USMLE Step `1 Biochemistry

Biochemistry Study Notes

Chromatin Structure

  • DNA and Chromatin Form: DNA exists in a condensed chromatin form to fit into the nucleus.

    • DNA loops around a histone octamer to form a nucleosome (referred to as "beads on a string").

    • H1 histone binds to the nucleosome and linker DNA, stabilizing the chromatin fiber.

  • Charges:

    • DNA has a negative charge from phosphate groups.

    • Histones are positively charged due to residues of lysine and arginine.

  • Mitosis: DNA condenses to form chromosomes during mitosis.

  • Synthesis Phase: DNA and histone synthesis occurs during the S phase of the cell cycle.

  • Mitochondrial DNA: Mitochondria have their own circular DNA and do not utilize histones.

  • Chromatin Types:

    • Heterochromatin:

    • Highly condensed, appears darker in electron microscopy.

    • Sterically inaccessible; thus, transcriptionally inactive.

    • DNA modifications: methylation decreases transcription, acetylation can increase transcription.

    • Example: Barr bodies (inactive X chromosomes).

    • Euchromatin:

    • Less condensed, appears lighter in electron microscopy.

    • Transcriptionally active and accessible.

    • Expressed DNA.

DNA Methylation and Histone Modifications

  • DNA Methylation: Changes the expression of DNA segments without altering the sequence.

    • Associated with aging, carcinogenesis, genomic imprinting, transposable element repression, and X chromosome inactivation (lyonization).

    • Methylation typically occurs in gene promoter regions (e.g., CpG islands) and represses gene transcription.

    • Example: Dysregulated DNA methylation is implicated in Fragile X syndrome.

  • Histone Methylation: Can cause either transcriptional suppression or activation depending on methyl group positioning.

    • Methylation primarily silences DNA.

  • Histone Acetylation:

    • Involves the removal of the positive charge from histones.

    • Results in relaxed DNA coiling, facilitating transcription.

    • Example: Acetylation of thyroid hormone receptor alters its synthesis.

  • Histone Deacetylation: Causes tightened DNA coiling, leading to reduced transcription.

    • Deactivated DNA associated with diseases such as Huntington's disease.

Nucleotides

  • Nucleoside and Nucleotide Definitions:

    • Nucleoside: Composed of a base + (deoxy)ribose (sugar).

    • Nucleotide: Composed of a base + (deoxy)ribose + phosphate (linked by a 3′-5′ phosphodiester bond).

  • Purines and Pyrimidines:

    • Purines: Adenine (A), Guanine (G) – 2 rings.

    • Pyrimidines: Cytosine (C), Uracil (U), Thymine (T) – 1 ring.

  • Deamination Reactions:

    • Cytosine → Uracil

    • Adenine → Hypoxanthine

    • Guanine → Xanthine

    • 5-Methylcytosine → Thymine (methylation transforms uracil to thymine).

  • Bond Strength:

    • C-G bond (3 hydrogen bonds) is stronger than A-T bond (2 hydrogen bonds).

    • Higher C-G content leads to increased melting temperature of DNA.

Amino Acids Necessary for Purine Synthesis

  • Amino acids required for purine synthesis include:

    • Glycine

    • Aspartate

    • Glutamine

  • Mnemonic: Cats Purr Until They GAG (Glycine, Aspartate, Glutamine).

De Novo Purine and Pyrimidine Synthesis

  • Various drugs affect nucleotide synthesis, including chemotherapeutics and antibiotics.

    • Implicated reactions include IMP, AMP, GMP, orotic acid synthesis, UMP, CTP, and thymidylate synthesis.

  • Drug Examples:

    • De novo purine synthesis inhibitors: 6-mercaptopurine (6-MP), azathioprine (potential immunosuppression).

    • De novo pyrimidine synthesis inhibitors: 5-fluorouracil (5-FU) (inhibits thymidylate synthase).

Genetic Code Features

  • Unambiguous: Each codon specifies one amino acid.

  • Degenerate/Redundant: Multiple codons can encode the same amino acid.

  • Wobble Hypothesis: The first two nucleotides of the codon are essential for recognition, while the third can vary (exceptions include Met and Trp).

  • Universal: The genetic code is conserved across species, with mitochondrial exceptions.

DNA Replication

  • Direction: DNA replication occurs in the 5′ to 3′ direction via continuous and discontinuous (Okazaki fragments) synthesis.

  • Structure: Semiconservative process requiring a replication fork, where enzymes like helicase, primase, and DNA polymerases play key roles.

    • Origin of Replication: Specific sequences in the genome where replication starts, with AT-rich sequences commonly found.

