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Or, Chemistry class in one lecture! Key Concepts Elements, Atoms, Isotopes etc. Chemical formulas, Chemical bonds Solutions, Concentrations, pH Organic Chemistry / Biochemistry Element = Building block of matter Periodic Table of the Elements In human: 11 major essential elements C, O, H, Na, Se, P, Mg, Mn, K, Ca, Fe = trace elements Organic Chemistry = Chemistry of Carbon Structure of Atoms (AKA elements) • Some Terminology: – – – – Atomic Number Atomic mass Ion Isotope Isotopes = Atoms of an element that have different numbers of neutrons. Same Atomic Number, variable Atomic Mass Most common Much rarer Heavy water = ? Some isotopes are unstable: Radioisotopes 3 types of radiation: 1. radiation – protons and neutrons 1. Generally not dangerous to life unless inhaled or ingested 2. Commonly emitted from radioactive substances like uranium 3. Does not travel far Some isotopes are unstable: Radioisotopes 1. radiation - electrons 1. Relatively harmless 2. Medium penetrating power 3. Can mutate DNA if struck 4. Used to kill cancer cells Some isotopes are unstable: Radioisotopes 1. -Radiation 1. High energy waves, not particles 2. Gamma Radiation can penetrate thick material 3. Since Gamma Radiation is more penetrating it can cause the most damage to the human body 4. Gamma knife 1. Used for benign or malignant tumors of the brain Alpha radiation consists of helium-4 nucleus and is readily stopped by a sheet of paper. Beta radiation, consisting of electrons, is halted by an aluminium plate. Gamma radiation is eventually absorbed as it penetrates a dense material. Lead is good at absorbing gamma radiation, due to its density. http://www.youtube.com/watch ?v=3u_8frR0IpE • http://www.youtube.com/watch?v=rvAJ_u3 Q0Hw&feature=related • http://www.youtube.com/watch?v=_W_lLh Bt8Vg Nuclear Medicine: use of radioisotopes in diagnosis & treatment of disease. is “normal” iodine 131I has 4 extra neutrons 127I and radiation Medical Imaging ? Treatment? The Chemistry of Life • Elements = Atoms – Nucleus • Protons • Neutrons – Orbit • Electrons Atoms • Atomic number • The number of protons, usually also equals the number of electrons. • Atoms must be neutral • Atoms/molecules that are stable will not bond with other atoms/molecules. Electron Bonding • Outermost shell contains all pairs of electrons – Stable • Outermost shell contains at least one unpaired electron – Unstable • Lose, gain or share electrons to become stable • An atom is most stable when each electron is paired! Chemical Bonds Ionic: electrons pulled from one atom to another: Na+ and ClCovalent: electrons shared equally Hydrogen: weak attraction -Causes surface tension in water. Chemical Bonds • Ions – More (or less) electrons than protons • Ionic Bonds – Anions • Negative – Cations • Positive • Ions are often called electrolytes! Ionic Bonds • Give away or receive electrons to create ions and for each ion to become more stable • Ions of opposite charge bind with each other to form an ionic bond • An ionic bond typically includes a metal – NaCl Ionic Bonding Important Ions in Physiology cations anions Chemical Bonds • Covalent – Polar – Non-polar Covalent Bonds • Strong bonds that occur when two atoms share electrons in order to become more stable Covalent Bonds • Non-polar Covalent Bonds – If the electrons are shared equally between atoms • Polar Covalent Bonds – If electrons spend more time around one atom than the other – Molecules develop regions of partial positive and negative charges Covalent Bonds http://www.youtube.com/watch? v=QqjcCvzWwww Covalent bond: Water The electrons are shared equally If two electrons are shared, that is a “double bond.” Chemical Bonds • Hydrogen Bonds – Surface tension – Attractive force between water molecules that causes water to form spherical droplets – Weak attractive force between hydrogen and oxygen, nitrogen or fluorine atoms – Quickly forms and quickly breaks Reactions • Types of Reactions – Synthesis Reaction--Anabolic • A+B C – Decomposition Reaction--Catabolic • AB A+B – Exchange Reaction • AB + C AC + B • Oxidation-Reduction Reactions (REDOX) Chemical Reactions • Reactants form Products • First Type of Reaction – Anabolic or Synthesis Reaction Chemical Reactions • Decomposition Reaction – Catabolic Acid Base Reactions Acids – The concentration Hydrogen ions free in solution • Protons – H+ • Bases – Are proton