we will start our study of the body at the chemical level of organization

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1 Chemistry Hand Out Dr. Stewart i. Anatomy- the study of the form and structure of the body parts and their interrelationships, i.e. what the body is made of and how all the parts fit together. ii. Physiology- the study of the normal functioning of the body, i.e. how do the various parts of the body work. Principle of Complementarity of Structure and Function: Structure determines function and function reflects structure; what a structure can do depends of its form. In the class you should continually ask, "how does the structure of X relate to its function Y. Ascending hierarchy of structural organization of the human body: atoms----molecules---organelles----cells----tissues----organs---- organ systems----organism. Definitions: we will start our study of the body at the chemical level of organization 1) matter is defined as anything that takes up space and has mass for our purpose mass and weight will be equal 2) chemistry is the science that deals with the structure of matter 4) elements All matter is composed of elements, elements are unique substances that cannot be broken down into simpler substances by ordinary chemical means. There is 116 known elements. 92 of with occur in nature the rest are produced artificially. (look at periodic table of elements) the elements Carbon, Nitrogen, oxygen, and hydrogen make up 96% of the bodies weight, 20 other elements are present in trace amounts. The periodic table is a complete listing of the known elements. Each element is composed of similar particles or building blocks called atoms. More on atoms later The elements differ in the nature of the atoms they are made of. Atoms of the element gold are different from the atoms that make up the element silver. It is the differences in the atoms that make gold unique from silver. 1

2 4) molecule Atoms of the same or different elements combine to produce molecules Molecules are the simplest combination of atoms held together by chemical bonds that are chemically pure: atoms and molecules Atomic Structure: Includes Oxygen or O2; water or H2O and large complicated structures like DNA. Atoms consist of dozens of different subatomic particles only three are important for understanding chemical properties 1. protons with a positive charge 2. neutrons which have no charge Protons and neutrons have almost identical wieght 3. electrons negative charge very low mass nucleus contains protons and neutrons and accounts for 99.9% of the mass. A complete atom has equal numbers of protons and electrons and thus are electrically neutral All protons are alike and all electrons are alike. what makes the atoms of each element different or unique is the different number of protons, neutrons, and electrons. The number of electrons is particularly important in determining how reactive a compound is. Atomic Number; is equal to the number of protons in the nucleus. Since atoms are normally electrically neutral, the number of protons are always balanced by an equal number of electrons Mass Number; Equal to the sum of protons and neutrons. This number tells you the number of subatomic particles in the nuclei of an atom. Helium has 2 protons and 2 neutrons so it as a mass of 4. Helium has an atomic number of 2 Isotopes: atoms which have the same number of electrons and protons but vary in number of neutrons. Example is Carbon 12, 13, 14- each has 6 electrons and 6 protons but 6,7,8 neutrons receptively carbon has an atomic number of 6 carbon 12 has a mass number of 12 2

3 carbon 13 has a mass number of 13 carbon 14 has a mass number of 14 atomic weight: is the average mass number of an element that reflex the proportions of the different isotopes and includes the small mass the electrons add to the atom carbon s = thus in nature most carbon is carbon 12 Remember that isotopes of an atom have the some number of electrons and protons (which determines how atoms interact with each other) and thus typically have the same function in metabolic reactions. Exposure to isotopes results in there incorporation into your body the Radioisotopes: The heavier isotopes of many elements are unstable and their atoms decompose spontaneously into more stable forms. The disintegration of nucleus releases energy in the form of alpha particles packets of 2 protons and 2 neutrons. Has lest penetration power, beta particles electron-like particles gamma rays are electromagnetic energy similar to X-rays andhas the highest energy form, thus most penetration power Very dangerous weak radioisotopes are useful in medicine because they can be added to then followed through the body stronger radioisotopes are useful because the energy can be used to destroy cancerous cells (cobalt 60). the dense cancer cells absorb the energy and their DNA is destroyed How Matter (atoms) is Combined: Atoms of a particular element rarely exist alone in a free state, they are combined with other atoms to produce molecules. The atoms in a molecule are held together by chemical bonds. To understand how matter is combined it is necessary to discuses the electrons that surround an atom. It is ultimately these electrons that determine the reactivity or desire of an atom to combined with other atoms. Electron Shells: Electrons circle the nucleus in electron shells also called energy shells. Each electron shell represents an energy level (electron shell = energy level). 3

