Chemistry of Life

1. Chemistry of Life Green = IMPORTANT NOTES

2. How much do you already know?

3. Let’s start small • Matter: any physical substance that has mass and takes up space • Atom: the basic unit of matter • From the Greek word atomos – unable to be cut • Protons (+) and Neutrons (n) are found in the nucleus in equal amounts • Electrons (-) are in constant motion in the space around the nucleus

4. Element: a pure substance that consists of entirely one type of atom Atomic Number: # of protons Element symbol Atomic Mass: # of protons + # of neutrons Element name

5. Periodic Table of Elements Arranged from left to right by increasing atomic number Colors indicate similar atomic properties

6. Elements Important to Life

7. Isotopes • An isotope is a variation of chemical element due to a different number of neutrons. • Identify isotopes by the atomic mass • Since the number of electrons remains the same the chemical properties remain the same • Radioactive isotopes have an unstable nuclei and will eventually break down • Used to date fossils, trace atoms through metabolism, diagnosis cancer, etc…

8. Electron Energy Levels • Valence Electrons are the outer electrons that can participate in chemical bonding

9. Octet Rule • Atoms tend to gain, lose, or share one or more of their valence electrons to achieve a filled outer electron shell • Trying to achieve stability like the Noble Gases

10. Compounds • A compound is composed of 2 or more elements • Physical and chemical properties are usually very different from the original individual elements • This is achieved by chemical bonds • Ionic Bonds • Covalent Bonds • Van der Waals Forces • Hydrogen Bonds (We will get to this later with Water)

11. Ionic Bonds 1 valence electrons 7 valence electrons • 1 or more electrons transferred from 1 atom to another • Ions: an atom or molecule that has gained or lost one or more of its valence electrons. • Gain electron = NEGATIVE • Lose electron = POSITIVE • Resulting ions have a strong attraction for one another

12. Covalent Bonds 1 valence electrons 1 valence electrons • Electrons are shared by 2 atoms. • The electron travels between the 2 nuclei

13. Lewis Dot Model Ionic Bonds Covalent Bonds Valence Electrons are represented by dots around the symbol

14. Van Der Waals Forces • Intermolecular forces that are not ionic or covalent • Weak attraction between atoms, molecules, and surfaces

15. Metabolism • Metabolism: the sum of all chemical reactions within a living organism • Anabolism: chemical reaction in which simple substances are combined to form a more complex substance • Need energy = Endergonic • Catabolism: chemical reaction in which complex substances are broken down into more simple substances • Release energy = Exergonic

16. Chemical Reactions Example of Anabolism: • Dehydration Synthesis: monomers of organic compounds bind together through a chemical reaction to form a polymer (with water as a product of the reaction) Monomer + Monomer  Polymer +Water Example of Catabolism: • Hydrolysis: The reverse of the dehydration reaction

17. Chemical Reactions • A chemical reaction is a process that changes or transforms a set of chemicals into another CH3COOH + NaHCO3CO2 + H20 + CH3COONa Acetic Acid + Sodium Bicarbonate  Carbon dioxide + water + sodium acetate Reactants Products • Chemical reactions involve changes in chemical bonds that join atoms and compounds

18. Energy Transformations • Energy is released or absorbed whenever a chemical bond is broken or formed • Exergonic: releases energy – typically spontaneous • Endergonic: absorbs energy – requires a source of E • Living organisms obtain their energy from raw materials such as the sun or other living organisms

19. Activation Energy: Energy required to get a reaction started Exergonic Higher Energy Lower Energy Even though this is an energy releasing reaction, a small amount of activation energy is still needed to get this reaction started

20. Endergonic Higher Energy Lower Energy A larger amount of activation energy is needed in this reaction in order to achieve a higher energy state of the products

21. Enzymes • Chemical reactions that are too slow or have a high activation energy need a helping hand • Catalysts: substances that speed up the rate of a chemical reaction • Enzymes are proteins that act as biological catalysts • They speed up reactions that take place inside cells

22. Enzymes • How do they do this? • Catalysts lower the activation energy of a reaction allowing the reaction to occur quicker and with less energy • Enzymes are very specific and generally only catalyze one reaction

23. Regular Reaction Reaction with Catalyst The activation energy for the reaction with the catalyst is much smaller than the original activation energy

24. Enzyme-Substrate Complex • In order for a reaction to occur, reactants must collide together with enough energy to break and form bonds • Enzymes provide a site where the reactants can be brought together. • The reactants of an enzyme-catalyzed reaction are known as Substrates. • The site in which the substrate binds on the enzyme is called the ActiveSite. • The enzyme remains UNCHANGED after a reaction. This allows one enzyme to catalyze many reactions.