acceptors • Bind with hydrogen ions • Hydroxyl ion = OH• Bicarbonate ion = HCO3- Buffers • Buffers resist abrupt and large swings in the pH of body fluids. • To resist large changes in pH, the body releases hydrogen ions when the pH rises and binds hydrogen ions with bicarbonate ions when the pH drops. • Blood pH = 7.35 – 7.45 Buffers • CO2 + H2O H2CO3 H++ HCO3- BIOMOLECULES • Carbohydrates • Fats • Proteins Organic Compounds • Carbohydrates – A group that includes things like table sugars and starches. – Includes Simple and Complex groups Simple Carbohydrates – Simple • Monosaccharides – Fructose – Glucose • Disaccharides – Sucrose – Lactose Monosaccharides Disaccharides Polysaccharide Organic Compounds • Complex Carbohydrates • Polysaccharides are long branching chains of simple sugars, specifically glucose. – Starch is a storage carbohydrate in plants. – Glycogen is a storage carbohydrate in animals. • Liver and muscles Lipids • Most diverse group of biomolecules • Solid at room temp = fat; – liquid at RT = oil • Contain much less O2 than CHOs – Often long chains of C • 4 categories: Fatty Acids can be (un)saturated Mono-, di-, and triglycerides Phospholipids (polar) Steroids Eicosanoids (prostaglandins et al.) Functions? Triglycerides Unsaturated (mono- & polyunsaturated) fats are liquid at room temp. Trans fats have added hydrogen (hydrogenated) (p 29) Triglycerides: 3 FA + Glycerol Saturated Unsaturated Polyunsaturated Trans Fats • In cis bonds, the two pieces of the carbon chain on either side of the double bond are either both “up” or both “down,” such that both are on the same side of the molecule. • In trans bonds, the two pieces of the molecule are on opposite sides of the double bond, that is, one “up” and one “down” across from each other. • Naturally-occurring unsaturated vegetable oils have almost all cis bonds, but using oil for frying causes some of the cis bonds to convert to trans bonds. • If oil is used only once like when you fry an egg, only a few of the bonds do this so it’s not too bad. • However, if oil is constantly reused, like in fast food French fry machines, more and more of the cis bonds are changed to trans until significant numbers of fatty acids with trans bonds build up. • The reason this is of concern is that fatty acids with trans bonds are carcinogenic, or cancer-causing. Organic Compounds • Lipids, Fats or Triglycerides – Composed of Glycerol backbone plus 3 fatty acid chains – Saturated Fats • Contains only single bonds between the carbons on the fatty acid chains • Solid at room temperature – Unsaturated Fats • Contains one or more double bonds between the carbons on the fatty acid chains • Semi-solid or liquid at room temperature • Mono, di- and polyunsaturated fats – Will only dissolve in other lipids and insoluble in water. • Like Dissolves in Like Phospholipid Phospholipids Organic Compounds • Phospholipids – Modified triglycerides – Phosphorous head and two fatty acid tails – Amphipatic • Hydrophilic, as well as • Hydrophobic – Found only in human cell membrane as a bilayer • Hydrophobic – Tails on the inside of the membrane • Hydrophilic – Heads on the outside of the membrane Steroids Cholesterol decreases cell membrane permeability to small water-soluble molecules. Function? Steroids Organic Compounds • Steroids – Parent compound is cholesterol. – Used for the production of steroid hormones. – Can dissolve in fatty substances. – Dissolves through cell membrane and nuclear membrane and attaches directly to DNA • Starts Transcription of proteins – Such as enzymes – Cholesterol can be produced through denovo synthesis Organic Compounds • Proteins – composes 10 – 30% of cell mass and is the basic structural material of the body. – Some are structural. • Bones, hair, connective tissue – Some are functional. • Antibodies, enzymes, protein hormones Names of the 2 functional groups ? Proteins • Made up of amino acids – Amino = - NH2 • Peptide → oligopeptide → polypeptide → protein • Most versatile of biomolecules in structure and function Learn these Amino Acids Organic Compounds • Amino acids. – The Building Blocks of Protein – Composed of • an amine groups • a carboxyl group • a “R” or Functional group. – 20 different types of amino acids • 9 Essential – Must acquire these through the foods we eat • 11 Non-essential – Can be produced through de-novo synthesis Peptide Bond Peptide Bonds • Two united amino acids form