Molecules and Fundamentals of Biology PDF

# Molecules and Fundamentals of Biology: Enzymes ## Outline 1. Catalysts can be involved in a chemical reaction to increase the reaction rate; however, they will have no effect on equilibrium, reaction direction, or spontaneity. 2. Enzymes are biological catalysts and are most often proteins. 3....

# Molecules and Fundamentals of Biology: Enzymes ## Outline 1. Catalysts can be involved in a chemical reaction to increase the reaction rate; however, they will have no effect on equilibrium, reaction direction, or spontaneity. 2. Enzymes are biological catalysts and are most often proteins. 3. Enzymes possess active sites that bind very specific substrates to increase the rate of a reaction. 4. These active sites have what is called an *induced fit*, meaning that they will contort slightly to fit the incoming substrate. 5. Ribozymes are a non-protein enzyme that is instead made of RNA. 6. Cofactors are molecules of varying properties that can bind an enzyme and help it perform its function. 7. An enzyme bound to its appropriate cofactor is called a holoenzyme. 8. An enzyme without a cofactor is an apoenzyme. 9. Enzymes can catalyze reactions in many ways, including bringing substrates close together, acid or base presence, and electrostatic interactions. 10. Phosphatases are enzymes that cleave phosphate groups off of a substrate molecule. 11. Phosphorylases are enzymes that directly add phosphates to a substrate via bond breakage. 12. Kinases are enzymes that transfer phosphates from an ATP onto a substrate. # Molecules and Fundamentals of Biology: Enzyme Inhibition and Kinetics ## Outline 1. Manipulation of enzymes and their catalytic capacity can alter the reaction rates that they govern. 2. Manipulation occurs when a molecule other than the desired substrate for a reaction binds to either the active or allosteric site. 3. Feedback loops allow for the product of a reaction to influence the reaction. 4. Products increase the reaction in a positive feedback loop. 5. Products decrease the reaction in a negative feedback loop. 6. Products are examples of molecules that will bind to an enzyme's allosteric site. 7. In competitive inhibition, a competitive inhibitor directly competes with the normal substrate for an enzyme's active site. 8. In noncompetitive inhibition, an inhibitor binds to the allosteric site and conformationally changes the active site. 9. Enzyme kinetics plots can be used to track reaction velocities based on substrate concentration. 10. $V_{max}$ represents the maximum velocity of a reaction. 11. $K_M$ represents the substrate concentration needed to reach $\frac{1}{2}V_{max}$ 12. Competitive inhibition will increase $K_M$ but preserve $V_{max}$. 13. Noncompetitive inhibition will decrease $V_{max}$ but preserve $K_M$. # Molecules and Fundamentals of Biology: Lipids ## Outline 1. Lipids are generally composed of carbons, hydrogens, and oxygens. 2. Fatty acid tails are common lipid components and are long hydrocarbon tails with hydrophobic properties. 3. Lipids can be hydrophobic, hydrophilic, or amphipathic. 4. Fatty acids can be saturated or unsaturated depending on the presence of double bonds in the hydrocarbon chain. 5. Monounsaturated fatty acids only have one double bond while polyunsaturated fatty acids have multiple double bonds. 6. Unsaturated fatty acids can also be either in a cis- or trans- conformation which will determine how tightly the lipids pack together. 7. Glycerol backbones consist of three carbons that can anchor fatty acids. 8. Triglycerides are composed of a glycerol backbone attached to three fatty acid tails. 9. Triglycerides as a class of lipids are mostly hydrophobic. 10. Phospholipids are amphipathic lipids with a polar phosphate head group and nonpolar fatty acid tails. 11. Phospholipids spontaneously form lipid bilayers in aqueous solutions. # Molecules and Fundamentals of Biology: Lipid Subtypes ## Outline 1. Membrane fluidity can be affected by many factors including temperature, cholesterol presence in the membrane, and the degree of fatty acid unsaturation of the membrane lipids. 2. Cholesterol is an amphipathic lipid that serves as the foundation for steroid hormones, Vitamin D, and bile acids. 3. Lipoproteins are capable of transporting cholesterols and proteins through the blood. 4. Low density lipoproteins have a high concentration of cholesterol and a low concentration of proteins, depositing the cholesterol in peripheral tissues. 5. High density lipoproteins have a high concentration of proteins with a low concentration of cholesterol, delivering cholesterol to the liver for metabolism. 