BI151 Exam 1 Study Guide PDF

BI151 EXAM I STUDY GUIDE UNIT 1: INTRODUCTION TO ANATOMY INTRODUCTION A. The purpose of the chapter is to introduce anatomy and physiology as specific disciplines. 1. Organization of the human body. 2. Reveal shared properties of all living things. 3....

BI151 EXAM I STUDY GUIDE UNIT 1: INTRODUCTION TO ANATOMY INTRODUCTION A. The purpose of the chapter is to introduce anatomy and physiology as specific disciplines. 1. Organization of the human body. 2. Reveal shared properties of all living things. 3. Homeostasis is the major theme in every chapter of the book. II. ANATOMY AND PHYSIOLOGY DEFINED A. Through a study of anatomy and its subdivisions, the body may be examined at different levels of structural organization. 1. Anatomy may be defined as the study of structure and the relationships among structures. 2. Branches of anatomy include: Embryology, developmental biology, cell biology, histology, gross anatomy, systemic anatomy, regional anatomy, surface anatomy, imaging anatomy, and pathological anatomy as summarized in Table 1.1. B. A study of physiology deals with how body parts function: the structure of a part determines its function. 1. Physiology is the study of how body structures function. 2. Branches of physiology include; neurophysiology, endocrinology, cardiovascular physiology, immunology, respiratory physiology, renal physiology, exercise physiology, and pathophysiology, as summarized in Table 1.1 III. LEVELS OF STRUCTURAL ORGANIZATION AND BODY SYSTEMS A. The human body consists of several levels of structural organization (Figure 1.1).  1. The chemical level includes atoms, the smallest units of matter that participate in chemical reactions, and molecules, two or more atoms joined together. 2. Cells are the basic structural and functional units of an organism. 3. Tissues consist of groups of similarly specialized cells and the substances surrounding them that usually arise from a common ancestor and perform certain special functions. 4. Organs are structures of definite form that are composed of two or more different tissues and have specific functions. 5. Systems consist of related organs that have a common function. 6. The human organism is a collection of structurally and functionally integrated systems; any living individual. B. The eleven systems of the human body are the integumentary, skeletal, muscular, nervous, endocrine, cardiovascular, lymphatic, respiratory, digestive, urinary, and reproductive (Table 1.2).  C. Clinical Connection: Three noninvasive techniques of palpation, auscultation, and percussion are used to assess certain aspects of body structure and function (as seen in a Clinical Connection section). 1. In palpation the examiner feels body surfaces with the hands; an example would be pulse and heart rate determination. 2. In auscultation, the examiner listens to body sounds to evaluate the functioning of certain organs, as in listening to the lungs or heart. 3. In percussion, the examiner taps on the body surface with the fingertips and listens to the resulting echo. IV. CHARACTERISTICS OF THE LIVING HUMAN ORGANISM A. Basic Life Processes 1. All living things have certain characteristics that distinguish them from nonliving things. 2. Among the life processes in humans are metabolism, responsiveness, movement, growth, differentiation, and reproduction. a. Metabolism is the sum of all chemical processes that occur in the body, including catabolism and anabolism. b. Responsiveness is the ability to detect and respond to changes in the external or internal environment. c. Movement includes motion of the whole body, individual organs, single cells, or even organelles inside cells. d. Growth refers to an increase in size and complexity, due to an increase in the number of cells, size of cells, or both. e. Differentiation is the change in a cell from an unspecialized state to a specialized state. f. Reproduction refers either to the formation of new cells for growth, repair, or replacement, or the production of a new individual. 3. An autopsy (as discussed in a Clinical Connection) is a postmortem examination of the body and dissection of its internal organs to confirm or determine the cause of death. B. Homeostasis 1. A condition of equilibrium in the body’s internal environment produced by the ceaseless interplay of all the body’s regulatory processes. C. Body Fluids 1. For the body’s cells to survive, the composition of the surrounding fluids must be precisely maintained at all times. a. Fluid inside body cells is called intracellular fluid. b. Fluid outside body cells is called extracellular fluid (ECF) and is found in two principal places. (i) ECF filling the narrow spaces between cells of tissues is called interstitial fluid, intercellular fluid, or tissue fluid.  (ii) ECF in blood vessels is termed plasma, within lymphatic vessels it is called lymph, in and around the brain and spinal cord it is called cerebrospinal fluid, in the joints it is called synovial fluid and within the eyes it is called aqueous humor or vitreous humor. (iii) Since ECF is in constant motion throughout the body and also surrounds all body cells, it is often called the body’s internal environment. V. CONTROL OF HOMEOSTASIS A. Homeostatic imbalances occur because of disruptions from the external or internal environments. B. Homeostasis is regulated by the nervous system and endocrine system, acting together or independently. 1. The nervous system detects changes and sends nerve impulses to counteract the disruption. 2. The endocrine system regulates homeostasis by secreting hormones. 3. Whereas nerve impulses cause rapid changes, hormones usually work more slowly. C. Feedback Systems 1. General Principles a. A feedback system is a cycle of events in which information about the status of a condition is continually monitored and fed back (reported) to a central control region (Figure 1.2). b. Any disruption that changes a controlled condition is called a stimulus. c. A feedback system consists of three basic components. (i) A receptor monitors changes in a controlled condition and sends input in the form of nerve impulses or chemical signals to a control center. (ii) The control center sets the range of values within which a controlled condition should be maintained, evaluates the input it receives from the receptors, and generates output commands when they are needed. (iii) An effector is a body structure that receives output from the control center and produces a response or effect that changes the controlled condition. d. If a response reverses the original stimulus, the system is a negative feedback system. e. If a response enhances the original stimulus, the system is a positive feedback system. D. Negative Feedback Systems 1. A negative feedback system reverses a change in a controlled condition. 2. Homeostasis of Blood Pressure (BP): Negative Feedback (Figure 1.3) a. If a stimulus (stress) causes blood pressure (controlled condition) to rise, pressure- sensitive cells (baroreceptors) in certain arteries send impulses (input) to the brain (control center). The brain sends impulses (output) to the heart (effector), causing the heart rate to decrease (response) and return of blood pressure to normal (restoration of homeostasis).  b. The activity of the effector produces a result, a drop in blood pressure that opposes the stimulus, an increase in blood pressure. E. Positive Feedback System 1. A positive feedback system tends to strengthen or reinforce a change in one of the body’s controlled conditions. 2. Normal childbirth provides a good example of a positive feedback system (Figure 1.4). a. When labor begins, the uterus is stretched (stimulus) and stretch-sensitive nerve cells in the cervix of the uterus (receptors) send impulses (input) to the hypothalamus (control  center). The hypothalamus causes the release of oxytocin (output), which stimulates the uterus (effector) to contract more forcefully (response). Movement of the baby’s head down the birth canal causes further stretching, the release of more oxytocin, and even more forceful contractions. The cycle is broken with the birth of the baby. b. The positive feedback system reinforces a change in a controlled condition. F. Homeostatic Imbalances 1. Disruption of homeostasis can lead to disease and death. 2. Disorder is a general term for any abnormality of structure or function. 