Human Anatomy & Physiology, Exam 1 Study Guide
Human Anatomy & Physiology, Exam 1 Study Guide HPHY 241-04 (McCann, Human Physiology)
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This 24 page Study Guide was uploaded by Elayne Ingram on Tuesday September 20, 2016. The Study Guide belongs to HPHY 241-04 (McCann, Human Physiology) at Gonzaga University taught by Dan McCann in Fall 2016. Since its upload, it has received 35 views. For similar materials see Human Physiology in Human Physiology at Gonzaga University.
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Date Created: 09/20/16
HPHY 241: Human Anatomy & Physiology – Exam 1 Study Guide Professor: Dan McCann Chapter 1 – Introduction to Physiology Overview: In this chapter, we briefly learned what physiology is and what it covers, homeostasis, and the various themes we will see throughout the semester. It also demonstrates different kinds of concept maps, graphs, and flow charts we can make to help us learn material. I. Introduction to Physiology Physiology is the study of the normal functioning of a living organism and its component parts, including all chemical and physical processes. *Structure and function are key to understanding what something is. This ties into the idea that we cannot, through science, truly ever know why something is happening. We can only describe the how. This idea is called the mechanistic approach. A teleological approach continually searches for the why. II. Physiology Is an Integrative Science Physiology is considered an “integrative science” because it includes all levels of organization from atom to biosphere and encompasses all related fields of study. Physiology also employs translational research, which uses insights and results gained from basic research on mechanisms to develop treatments and strategies for preventing disease. This is sometimes called the “bench to bedside” approach. III. Themes in Physiology There are 5 themes in physiology (the book only outlines four): (1) Structure and function are closely related a. Molecular interactions are essential for biological function and depend on structure/shape b. Compartmentation is the division of space into separate compartments, allowing cells, tissues, or organs to specialize and isolate functions (2) Living organisms need energy to carry out all biological processes (3) Information flow coordinates body functions using chemical and electrical signals (4) Homeostasis maintains internal stability (5) Evolution is the change in genetic composition of a population over several generations and is affected by homeostasis and consequent changes in structure and function. IV. Homeostasis Homeostasis is the maintenance of relatively stable internal conditions even while the outside environment undergoes change. True equilibrium is a constant, dynamic, balanced exchange of materials within the organism. Failure to maintain homeostasis usually results in pathology (suffering) and sometimes death of the organism. The general concept of homeostasis was discussed in the mid1800s by Claude Bernard as a “‘constancy’ of the internal environment”. The term “homeostasis” was actually coined by Walter B. Canon in 1929, emphasizing that the goal of homeostasis is not constancy, but stability. Homeostasis involves shortterm physiological responses to a changing outside environment. However, the need to maintain homeostasis also drives longterm adaptations to longterm environmental change (i.e. evolution). *Note that there is a difference between a response (short term) and an adaptation (longterm). *The response process of homeostasis is outlined in a very nice little flowchart in fig. 1.4! Also see fig. 1.5 if you need a review of what qualifies as an “internal environment”. Finally, homeostasis requires mass balance (described in detail in fig. 1.6). In other words, the input must equal the output. “Input” comes from the foot, water, and other things we ingest or absorb through our skin. “Output” includes everything eliminated from the body through feces, urine, lungs, and skin. V. Control Systems and Homeostasis Homeostasis is maintained through various different control systems. Regulated variables, such as blood pressure and blood glucose, are kept within a “normal” range by physiological control mechanisms. These mechanisms turn on only if the variable strays too far from its setpoint (optimal value). This is demonstrated in fig. 1.11. Controlled variables do not have a setpoint and may be changed dramatically to keep regulated variables within a specific range. All variables are controlled via either local control or longdistance reflex control. Local control is restricted to the tissue or cell involved and is the simplest form of control. Longdistance reflex control uses a more complex control system to monitor systemic changes (widespread throughout the body). No matter how simple the control, all control systems have the same three components: (1) Input signal (2) Integrating center (controller) – initiates appropriate response (3) Output signal – creates response *Fig. 1.8 shows a very simple control system* A feedback loop allows the response at the end of the control system to monitor and modulate the response loop. Negative