The Building Blocks of Matter
All matter, from a rock to an animal to the magma at the center of the Earth, is made from different combinations of 92 naturally occurring substances known as elements. The smallest quantity of an element that still exhibits the characteristics of that element is known as an atom. One atom of carbon, for example, is the smallest piece of matter that still retains the chemical and physical characteristics of carbon.
Atoms are made up of even smaller particles called electrons, protons, and neutrons. Each of these particles has a different electrical charge. Protons are positively charged, neutrons have no charge, and electrons are negatively charged. The protons and neutrons of an atom reside in a central body called a nucleus. Electrons appear around the nucleus within orbitals of varying energy. Overall, the atom is neutrally charged with equal numbers of positively charged protons and negatively charged electrons.
Elements are distinguished by the number of protons in their nuclei. All atoms containing six protons are called carbon. Any element with one proton is called hydrogen. Only the number of protons—and not the number of neutrons or electrons—distinguishes elements from each other.
Isotopes and Ions
Though the number of neutrons and electrons in an atom won’t change the atom’s status as a particular element, it can affect the properties of an element in subtle ways. An atom that contains a larger or smaller number of neutrons than usual is called an isotope. Carbon usually has six protons and six neutrons and can be called carbon-12 because the number of its protons and neutrons add up to 12. But some carbon atoms have seven or even eight neutrons. These two isotopes are called carbon-13 and carbon-14. Isotopes do not have charge, because the numbers of positive and negative particles remain balanced. Even though they have different masses, isotopes of the same element all have similar chemical properties, because the number of electrons (not the number of neutrons or protons) determines the way an atom will interact with other atoms.
Ions are atoms that either lack or have extra electrons. Because these atoms have unequal numbers of electrons and protons, they are charged particles and are often quite chemically interactive with other atoms. Though the SAT II Biology Test rarely asks direct questions about ions, ions do play an important role in many biological processes and phenomena, so understanding the basics of ions can help you understand the processes that the test covers.
Molecules and Compounds
Atoms combine with each other in chemical reactions to create molecules, unique substances with physical and chemical properties distinct from those of their constituent elements. Combining two hydrogen atoms with one oxygen atom creates water, which has very different characteristics than hydrogen or oxygen do alone. Molecules such as water containing more than one type of element can also be called compounds. A water molecule made up of oxygen and hydrogen can be called a compound; a hydrogen molecule, which contains only two hydrogen atoms, cannot be called a compound.
You may have heard water referred to as H2O. This notation is the standard way of representing molecules and compounds by shorthand. The “H” and “O” stand for the elements hydrogen and oxygen, and the subscript indicates that water contains two parts hydrogen for every one part oxygen. You can create the formula for any compound by writing down the letter symbol of each of its constituent elements and using subscripted numbers to indicate how many atoms of each element are present.
Chemical Bonds
The connections between the atoms in a compound are called chemical bonds. Atoms form bonds by sharing their electrons with each other, relying on the power of electric charge to keep themselves attached. Molecules and compounds can also bond with each other. Important bonds between atoms are covalent and ionic bonds. Bonds between molecules or compounds are called dipole-dipole bonds.
Covalent bonds
Bonds formed through the more or less equal sharing of electrons between atoms are known as covalent bonds.
If the electrons in a covalent bond are shared equally, the resulting bond is called a nonpolar covalent bond. When one atom pulls the shared electrons toward itself a little more tightly than the other, the resulting covalent bond is said to be a polar bond. In a polar bond, the atom that pulls electrons toward itself gains a slight negative charge (because electrons have a negative charge). Since the other atom partially loses an electron, it gains a slight positive charge. For example, the atoms in water form polar bonds because oxygen, which has eight protons in its nucleus, has a greater pull on electrons than hydrogen, which has only one proton.
Ionic Bonds
Polar covalent bonds involve the unequal sharing of electrons. This inequality is brought to an extreme in a bonding arrangement called an ionic bond. In an ionic bond, one atom pulls the shared electrons away from the other atom entirely. Ionic bonds are stronger than polar bonds.
One example of ionic bonding is the reaction between sodium (Na) and chlorine (Cl) to form table salt (NaCl). The chlorine atom steals an electron from the sodium atom. Because it loses an electron, the sodium atom develops a charge of +1. The chlorine atom has a charge of –1, since it gained an electron.
