        'Trans fats" are partially hydrogenated oils (hardened unsaturated fat) and are classified as saturated fats. They are associated with heart disease by raising LDL cholesterol and also lower the "good" HDL cholesterol levels. Trans fats are found in some margarines, cakes, fast food, vegetable shortenings. They are made by adding hydrogen to polyunsaturated or monounsaturated fat.        Monounsaturated oils: Lower LDL and raise HDL, believed to protect against some forms of cancer and may explain the benefits of the Mediterranean diet. Ex. Olive, canola, peanut oil, cashews, olives, almonds, avocadoes. "Mono" refers to a fatty acid with a single double bond.       Polyunsaturated oils: Ex. corn oil, soybean oil, sunflower oil, safflower oil, walnut oil. Believed to help prevent heart disease and include the omega-3 and omega-6 lipids.       Omega -3 in fish, walnuts, canola oil and flaxseed oil. Omega-3 lowers triglycerides but little effect on cholesterol. Eating fish is believed to lower the risk of heart disease and ischemic stroke (caused by a blood clot in the brain).        Omega - 6 in corn, soybean and sunflower oils, lowers LDL and raises HDL, may reduce the risk of heart disease and diabetes. Oils are actually a mixture of saturated, monounsaturated and polyunsaturated fatty acids (ex. canola oil has monounsaturated, omega-3 and polyunsaturated fatty acids).        Fat soluble vitamins: A, D, E and K. It is recommended that no more than 30 -35% of total calories per day should be derived from lipids. No more than 1/3 of these calories should come from saturated fat.      2. Phospholipids - found in cell membranes, nerve and brain cells. They are composed of: A)  2 fatty acids, B) a molecule containing phosphorus and C) glycerol.      3. Waxes - Ex. Ear wax,  cutin - a plant wax found on the surface of leaves and forming a layer called the cuticle. Suberin (cork cells). B. Lipids without fatty acids:      Steroids- Ex. cholesterol (LDL vs. HDL), hormones, anabolic steroids      The cholesterol in the blood is of two major types: LDL cholesterol (low-density lipoprotein cholesterol) and HDL cholesterol (high-density lipoprotein cholesterol).  The LDL is harmful because it can form plaque deposits in the walls of arteries. This can  buildup leading to a narrowing of the arteries that can slow or block blood flow leading to a heart disease/stroke. HDL cholesterol is beneficial because it is believed to keep LDL cholesterol from forming in the arteries.          3. PROTEINS - Importance, kinds and functions     A.  4 calories/gram      B. There are 7 groups of proteins: 1. structural proteins (ligaments, tendons, cartilage, keratin in hair and nails, collagen in bones and spider silk).  2. Contractile proteins in muscles for movement  3. Storage protein (albumen in egg white to feed embryo).  4. Defensive proteins (antibodies to fight infections).  5. Transport proteins (hemoglobin to carry oxygen).  6. Some hormones (insulin to control glucose metabolism).  7. Enzymes.     C. 20 amino acids (8 essential, 12 nonessential amino acids), amino group, alpha carbon, carboxyl group      D.    Protein structure, the peptide bond unites amino acids to form a protein.          E. Enzymes - enzyme kinetics, factors influencing enzyme action     F. Primary, secondary, tertiary and quaternary structure of a protein: text p.43 - 45. 4. NUCLEIC ACIDS - Importance, kinds and functions      A. Nucleotides - nitrogen bases (purines, pyrimidines), pentoses, and phosphate groups      B. RNA - (ribonucleic acid) genetic information      C. DNA (deoxyribonucleic acid)- double helix, genetic information      D. ATP - is a nucleotide important in the transfer of energy in the cell. Energy is packaged in a convenient form as ATP for ready use by the cell. When energy is needed, ATP is converted to ADP + P. The stored energy is released from the terminal high energy bond - this is the energy that is used to do biologic work. Week 3 - Chapter 4. A Tour of the Cell Lecture Outline: Ultrastructure of the Cell: prokaryotes, archaea and eukaryotes protoplasm, cytoplasm, prokaryotic, eukaryotic, , endosymbiont theory cell wall in plants;  penicillin inhibits cell wall formation in susceptible bacteria Summary of Organelles and Their Functions - For overview see text p.69.   Table 4.23 Eukaryotic Cell Structures and Functions A. General Function: manufacture      1. Nucleus - Contains the genetic information and directs cellular activities. DNA, RNA synthesis, chromatin, chromosomes       2. Ribosome - protein synthesis, streptomycin inhibits protein synthesis in susceptible bacteria.       3. ER (endoplasmic reticulum) - two types:  A) smooth ER: lipid synthesis, detoxification of chemicals (ex. in liver), muscle contraction involving the release and uptake of calcium.                                                                          