  • Key Enzymatic Actions:

    • Helicase: Unwinds the DNA template at the replication fork.

    • Single-Stranded Binding Proteins: Prevent strands from reannealing.

    • DNA Topoisomerases: Manage supercoiling by introducing breaks.

    • DNA Polymorphisms: Perform synthesis and proofreading.

    • DNA Ligase: Joins Okazaki fragments.

    • Telomerase: Adds telomeric sequences to replicate ends of chromosomes in eukaryotes.

DNA Repair Mechanisms

  • Nonhomologous End Joining: Repairs double-stranded breaks, does not require homologous templates.

  • Homologous Recombination: Uses a homologous DNA template for repair, involved in mechanisms of breast/ovarian cancers.

  • Nucleotide Excision Repair: Removes bulky base lesions, occurs during G1 phase, defects lead to conditions like xeroderma pigmentosum.

  • Base Excision Repair: Base-specific glycosylase removes altered base.

  • Mismatch Repair: Corrects mismatches during DNA replication, critical in maintaining genomic integrity.

Mutations in DNA

  • Types: Silent, missense, nonsense, frameshift, splice site mutations.

    • Missense Mutation: Falsely coded amino acid (example: sickle cell disease).

    • Nonsense Mutation: Early stop codon, producing truncated proteins.

    • Frameshift Mutation: Causes extensive downstream downstream misreading.

  • Lac Operon: Adaptive genetic response to environmental changes in the availability of glucose and lactose in E. coli.

Functional Organization of Eukaryotic Genes

  • Structural components include promoters, enhancers, silencers, exons, and introns associated with transcriptional regulation.

  • Enhancer: Site for regulatory proteins enhancing gene expression (possibly located distally);

  • Promoter: Binds RNA polymerase II and transcription factors to start transcription.

Epigenetics and Gene Expression Regulation

  • Epigenetic Modifications: Changes such as DNA methylation and histone modification can alter gene expression without changing DNA sequence.

  • RNA Processing: Include steps like capping, polyadenylation, and splicing out introns to form mature mRNA.

    • Capping: 7-methylguanylate cap added to the 5' end.

    • Polyadenylation: Addition of a poly-A tail at the 3' end for stability and nuclear export.

  • Abnormal processing can lead to diseases, displaying the crucial nature of accurate RNA modification.

Protein Synthesis

  • Initiation: Process begins when eukaryotic initiation factors assemble around the 5' cap leading to ribosome formation and start codon recognition.

  • Translation Process: Includes elongation where amino acids are added per the sequence dictated by mRNA.

    • Uses sites: A (aminoacyl), P (peptidyl), and E (exit) to facilitate tRNA interaction.

  • Termination: Occurs upon codon recognition by release factors, detaching the completed polypeptide chain.

Cell Cycle Phases and Regulation

  • Checkpoints: Cyclins and CDKs control transition through cell cycle phases; mutations in tumor suppressors can lead to unregulated division.

  • Phases: G1 (variable duration), S (DNA synthesis), G2 (preparation for mitosis), M phase (mitosis).

Endoplasmic Reticulum Functions

  • Rough ER: Synthesis of secretory proteins.

  • Smooth ER: Functions in steroid synthesis and detoxification of harmful substances, lacking ribosomes.

Lysosomes and Proteasomes

  • Lysosomes: Involved in degradation of biomolecules using hydrolytic enzymes; dysfunction can lead to storage diseases.

  • Proteasomes: Degrade ubiquitinated proteins: important for cellular regulation and protein turnover.

Cytoskeleton and Cell Structure

  • Composed of microfilaments (actin), intermediate filaments (structure), and microtubules (movement).

  • Molecular Motor Proteins: Kinesin and dynein transport cargo along microtubules.

Signal Transduction Mechanisms

  • Cell Surface Receptors: Transmitter-dependent targeting activates downstream signal pathways impacting various cellular responses.

  • Understanding of these sequences is essential for pharmacological and therapeutic interventions.

Nutritional Biochemistry

  • Covers essential nutrients, including vitamins and minerals, needed for metabolic reactions and functioning.

  • Deficiency and Toxicity: Both can yield important physiological disturbances, showcasing the role of balanced dietary intake.

Urea Cycle

  • Involves converting excess nitrogen into urea for excretion.

  • Disorders of this cycle lead to hyperammonemia, highlighting the importance of ammonia metabolism.

Summary of Metabolic Processes

  • Detailed pathways demonstrate the connections between energy metabolism, nutrition, and enzymatic functions.

  • Examples include glycolysis, TCA cycle, and the influence of different substrates on cellular energy production.