feedback loops are pathways in which the response opposes the signal, effectively “turning off” the signal when the desired response is achieved. Ex. insulin production Positive feedback loops have a response at the end of the pathway that reinforce, rather than remove, the stimulus. In this pathway, the cycle continues until the signal causing it is eliminated. Ex. labor, cycle stopped by delivery of baby Feedforward controls anticipate changes and start response loops to maintain homeostasis. Ex. salivation As you know, regulated variables do exhibit small changes within a range. Some of these variables change in predictable repeating patters or cycles called biological rhythms or biorhythms. Circadian rhythms are daily biological rhythms that control many body functions, including blood pressure, body temperature, sleep cycle, and metabolic processes. VI. The Science of Physiology Any good experiment starts with a testable hypothesis. If you can’t test it, it isn’t a hypothesis! Next, you must collect data through scientific inquiry (observation and experimentation) and isolate dependent and independent variables. Independent variables are altered variables that the experimenter believes are key aspects of an observed phenomenon. The dependent variable is the observed phenomenon that is affected by the independent variable. Ex. A child has an allergic reaction when he eats pepperoni pizza. The dependent variable is the allergic reaction. The doctor tests him for allergies to wheat, dairy, and pepperoni. His tests positive for a lactose intolerance. The wheat, dairy, and pepperoni are all independent variables, dairy being the variable on which the allergic reaction is dependent. Human experimentation has many ethical factors that must be considered. That being said, there are several types of human studies: Longitudinal studies are carried out over a long period of time and normally follows individuals for several years. These include prospective studies (studies that look forward). Crosssectional studies survey a single population for the prevalence of a particular disease or condition, identifying trends such as age, profession, or socioeconomic class. These include retrospective studies (studies that look backward and match previous groups with a specific condition to current similar groups without the condition). The results of human experiments can sometimes be hard to interpret because of a high level of genetic and environmental variability. There are several ways to reduce this variability when doing studies: A crossover study uses the individual experimental subject as his/her own control, comparing his/her response in the experiment to his/her own baseline or control value. A placebo, an inactive substance (often in the form of a sugar pill), may be administered to an individual or group in place of the active substance being tested. This eliminates skewed results due to a purely psychological response to the active substance. The phenomenon of an experiment group/subject responding to the placebo with the same response elicited by the active substance is known as the placebo effect. Similarly, a group warned of potential side effects for a substance will report higher incidence of those side effects. This is known as the nocebo effect. A blind study is a study in which the subjects do not know whether they are getting the active substance or a placebo. A doubleblind study is a study in which neither the subjects nor the experimenters know who is getting the active substance or the placebo. This knowledge is held by a third party not involved in the experiment. A doubleblind crossover study, perhaps the most sophisticated experimental design for minimizing psychological effects, is a doubleblind study in which the control group and the subject group switch for the second half of the study. Another type of study researchers sometimes perform is a metaanalysis, which is an analysis of the data, itself, in comparison to other similar studies, the goal being to resolve any contradictory results. Once a researcher has gathered sufficient date, he or she often writes it up in a report and presents it in different graphs and tables. These may include bar graphs, histograms, line graphs, scatter plots, pie charts, etc. Fig. 1.15 talks about these, but it should not be new information for you. A model is a hypothesis that is supported by evidence from multiple experiments. A theory is a model with substantial supporting evidence from many different experiments/investigations. Keep in mind that a theory is generally widely accepted to be true, but could potentially be disproven in future. This is why it is a theory, not a law. Chapter 3 – Compartmentation: Cells and Tissues Overview: In this chapter, we covered compartments of the body, biological membranes (focusing on the cell membrane), intracellular components, and tissues of the body (including death and remodeling). We also saw an introduction to the organs of the body. Chapter Breakdown I. Functional Compartments of the Body The three major compartments, or cavities, of the body are: the cranial cavity, the thoracic cavity, and the abdominopelvic cavity. Some organs are hollow and have an interior