B) rough ER: Protein synthesis such as membrane proteins as well as phospholipids also makes transport vesicles to ship proteins to other locations in the cell for further processing (for ex. to the Golgi apparatus).       4. Golgi apparatus (also known as Golgi complex)- packaging, modification, temporary storage of proteins, produces membrane-bound lysosomes (digestion of nutrients, etc.) and membrane-bound  vesicles (storage and transport of molecules). B. General function: Breakdown       5. Lysosome -  the lysosome is a membranous sac containing digestive (hydrolytic) enzymes. Multiple functions including the destruction of some cells during embryonic development. Tay-Sachs disease (due to the lack of an enzyme required to digest lipids, cells accumulate lipids as well as glycogen resulting in loss of vision and hearing, paralysis and death).       6. Peroxisome - separates certain chemical reactions from the remainder of the cell. Involved in the digestion of fatty acids, amino acids, detoxification, reactions produce hydrogen peroxide. Catalase detoxifies the hydrogen peroxide which is unstable and produces oxygen free radicals. Catalase prevents free-radical buildup by removing an oxygen atom from the hydrogen peroxide and combines it with 2 hydrogens to produce water.  Adrenoleukodystrophy (ALD) - victims lack a membrane protein that permits an enzyme to enter the peroxisome to digest very long chain fatty acids, results in accumulation of fatty acids in brain, spinal cord resulting in illness. Oxygen free radicals damage LDL cholesterol, believed that this altered form of cholesterol is what damages arteries leading to heart attack and stroke. Antioxidants neutralize oxygen free radicals, help to prevent the LDL cholesterol from being damaged.        7. Vacuoles - digestion, storage of chemicals including waste materials, water balance. C. General function: Energy Processing: provides chemical energy:       8. Chloroplast - membrane-bound organelle functioning in photosynthesis by converting light energy to carbohydrates. Has inner membranes termed thylakoids that house chlorophyll. Thylakoids are arranged in stacks to form grana (sing. granum). The stroma is the portion of the chloroplast surrounding the grana and  ribosomes. The chloroplast is a type of plastid green in color. The  chromoplast is a plastid with a pigment other than green such as red due to the pigment lycopene (tomatoes). The leucoplast is white or colorless and stores starch (white potato).      9. Mitochondrion - membrane-bound organelle functioning in cellular respiration by converting the chemical energy in food to ATP. Has inner folded membrane forming cristae. Surrounding portion is the matrix which contains ribosomes. Note: Chloroplasts and mitochondria have their own DNA and ribosomes. D. Support, Movement, and Communication Between Cells. ex. cell walls, cytoskeleton, cell junctions. ------------------------------------------------------------------------------------------------------------------------- Chap. 5: The Working Cell  Transport Across Plasma Membranes - p. 74 - 80. Ways Substances Enter and Exit the Cell: diffusion: The movement of molecules from a region of greater concentration to a region of lesser concentration. osmosis: The diffusion of water molecules across a selectively permeable membrane from a region of greater concentration to a region of lesser concentration. solute, solvent, hypotonic, hypertonic, isotonic, net flow plasma membrane: fluid mosaic model, phospholipid bilayer, carrier proteins Applying osmosis to the plasma membrane in cells is known as "passive transport". Like osmosis, passive transport does not require carrier proteins. No energy is required because it is a natural tendency to go from a greater to a lesser concentration and describes how small molecules pass the plasma membrane (ex. how red blood cells exchange oxygen and carbon dioxide in the lungs). Passive transport is diffusion across a membrane, down its concentration gradient (from a region of greater concentration to a region of lesser concentration). Facilitated diffusion - The movement of a molecule across a membrane down a concentration gradient  assisted by a specific transport protein and does not require energy. Explains how sugars, amino acids and water are transported across the plasma membrane. Note: Water is also capable of passing through the membrane by passive transport but this occurs at a slower rate because the membrane is hydrophobic. Active transport: Describes the transport of a molecule across a membrane against a concentration gradient assisted by a specific transport protein. Always requires a source of energy - usually ATP. Bulk Transport - Types: A. Endocytosis: phagocytosis vs. pinocytosis B. Exocytosis Week 4:    Cellular Respiration Chapter 6  How Cells Harvest Chemical Energy (from food) Cellular Respiration - The energy in glucose