4 Therefore the further out the electron shell is (further from nucleus) the more reactive that type of atom is. The outer most shell is called the valence shell Each electron shell can hold a finite number of electrons. First shell (shell closest to the nucleus) can hold only 2 Second shell can hold 8 Third can hold 8 Note: the third shell of elements with atomic numbers greater then 18 can hold 18 electrons There is seven shells in the large atoms of the elements of berkelium, einsteinium ect Two important concepts are; first, shells fill consecutively and second only elements with partially full shells are reactive (hydrogen vs. helium) Atoms that have full outer energy shells (called valence shell) or outer shells with eight (8) electrons tend to be stable (rule of eight s or octet rule). If this is not meet, the atom wants to loose or gain electrons to achieve a full outer shell or 8 outer electrons. 1. helium 2 electrons 2. neon 10 electrons; 2 in first shell and 8 electrons in second shell both have full outer shells and are inert or noble gases (very low reactivity) Atoms normal do not exist in a free state but are chemically combined with other atoms forming molecules (2 hydrogens and one oxygen yields a molecule of water). remember: a Molecule is the simplest combination of atoms held together by chemical bonds. The object of chemical bonds is to achieve a stable number of electrons in the valance shell (outer) or to gain electro neutrality 3 types of chemical bonds: 1. ionic 2 covalent 3 hydrogen 1. Ionic Bonds Atoms are electrically neutral. However electrons can be transferred from one atom to another which forms anions (-) the electron acceptor, and cations (+) the electron donator.these charge atoms (ions) will now be attracted to each other resulting in an ionic bond. This functions to maintain electro neutrality. 4

5 shell for 2. Covalent Bonds Covalent bonds occur when electrons are shared instead of transferred. This allows each atom to fill its outer electron at least part of the time. H2 and CH4 single covalent bond= atoms share only one pair of electrons Double or triple share 2 or 3 pairs of electrons. (O=O) NonPolar molecules occur if the electrons are shared equally between the atoms (Carbon dioxide CO2 is a linear). Polar molecules (dipole) occur in the electrons are shared unequally, that is the electrons spend more time at one end of the molecule. (water H2O). This is due to oxygen having a stronger attraction for electrons than hydrogen (oxygen is electronegative) and the triangular shape of the molecule. 3. Hydrogen bonds (see figure 2-6) are very weak and don t bind atoms together to form molecules. First must have a polar covalent bond. Polar covalent bonds form when hydrogen bonds to strong electronegative atoms like oxygen and nitrogen (remember electro negative atoms are electron greedy), resulting in a weak (+) charge to the H (electron spends less time on the hydrogen side of the molecule) and a weak (-) charge on the oxygen or nitrogen (electron spends more time on the oxygen or nitrogen side of the molecule). The (-) end of the molecule will be attached to the (+) end of nearest neighboring molecule. This attraction is a hydrogen bond Chemical reactions the existence of a cell depends on the ability to control chemical reactions chemical reactions involve the formation of new bonds between atoms or the braking of existing chemical bonds between atoms the formation of new bonds and the braking of existing bonds both involve the transfer of energy so a basic understanding of energy is necessary General back ground on energy 5

6 Energy has no mass and does not occupy space. It can be measured only by its effects on matter. Energy is defined as the capacity to do work or in other words to put matter into motion. Energy exists in two forms or work capacities 1. Kinetic is energy in action 2 Potential is stored or inactive energy Biologically relevant forms of energy: 1. Chemical- energy stored in the bonds of chemical 2. Electrical- movement of charged particles 3. Mechanical- energy directly involved in moving matter 4. Radiant or electromagnetic- energy that travels in waves or the electromagnetic spectrum. This includes visible light, radio waves, ultraviolet waves, and X-rays * Energy can be converted from one form to another but it can not be destroyed* the conversation of potential energy to kinetic energy is never 100 percent and some energy is released in the form of heat types of chemical reactions 1) decomposition reactions breaking down of a molecule into smaller fragments AB A + B energy is released digestion involves the breakdown of complex carbohydrates to sugars et. catabolism is a decomposition reaction that occurs in the cell covalent bonds (potential energy) is broken down to release kinetic energy that can perform cellular work like muscle contraction 2) synthesis reactions larger molecules are produces from smaller fragments A + B AB involves the formation of new bonds energy must be added anabolism is a synthesis reaction occurring in the cell resulting in the synthesis of new compounds 3) exchange reactions 6