a peptide bond or dipeptide. • 50 or more amino acids are called a protein or polypeptide. • Most proteins contain from 1500 to 50,000 amino acids in the human body. Protein Structure Structural Levels of Proteins • Primary Structure – Polypeptide chain • Secondary Structure – Alpha Helix – Beta pleated sheet • Tertiary Structure – Alpha helix folds on itself. • Quaternary Structure – Hemoglobin molecule Proteins • Hydrogen bonds are created within the Functional Group of the primary polypeptide chain • Hydrogen bonds form and break quickly and can thereby change the protein shape and its function Protein Structure • Globular Proteins – Compact, spherical proteins – Have tertiary or quaternary structures – Also known as functional proteins • • • • • Antibodies Hormones Enzymes (catalysts) Membrane Transporters DNA Regulatory Proteins for transcription Proteins • Fibrous proteins are stable. • Globular proteins are very unstable. – Hydrogen bonds can form and break easily. – Hydrogen bonds can break when: • pH drops. • Temperature rises above normal levels. • Add a PO4 group or other molecules Adenosine Triphosphate • The transfer of a high energy phosphate group to an enzyme causes a change in confirmation • The change in enzyme shape allows the enzyme to quickly catalyze the reaction Protein Structure • Change in shape of protein = – Change in conformation = – Change in configuration • Denatured – When globular proteins lose their shape they can’t perform their function any longer. Cellular Metabolism • Energy as it relates to Biology – Energy for synthesis and movement – Energy transformation • Enzymes and how they speed reactions • Metabolism and metabolic pathways – Catabolism (ATP production) – Anabolism (Synthesis of biologically important molecules) Enzymes • Enzymes are globular proteins that act as catalysts. – A catalyst speeds up a chemical reaction but it itself is not used up – Enzymes are recycled • The function of a globular protein depends on the arrangement of the atoms • A ligand is any molecule that binds to another molecule – A substrate is a ligand that binds to an enzyme Mechanism of Enzymes • Three Basic Steps – The Enzyme binds with a substrate at its active site. – The Enzyme-Substrate Complex is rearranged to form a product. – The Enzyme releases the product and goes back to its original shape • The Enzyme can be used again to catalyze another reaction Enzymes – The shape of the substrate matches with the shape of the active site. – The shape of the active site changes when the protein is denatured so the substrate can no longer bind. Enzymes • The job of an enzyme is to lower the activation energy – Some enzymes carry a helper of “cofactor” such as iron or copper. • Vitamins, especially B complex. Activation Energy Fig 4-3 Enzyme = Biol. Catalyst Some important characteristics of an enzyme: 1. Enzymes are proteins 2. rate of chemical reaction by lowering activation energy 3. is not changed itself 1. It may change DURING the reaction 4. does not change the nature of the reaction nor the result 5. is specific Some more characteristics of enzymes: • Usually end in –ase • Inactive form: -ogen • in few cases RNA has enzymatic activity (eg: rRNA peptide bond) • Isoenzymes may be produced in different areas of the body – E.g., LDH Naming of Enzymes mostly suffix -ase first part gives info on function examples • Kinase • Phosphatase • Peptidase • Dehydrogenase Protein Molecules • Specificity – The ability of a protein to bind to a certain ligand or a group of related ligands – Some proteins are very specific about the ligands they bind, others bind to whole groups of molecules Affinity • The degree to which a protein is attracted to a ligand is referred to as its Affinity. – High affinity proteins are more likely to bind a certain molecule than a low affinity protein Enzyme Activity Proteolytic Activation (for some) Cofactors & coenzymes (for some) Temperature pH 1. Other molecules interacting with enzyme 1. Competitive inhibitors 2. Allosteric modulators depends on Which of the following statements about proteins is false? A. All proteins are enzymes B. A given protein may contain over twenty different amino acids C. The tertiary structure of a protein results from interactions between its amino acids D. Proteins are gigantic polypeptides E. All of the above statements are true. Fatty acids with one or more double bonds are A. Unsaturated