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.


Attributes of Living things

1-They are composed of cells. Cells consist of a membrane around the outside, a nucleus containing DNA, and the cytoplasm.
2-Growth
3-Reproduction
Sexual reproduction: the offspring vary from the parents
Asexual reproduction: the offspring are identical clones
4-Respond to stimuli: for example plants respond to light, water, gravity, touch.
5-Metabolism: all the chemical reactions in an organism. The most critical reactions are respiration and photosynthesis.
6-Movement: for example sperm can swim, whole plants grow in particular directions, or there is cyclosis in cells.
7-Complexity: they are made of molecules and organelles.
8-Adaptation and evolution: populations evolve to become better adapted to their environment.

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. Living things contain a maximum of 25 elements.

c. Six elements (C, H, N, O, P, S) make up 98% of most organisms


II. Atoms form compounds and molecules
Atom - the smallest unit of an element.

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)

Atomic number = Number of Protons per atom. Atomic number also equals the number of electrons.
Example : Carbon has 6 protons and 6 electrons (Table 2.1).

Atomic mass = Number of Protons + Neutrons.
Example: carbon 14 has 8 neutrons (14 minus 6 ).

Isotopes : atoms of the same element that differ in the number of neutrons.

Radioactive atoms : large isotopes that break apart, releasing energy. The energy is either:
Alpha particles : weak, cannot penetrate paper.
Beta particles : stronger, can penetrate paper but not metal.
Gamma rays : very strong, can penetrate metal and harm living things.

Chemical Bond
Chemical bonds only involve electrons. Valence electrons - electrons in the outer shell ( the valence shell ) of an atom. All atoms try to fill their valence shell of electrons. Maximum number of electrons per shell :
First shell 2
Second shell 8
Third shell 8
Bonds are not physical links, they are links of pure energy.
Types Of Bond
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

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. Hydrogen bonds are important in holding together proteins.

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

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 50,00 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 (see figure 2-26a, p. 33). 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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