covered by a lumen. Examples of hollow organs are the heart, lungs, blood vessels, and intestines. Hollow organs can be filled with either air or fluid. Functionally, the body has 3 fluid compartments, but it may be divided into 2 main ones: (1) Extracellular fluid (ECF) – divided further into plasma and interstitial fluid (2) Intracellular fluid (ICF) within the cells II. Biological Membranes A cell membrane is a bilayer of phospholipids, interspersed with protein molecules, that separates the aqueous fluids of the interior and exterior environments. Cell membranes have four general functions: (1) Physical isolation (2) Regulation of exchange with the environment (3) Communication between the cell and its environment (4) Structural support Cell membranes are made up of different proportions of protein, lipid, and carbohydrate. If you wish to study the structure and components of cell membranes, including the fluid mosaic model of the membrane, see fig. 3.2. Here you will also find depictions of the three formations of membrane phospholipids: Bilayer Micelle (droplet of phospholipids) Liposome (droplet of phospholipids with an aqueous center) Remember that the polar head of the phospholipid is hydrophilic, while the nonpolar fatty acid tail is hydrophobic. Many proteins are suspended in the cell membrane: Integral proteins (tightly bound to the membrane) Peripheral proteins (include structural binding proteins that anchor to the cytoskeleton) Transmembrane proteins (form intra and extracellular loops to which phosphate groups and carbohydrates may attach, respectively) Lipidanchored proteins (previously thought to be transmembrane proteins, they bond covalently to lipid tails that insert themselves into the bilayer. The cell membrane incorporates lipid rafts made up of sphingolipids. These lipid rafts float through the cell membrane accomplishing different tasks and functions. Finally, the cell membrane includes carbohydrates (mostly in the form of sugars) that are found exclusively on the external surface of the cell. Here, they form a protective layer known as the glycocalyx. III. Intracellular Compartments Within the cell are many different compartments. In the cytoplasm, we find: Cytosol, or intracellular fluid, contains dissolved nutrients and proteins, ions, and waste products Inclusions are particles of insoluble materials (sometimes stored nutrients) – also referred to as “nonmembranous organelles”, these include ribosomes Insoluble protein fibers form the cytoskeleton (internal support system) and include actin fibers or microfilaments (the thinnest), intermediate filaments, and hollow microtubules (made of the protein tubulin) Microtubules are assembled in the centrosome, which contains two centrioles (think mitosis – or see fig. 3.4e) made out of these microtubules. Microtubules also form cilia (short, hairlike structures projecting from a cell surface) and flagella (longer, whiplike structures found only on the male sperm cell [in humans]). Organelles are membranebound compartments that play specific roles in cellular function The cytoskeleton, made up of those valuable protein fibers, is a flexible, changeable structure that has at least 5 important functions (the book says “at least five and then lists those five”): (1) Cell shape – cytoskeletal fibers support microvilli, which increase the surface area of the cell for absorption purposes (2) Internal organization – cytoskeletal fibers stabilize the positions of the various organelles (3) Intracellular transport – the cytoskeleton helps transport materials into and throughout the cell by serving as a “railroad track” for organelles (4) Assembly of cells into tissues – cytoskeletal fibers connect with extracellular fibers to link cells together, both providing strength and allowing for information flow (5) Movement – the cytoskeleton is responsible for cilia, flagella, and special motor proteins that facilitate cell movement Those special motor proteins convert stored energy into directed movement and involve three groups: (1) Myosins – bind to actin fibers and play a role in muscle contraction (2) Kinesins – assist in movement of vesicles along microtubules (3) Dyneins – assist in movement of vesicles along microtubules and help cilia and flagella beat/whip Next, we have the organelles: Mitochondria Endoplasmic reticulum (rough and smooth) Golgi apparatus Cytoplasmic vesicles (includes lysosomes, endosomes, and peroxisomes) *If you’d like to study the organelles more in depth, please refer to the textbook! I’m assuming that you already know as much about the organelles as you will need to for this exam since they’re covered in both Biology and Microbiology. And finally…the nucleus! Contained within the bimembranous nuclear envelope dotted with pores and nuclear pore complexes (for communication purposes), the nucleus holds chromatin (composed of DNA and associated proteins) and nucleoli (which contain the genes and proteins that control RNA synthesis). IV. Tissues of the Body: Histology Histology is the study of tissue structure and function. Histologists describe tissues by their physical features: (1) Shape and size of cells (2) Arrangement of cells in the tissue (e.g. layers, scattered, etc.) (3) The