1. UNIT 2: BIOCHEMISTRY Standards BIO.2 a-c

2. Biochemistry Vocabulary 1. Atom 2. Element 3. Compound 4. Ion 5. Ionic bond 6. Covalent bond 7. Molecule 8. Hydrogen bond 9. Polar 10. Cohesion 11. Adhesion 12. Acid 13. Base 14. pH 15. Buffer 16. Macromolecule 17. Monomer 18. Polymer 19. Dehydration Synthesis 20. Hydrolysis 21. Carbohydrate 22. Monosaccharide 23. Lipid 24. Fatty Acid 25. Protein 26. Amino Acid 27. Nucleotide 28. Nucleic Acid 29. Enzyme 30. Catalyst 31. Activation Energy 32. Active Site 33. Substrate 34. Denature

3. Photosynthesis + Cellular Respiration Vocabulary ATP Autotroph Chloroplasts Heterotroph Photosynthesis

4. ATOMS, IONS, AND MOLECULES Standard BIO. 2a

5. Everything is composed of matter The ‘stuff’ of life An atom is the smallest basic unit of matter; nonliving 3 subatomic particles: Proton Neutron Electron Element: one particular type of atom and it cannot be broken down into a simpler substance by ordinary chemical means The Periodic Table lists all known elements.

7. The Periodic Table Elements are arranged by increasing atomic number (# of protons) Rows are called periods Indicate number of energy levels Columns are called groups or families Indicate number of outermost electrons  Valence Electrons Valence electrons are involved in bonding two or more atoms together

8. Atoms Overall neutral charge Protons  Positive Neutrons  Neutral Electrons  Negative Protons and neutrons are held together in the nucleus of the atom Electrons stay in constant motion in paths around the nucleus

9. Calculating Protons, Neutrons, and Electrons Atomic Number = # of protons and electrons This number will NEVER change! Atomic Mass = # of protons + neutrons

10. Practice! Using your periodic tables fill in the following table ElementProtonsNeutronsElectrons Oxygen Nitrogen Lead Iron Hydrogen

11. Answers ElementProtonsNeutronsElectrons Oxygen888 Nitrogen777 Lead8212582 Iron263026 Hydrogen101

12. Ions Ions form when atoms gain or lose electrons *Electrons are negative* When an atom gains an electron it becomes negative O -2 Oxygen has gained 2 electrons When an atom loses an electron it becomes positive H + Hydrogen has lost 1 electron The number of protons remains the same the only thing that changes are the number of electrons

13. Practice! ElementProtonsNeutronsElectrons Cl - Fe +3 O -2 Na +

14. Answers ElementProtonNeutronElectron Cl -1718 Fe +3263023 O -28810 Na +111210

15. Isotopes Isotopes: atoms of the same element with different numbers of neutrons Ex. Carbon-14 Radioactive isotopes have unstable nuclei that break down

16. Compounds A compound is a substance made of atoms of different elements bonded together in a certain ratio. H 2 O (water) CO 2 (carbon dioxide) C 6 H 12 O 6 (glucose) A compounds properties differ from the individual properties of the elements that make it up

17. Bonding Ionic Bond: when two oppositely charged ions are joined NaCl, (Na+ --- Cl -) Molecule: two or more atoms held together by covalent bonds. Covalent Bond: when atoms share a pair of electrons Nonpolar: equal sharing of electrons within a molecule CH 4 Polar: unequal sharing of electrons within a molecule H 2 O

18. WATER CHEMISTRY Standard BIO. 2a

19. Your cells and body are mostly water. Blood is about 95% water Water gives cells their structure and allows them to transport materials within the organism. ALL of the processes necessary for life take place in a watery environment.

20. Structure of Water Water molecules are polar; this means there is an unequal sharing of electrons resulting in the oxygen atom being slightly negative while the hydrogen atoms are slightly positive. This polarity makes water a ‘Universal’ Solvent

21. Hydrogen Bonds A hydrogen bond is an attraction between the slightly positive hydrogen atom and the slightly negative oxygen atom of different water molecules. Hydrogen bonds in water are strong and a large amount of energy is needed to break them.

