Biology I Essentials
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CHAPTER 1
The Chemical and Molecular Basis of Life
1.1 The Elements
Element – An element is a substance which cannot be decomposed into simpler or less complex substances by ordinary chemical means.
Compound – Compounds are a combination of elements present in definite proportions by weight. These are substances which can be decomposed by chemical means.
Mixtures – Mixtures contain two or more substances, each of which retains its original properties and can be separated from the others by relatively simple means. They do not have a definite composition.
Atoms – Each element is made up of one kind of atom. An atom is the smallest part of an element which can combine with other elements. Each atom consists of:
atomic nucleus – small, dense center of an atom.
proton – positively charged particle of the nucleus.
neutron – electrically neutral particle of the nucleus.
electron – negatively charged particle which orbits the nucleus.
In normal, neutral atoms, the number of electrons is equal to the number of protons.
Figure 1.1 Atomic structure of carbon and nitrogen
Atomic Mass – The total number of protons and neutrons in a nucleus is the atomic mass. This number approximates the total mass of the nucleus.
Atomic Number – The atomic number is equal to the number of protons in the nucleus of an element.
Isotope – Atoms of the same element that have a different number of neutrons are known as isotopes. All isotopes of the same element have essentially the same chemical properties but their physical properties may be affected.
Ions – Atoms or groups of atoms which have lost or gained electrons are called ions. One of the ions formed is always electrically positive and the other electrically negative.
Figure 1.2 Representation of oxygen from Periodic Table of the Elements
1.2 Chemical Bonds
Ionic Bond – This involves the complete transfer of an electron from one atom to another. Ionic bonds form between strong electron donors and strong electron acceptors. Ionic compounds are more stable than the individual elements.
Covalent Bond – This involves the sharing of pairs of electrons between atoms. Covalent bonds may be single, double, or triple.
Polar Covalent Bond – A polar covalent bond is a bond in which the charge is distributed asymmetrically within the bond.
Non-Polar Covalent Bond – A non-polar covalent bond is a bond where the electrons are distributed equally between two atoms.
Hydrogen Bond – A hydrogen bond is the attraction of a hydrogen atom, already covalently bonded to one electronegative atom, to a second electronegative atom of the same molecule or adjacent molecule. Usually these bonds are found in compounds that have strong electronegative atoms such as oxygen, fluorine, or nitrogen.
Van der Waals Forces – Van der Waals forces are weak linkages which occur between electrically neutral molecules or parts of molecules which are very close to each other.
Hydrophobic Interactions – Hydrophobic interactions occur between groups that are insoluble in water. These groups, which are non-polar, tend to clump together in the presence of water.
1.3 Acids and Bases
Acid – An acid is a compound which dissociates in water and yields hydrogen ions [H+]. It is referred to as a proton donor.
Base – A base is a compound which dissociates in water and yields hydroxyl ions [OH-]. Bases are proton acceptors.
Figure 1.3 Reaction between hydrochloric acid (proton donor) and ammonia (proton acceptor)
pH – The degree of acidity or alkalinity is measured by pH.
pH = 7 → neutral
pH < 7 → acidic
pH > 7 → basic
1.4 Chemical Changes
Chemical Reaction - A chemical reaction refers to any process in which at least one bond is either broken or formed. The outcome of a chemical reaction is a rearrangement of atoms and bonding patterns.
Laws of Thermodynamics
First Law of Thermodynamics (conservation of energy) - In any process, the sum of all energy changes must be zero.
Second Law of Thermodynamics - Any system tends toward a state of greater entropy meaning randomness or disorder.
The Third Law of Thermodynamics - A perfect crystal which is a completely ordered system, at absolute zero (0 Kelvin) would have perfect order, and therefore its entropy would be zero.
Stability of chemical system depends on:
enthalpy - total energy content of a system.
entropy - energy distribution.
Exergonic Reaction – Exergonic reactions release free energy; all spontaneous reactions are exergonic... ,
Endergonic Reaction – Endergonic reactions require the addition of free energy from an external source.
Figure 1.4 Exergonic and Endergonic Reactions
1.5 Organic Chemistry
Hydrocarbons - The simplest organic molecules are the hydrocarbons. These compounds are composed solely of carbon and hydrogen. They can exist as chains (e.g., butane) or rings (e.g., benzene).
Figure 1.5
Lipids – Lipids are organic compounds that dissolve poorly, if at all, in water (hydrophobic). All lipids (fats and oils) are composed of carbon, hydrogen, and oxygen where the ratio of hydrogen atoms to oxygen atoms is greater than 2:1. A lipid molecule is composed of 1 glycerol and 2 fatty acids.
Phospholipid – A phospholipid is a variety of a substituted lipid which contains a phosphate group.
Figure 1.6 (A)An example of the addition which makes a lipid a phospholipid
Steroids - Steroids are complex molecules which contain carbon atoms arranged in four interlocking rings. Some steroids of biological importance are vitamin D, bile salts, and cholesterol.
Figure 1.6 (B)Structural formula of cholesterol
Carbohydrates - Carbohydrates are compounds composed of carbon, hydrogen, and oxygen, with the general molecular formula CH2O. The principal carbohydrates include a variety of sugars.
monosaccharides - a simple sugar or a carbohydrate which cannot be broken down into a simpler sugar. Its molecular formula is