Biochemistry & Molecular Biology Exam Review

Vocabulary flashcards covering key enzymes, molecules, pathways, and experimental techniques from the lecture notes to aid exam preparation.

Nitrogen Fixation

Biological conversion of atmospheric N₂ to ammonia, catalyzed by nitrogenase and requiring iron (Fe) and molybdenum (Mo) cofactors.

Fe-Mo Protein

The molybdenum-iron component of nitrogenase that carries out electron-dependent reduction of N₂.

Fe Protein

Iron–sulfur protein of nitrogenase that delivers electrons (from ferredoxin) to the Fe-Mo protein using ATP hydrolysis.

Ferredoxin

Iron–sulfur electron-carrier protein that donates reducing equivalents to the Fe protein in nitrogen fixation.

Biotin

Vitamin coenzyme that transports single-carbon units as CO₂ in carboxylation reactions.

Tetrahydrofolate (THF)

Reduced form of folate that carries one-carbon groups at various oxidation levels in metabolism.

S-Adenosylmethionine (SAM)

Activated methyl donor formed from methionine and ATP; participates in methylation and some one-carbon transfers.

Methotrexate

Anticancer drug that competitively inhibits dihydrofolate reductase, blocking regeneration of THF.

Dihydrofolate Reductase (DHFR)

Enzyme that reduces dihydrofolate to THF using NADPH; target of methotrexate.

Asparagine Synthetase

Enzyme that uses glutamine (as NH₃ donor), ATP, and aspartate to form asparagine.

Ubiquitination

Covalent attachment of ≥4 ubiquitin molecules to a lysine on a protein, marking it for proteasomal degradation.

Purine Bases

Nitrogenous bases adenine, guanine, hypoxanthine (NOT thymine) that have a fused bicyclic ring.

Inosine Monophosphate (IMP)

First complete purine nucleotide formed on ribose during de novo purine biosynthesis.

Phosphodiesterase (Exonuclease)

Enzyme that sequentially removes nucleotides from oligonucleotides, releasing nucleoside monophosphates.

Nucleotidase

Enzyme that hydrolyzes nucleoside monophosphate + H₂O → nucleoside + Pi.

Ribonucleotide Reductase (RNR)

Enzyme that converts ribonucleotides (NDPs) to deoxyribonucleotides (dNDPs) via free-radical chemistry.

RNR Class II/III Radicals

Classes that initiate catalysis with radicals generated by B₁₂ (class II) or S-adenosylmethionine (class III), unlike Tyr• in class I.

dTTP Precursors

dUDP and dCDP are the dNDPs that can be converted downstream to dTTP.

Guanine (Purine Catabolism)

Product formed when guanosine is de-ribosylated during purine degradation.

Inosine

First intermediate in adenosine catabolism toward uric acid (adenosine → inosine → hypoxanthine → xanthine → uric acid).

GPCR α-Subunit

Intracellular G-protein subunit that exchanges GDP for GTP, dissociates, and activates downstream effectors.

Nuclear Receptor

Intracellular hormone receptor (e.g., steroid receptors) that functions as a ligand-activated transcription factor.

DNA Phosphodiester Backbone

Repeating polymer of sugar-phosphate units that forms the structural framework of DNA strands.

Single Nucleotide Polymorphism (SNP)

Point mutation present in ≥1% of a population; contributes to genetic diversity.

Hershey–Chase Experiment

Used T2 bacteriophage labeled with ³²P (DNA) and ³⁵S (protein) to show DNA is the genetic material.

Base-Stacking Interactions

Hydrophobic and van der Waals forces between adjacent bases that stabilize the DNA helix (not phosphodiester bonds).

DNA Polymerase I (Prokaryotes)

Enzyme that removes RNA primers and fills gaps with DNA on the lagging strand during replication.

DNA Ligase (Eukaryotic)

Seals nicks in DNA; uses ATP to form a ligase-AMP intermediate (adenylation) required for phosphodiester bond formation.

Random Hexamer Primers

Mixture of random six-nucleotide sequences used to prime diverse sites on mRNA for reverse transcription.

Oligo dT Primers

Poly-dT sequence that anneals to the poly-A tail of eukaryotic mRNA for reverse transcription.

Enhancer Element

Distal DNA sequence (often in paired sites) that binds activator proteins and increases transcription from a promoter.

7-Methylguanosine Cap

Modified guanine nucleotide added to 5′ end of eukaryotic mRNA; stabilizes RNA and aids in translation initiation and splicing.

Alternative Splicing

Process by which different combinations of exons are joined to produce multiple, cell-type-specific mRNAs from one gene.

tRNA Acceptor Stem

3′ CCA terminus of tRNA that carries the amino acid during translation.

Release Factor RF3

Prokaryotic GTP-ase that promotes dissociation of RF1/RF2 and ribosomal subunits during translation termination.

SecB

Cytosolic chaperone that binds newly synthesized pre-proteins and prevents folding prior to Sec-dependent secretion.

Ran GTPase

G-protein that regulates nuclear import/export by binding importin and hydrolyzing GTP to drive transport directionality.

Rough Endoplasmic Reticulum

Cellular site where nascent polypeptides enter lumen and begin N-linked glycosylation during protein sorting.

cAMP in Lac Operon

Required co-activator (with CAP) for efficient transcription of lac genes when glucose is low; absent when glucose is high.

Histone H1

Linker histone that binds DNA between nucleosomes, aiding higher-order chromatin compaction.

Glutamine (Purine Nitrogen Donor)

Provides the N at position B (N-3 and N-9) during purine ring assembly.

Thioredoxin (Reduced Form)

Dithiol protein (–SH SH) that donates electrons to ribonucleotide reductase; oxidized form has disulfide (–S–S–).

Chargaff’s Rule

Empirical finding that in DNA, %A = %T and %C = %G.

Urea Cycle

Metabolic pathway that converts toxic ammonia to urea for safe excretion, efficiently eliminating excess nitrogen.

Meselson–Stahl Experiment

Density-gradient test showing semiconservative DNA replication; with successive rounds, light-DNA peak intensifies.

siRNA Knockdown

Use of small interfering RNA to trigger degradation of specific mRNA, confirming gene function by reduced protein expression.

Western Blot

Immunoassay that separates proteins by SDS-PAGE and detects specific proteins using antibodies.

Real-Time PCR (qPCR)

Technique that monitors amplification of cDNA during PCR to quantify initial mRNA levels indirectly.