Basic Chemistry for Understanding BiologyChapter 2 The Chemistry of LifeBiologyMrs. Douma

Terms to Know

Matter Anything that takes up space and has mass

Element Pure matter composed of the same kind of atoms Cannot be broken down into other substances by

chemical reaction Compound

A substance consisting of two or more elements combined in a fixed ratio

C,H,O,N make up 96% of all living matter Only about 25 of the known natural elements are

essential to life. Trace elements

Those required by an organisms in only minute quantities

E.g. Iron, iodine

Terms to Know

Atom the smallest component of an element that still has properties of the element, consisting of a positively charged nucleus made up of protons

and neutrons, surrounded by a charged cloud of electrons. Proton particle in the nucleus with a positive charge of +1

and an atomic mass number of 1 Dalton. Neutron a non-charged nuclear particle with the same

mass as the proton. Can vary in number creating Isotopes of the element

Electron negatively charged particle (-1) with a mass 1/1837 of that of a proton. Found in electron shells around the nucleus Determine the chemical properties and reactivity of the element

Atomic number is the number of protons an element possesses. Unique

Mass number of an element is the sum of its protons and neutrons.

Elements of Life

The names of the elements are abbreviated. Often, the abbreviation makes perfect sense (C for carbon) and sometimes it does not (Na for sodium). There is an abundance of elements on earth and in living systems (over 100 on the Periodic Table) but only 4 elements make up 96% of living organisms. These elements are hydrogen - H, oxygen - H, nitrogen - N, and carbon - C

Electrons determine chemical properties of elements

Chemical Bonds are defined as interactions between the valence electrons of different atoms

Electrons move about the nucleus in atomic orbitals.

Absorption of energy can cause an electron to move up to a higher energy level.

The atom is stable when the outermost energy level of most atoms has eight electrons. (The Octet Rule)

Electrons determine chemical properties of elements

Electrons can be transferred carrying energy to another molecule. The H atom can carry

electrons for transferring energy.

Oxygen has a strong affinity for electrons.

Oxidation - Reduction Reaction is the transfer of electrons from one molecule (oxidized) to another (reduced). Stability can be achieved by adding, losing, or sharing electrons.

Chemical Bonds and Attractive Forces

Sharing electrons leads to the formation of covalent bonds.

Methane has four covalent bonds between carbon (C) and hydrogen (H). The figure below shows the methane molecule in four different views.

Chemical Bonds and Attractive Forces

Sharing electrons is not always equal.

Electronegativity is a measure of the tendency of an atom to attract a bonding pair of electrons

Chemical Bonds and Attractive Forces

Ions are produced when atoms can obtain a stable number of electrons by giving up or gaining electrons.

For example Na (sodium) can donate an electron to Cl (chlorine) generating Na+ and Cl-. The ion pair is held together by strong electrostatic attractions called ionic bonds

The Chemistry of Water

Water has a simple molecular structure. It is composed of one oxygen atom and two hydrogen atoms. Each hydrogen atom is covalently bonded to the oxygen via a shared pair of electrons.

Polar Bonding aka Hydrogen Bonding

Water is a "polar" molecule, meaning that there is an uneven distribution of electron density. Water has a partial negative charge (-) near the oxygen atom due the unshared pairs of electrons, and partial positive charges (+) near the hydrogen atoms.

Polar Bonding aka Hydrogen Bonding

An electrostatic attraction between the partial positive charge near the hydrogen atoms and the partial negative charge near the oxygen results in the formation of a hydrogen bond as shown in the illustration.

Just as a summary to what each bond looks like…

Bonding by Analogy: Dog - Bone Bonds

Ionic Bonds: One big greedy thief dog!Ionic bonding can be best imagined as one big greedy dog steeling the other dog's bone.  If the bone represents the electron that is up for grabs, then when the big dog gains an electron he becomes negatively charged and the little dog who lost the electron becomes positively charged. 

Covalent Bonds: Dogs of equal strength.