7 involves the shuffling around of molecules AB + CD AD + CB is a combination of a decomposition reaction followed by a synthesis reaction may release or require energy if released energy is exergonic reaction if absorbs energy is endergonic reaction chemical reactions are reversible A + B AB thus AB A + B sense reactions are reversible they establish an equilibrium where the rate of synthesis is equal to the rate of decomposition A + B AB for a reaction to occur there must be enough energy available for the reaction this is called the activation energy most chemical reactions occur to slow (require high activation energy) to be useful for living cells. to lower the activation energy cells produce enzymes with promote chemical reactions. enzymes are catalysts: they accelerate chemical reactions without themselves being permanently changed or consumed. Basic Biochemistry Two major classes of compounds that contribute to body structure and function 1. Organic compounds; they contain carbon and all atoms are covalently bonded in the molecule. 2. Inorganic compounds; no carbon and atoms are not always covalently bond. Major types for us are water, salts, and inorganic acids and bases. Exceptions: Carbon dioxide, carbon monoxide, and carbides all have carbon atoms but are not considered organic but inorganic. Major biologically important inorganic compounds WATER (60-80% of volume of living cells) Is the single most important constituent of the body. 7

8 important properties of water in biological systems? a. high heat capacity; absorbs and releases large quantities of heat before changing temperature much. important in temp regulation. once a temperature is reached it changes temperature only slowly (thermal inertia) b. high heat of vaporization; requires a large amount of heat to transform from a liquid to a gas (due to hydrogen bonds). Important in sweating or body cooling. c. Polarity; (see above) makes water a great solvent for chemical reactions; stuff can dissolve in it. polarity important in dissolving ionic compounds, by forming hydration (water) layers around large charged molecules that shield them. For example sodium chloride will dissolve in water. the slight positive charge of the hydrogen side of the water molecule will surround the negatively charged chloride ion and the slightly negatively charged oxygen side of the water molecule will surround the positively charged sodium ion this hydration layer will allow the sodium and the chloride to separate from each other thus sodium chloride (table salt) dissolves into the water d. reactivity; important part of many types of reactions. decomposition reaction called hydrolysis is important part of metabolism. e. lubricant; there is little friction between water molecules. aqueous solutions (water solutions) the polarity of water makes it an unusually effective solvent because water is slightly negative on one side and slightly positive on the other water can slip between ionic bonds or other polar molecules allowing the atoms to separate or to undergo ionization or dissociation causing the molecule to dissolve water will form hydration spheres any molecule that contains ionic bonds or is polar attracts water and thus dissolves or goes into solution easy this molecules are called hydrophilic nonpolar molecules do not readily interact with water and are called hydrophobic when exposed to water they do not form hydration spheres and don t dissolve 8

9 Acid and base concentrations Acids and bases are extremely reactive and thus the concentration is closely regulated An acid is any compound the liberates hydrogen ions [H+] A base is any compound that accepts hydrogen ions. In an aqueous solution it results in the formation OH- Hydrogen ions concentrations can be measured in grams of ion per liter of solution Stomach juice has.01 grams of H+/liter Ammonia has grams of H+/liter The ph scale is a shorthand system to more easily tract the decimal place of the H+ concentration H+ concentration of.1 grams/liter = ph of 1 H+ concentration of.01 grams/liter = ph of 2 H+ concentration of.001 grams/liter = ph of 3 in pure water a small amount of water dissociated to yield hydrogen ions (H) and hydroxide ions (OH) (H2O H + OH) pure water contains grams/liter (mols) of hydrogen ion can be written [H] = 1 X 10-7 or ph = 7 thus the ph = negative logarithm of the hydrogen ion concentration ph scale ranges from 0 to 14 a change by 1 along this scale is a difference in hydrogen ion concentration of 10 times ph 7 has 10 times less hydrogen ion then ph 6 (remember is a negative log scale, less is more!) ph of 7 is neutral equal amounts of H and OH ph less than 7 is acidic greater concentration of H than OH ph greater than 7 is basic or alkaline greater concentration of OH than H blood ph is 7.35 to 7.45 acidosis is abnormally low blood ph alkalosis is abnormally high blood ph inorganic acids 9

