Chapter 2 Chemistry of Life

2.1 Nature of Life

Atoms

The greek philosopher, Democritus, first came up with the concept of the basic unit of matter, the atom. (atomos means unable to be cut)

Atoms are made up of subatomic particles called protons, neutrons, and electrons.

Atoms are incredibly small. Placed side by side, 100 million atoms would make a row only 1 cm long.

Protons and neutrons have about the same mass.
Protons are positively charged particles (+)
Neutrons carry on charge.

Strong forces bind protons and neutrons together to form the nucleus, the center of the atom.

Electrons are negatively charged particles (-) with only 1/1840 the mass of a proton.

Electrons are in constant motion in the space outside of and surrounding the nucleus and are attracted to the positively charged nucleus by the opposite charges.

Atoms have equal numbers of electrons and protons so their charges balance out. Therefore, they are electrically neutral.

Elements and Isotopes

An element is a pure substance that consists entirely of one type of atom. There are more than 100 known elements, but only about 24 of them reside in living organisms.

Mercury, a silvery-white metallic element, is liquid at room temperature and forms droplets. It is extremely poisonous.

                                        

Atoms of the same element may have different numbers of neutrons. These are known as isotopes.

Isotopes of the same element have the same number of protons but a different number of neutrons.

The total number of protons + neutrons in the nucleus is called its mass number.

mass # = protons + neutrons

Isotopes are identified by their mass numbers

Because they have the same number of electrons, all isotopes of an element have the same chemical properties.

(it is the number of electrons in the outer (valence) shell which determines an elements chemical properties)

Some isotopes have such uneven ratios of protons to neutrons, their nuclei are unstable and break down at a constant rate over time. This means they are radioactive. 

Radiation is dangerous, but these isotopes have a number of important scientific and practical uses such as C14 dating, medical diagnostics and treatments.

Chemical Compounds

In nature, most elements are found combined with other elements in compounds. A chemical compound is a substance formed by the chemical combination of two or more elements in definite proportions.

The composition of compounds is like an exact recipe. It tells how many atoms of each element are contained within the compound. 

H2O - two hydrogen atoms for every one oxygen atom

NaCl - one sodium atom for every chlorine atom

The physical and chemical properties of a compound are usually very different from those of the elements from which it is formed.

ex: NaCl (table salt)

Na - silver-colored metal

Cl - poisonous yellow-green gas

Chemical Bonds

There are 2 main types of chemical bonds.

Ionic and Covalent bonds.

Bond formation involves the electrons in the outermost shell surrounding the nucleus.

Ionic Bonds

An ionic bond is formed when one or more electrons are transferred from one atom to another. 

When an atom loses an electron (-) to another atom it becomes positively charged. When an atom gains an electron (-), it becomes negatively charged. These charged atoms are called ions. 

This transfer of electrons causes the ions to have a strong attractions to each other forming an "ionic bond." 

The compound sodium chloride forms when sodium loses its valence electron to chlorine.

Covalent Bonds

Sometimes electrons are shared by atoms instead of being transferred. This means that the moving electrons are actually traveling about about the nuclei of both atoms, forming a covalent bond.

When atoms share 2 bond, the bond is called a single covalent bond, and so on.

share 2 bonds - single covalent bond

share 4 bonds - double covalent bond

share 6 bonds - triple covalent bond

Molecule - structure that results when atoms are joined together by covalent bonds.

In a water molecule, each hydrogen atom shares two electrons with the oxygen atom.

                                        

Van der Waals Forces

Because of their structures, atoms of different elements do not all have the same ability to attract electrons. Some atoms have a stronger attraction for electrons than do other atoms. When the atomsin a covalent bond share electrons, the sharing is not always equal. This can create regions on a molecule that have a tiny positive or negative charge.

When molecules are close together, a slight attraction can develop between the oppositely charged regions of nearby molecules call van der Waals forces.

These are not as strong as bonds, but they can hold different molecules together. 

A gecko foot is covered by as many as half a million tiny hairlike projections. Each projection is further divided into hundreds of tiny, flat-surfaced fibers. This design allows the gecko's foot to come in contact with an extremely large area of the wall at the molecular level. Van der Waals forces form between molecules on the surface of the gecko's foot and molecules on the surface of the wall.

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2.2

Properties of Water

The Water Molecule

How does the structure of water contribute to its unique properties?

Water is one of the few compounds found in a liquid state over most of the Earth's surface. 

Water is neutral. Its positive (+) charges on its 10 protons balance out its negative (-) charges on its 10 electrons. 

Polarity

With 8 protons, water's oxygen nucleus attracts electrons more strongly than the single protons of water's two H nuclei. As a result, water's "shared" electrons spend more time around the O than the H. This causes the end of the molecule which the electrons are pulled toward to become more negative and the end of the molecule the electrons are being pulled away from to become more positive. 
A molecule in which the charges are unevenly distributed is said to be polar.
The partial charges on polar molecules are written in parentheses (-) and (+) to show that they are weaker than the charges on ions.