3. Disease is a more specific term for an illness characterized by a recognizable set of signs and symptoms. a. A local disease is one that affects one part or a limited region of the body. b. A systemic disease affects either the entire body or several parts. c. Symptoms are subjective changes in body functions that are not apparent to an observer; e.g., headache or nausea. d. Signs are objective changes that a clinician can observe and measure; e.g., fever or rash. e. Epidemiology deals with how diseases are transmitted among individual. Pharmacology is the science that deals with the effects and uses of drugs in treatment. 4. Diagnosis is the art of distinguishing one disease from another or determining the nature of a disease; a diagnosis is generally arrived at after the taking of a medical history and the administration of a physical examination (Clinical Connection). VI. BASIC ANATOMICAL TERMINOLOGY A. Body Positions 1. Anatomical Position a. The anatomical position is a standard position of reference. b. When in the anatomical position, the subject stands erect facing the observer, the upper extremities are placed at the sides, the palms of the hands are turned forward, and the feet are flat on the floor (Figure 1.5). 2. Reclining Position a. If the body is lying face down, it is in the prone position. b. If the body is lying face up, it is in the supine position. B. Regional Names 1. Regional names are names given to specific regions of the body for reference.  2. Study all of the regional names in Figure 1.5. (cephalic = head, cranial = skull, facial = face, frontal = forehead, temporal = temple, orbital or ocular = eye, otic = ear, buccal = cheek, nasal = nose, oral = mouth, mental = chin, occipital = base of skull, cervical = neck, thoracic = chest, sternal = breastbone, mammary = breast, scapular = shoulder blade, vertebral = spinal column, dorsal = back, axillary = armpit, brachial = arm, antecubital = front of elbow, olecranal or cubital = back of elbow, antebrachial = forearm, carpal = wrist, manual = hand, palmar or volar = palm, dorsum = back of hand, digital or phalangeal = fingers, pollex = thumb, abdominal = abdomen, lumbar = loin, sacral = between hips, inguinal = groin, pelvic = pelvis, gluteal = buttock, perineal = region of anus and external genitals, femoral = thigh, patellar = anterior surface of knee, popliteal = hollow behind knee, crural = leg, sural = calf, tarsal = ankle, pedal = foot, dorsum = top of foot, plantar = sole, calcaneal = heel, digital or phalangeal = toes, hallux = great toe) C. Directional Terms  1. Directional terms are used to precisely locate one part of the body relative to another and to reduce length of explanations. 2. Study all of the directional terms in Exhibit 1.A and Figure 1.6. (superior = higher, inferior = lower, anterior = towards front, posterior = towards rear, medial = nearer to midline, lateral = further from midline, intermediate = between two structures, ipsilateral = on same side as another structure, contralateral = on opposite side as another structure, proximal = nearer to attachment of limb to trunk, distal = further from attachment of limb to trunk, superficial (external) = towards surface, deep (internal) = away from surface) D. Planes and Sections 1. Planes are imaginary flat surfaces that are used to divide the body or organs into definite areas (Figure 1.7). Principal planes include: midsagittal (medial) and parasagittal, frontal (coronal), transverse (cross-sectional or horizontal) and oblique. a. A sagittal plane is a vertical plane that divides the body into right and left sides. (i) A midsagittal plane divides the body into equal right and left sides. (ii) A parasagittal plane divides the body into unequal right and left sides. b. A frontal plane divides the body into anterior and posterior portions. c. A transverse plane divides the body into superior and inferior portions. d. An oblique plane passes through the body at any angle other than 90 degrees.  2. Sections are flat surfaces resulting from cuts through body structures. They are named according to the plane on which the cut is made and include transverse, frontal, and midsagittal sections (Figure 1.8). E. Body Cavities 1. Body cavities are spaces within the body that help protect, separate, and support internal organs. 2. Cranial cavity and vertebral canal a. The cranial cavity is formed by the cranial bones and contains the brain. b. The vertebral (spinal) canal is formed by the bones of the vertebral column and contains the spinal cord. c. Three layers of protective tissue, called meninges, line these cavities. 3. Body cavities of the trunk a. The trunk is subdivided by the diaphragm into an upper thoracic cavity and a lower abdominopelvic cavity. (Figure 1.9)  b. The thoracic cavity contains two pleural cavities, and the mediastinum, which includes the pericardial cavity (Figure 1.10). (i) The pleural cavities enclose the lungs, while the pericardial cavity surrounds the heart (Figure 1.10). (ii) The mediastinum is a broad, median partition between the lungs that extends from the sternum to the vertebral column; it contains all contents of the thoracic cavity except the lungs. 4. The abdominopelvic cavity is divided into a superior abdominal and an inferior pelvic cavity (Figure 1.11). a. Viscera of the abdominal cavity include the stomach, spleen, pancreas, liver, gallbladder, small intestine, and most of the large intestine (Figure 1.11). b. Viscera of the pelvic cavity include the urinary bladder, portions of the large intestine and internal female and male reproductive structures (Figure 1.11). 5. Thoracic and abdominal cavity membranes a. A thin, slippery serous membrane covers the viscera within the thoracic and abdominal cavities and also lines the walls of the thorax and abdomen. b. Parts of the serous membrane are the parietal layer, which lines the walls of the cavities, and the visceral layer, which covers and adheres to the viscera within the cavities.  c. Serous fluid between the two layers reduces friction and allows the viscera to slide somewhat during movements. d. The serous membranes include the pleura, pericardium and peritoneum. (i) The pleural membrane surrounds the lungs, with the visceral pleura clinging to the surface of the lungs and the parietal pleura lining the chest wall. (ii) The serous membrane of the pericardial cavity is the pericardium, with visceral pericardium covering the surface of the heart and the parietal pericardium lining the chest wall. (iii) The peritoneum is the serous membrane of the abdominal cavity, with the visceral peritoneum covering the abdominal viscera and the parietal peritoneum lining the abdominal wall. 6. Abdominopelvic Regions and Quadrants a. To describe the location of organs easily, the abdominopelvic cavity may be divided into nine regions by drawing four imaginary lines as shown in Figure 1.12 (note that some organs are labeled in Fig. 1.6). (i) The liver is mostly found in the right hypochondriac and epigastric regions. Note that hypo means below, and chondro refers to the pieces of cartilage that attach the ribs to the sternum, so that hypochondriac means under the rib cartilage. (ii) The stomach is found in the epigastric and left hypochondriac regions. The term gastric refers to the stomach. (iii) The ascending colon is mostly in the right lumbar region. (iv) The descending colon is mostly in the left lumbar region. (v) The urinary bladder is in the hypogastric region. (vi) Most of the small intestine is in the umbilical region. b. To locate the site of an abdominopelvic abnormality in clinical studies, the abdominopelvic cavity may be divided into quadrants by passing imaginary horizontal and vertical lines through the umbilicus (Figure 1.12). (i) The gallbladder is in the right upper quadrant (RUQ). (ii) The spleen is in the left upper quadrant (LUQ). (iii) The appendix is in the right lower quadrant (RLQ). VII. MEDICAL IMAGING A. A very specialized branch of anatomy and physiology that is essential for the diagnosis of many disorders is medical imaging. Medical imaging techniques allow physicians to peer inside the  body to provide clues to abnormal anatomy and deviations from normal physiology in order to help diagnose disease. B. Radiography uses x-rays to produce a two-dimensional image called a radiograph. 1. Low dose x-rays can be useful for examining soft tissues such as the breast (mammography) and for determining bone density (bone densitometry). 