way cells are connected to one another (4) Amount of extracellular material present in the tissue There are four basic types of tissue, which should be very familiar to you: (1) Epithelial (2) Connective (3) Muscle (4) Nerve *See Table 3.4 “Characteristics of the Four Tissue Types” – outlines matrix amount and type, unique feathers, surface features, locations, and cell arrangement and shapes The extracellular matrix (ECM) is made up of material synthesized and secreted by the cells of a tissue. Its composition varies from tissue to tissue, its mechanical properties (e.g. elasticity, flexibility, etc.) determined by the amount and consistency. The matrix always has 2 basic components: (1) Proteoglycans: glycoproteins (proteins covalently bonded to polysaccharide chains, which are chains of sugars) (2) Insoluble protein fibers (e.g. collagen, fibronectin, laminin), which provide strength and anchor cells to the matrix Cell junctions are more permanent cellcell adhesions that form the structure for tissues. There are 3 major types of cell junctions: (1) Gap junctions (i.e. communicating junctions) are the simplest cellcell junctions and allow direct and rapid celltocell communication through cytoplasmic bridges between adjoining cells. They allow both chemical and electrical signals to pass. Their aiding proteins are connexins. (2) Tight junctions (i.e. occluding junctions) restrict the movement of material between cells by partially fusing the membranes of adjacent cells. Their aiding proteins are claudins and occludins. (3) Anchoring junctions attach cells to one another (cellcell anchoring junctions) or to the ECM (cellmatrix anchoring junctions). Cellcell anchoring junctions are created by cadherins and take the form of either adherins junctions, which link actin fibers in adjacent cells together, or desmosomes, which attach to intermediate filaments of the cytoskeleton (these are the strongest cellcell junctions). Cellmatrix anchoring junctions are created by ingetrins and take the form of either hemidesmosomes, which are strong junctions that anchor intermediate fibers of the cytoskeleton to fibrous matrix proteins such as laminin, or focal adhesions, which tie intracellular actin fibers to different matrix proteins, such as fibronectin. *Figure 3.8 shows you all of the different cell junctions in greater detail. I highly recommend taking a look! Cell adhesion molecules (CAMs) are membranespanning proteins responsible for cell junction and for transient cell adhesions. Table 3.3 gives the names and some examples of the four major CAMs, but we only need to know the FIRST TWO: Cadherins: cellcell (see above) Integrins: cellmatrix (see above) The paracellular pathway describes the movement of materials between cells, which involves the above junctions. Epithelial tissue (a.k.a. epithelia) protects the internal environment of the body, regulates the exchange of materials between the internal and external environments, and manufactures and secretes chemicals into the blood or external environment. Any substance that enters or leaves the body must cross an epithelium. *Epithelial tissue is complex and covers a lot of ground, so bear with me. I will try to summarize as much as possible. Structure: Epithelia typically consists of one or more layers of cells connected to one another, with a thin layer of ECM lying between the epithelial cells and underlying tissues. The basal lamina is the matrix layer and is composed of a network of collagen and laminin filaments embedded in proteoglycans. Basal lamina (cellmatrix connection) There are 2 types of layering and 3 cell shapes by which epithelial cells are classified: (1) Simple (one cell thick) (2) Stratified (multiple cell layers) (1) Squamous (flat) (2) Cuboidal (cubeshaped) (3) Columnar (taller than it is wide) These two groupings are then combined to gives us the various types of epithelium. Transitional epithelia are epithelial cells that do not fit into the other categories, but instead appear to be a combination. Epithelia are also classified as either “leaky” or “tight”, depending on how easy it is for substances to pass from one side of the epithelial layer to the other. “Leaky” epithelia allow most dissolved molecules (except for large proteins) to pass through gaps between the cells. “Tight” epithelia require that most substances enter the epithelial cells and go through them to get to the other side. Function: There are 5 different functional types of epithelia, which you WILL need to know: Exchange epithelia are composed of very thin, flattened cells that allow gasses to pass rapidly across the epithelium. This type of epithelium lines the blood vessels and the lungs (two major sites of gas exchange). *The epithelium lining the heart and blood vessels is also called the endothelium. Transporting epithelia actively and selectively regulate the exchange of nongaseous materials, such as ions and nutrients, between the internal and external environments. They line the hollow tubes of the digestive system and the kidney (places where lumens open into the external environment). Transporting epithelia have some special identifiable characteristics: Cell shape: thicker cells than exchange epithelia Membrane modifications: