BIOLCHEM 415Exam # 1 Study Guide Lectures: 1 - 10Lecture 1 (January 7)Biochemistry and the Unity of LifeWhat are the four classes of biomolecules? Name each and describe them and what purpose they serve.The four classes of biomolecules are amino acids, nucleic acids, carbohydrates, and lipids. Proteins are amino acid polymers. The amino acids are linked together with peptide bonds. Proteins fold into 3D shapes that affect their functions. Amino acids can act as signals, receptors, catalysts, building blocks, and molecular motors. Carbohydrates are used mainly as a fuel source and as energy storage for biological processes. They can also act as signaling molecules when linked with certain proteins. Nucleic acids are formed from nucleotides. These biomolecules store and transmit genetic info. They are composed of a base, a sugar, and a phosphate and serve functions such as enzymes, structural, and signaling. Nucleic acids make up DNA and RNA in cells. Lipids are amphipathic molecules meaning that they have both a hydrophobic component (hydrocarbon tails) and a hydrophilic component (polar head). Lipids can serve as a fuel source, a signal, and as a membrane component. Lipids form bilayer membranes that have limited permeability and protect cells. What is the difference between DNA and RNA?DNA is double stranded and forms a helix (a double helix). The two nucleotide strands are antiparallel and composed to the four bases adenine, guanine, cytosine, and thymine. The sugarthat is part of DNA is 2’ deoxyribose (hence Deoxyribose Nucleic Acid). RNA is typically a single strand polymer of nucleotides, but can be double stranded and form complex structures. The sugar that helps make up RNA is ribose (Ribose Nucleic Acid). It is composed of the four bases adenine, guanine, cytosine, and uracil. What is the Central Dogma? Describe each part.The central dogma describes the flow of genetic information. DNA is replicated each time a cell divides. DNA polymerase catalyzes it and new polymers of DNA are created. Transcription is the process of creating a strand of RNA based on the existing DNA strand. RNA polymerase catalyzesthis process. The last step is translation, which is the process of reading the RNA molecules and creating proteins. This happens in ribosomes. The nucleotide sequence specifies the amino acid sequence of the protein.Lecture 2 (January 9) Biochemistry and the Unity of Life AND Water, Bonding, and EntropyDescribe the differences between prokaryotic and eukaryotic animal cells.Prokaryotic cells lack intracellular membranes. They have an inner plasma membrane, a cell wall, and an outer membrane. Their genetic information is not contained in a nucleus. Eukaryotic cells contain membrane bound organelles and a single outer plasma membrane (no cell wall).Explain cellular import and export. Give an example of a disease related to one of these. Cellular export is called exocytosis. During exocytosis proteins are deposited outside of the cell. Import is called endocytosis and is the mechanism of bringing biomolecules into cells. An endosome forms when the plasma membrane invaginates and buds off. Another form of importis phagocytosis. This is when large amounts of material are taken into the cell.Familial Hypercholesterolemia is defective endocytosis of cholesterol from the blood. This can lead to high blood cholesterol levels and heart attacks. What is Brownian motion and why is it important?Brownian motion is the random movement of molecules powered by random fluctuations of environmental energy. This is important because it initiates many biochemical interactions and causes the diffusion of biomolecules throughout cells, within organisms, and within the environment.List the different chemical bonds/stabilizing forces in order from strongest to weakest.Covalent, electrostatic, hydrogen bonds, Van de Waals, hydrophobicWhat is the hydrophobic effect? Give an example.The hydrophobic effect is the spontaneous clustering of hydrophobic molecules. This is poweredby increased entropy. H2O molecules form ‘cages’ around nonpolar (hydrophobic) molecules. When these molecules cluster is means that less water molecules are needed to form a cage and therefore entropy increases. Examples include oil and water and the formation of lipid membranes. Why is it important to control pH? Give a specific examplepH is an important parameter in biological functions. It is important to control it so thatbiological systems are not damaged by anything too acidic or basic. Gastric Esophageal Reflux Disease is a pathological condition that results when the esophagus is exposed to stomach acid.Lecture 3 (January 12)Amino Acids and Protein StructureWhat are the two simplest amino acids? Give their side chains and their three letter abbreviations.The simplest amino acids are glycine (Gly) and alanine (Ala). Glycine’s R group is H and it is the only nonchiral amino acid. Alanine’s R group is CH3.Which amino acids are considered aliphatic? Give their side chains and three letter abbreviations. Define aliphatic.Aliphatic means that the amino acid has a hydrocarbon side chain. Aliphatic amino acids are valine(Val)(1), leucine(Leu)(2), isoleucine(Ile)(3), methionine(Met)(4), and proline(Pro)(5). Proline’s side chain is cyclic.1 2 3 4 5Which amino acids are aromatic? Give their R groups and three letter abbreviations.Aromatic amino acids have rings with double bonds and include Phenylalanine(Phe)(1), Tyrosine(Tyr)(2), and Tryptophan(Trp)(3). 1 2 3 Which amino acids have hydroxyl group side chains? Give their R groups and three letter abbreviations.These amino acids are Serine(Ser)(1) and Threonine(Thr)(2). 1 2 Which amino acid is related to closely to Serine?Cysteine(Cys). Instead of the –OH in the side chain it contains an –SH. It can form weak hydrogen bonds as well as stronger disulfide bonds.Which amino acids are basic and what charge do they tend to have at a pH of 7. Include their R groups and three letter abbreviations.The basic amino acids are Lysine(Lys)(1), Arginine(Arg)(2), Histidine(His)(3). They tend to have a positive charge at a pH of 7. 1 2 3 Which amino acids are acidic? What are their carboxamide derivatives? Include their R groups and three letter abbreviations. The acidic amino acids are