2. Contrast x-rays use a contrast medium to image blood vessels (angiography) the urinary system (intravenous urography), and the gastrointestinal tract (barium contrast x-ray). C. Magnetic resonance imaging (MRI) uses a high-energy magnetic field to align protons inside atoms, and radio waves to then create an image related to the chemical environment around the protons. MRI shows fine details for soft tissues, but not for bones. D. Computed tomography (CT) uses computer-controlled x-rays to create three-dimensional views of the body. E. Ultrasound scanning uses high-frequency sound waves to image body organs. F. Coronary (cardiac) computed tomography angiography (CCTA) scan uses an iodine-containing contrast medium injected into a vein to image the coronary blood vessels. G. Positron emission tomography (PET) uses substances that emits positrons (typically a radioactive form of glucose) to image organs. Organs that are more active take up more glucose (which is a major source of energy for cells), and show up with brighter images. PET thus shows physiological activity. H. Endoscopy involves the visual examination of the inside of body organs or cavities using a lighted tube-shaped instrument. 1. A colonoscopy examines the inside of the colon. 2. A laparoscopy examines the organs within the abdominopelvic cavity. 3. Arthroscopy is used to examine the interior of a joint. I. Radionuclide scanning involves the intravenous injection of radionuclides (radioactive substances) to image organs or tissues that take up the radionuclide. UNIT 2: ORGANIZATION OF MATTER INTRODUCTION A. Chemistry is the science of the structure and interactions of matter.. B. Matter is anything that occupies space and has mass  C. Mass is the amount of matter a substance contains; weight is the force of gravity acting on a mass. II. HOW MATTER IS ORGANIZED A. Chemical Elements 1. Matter exists in three forms: a. solid (such as bones and teeth) b. liquid (such as blood plasma) c. gas (such as oxygen and carbon dioxide) 2. All forms of matter are composed of chemical elements, which are substances that cannot be split into simpler substances by ordinary chemical means. 3. Elements are given letter abbreviations called chemical symbols. 4. Oxygen (O), carbon (C), hydrogen (H), and nitrogen (N) are the major elements in the body, and make up about 96% of body weight. (You do not need to memorize the “% of Total Body Mass” and “Significance” listed for the chemical elements in Table 2.1.) B. Structure of Atoms 1. Units of matter of all chemical elements are called atoms. An element is a quantity of matter composed of atoms of the same type. 2. Atoms: the smallest units of matter that retain the properties and characteristics of the element  a. subatomic particles: compose individual atoms. 1) protons: positively charged (p+), located within the nucleus 2) neutrons: uncharged (neutral; n0), located within the nucleus 3) electrons: tiny, negatively charged (e-) 2. Atoms consist of a nucleus, which contains positively charged protons and neutral (uncharged) neutrons, and negatively charged electrons that move about the nucleus in energy levels (Figure 2.1a). 3. Electrons revolve around the nucleus of an atom tending to spend most of the time in specific atomic regions, called shells (Figure 2.1b). a. Each shell can hold a certain maximum number of electrons. b. The first shell, the one nearest the nucleus, can hold a maximum of 2 electrons; the second shell, 8; the third shell, 18; the fourth shell, 18; and so on (Figure 2.1b). 4. The number of electrons in an atom of a neutral element always equals the number of protons. C. Atomic Number and Mass Number 1. Atomic Number: The number of protons in the nucleus of an atom  a. The number of protons in the nucleus makes the atoms of one element different from those of another as illustrated in Figure 2.2 (You do not need to memorize the atomic numbers, mass numbers, or atomic masses of the elements in this figure.) b. Since all atoms are electrically neutral, the atomic number also equals the number of electrons in each atom. 2. The Mass Number of an atom is the total number of protons and neutrons. 3. Different atoms of an element that have the same number of protons but different numbers of neutrons are called isotopes. a. Stable isotopes do not change their nuclear structure over time. b. Certain isotopes called radioactive isotopes are unstable because their nuclei decay to form a simpler and thus more stable configuration. c. The half-life of a radioactive isotope is the time required for half of the radioactive atoms to decay into a more stable form. D. Atomic Mass 1. The standard unit for measuring the mass of atoms and their subatomic particles is a dalton, also known as an atomic mass unit (amu). a. a neutron has a mass of 1.008 daltons b. a proton has a mass of 1.007 daltons c. an electron has a mass of 0.0005 daltons  2. The atomic mass, also called the atomic weight, of an element is the average mass of all its naturally occurring isotopes and reflects the relative abundance of isotopes with different mass numbers. 3. The mass of a single atom is slightly less than the sum of the masses of its neutrons, protons, and electrons because some mass (less than 1%) was lost when the atom’s components came together to form an atom. E. Ions, Molecules, and Compounds 1. If an atom either gives up or gains electrons, it becomes an ion - an atom that has a positive or negative charge due to having unequal numbers of protons and electrons. 2. When two or more atoms share electrons, the resulting combination is called a molecule (Figure 2.3a). 3. Clinical Connection: A free radical is an electrically charged atom or group of atoms with an unpaired electron in its outermost shell (Figure 2.3b). a. Free radicals become stable by either giving up their unpaired electron or by taking on an electron from another molecule. b. Antioxidants are substances that inactivate oxygen-derived free radicals. 4. A compound is a substance that contains atoms of two or more different elements. III. CHEMICAL BONDS A. The atoms of a molecule are held together by forces of attraction called chemical bonds. 1. The likelihood that an atom will form a chemical bond with another atom depends on the number of electrons in its outermost shell, also called the valence shell. 2. An atom with a valence shell holding eight electrons (2 electrons for helium) is chemically stable, which means it is unlikely to form chemical bonds with other atoms. 3. To achieve stability, atoms that do not have eight electrons in their valence shell (or 2 in the case of H) tend to empty their valence shell or fill it to the maximum extent (figure 2.2). 4. Atoms with incompletely filled outer shells tend to combine with each other in chemical reactions to produce a chemically stable arrangement of eight valence electrons for each atom. This chemical principle is called the octet rule. B. Ionic Bonds 1. When an atom loses or gains a valence electron, ions are formed (Figure 2.4a).  Positively and negatively charged ions are attracted to one another. b. When this force of attraction holds ions having opposite charges together, an ionic bond results. 2. Cations are positively charged ions that have given up one or more electrons (they are electron donors). 3. Anions are negatively charged ions that have picked up one or more electrons that another atom has lost (they are electron acceptors). 4. In general, ionic compounds exist as solids but some may dissociate into positive and negative ions in solution. Such a compound is called an electrolyte. 5. Table 2.2 lists the names and symbols of the most common ions in the body. C. Covalent Bonds 1. Covalent bonds are formed by the atoms of molecules sharing one, two, or three pairs of their valence electrons. 2. Covalent bonds are the most common chemical bonds in the body. 3. Single, double, or triple covalent bonds are formed by sharing one, two, or three pairs of electrons, respectively (Figure 2.5b,c). 4. Covalent bonds may be nonpolar or polar. a. In a nonpolar covalent bond, atoms share the electrons equally; one atom does not attract the shared electrons more strongly than the other atom (Figure 2.5a-d).  b. In a polar covalent bond, the sharing of electrons between atoms is unequal; one atom attracts the shared electrons more strongly than the other (Figure 2.5e). D. Hydrogen Bonds 1. In a hydrogen bond, a hydrogen atom with a partial positive charge attracts the partial negative charge of neighboring electronegative atoms (usually oxygen or nitrogen) (Figure 2.6). 2. Hydrogen bonds are weak and cannot bind atoms into molecules. They serve as links between molecules. 3. They provide strength and stability and help determine the three- dimensional shape of large molecules. 4. Hydrogen bonds linking neighboring water molecules (Figure 2.6) give water considerable cohesion which creates a very high surface tension. IV. CHEMICAL REACTIONS A. A chemical reaction occurs when new bonds are formed or old bonds break between atoms (Figure 2.7). 1. The starting substances of a chemical reaction are known as reactants. 