1. BASIC CHEMISTRY / BIOCHEMISTRY
Reference:
Chapter 2 of text
THE CHEMISTRY OF LIFE

2. BASIC CHEMISTRY

3. MEET THE ELEMENTS

4. ATOMIC THEORY OF MATTER (vocabulary)
Atoms = building blocks of matter that cannot be divided any further by ordinary chemical means
Molecule = two or more atoms combined that act as a single particle, the smallest particle that retains the properties
Elements = substances made of only one kind of atom

5. ATOMIC THEORY OF MATTER (vocabulary)
Compounds = two or more kinds of atoms in a substance in definite proportions
Isotopes = varieties in the normal number of neutrons on the nucleus
(The atomic number stays the same, the mass number changes)
Radioactivity = a nuclear process in which an atom is undergoing changes by emitting charged particles

6. A “Happy Atom” has all its orbital places filled.
STRUCTURE OF THE ATOM
particle charge mass location
proton (+) amu in nucleus
electron (-) in orbitals
neutron ( ) amu in nucleus
A “Happy Atom” has all its orbital places filled.
Atomic number = # of protons (also the number of electrons in a neutral atom)
Atomic mass or mass number = number of protons plus the number of neutrons in the nucleus.

7. ATOMIC ORBITALS (energy levels)
2 electrons orbit
nucleus
Level 2
8 electrons orbit
Level 3
8 electrons orbit
Remember: A “Happy Atom” has all its orbital places filled.

8. CHEMICAL BONDING
1. Chemical bond = force of attraction that holds atoms together
There are two kinds of bonds between atoms
Covalent Bonds = chemical bond that is formed by the sharing of electrons
Ionic Bonds = chemical bond that is formed by transfer of electrons

9. COVALENT BOND
HYDROGEN ATOM
HYDROGEN ATOM
OXYGEN ATOM
Covalent Bond = chemical bond that is formed by the sharing of electrons (covalent bonds form molecules)
Remember: A “Happy Atom” has all its orbital places filled.

10. IONIC BOND
Ionic bond = chemical bond that is formed by transfer of electrons
Remember: A “Happy Atom” has all its orbital places filled
Sodium (Na) has 1 electron in its outer energy level – is it happy?
Chlorine (Cl) has 7 electron in its outer energy level – is it happy?

11. IONIC BOND
Sodium and Chlorine ions are formed – What is an ion? 2. Ion = atom with an excess charge by the loss or gain of electrons
Sodium has lost one electron (one less (–) charge) so it now has a net charge of +1 Na Cl Na Cl
Chlorine has gained one electron (one more (–) charge) so it now has a net charge of -1
The (+) charge of Na is attracted to the (-) of the Cl and this attraction forms an ionic bond!

12. CHEMICAL FORMULAS
Each elements (symbol) and its proportions (subscripts) are represented information
All elements are listed in the periodic table
6 atoms of Carbon (C)
12 atoms of hydrogen (H)
6 atoms of oxygen (O)
For example C6H12O6 means:

13. CHEMICAL FORMULAS
Examples are:
H2O
CO2
C6H12O6
CH4

14. STRUCTURAL FORMULAS
4. A Structural formula shows the kinds and number of atoms as well as the chemical bonds
glucose H H C C H O
acetylene H
water
benzene

15. CHEMICAL EQUATIONS
5. Reactants = the original substances before a chemical reaction (left of the arrow)
6. Products = new substances formed after a chemical reaction (right of the arrow)

16. + 1 molecule of oxygen (O2)
7. Law of Conservation of Mass = mass can neither be created or destroyed (chemical reaction formulas must balance) +
2 molecules of hydrogen
(2H2)
molecule of oxygen (O2)
2 molecules of water
(2H2O)

17. Complete pages 6 and 7 in your packet

18. BIOCHEMISTRY The Chemical Compounds of Life

19. BIOLOGICALLY IMPORTANT COMPOUNDS
ORGANIC COMPOUNDS:
Species that naturally contain carbon and hydrogen (living organisms and their products)
Most also contain O (oxygen) and N (nitrogen)
Only a few elements are found in organic compounds
May also have P (phosphorous), S (sulfur), Fe (iron), Ca (calcium), Na (sodium), Cl (chlorine), Mg (magnesium), K (potassium)

20. BIOLOGICALLY IMPORTANT COMPOUNDS
INORGANIC COMPOUNDS:
DO NOT CONTAIN CARBON (with hydrogen)
May have carbonate compounds (CO2, CaCO, etc.) but not carbon with hydrogen.
Living organisms do contain inorganic compounds

21. IMPORTANT INORGANIC COMPOUNDS
WATER
The most important inorganic compound in living organisms
65% of the body
Many biological processes require water
SALTS
Help maintain water balance in the cells
Provide ions for many biological processes
ACIDS and BASES
Help maintain homeostasis

22. The Structure of Organic Compounds
Organic compounds are large and complex because of the carbon atom
Four vacancies for electrons allow 4 covalent bonds
Carbon has an atomic # of 6 which means it has 6 protons and 6 electrons
It has 4 vacancies in the outer energy level 2. 1.
6 + 3. 4.

