Study Guide from Chat 2

Cell Cycle & Mitosis

Overview of the Cell Cycle

The cell cycle is the orderly sequence of events that leads to cell growth, DNA replication, and cell division. It ensures that genetic material is accurately duplicated and distributed to daughter cells.

• Interphase: The "living" phase, comprising over 90% of a cell's life. It is divided into three sub-phases:

  • G1 phase: Cell growth and normal metabolism.

  • S phase: DNA replication occurs.

  • G2 phase: Further growth and preparation for division.

• M phase: Includes mitosis (nuclear division) and cytokinesis (cytoplasmic division).

• G0 phase: A resting state where the cell exits the cycle and does not divide (e.g., most neurons).

Cell Cycle Checkpoints

Checkpoints are control mechanisms that ensure the cell cycle progresses only when certain conditions are met, preventing the division of damaged cells.

• G1 checkpoint: Checks for adequate nutrients, growth factors, and undamaged DNA.

• G2 checkpoint: Ensures DNA has been accurately and completely replicated and the cell is large enough to divide.

• M (metaphase) checkpoint: Verifies that all chromosomes are properly attached to the spindle apparatus before separation.

Molecular Control of the Cell Cycle

• Cyclins: Regulatory proteins whose concentrations fluctuate throughout the cell cycle.

• Cyclin-dependent kinases (Cdks): Enzymes activated by binding to cyclins; they phosphorylate target proteins to advance the cell cycle.

• MPF (Maturation-Promoting Factor): A cyclin-Cdk complex that triggers passage from G2 into mitosis.

Phases of Mitosis

Mitosis produces two genetically identical daughter cells for growth, repair, and replacement.

• Prophase: Chromatin condenses into chromosomes; mitotic spindle forms.

• Prometaphase: Nuclear envelope breaks down; spindle fibers attach to kinetochores.

• Metaphase: Chromosomes align at the metaphase plate.

• Anaphase: Sister chromatids separate and move to opposite poles.

• Telophase: Nuclear envelopes reform; chromosomes decondense.

• Cytokinesis: Cytoplasm divides, forming two cells (in animals, via a cleavage furrow).

Memory Aid: PMAT = Prophase, Metaphase, Anaphase, Telophase.

Chromosome Numbers and Variation

• Chromosome number varies widely among species and does not correlate with organismal complexity.

• Examples: Humans (46), Cabbage (18), Elephants (56), Adders-tongue plant (1,260).

• Genome size also varies: E. coli (4.6 million base pairs), Humans (3.2 billion), Paris japonica (150 billion).

Cancer and Cell Cycle Dysregulation

• Cancer results from cells bypassing checkpoints and dividing uncontrollably.

• Cancer cells often have abnormal chromosome numbers (e.g., colorectal cancer cells may have 59 chromosomes).

• Many chemotherapy drugs (e.g., Taxol) disrupt microtubule function, blocking mitosis.

Meiosis & Sexual Reproduction

Purpose and Process of Meiosis

Meiosis is a specialized cell division that produces gametes (sperm and eggs), reducing chromosome number by half to maintain species stability across generations.

• 1 diploid cell (2n) produces 4 unique haploid cells (n).

Stages of Meiosis

• Meiosis I: Homologous chromosomes separate (reductional division).

• Meiosis II: Sister chromatids separate (resembles mitosis but in haploid cells).

Genetic Variation: Crossing Over

• During Prophase I, homologous chromosomes exchange DNA segments at chiasmata, increasing genetic diversity among offspring.

Comparison: Mitosis vs. Meiosis

Feature	Mitosis	Meiosis
Purpose	Growth, repair	Gamete production
Daughter cells	2 identical diploid	4 unique haploid
Number of divisions	1	2
Crossing over	No	Yes (Prophase I)

Human Life Cycle Numbers

• Females: ~50 mitotic divisions before meiosis produces an egg.

• Males: 100+ mitotic divisions before sperm formation.

• High number of divisions increases mutation opportunities.

The Central Dogma: DNA → RNA → Protein

Overview

The central dogma describes the flow of genetic information: DNA is replicated, transcribed into RNA, and translated into protein.

1. DNA Replication

• Occurs during S phase of the cell cycle.

• Each DNA strand serves as a template for a new strand (semi-conservative replication).

• Key enzymes:

  • DNA polymerase III: Synthesizes new DNA strands.

  • Primase: Lays down RNA primers.

  • DNA ligase: Joins Okazaki fragments on the lagging strand.

• Leading strand: Synthesized continuously.

• Lagging strand: Synthesized discontinuously in Okazaki fragments.

• Replication is highly accurate (error rate ~1 per billion nucleotides).

2. Transcription (DNA → RNA)

• Occurs in the nucleus (eukaryotes).

• Three steps:

  • Initiation: Transcription factors and RNA polymerase II bind to the promoter (often containing a TATA box).

  • Elongation: RNA polymerase synthesizes mRNA in the 5′ → 3′ direction.