2. The ending substances of a chemical reaction are the products. 3. In a chemical reaction, the total mass of the reactants equals the total mass of the products (the law of conservation of mass). 4. Metabolism refers to all the chemical reactions occurring in an organism. B. Forms of Energy and Chemical Reactions 1. Energy is the capacity to do work. a. Potential energy is energy stored by matter due to its position. b. Kinetic energy is the energy associated with matter in motion. c. Chemical energy is a form of potential energy stored in the bonds of compounds or molecules. 2. The total amount of energy present at the beginning and end of a chemical reaction is the same; energy can neither be created nor destroyed although it may be converted from one form to another (law of conservation of energy). C. Energy Transfer in Chemical Reactions 1. Breaking chemical bonds requires energy and forming new bonds releases energy. a. An exergonic reaction is one in which the bond being broken has more energy than the one formed so that extra energy is released, usually as heat (occurs during catabolism of food molecules). b. An endergonic reaction is just the opposite and thus requires energy, usually from a molecule called ATP, to form a bond, as in bonding amino acid molecules together to form proteins  2. Activation energy is the collision energy needed to break chemical bonds in the reactants (Figure 2.8). a. Activation energy is the initial energy needed to start a reaction. b. Factors that influence the chance that a collision will occur and cause a chemical reaction include 1) Concentration: The more particles of matter present in a confined space, the greater the chance that they will collide 2) Temperature: As temperature rises, particles of matter move about more rapidly. 3. Catalysts are chemical compounds that speed up chemical reactions by lowering the activation energy needed for a reaction to occur (Figure 2.9). a. A catalyst does not alter the difference in potential energy between the reactants and products. It only lowers the amount of energy needed to get the reaction started. b. A catalyst helps to properly orient the colliding particles of matter so that a reaction can occur. c. The catalyst itself is unchanged at the end of the reaction. D. Types of Chemical Reactions 1. Synthesis reactions occur when two or more atoms, ions, or molecules combine to form new and larger molecules. These are anabolic reactions, meaning that bonds are formed. 2. In a decomposition reaction, a molecule is broken down into smaller parts. These are catabolic reactions, meaning that chemical bonds are broken in the process. 3. Exchange reactions involve the replacement of one atom or atoms by another atom or atoms. 4. In reversible reactions, end products can revert to the original combining molecules. 5. Oxidation-reduction reactions: These reactions are concerned with the transfer of electrons between atoms and molecules. a. Oxidation refers to the loss of electrons b. Reduction refers to the gain of electrons V. INORGANIC COMPOUNDS AND SOLUTIONS A. Inorganic compounds usually lack carbon and are simple molecules; whereas organic compounds always contain carbon, usually contain hydrogen, and always have covalent bonds. B. Water 1. Water is the most important and abundant inorganic compound in all living systems. a. The most important property of water is its polarity, the uneven sharing of valence electrons that confers a partial negative charge near the one oxygen atom and two partial positive charges near the two hydrogen atoms in the water molecule (Figure 2.5e). b. Water enables reactants to collide to form products. 2. Water as a solvent  a. In a solution the solvent dissolves the solute. b. The polarity of water allows it to interact with several neighboring ions or molecules (Figure 2.10). c. Substances which contain polar covalent bonds and dissolve in water are hydrophilic, while substances which contain nonpolar covalent bonds are hydrophobic. d. Water’s role as a solvent makes it essential for health and survival. 3. Water in Chemical Reactions a. Water is the ideal medium for most chemical reactions in the body and participates as a reactant or product in certain reactions.  b. Hydrolysis breaks large molecules down into simpler ones by adding a molecule of water. c. Dehydration synthesis occurs when two simple molecules join together, eliminating a molecule of water in the process. 4. Thermal properties of Water a. Water has a high heat capacity. 1) It can absorb or release a relatively large amount of heat with only a modest change in its own temperature. 2) This property is due to the large number of hydrogen bonds in water. b. Water has a high heat of vaporization. It requires a large amount of heat to change from a liquid to a gas. 5. Water as a Lubricant a. Water is a major part of mucus and other lubricating fluids. b. It is found wherever friction needs to be reduced or eliminated. C. Solutions, Colloids, and Suspensions 1. A mixture is a combination of elements or compounds that are physically blended together but are not bound by chemical bonds. Three common liquid mixtures are solutions, colloids, and suspensions. a. In a solution, a substance called the solvent dissolves another substance called the solute. Usually there is more solvent than solute in a solution. b. A colloid differs from a solution mainly on the basis of the size of its particles with the particles in the colloid being large enough to scatter light. c. In a suspension, the suspended material may mix with the liquid or suspending medium for some time, but it will eventually settle out. 2. Percentage and molarity are ways of describing the concentration of a molecule or the amount of that molecule dissolved in solution (Table 2.3).  a. Percent gives the relative mass of a solute found in a given volume of solution. b. A mole is the name for the number of atoms in an atomic weight of that element, or the number of molecules in a molecular weight of that type of molecule, with the molecular weight being the sum of all the atomic weights of the atoms that make up the molecule. D. Inorganic Acids, Bases, and Salts 1. When molecules of inorganic acids, bases, or salts dissolve in water, they undergo ionization or dissociation; that is, they separate into ions. 2. Acids are proton donors, and ionize into one or more hydrogen ions (H+) and one or more anions (negative ions) (Figure 2.11a). 3. Bases are proton acceptors. Many bases dissociate into one or more hydroxide ions (OH-) and one or more cations (positive ions) (Figure 2.11b). 4. A salt, when dissolved in water, dissociates into cations and anions, neither of which is H+ or OH- (Figure 2.11c). Many salts are present in the body and are formed when acids and bases react with each other. E. Acid-Base Balance: The Concept of pH 1. Body fluids must constantly contain balanced quantities of acids and bases. 2. Biochemical reactions are very sensitive to even small changes in acidity or alkalinity. 3. A solution’s acidity or alkalinity is based on the pH scale, which runs from 0 (=10 0 = 1.0 moles H+/L) to 14 (= 10-14 = 0.00000000000001 moles H+/L) (Figure 2.12) a. pH 7.0 = 10-7 = 0.0000001 moles H+/L = neutrality or equal numbers of [H+] and [OH-]. b. Values below 7 indicate acid solutions ([H+] > [OH-]). c. Values above 7 indicate alkaline solutions ([H+] < [OH-]).  F. Maintaining pH: Buffer Systems 1. The pH values of different parts of the body are maintained fairly constant by buffer systems, which usually consist of a weak acid and a weak base. 2. The function of a buffer system is to convert strong acids or bases into weak acids or bases. 3. One important buffer system in the body is the carbonic acid-bicarbonate buffer system. a. Bicarbonate ions (HCO3-) act as weak bases and carbonic acid (H2CO3) acts as a weak acid. VI. ORGANIC COMPOUNDS A. Carbon and Its Functional Groups 1. The carbon that organic compounds always contain has several properties that make it particularly useful to living organisms. a. It can react with one to thousands of other carbon atoms to form large molecules of many different shapes. b. Some carbon compounds do not dissolve easily in water, making them useful materials for building body structures. c. Carbon compounds are usually held together by covalent bonds.  d. The chain of carbon atoms in an organic molecule is the carbon skeleton. Attached to the carbon skeleton are distinctive functional groups, in which other elements form bonds with carbon and hydrogen atoms. 1) Each type of functional group has a specific arrangement of atoms that confers characteristic chemical properties upon organic molecules. 