BIOCHEMISTRY

*Only 27 naturally occurring chemical elements are indispensable in living organisms.

Four most abundant Four most abundant elements-

elements- Living
Earth's crust organisms
Oxygen Carbon 9.5%
Silicon Hydrogen 25.2%
Aluminum Oxygen 63.0%
Iron Nitrogen 1.4%

I. BIOMOLECULES/ORGANIC COMPOUNDS
large molecules that serve as building blocks of life and provide structural
components of cells
combinations of many smaller molecules (monomers) joined together in chainlike
structures through the process of polymerization
carbohydrates, lipids, nucleic acids, and proteins

A. CARBOHYDRATES (C,H,O)
• Known as saccharides or carbs
• names end in-ose
• general formula: Cn(H2O)n
• primary source of energy
• forms part of the structures of plants and animals

Three Classifications:
1. Monosaccharides-simple sugars; smallest units that have the
characteristics of carbohydrates and can be combined to make
larger complex carbohydrates
a. Glucose- most common monosaccharide
- only form of sugar used by the body to produce energy

b. Galactose- obtain from milk

c. Fructose- fruit sugar
- sweetest amongthe sugars

2. Disaccharides- composed of 2 monosaccharides

- joined by a glycosidic bond by removal of water
- C12H22011
a. Sucrose (glucose+ fructose)
- table sugar; most common disaccharide
b. Lactose (glucose+ galactose)
 - milk sugar
- first carbohydrates that newborn mammals consume
c. Maltose (glucose+ glucose)
- malt sugar
- the grain used in brewing beer

3. Polysaccharides- polymers of sugars joined together by glycosidic

bonds
- can be classified as structural or storage
Structural:
a. Cellulose- most abundant organic molecule on Earth
- main component of the cell walls of plants
- cows, goats, sheep, cattle (ruminants) have microbes
in their stomach to digest cellulose
b. Chitin- forms the hard, protective covering of insects and
shellfish, such as crabs and lobsters
-found in fungi cell wall
Storage:
c. Starch- energy-storage molecule of plants
d. Glycogen- animal starch; excess sugar in a polysaccharide
stored in animals

B. LIPIDS
• Non polar and hydrophobic
• Soluble in nonpolar organic solvents, insoluble in water
• Function mainly as an energy source; insulator

1. Fats
Called triglycerides or triglycerols
Composed of one molecule of glycerol and
three fatty acids

• Saturated Fats- have single hydrogen bond

- fairly straight, packed closely together
- solid at room temperature (lard, butter, margarine)
• Unsaturated Fats- have double bonds
- kink (bend), cannot be packed closely
- liquid at room temperature (corn oil, palm oil)
• Polyunsaturated Fats- more than one double bond
 2. Phospholipids
Major structure of the cellmembrane
1 glycerol, 2 fatty acids, phosphate
group Have hydrophilic (water-loving)
heads and hydrophobic (water-fearing)
tails

3. Waxes

Simple lipids (along chain of alcohol and a fatty acid joined by

ester bond)
Harder and less greasy than fats
Found in coatings of leaves and stems and in body surface across
cuticle (some insects)

4. Steroids
Have ring system structure where
various functional groups can be
attached
E.g. cholesterol, sex hormones

C. Nucleic Acids
• Discovered by Friedrich Miescher
• Made up of nucleotides joined by phosphodiester bonds
• Store genetic information
• TwoTypes:
1. Deoxyribonucleic acid (DNA)- main carrier of genetic information;
double-stranded
2. Ribonucleic acid (RNA)- a copy from a portion of the DNA and
becomes the template for the production
of a specific protein; single stranded

Nucleotide is made up of three components:

I
 1. Nitrogenous bases- classified according to the number of rings found in
the molecule
Purines (double ring)
-Adenine (A)
-Guanine (G)
Pyrimidines (single ring)
- Cytosine (C)
- Thymine (T)
- Uracil (U)- RNA

Complementary Bases

DNA RNA
Adenine and Thymine Adenine and Uracil
(two H-bond) (two H-bond)
Cytosine and Guanine Cytosine and Guanine
(three H-bond} (three H-bond)

2. Five-carbon sugar (pentose sugar)

• RNA- ribose; a sugar with oneoxygen atom bonded to
each carbon atom
• DNA- deoxyribose; a sugar which lacks one oxygen atom
3. Phosphate group
*The phosphate group and the sugar molecule form the backbone.

