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BASIC BIOCHEMISTRY
Philosophical considerations aside, organisms are basically ordered aggregations
of chemicals and biological processes are merely biochemical reactions. Therefore an understanding of basic biochemistry is necessary in order to
understand biology.
I. Matter is composed of elements
A. Matter
1. Matter refers to anything that takes up space and has mass
2. All matter (living and nonliving) is composed of basic elements
a. Elements
= fundamental forms of matter that occupy space and have mass, cannot be broken down to substances with different chemical
or physical properties
b. There are 92 naturally occurring elements
b. Six elements (C, H, N, O, P, S) make up 98% of most organisms
II. Atoms form compounds and molecules
A. Molecules =
two or more atoms of same element bonded together (e.g., O2)
B. Compound = two or more different elements bonded together (e.g., H2O)
C. Bonds are not physical links, they are links of pure energy.
Types of bonds:
1. Covalent bond -
involves sharing of electron(s). Electrons possess energy; bonds that
exist between atoms in molecules contain energy.
a. Sharing of a pair of electrons creates a single bond represented by
single dash, e.g. water H2O is made of two single bonds H-O-H.
Sharing two pairs of electrons is represented by two dashes, C=C
b. Know the number of covalent
bonds each of the six most important elements can form.
|
Element
|
# of covalent bonds |
| Hydrogen (H) |
1 |
| Oxygen (O) |
2 |
| Nitrogen (N) |
3 |
| Carbon (C) |
4 |
| Phosphorous (P) |
5 |
| Sulfur (S) |
2 |
2. Ionic bond - electrons are transferred
from one atom to another, e.g. salt NaCl
3. Hydrogen bond - weak
attractive force between slightly positive hydrogen atom of one molecule and
slightly negative atom in another or the same molecule
a. E.g. in a water molecule the electrons spend more time orbiting the
oxygen than the hydrogens, therefore the oxygen becomes slightly negative
and the two hydrogens become slightly positive
b. Such polar molecules attract each other like magnets
BASIC ORGANIC CHEMISTRY
Because carbon needs four electrons to fill its outer shell it can form
millions of different combinations with other atoms - ten times more than all
other atoms put together.
I. Organic molecules
A. Life as we know it is based on carbon
1. Carbon has four electrons in outer shell; bonds with up to four other
atoms (usually H, O, N, or another C)
2. Ability of carbon to bond to itself makes possible carbon chains and
rings which serve as the backbones of organic molecules
3. Organic molecules - contain carbon and hydrogen, most also
contain nitrogen, and oxygen
4. Functional groups
- clusters of atoms with characteristic structure and functions
B. Monomers and polymers
1. Most important biological compounds are polymers
a. Polymers - large compounds made of identical or nearly
identical repeating subunits
b. Monomers - the subunits of polymers
2. Making and breaking polymers
a. Condensation
- making polymers by lining up monomers and eliminating a water molecule,
a hydroxyl (OH) group is removed from one monomer and a hydrogen (H) is
removed from the other
b. Hydrolysis -
breaking polymers apart by introducing a water molecule
PRINCIPLE ORGANIC POLYMERS
I. Carbohydrates- contain C, H and O
in the proportion 1:2:1 (CH2O).
A. Most abundant organic compounds in nature
B. Serve both as structural compounds and as energy reserves to fuel life
processes
C. Carbohydrate monomers are called monosaccharides
1. Alpha Glucose, a six
carbon sugar (C6H12O6) is the
immediate energy source to cells. You should know its structure
D. Carbohydrate polymers are called polysaccharides
1. Starch is straight chain of alpha glucose molecules with
few side branches, mostly from plant sources
2. Glycogen is highly branched polymer of alpha glucose with
many side branches; called "animal starch," it is storage
carbohydrate of animals
3. Cellulose is a polymer of beta glucose
molecules, it is primary constituent of plant cell walls
E. Disaccharides - 2 monosaccharides linked together
1. Sucrose (table sugar ) - glucose and fructose linked together,
transported throughout plants
2. Lactose (milk sugar) is glucose + galactose
F. Virtually all carbohydrates come from plants which use the sun's energy
to make alpha and beta glucose.