10 an acid is any solute that dissociates in solution and releases hydrogen ions thus lowering the ph because hydrogen ion has no electron it is just a proton and acids are called proton donors strong acids dissociate completely in solution HCL H +Cl weak acids fail to dissociate completely so establish an equilibrium H2CO3 H + HCO3 inorganic bases a base is a solute that removes hydrogen ions from a solution they are proton acceptors NaOH Na + OH the OH will accept H to form water (OH + H H2O) strong bases dissociate completely in solution weak bases fail to dissociate completely buffers Are chemicals both inorganic and organic that resist changes in the ph of a solution. The can release a H+ when ph rises to curve the rise in ph and can accept a H+ when ph drops (becomes more acidic). Buffers are actually weak acids or weak bases. they can act as proton acceptors or donators depending on the concentrations that are present (bicarbonate buffer system) H2CO3 H + HCO3 if H levels are low then more H2CO3 will break down to yield H + HCO3 if H levels are high more HCO3 will bind with H to yield H2CO3 so act to hold H concentrations at a steady level Salts; a salt is an compound that dissolves in water to produce ionic or charged particles. The positive charges particles are called cations The negative particles are called anions 10

11 exception: the anion cannot be H+ and the cannot be the hydroxyl ion OH _ ions are called electrolytes. 1. importance; carry electrical charges in the body (nerve impulses, muscle contraction) 2. contribute to the hardness of bones and teeth (Calcium phosphates 3. ionic iron is part of hemoglobin biologically important salts: 1. NaCl 2. KCl 3. Ca 2 CO 3 4. Ca 2 PO 4 Major biologically important organic compounds Proteins, carbohydrates, lipids and nucleic acids 1. Carbohydrates molecules include sugars and starches and are made of carbon hydrogen, and oxygen a. functions of carbohydrates i. cellular fuel to produce ATP ii. Structural purposes iii. Signaling molecules (androgens) Major types of carbohydrates: 1 monosaccharides; a single-chain or single ring structure are simplest form and linked together to form larger polysaccharide molecules glucose, galactose, fructose and deoxyribose (part of DNA) 2 Disaccharides = two monosaccharides joined together sucrose = glucose + fructose 3 polysaccharides = a long chain of simple sugars linked together resulting from a dehydration synthesis or removal of a water molecule the longer the polysaccharide the less soluble in water starch is a digestible polysaccharide cellulose is a nondigestible polysaccharide 11

12 glycogen is a storage carbohydrate (polysaccharide) used by animals 2. Lipids; organic compounds that are insoluble in water but dissolve readily in other lipids and in organic solvents such as alcohol, chloroform and ether. Major types are neutral fats, phospholipids, steroids, and eicosanoids 1 Neutral fats; commonly known as fats when solid or oils when liquid. made from fatty acids and glycerol (see figure 2-14) three fatty acids on a glycerol backbone function is to supply energy and insulation for the body 2 Phospholipids; are modified triglycerides with a phosphorus containing group and two not three fatty acid chains. the hydrocarbon portion (fatty acids) of the molecule is nonpolar and interacts only with nonpolar compounds the phosphoruscontaining head is polar and attracts other polar particles such as water. function: major part of the cell membrane other functions 3 Steroids; are flat molecules formed of four interlocking hydrocarbon rings most abundant is cholesterol important precursors of other molecules like steroid hormones and bile salts function: important for cell membrane rigidity 4 Eicosanoids: derived from a 20 carbon fatty acid called arachidonic acid found in cell membranes. most important are prostaglandins and leukotrienes function: is blood clotting inflammation labor contractions and intracellular signaling 3. Proteins; 10-30% of cell mass. Is both structural and non structural. composed of carbon, oxygen, hydrogen, and nitrogen, and sum have sulfur and phosphorus. 12

13 are most abundant organic components of the human body different proteins in the body Amino acids are the building blocks of proteins there are 20 different types of amino acids. Each amino acids has unique properties all amino acids have an amine group -NH2 and a organic acid group -COOH. because of the acid group amino acids can act as proton acceptors or release protons thus proteins are a very important ph buffer in the body. Amino Acids are joined by peptide bonds is a bond between the carboxylic acid of one amino acid and the amine group of a second amino acid Two amino acids form a dipeptide three = a tripeptide, 10 or more = polypeptide, 50 or more = a protein. The different types of amino acids assembled yield proteins that have very different properties. protein shape Primary, secondary, tertiary, quaternary structure 1. primary; linear sequence of amino acids in a protein 2. secondary structure; twisting and or folding of the chain upon itself to form a more complex structure. is primarily the result of hydrogen bonding between neighboring amino acids alpha helix; coiled beta pleated sheet; side-by-side 3. tertiary structure; this results from the helix or plated sheet folding upon itself to produce a more compact structure. 4. quaternary structure; when two or more separate polypeptide chains interact to produce a complex protein. Proteins are found in two major forms 13

