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| Extended Lecture Outline |
Chapter 3: The Chemistry Of Biology |
3.1 Basic principles of chemistry are fundamental to biology.
a. Matter is made of atoms.
b. An element (e.g. iron) is a basic substance that cannot be broken down into simpler substances by a chemical process.
c. An atom is the smallest particle of an element that has any of the element's characteristic properties.
d. An electron is a subatomic particle with a negative electrical charge. Electrons surround the atomic nucleus.
e. A proton is a subatomic particle with a positive electrical charge. Protons are located in the atomic nucleus.
f. A neutron is a subatomic particle with no electrical charge. Neutrons are located in the atomic nucleus.
g. An atomic nucleus (not to be confused with a cellular nucleus) is comprised of protons and neutrons at the center of an atom.
h. Atoms form molecules; elements form compounds.
i. Molecules are combinations of two or more atoms.
j. When two or more atoms combine to form molecules, they are said to have formed a bond. A bond is established when two atoms are held in a stable arrangement at a specific distance.
k. Elements combine naturally to form compounds. A compound is a substance with well-defined properties that are quite different from those of their components.
l. The distinctive shapes of biomolecules and their abilities to change shapes are the keys to their functions.
m. Complementary molecules are those whose shapes allow them to fit together like jigsaw-puzzle pieces. These molecules interact in very specific ways and these interactions produce biological activities.
n. Each element has a particular atomic number and mass.
1. Atomic number is the number of protons in each atom of a given element.
2. Atomic mass is the total mass of the protons and neutrons in each atom of a given element.
3. Atomic mass unit (amu) is the standard unit in which all atomic masses are given.
4. The molecular mass of a compound is the sum of the masses of the atoms in one molecule.
o. Most elements have isotopic variants.
1. Isotopes are variant forms of an element with the same number of protons, but with different numbers of neutrons.
2. When stating the atomic mass of an element, one must average the atomic masses of its isotopes.
3. Radioisotopes regularly and spontaneously change into more stable atoms by giving off radiation, usually in the form of electrons.
p. Each atom has a distinctive arrangement of electrons.
q. The periodic table, first devised in 1869 by Dmitri Mendeleev, arranges elements in order of their atomic numbers and relates their properties to their atomic structures (Figure 3.2).
1. Each horizontal row of the periodic table is called a period.
2. Each column of the periodic table is called a family.
3.2 Some atoms form molecules by sharing electrons.
a. All biomolecules are basically made of only six elements: hydrogen, carbon, nitrogen, oxygen, phosphorus, and sulfur.
b. Covalent bonds exist when two atoms share electrons, making strong bonds with one another to form a stable molecule.
c. Every hydrogen atom has one electron.
d. Hydrogen's electron resides in a small spherical region around the atomic nucleus called an orbital.
e. Methane is a colorless, odorless natural gas with the formula CH4.
f. Ammonia (NH3) is formed when an atom of nitrogen combines with three hydrogen atoms.
g. Water (H2O) is formed when an oxygen atom combines with two hydrogen atoms.
h. Water is a V-shaped molecule with an angle of about 105û between bonds.
i. Electronegativity is a characteristic of an atomic nucleus that describes its affinity for valence electrons.
j. Polar covalent bonds are achieved when two atoms bond by sharing electrons and when one is much more electronegative than the other. This results in one atom holding the electrons more tightly than the other atom.
k. Polar molecules, such as water, have an uneven distribution of electrical charge.
l. An ion is an atom or molecule with an electric charge that results from unequal numbers of protons and electrons.
m. A hydrogen ion (H+) is produced when one hydrogen atom in water becomes unbonded and leaves the rest of the molecule. When this occurs, the hydrogen atom leaves its sole electron with the oxygen atom and becomes a hydrogen ion. Another way to look at a hydrogen ion is as a lone proton.
n. A hydroxyl ion (OH-) is what remains of a water molecule when one hydrogen atom leaves the rest of the molecule. A hydroxyl ion has a single negative charge.