is stored in its chemical bonds. To obtain this energy, enzymes cleave the bonds of the carbohydrate and convert the energy into a form the cell can use: ATP. During cellular respiration, glucose is completely catabolized (broken down) to carbon dioxide and water with the released energy from glucose used to make ATP. Cellular respiration is the aerobic harvesting of this energy by cells. ATP can be synthesized in two ways: substrate-level  phosphorylation and by chemiosmosis using ATP synthase. NADH and FADH2 are electron carrying molecules. Cellular respiration occurs in 3 stages:    1. Glycolysis - Cellular respiration begins with glycolysis which does not require oxygen. It occurs in all organisms and most likely in even the first forms of life when there was no oxygen. It involves the formation of ATP (substrate-level phosphorylation)and NADH (from its oxidized form) in the cytoplasm where one glucose molecule is converted into two molecules of pyruvate. Glycolysis ends with the synthesis of pyruvate (pyruvic acid). See Fig. 6.7C (p. 95).  Each pyruvate (having 3 - carbons) then enters the mitochondrion where it undergoes a decarboxylation and produces NADH (from its oxidized form). in its conversion to a 2-carbon group (acetyl) that combines with coenzyme A to form acetyl CoA.    2. Citric acid cycle (also known as the Krebs cycle) - occurs in the matrix of the mitochondrion. Decarboxylations occur along with the formation of ATP, NADH, FADH2 as citric acid is converted to oxaloacetic acid. See p. 96,97.    3. Oxidative phosphorylation (also known as the electron transport chain).  Involves chemiosmosis and ATP synthases.  Occurs on the inner mitochondrion membrane which is repeatedly folded to form cristae. The cristae  divide the mitochondrion into 2 compartments, the inner matrix and the intermembrane space (the portion between the outer and inner membranes of the mitochondrion). The reduced NADH and FADH2 molecules that formed during the earlier stages of respiration by the removal of electrons from glucose are delivered to the electron transport chain. The chain consists of electron carrier molecules that are situated on the cristae. The NADH and FADH2 become oxidized when they give up their electrons and hydrogen protons to the chain. As electrons pass along the carriers in the chain, the hydrogen protons are pumped from the mitochondrial matrix to the intermembrane space thereby creating a concentration gradient and an electrical gradient. The accumulating protons are able to return to the matrix through ATP synthase passageways where their energy is utilized to phosphorylate ADP to produce ATP. Most of the ATP produced during cellular respiration occurs during oxidative phosphorylation. See p. 98 - 100. Alternate pathways: Fermentations -  fermentations are alternate pathways to cellular respiration when oxygen is not available:  A. Lactic acid fermentation - When oxygen is not available, glucose is converted to pyruvate (glycolysis) but does not enter the citric acid cycle. Instead, pyruvate (3 carbon molecule) is converted to lactic acid (also 3 carbons) making NAD+  from NADH . p. 101, Fig. 6.13 A.  B. Alcoholic fermentation - In the absence of oxygen, glycolysis occurs with the end product pyruvate (3 carbon molecule) converted to ethanol (2 carbon molecule) which involves a decarboxylation (formation of carbon dioxide) and produces NAD+  from NADH + H+ . Note: see text p. 101 Fig.6.13 B. Note: Fermentations do not involve the citric acid cycle and oxidative phosphorylation. Consequently, far less ATP is synthesized during fermentations.   ====================================================================== Photosynthesis Chapter 7 Photosynthesis:  Using Light to Make Food Photosynthesis - occurs in 2 stages:     1. The Light Reactions - Converts solar energy to chemical energy. Reactions require light and involves membranes in the chloroplast termed thylakoids which are arranged in stacks or grana (singular: granum). These membranes house the chlorophyll molecules. The light reactions generate ATP, NADPH and oxygen. "Water splitting" reactions produce oxygen, hydrogen ions and electrons.  Two photosystems are involved in the light reactions: Photosystem I contains P700,  Photosystem II P 680. Products of the light reactions are ATP (from ADP + P), NADPH (from its oxidized form) and oxygen.     2. The Calvin Cycle: Converts carbon dioxide to sugars.  - Involves the remaining portion of the chloroplast termed the stroma, The Calvin cycle utilizes ATP, NADPH, RuBP (ribulose biphosphate) and carbon dioxide for the synthesis of carbohydrate. Carbon fixation (the addition of inorganic carbon to an organic molecule) occurs during this cycle when RuBP combines with carbon dioxide.  Overview of light reactions and Calvin cycle: p. 111. Six turns of the Calvin cycle produces one molecule of glucose and six molecules of RuBP.