BSC 1084 Dr.

Presley

Chapter 2 6th edition

CHEMISTRY OF LIFE
ELEMENT = substance made up of only one type of atom CHNOPS + Ca = 99% of the human body (by weight) Elements of the body -- See Table 2-1, p. 25 and Table 2-2, p. 32 You need to know the names and symbols of biologically important elements: C, O, H, N, Ca, P, K, S, Na, Cl, Mg, I, Fe ATOM = smallest part of an element with properties of that element (Fig 2-1, p. 25) Nucleus: proton (p+) - is positively charged - has weight of one atomic mass unit (1 amu) neutron (n0) - no charge (neutral) - 1 amu ATOMIC NUMBER = number of protons **CHEMICAL NATURE of an element is determined by its number of protons. (Notice that the chemical name (and its properties) is related to the number of protons in its nucleus.) ATOMIC WEIGHT (also known as the average atomic mass) = number of protons plus the number of neutrons (involves nucleus) - mass vs. weight because we are studying life on this planet, we can refer only to weight. However note that the human on the moon would have the same mass as on Earth, but will have less weight on the moon because of its lower gravitational pull on objects. - Look at the decimal fractions in the table below. This represents the average weight of all of the atoms for the element. These atoms of an element have different numbers of neutrons in their nucleus and therefore different weights. ISOTOPES are atoms of an element with different weights(# of n0s). - ex. 12C , 13C , 14C (Only 14C is radioactive) Radioisotope unstable isotope, decay, emit radiation - used in carbon dating & metabolic tracers Energy shells (orbitals) electron (e-) - is negatively charged - has little mass, extremely small particle - constantly moving around nucleus Energy related to position of shell: First shell has the lowest energy level. Shell farthest away from nucleus has greatest energy level. Number of electrons that a shell can hold: First shell holds a maximum of 2 electrons. Second shell holds a maximum of 8 electrons. Third shell can holds a maximum of 18 electrons.
Ch 2 1 of 10

BSC 1084 Dr. Presley

Chapter 2 6th edition

***CHEMICAL REACTIVITY of an element related to number of electrons in outermost shell (valence electrons) The Atom Is Electrically Neutral. Therefore number of electrons exactly equals the number of protons. Use information from the PERIODIC TABLE OF ELEMENTS to diagram some of the biologically important elements. This will give you a feel for the chemical nature of elements. ELEMENT SYMBOL ATOMIC NUMBER ATOMIC WEIGHT Hydrogen H 1 1.008 Carbon C 6 12.01 Nitrogen N 7 14.01 Oxygen O 8 15.99 Sodium (Natrium) Na 11 22.99 Phosphorus P 15 30.97 Sulfur S 16 32.06 Chlorine Cl 17 35.45 Potassium (Kalium) K 19 39.10 Calcium Ca 20 40.08 Iron (Ferrum) Fe 26 55.85 Calculate the following in order to diagram the structure of a typical atom for the element: # p+ = Atomic number # n0 = Atomic weight (rounded off) - Atomic number (# p+ + # n0 ) (# p+) + #e = #p arrange the electrons into their shells: fill first shell with 2, then the second with 8, and remainder in third shell up to 18 Now you know the basic structure of atoms. Need to use this information on the test. Most of them are unhappy with the way they exist in nature. They will enter into chemical reactions to become happy. OCTET RULE Atoms are most stable when the outer most shell is full or has 8 electrons (exception is Hydrogen which is happy with 2 electrons). Atoms lacking this happy condition will react by: 1. Gaining or losing electrons 2. Sharing electrons Chemical reactions produce: Molecule chemical combination of 2 or more atoms Compound chemical combination of 2 or more elements TYPES OF CHEMICAL BONDING: (forces or attractions that keep atoms closely associated) 1. Ionic bonds p. 26 ion = charged atom which has gained or lost one or more electrons Cation = positive ion due to loss of electron(s) Anion = negative ion due to gain of electron(s) Ionic bonds = attraction between oppositely charged ions Example: Na+ + Cl- NaCl (table salt) (Fig. 2-2, p. 26) These are weak bonds in aqueous solutions **View WCB Life Science Animations tape 1 Chemistry, the Cell, Energetics concept 1 formation of ionic bonds at Main Campus Library and other ASCs
Ch 2 2 of 10

