Final exam key concepts for exams 1 3 20 questions 50 points total Water pH and buffers Water is an excellent solvent due to its polar nature The ion product of water is given by Kw H OH 10 14 pH is the negative log of H 7 0 for water Buffers help maintain the pH of a solution Amino acids General structure of an amino acid Formation of peptide bonds The ionization behavior of amino acids The importance of amino acid side chains Proteins The levels of protein structure primary secondary tertiary quaternary Noncovalent forces that underlie the higher levels of protein structure Methods for protein purification are based on certain properties of proteins helix versus sheet and stabilization by hydrogen bonding Carbohydrates Structure for simple aldoses and ketoses Difference between enantiomers diastereomers and epimers Polysaccharides general roles and which types of polysaccharides serve each role Lipids Saturated versus unsaturated fatty acids what does this mean and what is the effect of each Nomenclature naming convention Role of triacylglycerols triglycerides versus glycerophospholipids Membranes and membrane transport General functions structure of membranes Peripheral versus integral membrane proteins Fluid mosaic model of membrane structure Differences between passive diffusion facilitated diffusion and active transport Enzymes Meaning of Km kcat and kcat Km Michaelis Menton plot versus Lineweaver Burk plot Competitive versus non competitive versus mixed inhibition plots Allosteric effects and cooperativity Nucleic acids Similarities and differences between DNA and RNA General structure of DNA double helix Chargaff s rules Pyrimidines versus purines general structure and which nucleotides belong to each DNA replication DNA replication is semiconservative bidirectional and semidiscontinuous DNA polymerase requires a primer with a free 3 OH group and proceeds in the 5 to 3 direction DNA polymerase holoenzyme has two core DNA polymerase units one for each strand The clamp makes DNA polymerase processive by holding onto the DNA Primase makes the RNA primer helicase unwinds the double helix and ligase seals nicks Transcription RNA polymerase synthesizes RNA complementary to a DNA template and does not require a primer RNA polymerase recognizes a promoter to know where to start transcription Eukaryotic mRNAs are highly processed 5 cap splicing and polyadenylation Bacteria have a single RNA polymerase and eukaryotes have three RNA polymerases Translation The genetic code is a triplet code that is universal degenerate and unambiguous Codons are recognized by the tRNA anticodon and wobble can occur at the third base of the codon Ribosomes have a large and a small subunit and three tRNA sites A P and E Three codons do not encode for an amino acid do not bind a tRNA and instead signal termination GTP hydrolysis is important in initiation elongation and termination Gene regulation Negative and positive regulation refer to regulatory proteins Inducible and repressible refer to the small molecules that bind to the regulatory proteins Four modes of transcriptional regulation General metabolism ATP is the key high energy compound that fuels many metabolic processes NAD is a key electron carrier in catabolic processes G signals whether a reaction will proceed spontaneously poor reactions can be coupled to favorable reactions Glycolysis Requires 2 ATP in the preparatory phase and generates 4 ATP in the payoff phase Generates 1 NADH Three strongly favored reactions are regulated Glucose is broken down to two pyruvate TCA cycle Each pyruvate is converted to acetyl CoA which enters the TCA cycle Oxaloacetate is required for the first step and is regenerated at the end of the cycle The TCA cycle generates many NADH but only one ATP Electron transport and oxidative phosphorylation Electron transport through the electron transport chain is used to create a proton gradient across the inner mitochondrial membrane Complexes I III and IV transport protons Complex II does not Complex I uses NADH Complex II uses FADH 2 O2 is the final electron acceptor ATP synthase generates ATP from ADP P The proton gradient is used to drive conformation changes in ATP synthase for ATP release Gluconeogenesis Glycolysis and gluconeogenesis share some enzymes but the highly favored reactions are unique to each pathway Gluconeogenesis requires ATP Energy charge The energy charge of the cell is maintained at a high level Energy charge relates the levels of ATP ADP and AMP