II. Lipids - fats, oils, fatlike substances, some vitamins and
steroids
A. Primarily energy sources and structural compounds
B. Two principle characteristics:
1. Hydrophobic - insoluble in water
2. Large number of bonded hydrogens - therefore release a larger amount
of energy than other organic compounds. Fats yield 9 cal/gm, carbohydrates 4
cal/gm
C. Major lipids:
1. Triglycerides (fats and oils) - three
fatty acids joined to a glycerol molecule:
a. Fatty acid - long hydrocarbon chains
with terminal carboxyl (COOH) group
Saturated fatty
acids have no double bonds between their carbon atoms
Unsaturated
fatty acids have double bonds in the carbon chain
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% saturated/unsaturated fat in
some common foods
|
|
Unsaturated
|
Saturated
|
| safflower |
72 |
beef |
48 |
| soybean |
59 |
butter |
55 |
| corn |
53 |
fish |
15 |
| |
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coconut oil |
86 |
| |
|
chocolate |
56 |
b. Glycerol - three carbon molecule
1) Fats - triglycerides containing saturated fatty acids (e.g. butter
is solid at room temperature)
2). Oils - triglycerides with unsaturated fatty acids (e.g. corn oil
is liquid at room temperature)
c. Triglycerides are synthesized via condensation
2. Phospholipids - two fatty acids
attached to phosphate group
a. phosphate heads are hydrophilic (water soluble) but tails are
hydrophobic (water insoluble) therefore they spontaneously line up to form
a lipid bilayer
b. very important because they form biological membranes
III. Polypeptides - polymers of nitrogen containing molecules called amino
acids, joined together by peptide bonds
A. Amino acids consist
of:
1. Amino group - NH2 (positive charge)
2. Carboxyl group - COOH (negative charge)
3. Central carbon atom
4. R group - different substitution to the molecule, determines nature
of the amino acid
B. About 50,000 different proteins in humans, serve a variety of functions:
1. Structural - e.g. muscles, hair, fingernails, collagen
2. Enzymes - biological catalysts which regulate biochemical reactions
C. Proteins - large polypeptides with molecular weights from 10,000
- 1,000,000
D. Enzymes - large globular proteins from 12,000 to 1 million
molecular weights that act as catalysts
1. Catalysts - substances that accelerate chemical reactions but which
remain unchanged or unused in the process
2. Enzymes generally named by adding -ase to root name of substrate they
react upon, e.g. amylase breaks down amylose (starch)
E. Polypeptide structure - due to interactions between adjacent hydrogen
bonds and R groups proteins form complex
three dimensional structures
C. Polypeptides can be denatured
1. Both temperature and pH can change polypeptide shape
a. Examples: heating egg white causes albumin to congeal; adding acid
to milk causes curdling. When such proteins lose their normal
configuration, the protein is denatured
b. Once a protein loses its normal shape, it cannot perform its usual
function
IV. Nucleic Acids - polymers of nucleotides
A. Nucleotides made up of:
1. Phosphate group - PO4
2. Five carbon sugar called ribose (or deoxyribose)
3. Nitrogenous base - ring structure containing C & N
B. Important Nucleic Acids:
1. DNA (deoxyribonucleic
acid) - the molecule which stores the genetic information passed on form
parent to offspring
2. RNA (ribonucleic acid) - serves as the translator of the
genetic information contained in DNA
SECONDARY METABOLITES
I. Proteins, lipids, carbohydrates and nucleic acids are called primary
metabolites because they occur in all plant cells and they are necessary for the
life of the plant.
II. Secondary metabolites are an assortment of many different
compounds which serve a variety of functions, and that are restricted to different species
of plants. They include:
A. Alkaloids - alkaline, nitrogen containing compounds which affect
the human nervous system. At least 10,000 alkaloids have been isolated from plants. Many
names end in -ine, e.g. morphine, caffeine, cocaine, nicotine, atropine.
B. Terpenoids - polymers of isoprene.
Isoprene is emitted by leaves, causing a haze over forests on hot days. Other terpenoids
include essential oils (volatile compounds) such as mint and menthol, taxol (cancer drug),
digitalis (heart medicine) and rubber.
C. Phenolics - compounds based on an aromatic ring with an attached
OH group. Flavonoids are important pigments, tannins are bitter tasting compounds which
probably act as deterrents to herbivores, lignin is an important compound secreted into
the cells of woody plants to provide structural support. Salicylic acid is the active
ingredient in aspirin.
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