2) Table 2.5 lists the most common functional groups. 3) Fig 2.13 shows two ways to indicate the structure of the sugar glucose. 2. Small organic molecules can combine to form very large molecules (macromolecules, or polymers, when composed of repeating units called monomers). a. When two monomers joint together, the reaction is usually dehydration synthesis. b. Macromolecules break down into monomers usually by hydrolysis. 3. Molecules that have the same molecular formula but different structures are called isomers. B. Carbohydrates 1. Carbohydrates provide most of the energy needed for life and include sugars, starches, glycogen, and cellulose. a. Some carbohydrates are converted to other substances, which are used to build structural units such as DNA. b. The general structural rule for carbohydrates is one carbon atom for each water molecule (CH2O). c. Carbohydrates are divided into three major groups based on their size: monosaccharides, disaccharides, and polysaccharides (Table 2.6). 2. Monosaccharides and Disaccharides: The Simple Sugars a. Monosaccharides contain from three to seven carbon atoms and include glucose, a hexose that is the main energy-supplying compound of the body (Figure 2.14) b. Disaccharides are formed from two monosaccharides by dehydration synthesis; they can be split back into simple sugars by hydrolysis (Figure 2.15). Glucose and fructose combine, for example, to produce sucrose.  3. Polysaccharides a. Polysaccharides are the largest carbohydrates and may contain hundreds of monosaccharides. b. The principal polysaccharide in the human body is glycogen, which is stored in the liver or skeletal muscles. Starches are polysaccharides formed from glucose in plants. Celluose is a polysaccharide formed from glucose but cannot be digested in humans (Figure 2.16) C. Lipids 1. Lipids, like carbohydrates, contain carbon, hydrogen, and oxygen; but unlike carbohydrates, they do not have a 2:1 ratio of hydrogen to oxygen.  a. They have fewer polar covalent bonds and thus are mostly insoluble in polar solvents such as water (they are hydrophobic). To become soluble they join with proteins to become lipoproteins. b. Table 2.7 summarizes the various types of lipids and highlights their roles in the human body. (You do not need to memorize the functions listed in this table.) 2. Fatty acids a. Fatty acids are used to form triglycerides (which provide cellular energy) and phospholipids. b. Fatty acids can be saturated, with only single covalent bonds, and unsaturated, with one or more double covalent bonds. c. Essential fatty acids cannot be made by the human body, and must be obtained from food or supplements. 3. Triglycerides  a. Triglycerides are the most plentiful lipids in the body and provide protection, insulation, and energy (both immediate and stored). 1) At room temperature, triglycerides may be either solid (fats) or liquid (oils). 2) Triglycerides provide more than twice as much energy per gram as either carbohydrates or proteins. 3) Triglyceride storage is virtually unlimited. 4) Excess dietary carbohydrates, proteins, fats, and oils will be deposited in adipose tissue as triglycerides. b. Triglycerides are composed of glycerol and fatty acids (Figure 2.17). c. The type of covalent bonds (and by inference, number of hydrogen atoms) found in the fatty acids determines whether a triglyceride is saturated, monounsaturated, or polyunsaturated. 4. Phospholipids  a. Phospholipids have two fatty acids and a phosphate group attached to the three carbons on a glycerol backbone. b. Phospholipids are important membrane components. c. They are amphipathic, with both polar and nonpolar regions (Figure 2.18). 5. Steroids a. Steroids have four rings of carbon atoms (Figure 2.19).  b. The commonly encountered steroids in the body (including sex hormones and cholesterol) are known as sterols because they have at least one hydroxyl group, which makes them weakly amphipathic. c. Cholesterol serves as an important component of cell membranes and as starting material for synthesizing other steroids. 6. Other Lipids a. Eicosanoids include prostaglandins and leukotrienes. 1) Prostaglandins modify responses to hormones, contribute to inflammatory responses, prevent stomach ulcers, dilate airways to the lungs, regulate body temperature, and influence blood clots, among other things.  2) Leukotrienes participate in allergic and inflammatory responses. b. Body lipids also include fat-soluble vitamins such as beta-carotenes; vitamins D, E, and K; and lipoproteins. D. Proteins 1. Proteins give structure to the body, regulate processes, provide protection, help muscles to contract, transport substances, and serve as enzymes (Table 2.8). 2. Amino Acids and Polypeptides a. Proteins are constructed from monomers of amino acids. b. Amino acids contain carbon, hydrogen, oxygen and nitrogen in amino and carboxyl (acid) groups (Figure 2.20).  c. Amino acids are joined together in a stepwise fashion with each covalent bond joining one amino acid to the next using a peptide bond (Figure 2.21). d. Resulting polypeptide chains may contain 10 to more than 2,000 amino acids. 3. Levels of Structural Organization a. Levels of structural organization include primary, secondary, tertiary, and quaternary structures (Figure 2.22).  b. The resulting shape of the protein greatly influences its ability to recognize and bind to other molecules. c. Denaturation of a protein by a hostile environment causes loss of its characteristic shape and function. 4. Enzymes a. Catalysts in living cells are called enzymes. b. Some enzymes consist of a protein portion called an apoenzyme and a nonprotein portion called a cofactor. c. The names of enzymes usually end in the suffix -ase; oxidase, kinase, and lipase, are examples. c. Although enzymes catalyze select reactions, they do so with great efficiency and with many built-in controls.  1) Enzymes are highly specific in terms of the substrate with which they react. 2) Enzymes are extremely efficient in terms of the number of substrate molecules with which they react. 3) Enzymes are subject to a great deal of cellular controls. d. Enzymes speed up chemical reactions by increasing frequency of collisions, lowering the activation energy and properly orienting the colliding molecules (Figure 2.23a). E. Nucleic Acids: Deoxyribonucleic Acid (DNA) and Ribonucleic Acid (RNA) 1. Nucleic acids are huge organic molecules that contain carbon, hydrogen, oxygen, nitrogen, and phosphorus. a. Deoxyribonucleic acid (DNA) forms the genetic code inside each cell and thereby regulates most of the activities that take place in our cells throughout a lifetime.  b. Ribonucleic acid (RNA) relays instructions from the genes in the cell’s nucleus to guide each cell’s assembly of amino acids into proteins by the ribosomes. 2. The basic units (monomers) of nucleic acids are nucleotides, composed of a nitrogenous base, a pentose sugar, and a phosphate group (Figure 2.24a). 3. DNA molecules consist of a double-stranded helix of nucleotides containing adenine, thymine, cytosine, and guanine nitrogenous bases, and deoxyribose sugars. RNA molecules consist of a single strand of nucleotides containing adenine, uracil, cytosine, and guanine nitrogenous bases, and ribose sugars. F. Adenosine Triphosphate 1. Adenosine triphosphate (ATP) is the principal energy-transferring molecule inside cells.  2. Among the cellular activities for which ATP provides energy are muscular contractions, chromosome movement during cell division, cytoplasmic movement within cells, membrane transport processes, and synthesis reactions. 3. ATP consists of three phosphate groups attached to an adenosine unit composed of adenine and the five-carbon sugar ribose (Figure 2.25). a. When energy is liberated from ATP, it is decomposed to adenosine diphosphate (ADP) and phosphorus (P), with the enzyme ATPase catalyzing the reaction. b. ATP is manufactured from ADP and P using the energy supplied by various decomposition reactions, particularly that of glucose. UNIT 3: CELLULAR ORGANIZATION I. INTRODUCTION A. A cell is the basic living, structural, and functional unit of the body.  B. Cell biology or cytology is the study of cell structure and function. II. PARTS OF A CELL A. A generalized view of the cell is a composite of many different cells in the body as seen in Figure 3.1. No single cell includes all of the features seen in the generalized cell. B. The cell can be divided into three principal parts for ease of study. 