microvilli on apical membranes and folds on basolateral membranes Cell junctions: moderately tight to very tight junctions Cell organelles: most have numerous mitochondria Ciliated epithelia are nontransporting tissues that line the respiratory system and parts of the female reproductive tract. They are called “ciliated” because the surface of the tissue facing the lumen is covered with cilia that beat in a coordinated, rhythmic fashion that moves fluid and particles across the tissue surface. Protective epithelia prevent exchange between the internal and external environments and protect areas subject to mechanical or chemical stress. These are stratified tissues toughened by the secretion of keratin. They form the epidermis and the linings of the mouth, pharynx, esophagus, urethra, and vagina. These cells have a short life span and are continuously replaced. Secretory epithelia are composed of cells that produce and secrete a substance into the extracellular space. They may be scattered among other epithelial cells, or they may group together to form a multicellular gland. There are 2 types of secretory glands: Exocrine glands release secretions to the body’s external environment, mostly through ducts. Serous secretions are watery solutions, many containing enzymes (e.g. tears, sweat, digestive enzyme solutions). Mucous secretions (a.k.a. mucus) are sticky solutions containing glycoproteins and proteoglycans. Goblet cells are single exocrine cells that produce mucus. *Salivary glands are an example of an exocrine gland that contains more than one type of secretory cell and produces both serous and mucous secretions.* Endocrine glands are ductless glands that secrete hormones into the body’s extracellular environment. Connective tissue provides structural support and, in some cases, a physical barrier that helps defend the body from foreign invaders such as bacteria. All types of connective tissue have an ECM composed of proteoglycans, water, and suspended protein fibers that is called ground substance. Connective tissue cells interact closely with the matrix. There are three types of connective tissue cells that may be identified and defined by their suffixes: blast: cell that is either growing or actively secreting ECM clast: cell that is actively breaking down matrix cyte: cell that is neither growing, secreting matrix components, nor breaking down matrix ex. fibroblast: connective tissue cell that secretes collagenrich matrix Connective tissues produce four different types of matrix fibers, found throughout the body. These fibers are: (1) Collagen: this is the most abundant protein in the human body (it accounts for almost 1/3 of the body’s dry weight) and is also the most diverse (it has 12 variations) (2) Elastin: a coiled, wavy protein that returns to its original length after being stretched (3) Fibrillin: composed of very thin, straight fibers that connect with elastin to form filaments and sheets of elastic fibers (4) Fibronectin: connects cells to the ECM (also plays an important role in would healing and blood clotting) *The matrix includes connective tissue cells that may be described as fixed (local maintenance, tissue repair, energy storage) or mobile (defense), but the book says that the distinction between these types is often unclear or not absolute. For this reason, I wouldn’t worry about it for the exam. Connective tissue is found in all parts of the body and is divided into 8 basic types (outlined in fig. 3.12b): (1) Loose connective tissue is an elastic tissue that underlies skin and provides support for small glands. Also called “areolar” connective tissue. Loose and dense connective tissues are referred to as “CT proper”. (2) Dense connective tissue provides strength and flexibility and is found in tendons, ligaments, and the sheaths that surround muscles and nerves. Regular: collagen runs in a single direction (tendons and ligaments) Irregular: more fibers than ground substance, collagen runs in many directions (muscle and nerve sheaths) (3) Tendons cannot stretch and attach skeletal muscles to bones. (4) Ligaments have a limited ability to stretch and connect one bone to another. (5) Cartilage (hyaline, elastic, and fibrocartilage) is solid, flexible, and lacks blood supply; it is found in structures such as the nose, ribs, spinal discs, ears, knee, and windpipe. (6) Bone has a calcified ECM that contains mineral deposits (primarily calcium, such as calcium phosphate) (7) Blood is characterized by its watery ECM known as plasma, which is a dilute solution of ions and dissolved organic molecules (8) Adipose tissue is made up of adipocytes (a.k.a. fat cells). An adipocyte of white fat (the most common form in adults) typically contains a single, large lipid droplet that occupies most of the volume of the cell. An adipocyte of brown fat contains multiple lipid droplets and plays an important role in temperature regulation in infants. Muscle tissue has the ability to contract and produce force and movement. There are three types of muscle: (1) Cardiac muscle – found in the heart, involuntary (controls itself with help from nervous and endocrine systems) (2) Smooth muscle – forms most internal organs and blood vessels, involuntary (controlled