Covalent bonds can be thought of as two or more dogs with equal attraction to the bones.  Since the dogs (atoms) are identical, then the dogs share the pairs of available bones evenly.  Since one dog does not have more of the bone than the other dog, the charge is evenly distributed among both dogs. The bond is not “polar” because the dogs share equally.

Polar Covalent Bonds: Unevenly matched but willing to share.

These bonds can be thought of as two or more dogs that have different desire for bones.  The bigger dog has more strength to possess a larger portion of the bones.  Sharing still takes place but is an uneven sharing.  In the case of the atoms, the electrons spend more time on the end of the molecule near the atom with the greater electronegativity (desire for the electron) making it seem more negative and the other end of the molecule seem more positive.

The Chemistry of Water

The ability of ions and other molecules to dissolve in water is due to polarity. A hydration shell forms as water surrounds an ion.

The Chemistry of Water

Each water molecule can form a maximum of four hydrogen bonds at a time

The Chemistry of Water

high specific heat• Water is slow to undergo

changes in temperature. • Much heat must be added or

removed before the temperature of water changes much.

• The temperature of the water within living organisms tends to change more slowly than does that of the surrounding air or soil, so that the living cells are buffered somewhat against temperature fluctuations.

• HOMEOSTASIS IS POSSIBLE BECAUSE OF WATER

• Biochemical reactions take place only within a narrow range of temperatures.

Water Holds Immense Amounts of Heat

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Forecast for San Diego and Gallup 1/11/06-1/15/06

Water’s high heat capacity has profound effects on climate and ecology.

The Chemistry of Water Unique physical

properties, include a high heat of vaporization:In order for water to reach the gaseous state, it must absorb a great deal of heat from the surroundings. For many plants and animals, this property is the basis of a natural cooling

system. Water evaporating from leaves, skin or lungs uses up heat from the organisms in the process of changing from liquid to gas. That is the reason mammals have evolved sweat glands, when the body is overheated, the glands pour watery "sweat" onto the skin, as the water evaporated, large amounts of body heat are used up and the body is cooled.

The Chemistry of Water

Tensile strength is related to cohesion and is a measure of the resistance of molecules to being pulled apart. This phenomena is responsible for "surface tension" that you see above. The water strider can "walk on water" because its feet don’t push hard enough to force the water molecules apart.

Unique physical properties include strong surface tension.

The Chemistry of Water

This is the result of the polar nature of water molecules and the resulting hydrogen bonding. In the photos, water is transported up inside trees and other vascular plants inside tiny tubes call "xylem vessels". As water transpires off the leaves the cohesion pulls more water up through the vessels.

cohesion = the tendency of "like" molecules to stick together (water to water).

The Chemistry of Water

Adhesion = tendency of "unlike" molecules to cling together

High surface tension allows long water columns to be drawn from roots to leaves – even in a redwood.

Water Is Lighter as Solid than as a Liquid

This means that ice forms an insulating blanket over water.

Water is a wonderful solvent

.

Dissolving table salt (sodium chloride) Solution: a mixture where everything is equally distributed

Acids and Bases

In biology, keeping H+ levels within a narrow range is critically important.

Water is neutral!!! pH = 7 pH is a measure of

proton concentration. Low pH = lots of H+s =

Acid High pH = few H+s =

Base

Acids and BasesA base absorbs H+An acid produces H+

Put them together and you get SALTS!!!!

Acids and Bases

Buffers are substances that minimize changes in pH. They accept H+ from solution when they are in excess and donate H+ when they are depleted.

Carbonic acid (H2CO3) is an important buffer in living systems. It moderates pH change in blood plasma and the ocean.

A little bit of history…

In the seventeenth century, chemist Robert Boyle first labeled substances as either acids or bases according to the following characteristics:

•Acids taste sour, are corrosive to metals, change litmus (a dye extracted from lichens) red, and become less acidic when mixed with bases. •Bases feel slippery, change litmus blue, and become less basic when mixed with acids.