Atoms-- “Unable to be cut” Protons (+) charged Neutrons (o) charged Electrons (-) charged with 1/1840 the mass of a proton. They are in constant motion Have about the same mass.

Element Pure substance that consits entirely of one type of atom.

Organic chemistry- chemistry of carbon compounds. Biochemistry is a branch of organic chemistry which attempts to explain the chemistry in living organisms.

The majority of organic molecules can be classified into one of the four: - Carbohydrates - Lipids - Proteins - Nucleic acids

3.1 Chemical elements and water What elements (most common) are found in living organisms?

- Carbon - Hydrogen - Oxygen - Nitrogen These elements are used in the molecular structures of all carbohydrates, proteins, lipids, and nucleic acids.

BUT Living organisms contain a variety of other elements which are extremely important, but are less common.

Sulfur Some amino acids contain sulfur and can form a bond with another amino acid which also contains sulfur. These connections are called disulfide bridges. They can occur within a polypeptide chain which causes folding of the chain. They can also occur between polypeptide chains and keep the chains together.

Phosphorus A schematic diagram of a molecule of ATP. Note that the three phosphates have high energy bonds between them. Each phosphate contains the elements phosphorus and oxygen.

Calcium Calcium is needed to form bone tissue. In the figure shows normal bone on the left and bone with osteoporosis on the right. Notice the decrease in bone material and hence in strength.

Iron In the figure shows the structure of one of the four polypeptide chains that makes up hemoglobin. Each chain has a ‘heme’ group containing iron associated with it. The heme group containing the iron is indicated by a pointer. Iron is also important in myoglobin and cytochromes.

SODIUM During a nerve impulse, in the first part of an action potential, sodium channels open across the plasma membrane and sodium will diffuse into the neuron.

Structure of water - Is the solvent of life. - All cells have water within (cytoplasm) and water in the surroundig environment (intercellular fluir, pond water, etc.)

A typical person could survive for about a month without food. They would survive only a week or less without water.

Covalent Bonds Are formed when electrons are shared between atoms. Shared electrons by atoms instead of being transferred.

A simulation of polar covalent bonding in the H 2 O molecule (Only valence electrons are shown)

Polarity Oxygen atom has a stronger attraction for electrons than does the hydrogen atom with a single proton in its nucleus. In the oxygen end of the molecule it has a slight negative charge and the hydrogen end of the molecule has a positive charge.

A water molecule is polar because there is an uneven distribution of electrons between the oxygen and hydrogen atoms.

Hydrogen Bonds Because of their partial positive and negative charges, polar molecules such as water can attract each other. Hydrogen bonds are not as strong as covalent bonds or ionic bonds, but water´s ability to form multiple hydrogen bonds is responsible for its properties.

Thermal properties Water can absorb or give off a great deal of heat without changing temperature greatly.

Think of a body of water on a very cold night; even though the air may be very cold, the body of water is relatively stable in temperature.

All living things are composed of a great deal of water and thus you can think of your water content as a temperature stabilizer.

Water also has a high heat of caporization. This means that water abosrbs a great deal of heat when it evaporates. This mechanism is used by us to cool down.

Heat turns water molecules from liquid to vapor from your body and thus sweating not only makes you feel cooler, it really does lower your temperature.

Cohesion An attraction between molecules of the same substance. Water cohesion causes molecules on the surface of water to be drawn inward.

When water cools below the freezing point, molecular motion has slowed to the point where these polar attractions become locked into place and an ice crystal forms.

Cohesion between liquid water molecules explain a variety of events, including: Why water forms into droplets when spilled Why water has a surface tension that allows some organisms to “walk on water”, somo run How water is able to move as a column in the vascular tissue of plants Why water has a high heat capacity and high heat of vaporization as discussed earlier.

Adhesion Attraction between molecules of different substances.

Solvent properties Water is an excellent solvent of other polar molecules. ‘Like disolves like’ The majority of molecules typically found inside and outside of most cells are polar; including carbohydrates, proteins, and nucleic acids. Lipids are non- polar BUT most organisms have special strategies to deal with the transport and biochemistry of lipids.

Water is an excellent solvent for biochemically important molecules, it is also the medium in which most of the biochemistry of a cell occurs. A cell contains a wide variety of fluids, all of which are primarily water. We refer to such solutions as aqueous solutions.

Aqueous solutionLocationCommon reactions CytioplasmFluid inside cell but outside organelles Glycolysis/ protein synthesis reactions NucleoplasmFluid inside nuclear membrane DNA replication/ transcription StromaFluid inside chloroplast membrane Light- independent reactions of photosynthesis Blood plasmaFluid in arteries, veins and capillaries Loading and unloading of respiratory gases/ clotting

Examples of water as a solvent in plants and animals The properties of water make it an excellent medium for transport. Vascular tissue in plants carries water and a variety of dissolved substances.

Xylem carries water and dissolved minerals up from the root system to the leaves of a plant. Phloem then transports dissolved sugars from the leaves to the stems, roots and flowers of a plant.

Blood is the most common transport medium in animals and is largely made up of water. Blood is transport medium for red blood cells, white blood cells, platelets and a wide variety of dissolved molecules.

The liquid portion of blood plasma are: - glucose (blood sugar) - amino acids - fibrinogen (protein involved in blood clotting) - hydrogencarbonate ions (as a means of transporting CO 2 ).