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Organic Molecules Molecules that have carbon atoms are said to be organic. Macromolecules can contain hundreds or thousands of atoms and most are polymers or molecules that consist of a single unit (monomer) repeated many times. Four of carbon’s six electrons are available to form bonds. This is always depicted with four lines connecting carbon to other atoms. Complex molecules consist of a line or a ring of carbon atoms. Functional groups are organic molecules that share similar properties because of the types of atoms clustered together. Often, nitrogen, oxygen, and other atoms add variety to carbon molecules and identify those clusters. Draw the bonds that are missing. They can be single or double. Use your knowledge of valence electrons for carbon, nitrogen and phosphorous. Functional group class name examples characteristics Alcohols Ethanol, glycerol, sugars Polar, hydrophilic Carboxylic acids Acetic acid, amino acids, fatty acids, sugars Polar, hydrophilic, weak acid Amines Amino acids Polar, hydrophilic, weak base Organic phosphates DNA, ATP, phospholipids Polar, hydrophilic, acid Ketones Acetone, sugars Polar, hydrophilic Aldehydes Formaldehyde, sugars Polar, hydrophilic ---- Fatty acids, oils, waxes Nonpolar, hydrophobic -OH Hydroxyl O -C OH H Carboxyl -N H O -P OOO Amino Phosphate -CO Carbonyl -C-H H C H H Carbonyl Methyl Cliffs AP Biology 3rd edition Chemical reactions Chemical reactions occur when reacting molecules collide with enough activation energy to trigger the formation of new bonds. Many reactions occur spontaneously, however a catalyst can accelerate the rate of reaction because it lowers the activation energy required. A catalyst is any substance that accelerates a reaction but does not undergo a chemical change itself, thus making the catalyst usable again and again. Chemical reactions in biological systems are called metabolism, which includes the breakdown of substances (catabolism), the formation of new substances (synthesis or anabolism), or the transfer of energy. Metabolic process: 1.result in a net direction that is determined by the concentration of reactiants and the products. Chemical equilibrium describes the condition where the rat of reaction in the forward direction equals the rate in the reverse. 2.can utilize enzymes as proteins that act as catalysts. Enzymes act on substrates, like when the enzyme amylase catalyzes the breakdown of the substrate amylose. Enzymes are substrate specific. Enzymes perform their function repeatedly, unchanged. Enzymes can work toward the product or in reverse to the reactants. Enzyme efficiency is affected by temperature and pH. Beyond their ideal temperature or pH they begin to denature, or break down. Enzymes are typically easy to identify because they end in the root –ase. Enzymes interact with substrates to change shape which allows for a new position to allow for substrate reaction. Once the reaction takes place, the product is released. This is called the induced-fit model. 3.can utilize cofactors that are nonprotein molecules that assist enzymes. A holoenzyme is the union of the cofactor and the enzyme. 4.can utilize adenosine triphosphate (ATP) as a source of activation energy. ATP is essentially an RNA adenine nucleotide with two additional phosphate groups. When ATP supplies energy to a reaction, it is usually the energy in the last bond that is delivered to the reaction. In the process of giving up this energy, the last phosphate bond is broken and the ATP molecule is converted to adenosine diphosphate, ADP and a phosphate group. In contrast, new ATP molecules are assembled by phosphorylation when ADP combines with a phosphate group using energy obtained from an energy =-rich molecule, like glucose. Regulation of enzymes equals regulation of chemical reactions Four common ways to regulate enzymes. 1. Allosteric enzymes have one active binding site for a substrate, one for an allosteric effector. a. Allosteric activator binds to the enzyme and induces the enzyme’s active shape. b. Allosteric inhibitor binds to the enzyme and induces the enzyme’s inactive shape. 2. Competitive inhibition is when a substance mimics the substrate and inhibits an enzyme by occupying the active site. This results in prevention of the enzyme catalyzation. 3. Noncompetitive inhibition is when a substance inhibits the action of an enzyme by binding to the enzyme at a location other than the active site. The inhibitor changes the shape of the enzyme which disables it. Many toxins and antibiotics perform this way. 4. Cooperativity is when an enzyme becomes more receptive to additional substrate molecules after one substrate molecule attaches to an active site. Enzymes can have two or more subunits, (quaternary structure) with two active sites. Hemoglobin, albeit not an enzyme, acts in cooperativity. Four Organic Molecule Classes Carbohydrates: divided by the number of sugar molecules 1. monosaccharide: 1 sugar molecule 2. disaccharide: 2 sugar molecules linked by glycosidic linkage 3. polysaccharide: serried of connected monosaccharides (it’s a polymer, folks!) Lipids: three groups 1. triglycerides (or tricylglycerols) 2. phospholipids 3. steroids Proteins: divided by their function, however it is their structure that identifies them o structural proteins o storage proteins o transport proteins o defensive proteins o enzymes 1. primary structure 2. secondary structure 3. tertiary structure 4. quaternary structure Nucleic Acids: two types 1. DNA 2. RNA