B. Have less hydrogen than fatty acids with no double bonds C. Generally found in plants D. All of the above Cholesterol, while it is not an energy molecule, has importance in the body because: A. It is a stabilizing component of the plasma membrane and is the parent molecule of steroid hormones B. It helps provide essential nutrients to the brain and lungs C. It helps mobilize fats during periods of starvation D. It enters the glycolytic pathway without being altered When ketone bodies are present in the blood and urine in large amounts, it indicates increased metabolism of: A. B. C. D. Amino acids Fatty acids Glycogen Lactic acid The atomic mass of an atom indicates the average total number of A. Protons B. Neutrons C. Electrons D. Protons, neutrons and electrons E. Protons and electrons Elements that have full outer shells of electrons A. Will form many compounds B. Will normally form anions C. Will normally form cations D. Frequently form hydrogen bonds E. Are inert, and don’t bond readily with other atoms Deuterium and Tritium are examples of A. Elements B. Ions C. Buffering compounds D. Isotopes E. None of these When a molecule is referred to as polar, it means that A. The positive and negative charges of the molecule are unevenly distributed B. The molecule is ionized and now carries a charge C. The molecule is likely to dissolve in water D. A and C are true E. All of the Above When a molecule is referred to as polar, it means that A. The positive and negative charges of the molecule are unevenly distributed B. The molecule is ionized and now carries a charge C. The molecule is likely to dissolve in water D. A and C are true E. All of the Above The number of protons in the nucleus of an atom constitutes the A. Atomic weight B. Atomic number C. Atomic mass D. Nuclear number A sodium ion, with 11 protons but 10 electrons is A. Neutral B. Positively charged C. Negatively charged D. Isotope Suppose you dissolve a little acid in water and determine that the pH of the solution if 5.2. Now you add 100 times as much acid to the solution. Which of the following is the best estimate of the new pH? A. 3.2 B. 6.2 C. 7.2 D. 8.2 A polypeptide consists of 100 amino acids. How many peptide bonds does it contain? A. 50 B. 100 C. 99 D. 101 E. Impossible to say without knowing the exact amino acid composition Each of the following is a function of proteins except one. Identify the exception. A. Support and structure B. Transport C. Carrying of messages D. Body defense E. Storage of genetic information A fatty acid that contains three double bonds in its carbon chain is said to be A. Saturated B. Monounsaturated C. Polyunsaturated D. Hydrogenated E. Carboxylated Carbohydrates are stored in the liver and muscles in the form of: A. B. C. D. Glucose Triglycerides Glycogen Cholesterol The subunits of proteins are called A. B. C. D. Fatty acids Carboxyl groups Sugars Amino acids The bond between an oxygen and a hydrogen atom in a water molecule is a(n) A. Non-polar covalent bond B. Polar covalent bond C. Hydrogen bond D. Ionic bond 4) Molecules interacting with enzyme, cont’d Allosteric modulators: bind to enzyme away from active site change shape of active site (for better or for worse) Special case: = end product inhibition 4) Molecules interacting with enzyme Competitive inhibitors: bind to active site block active site Fig 4-13 E.g.: Penicillin binds covalently (= irreversibly to important bacterial enzyme active site) Active Site: Small region of the complex 3D structure is active (or binding) site. Enzymes bind to substrate Old: Lock-and-key model / New: Induced-fit model Reversible Reactions Follow The Law of Mass Action Isoenzymes = different models of same enzyme (differ in 1 or few aa) Catalyze same reaction but under different conditions and in different tissues/organs Examples: 1. Amylase 2. LDH → importance in diagnostics – (LDH) Lactate dehydrogenase - Total LDH will begin to rise 2 to 5 days after an MI; the elevation can last 10 days. • • 140-280 U/L Normal Adult Range: 0 - 250 U/L Optimal Adult Reading: 125 1) Proteolytic Activation Also 1. Pepsinogen 2. Trypsinogen Pepsin Trypsin 2) Cofactors & Coenzymes Structure: Inorganic molecules Cu, Fe, Mg Function: conformational change of active site Structure: Organic molecules (vitamin derivatives, FADH2 ....) Function: act as receptors & carriers for atoms or functional groups that are removed from substrate