Chapter 2: Chemistry

Molecules and compounds

A molecule is two or more elements bonded together. It is the smallest part of a compound that retains its chemical properties. A compound is a molecule containing at least two different elements bonded together. A formula tells the number of each kind of atom in a molecule.

Chemistry of water cont.

A hydrogen bond is a weak attraction between a slightly positive hydrogen atom and a slightly negative atom. In water, hydrogen bonds occur between atoms of different molecules. Help to maintain the proper structure and function of complex molecules such as proteins and DNA. A single hydrogen bond is easily broken while multiple hydrogen bonds are collectively quite strong.

6 C 12

6 is the atomic number - this means this element has 6 protons and 6 electrons 12 is the mass number - this means this element has 6 protons and 6 neutrons

Ionic bonding

An ion is an atom that has lost or gained an electron

Properties of water

Frozen water (ice) is less dense than liquid water. At temperatures below 4C, hydrogen bond between water molecules become more rigid but also more open. Water expands as it reaches 0C and freezes. Ice floats on liquid water. Without this property, ice would sink and oceans freeze solid, instead of from the top down. Acts as an insulator on top of a frozen body of water.

Electron shells

Orbiting clouds around nucleus

Radiation

Radioactive isotopes give off energy in the form of rays and subatomic particles. They can be helpful or harmful. Carbon 14 is an example of a radioactive isotope. Low levels of radiation is used to diagnose diseases: MRI, PET scan. High levels of radiation can be used to sterilize medical products, preserve food, and kill cancer cells.

Matter

Refers to anything that has mass and occupies space. Exists in 3 states. Solid, liquid, and gas. All matter (both living and non-living) is called elements.

Buffers and pH cont.

A buffer is a chemical or a combination of chemicals that keeps pH within normal limits. Health of organisms requires maintaining the pH of body fluids within narrow limits. Human blood is normall pH 7.4 (slightly basic). If blood pH drops below 7.0, acidosis results. If blood pH rises above 7.8, alkalosis results. Both are life threatening situations.

Atoms

An atom is the smallest part of an element that displays the property of the element. An element and its atom share the same name. Composed of subatomic particles: protons, neutrons, and electrons. Central nucleus: protons - positively charged, neutrons - no charge, electrons - negatively charged - negligible in calculations.

Elements

An element is a substance that cannot be broken down into substances with different properties; composed of one type of atom. 92 elements are naturally occurring. Six elements make up 95% of the body weight of organisms (acronym CHONPS: Carbon, hydrogen, oxygen, nitrogen, phosphorus and sulfur.

Periodic table

Atoms of an element are arranged horizontally by increasing atomic number in rows called periods. Atoms of an element arranged in vertical columns are called groups. Atoms within the same group share the same chemical binding characteristics. Group VIII are the noble gases and are inert - meaning their valence shells are stable and that they do not react. Atoms shown in the periodic table are electrically neutral.

Chemical bonding

Bonds that exist between atoms in molecules contain energy. Bonds between atoms are caused by the interactions between electrons in the outermost energy shells. An atom must have vacancy in its outermost electron shell to bond with other atoms. The process of bond formation is called a chemical reaction.

Compounds and molecules

C6H1206 indicates 6 atoms of carbon, 12 atoms of hydrogen, and 6 atoms of oxygen.

Water as a transport medium

Cohesion and adhesion account for water transport in plants as well as transport in blood vessels.

Properties of water: cohesion and adhesion

Cohesion: Hydrogen bonds hold water molecules tightly together i.e. allows water to flow freely without molecules separating. Adhesion: hydrogen bonds between water and other polar materials. Both allow water to be drawn many meters up a tree in a tubular vessel. High surface tension: Water molecules at the surface hold more tightly than below the surface. Amounts to an invisible "skin" on water surface. Allows small nonpolar objects (like a water strider) to sit on top of water.

Atomic number and mass number

Each element is represented by one or two letters to give it a unique atomic symbol. H = hydrogen, Na = sodium, C = carbon. The atomic number is equal to the number of protons in each atom of an element. The mass number of an atom is equal to the sum of the number of protons and neutrons in the atom's nucleus. The atomic mass is approximately equal to the mass number.

Electrons and energy

Electrons are attracted to the positively charged nucleus; thus, it takes energy to hold electrons in place. It takes energy to push them away and keep them in their own shell. The more distant the shell, the more energy it takes to hold it in its place. Electrons have energy due to their relative position (potential energy). Electrons determine chemical behavior of atoms.

Properties of water: heat of fusion

Heat of fusion (melting) To raise ice from -2 to -1 degree celsius, 1 calorie is required. To raise ice from 1 degree to 0 degree celsius, 1 calorie is required. To raise water from 0 to 1 degree celsius, 80 calories are required. This is why ice at 0 degrees celsius keeps items cold much longer than water at 1 degree celsius. This is why ice is used for cooling, not due to its low temperature but because it absorbs so much heat before it will warm by one degree.

Isotopes

Isotopes are atoms of the same element that differ in the number of neutrons (and therefore different atomic masses). Some isotopes spontaneously decay.

Properties of water

Living things contain 70 - 90% water. Due to hydrogen bonding, water molecules cling together. Water has very unique characteristics that makes the existence of life on earth possible. Many of the important properties of water are the result of hydrogen bonding.