unconsciously) (3) Skeletal muscle – attaches to bones, responsible for gross movement, 600+ throughout the body, voluntary (controlled consciously) Neural tissue has two types of cells: Neurons (a.k.a. nerve cells): carry information by chemical or electrical signals; they are concentrated in the brain and spinal cord, but they are found in every part of the body Glial cells (a.k.a. neuroglia): these are the support cells for the neurons; they are extremely important and greatly outnumber neurons in the body *What do muscle and neural tissues have in common? They are both known as excitable tissues because of their ability to generate and propagate action potentials. Additionally, the ECM for both of these tissues is usually limited to a supportive layer known as the external lamina. V. Tissue Remodeling Tissue is plastic, which means that it is constantly undergoing cell death and replacement. Necrosis: cell death caused by physical trauma, toxins, or lack of oxygen (this type of cell death is unplanned and is damaging to neighbor cells) Apoptosis: programmed cell death (this type of cell death is isolated and does not affect neighboring cells) The book also talks about stem cells and differentiation, but you only need to have a brief understanding of the following: Totipotent cells, the first cells of life, are so named because they have to ability to develop into any and all types of tissue. One totipotent cell has the capability to become a complete, functioning organism. Around day 4 of development, these totipotent cells begin to differentiate (specialize) and become pluripotent. In other words, they can still develop into many different cell types, but their capabilities are more limited. A single pluripotent cell cannot develop into an organism. Undifferentiated stem cells that retain the ability to divide and reproduce are said to be multipotent and can develop only into the specific tissue type for which they were destined during differentiation. Stem cells are special because, while they can undergo mitosis (cell reproduction via division), most cells lose this ability as the organism forms. VI. Organs Organs are tissues that carry out related functions as part of a structure. Organs contain all four types of tissue (epithelial, connective, muscle, neural) in varying amounts. The organ systems of the body are: circulatory, digestive, endocrine, immune, integumentary, musculoskeletal, nervous, reproductive, respiratory, and urinary (see fig. 1.2). Fun fact: The skin is the heaviest single organ (16% of total body weight). *You really don’t need to know much at all about organs or organ systems. Basically, just know what an organ/organ system is, and be aware of the 10 different systems. Chapter 4 – Energy and Cellular Metabolism Overview: In this chapter, we started learning about energy (types, production, sources, and use), chemical reactions, enzymes, and metabolism (including glycolysis and the citric acid cycle). Chapter Breakdown I. Energy in Biological Systems Energy is defined as the capacity to do work. It comes in two forms: kinetic energy (energy of motion) and potential energy (stored energy). Energy is quantified in kcals (kilocalories or Calories). Excess energy is stored as glycogen and lipid molecules. Potential energy has the ability to become kinetic energy and vice versa. The amount of energy lost in the transformation depends on the efficiency of the process. There are also three types of work: Chemical work: the making and breaking of chemical bonds Transport work: enables cells to move ions, molecules, and larger particles through the cell membrane and the membranes of organelles in the cell (especially useful for creating concentration gradients) Mechanical work: mediated by motor proteins, it includes muscle contraction, organelle movement, cells changing shape, and cilia and flagella beating First law of thermodynamics (law of conservation of energy): The total amount of energy in the universe is constant. Second law of thermodynamics: Natural spontaneous processes move from a state of order to a condition of randomness or disorder (i.e. entropy). A “spontaneous process” is a reaction that, once started, will go to completion. It does not “occur from nothing”. An example is a campfire: it was started by a spark and, if left unattended, will continue to burn until all its resources are used up. Another example is pouring vinegar onto baking soda. Closed system: nothing enters, nothing leaves (ex. the universe) Open system: exchanges materials and energy with its surroundings; requires the input of energy to create and maintain order (ex. the body) Respiration: a process which consumes O and produces CO and H O, used by animals to 2 2 2 extract energy from biomolecules Food sources of energy: Carbohydrates: limited reserves, must be replenished; stored as glycogen Lipids: larger body stores than carbs, but less accessible for metabolism (they must first be reduced from triglycerides to form glycerol and free fatty acids [FFA], both of which can then be used to make ATP) Protein: can be converted to glucose through glucogenesis or FFAs through lipogenesis; excess amino acids are stored as fat (converted through lipogenesis) after