Chapter 3 Biochemistry

Pheromones Revisited The chemical scent between the queen bee and all of the worker bees is nearly identical. The only difference: the bonding of the hydroxyl (OH) group to the first or the second carbon atom in the chain (see figures below). This one slight difference allows the bees to recognize the difference between “royalty” and the commoners!  

Carbon Compounds All compounds can be classified in two broad categories Organic Compounds: contain the element carbon and at least one hydrogen atom. Inorganic Compounds: do not contain the element carbon.

Carbon Bonding A carbon atom has four valence electrons and is able to bond with most atoms. This is why carbon can form many complex structures like… Straight chains Branched Chains Rings

Carbon Bonding Carbon can form single, double, or triple covalent bonds. Each line between atoms in a molecular drawing represents one covalent bond.

Carbon Compounds Functional Groups Functional groups are groups of atoms that influence the properties of molecules and the chemical reactions in which the molecules participate. Hydroxyl: In alcohols, sugars, and amino acids- water soluble Methyl: In fatty acid chains- insoluble in water.

Functional Groups Carbonyl: In sugars, amino acids, nucleotide bases- water soluble. An aldehyde if at end of a carbon backbone; a ketone if attached to on e of the backbone’s interior carbons. Carboxyl: In amino acids, fatty acids- water soluble. Highly polar and acts as an acid (releases H+)

Functional Groups Amino: in amino acids and certain nucleotide bases- water soluble. Acts as a weak base (accepts H+) Phosphate: In ATP, other nucleotides’ also in DNA, RNA, many proteins, phospholipids- water soluble, acidic.

Functional Groups Sulfhydryl: In amino acid cysteine; helps stabilize protein structure (at disulfide bridges). Water soluble.

Large Carbon Molecules Many carbon compounds are built up from smaller, simpler molecules know as monomers. Monomers can bond to one another to form polymers, through a process called polymerization. A polymer is a molecule that consists of repeated, linked units.

Carbon Bonding Dehydration synthesis removes OH and H during synthesis of a new molecule. Hydrolysis breaks a covalent bond by adding OH and H.

Energy Currency Life processes require a constant supply of energy. This energy is available to cells in the form of certain compounds that store a large amount of energy in their overall structure. The primary energy compound in living systems is adenosine triphosphate (ATP)

Macromolecules The four groups of biomolecules or macromolecules found in living things which are essential to life are: Proteins Carbohydrates Lipids Nucleic Acids

Proteins Proteins are organic compounds composed mainly of carbon, hydrogen, oxygen, and nitrogen. Proteins are the principle component of all cells. Proteins, for example, makeup most of your skin, muscles, and many biological catalyst.

Proteins Amino acids are the monomers that makeup proteins. Amino acids are compounds with an amino group on one end and a carboxyl group on the other end. More than 20 different amino acids are found in nature.

Proteins All amino acids are identical where they join in covalent bonds. This allows amino acids to join with any other amino acid. The portion of the amino acid that is different is a side chain called an R-group. R-groups can be complex or simple.

Enzymes Some proteins control the rate of reactions, these proteins are know as enzymes. (We will return to this subject in more detail later on)

Enzymes Enzyme reactions depend on a physical fit between the enzyme molecule and its specific substrate (the reactant being catalyzed). The active site is the folded region on the enzyme that fits together with the substrate.

Carbohydrates Composed of the elements: carbon, hydrogen, and oxygen. Living things use carbohydrates as their main source of energy. Plants (and some animals) use carbohydrates for structural (support) purposes.

Carbohydrates Breaking down sugars provides immediate energy for the cell. The formula for glucose is C6H12O6 Living things store extra complex carbohydrates (sugar) in the form of glycogen

Carbohydrates Monosaccharides are single sugar molecules. Examples: Glucose- main source of energy Galactose- found in milk Fructose- found in fruit

Carbohydrates Disaccharides consist of two sugars linked together. Examples: Sucrose = glucose + fructose Lactose = galactose + glucose Maltose = glucose + glucose

Carbohydrates Polysaccharides are large macromolecules formed from many monosaccharides. Animals store extra polysaccharides in the form of glycogen and it is held in the liver or muscles and is ready to be used for quick energy.

Carbohydrates Plants store extra polysaccharides in the form of starch or as cellulose. Starch is similar to glycogen Cellulose gives strength and rigidity to plant cells, makes up 50% of wood.

Lipids Lipids, also called fats, are biomolecules that are usually not soluble in water. Lipids can be used to store energy and are important parts of biological membranes and waterproof coverings.

Lipids Common categories of lipids are: fatty acids, waxes, and steroids. Lipids form when a glycerol molecule combines with several molecules called fatty acids.

Lipids If each Carbon atom has bonded with the maximum number of Hydrogen atoms, the lipid is said to be saturated. Saturated fats are solid at room temperature. For example: butter and fats in red meat.

Lipids If there is at least on Carbon-Carbon double bond in a fatty acid, the lipid is said to be unsaturated. Lipids whose fatty acids contain more than on double bond is said to be polyunsaturated.

Lipids Unsaturated fats, like olive oil, are liquid at room temperature. Some examples are: vegetable oils, corn, sunflower, and soy.

Lipids The hydrophilic “head” is water loving while the hydrophobic “tail” is water hating. Phospholipids are components of cell membranes

Nucleic Acids Nucleic acids are “giant molecules”, polymers which contain the elements: carbon, nitrogen, oxygen, phosphorous, and hydrogen. Nucleic acids are polymers. Polymers are made of monomers. The monomers that make up nucleic acids are called nucleotides.

Nucleic Acids Nucleotides are made of three parts A. Nitrogen containing base B. Phosphate group 5 carbon sugar

Nucleic Acids When several nucleotides join by covalent bonds, a polynucleotide is formed. A polynucleotide is also called a nucleic acid Nucleic Acids store and transmit genetic material, or genetic information.

Nucleic Acids The two kinds of nucleic acids are: A. Ribonucleic acid (RNA) B. Deoxyribonucleic acid (DNA)