23. CHEMICAL COMPOUNDS OF LIFE
Living organisms depend upon a variety of molecules for their survival. Some are used to build complex parts of an organism; some supply energy; while others provide instructions for the operation of the organism.
There are many organic compounds found in organisms, but they can be classified into 4 main types:
CARBOHYDRATES
LIPIDS
NUCLEIC ACIDS
PROTEINS

24. CARBOHYDRATES
Carbohydrates are compounds of C (carbon), H (hydrogen), and O (oxygen)
They have the same ratio H:O as in water (H2O) = 2:1 (twice as many H as O)
Monosaccharides = simple sugars = C6H12O6
ALWAYS END IN “OSE”
EX: MALTOSE, FRUCTOSE, GLUCOSE
RELEASE ENERGY WHEN BREAKING DOWN GLUCOSE INTO CO2 AND H2O
C6H12O CO H2O
MOST ORGANISMS USE GLUCOSE AS A SOURCE OF ENERGY

25. CARBOHYDRATES
THIS IS A MONOSACCHARIDE MOLECULE! THIS IS A SIMPLE SUGAR! THIS IS GLUCOSE! THIS IS C6H12O6 !

26. CARBOHYDRATES DISACCHARIDE = two simple sugars joined
POLYSACCHARIDE = several simple sugars joined
POLYMERS = long chains of repeating molecules
(many) (molecules)

27. CARBOHYDRATES Sugars stored in plants are called STARCH
Sugars stored in the liver of animals are called GLYCOGEN
Glycogen will be changed into glucose when the body needs it for energy!

28. CARBOHYDRATES BUILDING BLOCKS OF CARBOHYDRATES ARE
SIMPLE SUGARS OR MONOSACCHARIDES

29. LIPIDS (fats, oils, and waxes)
Made of carbon, oxygen, and hydrogen
(there is less oxygen in lipids than in carbohydrates)
Reserve energy supply in an organism
2 times as much energy as carbohydrates
Plants store oils in seeds
Mammals store fats under the skin
Waxes are formed from fatty acids and substances similar to glycerol
Fats and oils are formed from fatty acids and glycerol

30. LIPIDS (fats, oils, and waxes)
BUILDING BLOCKS of LIPIDS (fats and oils) ARE
1 GLYCEROL + 3 FATTY ACIDS

31. The Structure of a Fatty Acid
Lipid molecule
The Fatty Acid has 2 parts:
Chain of carbon atoms with hydrogen atoms bonded
(hydrocarbon chain)
Carboxyl group

32. SATURATED vs UNSATURATED FATTY ACIDS
Fats that have all single carbon-to-carbon bonds
Tend to be solids at room temperature (ie. butter)
Tend to increase the amount of cholesterol in the body
Cause deposits that lead to hardening and narrowing of arteries

33. SATURATED vs UNSATURATED FATTY ACIDS
UNSATURATED FATS
Fats that have a double or triple carbon-to-carbon bond
Tend to be oils at room temperature
Tend to decrease blood cholesterol
Polyunsaturated fats = a chain that has more than one double or triple bond

34. Complete the crossword puzzle on page 11 in your packet

35. NUCLEIC ACIDS
Compounds that contain phosphorus (P) and nitrogen (N)
Also carbon, hydrogen, and oxygen
Two types of Nucleic Acids:
DNA
RNA

36. NUCLEIC ACIDS (DNA) DNA = deoxyribonucleic acid
Found in the nucleus of the cell
Directs and controls heredity information and the development and activities of the cell

37. THE STRUCTURE OF DNA DNA is made of: Repeated chains of nucleotides
Nucleotides are made of:
5 carbon sugar (deoxyribose)
Phosphate group (PO4)
Nitrogenous base (A,T,C,G)

38. THE STRUCTURE OF DNA DNA
The DNA molecule is made of repeating chains of nucleotides
The sugar and phosphate groups are the sides of the ladder
Nitrogenous base pairs are the rungs of the ladder
The bases are adenine (A), thymine (T), cytosine (C), and guanine (G)
adenine (A) always pairs with thymine (T)
cytosine (C) always pairs with Guanine (G)

