BIO 205Exam # 1 Study Guide: Chapters 1 – 7Part I: Chemical Foundations of BiochemistryChapter 1: Structure and Function - Proteinso Proteins have many different functions in our body. They range from hormones, such as insulin, to structural, such as collagen.o Proteins are formed by linking amino acids together. Each amino acid is composed of an amino group (NH2), a carboxyl group (COOH), a hydrogen, and a side chain. o The side chain gives each of the 20 amino acids their unique identity. The classes of side chains are nonpolar, polar uncharged, and polar charged (acidic and basic).o Amino acids are linked together via a condensation reaction, which in simplest of terms, is a carboxylic acid plus an amine, which yields an amide and water. The polymerization of amino acids proceeds from the N (amino) terminus to the C (carboxyl) terminus.o Proteins are usually chains of varying amino acids, which makes it a heteropolymer.o Due to the varying composition of proteins, they will fold into different shapes in orderfor the amino acids to arrange themselves in a favorable environment. For example, a nonpolar amino acid will fold inward to avoid interaction with water.- Nucleic Acidso Nucleic acids have two main functions. One is carrying genetic information in the form of DNA or RNA while the other is storing of energy in the form of ATP and other similarstructures.o Nucleic acids are made from nucleotides. Each nucleotide consists of a phosphate group attached to the 5’ carbon of a 5 carbon sugar (ribose for RNA and deoxyribose for DNA) along with a base (A, C, T, G, or U (RNA)) attached to the 1’ carbon.o The bases A and G are composed of two large rings while T, U and C only have one small ring. A and T (U in RNA) only join to make 2 hydrogen bonds and G and C make 3 hydrogens bonds. o Base pairing is complementary so that when only given the sequence for one strand, you automatically know the sequence for the other strand. DNA and RNA always polymerize from 5’ to 3’. o Transcription is the process where mRNA is made by base pairing with a strand of DNA in the nucleus of a cell. The mRNA then leaves the nucleus to participate in translation where groups of three bases (codons) are translated into an amino acid, forming a polypeptide chain. o ATP has such a large energy capacity (large ∆G) because of the many negative charges placed in such close proximity to each other. The phosphate groups want to be separated, so hydrolysis of ATP releases a lot of energy due to the favorable separation.- Carbohydrateso The two major classes of carbohydrates are aldoses and ketoses. o The overall formula for a carbohydrate is (CH2O)n.o The antigens on our blood cells are made from carbohydrates. Every human has the type-O core structure and by adding different monomers on to the end of the core structure differentiates A and B blood types. o Carbohydrates are the only biomolecules that can be either homopolymers or heteropolymers. o Cellulose, an example of a homopolymer of glucose, gives plant cells their rigid shape due to extensive hydrogen bonding.- Lipidso Just like proteins, lipids can serve as hormones, such as testosterone, or they can provide cellular structure in the form of phospholipids.o Due to their long chains of saturated carbons, fatty acids resemble hydrocarbon fuels. o In the combustion of natural gas (methane), heat energy is released in the favorable reaction due to the change in bonds. The nonpolar bonds of the reactants (CH4 and O2)are less stable than the polar bond of the reactants (CO2 and H2O).o Phospholipids are unique because the phosphate group gives fatty acids a hydrophilic head in addition to a hydrophobic tail. This amphipathic property is what forms the lipid bilayer of cell membranes. Chapter 2: Stereochemistry of Biomolecules - Constitutional isomers are molecules that share the same chemical formula, but have different connections between those molecules.- Conformations are molecules that have been simply rotated along a single bond. - Configurations are molecules that cannot be interconverted by rotation. R and S isomers have chiral carbons that cannot be superimposed, while cis and trans isomers cannot be rotated because of the double bond. - Determining R/S configurations depends on the order of the four different groups attached to the central, chiral carbon based on molecular weight. If the order of the groups proceeds in a clockwise rotation going from 1 to 2 to 3 with the 4th priority group going in the back, then the molecule has an R configuration. Remember, there must be 4 different groups in order for the molecule to be chiral.- The d/l system cannot be determined based solely on molecular structure. The only way to determine if a molecule is d or l is to put it in a polarimeter. A d molecule will bend lightto the right. - The only molecule that has a known d or l rotation is glyceraldehyde. The D/L naming system is based on the fact that d-glyceraldehyde is also D-glyceraldehyde. - Carbohydrates are named using the D/L system. All biological sugars are D, which can be determined by looking at the chiral carbon that is furthest from the carbonyl (in both aldoses and ketoses). If the hydroxyl group of the sugar is pointing to the right, then the sugar is D. - The number of different stereoisomers for a molecule depends on the number of chiral centers (n). By taking that number and having 2 raised to that power, you get the total number of stereoisomers (2n).- The D/L system is applied to the chiral carbon in the backbone of an amino acid. All naturally occurring amino acids are L, except for glycine because it is not chiral. - In an alpha helix, each amino acid residue has two hydrogen bonds. The amino group of one amino acid will hydrogen bond with the carbonyl of the amino acid below. Furthermore, the carbonyl of the original amino acid residue will hydrogen bond with the amino group above. - Amino acids need to have an L configuration because of the unique structure of the alpha helix. With an L configuration, the peptide chain avoids unfavorable interactions betweenthe large carbonyl group and the side chain of an amino acid. In a D configuration, these steric interactions are realized and create unfavorable repulsions. - An enzyme requires that there are at least three points of contact with a substrate. This implies that one stereoisomer is favored over another, which makes enzyme-substrate