BSC 1084 Dr. Presley

Chapter 2 6th edition

2. Covalent bonds - sharing of electrons between two atoms (Fig 2-3, p. 27) Non-polar covalent bond = equal sharing of electrons between two atoms; Single covalent bond share one pair of electrons Double covalent bone share two pairs of electrons Examples: O2, glucose Polar covalent bond = unequal sharing of electrons between two atoms. One atom is more strongly electronegative (as oxygen and nitrogen) and will have a greater attraction for the shared electrons. This produces a negative charge on that part of the molecule while the atom with the weaker attraction on the shared electron will have a positive charge. Charges on these molecules allow for electrical attractions between molecules or portions of large molecules. Example: in a water molecule (described as polar because of charged regions on the molecule) Covalent bonds are strong, stable type of bonds, even in aqueous environments 3. Disulfide Bond covalent bridge between two sulfur atoms usually found in same protein structure aids in formation of normal shape of protein molecule - insulin, antibodies, keratin of skin and hair (modify in perms or straighteners) 4. Hydrogen bond - attraction between the partially positive H atom of one molecule and a partially negative O or N of another molecule or portion of the same large molecule. Know these three important examples: 1. between water molecules (cohesiveness of water) 2. in protein secondary and higher structure 3. between DNA bases Fig 2-10, p. 44 TYPES OF CHEMICAL REACTIONS: p. 28 1. Dehydration synthesis (Condensation) reactions = - bonds form between molecules to produce a larger product and gives water - requires energy input 2. Hydrolysis (Decomposition) reactions = - bonds broken between molecules to produce smaller products - uses water to add across bonds - releases (potential) energy stored in chemical bonds INORGANIC vs. ORGANIC Inorganic compounds - usually small - usually do not contain chains of carbon - include: oxygen (O2), water (H2O), carbon dioxide (CO2) salts, acids and bases Organic compounds - usually large - always contain chain of carbons - include: carbohydrates, lipids, proteins and nucleic acids

Ch 2

3 of 10

BSC 1084 Dr. Presley

Chapter 2 6th edition

WATER p. 29 - inorganic compound - polar molecule (dipole = has positive and negative ends), hydrogen bonding important - an excellent solvent; solutes dissolved in water include: nutrients, wastes, vaporized foods to stimulate sensory receptors in nose or taste buds - cohesive - water molecules stick to each other by H-bonding - adhesive (lubricant) - water molecules are attracted to charged surfaces, prevents friction - liquid at room temperature - provides for temperature stability - high specific heat water can absorb lots of energy (heat) - high heat of vaporization - can release energy when water evaporates - makes up 60-75% of human body Compartments: Fig. 2-4, p. 30 ICF intracellular fluid (65%): cytoplasm, matrix of mitochondria, etc. ECF extracellular fluid (35%): blood plasma, lymph, tissue fluid, CSF, etc. CELLULAR RESPIRATION: p. 30 Cells break glucose in presence of oxygen to release carbon dioxide, water, and energy in the form of heat and store energy in ATP molecules Rx: Glucose + O2 ------> CO2 + H2O + ATP + heat This process takes place mainly in the mitochondria of cells ACIDS, BASES AND pH Dissociation (separation) of water into H+ (hydrogen ion) and OH- (hydroxide ion) Electrolytes - substances dissociate to release charged particles (ions) in solution Acid = substance that dissociates in water to release a H+ ion. Base =substance that dissociates in water to release an OH- ion (decreasing H+ conc). (SALT = substance made of ions other than H+ or OH- ions, (p. 26: CaCl2 ) pH = scale used to measure the degree of acidity or basicity of a solution = - log [H+] *** an inverse relationship between pH value and conc. of H+ = represents amount of H+ (acidic protons) in a value that is a power of 10 ** a pH change of 1 is a 10 fold change in H+ ion concentration neutral pH = pH 7 (equal amounts of H+ and OH-) acidic pH = pH 1 to 6.9 (greater conc. of H+) basic pH = pH 7.1 to 14 (greater conc. of OH-) Identify the pH of some common biological and household items (See Fig 2-5, p. 33) Check out blood, orange juice, cola, coffee. Acidosis increased hydrogen ion concentration of a solution, lowered pH Alkalosis increased blood alkalinity due to reduced acids or increased bases IMPORTANCE OF pH Every living thing has a limited tolerance to pH changes. An important homeostatic concern pH of blood plasma is 7.4 (slightly basic) -- What do you expect to happen during exercise when your cells are releasing
Ch 2 4 of 10

