BMB 251 1st EditionExam # 1 Study Guide Lectures: 1 - 7Question Set One Review/Answers Methyl group: neither hydrogen bond donors not acceptorsHydroxyl group: both hydrogen bond donors and acceptorsCarboxyl group: both hydrogen bond donors and acceptorsCarbonyl group: hydrogen bond donorAmine group: both hydrogen bond donors and acceptorsSulfhydryl group: hydrogen bond donor; Sulfur atom can give H awayPhosphate group: hydrogen bond acceptorWhy are a lot of proteins comprised of many domains? (These domains can appear either in many different proteins or multiple times within the same protein)-Multiple copies of a domain can appear in a protein or many different proteins due to gene duplication and shuffling throughout evolutionBiological Macromolecules: -Polysaccharides, proteins, fatty acids and nucleic acidsWhich of the four contain both a carboxyl and amino group?-Proteins (amino acid monomers)Which of the four contain only a carboxyl group?-Fatty acids (lipid monomers)Which of the four contain only an amino group?-Nucleic acids (nucleotide monomers)Which of the four contain neither a carboxyl nor amino group?-Polysaccharides (carbohydrate monomer)-**Carbs contain a carbonyl group and many hydroxyl groupsWhich category contains Sulfur atoms?-ProteinsWhat is the reason that mitochondria have two membranes?-Mitochondria are thought to have originally been free-living bacteria that were engulfed by the predator eukaryotic cells. As time went on, the mitochondria evolved within the eukaryotic cells through endosymbiosis, yet they retained their double membranes and personal circular DNA from when they were free-living organismsCondensation synthesis: process of building substrate molecules into larger macromolecules by removing a water molecule **In protein synthesis, an –OH group is taken from the carboxyl group of one amino acid and an H is taken from the amino group of another amino acid, releasing an H2O molecule while forming a peptide bond between the two amino acidsHydrolysis: the reverse reaction of condensation synthesis where a larger molecule is broken up into its smaller substrates by adding a molecule of waterWhy does salad dressing separate into two different substances, even after being shaken thoroughly?-This is the result of the hydrophobic effect. The oil and aqueous phases within the salad dressing separate because it is amphiphilic, meaning that is has both a hydrophilic and hydrophobic nature. The hydrophilic heads face the water part of the dressing while the hydrophobic tails face each other, forming a type of barrier and separating the –phobic tails (oil) from the water.Greatest to least strength within bonds Covalent bonds > ionic bonds > hydrogen bonds > London Dispersion ForcesCentral Dogma: DNA (templated polymerization aka transcription)  RNA (translation)  proteinsQuestion Set Two Review/AnswersWhat is the difference between spontaneous and nonspontaneous reactions?-A spontaneous reaction has negative free energy (−∆ G), happens automatically, is favored,and releases energy that can be used to initiate nonspontaneous reactions. Nonspontaneous reactions have positive free energy (−∆ G), are unfavored in the environment, and must be either coupled with a spontaneous reaction or acquire an activation energy to occurStages in the Oxidation of GlucoseStep 1: Glycolysis-Glucose is initially broken down in the cytosol of the cell; this step produces 4 ATP (net gain of 2 because 2 were used to initiate reaction), 2 NADH, and 2 molecules of pyruvate. There is no oxygen required for this step, so it is anaerobic.Step 2: Citric Acid Cycle-Pyruvate molecules move into mitochondrial matrix and are broken down into acetyl CoA before this reaction can occur. This produces a molecule of GTP (similar to ATP), 2 CO2, 3 NADH, and 1 FADH2Step 3: Oxidative Phosphorylation (ETC)-High-energy carriers (NADH and FADH2) move into the mitochondrial membrane and give off their electrons to a series of oxidation steps. As the electrons move from one molecule down the train toanother, more electronegative molecule, they release energy and move into a lower energy state. This energy is used to move H+ protons across the membrane, creating an energy gradient. Once the electrons reach the end of the train and are in their lowest energy state, they are given off to oxygen, which is the final electron acceptor. The energy gradient helps phosphorylate ADP and an inorganic phosphate into ATP; this reaction alone can create up to 30 molecules of ATP per one glucose molecule.Roles of ATP, NADH and NADPHATP: most abundant and important source of energy within the cells of living organisms. It gives off its energy via hydrolysis reactions, more specifically from breaking the bonds between the second and third phosphates (creating ADP and an inorganic phosphate)NADH: an energy/electron carrier; it oxidizes molecules with higher energy in order to gain H+ proton andelectrons and then transports them to wherever energy is neededNADPH: another energy carrier (similar to NADH) which is mostly used within photosynthetic reactions Which level of protein folding could function as an enzyme?-Tertiary structure. The primary structure is simply the amino acid sequence and the secondary structure consists of the alpha helices/beta sheets, so these are not completed proteins and therefore could not function as enzymes. The tertiary structure is where the protein folds itself into its 3-D conformation, and is then a functional macromolecule. Additionally, not all proteins have a quaternary structure; only some combine with other polypeptides to create this super-macromolecular structure.What is the role of covalent bonding within a polypeptide chain?-Covalent bonds are only used during the creation of the primary structure; it binds the amino acids together via peptide bonds. The noncovalent bonds (or H-bonds) are used in making the other structures.Lecture One (Wednesday, Jan 14)What makes cell types different?-In any cell, most genes are turned off; a minority of genes are turned on, and only specific proteins are made for what this cell type needs-Example: photoreceptor genes in eyes are NOT turned on in muscle cells-All cells have the same genotype, but the different phenotypes are due to which genes are actually turned onALL living cells store their hereditary indo in the form of double-stranded DNA ALL cells require phosphorylated nucleotide ATP as building block for