25. Enzyme-Substrate Complex

26. Enzyme-Substrate Complex Substrate Substrate Active Site Active Site Lock and Key Analogy

27. Organic Compounds • Organic compounds all contain carbon • Carbon has 4 valence electrons which allows it to bond with 4 other elements including itself • Compounds that make up Organic compounds: C, H, O, N, P, S • Or NHCOPS • There are 4 types of organic compounds: • Carbohydrates • Lipids • Proteins • Nucleic Acids

28. Macromolecules • Macromolecules “giant molecules” are made out of many small molecules • Polymerization: large compounds are built by joining smaller units together • Monomers “single” • Polymers “many parts”

29. Chemical Reactions • Dehydration Synthesis: monomers of organic compounds bind together through a chemical reaction to form a polymer (with water as a product of the reaction) Monomer + Monomer  Polymer +Water • The reverse of this reaction is called Hydrolysis

30. Carbohydrates • Compounds made of C, H, O • Usually a 1:2:1 ratio • 4 calories/gram • Living things use carbohydrates as a main source of energy and sometimes for structural purposes • Monomer: Monosaccharide “simple sugars” • Glucose: supplies immediate energy for cells • Fructose • Galactose • Polymer: Polysaccharide “complex sugars” • Glycogen: Animal storage • Starch: Plant storage • Cellulose: Plant structures

31. Carbohydrates Glucose Glycogen

32. Lipids • Compounds made of C,H, O • Not water soluble • Fats, oils, waxes, steroids • 9 calories/gram • Living things use lipids for stored energy sources, insulation, membrane structure, vitamin and mineral storage. • Composed of one glycerol molecule (alcohol) and 3 fatty acids

33. Lipids Triglyceride Molecule:1 glycerol + 3 Fatty Acids

34. Phospholipid Bilayer • Makes up almost all living organisms cell membranes • Barrier that prevents water soluble molecules from diffusing across • Composed of 2 layers of phospholipids • Phospholipids have a hydrophilic head and 2 hydrophobic tails

35. Lipids • Cholesterol: is a steroid produced by the liver • It is both fat soluble and water soluble • It is an essential component of the cell membrane • Also important in the manufacturing of other steroids, bile acids, and vitamin D

36. Lipids • Saturated fats: all single bonds with maximum number of Hydrogen • Solid at room temperature • Monounsaturated fats: 1 double bond • Polyunsaturated fats: more than one double bond • Both mono and polyunsaturated fats are liquid at room temperature

37. Fat gets a bad rap • In the 1950s biochemist Ancel Keys conducted “The Seven Countries Study” • This study demonstrated a strong positive correlation between amount of fat consumed and heart disease • Although these results were published, the results are actually inconclusive since Ancel Keys left a number of countries out of his study. • From Ancel Key’s Study, the Low Fat Diet/Heart Healthy Diet was born

38. Saturated Fats • Examples: • Lauric Acid: coconuts, breast milk • Palmitic Acid: animal products • Stearic Acid: meat and eggs • Benefits: improve memory, increase levels of “good cholesterol” • High levels of saturated fats in combination with a poor diet is not recommended, however you do not need to avoid saturated fats like the plague

39. Unsaturated Fats • Examples of Monounsaturated Fats: • Oleic Acid: olive oil, avocados, nuts • Benefits of Monounsaturated Fats: antioxidants, decrease “bad cholesterol” • Examples of Polyunsaturated Fats: • The most common types are Omega-3 and Omega-6 fatty acids • Essential fats: cannot make these in our body • A 1:1 ratio of Omega-3:Omega-6 is ideal - however, most of standard American diets do not have this ratio • Benefits of Polyunsaturated Fats: anti-inflammatory

40. Trans-fats • Trans fats are created when a polyunsaturated fat is transformed into a saturated fat • Hydrogen atoms are added to the molecule until it becomes a saturated fat. This process is called hydrogenation. • Examples: Margarine • Trans fats can lead to heart disease by increasing blood lipids

41. Proteins • Compounds made of C, H, O, N • 4 calories/gram • Living things use proteins for growth and repair, controls rates of chemical reactions (enzymes), cell membrane, transport, NOT an energy source • Monomers: Amino Acids • 20 different amino acids • Polymers: Polypeptides • Different structures of polypeptide chains • Sequence of amino acids is dictated by DNA

42. Amino Acid • Amine Group • Carboxyl Group • R group • Accounts for variability and diversity

43. Primary Structure: • Sequence of amino acids • Secondary Structure: • Alpha-helices • Beta-sheets • Held together by H-bonds • Tertiary Structure: • Secondary structure folded onto itself • Quaternary Structure: • 2 or more tertiary structures combined together.

44. Nucleic Acids • Compounds made up of C, H, O, N, P • NHCOPS • Nucleic Acids store and transmit heredity or genetic information (DNA and RNA) • Monomers: Nucleotides • Nucleotides composed of: a sugar, triphosphate, and a nitrogenous base • 5 nitrogenous bases: Adenine, Guanine, Thymine, Cytosine, Uracil • Polymers: DNA & RNA • DNA: deoxyribonucleic acid • RNA: ribonucleic acid

45. Nucleic Acids Nucleotide DNA

46. Water

47. Properties of Water • Water is a POLAR MOLECULE!!!! • In a covalent bond, electrons are not equally shared among atoms • This unequal sharing of electrons causes a slight positive and slight negative charge on the molecule

48. Properties of Water 2. Water is able to form many Hydrogen Bonds • Polar molecules can attract one another via the slight charges on the molecule. These are very weak bonds. • This gives water unique properties

49. Properties of Water • Water can be found in all 3 phases of matter: solid, liquid, gas • Water molecules expand when frozen causing it to be less dense than in the liquid state.

50. Properties of Water • Water is cohesive. • Cohesion is the attraction between molecules of the same substance • “Like attracts Like” • Water molecules “stick” to one another • This also creates surface tension