1. BIOCHEMISTRY

2. CHEMISTRY OF LIFE
Elements: simplest form of a substance - cannot be broken down any further without changing what it is
Atom: the actual basic unit - composed of protons, neutrons, and electrons

3. THE ATOM
Just like cells are the basic unit of life, the ATOM is the basic unit of matter.
They are very small. If placed side by side one million would stretch a distance of 1cm.
The atom is made up of 3 particles.
Particle
Charge
PROTON +
NEUTRON
NEUTRAL
ELECTRON -

4. ATOMIC MASS = 4 (PROTONS & NEUTRONS)
Electrons are not present within the atom, instead THEY REVOLVE AROUND THE NUCELUS OF THE ATOM & FORM THE ELECTRON CLOUD
Draw a helium atom. Indicate where the protons, neutrons and electrons are.
NEUTRONS
PROTONS -
ATOMIC # = 2 (PROTONS)
ATOMIC MASS = 4 (PROTONS & NEUTRONS) + +
ELECTRONS -

5. ISOTOPES
atoms of the same element that HAVE A DIFFERENT NUMBER OF NEUTRONS
Some isotopes are radioactive. This means that their nuclei is unstable and will break down at a CONSTANT RATE over time.
There are several practical uses for radioactive isotopes:
CARBON DATING
TRACERS
KILL BACTERIA / CANCER CELLS

6. COMPOUNDS
a substance formed by the chemical combination of 2 or more elements in definite proportions
Ex: water, salt, glucose, carbon dioxide
H20
CO2
NaCl

7. The cell is a COMPLEX CHEMICAL FACTORY containing some of the same elements found in the nonliving environment.
carbon (C), hydrogen (H), oxygen (O), and nitrogen (N) are present in the greatest percentages

8. Inorganic - usually "support" life - no specific ratio of C, H, and O
TWO TYPES OF COMPOUNDS
Organic - Contain C, H, and O in some ratio (usually referred to as chemicals of life)
Carbohydrates, Proteins, Lipids, Nucleic Acids
Inorganic - usually "support" life - no specific ratio of C, H, and O
Water (H2O), Carbon Dioxide (CO2)

9. CHEMICAL BONDS Chemical bonds hold the atoms in a molecule together.
There are 2 types of chemical bonds IONIC and COVALENT

10. IONIC BONDS
Occur when 1 or more electrons are TRANSFERRED from one atom to another.
When an atom loses an electron it is a POSITIVE charge.
When an atom gains an electron it is a NEGATIVE charge
These newly charged atoms are now called IONS
Example: NaCl (SALT)

12. COVALENT BONDS Occur when electrons are SHARED by atoms.
These new structures that result from covalent bonds are called MOLECULES
** In general, the more chemical bonds a molecule has the more energy it contains
SHARING IS CARING!

13. MIXTURES
Water is not always pure. It is often found as part of a mixture.
A mixture is a material composed of TWO OR MORE ELEMENTS OR COMPOUNDS THAT ARE PHYSICALLY MIXED
Ex: salt & pepper mixed, sugar and sand – can be easily separated

14. SOLUTION
Two parts:
SOLUTE – SUBSTANCE THAT IS BEING DISSOLVED (SUGAR / SALT)
SOLVENT - the substance in which the solute dissolves
Materials that do not dissolve are known as SUSPENSIONS.
Blood is the most common example of a suspension.
Cells & other particles remain in suspension.

15. FORMULA
The chemical symbols and numbers that compose a compound ("recipe")
Structural Formula – Line drawings of the compound that shows the elements in proportion and how they are bonded
Molecular Formula – the ACTUAL formula for a compound
C2H6O

16. ACIDS & BASES
Acids: always (almost) begin with "H" because of the excess of H+ ions (hydrogen)
Ex: lemon juice (6), stomach acid (1.5), acid rain (4.5), normal rain (6)
Facts about Acids
Acids turn litmus paper BLUE and usually taste SOUR.
You eat acids daily (coffee, vinegar, soda, spicy foods, etc…)

17. ACIDS & BASES
Bases: always (almost) end with -OH because of the excess of hydroxide ions (Oxygen & Hydrogen)
EX: oven cleaner, bleach, ammonia, sea water, blood, pure water
Facts about Bases
Bases turn litmus BLUE.
Bases usually feel SLIPPERY to touch and taste BITTER.

18. Neutralization Reactions
When an acid reacts with a base to produce a salt and water.

19. pH SCALE measures degree of substance alkalinity or acidity
Ranges from 0 to 14
0 – 5 strong acid
6-7 neutral
8-14 strong base

20. The goal of the body is to maintain HOMEOSTASIS (neutrality) – to do this when pH is concerned, we add weak acids & bases to prevent sharp changes in pH.
These are called BUFFERS

21. And now for the Biochemistry portion of things….

22. ORGANIC COMPOUNDS
LIPIDS
PROTEINS
NUCLEIC ACIDS
CARBOHYDRATES

23. CARBOHYDRATES
Living things use carbohydrates as a key source of ENERGY!
Plants use carbohydrates for structure (CELLULOSE)
include sugars and complex carbohydrates (starches)
contain the elements carbon, hydrogen, and oxygen (the hydrogen is in a 2:1 ratio to oxygen)

24. Monosaccharides (simple sugars)
all have the formula C6 H12 O6
all have a single ring structure
(glucose is an example)

25. Disaccharides (double sugars)
all have the formula C12 H22 O11
sucrose (table sugar) is an example

26. Polysaccharides Formed of three or more simple sugar units
Glycogen - animal starch stored in liver & muscles
Cellulose - indigestible in humans - forms cell walls
Starches - used as energy storage