  • Termination: Polymerase encounters a polyadenylation signal (AAUAAA), releasing pre-mRNA.

mRNA Processing (Eukaryotes)

• 5′ Cap: Modified guanine added for stability and ribosome binding.

• 3′ Poly-A tail: 50–250 adenines added for protection.

• Splicing: Removal of introns and joining of exons by spliceosomes (snRNPs and snRNA).

• Alternative splicing: Allows one gene to code for multiple proteins.

3. Translation (RNA → Protein)

• Occurs in the cytoplasm on ribosomes.

• Key players:

  • mRNA: Carries the genetic code.

  • tRNA: Brings amino acids; contains anticodons complementary to mRNA codons.

  • Ribosome: Site of protein synthesis; composed of rRNA and proteins.

• Process:

  • Initiation: Ribosome assembles at the start codon (AUG).

  • Elongation: tRNAs bring amino acids; peptide bonds form via dehydration reactions.

  • Termination: Stop codon triggers release of the completed protein.

• Wobble: Flexibility in the third base of the codon allows one tRNA to recognize multiple codons.

• Polyribosomes: Multiple ribosomes translate a single mRNA simultaneously.

DNA Damage, Mutations & Evolution

Types of Mutations

• Point mutations (single nucleotide changes):

  • Silent: No change in amino acid sequence.

  • Missense: One amino acid is changed (e.g., sickle-cell anemia).

  • Nonsense: Early stop codon truncates the protein.

  • Frameshift: Insertion or deletion shifts the reading frame, altering downstream amino acids.

• Chromosomal mutations: Large-scale changes (deletions, duplications, inversions, translocations).

Sources of DNA Damage

• Metabolism: Reactive oxygen species (ROS) can oxidize DNA bases (e.g., guanine to 8-oxoG).

• UV light: Causes pyrimidine dimers, distorting DNA structure.

• Chemicals: Carcinogens like benzo[a]pyrene bind DNA, causing bulky lesions.

DNA Repair Mechanisms

• Homologous recombination: Uses a sister chromatid as a template for accurate repair.

• Non-homologous end joining (NHEJ): Directly joins broken DNA ends; error-prone.

Evolution and Mutation

• Most mutations are neutral or harmful; beneficial mutations can be favored by natural selection, driving evolution.

• Example: Evolution of circulatory systems in vertebrates for improved oxygen delivery.

Biotechnology Tools & Applications

Key Techniques

• Gel Electrophoresis: Separates DNA fragments by size using an electric field; smaller fragments move faster through agarose gel.

• DNA Sequencing (Sanger method): Uses chain-terminating nucleotides to determine DNA sequence.

• Restriction Enzymes: Bacterial enzymes that cut DNA at specific palindromic sequences; used in genetic engineering.

• PCR (Polymerase Chain Reaction): Amplifies specific DNA segments using cycles of heating and cooling and a heat-stable DNA polymerase (Taq polymerase).

• CRISPR-Cas9: Gene-editing tool that uses a guide RNA to direct Cas9 to a target sequence for precise DNA modification.

Applications

• Insulin production: Human insulin gene inserted into bacteria for large-scale production.

• Golden Rice: Genetically engineered to produce beta-carotene, addressing vitamin A deficiency.

• GFP (Green Fluorescent Protein): Used as a marker to visualize proteins in living cells.

Viruses — Biological Hackers

General Viral Life Cycle

• Attachment and entry into host cell via specific receptors.

• Uncoating of viral genome.

• Replication of viral genome.

• Transcription/translation of viral proteins using host machinery.

• Assembly of new virus particles.

• Exit from the cell (often causing cell lysis).

Notable Viruses

• Retroviruses (e.g., HIV): RNA genome; reverse transcriptase converts RNA to DNA, which integrates into host genome as a provirus.

• Coronaviruses: Bind to ACE2 receptor; entry facilitated by TMPRSS2 protease.

Vaccines

• Expose immune system to viral components (attenuated virus, protein fragments, or mRNA) to stimulate antibody and memory cell production without causing disease.

Bioethics & Economics

Clinical Research Ethics

• Institutional Review Boards (IRBs) oversee research involving humans to ensure ethical standards.

• Prevent "undue influence"—excessive payment that could coerce participation.

• Informed consent must be voluntary and genuine.

Economic Considerations in Drug Development

• Developing a new drug costs approximately $879 million.

• Profit motives may favor treatments over cures or vaccines, influencing research priorities.

Quick Reference — Essential Terms

• Diploid (2n): Two sets of chromosomes (body cells).

• Haploid (n): One set of chromosomes (gametes).

• Homologous chromosomes: Chromosome pairs, one from each parent.

• Sister chromatids: Identical copies of a chromosome joined at the centromere.

• Gene: DNA segment coding for a protein or functional RNA.

• Allele: Variant form of a gene.

• Genome: Complete set of an organism's DNA.

• Codon: Three-nucleotide mRNA sequence coding for an amino acid.

• Anticodon: Three-nucleotide tRNA sequence complementary to a codon.

• Promoter: DNA sequence where transcription begins.

• Exon: Coding region retained in mRNA.

• Intron: Non-coding region removed during mRNA processing.