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 FADH2
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