Dipole-Dipole Bonds
As seen in polar covalent compounds, due to the unequal sharing of electrons, some molecules have a slightly positive and a slightly negative end to them, or a dipole (di-pole = two magnetic poles). These compounds can form weak bonds with one another without combining together completely to create new compounds. This type of bonding, known as dipole-dipole interaction, takes places when the positively charged end of one polar covalent compound (d+) comes in contact with the negatively charged end of another polar covalent compound (d–):
Dipole-dipole interactions are much weaker than the bonds within molecules, but they play a very important role in the chemistry of life. Perhaps the most important dipole-dipole bond in biochemistry (and on the SAT II Biology) is the dipole-dipole interaction between positively charged hydrogen molecules and negatively charged oxygen molecules. This reaction is so important, it gets its own special name: hydrogen bond. These bonds account for many of the exceptional properties of water and have important effects on the structure of proteins and DNA.
Acids and Bases
Sometimes atoms give their electrons up altogether instead of sharing them in a chemical bond. This process is known as disassociation. Water, for instance, dissociates by the following formula:
H2OH+ + OH–
The hydrogen atom gives up a negatively charged electron, gaining a positive charge, and the OH compound gains a negatively charged electron, taking on a negative charge. The H+ is known as a hydrogen ion and OH– ion is known as a hydroxide ion.
The disassociation of water produces equal amounts of hydrogen and hydroxide ions. However, the disassociation of some compounds produces solutions with high proportions of either hydrogen or hydroxide ions. Solutions high in hydrogen ions are known as acids, while solutions high in hydroxide ions are known as bases. Both types of solution are extremely reactive—likely to form bonds—because they contain so many charged particles.
The technical definition of an acid is that it is a hydrogen ion donor, or a proton donor, as hydrogen ions are consist of only a single proton. Acids put H+ ions into solution. The definition of a base is a little more complicated: they are H+ ion or proton acceptors, which means that they remove H+ ions from solution. Some bases can directly produce OH– ions that will take H+ out of solution. NaOH is an example of this type of base:
NaOHNa+ + OH–
A second type of base can directly take H+ out of an H2O solution. Ammonia (NH3) is a common example of this sort of base:
NH3 + H2ONH4+ + OH–
From time to time, the SAT II Biology has been known to ask whether ammonia is a base.
The pH Scale
The pH scale, which ranges from 0 to 14, measures the degree to which a solution is acidic or basic. If the proportion of hydrogen ions in a solution is the same as the proportion of hydroxide ions or equivalent, the solution has a pH of 7, which is neutral. The most acidic solutions (those with a high proportion of H+) have pHs approaching 0, while the most basic solutions (those with a high proportion of OH– or equivalent) have pHs closer to 14.
Water has a pH of 7 because it has equal proportions of H+ and OH– ions. In contrast, when a compound called hydrogen fluoride (HF) disassociates, it forms only hydroxide ions. HF is therefore quite acidic and has a pH well below 7. Some acids are more acidic than others because they put more H+ ions into solution. Stomach fluid, for example, is more acidic than saliva.
When sodium hydroxide (NaOH) disassociates, it forms only hydroxide ions, making it a base and giving it a pH above 7. Like acids, bases can be strong or weak depending on how many hydroxide ions they put in solution or how many hydrogen ions they take out of solution.
Buffers
Some substances resist changes in pH even when acids or bases are added to them. These substances are known as buffers. The cell contains many buffers because wide swings in pH can negatively impact the chemical reactions of cell processes.
The Chemistry of Life
Of the 92 naturally existing elements on the Earth, only 25 play a role in the chemical processes of life. Of these 25, four elements constitute more than 98 percent of all biological matter: carbon (C), oxygen (O), hydrogen (H), and nitrogen (N). Virtually every important organic compound is made up of these four elements. The Big 4 of organic elements can be cut down even further to a Supreme 1: carbon is the most important biological molecule, both for life as we know it and on the SAT II.
Carbon
Carbon is the central element of life. Its important role stems from its ability to form four chemical bonds with other elements at the same time:
Carbons often attach to other carbon atoms, forming long chains called hydrocarbons. These molecules get their name because the central carbons also bond to hydrogen:
In addition to making a connection to four other atoms, carbon also has the ability to make two or three separate connections with the same single partner (and make its remaining one or two bonds with other substances). These bonds, which are stronger than single bonds, are known as double or triple bonds, respectively.
Monomers and Polymers
Many biological molecules consist of basic units that are strung together to form long chains, much like beads are placed on a string to make a necklace. There can be some variation in these basic units, which are known as monomers. Two monomers connected to each other are known as a dimer; a chain of monomers is called a polymer.
Polymers can be formed by many different types of chemical reactions. One special reaction, however, is particularly important in producing the polymers found in the chemistry of life. This reaction involves a carbon that has a hydrogen atom attached and a carbon that has an OH– group attached. When the carbons bond to each other, they release a water molecule formed from the oxygen atom and the two hydrogen atoms.
Because a water molecule is created in order to join the two monomers, this reaction is known as dehydration synthesis. The reverse of dehydration synthesis, when a water molecule is inserted into a polymer to break off a monomer, is called hydrolysis.