1. Plasma (cell) membrane 2. Cytoplasm a. Cytosol = fluid portion b. Organelles (except for the nucleus) = little organs 3. Nucleus a. Chromosomes = each is single DNA molecule b. Genes = sequences of DNA that codes for a particular RNA III. THE PLASMA MEMBRANE A. The plasma membrane is a flexible, sturdy barrier that surrounds and contains the cytoplasm of the cell. 1. The fluid mosaic model describes its structure (Figure 3.2).  2. The membrane consists of proteins in a sea of lipids. B. The Lipid Bilayer 1. The lipid bilayer is the basic framework of the plasma membrane and is made up of three types of lipid molecules: phospholipids, cholesterol, and glycolipids (Figure 3.2). 2. The bilayer arrangement occurs because the lipids are amphipathic molecules. They have both polar (charged) and nonpolar (uncharged) parts with the polar “head” of the phospholipid pointing out and the nonpolar “tail” pointing toward the center of the membrane. a. cholesterol molecules are weakly amphipathic C. Arrangement of Membrane Proteins 1. The membrane proteins are divided into integral and peripheral proteins (Figure 3.2)  a. Integral proteins extend into or across (transmembrane) the entire lipid bilayer among the fatty acid tails of the phospholipid molecules. b. Peripheral proteins are found at the inner or outer surface of the membrane and can be stripped away from the membrane without disturbing membrane integrity. 2. Integral membrane proteins are amphipathic. a. Those that stretch across the entire bilayer and project on both sides of the membrane are termed transmembrane proteins. b. Many integral proteins are glycoproteins. 1. Glycocalyx: formed by the carbohydrate portions of glycolipids and glycoproteins 3. The combined glycoproteins and glycolipids form the glycocalyx which helps cells recognize one another, adhere to one another, and be protected from digestion by enzymes in the extracellular fluid. D. Functions of Membrane Proteins  1. Membrane proteins vary in different cells and functions as ion channels, carriers (transporters), receptors, enzymes, linkers, and cell-identity markers (Figure 3.3). 2. The different proteins help to determine many of the functions of the plasma membrane. E. Membrane Fluidity 1. Membranes are fluid structures, rather like cooking oil, because most of the membrane lipids and many of the membrane proteins easily move in the bilayer. 2. Membrane lipids and proteins are mobile in their own half of the bilayer. 3. Cholesterol serves to stabilize the membrane and reduce membrane fluidity (figure 2.18). F. Membrane Permeability  1. Plasma membranes are selectively permeable, meaning that some things can pass through and others cannot. 2. The lipid bilayer portion of the membrane is permeable to small, nonpolar, uncharged molecules but impermeable to ions and charged or polar molecules, with the exception of water and urea, which are thought to pass through gaps between the fatty acid tails of membrane phospholipids and glycolipids. 3. Transmembrane proteins that act as channels or transporters increase the permeability of the membrane to molecules that cannot cross the lipid bilayer. 4. Macromolecules are unable to pass through the plasma membrane except by vesicular transport. G. Gradients Across the Plasma Membrane 1. A concentration gradient is the difference in the concentration of a chemical between one side of the plasma membrane and the other. a. Oxygen and sodium ions are more concentrated outside the cell membrane with carbon dioxide and potassium ions more concentrated inside the cell membrane. b. The inner surface of the membrane is more negatively charged and the outer surface is more positively charged. This sets up an electrical gradient, also called the membrane potential. 2. Maintaining the concentration and electrical gradients are important to the life of the cell. 3. The combined concentration and electrical gradients are called the electrochemical gradient. IV. TRANSPORT ACROSS THE PLASMA MEMBRANE A. Processes to move substances across the cell membrane are essential to the life of the cell. 1. Some substances cross the lipid bilayer while others cross through ion channels. 2. Transport processes that move substances across the cell membrane are either active or passive. a. Passive processes include simple diffusion, facilitated diffusion, and osmosis and are driven by concentration gradients b. Active processes include active transport and vesicular transport and these require cellular energy. B. Passive Processes 1. The principle of diffusion a. Diffusion is the random mixing of particles that occurs in a solution as a result of the kinetic energy of the particles. (Figure 3.4) b. Diffusion rate across plasma membranes is influenced by several factors: steepness of the concentration gradient, temperature, mass of the diffusing substance, surface area, and diffusion distance. 2. Simple Diffusion a. Nonpolar, hydrophobic molecules such as respiratory gases, some lipids, small alcohols, water, urea, and fat-soluble vitamins can diffuse across the lipid bilayer without the help of transport proteins (Figure 3.5) b. It is important for gas exchange, absorption of some nutrients, and excretion of some wastes. 3. Facilitated Diffusion Solutes that are too polar or highly charged to move through the lipid bilayer by simple diffusion can cross the plasma membrane by a passive process called facilitated diffusion. In this process, an integral membrane protein assists a specific substance across the membrane. The integral membrane protein can be either a membrane channel or a carrier. a. Channel-mediated facilitated diffusion: a solute moves down its concentration gradient across the lipid bilayer through a membrane channel. (Figure 3.6)  1) Most membrane channels are ion channels 2) Some membrane channels are gated b. Carrier-mediated facilitated diffusion: a solute binds to a specific transporter on one side of the membrane and is released on the other side after the transporter undergoes a conformational change. (Figure 3.7) c. Substances that move across the plasma membrane by carrier mediated facilitated diffusion include glucose, fructose, galactose, and some vitamins 4. Osmosis a. Osmosis is the net movement of a solvent through a selectively permeable membrane, or in living systems, the movement of water (the solute) from an area of higher concentration to an area of lower concentration across the membrane (Figure 3.8a).  b. Water molecules penetrate the membrane by diffusion through the lipid bilayer or through aquaporins, transmembrane proteins that function as water channels. c. Water moves from an area of lower solute concentration to an area of higher solute concentration. Movement of water can generate hydrostatic pressure (figure 3.8b). d. Osmosis occurs only when the membrane is permeable to water but not to certain solutes. The solution with the impenetrable solute exerts a force called the osmotic pressure. e. Tonicity of a solution relates to how the solution influences the volume of body cells (Figure 3.9) 1) In an isotonic solution, red blood cells maintain their normal shape. 2) In a hypotonic solution, red blood cells undergo hemolysis. 3) In a hypertonic solution, red blood cells undergo crenation. f. Clinical Connection: Medical Uses of Isotonic, Hypertonic, and Hypotonic Solutions C. Active Processes Active Transport: energy is required for the carrier proteins to move solutes across the membrane against the concentration gradient. 1. Primary Active Transport a. In primary active transport, energy derived from ATP changes the shape of a transporter protein, which pumps a substance across a plasma membrane against its concentration gradient. b. The most prevalent primary active transport mechanism is the sodium- potassium pump, or Na+-K+ATPase (Figure 3.10). c. Clinical Connection: Digitalis slows the sodium ion-calcium ion antiporters, allowing more calcium to stay inside heart muscle cells, which increases the force of their contraction and thus strengthens the heartbeat. 2. Secondary Active Transport a. In secondary active transport, the energy stored in the form of a sodium or hydrogen ion concentration gradient is used to drive other substances against their own concentration gradients. b. Plasma membranes contain several antiporters and symporters powered by the sodium ion gradient (Figure 3.11). 3. Transport in Vesicles a. Endocytosis 1) In endocytosis, materials move into a cell in a vesicle formed from the plasma membrane. 2) Receptor-mediated endocytosis is the selective uptake of large molecules and particles (ligands) by cells (Fig 3.12). a) The steps of receptor-mediated endocytosis include binding, vesicle formation, uncoating, fusion with endosome, recycling of receptors, and degradation in lysosomes.  b) Some viruses (such as HIV) can take advantage of this mechanism to enter cells. 