Biochemistry I

• The three domains of life are bacteria, eukarya, and archaea.
• Bacteria have circular or linear DNA and are prokaryotes, which lack organelles and are unicellular.
• Eukarya have linear DNA within a nucleus and can be unicellular or multicellular.
• Archaea have mostly circular DNA and are unicellular.
• Extremophiles have unique cell physiology and metabolism.
• The importance of unity in biological diversity is the preservation of the foundation, basic building blocks of life.
• The genetic code is similar in TATA-box binding proteins in archaea, plants, and humans.
• Suicide is the termination of a chemical reaction by the enzyme that participated in its own catalysis, using its own mechanism.
• Mechanism-based inhibition is the termination of a chemical reaction by the enzyme that participated in its own catalysis, using its own mechanism.
• London dispersion, dipole-dipole, and hydrogen bonding are important for secondary structure of proteins.
• Electrostatic interactions are important for tertiary protein structure.
• The First Law of Thermodynamics states that the conservation of energy is constant.
• The Second Law of Thermodynamics states that the entropy of the universe increases with spontaneous processes.
• Denaturation refers to the loss of protein function due to changes in its shape or conformation caused by heat, pH change, or other factors.
• The change in entropy is proportional to the change in enthalpy, meaning that heat released increases disorder.
• ΔG = ΔH - TΔS and is spontaneous if ΔG < 0.
• Amino acids are monomers that are “α-amino acids” with a center α carbon, which are chiral molecules with one predominant formation.
• Almost all biological amino acids are in the L isomer, not the D isomer.
• Amino acids are zwitterions, having both a negative and positive charge in the molecule, true for amino acids at biological pH.
• The pKa of carboxyl is 2-2.5 and of amino is 9-10.
• Nonpolar/hydrophobic amino acids include glycine, alanine, valine, leucine, isoleucine, proline, tryptophan, phenylalanine, methionine.
• Polar, but neutral (uncharged) amino acids include serine, threonine, tyrosine, cysteine, asparagine, glutamine.
• Positively charged amino acids include lysine, arginine, histidine.
• Negatively charged amino acids include aspartic acid, glutamic acid.
• Steady State Approximation in enzyme kinetics states that [ES] is constant (unknown, whatever that means, but constant), meaning that the rate of ES formation k1[E][S] = rate of its dissociation k-1[ES] + k2[ES], with k1 and k2 being both dissociation and formation rates.
• KM can vary for each substrate of a single enzyme, indicating that it depends on both substrate and enzyme.
• The fetal oxygen binding curve will be higher and closer to the myoglobin curve due to the difference in subunits.
• 2,3-BPG interacts with the T state of hemoglobin, stabilizing it and requiring that in order to convert to the R state, the interactions with 2,3-BPG must be broken.
• KD in enzyme kinetics is the actual quantitative measurement of substrate-binding affinity.
• The initial rate (v0) of a reaction is used in enzyme kinetics, as it is close to time=0 and little product has been formed, making calculations easier.
• The fetal hemoglobin has different subunits than adult hemoglobin, with 𝛾 (gamma) subunits instead of β subunits.
• Enzymes are mostly proteins, but can also have RNA (ribozymes), and increase the rate of reaction, lower the energy of transition state, and have specificity for catalyzing specific reactions.
• KM in enzyme kinetics is the sum of ES dissociation rate constants over ES formation rate constant, and can indicate/suggest substrate-binding affinity, with lower KM indicating greater affinity.
• CO poisoning stabilizes the T state of hemoglobin, making it harder for oxygen to bind and leading to tighter binding and preventing oxygen from leaving in tissues.
• Enzyme kinetics can provide insight into the mechanism of the enzyme, and is useful for understanding how enzymes work.
• The Bohr effect, which is the change in affinity of oxygen due to pH and CO2, affects the T state of hemoglobin, with higher pH destabilizing the T state and leading to higher binding curve, and CO2 stabilizing the T state and lowering the binding curve.
• Sickle-cell anemia is a disease caused by a single amino acid mutation that makes the T-state less soluble and causes it to aggregate into fibers, but it does not affect the R state.
• The T state of hemoglobin is important for oxygen delivery as it allows hemoglobin to let go at some point.
• Carboxyhemoglobin is formed when hemoglobin binds CO, which is not desirable.
• Peptides are formed by condensation and broken by hydrolysis.