22. Properties of Water Hydrogen bonds give water its unique properties. High Specific Heat: water resists change in temperature; water must absorb a lot of heat in order for the temperature to change. Cohesion: water molecules have a tendency to stick to each other; beads of water and surface tension Adhesion: water molecules have tendency to stick to other things; transport water from roots to leaves though plants  Ice is less dense than liquid water

23. Solutions Many compounds dissolve in water, when one substance dissolves in another a solution forms. Solvent: dissolves solute; greater amount Solute: substance that dissolves Concentration: amount of solute dissolved in a certain amount of solvent Polar molecules and ionic compounds dissolve in water Nonpolar substances do not dissolve in water Vitamin E (fat), oil, butter

24. PH Standard BIO. 2 a

25. Quick Review What happens when an atom gains or loses an electron? It becomes charged and is known as an ion When an atom gains an electron it becomes negatively charged When an atom loses an electron it becomes positively charged

26. Acids, Bases and PH Some compounds break into ions when dissolved in water. Acids release a proton, or hydrogen ions (H+) when dissolved in water. Bases remove H+ ions from a solution; increase the number of OH- (hydroxide ions) in a solution

27. Characteristics of Acids and Bases Acids Taste Sour Corrosive to Metal Have a pH < 7 Cause Litmus Paper to Turn Red Bases Taste Bitter Feel Slippery Have a pH > 7 Cause Litmus Paper to Turn Blue

28. What are some common examples of acids? Of bases? Acids Vinegar Lemon Juice HCl – Hydrochloric Acid Bases Blood Bleach NaOH – Sodium Hydroxide

29. The pH Scale pH measures the H+ ion concentration in a solution. The higher the concentration of H+ ions there are the more acidic that substance is, and the lower the pH is. pH < 7 acidic pH = 7 neutral pH > 7 basic

30. Buffers Substances that minimize changes in concentrations of acids and bases to help maintain a stable pH Accepts and donates H+ ions depending on what a solution needs Helps organisms maintain HOMEOSTASIS Our bodies have buffers in our blood system to help maintain our body’s pH

31. MACROMOLECULES Carbon based molecules. Standard BIO. 2b

32. What Can You Tell From This Pie Chart? The human body is composed mostly of Oxygen and Carbon Living things are mostly composed of only a few elements: Carbon Hydrogen Nitrogen Oxygen Phosphorus Sulfur The most important being Carbon

33. Carbon: The Building Block of Life All living things, or once living things, contain carbon. To be living and considered organic, an organism must contain carbon, hydrogen, and oxygen. Carbon only has 4 valence electrons so, carbon wants to make 4 bonds.

34. Carbon Chains and Rings Carbon can make rings, single/double/triple covalent bonds Carbon usually combines with other carbon atoms, oxygen, or hydrogen

35. Macromolecules “ Giant Molecules” made from hundreds or even thousands of smaller monomers linked together. Macromolecules include 4 groups: Carbohydrates Lipids Proteins Nucleic Acids Polymerization: linking several monomers together creating a polymer

36. Dehydration Synthesis When water is removed to join two molecules. Uses Energy; creates polymers

37. Hydrolysis Adding water to break a polymer apart Releases energy; creates monomers

38. CARBOHYDRATES

39. Carbohydrates Molecules made up of carbon, hydrogen, and oxygen atoms usually arranged in a 1 : 2 : 1 ratio. Example: Glucose C 6 H 12 O 6 Monomer: Glucose Function: Main source of energy for living things. The breakdown of sugars, such as glucose, supplies immediate energy for all cell activities.

40. Examples of Carbohydrates Carbohydrates are commonly known as sugars and starches Simple sugars (individual sugars) are known as monosaccharides Glucose Galactose Fructose Monosaccharides can be linked together to create disaccharides (two sugars) and polysaccharides (many sugars

42. Examples of Polysaccharides Starch: energy storage in plants; potatoes, wheat, corn, rice Glycogen: energy storage in animals; liver and muscle cells Cellulose: tough outer coating of plant cell walls; celery fibers

43. LIPIDS

44. Nonpolar molecules that include fats, oils, phospholipids and cholesterols Usually long chains of carbon bonded to oxygen and hydrogen Monomer: No true monomer Function: Store large amounts of energy Part of the cell membrane Insulation Protection