3) Phagocytosis is the ingestion of solid particles (Figure 3.13). a) Only a few body cells, termed phagocytes, are able to carry out phagocytosis. b) Two main types of phagocytes are macrophages and neutrophils. c) Phagocytosis begins with pseudopod formation. 4) Pinocytosis is the ingestion of extracellular fluid (Figure 3.14). Also called bulk phase endocytosis.  b. Exocytosis 1) In exocytosis membrane-enclosed structures called secretory vesicles that form inside the cell fuse with the plasma membrane and release their contents into the extracellular fluid. 2) Transcytosis is a transport process that includes both endocytosis and exocytosis. V. CYTOPLASM A. Cytosol, the intracellular fluid, is the semifluid portion of cytoplasm that contains inclusions and dissolved solutes (Figure 3.1). 1. Cytosol is composed mostly of water, plus proteins, carbohydrates, lipids, and inorganic substances. 2. The chemicals in cytosol are either in solution or in a colloidal (suspended) form. 3. Functionally, cytosol is the medium in which many metabolic reactions occur.  4. The cytoskeleton is a network of protein filaments that extends throughout the cytosol, and consists of microfilaments, intermediate filaments, and microtubules. a. Most microfilaments are composed of actin (some contain myosin) and function in movement and mechanical support (such as within microvilli). b. Intermediate filaments are exceptionally strong, are found in parts of cells subject to mechanical stress, help stabilize the position of organelles, and help attach cells to one another. c. Microtubules are composed of a protein called tubulin and help determine cell shape, and also function in the movement of organelles, chromosomes (during cell division), and specialized cell projections such as cilia and flagella. B. Organelles are specialized structures that have characteristic shapes and perform specific functions in cellular growth, maintenance, and reproduction. 1. Centrosomes are dense areas of cytoplasm containing the centrioles, which are paired cylinders arranged at right angles to one another, and serve as centers for organizing microtubules in interphase cells and the mitotic spindle during cell division. (Figure 3.16a-c) 2. Cilia and Flagella a. Cilia are numerous, short, hairlike projections extending from the surface of a cell and functioning to move materials across the surface of the cell (Figure. 3.17).  b. Flagella are similar to cilia but are much longer; usually moving an entire cell. The only example of a flagellum in the human body is the sperm cell tail (Figure 3.17). 3. Ribosomes a. Ribosomes are tiny spheres consisting of ribosomal RNA and several ribosomal proteins; they occur free (singly or in clusters) or together with endoplasmic reticulum (Fig 3.18). b. Functionally, ribosomes are the sites of protein synthesis. 4. Endoplasmic Reticulum a. The endoplasmic reticulum (ER) is a network of membranes that form flattened sacs or tubules called cisterns (Figure 3.19).  b. Rough ER is continuous with the nuclear membrane and has its outer surface studded with ribosomes. c. Smooth ER extends from the rough ER to form a network of membrane tubules but does not contain ribosomes on its membrane surface. d. The ER transports substances, stores newly synthesized molecules, synthesizes and packages molecules, detoxifies chemicals, and releases calcium ions involved in muscle contraction. e. Clinical Connection: The role of the smooth ER in chemical detoxification has a role in drug tolerance. 5. Golgi Complex a. The Golgi complex consists of 3 to 20 stacked, flattened membranous sacs (cisterns) referred to as cis, medial, and trans (Figure 3.20). b. The principal function of the Golgi complex is to process, sort, and deliver proteins and lipids to the plasma membrane (in membrane vesicles), lysosomes (in transport vesicles), and secretory vesicles (Figure 3.21). 6. Lysosomes a. Lysosomes are membrane-enclosed vesicles that form in the Golgi complex and contain powerful digestive enzymes (Figure 3.22).  b. Lysosomes function in intracellular digestion, digestion of worn-out organelles (autophagy), destruction of the entire cell (autolysis), and extracellular digestion. c. Clinical connection: Tay-Sachs disease is an example of a disorder caused by faulty lysosomes. 7. Perioxosomes a. Peroxisomes are similar in structure to lysosomes, but are smaller (figure 3.1). b. They contain enzymes called oxidases, that use molecular oxygen to oxidize various organic substances. 8. Proteasomes a. Proteosomes are structures that destroy unneeded, damaged, or faulty proteins. b. They contain proteases, which cut proteins into small peptides. c. Clinical Connection: Proteosomes are thought to be a factor in several diseases, such as Parkinson’s and Alzheimer’s diseases. 9. Mitochondria  a. The mitochondrion is bound by a double membrane. The outer membrane is smooth with the inner membrane arranged in folds called cristae (Figure 3.23). b. Mitochondria are the site of ATP production in the cell by the catabolism of nutrient molecules. c. Plays an important role in apoptosis d. Mitochondria self-replicate, using their own DNA. e. Mitochondrial DNA (genes) is inherited only from the mother. II. NUCLEUS The nucleus is usually the most prominent feature of a cell (Figure 3.24).  1. Most body cells have a single nucleus; some (red blood cells) have none, whereas others (skeletal muscle fibers) have several. 2. The parts of the nucleus include the nuclear envelope which is perforated by channels called nuclear pores, nucleoli, and genetic material (DNA) a. nucleoli: function in producing ribosomes. Each nucleolus is simply a cluster of protein, DNA, and RNA; it is not enclosed by a membrane  3. Within the nucleus are the cell’s hereditary units, called genes, which are arranged in single file along chromosomes. a. Each chromosome is a long molecule of DNA that is coiled together with several proteins (Figure 3.25). b. Human somatic cells have 46 chromosomes arranged in 23 pairs. 4. The various levels of DNA packing are represented by nucleosomes (= DNA + histones), chromatin fibers, loops, chromatids (which condense into chromosomes during cell division) (Figure 3.25). 5. The main parts of a cell and their functions are summarized in Table 3.2. 6. Clinical Connection: Genomics, the study of the genome and its relationship to body function, has the potential for increasing our understanding of normal and abnormal conditions. VII. PROTEIN SYNTHESIS A. Much of the cellular machinery is devoted to synthesizing large numbers of diverse proteins.  1. The proteins determine the physical and chemical characteristics of cells. a. proteome refers to all of an organism’s proteins 2. The instructions for protein synthesis are found in the DNA in the nucleus. a. genetic information in DNA is stored in sets of three nucleotides called base triplets 3. Protein synthesis involves transcription and translation (Figure 3.26). B. Transcription 1. Transcription is the process by which genetic information encoded in DNA as base triplets is copied onto a strand of RNA called messenger RNA (mRNA) as three- nucleotide sequences called codons, which then direct protein synthesis (Figure 3.27). a. Besides serving as the template for the synthesis of mRNA, DNA also synthesizes two other kinds of RNA, ribosomal RNA (rRNA), and transfer RNA (tRNA). b. tRNA functions later during translation, to transport amino acids to the ribosomes. c. Transcription of DNA is catalyzed by RNA polymerase.  1) RNA polymerase uses a region of the mRNA called the promoter to start synthesis of a new strand 2) Transcription of the DNA strand ends at another special nucleotide sequence called a terminator d. Not all parts of a gene actually code for parts of a protein. Regions within a gene called introns do not code for parts of proteins. They are located between regions called exons that do code for segments of a protein C. Translation 1. Translation is the process of reading the mRNA nucleotide sequence to determine the amino acid sequence of the protein (Figure 3.28). 2. The sequence of translation is as follows (Figure 3.29). a. Messenger RNA associated with ribosomes, which consist of rRNA and proteins. b. Specific amino acids attach to molecules of tRNA. Another portion of the tRNA has a triplet of nitrogenous bases called an anticodon (a codon is a segment of three bases of mRNA). c. Transfer RNA delivers a specific amino acid to the codon; the ribosome moves along an mRNA strand as amino acids are joined to form a growing polypeptide.  