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K. Muma Bio 6 Chapter 2 Chemistry Study Objectives: 1. Define the terms matter, elements, and atoms 2. Differentiate between ionic, covalent, and hydrogen bonds 3. Differentiate between polar and non-polar molecules: how do they interact? 4. Describe the unique properties of water and their importance to the human body 5. Distinguish between inorganic and organic compounds 6. Describe acids and bases, and explain the concept of the pH scale 7. Explain the importance of buffer systems and how they work 8. Describe the building blocks, structure, and functions of carbohydrates: monosaccharide, disaccharides, and polysaccharides 9. Describe the building blocks, structure, and functions of lipids: neutral fats, phospholipids, steroids, and eicosanoids 10. Describe the building blocks, structure, and functions of proteins: fibrous and globular 11. Explain how acidity and high temperature affect the functioning of globular proteins 12. Describe the building blocks, structure, and functions of nucleic acids: DNA and RNA Chapter 2 Outline Molecular Interaction / Biochemistry I. Matter - anything that occupies space and has mass a. Elements are substances that cannot be broken down into other substances b. Atoms - the smallest unit of matter that still retains the properties i. Structure of atoms - composed of subatomic particles 1. Protons - that are positively charged and are found in the nucleus (center) of an atom 2. Neutrons - are neutral or have no charge; are also found in the nucleus 3. Electrons - are negatively charged and exist in the orbits/shells around the nucleus. a. Maximum number of electrons per shell = 2 in the first shell; 8 in the other shells b. Number of electrons on the outer shell determines the atoms chemical behavior c. Chemical Bonds i. Ionic Bonds - formed between oppositely charged ions 1. When an atom loses or gains electrons, it becomes electrically charged 2. Ions are charged atoms ii. Covalent Bonds - form when electrons are shared between atoms 1. non-polar covalent bonds – electrons shared equally 2. polar covalent bonds – electrons are NOT shared equally iii. Hydrogen bonds – interaction between a hydrogen atom bound to an electromagnetic atom and another electromagnetic atom. 1. The polarity of water results in hydrogen bonds between neighboring water molecules 2. Gives water some unique vital properties: a. High heat capacity - requires a lot of energy to increase in temperature, and releases a lot of energy when it cool b. High heat of vaporization - as water evaporates it takes large amounts of heat with it c. Good solvent properties –dissolves chemicals, making it a good medium for transporting biological molecules i. Solution - is a liquid consisting of two or more substances evenly mixed 1. Solvent: is the dissolving agent 2. Solute: is the substance being dissolved ii. Hydrophilic – water soluble (likes water) 1. Polar molecules iii. Hydrophobic – does not dissolve in water (water fearing) 1. Non – polar molecules iv. Amphiphilic – molecules that is both hydrophilic and phobic 1. Polar and non-polar ends d. Chemical reactivity i. Hydrolysis – water breaks bond apart ii. Dehydration – removing water to form bonds e. Cohesion - stickiness of water molecules f. Cushioning II. Acid and Base Concepts a. Acid – a chemical compound that donates H+ ions to solutions i. HCl H+ + Cl- b. Base - a compound that accepts H+ ions and removes them from solution i. NaOH Na+ + OH- c. pH scale - measures concentration of hydrogen ions i. Logarithmic scale – each pH unit is a tenfold change in H+ concentration 1. pH 7 = neutral 2. pH below 7 = acidic 3. pH above 7 = basic d. Buffers - substances that resist pH change i. They accept H+ ions from the solution when they are in excess ii. They donate H+ ions to the solution when they are depleted III. Biochemistry a. Organic molecules – large molecules containing carbon (macromolecules) i. Have a unique three-dimensional shape that defines its function in an organism ii. The molecules of your body recognize one another based on their shapes iii. Most macromolecules are polymers. Polymers are made by stringing together many smaller molecules called monomers (subunits) b. Four types of macromolecules found in cells i. Carbohydrates - includes sugars and starches 1. Contain carbon, hydrogen, and oxygen (1:2:1 ratio) 2. Monomer = monosaccharide 3. Classified according to size: a. Monosaccharides – one sugar, referred to as simple sugars b. Disaccharide - a double sugar c. Polysaccharides - complex carbohydrates formed by long chains of monosaccharides i. Starch, cellulose (plants), glycogen (animals) ii. Lipids 1. Carbon and hydrogen outnumber oxygen 2. Lipids are hydrophobic 3. Functions: a. Energy storage b. Cushioning c. Insulation 4. Types of lipids: a. Neutral fats – mostly triglycerides i. A combination of glycerol and three fatty acids ii. Found in fat deposits (adipose tissue) iii. Source of stored energy and insulation iv. Cushions organs v. Unsaturated fatty acids - have less than the maximum number of hydrogen bonded to the carbons 1. Examples: Most plant oils; vegetable or corn oil vi. Saturated fatty acids - have the maximum number of hydrogen bonded to the carbons 1. Example: Most animal fats vii. What is trans fat then??? b. Phospholipids – composed of phosphate head (hydrophilic) and two lipid tails (hydrophobic) i. Forms cell membranes and the myelin sheaths of neurons c. Eicosanoids – a 20 carbon fatty acid with a 5 or 6 carbon ring i. Examples: prostaglandins, leukotrienes, thromboxanes d. Steroids - the carbon skeleton is bent to form four fused rings i. Cholesterol is the “base steroid” from which your body produces other steroids ii. Example: testosterone, estrogen, cortisol, bile salts iii. Protein - a polymer constructed from chains of amino acid monomers 1. Contains C, H, O, N, and sometimes S 2. Monomer = Amino Acids a. There is 20 different amino acids b. The arrangement and combination of amino acids makes each protein different c. Amino acids are held together by peptide bonds 3. Types of Proteins a. Fibrous proteins i. Provides for construction materials for body tissues ii. Important role in structure iii. Examples: collagen, elastic fibers, myosin and actin b. Globular Proteins i. Relies on complex folded structure to function ii. Plays a vital role in cell function iii. Act as enzymes, hormones, transport proteins or antibodies iv. Protein Shape - protein’s shape is sensitive to the surrounding environment 1. Primary structure – order of amino acids 2. Secondary structure -polypeptide folded into a helix or a sheet 3. Tertiary structure- sheets and helices folded into a 3-D globule 4. Quaternary structure - several tertiary units put together 5. A slight change in the primary structure of a protein affects its ability to function a. Example: sickle cell anemia 6. Denaturation - unfavorable temperature and pH changes can cause a protein to unravel and lose its shape iv. Nucleic Acids - information storage molecules 1. Monomer = nucleotides a. 5 carbon sugar b. Phosphate group c. Nucleic base 2. Types of Nucleic Acids a. Deoxyribonucleic Acid i. Composed of 4 types of nucleotides 1. Purines – Adenine (A) and Guanine (G) 2. Pyrimidines – Thymine (T) and Cytosine (C) ii. Organized by complimentary base pairing to form a double stranded helix 1. A = T 2. C = G iii. The nucleotides of the two stands are joined by hydrogen bonds iv. Contains a sugar-phosphate backbone b. Ribonucleic acid i. RNA is different from DNA in that: 1. Its sugar is ribose instead of deoxyribose 2. It has the base uracil (U) instead of thymine (T) 3. It’s single stranded c. Some other nucleotides: i. ATP used for cellular work ii. NAD and FAD, used as electron carriers in cellular respiration iii. GTP, cyclic AMP, ADP in cell signaling Post-Lecture Practice 1. List at least four vital properties of water and describe why this is important to the human body. 2. Draw two or three water molecules interacting with each other by accurately depicting where the hydrogen bonds would take place in your illustration. 3. Bicarbonate ions, HCO3- is an important ion in the body. It reacts in the following way: HCO3- + H+ H2CO3 a. Are bicarbonate ions acids or bases? _________________ b. Why? 4. HNO3 reacts in the following way when dissolved in water: HNO3 H+ + NO3- a. Is HNO3 an acid or a base? ___________ b. Why? 5. How much more H+ is in a solution that has a pH of 3 when compared to a pH of 6? 6. How much OH- is in a solution with a pH of 11 when compared to a pH of 7? Organic Molecules Name Monomers (subunits) List examples of: Monosaccharide Carbohydrates Disaccharide Polysaccharide Neutral Fats Lipids Phospholipids Steroids Eicosanoids biological function Name Monomers (subunits) List examples of: Fibrous Proteins Globular DNA Nucleic acids RNA biological function