the excess nitrogen is processed by the kidneys and expelled in the urine as urea Note: except for excess stored as fat, protein (unlike carbs and lipids) is NOT stored – it is used for structure and other functions (including energy if need is great) II. Chemical Reactions Bioenergetics is the study of energy flow through biological systems. In these biological systems, chemical reactions are crucial in the transfer of energy from one part of the system to another. In a chemical reaction, one or more reactants undergo chemical change (usually via the breaking and/or making of covalent bonds) to form one or more products. The speed with which this takes place is called the reaction rate. There are four basic types of chemical reactions (combination, decomposition, single displacement, and double displacement), but YOU DO NOT NEED TO KNOW THESE FOR THE EXAM. If you wish to study them for your own knowledge, see table 4.2. When talking about energy, I mentioned potential energy. This energy is converted from kinetic energy and stored up for later use. The potential energy stored in the chemical bonds of a molecule is called free energy and can be used to fuel the cell. The purpose of chemical reactions in cells is to: (1) Transfer energy from one molecule to another. (2) Use energy stored in reactant molecules to do work. Activation energy is the initial energy input required to start a reaction. All chemical reactions have an activation energy, but some have a higher activation energy than others. There will be more on this when we talk about enzymes. There are 4 kinds of basic chemical reactions that we need to worry about: (1) Exergonic reactions: reactions that release energy (i.e. the free energy of the products is lower than that of the reactants) – there is a negative Gibbs free energy change (ΔG) ex. ATP + H 0 ADP + P + H + energy (ΔG = 7.3 kcal/mol) 2 i (2) Endergonic reactions: reactions that require a net input of energy (i.e. the free energy of the products is higher than that of the reactants) – there is a positive Gibbs free energy change (ΔG) ex. synthesis reactions (reactions that form complex molecules from smaller molecules – complex molecules have more bonds and can store more free energy than smaller molecules) (3) Reversible reactions: reactions that can proceed in both directions – most biological reactions are reversible because they are aided by enzymes (4) Irreversible reactions: reactions that can proceed in one direction, but not the other III. Enzymes Enzymes are specialized proteins that speed up the rate of chemical reactions. They are catalysts, meaning they are neither changed in any way nor used up. Isozymes are enzymes that come in a variety of related forms (called isoforms). They catalyze the same reactions, but under different conditions or in different tissues. Coenzymes are organic cofactors (nonprotein molecule required for the activation of a protein) that act as receptors and carriers for atoms or functional groups that are removed from the substrates during the reaction. Vitamins are precursors of coenzymes. Diagnostically important enzymes: Enzyme Related Diseases Acid phosphatase prostate cancer Alkaline phosphatase diseases of the bone or liver Amylase pancreatic disease Creatine kinase (CK) myocardial infarction, muscle disease Lactate dehydrogenase (LDH) tissue damage to heart, liver, skeletal muscle, red blood cells There are four basic types of enzymatic reactions: Oxidationreduction (redox): transfers electrons from one molecule to another (THIS IS THE MOST IMPORTANT REACTION IN ENERGY EXTRACTION AND TRANSFER IN CELLS) OIL RIG oxidation is loss, reduction is gain Hydrolysisdehydration: breaks down molecules with the addition of water (hydrolysis) and synthesizes larger molecules while losing water (dehydration) *When an enzyme name consists of the substrate name plus the suffix “ase”, we know that the enzyme causes a hydrolysis reaction. Additionsubtractionexchange: moves functional groups (e.g. phosphate groups, amino groups, etc.) among molecules Kinases: transfer a phosphate group from a substrate to an ADP molecule to create ATP, or from an ATP molecule to a substrate Amination: addition of an amino group to a molecule Deamination: removal of an amino group from an amino acid or peptide Transamination: transfer of an amino group from one molecule to another Ligation: joins two molecules together using enzymes known as synthetases and energy from ATP IV. Metabolism Metabolism encompasses all chemical reactions that take place in an organism. It is divided into catabolism, which is the release of energy through the breakdown of large biomolecules (yields ATP), and anabolism, which is the synthesis of large biomolecules from smaller molecules (uses ATP). Metabolism has two main functions: (1) To extract energy from nutrient biomolecules (i.e. proteins, carbohydrates, and lipids) (2) To synthesize and break down molecules *The most important thing you need to know from this section is the metabolic pathway, which includes glycolysis and the Krebs cycle (also called the citric acid cycle). Within the metabolic pathway, each step is a different enzymatic reaction, proceeding in sequence, involving molecules that are called