BIO 205Exam # 2 Study Guide: Chapters 8-15 Part II: Protein Structure and FunctionChapter 8: Amino Acids- Hydrocarbon groups where all the C-C bonds are single bonds are called aliphatic.- The tetrahedral carbon in the backbone of amino acids is called the alpha carbon. The first side chain carbon atom is then referred to as the beta carbon, and so on. - Cysteine is the only amino acid that can form a disulfide bond with another cysteine in the same molecule.- At a pH of 7, the side chains of lysine and arginine are fully protonated, giving them a positive charge. Histidine has a pKa of 7, so half of its side chains will be positively charged, and the other half will be neutral. - At a pH of 7, the side chains of glutamic acid and aspartic acid are negatively charged, giving the amino acid an overall negative charge. The NH2 groups of these two amino acids never become protonated to NH3+. - When referring to a tripeptide, the molecule actually only has two peptide bonds, but since there are three amino acids, it is referred to as a tripeptide. - When determining the orientation of a polypeptide chain, the first step is to draw boxes around amino acid residues by first finding the central carbon with the side chain. Once all the available residues have been boxed in, draw an arrow going from the N (amino) terminus to the C (carbonyl) terminus. - Tyrosine, serine and threonine are the only amino acids that are phosphorylated for post-translational modifications.- Epinephrine is a hormone that activates an enzyme cascade through the use of cyclic AMP (cAMP). Binding of the hormone changes the shape of the receptor, which activates enzyme #1, converting ATP into cAMP. cAMP binds to regulatory subunits on enzyme #2, causing dissociation into two catalytic subunits and one regulatory subunit. A phosphate group from ATP is transferred to enzyme #3, leaving behind ADP and activating the enzyme to catalyze an additional reaction.- Cysteine can be farnesylated, which acts as an anchor for proteins found on the outer surface of the lipid membrane. - Histamine is derived from histidine while thyroxine is derived from tyrosine.- A disulfide bond between two cysteine amino acids is formed by an oxidation by oxygen.The pair of the two cysteines now covalently bonded together is called cystine. - An intrachain disulfide bond means within the chain while interchain means between two separately synthesized chains. - An antibody is made from two copies of a short chain (light) and two copies of a long chain (heavy). The top spans of the antibody are called variable regions because they aredifferent for each type of antibody. The very tops of each antibody serve as the binding sites for foreign antigens.- Insulin is made from two chains (A and B) that are connected by disulfide bonds. The precursor called proinsulin has a C chain that does not add to the function of insulin but may be present so that the proper connections between the A and B chains can form. - In the digestive system, there are many enzymes that need to first be cut in order to start digesting food. These are called zymogens and include trypsinogen and chymotrypsinogen. The activation first starts with the secretion of enterokinase from thebrush border cells of the intestine that cleaves trypsinogen, forming trypsin, which thengoes on to activate chymotrypsin. Trypsin cuts after arginine 15, generating pi-chymotrypsin. The molecule then finishes its own activation, turning into chymotrypsin with three disulfide bonds connecting the three separate pieces. - In a separatory funnel, water and octanol are mixed together, forming two separate layers with the less dense and nonpolar octanol rising to the top of the funnel. When derivatized amino acids (amino and carbonyl groups changed to nonreactive amide group) are added, the nature of their side chain will sort them into one of the layers. Polar side chains will be found in the water layer while nonpolar side chains will be found in the octanol layer. - Data for the separatory funnel experiment displays the ∆G for the favorability of an amino acid to dissolve in water or octanol as well as the ∆G for the tendency of an amino acid to distribute itself between the inside and outside of a protein. A positive ∆G for solvent favorability means that the amino acid likes to dissolve in water while a positive ∆G for position tendency means that amino acid is most likely found on the outside of a protein.SidechainGroupAminoAcid∆G water to octanol ∆G surface vs buried+ charge Arg +1.01 +1.40+ charge Lys +0.99 +2.06- charge Asp +0.77 +0.78- charge Glu +0.64 +1.15C=O NH Asn +0.60 +0.75C=O NH Gln +0.22 +0.80OH Ser +0.00 +0.40Gly 0 0NH His -0.13 +0.02OH Thr -0.26 +0.31Ala -0.31 -0.14CH Pro -0.72 +0.50CH OH Tyr -0.96 +0.28CH Val -1.22 -0.55CH S Met -1.23 -0.65CH S Cys -1.54 -0.61CH Leu -1.70 -0.59CH Phe -1.79 -0.61CH Ile -1.80 -0.68CH NH Trp -2.25 -0.38- At extremely low pH, proteins are positive and at extremely high pH, they are negative.- Hemoglobin has a tense state and a relaxed state. In the tense state, found in muscles where the pH is 6.8 (acidic), the positively charged side chain (NH+) of a histidine is electrostatically attracted to the negative side chain (O-) of an aspartate. In the relaxedstate, found in the lungs where the pH is 7.4 (basic), there no longer exists the electrostatic attraction because histidine’s side chain is deprotonated. The relaxed state binds oxygen more favorably, which makes sense from a physiological standpoint. - Tyrosine and tryptophan strongly absorb light in the UV spectrum at a wavelength of 280nm. Tyrosine has a molar extinction coefficient value of 1200 units, while tryptophanhas a molar extinction coefficient value of about 5000 units.- Proline is the least flexible amino acid because its side chain attaches directly to the amino group, actually making rotation impossible. Furthermore, since the side chain is directly attached to the amino group, there is no longer a hydrogen atom available for hydrogen bonding. As a result, proline is rarely found in an alpha helix because it would essentially “break” the structure. Chapter 9: Molecular Evolution – Comparison of Protein Sequences- Proteins can be sequenced by breaking apart its peptide links in order to identify the amino acids.- First, the protein needs to be cleaved into manageable segments. Trypsin cleaves at the