39. RNA RNA = ribonucleic acid RNA structure:
A single strand or chain of bases
The sugar is ribose
The base thymine is replaced with uracil
RNA is involved with protein synthesis

40. AMINO ACIDS ARE THE BUILDING BLOCKS OF PROTEINS
Compounds that contain nitrogen, carbon, hydrogen, and oxygen
Many contain sulfur and phosphorus
Great range of properties that give life complexity
20 different amino acids found in proteins
AMINO ACIDS ARE THE BUILDING BLOCKS OF PROTEINS

41. STRUCTURE OF AN AMINO ACID
One central carbon atom (C)
One carboxyl group (COOH)
One amino group (NH3)
One hydrogen atom (H)
One side chain (R)
GLYCINE is the simplest amino acid – the side chain is only one H atom

42. Examples of the different amino acids

43. PROTEIN VOCABULARY Dipeptide = two amino acids bonded together
The peptide bond = the bond between amino acids
Polypeptide = a long chain of amino acids

44. ORGANIC COMPOUND ATOMS BUILDING BLOCKS EXAMPLES USES
CARBOHYDRATES
C H O
H:O is 2:1
ex: C6H12O6
glucose
Monosaccharides
(simple sugars)
Disaccharides
(2 sugars)
Polysaccharides
(many sugars)
glucose, fructose, galactose
maltose, sucrose, lactose
starch, cellulose, glycogen, chitin
Quick energy
“ose” ending
carbon ring shape

45. ORGANIC COMPOUND ATOMS BUILDING BLOCKS EXAMPLES USES
CARBOHYDRATES
C H O
H:O is 2:1
ex: C6H12O6
glucose
Monosaccharides
(simple sugars)
Disaccharides
(2 sugars)
Polysaccharides
(many sugars)
glucose, fructose, galactose
maltose, sucrose, lactose
starch, cellulose, glycogen, chitin
Quick energy
“ose” ending
carbon ring shape
LIPIDS
H:O is › 2:1
ex: C20H24O3
1 glycerol
3 fatty acids
(hydrocarbon chain)
fats, oils, waxes
Stored energy
makes up cell membrane

46. ORGANIC COMPOUND ATOMS BUILDING BLOCKS EXAMPLES USES
CARBOHYDRATES
C H O
H:O is 2:1
ex: C6H12O6
glucose
Monosaccharides
(simple sugars)
Disaccharides
(2 sugars)
Polysaccharides
(many sugars)
glucose, fructose, galactose
maltose, sucrose, lactose
starch, cellulose, glycogen, chitin
Quick energy
“ose” ending
carbon ring shape
LIPIDS
H:O is › 2:1
ex: C20H24O3
1 glycerol
3 fatty acids
(hydrocarbon chain)
fats, oils, waxes
Stored energy
makes up cell membrane
PROTEINS
C H O N
20 amino acids
dipeptide (2)
polypeptide (many)
glycine, alanine
insulin, hemoglobin
Build and repair
ie: muscles hormones
enzymes

47. ORGANIC COMPOUND ATOMS BUILDING BLOCKS EXAMPLES USES
CARBOHYDRATES
C H O
H:O is 2:1
ex: C6H12O6
glucose
Monosaccharides
(simple sugars)
Disaccharides
(2 sugars)
Polysaccharides
(many sugars)
glucose, fructose, galactose
maltose, sucrose, lactose
starch, cellulose, glycogen, chitin
Quick energy
“ose” ending
carbon ring shape
LIPIDS
H:O is › 2:1
ex: C20H24O3
1 glycerol
3 fatty acids
(hydrocarbon chain)
fats, oils, waxes
Stored energy
makes up cell membrane
PROTEINS
C H O N
20 amino acids
dipeptide (2)
polypeptide (many)
glycine, alanine
insulin, hemoglobin
Build and repair
ie: muscles hormones
enzymes
NUCLEIC ACIDS
C H O P N
Nucleotides
(sugar, phosphate nitrogenous base)
DNA = deoxyribonucleic acid
RNA = ribonucleic acid
hereditary material
protein synthesis

48. Complete page 15 in your packet

49. DEHYDRATION SYNTHESIS
DEHYDRATION = to remove water SYNTHESIS = to make more complex
H and OH are removed from the glucose molecules (to make water), this is the dehydration part
Then the two glucose molecules have open bonding sites so they can join together to make more complex, this is the synthesis part.
Dehydration synthesis =
to make more complex by removing water

50. To break down by adding water
HYDROLYSIS
To break down by adding water

51. Dehydration Synthesis of a Carbohydrate
In carbohydrates, two monosaccharides form a bond to create a disaccharide

52. Dehydration Synthesis of a Protein
In proteins, two amino acids form a peptide bond to create a dipeptide molecule

53. Dehydration Synthesis of a Fatty Acid
In lipids, we remove 3 molecules of water!
Then the glycerol molecule bonds with the 3 fatty acids

