principles of biology by frank h. osborne, ph. d. chemistry of life

Principles of Biology

By

Frank H. Osborne, Ph. D.

Chemistry of Life

The Scientific Method

The Scientific Method has several steps:

•A natural phenomenon is observed

•A hypothesis (proposed explanation) is made

•An experiment is performed

•Results are obtained

•The hypothesis is supported or disproved

•Any scientific explanation is called a theory

The Scientific Method

How science works:

•We learn not by proving something but by disproving something else.

•Inquiry is used to make observations, formulate hypotheses and test them.

•Science works by asking questions and answering them.

The Metric System

The Metric System is used for measurement.

•Length is measured in units of the meter.

•Volume is measured in units of the liter.

•Mass is measured in units of kilograms.

•Time is measured in units of seconds.

The Metric System

Prefixes used in the Metric System

Scientific Notation

Numbers are represented as a number between 1 and 10 x 10 raised to an appropriate power. Examples:

2800 = 2.8 x 103

.00055 = 5.5 x 10-4

Simple Chemistry

Biology involves understanding some simple concepts of chemistry.

•Atoms

•pH scale

•Chemical bonding

ATOMSAtoms are composed of protons, neutrons and electrons.•The nucleus is made of protons and neutrons.•The electrons travel in orbits around the nucleus.•Atomic number is the number of protons.•Atomic mass is the number of protons and neutrons. Find the number of neutrons by subtraction.

Atomic StructureStructure of the Atom

•Each atom (element) has its own symbol.

•Example: Helium

Examples of Atoms

Examples of Atoms

Examples of Atoms

Examples of Atoms

Examples of Atoms

Dot Structures

The outer electrons of the atom are all that matter in chemical bonding. It is customary to represent them using dots.

Principal Elements in Protoplasm

Water is most CHON are mostabundant abundant elementscompound

Element Symbol Percentage

Hydrogen H 63

Oxygen O 25.5

Carbon C 9.1

Nitrogen N 1.4

Phosphorus P < 1

Sulfur S < 1

Molecules

• Molecules are electrically neutral aggregates of atoms bonded together.

• "Electrically neutral" means that the number of protons equals the number of electrons.

Compounds and Molecules

•A compound is a substance with a definite composition that can be decomposed into two or more substances (examples are salt (NaCl) and water H2O)).

•A molecule is the smallest unit of a substance that has the chemical properties of the substance.

Bonding

•An ionic bond is formed by complete transfer of one or more electrons from one atom to another. Example: NaCl

•A covalent bond is formed by sharing of electrons between atoms. Example: H2O

Ionic Bonding

Covalent Bonding

Some Important Compounds

Counting Atoms

The pH Scale

•The pH scale shows the strength of an acid or a base. It ranges from 0 to 14.

•A pH of 7 is neutral.

•A pH less than 7 is acidic.

•A pH greater than 7 is alkaline (basic).

The pH Scale

ORGANIC CHEMISTRYOrganic chemicals contain carbon.The more important ones are:• carbohydrates• lipids• proteins• nucleic acids

CARBOHYDRATES

Carbohydrates contain carbon (C), hydrogen (H), and oxygen (O). The ratio of hydrogen to oxygen is 2:1 in carbohydrates. This means that there is twice as much hydrogen as there is oxygen.

Simple Sugars (Monosaccharides)Simple sugars contain from three to seven carbon atoms. Some of the larger ones can form rings.

Glucose Can Form Rings• Glucose makes a hexagonal ring form

Condensation Reactions

• A condensation reaction occurs between two molecules when an enzyme removes water from them and joins them together with a single bond. This process is known as dehydration synthesis.

• The water is always removed in the form of H from one molecule and OH from the other.

Disaccharides

Disaccharides consist of two monosaccharides connected by a condensation reaction. An example is maltose which is formed by reaction between two glucose molecules.