BSC 1084 Dr. Presley

Chapter 2 6th edition

acid wastes such as lactic acid and carbon dioxide which combines with water to form carbonic acid? -- If your blood plasma drops to 6.8, you better have medical attention to correct this problem immediately or you problem may be determined in your autopsy !! Yes, pH is that important. buffer - chemical(s) that take up excess H+ or OH- or release H+ or OH- in order to keep the pH of a solution stable. - Basically act as a quick sponge to clean up the excess. Examples: proteins in the blood plasma, bicarbonate buffer system in blood

ORGANIC COMPOUNDS
Learn for each macromolecule group: (carbohydrate, lipid, protein, nucleic acid) 1) elements; 2) building blocks, 3) structural description or categories, 4) functions, 5) examples 1. CARBOHYDRATES elements: C, H, O building block: monosaccharides structural characteristics - contain C:H:O in a ratio of 1:2:1 function chemical energy fuel that can be used in cellular respiration to provide cellular energy (ATP) categories (See Figure 2-6, p.34) (1) Monosaccharides (contain between 3 and 7 Carbons) simple sugars ex. Pentose (5-C): ribose, deoxyribose (in nucleic acids) Hexose (6-C): glucose, fructose, galactose Two forms of glucose exist: alpha () and beta () sugars are useful by our body in metabolism compounds of -glucose are indigestible fiber by humans (2) Disaccharides (two monosaccharides joined) Sweet tasting sugars ex. Sucrose = table sugar (glucose + fructose) Lactose = milk sugar (glucose + galactose) Maltose = malt sugar (glucose + glucose) (also called grain sugar) (3) Oligosaccharides (3-20 monosaccharides joined) Humans do not digest these Surface antigens on cell membrane (as type A, B, and AB red blood cells) Add to proteins to form self-identity markers on cells (immune function) (3) Polysaccharides (thousands of monosaccharides joined) Energy storage polysaccharides - starch in plants, - glycogen in skeletal muscles & liver Structural polysaccharide - Cellulose - indigestible -glucose fibers in plant materials Review Table 2-3, p. 36