The distribution of electrons

The Bohr model is a useful way to visualize electron location. Bohr model shows electron shells as concentric circles around nucleus. Electrons revolve around the nucleus in energy shells (energy levels). For atoms with atomic numbers of 20 or less, the following rules apply: 1. the first shell can hold up to 2 electrons 2. each additional shell can hold up to 8 electrons 3. each lower shell is filled first before electrons are placed in the next shell These rules cover most of the biologically significant elements

Electron sharing

The electrons in the periodic table are electrically neutral meaning that they always contain the same amount of electrons (negative charge) as protons (positive charge). These charges cancel each other out and thus leave the element with a neutral, or 0 charge. When an element shares its valence electron with another, it can become positive by losing an electron thus causing the proton/electron ratio to not be equal anymore and giving it one more proton than electron. This new element is now called an ion, or an ionic bond occurs when one element gives another element an electron.

Valence electrons cont.

The number of electrons in an atom's valence shell determines whether the atom gives up, accepts, or shares electrons to acquire eight electrons in the outer shell. Atoms that have their valence shells filled with electrons tend to be chemically stable. Atoms that do not have their valence shells filled with electrons are chemically reactive.

Valence electrons

The outermost energy shell of any atom is called the valence shell. The valence shell is important because it determines many of an atom's chemical properties. The octet rule states that the outermost shell is most stable when it has eight electrons. Exception: If an atom has only one shell, the outermost valence shell is complete when it has two electrons.

Noble gases

These include Kr -krypton, Ne - neon, Ar - argon, He - helium, Xe - xenon, and Rn - Radon.

The chemistry of water: heat capacity

Water has a high heat capacity. When heat is applied to most liquids: molecules bounce faster and the temperature increases. But, when heat is applied to water, hydrogen bonds restrain bouncing. Temperature rises more slowly per unit heat. Water at a given temperature has more heat than most liquids. Thermal inertia: resistance to temperature change. More heat is required to raise water 1 degree than most other liquids (1 calorie per gram). Temperature of water rises and falls slowly, organisms are therefore better able to maintain a steady internal temperature.

Properties of water: heat of vaporization

Water has a high heat of vaporization. To raise water from 98 degrees to 99 degrees, -1 calorie. To raise water from 99 to 100 degrees, -1 calorie. However, large numbers of hydrogen bonds must be broken to evaporate water. To raise water from 100 to 101, it takes 540 calories. This is why sweating and panting cools. Evaporative cooling is best when humidity is low because evaporation occurs rapidly.

Properties of water: water as a solvent

Water is a good solvent because of its polarity. Solutions consist of: a solvent (the most abundant part) and a solute (the less abundant part) that is dissolved in the solvent. Polar compounds readily dissolve; hydrophilic molecules dissolve in water. Hydrophobic molecules do not dissolve in water. Ionic compounds dissociate in water because it is polar. NA+: attracted to negative (O) H20. Each Na+ completely surrounded by H20. Cl-: Attracted to positive (H2), end of H20. Each Cl- completely surrounded by H20.

Chemistry of water

Water is a polar molcule. In H20, sharing of electrons by oxygen and hydrogen is not equal. The oxygen atoms with more protons attracts the electrons more. Oxygen is partially negative and hydrogen is partially positive.

Buffers and PH

When H+ is added to pure water at pH 7, pH goes down and water becomes acidic. When OH- is added to pure water at pH 7, pH goes up and water becomes alkaline. Buffers are solutes in water that resist change in pH. Keep pH within normal range. When H+ i added, buffer may absorb or counter by adding OH-. When OH- is added, buffer may reabsorb, or counter by adding H+.

2.4 acids and bases

pH is a measure of hydrogen ion concentration in a solution. When water ionizes or dissociates, it releases an equal number of hydrogen (H+) ions and hydroxide (OH-) ions. Acids are substances that dissociate in water, releasing hydrogen ions. Have a sour taste. Bases are substances that either take up hydrogen ions (H+), or release hydroxide ions (OH-). Has a bitter taste.

Ionic bond

An ionic bond forms wen electrons are transferred from one atom to another atom and the oppositely charged ions are attracted to each other. Example: formation of sodium chloride. Salts are solid substances that usually separate and exist as individual ions of water.

Nonpolar covalent bonds

Covalent bonds can be either non-polar or polar. In nonpolar covalent bonds, sharing of electrons is equal, i.e. the electrons are not attracted to either atom to a greater degree. The bonded electrons will spend about equal time with both atoms. Examples: hydrogen gas, oxygen gas, methane.

Covalent bond

Covalent bonds result when two atoms share electrons so each atom has an octet of electons in the outer shell. Note: in the case of hydrogen, the outer energy shell is complete when it contain two electrons. Single bond: when a single pair of electrons is shared between two atoms. Double covalent bond: when two pairs of electrons are shared between atoms.

Polar covalent bonds

In a polar covalent bond, electrons are shared unequally. Electronegativity is the ability of an atom to attract electrons toward itself in a chemical bond. In water, the oxygen atom is more electronegative than the hydrogen atoms and the bonds are therefore polar.

The PH scale

The PH scale is used to indicate the acidity or basicity (alkalinity) of a solution. Values range from 1 - 14. 0 to < 7 = acidic. 7 = neutral. >7 to 14 = basic (or alkaline). Logarithmic scale: each unit change in pH represents a 10-fold change in H+ concentration. pH of 4 is 10x as acidic as pH of 5. pH of 10 is 100x more basic than pH of 8.