D. Proteins
• the most versatile macromolecule
• Made up of amino acids joined by peptide bonds
• Same amino group (-NH2) and carboxyl group (-COOH), but differ in
side chain (R)
• Polypeptide- a polymer formed from linking many amino acid molecule
 Four Levels of Protein Structure
1. Primary- sequence of amino acids in a polypeptide chain.
- dictates the structure and function of the protein.

2. Secondary-the coiling or folding of the polypeptide into a repeating

configuration
- includes the alpha (a) helix and the beta (13) pleated sheet
3. Tertiary- the overall three-dimensional shape of a polypeptide
4. Quaternary- comprised of two or multiple separate polypeptide chains
a. Fibrous proteins- long strands of polypeptide chain adapted
for the structural function of a protein
b. Globularproteins -spherical shaped polypeptide chain
carrying out a wide array of protein function

II. INORGANIC COMPOUNDS

A. Water
• The "universal solvent"
 • The most abundant compound on Earth (its abundance is the
main reason why Earth is habitable)
• Comprises 60%-90% of the total compositions of the cells
• Tasteless, odorless, colorless, and almost incompressible liquid

Properties of Water
1. Polarity-results from the uneven partial charge {electron) distribution
making opposite sides of the molecule to have opposite charges
*The polarity of water:
- allows them to form hydrogen bonds with each other
(can easily dissociate and reform)
- leads to attractions with other substances which then
cause the molecules of the other substances to be mixed
uniformly
{dissolved} with the water molecules.
- contributes to the various properties water exhibits
2. Cohesion- attraction between like molecules
- hydrogen bonds between water molecules
- responsible for surface tension
* allows a water strider to walk across the top of the pond
3. Adhesion- attraction between unlike molecules
Ex: Water drops clinging in a leaf (The water molecule is attracted to
the leaf surface molecule)
5. Capillary action- only occurs when the adhesive forces are stronger than
the cohesive forces
- liquid climbing up into a narrow tube

B. Acids and
Bases ACIDS
• Substances that increase W (proton) when added in water
• Turn blue litmus to red
• Taste sour
• Ex: ascorbic acid (citrus food}, carbonic acid (soft drinks)
BASES
• Substances that increase OH- (proton) when added in water
• Accept H+(proton)
• Turn red litmus to blue
• Taste bitter
• Ex: ammonia, antacids, milk of magnesia, soap, shampoo
Buffers- solution that resists pH change upon the addition of acidic or basic
components
- consist of an acid-base pair that reversibly combines with
hydrogen ions
Ill. ENZYMES
- proteins that speed up chemical reactions
- biological catalysts
- demonstrates specificity
- enzymes catalyze only specific substrates (substance where
enzyme reacts) and specific reaction

*Enzymatic Activity
• Activation energy- needed to create sufficient energy for a reaction to occur.
• Enzymes speed up chemical reactions by lowering the activation energy.

1. Enzyme structure
a. Active site- pocket where the catalytic reaction takes place
b. Substrate- molecule that binds to the active site and is acted upon by
the enzyme

*Enzyme-substrate complex- recognizes each other through structural

complementarity
- bound by weak forces (hydrogen bonds, van der
Waals interactions)

2. Co-enzymes and Cofactors

- non-protein components that prepare the active site for catalytic activity
although most enzymes function on their own

a. Co-enzymes- organic molecules

- serve as intermediate carriers of functional groups in the
conversion of substrates to products

b. Cofactors- metal ions

3. Enzyme Kinetics
 • Saturation point- reached when all the active sites of the enzymes
are occupied by their substrates.

4. Factors Affecting Enzymes

a. Number of enzymes- directly proportional to the reaction rate
b. Temperature- increases the reaction rate up to maximum and
then declines
c. pH- changes in H+ and OH- ions affect the shape of the active site
d. Concentration of reactants and products
e. Pressure- the higher pressure, the better

*Enzyme Inhibition
a. Competitive inhibition- inhibitor mimics a portion of the substrate then
binds to the active site
- directly blocks the active site
- Ex: poisons, heavy metals, heavy drugs

b. Non-competitive inhibition- inhibitors bind to the allosteric site (other

parts of the enzyme) causing conformational
changes to the active site

c. Uncompetitive inhibition- occurs when the substrate causes the binding

of the inhibitor or causes a change in the structure of
the enzymes that allow the inhibitor to bind

d. Zymogens- inactive enzymes; causes enzymes to be transported

to different locations without performing their functions