14 fibrous- long filamentous proteins like collagen, elastin, et. are structural proteins. globular rounded or tightly compacted proteins-crucial in virtually all biological processes. important in immunity, hormones, enzymes, et. Protein Denaturation; change in protein shape that occurs in high temp, and acidic or basic ph. Results from breaking hydrogen bonds (first) this may be reversible. If conditions to extreme may brake peptide bonds now denaturation is irreversible.because the structure of a protein produces is active site denaturing will inactive these active sites so protein can perform its function. (hemoglobin cant transport oxygen if ph to high or to low) Enzymes are globular proteins that act as biological catalysts to greatly speed up chemical reactions (by a factor of 1 million). Enzymes are not used up in the reaction (see figure 2-19) enzymes are very sensitive to denaturation enzyme characteristics 1. specificity each enzyme will catalyze only one type of reaction 2. saturation limits an enzyme will catalyze the reaction faster as the concentration of substrate (starting material) increases up to a point when all enzymes are working at their maximally rate (the enzymes are saturated) 3. regulation a variety of factors can turn enzymes on or off to control reaction rates this allows the cell careful control over when a reaction will occur parts of an enzyme: holoenzyme: a complete and functioning enzyme is called a holoenzyme some enzymes require a non protein portion. apoenzyme: the protein part of the holoenzyme is called the apoenzyme 14

15 cofactor: the non protein part of a holoenzyme is the cofactor cofactor can be an ion of a metal element like cooper or zinc. if the cofactor is organic, derived from a vitamin it is called a coenzyme 4. Nucleic Acids (DNA and RNA) are composed of carbon oxygen, hydrogen, nitrogen, and phosphorous. These are the largest molecules in the body. DNA and RNA composed of the structural unit nucleotides. Nucleotides are made of a 1. nitrogen-containing base: there is five types of bases 1. adenine, 2 guanine 3 cytosine, 4 thymine, 5 uracil adenine and guanine are constructed of two large ring bases and are called purines (see figure 2-20) cytosine, thymine, and uracil are constructed of a single ring base and are called pyrimidines (see figure 2-20) DNA has adenine, guanine cytosine thymine RNA has adenine guanine cytosine uracil 2 pentose sugar: five carbon sugar the pentose sugar of DNA has one less oxygen molecule so is called deoxyribose thus the name for DNA deoxyribonucleic acid. RNA has one more oxygen molecule so is called ribose thus the name ribonucleic acid. 3. phosphate group: which is attached to the sugar DNA A molecule of DNA is a double stranded chain of nucleotides. The strains are attached by hydrogen bonds. Because of hydrogen bonding the chain of nucleotides are coiled so the structure is a double helix 15

16 to RNA each nucleotide in the strand is attracted by the phosphate group to the sugar group of the next nucleotide. The bases on opposite strands are held together by the hydrogen bonds between then adenosine binds to thymine and cytosine binds to guanine. (see figure 2-20) thus these base pairs are called complementary bases. function of DNA- found in the nucleus and is the storage molecule for the genetic code or information. heredity. A molecule of RNA is a single stranded chain of nucleotides that is made using the DNA as a template. The RNA will be complementary the DNA template. function of RNA- DNA is "read" producing RNA. this RNA is translated to produce a protein molecule. RNA contains the directions for how to assemble a protein then Adenosine Triphosphate (ATP) ATP is a molecule that is based on the adenosine molecule like that used in DNA and RNA but it as to more phosphate groups attached to the end for a total of three. The last two phosphate groups are held on by a unique chemical bond that contains a high amount of energy that can be easily used by the body. These bonds can be ruptured by hydrolysis liberating the energy. Normally only the last bond is uses to yield ADP and P + energy, but the last two can by broken to give AMP (adenosine monophosphate) and 2P + energy 16