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Basic Chemistry Concepts

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>Introduction > A knowledge of basic chemistry is important for understanding just about any area of biology from the function of cells to the behavior of organisms and the ecological relationships between organisms and their environment. Indeed, chemists are fond of teasing biologists by claiming that all biology is chemistry*. While this isn't quite true, in order to make sense of the structure of cells and organisms a little chemistry goes a long way. Ball and Stick" Model of a Heme group. This group is part of a larger molecule, hemoglobin. Grey=Carbon, Blue= Nitrogen, Red= Oxygen. Hydrogens not shown. *Of course the physicists say that all chemistry is physics!

Electrons, Chemical Bonds and Periodic Table.

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The chemical properties of an atom are determined largely by how full or empty the outer electron shell is. For example, atoms of fluorine(F), chlorine(Cl) and the other elements in that second from the last column of the periodic table need only one electron to fill the outer shell. These atoms have a very strong tendency to steal electrons from other atoms. Oxygen and sulphur have 6 electrons in their outer shell which again holds 8 maximum. Thus these elements tend to steal electrons. Elements such as Lithium(Li) Sodium(Na) and Potassium(K) on the left hand side of the periodic table have an almost empty shell and these elements readily give up those outer shell electrons to atoms such as oxygen and chlorine. Elements that tend to give up electrons to other atoms are called metals. Elements in the middle of the periodic table tend to share electrons rather than give them up or take them entirely. Many of these such as iron, copper or gold are also considered metals. The elements at ...

Chemical Bonds.

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A chemical bond is an attraction between atoms brought about by a sharing of electrons between to atoms or a complete transfer of electrons. There are three types of chemical bonds: Ionic, Covalent and Polar covalent. In addition chemists often recognise another type of bond called a hydrogen bond. Ionic Bonds:    Ionic  bonds arise from elements with low electronegativity(almost empty outer shells) reacting with elements with high electronegativity (mostly full outer shells). In this case there is a complete transfer of electrons A well known example is table salt, sodium chloride. Sodium gives up its one outer shell electron completely to chlorine which needs only one electron to fill its shell. Thus, the attraction between these atoms is much like static electricity since opposite charges attract. Covalent bond: Ionic, Covalent, Polar covalent, Hydrogen bond .     Covalent bonds involve a complete sharing of electrons and occurrs most commonly between atoms that have partially f...

Hydrogen Bond.

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The fact that the oxygen end of a water molecule is negatively charged and the hydrogen end positively charged means that the hydrogens of one water molecule attract the oxygen of its neighbor and vice versa. This is because unlike charges attract. This largely electrostatic attraction is called a hydrogen bond and is important in determining many important properties of water that make it such an important liquid for living things. Water can also form this type of bond with other polar molecules or ions such as hydrogen or sodium ions. Further, hydrogen bonds can occurr within and between other molecules. For instance, the two strands of a DNA molecule are held together by hydrogen bonds. Hygrogen bonding between water molecules and the amino acids of proteins are involved in maintaining the protein's proper shape. This picture represents a small group of water molecules. Hydrogen bonds between unlike charges are shown as lines without arrows on the ends. The double arrowed lines ...

Properties of Water

Water has a number of unusual properites which come about because the atoms that comprise a water molecule form apolar covalent bonds. The main properties of water that are important for living things are the following: Ice floats. Usually when a liquid freezes the solid ismore dense than the liquid. In water thesolidphase is less dense than the liquid phase under normal conditions. If ice sank, ponds and lakes would freeze solid to the bottom making things very difficult for fish and other creatures to obtain food and oxygen in the winter. Water is a great solvent especially for polar molecules of ionically bonded substances like salt. That's because the charged ends of the water molecules are attracted to the charges on other molecules. Water molecules will surround soluable molecules or ions in a hydration shell. This helps keep the molecules in solution. Many gases dissolve in water because the the combination of attractive and repulsive forces among water molecules leaves spac...

Fatty acids

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Fatty acids are organic acids which have a long chain of carbon and hydrogens attached to the carboxyl group. Oleic Acid is a common saturated fatty acid. Actually the bend in the carbon chain suggests that oleic acid is not completely saturated. I can't resist this cool looking fatty acid from Chrysanthamums. Notice the interesting triangular ring in the carbon chain. Finally this exotic looking fatty acid is vitamin A

Organic acids.

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Organic acids are very important compounds in living things. They are important components of structural molecules such as phospholipids and are an important source of energy. Organic acids have a carboxyl group and long a chain of carbons attached to it. This diagram shows formic acid, the simplest organic acid. The name formic comes from the Latin word(Formica) for ant. This acid is an important alarm and defensive compound for many ants. Acetic acid, the acid in vinegar, has one more carbon than formic acid.

Carbon: the Three Main Forms of the Element

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Introduction Carbon is important in biology because carbon forms the "back-bone" of just about all biologically important molecules. This is because carbon forms long and sometimes complex covalently bonded structures and also because carbon compounds vary greatly in the type of interactions they have with water. For example some carbon compounds, such as most lipids, have strictly hydrophobic interactions with water, others such as sugars are hydrophilic. Still others such as proteins and phospholipids are partly hydrophobic and partly hydrophilic. 1. Diamond 2. Graphite 3. Fullerine

The pH Scale.

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The concentration of hydrogen ions in a solution is very important for living things. This is because, since the hydrogen ions are positively charged they alter the charge environment of other molecules in solution. By putting different forces on the molecules, the molecules change shape from their normal shape. This is particularly important for proteins in solution because the shape of a protein is related to its function. The concentration of hydrogen ions is commonly expressed in terms of the pH scale. Low pH corresponds to high hydrogen ion concentration and vice versa. A substance that when added to water increases the concentration of hydrogen ions(lowers the pH) is called an acid. A substance that reduces the concentration of hydrogen ions(raises the pH) is called a base. Finally some substances enable solutions to resist pH changes when an acid or base is added. Such substances are called buffers. Buffers are very important in helping organisms maintain a relatively constant p...