intermediates because each is both the product of one reaction and the substrate of the next reaction. Cells regulate their metabolic pathways by: (1) Controlling enzyme concentration (2) Producing modulators that change reaction rates Modulators are molecules that alter the activity of a protein. These are produced and controlled by hormones and other signals coming from outside the cell. some metabolic pathways have feedback inhibition (a.k.a. endproduct inhibition), in which the end product of a pathway (ABCZ) acts as an inhibitory modulator of the pathway. (3) Using two different enzymes to catalyze reversible reactions (one enzyme for forward, another for backward) (4) Compartmentalizing enzymes within intracellular organelles Isolating the various enzymes and containing them in the mitochondria, ER, Golgi apparatus, or lysosomes allows for the resulting pathways also to remain separate. (5) Maintaining an optimum ratio of ATP to ADP This determines whether pathways that result in ATP synthesis are turned on or off. ATP stores energy in the highenergy phosphate bond attached to ADP in glycolysis and releases it when the bond is broken during removal of the phosphate group. ADP + P i energy ADP ~ P (=ATP) The free energy released highenergy bond in this reaction is estimated inorganic to phosphate group range from 712 kcals/mol of ATP. We need to store energy to fuel all of our metabolic activities. This can happen in the highenergy bonds of either ATP (adenosine triphosphate) or GTP (guanosine triphosphate). ATP Production Aerobic pathways require oxygen and yield a great deal of ATP through oxidative phosphorylation (the addition of a phosphate group to ADP). Anaerobic pathways do not require oxygen and produce far less ATP. They are not sustainable for most animal life, but they are nonetheless useful. There are 3 major processes that produce ATP: ATPPCr System: anaerobic; high rate, low capacity utilizes phosphocreatine (PCr) to replenish ATP You will need to know this chart: ATP creatine Muscle ATPase creatine kinase mitochondrion ADP + P phosphocreatine i Glycolytic System: anaerobic; intermediate rate and capacity; intimately involved in aerobic metabolism Oxidative System: aerobic; slow rate, high capacity The adenylate kinase reaction (a.k.a. myokinase reaction) also occurs as energy requirements increase. adenylate kinase ADP + ADP ATP + AMP AMP increases the activity of the enzyme phosphofructokinase (PFK), which is a key enzyme in glycolysis. This is all good to be familiar with, but the most common way of producing ATP is through the combination of glycolysis and the Krebs cycle. Glucose x1 C H O 6 12 6 NAD + optional glycerol NADH Required for ATP amino acids ADP ATP KNOW THIS!! Cytosol amino acids Pyruvate x2 *The most important contribution of this process to ATP synthesis is trapping energy in electrons carried by NADH and FADH , whi2h transfer the electrons to the electron transport chain (ETC), which uses energy from these electrons to make the highenergy phosphate bond of ATP. + + glucose + 2NAD + 2ADP + 2P 2 piruvate + 2ATP + 2NADH + 2H + 2H O 2 Some steps of glycolysis require energy, but overall the process is exergonic. Substratelevel phosphorylation: the transfer of a phosphate to ADP by an intermediate to form ATP Phosphofructokinase (PFK): a ratelimiting enzyme of glycolysis that is allosterically inhibited by ATP at higher concentrations (see representation below) Figures 4.12, 4.13, and 4.14 illustrate all the process of ATP production in detail, so study these hard! Dr. McCann will probably have a question on the exam asking us to draw out the citric acid (Krebs) cycle. The circle from fig. 4.13 will probably get you 7 or 8 points out of 10, but what he would really LOVE to see is the circle on slide 73 of his PPT, which is on BlackBoard (Chapter 4, Part 3). Output from the Krebs cycle incudes: ATP CO 2 NADH+H + FADH 2 You also need to know the three irreversible reactions in glycolysis, as well as all of the enzymes. The 3 irreversible reactions are: HK (hexokinase) PFK (phosphofructokinase) PK (pyruvate kinase) There are also 4 important irreversible reactions in the Krebs cycle that you must know: PDH (pyruvate dehydrogenase) – gets us in and preps for Krebs CS (citrate synthase) ISDH (isocitrate dehydrogenase) αKDH (αketoglutarate dehydrogenase complex) Dr. McCann encourages you to use abbreviations on the exam (for clarity’s and sanity’s sakes)! Glycolysis and the Krebs cycle seem entirely overwhelming, but you DO NOT need to know the how of everything (i.e. the mechanisms). You DO need to know the ingredients that go in, the steps (in order), and the results/products. I realize this is a huge amount of information, but I hope it will be useful to you. I tried to make it pretty comprehensive so that you could carry this with you and study in little pockets of time instead of having to lug around the giant textbook. REMEMBER: There is a review session in on Saturday 9/24 from 13pm in Jepson 109 just for you!! Also, if you have specific questions or want to inquire about getting tutoring for this class at any point, email Anna Fox. firstname.lastname@example.org Good luck!!!!
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