3.3 Many compounds are made from combinations of positive and negative ions.
a. Ionic bonds are formed when ions are held together by the mutual attraction of their positive and negative ions rather than by sharing electrons.
b. Cations are ions with positive charges, such as Li+, Na+, and K+.
c. Anions are ions with negative charges, such as F-, Cl-, and Br -.
d. The s and p orbitals are sometimes referred to as valence orbitals. The electrons in these orbitals are often called valence electrons.
e. The octet rule states that atoms form bonds by transferring or sharing electrons so that each atom is surrounded by 8 valence electrons.
f. The capacity of an atom to combine with others is described by its valence, the number of electrons it can donate or accept.
g. Elements such as sodium, potassium, fluorine, and chlorine have a valence of 1, and their ions are monovalent cations (e.g. Na+, K+) or monovalent anions (e.g. F-, Cl-).
h. Elements such as beryllium, magnesium, and calcium have a valence of 2, and their ions are divalent cations (e.g. Mg2+, Ca2+).
3.4 Atoms are rearranged in chemical reactions.
a. Chemical reactions are processes in which one kind of material is converted into another.
1. Elements can combine to form compounds.
2. Acids and bases can neutralize each other with the products being salts and water.
3. Compounds sometimes decompose into their elements.
b. The written description of a chemical reaction is called a chemical equation. These equations must account for all the material that goes into and comes out of the reaction. One is said to have balanced the equation when one adjusts the amounts of reactants and products so that they are equal.
c. A mole is the unit used to describe how much material takes part in a reaction.
1. A mole of any substance is about 6 x 1023 molecules (or atoms) of it.
2. The unit mole is often abbreviated as mol.
3. 6 x 1023 is Avogadro's number and has been determined experimentally to be the number of atoms in x grams of a substance with atomic (or molecular) mass x.
3.5 Acids and bases liberate or accept hydrogen ions.
a. An acid is a substance that liberates hydrogen ions.
b. A base is a substance that accepts hydrogen ions.
c. Water can act like an acid because it can dissociate into a hydrogen ion and a hydroxyl ion.
d. Water can act like a base because it can combine with a hydrogen ion to form a hydronium ion (H3O+).
3.6 Hydrogen ion concentrations are expressed as pH.
a. The concentration of a chemical solution is commonly expressed as molarity, the number of moles of solute (the substance dissolved) per liter of solution.
b. pH is defined as the negative logarithm (to the base 10) of the hydrogen ion concentration; pH = -log10 [H+].
1. A solution with more H+ ions than OH- ions is acidic. In an acidic solution, if [H+] = 10-4 M, the pH is 4.
2. A solution with more OH- ions than H+ is basic or alkaline. In a basic solution, if [H+] = 10-9 M, the pH is 9.
3. A solution is neutral if the concentrations of H+ and OH- are equal.
c. The pH scale is a logarithmic scale, and each unit means a hydrogen-ion concentration 10 times different from the next unit (Figure 3.3).
d. A buffer is a substance that absorbs and releases H+ ions in a way that keeps the pH of a solution constant. Blood is an example of a buffer.
3.7 Water has unusual properties that are essential for life.
a. All organisms are largely composed of water (Table 3.1), and chemical principles suggest that no substance could substitute for water in a biological system.
b. Hydrogen bonds are weak interactions where a hydrogen atom is shared between two relatively electronegative atoms and holds them together.
c. Hydrogen bonding within water gives it many biologically important properties.
1. Water is cohesive (water molecules stick together) and it is adhesive (it can form hydrogen bonds with many biomolecules).
2. Water has surface tension. Because the molecules of water on the surface of a body of water are held together by hydrogen bonding from within the water, small objects can rest on top of the water even if they are more dense than the water (Figure 3.6).
3. Water is an excellent solvent for many substances, can dissolve many kinds of organic compounds, and helps facilitate metabolism.
4. The cytosol is a mostly aqueous solution found inside of cells; it contains many kinds of molecules and ions.
5. Water has a high heat capacity. Heat capacity is defined as a substance's ability to hold heat. Specific heat, a measure of heat capacity, is the heat required to raise the temperature of one gram of a substance 1û C. The specific heat of water is 1 calorie (cal) per gram by definition.
