Fundamentals of Chemistry: Atoms to Proteins Journey

1. Chapter 2The Chemistry of Life

2. Warm-Up Look at the following words. Place each one in the table below and define if you think you can. atom proton neutron electron nucleus element compound

3. 2-1 The Nature of Matter A. Atom – The basic unit of matter 1. 3 types of subatomic particles in an atom • a. proton (+ charge) • b. neutron (no charge) • c. electron (- charge) • Protons and neutrons are in the NUCLEUS • Electrons are in constant motion around the nucleus. ---Atoms have a neutral charge!--

4. B. Elements and Isotopes 1. Element - is a pure substance that consists entirely of one type of atom. a. Atomic number- number of protons in an atom (C- Carbon 6) An atom has the same number of protons and electrons. 2. Isotopes – Atoms of the same element that differ in the number of neutrons. a. Mass number- sum of protons and neutrons b. Isotopes are named by their mass number

5. 3. Radioactive Isotopes a. Geologists determine age of rocks b. Radiation for cancer c. Used as tracers to follow substances in organisms • Chemical Compounds 1. A compound is a combination of two or more elements in definite proportions 2. Use chemical formula

6. D. Chemical Bonds 1. Ionic – valence electrons are transferred (ex: NaCl) 2. Covalent – valence electrons are shared (ex: H20) 3.Van der Waals Forces – When molecules are close together they can develop a slight attraction to the oppositely charged regions of nearby molecules

7. Warm-up • Draw a pH scale. Then place the following substances on the scale in the appropriate location according to their pH values. • Dr. Pepper • Fantastik cleaner • Water Answer: 0 7 14 Dr.P water Fantastik

8. 2-2 Properties of Water A. Characteristics of Water - It is the single most abundant compound in most living things - A water molecule is neutral 1. Polarity – the oxygen end of the molecule has a slight neg (-) charge and the hydrogen end has a slight pos(+) charge. There is an uneven distribution of e- between O and H

9. 2. Hydrogen Bonds - attraction between the partial positive and the negative charges of atoms. These bonds are not as strong as ionic or covalent bonds. (EX: Water) a. Cohesion – attraction between molecules of the same substance b. Adhesion - attraction between molecules of different substances.

10. B. Solutions and Suspensions 1. Mixture – material composed of two or more mixed compounds that are physically mixed together but not chemically combined. a. Solutions – all components are evenly distributed (ex: salt water) 1. solute – what is being dissolved 2. solvent – substance in which the solute dissolves b. Suspensions – mixture with non-dissolved particles (ex: blood)

11. Questions • 1. How do you know whether a sample is a mixture(physical) or a compound (chemical)? • Answer: a mixture can easily be separated into the component parts • 2. Are solutions only in the liquid state? • Answer: No, solutions can be solids, liquids, or gases

12. C. Acids and Bases 1. pH Scale – indicates the number of H+ ions in a solution. (Ranges from 1-14) 2. Acids – Contain a higher concentration of H+ ions than pure water and pH values below 7 3. Bases – Contain a lower concentration of H+ ions than pure water and pH values above 7. They also produce OH- 4. Buffers – weak acids or bases that can react with strong acids or bases to prevent sharp, sudden changes in pH

13. Chapter 2-3 Carbon Compounds What is a Valence Electron? What is an Organic Compound? A. Carbon 1. 4 Valence Electrons • Ability to bond with other elements and itself – millions of structures • Compounds containing carbon are considered ORGANIC

14. B. Macromolecules – “giant molecules” 1. Connecting monomers to make polymers 2. 4 groups of macromolecules a. Carbohydrates • carbon, hydrogen, oxygen – 1:2:1 ratio • main source of energy for organisms • starch – storage molecule • monosaccharides (ex. Glucose) and polysaccharides (glycogen and cellulose)

15. b. Lipids • not soluble in water • fats, oils, and waxes • glycerol + fatty acid • saturated (max # of H bonds) and unsaturated (at least one double bond=) c. Nucleic acids • H, O, N, C, P • Polymers of nucleotides – sugar, phosphate, and nitrogen base • Store and transmit hereditary or genetic information • RNA and DNA

16. d. Proteins • N, C, H, O • Polymers of amino acids • Amino group- NH2 and a carboxyl group – COOH • Proteins control rate of cell reaction(rxn), regulate cell processes, form bones and muscles, transport into and out of cells, and some fight diseases

17. 4 levels of organization of proteins Primary- sequence of amino acids in a protein chain Secondary- amino acid within a chain is twisted or folded Tertiary- the chain itself is folded Quaternary- if a protein has more than one chain

18. Protein Structure

19. Chapter 2-4 Chemical Reactions and Enzymes A. Chemical Reactions – process that changes one set of chemicals into another set of chemicals 1. reactants → products 2. breaking of bonds in reactants and forming new bonds in products

20. B. Energy in Reactions – released or absorbed 1. RXNS (reactions) that release energy are spontaneous – produce heat light and sound 2. RXNS that absorb energy must have a source of energy – plants (sunlight) and animals (food) 3. Activation Energy – energy needed to get reaction started

21. Catalyzed vs. UncatalyzedReaction

22. C. Enzymes – (Proteins) 1. Are biological catalysts 2. Catalyst – speed up RXN by lowering activation energy 3. Very specific – only one reaction

23. D. Enzyme Action 1. Enzyme-Substrate Complex a. substrates – reactants of enzyme-catalyzed reactions • active site – where substrates bind to enzyme (lock and key) • Catalase. It catalyzes the decomposition of hydrogen peroxide into water and oxygen. • 2H2O2 -> 2H2O + O2 • One molecule of catalase can break 40 million molecules of hydrogen peroxide each second

24. Competitive Inhibition Competitive inhibition The necessity for a close, if brief, fit between enzyme and substrate explains the phenomenon of competitive inhibition. One of the enzymes needed for the release of energy within the cell is succinic dehydrogenase. It catalyzes the oxidation (by the removal of two hydrogen atoms) of succinic acid (a). If one adds malonic acid to cells, or to a test tube mixture of succinic acid and the enzyme, the action of the enzyme is strongly inhibited. This is because the structure of malonic acid allows it to bind to the same site on the enzyme (b). But there is no oxidation so no speedy release of products. The inhibition is called competitive because if you increase the ratio of succinic to malonic acid in the mixture, you will gradually restore the rate of catalysis. At a 50:1 ratio, the two molecules compete on roughly equal terms for the binding (=catalytic) site on the enzyme.

25. 2. Regulation of Enzyme Activity a. pH values b. temperature c. cells regulate - proteins turn enzymes “on” or “off”

26. Feedback Inhibition • If the product of a series of enzymatic reactions, e.g., an amino acid, begins to accumulate within the cell, it may specifically inhibit the action of the first enzyme involved in its synthesis (red bar). Thus further production of the enzyme is halted.