Ch 2

5 of 10

BSC 1084 Dr. Presley

Chapter 2 6th edition

2. LIPIDS Characteristics - non-polar (hydrophobic), insoluble in water Elements: C, H, O (less oxygen than in carbohydrates) Categories: (1) Neutral (true) fats (Triglycerides) (See Figure 2-7, p.37) - 1 glycerol + 3 fatty acids - saturated versus unsaturated fatty acids - diets rich in saturated fatty acids associated with risk of cardiovascular disease - Unsaturated fatty acids do not have enough Hydrogens to meet the electron sharing needs, so carbons have to share 2 pairs of electrons producing a double bond. The double bond causes the molecule to kink. Trans fats (hydrogenated fats): for convenience in packaging or storage, hydrogens are added to unsaturated fatty acids; contribute to digestive and cardiovascular problems - Unsaturated fatty acids are liquid at room temperature while saturated fatty acids are solids. - functions = long term storage of energy (survival fuel), Insulation Protection (cushion) (2) Phospholipids (see Fig. 3-1, p.53 membrane) - 1 glycerol + 2 fatty acids + 1 phosphate group (inorganic polar group) - polar (hydrophilic) head and 2 non-polar (hydrophobic) tails - forms bilayer in water - function = major constituent of the cell membrane (lecithin, myelin) (3) Steroids - backbone of 4 fused carbon rings (Figure 2-7, p. 33) - function varies with type of steroid - examples: cholesterol, estrogen and testosterone, vitamin D, bile - Bile contains an emulsifier which breaks up large fat aggregates and allows them to mix with the water in the digestive tract. - See Box 2-4 , p. 36 LDL = bad cholesterol, HDL = good cholesterol Review the lipids in table 2-4, p, 39 3. PROTEINS Characteristics: large structure, polar regions, shape is essential for function Elements: C, H, O, N, S Building block: amino acids (See Fig 2-8, p. 40) consist of 5 components: a central carbon which is bound to each of following 4 groups an amino group a carboxyl group (acid group) an R group (variable portion of the amino acid) a Hydrogen polypeptide = protein made of amino acids joined by peptide bonds

Ch 2

6 of 10

BSC 1084 Dr. Presley

Chapter 2 6th edition

Levels Of Protein Structure primary = sequence of amino acids help by peptide bonds, resembles a string of beads. determined by nucleotide sequence in the gene (portion of a DNA) secondary = repetitive twisting or folding held by hydrogen bonds resembles a coil ( Slinky) or accordion folds (folded computer paper) tertiary = non-repetitive three dimensional shape held by bonds between R groups ** essential shape for function quaternary = 2 or more linked polypeptides ** example: hemoglobin shape is critical to normal function Denaturation - alteration of secondary or higher protein structure - does NOT break peptide bonds of primary structure - results in inactivation of the protein , especially enzymes - causes of denaturation: increased heat (high fever), change of pH ^ renaturation is possible in some cases Functional types of proteins: (Table 2-5, p. 41) - structural components of cells, tissues and organs (collagen, keratin) - hormones (insulin, human growth hormone) - transport (hemoglobin) - defense (antibodies) - contractile (actin and myosin of muscles) - catalysts (enzymes) ENZYMES = biological catalysts, recyclable in the cell - speed up the rate of a chemical reaction (million times) - specificity due to shape relationship of active site and substrate (p.43) - name frequently ends in -ase - allows chemical reactions to occur at warm body temperatures - one enzyme for each different chemical reaction step - study Fig. 2-9 on page 43 Observe the inactivation of enzyme by heat, heavy metals 4. NUCLEIC ACIDS Elements: C, H, O, N, P Building block: nucleotide nucleotide: composed of: a pentose sugar (ribose or deoxyribose) a phosphate group a nitrogen-containing base: PURINES (double ring) Adenine - A Guanine - G PYRIMIDINES (single ring) Cytosine - C Uracil U -- only in RNA Thymine T only in DNA

Ch 2

7 of 10

BSC 1084 Dr. Presley

Chapter 2 6th edition

Categories: (1) Deoxyribonucleic Acid (DNA) (Figure 2-10, p. 44) Sugar = deoxyribose Bases are Adenine (A), Thymine (T), Cytosine (C) and Guanine (G) Phosphate group Double sugar-phosphate backbone Helix (coiling) Complementary base pairing -- H bonds between A = T and G = C Function = stores genetic code (genes store codes for proteins) Controls cell activity by determining which proteins are being produced (2) Ribonucleic Acid (RNA) Sugar = ribose Bases = A, C, G or Uracil (U) Phosphate group Single sugar-phosphate backbone, single-stranded Functions as a helper in protein synthesis taking place in the cytoplasm (3) Adenosine Triphosphate (ATP) (Figure 2-11, p. 45) Sugar = ribose Base = adenine contains 3 phosphates joined by high energy bonds mainly produced during cellular respiration in the mitochondria - cellular respiration of the glucose molecule can provide energy to add a phosphate group to ADP to make it ATP (cellular energy) - break off terminal phosphate group to release energy to do work in cells leaving an ADP molecule - again energy from cellular respiration is used to add phosphate to make ATP - an ongoing cycle in the cell to meet its energy needs Function as the energy "currency" of cell only energy directly available to cells to do work such as cell division, protein synthesis, and muscle contraction THINGS TO CONSIDER: Mineral supplements: Why do people take them? What benefits are they hoping for? Are there any potential dangers? Food labels: What is in our food? What are all these chemicals for? Are they harmful or beneficial? Cellular respiration: What is the relationship between breakfast, inhaling and exhaling, and walking to class?