D. Clinical Connection: As a result of recombinant DNA techniques, genetic engineering has arisen; strains of recombinant bacteria produce important therapeutic substances such as human growth hormone, insulin, and vaccines against several viruses. VIII. CELL DIVISION A. Cell division is the process by which cells reproduce themselves. It consists of nuclear division (mitosis and meiosis) and cytoplasmic division (cytokinesis). 1. Cell division that results in an increase in body cells is called somatic cell division and involves a nuclear division called mitosis, plus cytokinesis. This results in two genetically identical cells, each with the same number and kind of chromosomes as the original cell (called diploid (2n) cells, with 23 pairs of chromosomes each). The two chromosomes that make up each pair are called homologous chromosomes. 2. Cell division that results in the production of sperm and eggs is called reproductive cell division and consists of a nuclear division called meiosis plus cytokinesis. The resulting sperm or egg cell has half of the original number of chromosomes (called haploid (n) cells, with a single set of 23 chromosomes). B. Somatic Cell Division 1. The cell cycle is an orderly sequence of events by which a cell duplicates its contents and divides in two. It consists of interphase and the mitotic phase (Figure 3.30). 2. Interphase a. During interphase the cell carries on every life process except division. Interphase consists of three phases: G1, S and G2 (Figure 3.30). 1) In the G1 phase, the cell is metabolically active, duplicating its organelles and cytosolic components except for DNA. a) Cells that remain in G1 for a very long time, perhaps destined never to divide again, are said to be in the G0 phase 2) In the S phase, DNA is replicated (Figure 3.31). 3) In the G2 phase, cell growth continues and the cell completes its preparation for cell division, including replication of centrosomes. b. A cell in interphase shows a distinct nucleus and the absence of chromosomes (Figure 3.32a). 3. Mitotic Phase a. The mitotic phase consists of mitosis (or nuclear division) and cytokinesis (or cytoplasmic division). b. Nuclear division: mitosis 1) Mitosis is the distribution of two sets of chromosomes, one set into each of two separate nuclei. 2) Stages of mitosis are prophase, metaphase, anaphase, and telophase. a) During prophase, the chromatin condenses and shortens into chromosomes (Figure 3.32b). b) During metaphase, the centromeres line up at the exact center of the mitotic spindle, a region called the metaphase plate or equatorial plane region (Figure 3.32c). c) Anaphase is characterized by the splitting and separation of centromeres and the movement of the two sister chromatids of each pair toward opposite poles of the cell (Figure 3.32d). d) Telophase begins as soon as chromatid movement stops; the identical sets of chromosomes at opposite poles of the cell uncoil and revert to their threadlike chromatin form, microtubules disappear or change form, a new nuclear envelope forms, new nucleoli appear, and the new mitotic spindle eventually breaks up. (Figure 3.32 e) c. Cytoplasmic Division: Cytokinesis 1) Cytokinesis is the division of a parent cell’s cytoplasm and organelles. The process usually begins in late anaphase with the formation of a cleavage furrow (Figure 3.32 d and e).  2) When cytokinesis is complete, interphase begins (Figure 3.32 f). d. Clinical Connection: Inhibiting the formation of the mitotic spindle has a role in the treatment of cancer. C. Control of Cell Destiny 1. The three possible destinies of a cell are to remain alive and functioning without dividing, to grow and divide, or to die. 2. Enzymes called cyclin-dependent protein kinase can regulate DNA replication. Turning these on and off is a function of proteins called cyclins. 3. Cell death, a process called apoptosis, is triggered either from outside the cell or from inside the cell due to a “cell-suicide” gene. 4. Necrosis is a pathological cell death due to injury. D. Clinical Connection: Tumor-suppressor genes can produce proteins that normally inhibit cell division resulting in the uncontrollable cell growth known as cancer. E. Reproductive Cell Division 1. The replication of DNA in meiosis is similar to mitosis. 2. Meiosis involves two stages (Figure 3.33a-b) a. Meiosis I 1) The two pairs of sister chromatids pair off to form a tetrad, in a process called synapsis. 2) In the tetrad, parts of the sister chromatids of the homologous chromosomes are traded, a process called crossing over. 3) As a result of crossing over, the resulting sister chromatids are not genetically identical, resulting in genetic recombination. 4) The net result is a haploid cell with only one of the pair of homologous chromosomes, but with paired sister chromatids. b. Meiosis II  1) The paired sister chromatids making up each homologous chromosome are separated 2) The net result of Meiosis II is a haploid cell with one chromatid 3) Net result of meiosis is the production of four haploid cells that are genetically different. 4) Compare mitosis and meiosis with Figure 3.34 IX. CELLULAR DIVERSITY A. Not all cells look alike, nor do they perform identical functional roles in the body.  B. The shapes of cells vary considerably (Figure 3.35). X. CELLS AND AGING A. Aging is a normal process accompanied by a progressive alteration of the body’s homeostatic adaptive responses; the specialized branch of medicine that deals with the medical problems and care of elderly persons is called geriatrics. 1. The physiological signs of aging are gradual deterioration in function and capacity to respond to environmental stresses. 2. These signs are related to a net decrease in the number of cells in the body and to the dysfunctioning of the cells that remain.  3. The extracellular components of tissues (e.g., collagen fibers and elastin) also change with age. B. Clinical Connection: Free Radicals. Many theories of aging have been proposed, including genetically programmed cessation of cell division, glucose addition to proteins, free radical reactions, and excessive immune responses. C. Clinical Connection: Progeria and Werner Syndrome are disorders of aging. XI. DISORDERS: HOMEOSTATIC IMBALANCES A. Cancer is a group of diseases characterized by uncontrolled cell proliferation. 1. Cells that divide without control develop into a tumor or neoplasm. 2. A cancerous neoplasm is called a malignant tumor or malignancy. It has the ability to undergo metastasis, the spread of cancerous cells to other parts of the body. A benign tumor is a noncancerous growth. B. Types of Cancer 1. Carcinomas arise from epithelial cells. 2. Melanomas are cancerous growths of melanocytes. 3. Sarcomas arise from muscle cells or connective tissues. 4. Leukemia is a cancer of blood-forming organs. 5. Lymphoma is a cancer of lymphatic tissue. C. Growth and Spread of Cancer 1. Cancer cells divide rapidly and continuously. 2. They trigger angiogenesis, the growths of new networks of blood vessels. 3. Cancer cells can leave their site of origin and travel to other tissues or organs, a process called metastasis. D. Causes of Cancer 1. Environmental agents can cause cancer growth. A chemical agent. or radiation that produces cancer is termed a carcinogen and induces mutations in DNA. 2. Viruses can cause cancer. 3. Cancer-causing genes, or oncogenes, can cause cancer. a. The normal counterparts of oncogenes are called proto-oncogenes; these are found in every cell and carry out normal cellular functions until a malignant change occurs via a mutation.  b. Some cancers may also be caused by genes called anti-oncogenes or tumor- suppressing genes. These genes may produce proteins that normally oppose the action of an oncogene or inhibit cell division. E. Carcinogenesis is a multistep process involving mutation of oncogenes and anti-oncogenes; as many as 10 distinct mutations may have to accumulate in a cell before it becomes cancerous. F. Treatment of Cancer 1. Treatment of cancer is difficult because it is not a single disease and because all the cells in a tumor do not behave in the same way. 2. Many cancers are removed surgically. 3. Cancer that is widely distributed throughout the body or exists in organs with essential functions, such as the brain, which might be greatly harmed by surgery, may be treated with chemotherapy and radiation therapy instead. 4. Another potential treatment for cancer that is currently under development is virotherapy, the use of viruses to kill cancer cells. 5. Researchers are also investigating the role of metastasis regulatory genes that control the ability of cancer cells to undergo metastasis. Scientists hope to develop therapeutic drugs that can manipulate these genes and, therefore, block metastasis of cancer cells.