45. Fats and Oils Called triglycerides Consist of 1 glycerol molecule bonded to 3 fatty acids (chains of hydrocarbons) Saturated: saturated with hydrogen Butter Unsaturated: double bond; cannot form a solid Olive Oil

46. Phospholipids Made up of 2 fatty acids and 1 glycerol plus a phosphate (hydrophilic) Arrange themselves into bilayers to create cell membranes

47. Cholesterol Ring structure Part of cell membranes Used to make steroid hormones Regulate stress Testosterone Estrogen

48. PROTEINS

49. Proteins A molecule containing carbon, hydrogen, oxygen, nitrogen, and sometimes sulfur Monomer: amino acids Amino acids are joined together by peptide bonds; polypeptides 20 different amino acids; organisms naturally produce 12 Function: Speeding up chemical reactions Structural support Storage Transport Communication Movement Defense Examples: Enzymes Keratin (hair) Collagen (skin) Albumin (egg)

50. Amino Acid Structure Amino Acids are composed of an amino group, a carboxyl group, a H atom and a variable group (R) Specific sequence of amino acids determine the type of protein

51. Protein Function Protein function depends entirely on the shape of the protein. Even a slight change in shape can affect a proteins function or render it useless Protein formation depends on pH, salt concentration, temperature, etc. and an imbalance in any of these may cause the protein to denature. When a protein denatures it basically unravels (loses its shape) and cannot do its job anymore.

52. NUCLEIC ACIDS

53. Molecules that are composed of the elements carbon, hydrogen, oxygen, nitrogen, and phosphorus Monomer: nucleotide Function: store and transmit genetic information and energy Examples: DNA RNA ATP

54. Nucleotides A nucleotide is composed of a sugar, a phosphate group, and nitrogen-containing molecule called a base

55. DNA, RNA, and Proteins DNA directs the cell but can’t actually carry out its directions DNA makes RNA to help direct a cell’s activities The RNA makes proteins to actually do the work necessary to keep the cell alive

56. ATP The main energy molecule for organisms Holds energy in the bond between the second and third phosphate

57. Macromolecule Table PolymerElements Present MonomerFunctionExample CARB LIPID PROTEIN NUCLEIC ACID

58. ENZYMES Standard BIO. 2 c

59. Chemical Reactions Chemical reactions change substances into different substances by breaking and forming chemical bonds C 6 H 12 O 6 + 6O 2  6CO 2 + 6H 2 O + Energy Reactants: substances changed during a chemical rxn (left) Products: substances made by a chemical reaction (right)

60. Types of Chemical Reactions Endothermic Absorbs more energy than it releases 6CO 2 + 6H 2 O + Energy  C 6 H 12 O 6 + 6O 2 (Energy is on the left) Exothermic Releases more energy than it absorbs C 6 H 12 O 6 + 6O 2  6CO 2 + 6H 2 O + Energy (Energy is on the right)

61. Activation Energy The amount of energy that needs to be absorbed for a chemical reaction to start. Activation Energy

62. Catalysts Lowers activation energy and as a result, increases the rate of the chemical reaction Without Catalyst With Catalyst

63. Enzymes Enzymes are catalysts for chemical reactions in living things. Usually reactions in living things need to take place very quickly Enzymes are very specific, they only catalyze one type of reaction Enzymes are proteins Can be denatured due to unfavorable conditions Work best in small temperature ranges around the organisms normal body temperature and neutral pH’s End in -ase

65. Lock and Key Model Enzyme’s unique shape allows only certain reactants to bind to the enzyme Substrate: reactant in a chemical rxn upon which an enzyme acts Example: amylase only breaks down starch, therefore, starch is the substrate for amylase Substrates bind to enzymes at their active sites The enzyme ‘bends’ around the substrate and starts to weaken the bonds within the substrate New products are released and the enzyme is left to catalyze another reaction

66. Lock and Key Model After the bonds in the substrate are weakened, new products form

67. Altering Enzymes Inhibitors: naturally occurring or synthetic molecules that decrease enzyme activity Competitive: binds to the enzyme at the active site preventing the substrate from binding Non-Competitive: binds to the enzyme changing it’s shape thus altering the active site, so that the substrate can no longer interact with the enzyme Activators: increase enzyme activity