6. Water has a high heat of vaporization. Heat of vaporization is defined as the amount of energy needed to vaporize a substance. This feature of water is biologically significant because the evaporation of water is one major way that terrestrial organisms cool themselves (Figure 3.7).
7. Water has a high heat of fusion. Heat of fusion is defined as the amount of energy that must be removed to freeze a substance. This feature of water is biologically significant because bodies of water help modulate sudden shifts of temperature on earth (Figure 3.8).
8. Water remains liquid over a wide temperature range, from 0û C to 100û C. This property of water makes possible a wide variety of habitats in which organisms can exist (Figure 3.9).
9. Ice is less dense than liquid water and consequently it floats. This allows the ice that forms on bodies of water to serve as an insulating layer. This insulation reduces heat loss from the water, which allows life below the ice to continue.
3.8 Organisms are composed of only about 25—30 elements.
a. Traces of all elements have been found in organisms, but only about 25—30 of them are known to have any biological function (Table 3.2).
b. The distribution of elements in organisms in general is remarkably similar to their distribution in the whole universe, with some exceptions (Figure 3.10).
c. The uniqueness of living things doesn't come from their constituent elements but rather from the molecules those elements form and the way the molecules react with one another.
d. The four major components of organic molecules and the elements that constitute the bulk of an organism's substance are: hydrogen, carbon, nitrogen, and oxygen.
e. The next group of important elements are somewhat less abundant: sulfur, phosphorus, sodium, magnesium, potassium, calcium, and chlorine.
f. Trace elements are a group of elements that are the lowest on the abundance scale and that often work as biological catalysts to help speed up metabolic processes.
3.9 Organisms are constructed of carbon-based molecules.
a. The weight of an organism after all the water is removed is referred to as its dry weight.
b. Organic compounds are composed of carbon and hydrogen, and most of them also contain oxygen and nitrogen.
c. Hydrocarbons are compounds containing only carbon and hydrogen.
1. The simplest hydrocarbon is methane (CH4), with one carbon atom bonded to four hydrogen atoms.
2. The next larger hydrocarbon is ethane (C2H6), with two carbon atoms bonded to each other and the three remaining bonds on each carbon atom are made to hydrogen atoms.
3. The next hydrocarbon in the series is propane (C3H8), with one more carbon atom and two more hydrogen atoms than ethane.
4. Butane (C4H10) is next in the series, but has two possible structures.
d. The two structures of butane are called isomers because they have the same composition but different structures.
1. One of these structures is unbranched and is labeled the straight chain. It is called n-butane, where the n stands for normal.
2. The other structure of butane is branched and is called isobutane. The prefix iso- means equal, which refers to the symmetrical shape of the molecule.
e. Saturated hydrocarbons are those characterized by a carbon atom carrying the maximum number of hydrogen atoms, either two or three.
f. Unsaturated hydrocarbons have fewer than the maximum number of hydrogen atoms.
g. Double bonds are said to exist when two carbon atoms share two pairs of electrons.
h. In many cases, carbon chains form ringed structures such as pentagons (five-sided rings) and hexagons (six-sided rings).
3.10 Organic molecules have distinctive shapes, and most can change shape without breaking bonds.
a. All organic molecules have distinctive three-dimensional shapes (Figure 3.11).
1. Methane (CH4) is a tetrahedron with a carbon atom in the center and a hydrogen atom at each of the four corners.
2. Ethane (C2H6) is like two linked tetrahedrons.
3. Hydrocarbon chains have a zigzag shape with the hydrogen atoms alternately forming a pair of knobs on apposite sides.
4. Branched-chain molecules have increasingly complex forms as the chains become longer.
b. Compounds called aromatic hydrocarbons have strong odors, and illustrate a common feature of some organic structures: electrons occupying large orbitals.
1. In benzene (C6H6), each of its carbon atoms is bonded to only one hydrogen atom, and the carbons form a ring that is conventionally drawn with alternating single and double bonds.