6. Waxes are simple lipids used mainly as hydrophobic coatings. 7. Carotenoids are long carbon chain lipids that are prominent in certain pigments. 8. Sphingolipids are useful for signal transduction, structural support, cell recognition, and plasma membrane composition. 9. Glycolipids are fatty acid chains attached to carbohydrates that are important components of cell membranes. # Molecules and Fundamentals of Biology: Biological Chemistry ## Outline 1. Matter is anything that takes up space and has mass. 2. Elements are pure substances that have specific chemical and physical properties and can't be broken down into a simpler substance. 3. Atoms are the smallest unit of matter that still retains the chemical properties of the element. 4. Molecules are two or more atoms joined together. 5. Intramolecular forces are attractive forces that act on atoms within a molecule. 6. Intermolecular forces are attractive forces between molecules. 7. Monomers are single molecules that can polymerize. 8. Polymerization is the linking of several monomer units. 9. Polymers are substances made of many monomers. 10. Dehydration (condensation) reactions are a mode of polymerization that releases water. 11. Depolymerization breaks polymers down into monomers. 12. Hydrolysis is a mode of depolymerization that uses water to break down bonds. # Nucleic Acids 1. Nucleic acids are a class of molecules that are all composed of either deoxyribose or ribose nucleic acids. 2. DNA and RNA and the overarching categories of nucleic acids. 3. Nucleosides are made of 1 sugar and 1 nitrogenous base. 4. Nucleotides are nucleosides with the addition of phosphate(s). 5. RNA molecules are composed of ribonucleic acids and are usually single stranded. 6. Ribose sugars are used to make RNA and have two hydroxyl groups (3' and 2'). 7. DNA molecules are composed of deoxyribonucleic acids and are usually double stranded. 8. Deoxyribose sugars are used to make DNA and have one hydroxyl groups (3'). 9. Phosphodiester bonds hold nucleotides together via a condensation reaction. 10. Sugars and phosphates bonded together form the sugar-phosphate backbone. 11. Nucleic acid polymerization requires nucleotides to be added to free 3' ends of growing nucleic acid molecules. 12. mRNA encodes the information for protein production. 13. tRNA transfers amino acids to ribosome enzymes. 14. rRNA helps to form the ribosome enzymes. 15. miRNA can silence gene expression by binding to mRNA. 16. dsRNA is used by viruses to store genetic information. # Molecules and Fundamentals of Biology: Carbohydrates ## Outline 1. Carbohydrates are molecules that are used for both fuel and structural support. 2. Carbohydrates will contain a combination of carbon, hydrogen, and oxygen atoms. 3. The formula for monosaccharides is $(CH_2O)_n$ where n represents the number of carbons. 4. Monosaccharide examples include 5 carbon ribose, 6 carbon fructose, and 6 carbon glucose. 5. Disaccharides are composed of two monosaccharides held together by glycosidic bonds. 6. A common disaccharide example is sucrose. 7. Polysaccharides are composed of many monosaccharides, all held together by glycosidic bonds. 8. Starch polysaccharides are glucose based, used by plants, held together by a-glycosidic bonds, and are fuel storages. 9. Amylose and amylopectin are other glucose polysaccharides. 10. Glycogen polysaccharides are glucose based, used by animals, held together by a-glycosidic bonds, and are fuel storages. 11. Cellulose is a structural polysaccharide used in plant cell walls. # Molecules and Fundamentals of Biology: Protein Structure ## Outline 1. Amino acids are protein monomers composed of carbon, hydrogen, nitrogen, and oxygen. 2. There are 20 amino acids, each with a unique structure including their differentiating R groups. 3. Peptide bonds hold amino acids together and are created via dehydration reactions. 4. Polypeptides are composed of many amino acids and have N and C termini. 5. Conjugated proteins include a non-protein component such as an ion cofactor or carbohydrate. 6. Primary protein structure describes the basic amino acids sequence of a protein. 7. Secondary protein structure describes the folding pattern of the amino acid chain. 8. Tertiary protein structure describes the three dimensional polypeptide structure, governed by interactions between R groups. 9. Quaternary structure describes a structure composed of multiple tertiary proteins. 10. When proteins denature, they lose their higher level structure and therefore their higher level function. 11. Protein functions include storage of amino acids, hormone activity, signal reception, structural support, immunity, and enzymatic activity.