27. How are complex carbohydrates formed and broken down?

28. Dehydration Synthesis
Combining simple molecules to form a more complex one with the removal of water
ex. monosaccharide + monosaccharide ----> disaccharide + water
(C6H12O6 + C6H12O6 ----> C12H22O11 + H2O
Polysaccharides are formed from repeated dehydration syntheses of water
They are the stored extra sugars known as starch

30. Hydrolysis
Addition of WATER to a compound to SPLIT it into smaller subunits
(also called chemical digestion)
ex. disaccharide + H2O ---> monosaccharide + monosaccharide
C12 H22 O11 + H2 O ---> C6 H12 O6 + C6 H12 O6

32. Lipids (Fats) Fats, oils, waxes, steroids
Chiefly function in energy storage, protection, and insulation
Contain carbon, hydrogen, and oxygen but the H:O is not in a 2:1 ratio
Tend to be large molecules -- an example of a neutral lipid is below

33. Neutral lipids are formed from the union of one glycerol molecule and 3 fatty acids
3 fatty acids + glycerol ----> neutral fat (lipid)
Fats -- found chiefly in animals
Oils and waxes -- found chiefly in plants
Oils are liquid at room temperature, waxes are solids
Lipids along with proteins are key components of cell membranes
Steroids are special lipids used to build many reproductive hormones and cholesterol

34. PROTEINS contain the elements carbon, hydrogen, oxygen, and nitrogen
composed of MANY amino acid subunits
It is the arrangement of the amino acid that forms the primary structure of proteins.
The basic amino acid form has a carboxyl group on one end, a methyl group that only has one hydrogen in the middle, and a amino group on the other end.
Attached to the methyl group is a R group.

35. AN R GROUP IS ANY GROUP OF ATOMS – THIS CHANGES THE PROPERTIES OF THE PROTEIN!

36. FUNCTIONAL GROUPS
There are certain groups of atoms that are frequently attached to the organic molecules we will be studying, and these are called functional groups.
These are things like hydroxyl groups which form alcohols, carbonyl groups which form aldehydes or ketones, carboxyl groups which form carboxylic acids, and amino groups which form amines.

38. Major Protein Functions
Growth and repair
Energy
Buffer -- helps keep body pH constant

39. Dipeptide formed from two amino acid subunits
Formed by the process of Dehydration Synthesis
amino acid + amino acid dipeptide + water

40. Hydrolysis of a dipeptide
Breaking down of a dipeptide into amino acids
dipeptide + H2O ---> aminoacid + amino acid

41. Polypeptide (protein)
composed of three or more amino acids linked by synthesis reactions
Examples of proteins include insulin, hemoglobin, and enzymes.
** There are an extremely large number of different proteins.
The bases for variability include differences in the number, kinds and sequences of amino acids in the proteins

42. NUCLEIC ACIDS in all cells composed of NUCLEOTIDES
store & transmit heredity/genetic information
Nucleotides consist of 3 parts:
1. 5-Carbon Sugar
2. Phosphate Group
3. Nitrogenous Base

44. DNA (deoxyribonucleic acid)
contains the genetic code of instructions that direct a cell's behavior through the synthesis of proteins
found in the chromosomes of the nucleus (and a few other organelles)

45. RNA (ribonucleic acid)
directs cellular protein synthesis
found in ribosomes & nucleoli

46. CHEMICAL REACTIONS
a process that changes one set of chemicals into another set of chemicals
REACTANTS – elements or compounds that enter into a chemical reaction
PRODUCTS – elements or compounds that are produced in a chemical reaction
Chemical reactions always involve the breaking of bonds in reactants and the formation of new bonds in products.

47. In a reaction, energy is either TAKEN IN (ENDOTHERMIC) or GIVEN OFF (EXOTHERMIC)
Can you think of an everyday example of each type of reaction?

48. Enzymes and Enzyme Action
catalyst: inorganic or organic substance which speeds up the rate of a chemical reaction without entering the reaction itself
enzymes: organic catalysts made of protein
most enzyme names end in -ase
enzymes lower the energy needed to start a chemical reaction. (activation energy)
begin to be destroyed above 45øC. (above this temperature all proteins begin to be destroyed)

49. It is thought that, in order for an enzyme to affect the rate of a reaction, the following events must take place.
The enzyme must form a temporary association with the substance or substances whose reaction rate it affects. These substances are known as substrates.
The association between enzyme and substrate is thought to form a close physical association between the molecules and is called the enzyme-substrate complex.
While the enzyme-substrate complex is formed, enzyme action takes place.
Upon completion of the reaction, the enzyme and product(s) separate. The enzyme molecule is now available to form additional complexes.

50. 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

51. "Lock and Key Theory"
each enzyme is specific for one and ONLY one substrate (one lock - one key)
this theory has many weaknesses, but it explains some basic things about enzyme function

52. Factors Influencing Rate of Enzyme Action
1. pH - the optimum (best) in most living things is close to 7 (neutral)
high or low pH levels usually slow enzyme activity
A few enzymes (such as gastric protease) work best at a pH of about 2.0

53. 2. Temperature - strongly influences enzyme activity
optimum temperature for maximum enzyme function is usually about C.
reactions proceed slowly below optimal temperatures
above 45 C most enzymes are denatured (change in their shape so the enzyme active site no longer fits with the substrate and the enzyme can't function)

55. 3. Concentrations of Enzyme and Substrate
** When there is a fixed amount of enzyme and an excess of substrate molecules -- the rate of reaction will increase to a point and then level off.