54. Vocabulary Review monomer = polymer = dehydration synthesis =
A small molecule that will combine with other small molecules to form a chain
monomer =
polymer =
dehydration synthesis =
hydrolysis =
A large molecule (chain) formed from combined repeated smaller units (monomers)
Combining molecules by the removal of water
Breaking down molecules by the addition of water

55. Complete pages 18, 19, and 20 in your packet

56. ENZYMES The importance of enzymes: Enzymes are proteins
Enzymes enter the chemical reaction temporarily and are not changed
Enzymes are used over and over again
Enzymes are organic catalysts

57. ENZYMES
A catalyst is a substance that brings about a chemical reaction without being changed itself The substrate is the substance the enzyme acts upon

58. HOW ENZYMES WORK The active site matches up with the substrate
Forms enzyme-substrate complex
Enzyme will either break down or bond molecules
Enzymes are very specific – one specific enzyme matches one specific substrate

59. substrate -------------> product
ENZYME SPECIFICITY
How do enzymes work? substrate: molecules upon which an enzyme acts. The enzyme is shaped so that it can only lock up with a specific substrate molecule.
(enzyme)
substrate > product
Each enzyme is specific for one and ONLY one substrate
(one lock - one key)
active site: part of the enzyme that fits with the substrate
Note that the active site has a specific fit for this particular substrate and no other.

60. REMEMBER: Each enzyme is specific for one and ONLY one substrate
If the substrate and enzyme are not a match – the reaction will not proceed

61. TWO ENZYME THEORIES
LOCK AND KEY THEORY
INDUCED FIT THEORY

62. Naming the Enzyme
The prefix comes from the substrate (the material acted upon)
Enzymes end in “ase” (the suffix)
For example:
Maltase (malt/ase) = an enzyme that breaks down ________
Lipases (lip/ases) = enzymes that break down ______
Proteases (prote/ases) = enzymes that break down ________
maltose
lipids
proteins

63. FACTORS AFFECTING ENZYME FUNCTION:
REMEMBER…
Enzymes are powerful
one enzyme molecule can catalyze thousands of substrate reactions each second
enzymes speed up the reaction without raising the temperature of the environment
BUT…

64. ENZYME REACTION vs TEMPERATURE
Enzymes work the best at certain temperatures, usually the temperature of the natural environment
Enzymes become denatured at high temperatures (the high temp will change the shape of the active site so the enzyme no longer fits)

65. ENZYME REACTION vs pH
Enzymes work the best at a certain pH, usually the pH of the natural environment

66. ENZYME REACTION vs CONCENTRATIONS
The rate of an enzyme controlled reaction depends upon the concentrations of enzymes and substrates

67. COENZYMES
SOME ENZYMES NEED SUBSTANCES CALLED COENZYMES IN ORDER TO FUNCTION
Coenzymes are organic substances
Coenzymes are not proteins
Most coenzymes are vitamins
A COENZYME ALLOWS AN ENZYME TO PERFORM ITS CATALYTIC FUNCTION

68. How Enzymes Work

69. Acids, Bases, and Salts

70. TERMS
Acids = any compound that produces hydrogen ions (H+) in solution
HCl = H Cl-
Base = any compound that produces hydroxide ion (OH-) in solution
NaOH = Na+ + OH-

71. TERMS
Neutralization = when quantities of acids and bases are mixed together and no extra H+ or OH- remain
HCl + NaOH NaCl + H2O
(acid) + (base) (salt) + (water)

72. TERMS
Salts = the ionic compound obtained from the neutralization reaction between and acid and a base
HCl + NaOH Na+ + Cl- + H2O
Solid NaCl (salt) found if water is evaporated

73. Neutral pure water, no excess of H+ or OH-
The pH scale
H2O H+ + OH-
Neutral pure water, no excess of H+ or OH-
(not an acid or a base)
If the H+ concentration increases, it becomes acidic
If the OH- concentration increases, it becomes basic

74. pH measures the concentration of H+
The pH scale
pH measures the concentration of H+
Scale runs
if the [H+] > [H2O] = acid
if the [H+] < [H2O] = base
The Scale
high [H+] = acids = low pH values = 0 - 6
neutral = 7
low [H+] = bases = high pH values = 8 – 14

75. Indicators
Indicator: substance that changes color when pH goes above or below a certain value
Litmus: Red = acid / Blue = base
Methyl orange: red to yellow indicates base
Phenolphthalein: colorless to red indicates base
(compare to indicator paper to read actual pH)