1. Unit 2 (Biochemistry) Notes, Part 1: Atomic And Molecular Structure

2. Element
A pure substance that is composed of only one type of atom; There are 92 natural elements
Ex: Sodium (Na), Chlorine (Cl), Hydrogen (H), Lead (Pb)

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Atoms
Basic unit of matter; smallest particle of
element with all properties of that element
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Placed side by side, 100 million atoms would make a row only about 1 centimeter long.
Atoms contain subatomic particles that are even smaller.
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The subatomic particles that make up atoms are
protons
neutrons
electrons
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Protons (+): positively charged particles in the nucleus
Neutrons (0): neutral particles (no charge) in the nucleus
Electrons (-): negatively charged particles outside the nucleus
Helium atoms contain protons, neutrons, and electrons. The positively charged protons and uncharged neutrons are bound together in the dense nucleus, while the negatively charged electrons move in the space around the nucleus.
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7. Isotopes
atom of same element w/ different number of neutrons (e.g., carbon-12, carbon-13, carbon-14)

8. Protons + Neutrons = Atomic Mass
Drawing An Atom
1) All the mass of an atom is in the center or nucleus.
2) The mass of an atom can be calculated by adding the number of protons and the number neutrons.
Ex: 6 C
12 (Atomic Mass)
Protons + Neutrons = Atomic Mass

9. Atomic Number = The # of Protons
Where can I find the number of protons?
Ex: 6 (atomic number) C 12
Atomic Number = The # of Protons

10. Atomic Mass – Atomic Number = The # of Neutrons
How do I find the number of neutrons?
Ex: 6 C 12
12 – 6 = 6 Neutrons
Atomic Mass – Atomic Number = The # of Neutrons

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Chemical Compounds
A chemical compound is a substance formed by the chemical combination of two or more elements in definite proportions.
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12. Examples of Chemical Compounds
Water H2O
Table salt NaCl
Carbon dioxide CO2
Sugar C6H12O6

13. Characteristics of Compounds
Always formed from a specific combination of elements
2. Always formed in a fixed ratio
Ex: H3O does not = water
Ex: CO4 does not = carbon dioxide

14. Characteristics of Compounds
Compounds are chemically and physically different from the elements they are made from:
Ex: Water (H2O) has different properties than hydrogen (H) or oxygen (O)

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Chemical Bonds
The atoms in compounds are held together by chemical bonds.
The electrons that are available to form bonds are called valence electrons.
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The main types of chemical bonds are:
Ionic bonds
Covalent bonds
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Ionic Bonds
force of attraction between oppositely charged ions (atoms that gain or lose electrons); electrons are transferred (e.g., NaCl)
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The chemical bond in which electrons are transferred from one atom to another is called an ionic bond. The compound sodium chloride forms when sodium loses its valence electron to chlorine.
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Covalent Bonds
chemical bond formed when 2 atoms combine by
sharing electrons (e.g., H2O)
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The structure that results when atoms are joined together by covalent bonds is called a molecule.
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One more bond type…Van der Waals Forces
When molecules are close together, a slight attraction can develop between the oppositely charged regions of nearby molecules.
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23. Unit 2 (Biochemistry) Notes, Part 2: Properties of Water

24. Why do we study water properties in biology class?
About 2/3 of the mass of a cell is water!
Most life-sustaining reactions occur in water solutions

25. Water Molecule
2 atoms of hydrogen linked by covalent bonds to 1 atom oxygen (H2O)
Polar Molecule: has positive hydrogen end and negative oxygen end

26. Water is Polar
Polarity: The electrons are unevenly distributed between the Oxygen and the two Hydrogen atoms.
Oxygen has 8 protons. Each hydrogen has 1.

27. Water is Polar
The atom with more protons (Oxygen) pulls electrons away from the atom(s)
A diagram of what’s happening:

28. Water forms Hydrogen Bonds
Hydrogen Bonds: Form due to attraction between water molecules.
Not as strong as ionic/covalent bonds

29. Water forms Hydrogen Bonds
Water can form up to 4 hydrogen bonds at once
A diagram of what’s going on:

30. Water is Cohesive
Cohesion: Water molecules are drawn tightly together (on the surface of a lake or a pond, this forms a film, which is called surface tension)
Explains why:
Water beads on a surface (like the lab table)
Insects can walk on water

31. A Cool Example of Cohesion / Surface Tension: Water Strider Insect

32. Water is Adhesive =
Adhesion = Water adheres (sticks) to different surfaces
Ex: Measuring water in a graduated cylinder
Water adheres (sticks) to the glass more than it adheres to itself.
That’s why there is a dip in the water when you read the volume

33. Cohesion Adhesion
Ex: Water Bubble
Ex: Water and Paper Towels

34. Water can undergo Capillary Action
Capillary Action= Water can flow up a tube, against gravity
Ex: Plants absorbing water through their roots

35. Water is an Excellent Solvent
Water often found as part of a mixture called a solution
Solution: one substance (solute) dissolves into another (solvent); water is called the “universal solvent”
Why is this important in humans?
Salt (NaCl) in Water

36. Water Has a Neutral pH
pH: measure of how acidic or basic a solution is
scale is 0 to 14
If pH = 7, then substance is neutral (not acid or base)

37. Water Has a Neutral pH
acid: forms hydrogen ions (H) in water; pH is less than 7
base: forms hydroxide ions (OH) in water; pH is greater than 7

38. Acid / Base Reactions
pH level determines rate & types of reactions that can take place
buffer: weak acid or base that can react with a strong acid or base to prevent sudden changes in pH
Buffers help maintain a constant pH.  A change in pH in living cells could denature proteins, DNA and other important molecules resulting in the death of the cells.