______________________
Ch 2 8 of 10

BSC 1084 Dr. Presley

FOR STUDY: Read Chapter 2. Follow my chapter notes to indicate the details required for the test. Answer the review questions at the end of the chapter. Practice drawing some atomic structures. Know how to use the atomic number and atomic weight to calculate numbers of protons, neutrons, and electrons for an atom of an element. Also know how to figure the number of electrons in each shell, especially the last shell (most energy). Make a table of the macromolecules to include: Name of macromolecule, building block, elements, subgroups, examples, and functions of each group or type Learn the key terms. Make flash cards of those that you need to learn. acid acidic proton active site adenine alkaline amino acids antibody anion atom atomic number atomic weight ATP base basic buffer carbohydrates catalyst cation cellular energy cellular respiration cellulose chemical bond chemical properties chemical reactivity cholesterol complementary bases covalent bond cytosine dehydration synthesis denaturation disaccharides DNA double bond electrolyte
Ch 1

electron element elements of body emulsifier enzyme estrogen extracellular fluids gene genetic code glucose glycogen guanine hexose hydrogen bond hydrogen ion hydrolysis (decomposition) hydrophilic hydrophobic intracellular fluid ion ionic bond isotope (notes p.1) lecithin levels of protein structure lipids monosaccharides myelin neutral neutral fats neutron nitrogen-containing base nucleic acid nucleotide
9 of 9

nucleus octet rule oligosaccharides orbitals (shells) pentose peptide bond pH pH scale phospholipids polar molecule polypeptide polysaccharides protein synthesis proteins proton R-groups RNA salt saturated fatty acid single bond solute solvent starch steroids substrate sucrose testosterone thymine trace elements triglyceride unsaturated fatty acid uracil vitamin D water

BSC 1084 Dr. Presley

Use the Essential Study Partner (ESP) tutorials: Levels of Organization: Chemistry: 1) atomic structure; 2) chemical bonding; 3) pH; 4) thermodynamics. Molecules of Life: 1) water; 2) organic chemistry; 3) carbohydrates; 4) lipids; 5) proteins; 6) enzymes; 7) pathways & feedback; 8) ATP; 9) respiration How to access ESP tutorials:
Step 1: Go to Tutorials in Lesson tab Step 2: click on step one www.mharris.com Step 3: Click on Students Step 4: Click on register for self study Step 5: Under subject tab highlight Anatomy and Physiology and enter Step 6: Scroll down to Human Anatomy 2c Saladin Step 7: Log in with email and set up password Step 8: Click on The Resources which is near the top it is highlighted blue Step 9: Scroll down to the bottom and open, link, articles, news Step 10: Click on Study Partner Step 11: click on blue highlighted essential study partner Step 12: Look on the left hand side and where it says click here to choose a unit...and click Step 13: click levels of organization Step 24: click on introduction If you are having trouble accessing the ESP tutorials from this site, you may find helpful activities in the Saladin textbook from its Chapter 2: The chemistry of life.

Remember that your medical dictionary may provide quick reference to terms not in the glossary of your text. I suggest Tabers Cyclopedic Medical Dictionary 20/21st edition Complete Chapter 2 in the Student Workbook. Especially practice the Multiple Choice Test #2 and Test #3. For a FUN Review go to Davis Plus: http://davisplus.fadavis.com (keyword: Scanlon).

Ch 1

10 of 9