2. This representation of benzene is actually unrealistic. The electrons are not localized, but rather are delocalized and able to occupy large doughnut-shaped orbitals spread around the whole ring.
3. Aromatic molecules are flat, with all the atoms in the ring lying in a plane, in contrast to the zigzag forms of saturated molecules such as cyclohexane.
c. When the atoms in organic molecules are joined only by single bonds, they can generally rotate around these bonds. This allows the molecule's shape to be changeable.
1. By rotating some atoms, but without breaking the bonds between them, a molecule can switch between two distinct conformations.
2. These two conformations, different arrangements of the atoms in space, are called the chair and boat forms.
3. The ability of large organic molecules to change conformations accounts for most of their biological activity.
3.11 The solubility of an organic molecule in water is important biologically.
a. Water-soluble molecules are hydrophilic, literally "water loving."
1. The general rule is that "like dissolves like." This means that polar molecules readily dissolve in water which is polar.
2. Salts readily dissolve in water.
b. Nonpolar materials such as hydrocarbons that are not water soluble, are hydrophobic or "water fearing."
1. The hydrophobic effect is explained by the fact that water molecules attract one another strongly but have very little attraction for hydrocarbon molecules. When hydrocarbons are mixed with water, they tend to disrupt the hydrogen-bonded water structure. Oil and water do not mix.
2. Within a droplet of hydrocarbon molecules, the hydrocarbons are held together by weak interactions called van der Waals forces. These weak forces can be disrupted by simple shaking, as in shaking the oil and vinegar in a salad dressing (Figure 3.12).
c. The affinity of a biomolecule for the water in cytosol or for the surrounding membranes determines where it resides and how it functions.
1. Water-soluble organic molecules are compatible with the water contained in cells, where most chemical reactions of metabolism occur.
2. The membranes that separate the cell from its environment consist of hydrophobic molecules.
3.12 Different types of organic molecules are characterized by their functional groups.
a. A few common groups of atoms, called functional groups, have the ability to change a hydrocarbon's character when added to the molecule.
1. Alcohols are organic molecules with a hydroxyl group (-OH). Hydroxyl groups are polar, making short-chain alcohols water-soluble. When the hydrocarbon chain is very long, a single polar group cannot make the molecule hydrophilic.
2. A carbonyl group (-C=O) is a carbon atom double-bonded to an oxygen atom. When a carbonyl group is located on the end of a chain it is an aldehyde (acetaldehyde; CH3HC=O). When a carbonyl group is located on an internal position in a chain it forms a ketone (acetone). Sugars are aldehydes or ketones that also have one or more hydroxyl groups.
3. A carboxyl group (-COOH) is a carbon with a double bond to an oxygen atom and a single bond to a hydroxyl group. Molecules that contain carboxyl groups are organic acids; vinegar is a dilute acetic acid (CH3COOH). Carboxyl groups are acidic because they dissociate by releasing a hydrogen ion.
4. Molecules containing amino groups (-NH2) are called amines. Amines are bases because an amino group acts very much like an ammonia molecule and can accept a hydrogen ion. An example of an amine is propylamine (CH3CH2CH2NH2).
5. Molecules containing sulfhydryl groups (-SF) are thiols or mercaptans. Thiols and their modifications are very important in protein structure. They are also remarkable for their pungent odors, such as those of rotten eggs, chopped onions, and garlic. An example of a thiol is mercaptoethanol (HO-CH2CH2SH).
6. Organic compounds called phosphates contain some form of phosphoric acid (H3PO4) and are very common and essential in biology. The phosphate group on an organic molecule can have different forms depending on the pH of the medium.
b. Molecules become more hydrophobic and less soluble in water if they carry nonpolar groups; most often these are small hydrocarbon chains such as methyl (-CH3) and ethyl (-CH2CH3) groups.
1. The suffix -yl indicates a portion of a molecule that is considered a group.
2. Methane, for example, is transformed into a methyl group, and acetic acid with its hydroxyl group removed becomes an acetyl group (CH3C=O).
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