39. Water is less dense in its solid form
Water is less dense in its solid form than it is in its liquid form (Ice floats!)
Why might it be a bad thing for ice to sink in a pond?

40. What does ice look like at the molecular level?

42. Water has a High Heat Capacity
Water absorbs a lot of heat from the air without having a large temperature change
So…lakes and oceans often stabilize air temperatures
Water absorbs heat when it evaporates; this is why sweating helps us cool down!

43. So why does it take so much heat to increase the temperature of water?!
You have to break the hydrogen bonds between water molecules first!

45. Unit 2 (Biochemistry) Notes, Part 3: Macromolecules

46. What elements are most common in our cells?
Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus, and Sulfur.
Remember CHNOPS!

47. What have we already talked about?
Water…which elements are found in water?

48. A carbon atom can form four covalent bonds with other atoms
Carbon Compounds
A carbon atom can form four covalent bonds with other atoms

49. Carbon Compounds
Organic chemistry is the study of all compounds that contain bonds between carbon atoms.
Lipids (Fats)
Nucleic Acids (DNA)
Carbohydrates
Proteins

50. Carbon Compounds
macromolecules: large molecules formed by process called polymerization
polymer: forms when many smaller molecules (called monomers) bond together, usually in long chains

52. Building and Breaking Down Molecules
1) Dehydration/Condensation Reaction: monomers are joined to form a polymer; molecules of water are released

53. 2) Hydrolysis: a polymer is broken into monomers when water molecules are added

54. Macromolecules in Living Things
4 Types
1) Carbohydrates
2) Lipids
3) Nucleic Acids
4) Proteins

55. 1) Carbohydrates
Functions: source of energy; also used to maintain plant structure
Made of: Carbon, Hydrogen, Oxygen (1 C: 2H: 1O)
Glucose

56. 1. Carbohydrates (Sugars)
monosaccharide: carbohydrate monomer, simple sugars
Example: glucose and fructose
disaccharide: 2 monosaccharides form 2-sugar carbohydrate
Example: sucrose

57. 1. Carbohydrates
polysaccharide: carbohydrate polymer (forms when sugars join together in a long chain)
Examples:
1) starch: used as food storage by plants
2) glycogen: form in which animals store food
3) cellulose: cell walls in plants

59. 2. Lipids (Fats) Made of: Carbon and Hydrogen (with a few Oxygens)
Functions: long-term energy storage, insulation, protective coatings (Some lipids are important parts of biological membranes and waterproof coverings.)
Examples: fats, oils, and waxes - insoluble in water
Steroids are also lipids. Many steroids serve as chemical messengers.

60. 2. Lipids
Structure: Usually 3 fatty acids (carbon-hydrogen chains) bonded to 1 glycerol molecule

61. Saturated Fat (Butter)
2. Lipids
Saturated vs. Unsaturated Fat…which is “worse” for you and why?
Saturated Fat (Butter)
Unsaturated Fat (Oil)

62. 3. Nucleic Acids Made of: C, H, O, N, and P
Functions: store & transmit information in cells in form of a code
Nucleotide: monomer of a nucleic acid ; 3 parts (nitrogen base, 5 carbon sugar, and phosphate group)
DNA or RNA: polymers made by linking nucleotides in a chain

63. 3. Nucleic Acids
Nucleotide
DNA

64. 3. Nucleic Acids
DNA : deoxyribonucleic acid; master copy of organism's genetic code
RNA: ribonucleic acid; forms copy of DNA; used to make proteins (protein synthesis)

65. 4. Proteins Made of: C,H,N,O and sometimes S Functions:
1) Structure (hair, nails)
2) Transport (hemoglobin in blood)
3) Movement (muscle fibers)
4) Defense (antibodies)
5) Regulating Cell Functions (hormones and enzymes)

66. 4. Proteins
Amino Acids : Monomers of proteins; 20 common amino acids ; Consists of a central Carbon atom bonded to 4 groups
4 Groups
1) Hydrogen Atom
2) Amino Group
3) Carboxyl Group
4) R group (changes in each Amino Acid!)

67. 4. Proteins Polypeptide: polymer; one chain of amino acids
Proteins: several polypeptides folded into complex structures.

68. 4. Proteins Four Levels of Protein Structure 1) Primary 2) Secondary
3) Tertiary
4) Quaternary
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69. Unit 2 (Biochemistry) Notes, Part 4: Enzymes

70. Why do we study chemical reactions in biology?
Chemistry isn’t just what life is made of, chemistry is also what life does
Everything that happens in an organism is based on chemical reactions (growth, response to environment, etc.)

71. Chemical Reaction A process that changes reactants into products.
Slow Reactions vs. Fast Reactions

72. Chemical reactions  breaking bonds in reactants and forming bonds in products

73. Energy Changes Some reactions release energy and some absorb energy
Activation Energy: the energy required to start a reaction

74. Speeding up Reactions
Slow reactions or reactions with high activation energies need a catalyst
Catalyst = any substance that lowers the activation energy of a reaction to “speed it up”
Enzymes are catalysts that are protein molecules.

76. Enzymes
Enzymes provide a site where reactants can be brought together to react.
In an enzyme-catalyzed reaction, the reactants are called substrates.
Each enzyme has a specific shape and a specific portion called the active site, where substrates bind.

77. The substrates must fit exactly into the active site
The substrates must fit exactly into the active site. This is called the lock and key model.
Once the reaction is complete, the enzyme releases the products of the reaction.
Enzymes can join or break substrates into products.

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Breaking 1 Substrate into 2 Products
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79. Joining 2 Substrates into 1 Product

80. Enzymes can break or join substrates into products.
Enzymes work best at a certain pH and temperature.
Roles of Enzymes:
1) regulating chemical pathways
2) making materials
3) releasing energy
4) transferring info