pre-midterm content

  1. Genetic Approach to Studying Mutants

    • Information gained from genetic studies of mutants can confirm amino acid functionalities and elucidate roles in biological processes.

  2. Permissive Conditions

    • In temperature-sensitive mutants, permissive conditions allow the mutated gene product to behave normally, obscuring the mutant phenotype.

  3. Roles of Model Organisms

    • Model organisms enable comprehensive insights into biological systems on cellular, tissue, organ, and systemic levels.

  4. Functions of DNA

    • Replication: Must replicate faithfully for proper growth and cell division.

    • Information Storage: Saves instructions for protein synthesis and essential functions.

    • Mutation: Allows for genetic variation through mutations, fostering natural selection and evolution.

  5. Roles of Bonds in DNA Structure

    • Phospho-diester Bonds: Stabilize the structure by linking phosphate and sugar in the backbone.

    • Hydrogen Bonds: Connect base pairs between DNA strands, essential for double helix stability.

    • Hydrophobic Interactions: Affect DNA’s interaction with water, influencing molecular structure.

  6. Non-Covalent Interactions

    • Interactions maintaining double-helical conformation include ionic, hydrogen, van der Waals, and hydrophobic interactions.

  7. Meselson-Stahl Experiment

    • Demonstrated semiconservative DNA replication using E. coli grown in N-15, transferring to N-14, and analyzing DNA density after centrifugation. Each daughter molecule contains one old and one new strand.

  8. Polarity of DNA Strands

    • DNA strands are antiparallel, with opposing 5’ and 3’ ends, and are complementary, meaning the sequence of one strand dictates the other.

  9. DNA Composition Ratios

    • If C content is 20%, then G also is 20%; thus, AT content is 60%, leading to T content of 30%.

  10. Nucleoside vs Nucleotide

    • Nucleosides consist of sugar and base; nucleotides include sugar, base, and phosphate. dNTP stands for deoxynucleotide triphosphate.

  11. High Salt Concentration and Denaturation

    • High salt stabilizes negatively charged phosphates in DNA, reducing strand repulsion, resulting in higher melting temperatures due to duplex stability.

  12. Classes of DNA Sequences

    • Highly Repetitive: Fast renaturation.

    • Moderately Repetitive: Slower renaturation.

    • Unique: Slowest renaturation.

  13. Cot Analysis

    • Measures genomic DNA complexity through DNA reassociation kinetics.

  14. Absorbance Comparison

    • Single-stranded DNA will show a higher concentration than double-stranded DNA at the same absorbance (260 nm).

  15. Bacterial vs Eukaryotic Genome Complexity

    • Bacterial genomes are primarily unique without repetitive sequences, while eukaryotic genomes feature high and moderate repeat sequences and unique sequences with varying renaturation kinetics.

  16. C-value Paradox

    • There is no correlation between genome size (C-value) and organismal complexity.

  17. Factors Influencing DNA Renaturation

    • High salt, low temperature, DNA concentration, fragment size, and overall genomic complexity.

  18. New Species DNA Complexity Evaluation

    • a) 3 classes found: 25% highly repetitive, 25% moderately repetitive, 50% unique.

  19. Prokaryotic Topoisomerase Distinctions

    • Topoisomerase I introduces positive supercoiling; Gyrase introduces negative supercoiling; Topoisomerase cuts single strands, while Gyrase cuts double strands and requires ATP.

  20. Topological Isomers of DNA

    • Variants of DNA differing in their supercoiling state.

  21. Importance of DNA Supercoiling

    • Ensures compact DNA packaging for cell survival, facilitates transcription, protects against damage, and provides energy for unwinding during replication/transcription.

  22. DNA vs RNA Structural Differences

    • Primary: Uracil (RNA) replaces thymine (DNA).

    • Secondary: DNA: double helix; RNA: folds into stem-loops and hairpins.

  23. Circular DNA Twisting and Writhe Calculation

    • 4800 bp circular DNA with L=450 results in 480 twist and -30 writhe (negatively supercoiled).

  24. Mutation Observation in Histones

    • Histones are conserved due to their essential, stable role in chromatin structure.

  25. Eukaryotic Chromosomes Features

    • Linear DNA with nucleosomes (histone structures) wound into higher-order folds, with centromeres for spindle attachment and telomeres for chromosome end protection.

  26. Histone Amino Acid Composition

    • Histones are rich in lysine and arginine, stabilizing DNA’s negative charge and facilitating its binding.

  27. Non-Histone Proteins in Chromatin

    • Proteins such as MARs and SMC that assist in structural organization and transcription regulation within chromatin.

  28. Heterochromatin vs Euchromatin

    • Heterochromatin: tightly packed, transcriptionally inactive; Euchromatin: loosely packed, active in transcription and replication.

  29. Histones per Kilobase Comparison

    • More histones are expected in heterochromatin due to its tightly packed structure requiring additional binding proteins.

  30. Gene Expression and Chromatin State

    • Genes in euchromatin are expressed in active cell types; genes in heterochromatin are usually not expressed.

  31. Developmental Chromatin Changes

    • Genes that become euchromatin in later development allow necessary muscle expression.

  32. Human Genomic Measurements

    • a) Diploid genome: 6 billion bp = 6 million kb.

    • b) Average chromosome length ~4.43 cm if in relaxed B-DNA.

    • c) ~13 million complete turns per chromosome.

    • d) Average of 1304-1739 genes per chromosome.

33-36. Homologous vs Non-Homologous Chromosomes- Homologous chromosomes: similar pairs from each parent.- Non-Homologous chromosomes: distinct and unrelated pairs.- Both genders have 23 homologous chromosomes.

  1. Cell Division Purpose

    • Eukaryotes: growth, repair, reproduction.

    • Prokaryotes: reproduction.

  2. DNA Replication vs Cell Division

    • DNA replication is the copying of genetic material, whereas cell division is the actual division into daughter cells.

  3. Mitosis vs Meiosis Purpose

    • Mitosis: tissue growth and repair.

    • Meiosis: production of gametes, promoting genetic variability.

  4. Genetic Variability

    • Results from crossing over in prophase I of meiosis.

  5. Cell Cycle Definition and Stages

    • A sequence of events leading to cell division; includes interphase and mitosis.

  6. Cell Cycle Checkpoints

    • G1: checks cell size/environment; S phase: replication progress; G2: checks DNA replication; M: ensures chromosome alignment.

  7. Triggers for Cell Cycle Arrest

    • DNA damage, improper mass, defective replication, lack of nutrients.

  8. Chromosome Segregation

    • Mitosis occurs in anaphase; meiosis occurs in meiosis I anaphase.

  9. Chromatid Segregation

    • Mitosis occurs in anaphase; meiosis occurs in meiosis II anaphase.