Biochemistry Exam Questions and Verified Answers — DNA Repair, PCR, Protein Structure, Metabolism, and Hemoglobin Study Guide (2024)

This document is a 2024 biochemistry study guide containing exam-style questions with verified correct answers covering the full scope of molecular and metabolic biochemistry. The content includes genetics and inheritance patterns such as autosomal dominant disorders affecting males and females equally, autosomal recessive inheritance of sickle cell anemia, heterozygous and homozygous genotypes, and X-linked dominant inheritance where a father affects only his daughters; molecular biology techniques including Polymerase Chain Reaction (PCR) as the process of copying DNA in the lab, its required components of template DNA, nucleotides (dNTPs), DNA polymerase, and DNA primers, its three steps of denaturing, annealing, and elongating, and ligase as the component not involved in PCR; DNA repair mechanisms including base excision repair with glycosylases, mismatch repair (MMR) occurring during replication and proofreading where a large section of nucleotide is removed so DNA polymerase can try again, nucleotide repair that cleans UV damage, homologous recombination for double-stranded breaks as a last effort, and non-homologous recombination that can lead to deletions, insertions, and frameshift mutations; transcription, RNA splicing where introns are removed and exons joined to form a contiguous coding sequence, gene expression as the ability to turn genes on and off, epigenetics as changes caused by modification of gene expression rather than alteration of the gene code, and DNA packaging around histone proteins into nucleosomes and chromatin where genes are ON when nucleosomes are widespread and OFF when tightly packed; mutation types including nonsense mutations producing a premature STOP codon, silent mutations with no observable phenotypic effect, and missense mutations coding for a different amino acid; amino acid chemistry including polar amino acids preferring water, non-polar hydrophobic amino acids, ionized amino acids with a charge, the hydrogen bond formed from two polar amino acids, and what happens when alanine loses an electron to become ionized alanine; protein structure including primary, secondary, tertiary, and quaternary levels, peptid bonds in primary structure, hydrogen bonds in secondary structure, side chain interactions in tertiary structure, multiple polypeptides in quaternary structure, beta sheets and alpha helices, how the amino acid sequence determines the 3D shape of a protein, denaturing where primary structure is unaffected, molecular chaperones that assist proper folding, and protein aggregation associated with Alzheimer's disease including amyloid-beta senile plaques, TAU protein filaments, and neurodegenerative aggregation in Parkinson's, Huntington's, ALS, and prion diseases; enzyme kinetics including substrates, substrate-enzyme complexes, active sites, allosteric sites, competitive inhibitors similar to substrates, non-competitive inhibitors binding at allosteric sites, feedback inhibition, and how methotrexate blocks enzyme processes in cancer cells; metabolic pathways including the citric acid cycle started by acetyl CoA producing NADH and FADH2, fermentation allowing glycolysis to continue when oxygen is scarce, anabolic pathways requiring energy to synthesize larger molecules, catabolic pathways generating energy by breaking down larger molecules, substrate-level phosphorylation as the only way to make ATP without oxygen, the Cori cycle supplying glucose for red blood cells through gluconeogenesis converting lactate to glucose, glycogenesis, glucagon stimulating glycogenolysis, metformin inhibiting liver glucose output, gluconeogenesis converting amino acids into glucose, glycolysis, glycation contributing to atherosclerosis, and insulin stimulating glucose uptake; lipid metabolism including beta oxidation occurring in the mitochondrial matrix during fasting, fatty acyl CoA formation, ATP/NADH/FADH2 production, C18 fatty acid beta oxidation rounds, MCAD deficiency and its low-fat complex-carbohydrate diet, omega-6 and omega-3 double bond positions, unsaturated fat characteristics, CIS and TRANS configurations, triglycerides as the greatest energy reserve, eicosanoids as signaling molecules from polyunsaturated fatty acids, the fluid mosaic model, phospholipids with two fatty acid tails, cholesterol structure and membrane fluidity role, and fatty acid synthesis in the cytoplasm; and hemoglobin and oxygen transport including cooperative binding, carbon monoxide poisoning, 2,3-BPG differences between mother and fetus, the tense domed state of hemoglobin without oxygen, hemoglobin versus myoglobin affinity, the Bohr effect and pH influence on oxygen saturation, LDL and high cholesterol, myoglobin and troponin in myocardial infarction, and the CHART mnemonic for low pH, high carbon dioxide, high hydrogen, acidic, right shift, and tense state.