A water molecule is polar because there is an uneven distribution of electrons between the O and H atoms. The negative pole is near the O atom and the positive pole is between the H atoms.

Hydrogen Bonding

Because of their partial positive and negative charges, polar molecules like water can attract each other. This attraction of opposite charges involving a H with a partial positive charge and a partial negative charge on a different molecule is called a Hydrogen Bond. 
Hydrogen bonds usually bond with O, N, and F. (FON)

H bonds are not as strong as covalent or ionic bonds. Because water is a polar molecule, it is able to form multiple H bonds which account for many of water's special properties.

Each molecule of water can form multiple H bonds with other water molecules.

Cohesion

Cohesion is an attraction between molecules of the same substance. Water is extremely cohesive and can form as many as 4 H bonds at a time. Cohesion causes the water molecules to stick together. This accounts for why drops of water form beads on a smooth surface, and why some insects can walk on water.

The strong attraction between water molecules produces a force sometimes called "surface tension," which can support very lightweight objects, such as this raft spider.

Adhesion

Adhesion is an attraction between molecules of different substances, like water and glass, and is responsible the the meniscus that forms when water is in a glass container. It is also responsible for the capillary action that draws water out of the roots of a plant and up into the stem against gravity.

Adhesion between water and glass molecules is responsible for causing the water in these columns to rise. The surface of the water in the glass column dips slightly in the center, forming a curve called a meniscus.

Heat Capacity

It takes a large amount of heat energy to cause the H bonded molecules of water to move faster, which raises the temperature of water. Water's heat capacity, the amount of heat energy required to increase its temperature, is relatively high. This fact keeps large bodies of water from drastic fluctuations in temperature. This is important for the organisms who live there. At the cellular level, water absorbs the heat produced by cell processes. Cells would not be able to tolerate rapid fluctuations in temperature. 

Solutions and Suspensions

A mixture is a material composed of two or more elements or compounds that are physically mixed together but not chemically combined. Salt and pepper, sugar and sand, and salad are all mixtures. Living things are in part composed of mixtures, and other gases. 

Two types of mixtures that can be made with water:

solutions and suspensions

Solutions

If table salt (NaCl) is placed in a glass of water, the polar ends of the water molecule pull the ions away from each other and "dissolve" them in the water molecules. The water molecules will surround the ions until the NaCl is completely dissolved forming a solution, or until there are no more available and the solution is said to be "saturated." All the components of a solution are evenly distributed throughout the solution.
In a solution, the substance in which the solute dissolves is the solvent. The substance being dissolved is the solute.

Water's polarity gives it the ability to dissolve both ionic compounds and other polar molecules.

When an ionic compound such as sodium chloride is placed in water, water molecules surround and separate the positice and negative ions.

Acids, Bases, and pH

Water molecules sometimes split apart to form ions. 

In pure water, only 1/550million molecules split into ions. Since the positive ions = the negative ions, water remains neutral.

 The pH Scale

The pH scale is a measurement system which indicates the concentration of H ions in solution. It ranges from 0 to 14. A pH of 7 means the concentration of H ions and OH ions is equal. Pure water has a pH of 7. Solutions with a pH below 7 are called acids because they have more H ions that OH ions. The lower the pH, the greater the acidity. Solutions with a pH above 7 are called basic because they have more OH ions than H ions. The higher the pH, the more basic the solution. 

pH - the concentration of H ions in solution

Each step on the pH scale represents a factor of 10.

A liter of solution with a pH of 4 has 10x as many H as a liter of solution with a pH of 5.

Acids

An acid is any compound that forms H ions in solution. Acidic solutions contain higher concentrations of H ions than pure water and have pH values below 7. Strong acids have pH values from 1 to 3. (HCl)

Bases

A base is a compound that produces hydroxide (OH) ions in solution. Basic, or alkaline, solutions contain lower concentrations of H ions that pure water and have pH values above 7. Strong bases have pH values ranging from 11 to 14. (Lye soap, NaOH)

Buffers

The pH in the fluids within most cells in the human body must generally be kept between 6.5 and 7.5. If the pH is higher or lower, it will affect the chemical reactions that take place within the cells. Controlling pH is important for maintaining homeostasis.

Buffers are one way organisms can control pH through dissolved compounds. Buffers are weak acids or bases that can react with strong acids or bases to prevent sharp, sudden changes in pH.  

Buffers dissolved in life's fluids play an important role in maintaining homeostasis in organisms.

Buffers help prevent drastic changes in pH. Adding acid to an unbuffered solution causes the pH of the unbuffered solution to drop. If the solution contains a buffer, however, adding the acid will cause only a slight change in pH.