Formation of Maltose

Polysaccharides

Polysaccharides contain many monosaccharides linked together by condensation reactions. These consist of long chains called polymers. The three polymers of glucose are starch, cellulose and glycogen.

The Hydrolysis-Synthesis Cycle

The Carbohydrate PyramidMany sugars(many glucose)

Two glucose (maltose)

One glucose

LIPIDS

• triglycerides

• waxes

• phospholipids

• steroids

• Lipids contain carbon, hydrogen and oxygen. There is much less oxygen in a lipid than there is in a carbohydrate.

• The types of lipids are:

Fats and Oils

Fats and oils are examples of triglycerides. Fat is solid at room temperature, oil is liquid.

The building blocks of triglycerides are fatty acids and glycerol.

Molecules of triglycerides contain one glycerol and three fatty acids.

Forming a Triglyceride (1)

Forming a Triglyceride (2)

Saturated/Unsaturated FatsSaturated fats do not have double bonds between the carbon atoms.

Unsaturated Fats have double bonds between the carbon atoms.

Types of Fatty Acids

Waxes

Waxes are formed by condensation reactions between long-chain fatty acids and long-chain alcohols. They are found in various places, such as the surfaces of leaves.

Phospholipids

Phospholipids contain glycerol, two fatty acids, phosphorus and sometimes nitrogen. They have polar heads and non-polar tails.

The polar end is hydrophilic.

The non-polar end is hydrophobic.

These molecules are the major component of all biological membranes

Phospholipids

Diagram of a phospholipid molecule.

SteroidsSteroid molecules have a complicated structure of interlocking carbon rings. This is an important type of lipid. It includes the sex hormones, cortisone, cholesterol, and related molecules.

PROTEINSProteins are long-chain polymers of amino acids which are linked together by condensation reactions (dehydration synthesis). They are the fundamental structural molecules in biology.

The structural properties of proteins are due to the presence of nitrogen.

Amino AcidsThere are 20 different types of amino acids. They can combine in a variety of ways. Amino acids are required for synthesis of proteins.

Formation of ProteinsProteins are formed by condensation reactions (dehydration synthesis).

When two amino acids are joined together, the result is a dipeptide (two amino acids) joined by a peptide bond, and the water molecule which was removed.

Formation of Proteins

Peptide Bond

The Protein Pyramid

Functions of ProteinsStructural proteins. Structural proteins hold biological structures together or form body structures. An example is keratin. Keratin is found in hair, skin, nails, and the corresponding parts of other animals such as fur, hooves, claws, as well as fish and reptile scales.

Functions of ProteinsEnzymes. An enzyme is a catalyst that allows the occurrence of a chemical reaction at body temperature. All enzymes are proteins. Condensation reactions are examples of biological reactions that are catalyzed by enzymes. There is also an enzyme called catalase. Catalase is another example of an enzyme.

NUCLEIC ACIDSThere are two types of nucleic acids. These are known as:• Deoxyribonucleic acid (DNA)• Ribonucleic acid (RNA)

Nucleotides Nucleotides are the building blocks of nucleic acids. They have three components: a base, a sugar and a phosphate. The bases are rings of carbon and nitrogen atoms and are sometimes called nitrogenous bases. Phosphate is derived from phosphoric acid. The sugar found in DNA is called deoxyribose while the sugar found in RNA is called ribose.

Formation of Nucleic AcidsThe phosphate from one nucleotide becomes joined to the sugar of another nucleotide by a condensation reaction. This process builds very long chains of nucleotides.

The Nucleic Acid Pyramid

Functions of the Nucleic AcidsDeoxyribonucleic acid (DNA). DNA is found in the chromosomes of the nucleus of the cell. It directs all aspects of cell function. It is organized into genes which determine the properties of the organism.

Functions of the Nucleic AcidsRibonucleic acid (RNA). There are three types of RNA. Each is associated in some way with protein synthesis. The structure of proteins (the sequence of the amino acids in the protein) is ultimately determined by the DNA of the cell.

The End

Principles of Biology

Chemistry of Life