Molecular Genetics: Human Genome and Cell Division Structure, Cell Cycle, and Clinical Genomics and the Human Genome Project

Human Cell Structure and the Nucleus

• Cell Basics: A cell is the structural and functional unit of all living organisms, capable of carrying out the processes of life independently. The human body contains approximately $100$ trillion of these cells.
• Major Cell Compartments:
  • Cell Membrane / Plasma Membrane: This structure separates the contents of the cell from its external environment and controls the exchange of materials between the extracellular fluid (ECF) and the intracellular fluid (ICF).
  • Protoplasm: This includes the cytoplasm (an aqueous substance) and the nucleus.
  • Cytoskeleton: A complex fiber network that maintains cell structure, shape, and facilitates movement.
  • Organelles: Sub-cellular structures including the mitochondria, ribosomes, centrioles, Golgi apparatus, vacuoles, endoplasmic reticulum (Rough and Smooth), and lysosomes.
  • Inclusion Bodies: Stored nutrients or cell products, such as granules.
• The Cell Nucleus: The nucleus serves as the center of cellular operations. It is composed of a nuclear membrane (nuclear envelope), nucleoplasm, chromosomes, and the nucleolus.
  • Nuclear Envelope: A ribosome-studded double membrane that surrounds the nucleus and contains a perinuclear space.
  • Nuclear Pores: Openings in the nuclear envelope that allow the nucleus to communicate with the cytoplasm.
  • Nucleoplasm: The liquid within the cell nucleus, which is similar in consistency and function to the cytoplasm outside the nucleus.
  • Cisternae: Flattened membrane disks within the nuclear structure.
  • Nuclear Functions:
    • Control of all cellular activities, including metabolism, growth, reproduction, and protein synthesis.
    • Synthesis of RNA.
    • Formation of the subunits of ribosomes.
    • Transmission of genetic instructions to the cytoplasm via messenger RNA (mRNA) for protein synthesis.
    • Control of cell division through genes.
    • Storage of hereditary information (DNA) and the transformation of this information from one generation to the next.

Biological Flow of Information and the Central Dogma

• The Central Dogma (Francis Crick): Describes the one-way flow of information in a normal cell: DNA $\rightarrow$ RNA $\rightarrow$ Protein.
• Two-Step Gene Expression:
  1. Transcription: DNA is copied into RNA (specifically mRNA) within the nucleus by RNA polymerases and transcription factors.
  2. Translation: mRNA is translated into polypeptides (proteins) at the ribosomes in the cytoplasm using transfer RNA (tRNA).
• Post-Translational Modification: After translation, polypeptides undergo modifications to become functional proteins.
• Information Types:
  • Sequential Information: DNA and RNA.
  • Conformational Information: Proteins and resulting Traits.
• Exceptions to the Rule:
  • Reverse Transcription: Found in retroviruses such as HIV and many tumor viruses. The rule is reversed: RNA $\rightarrow$ DNA using the enzyme viral Reverse Transcriptase.
  • Other RNA Viruses: These viruses exclude DNA entirely, moving directly from RNA to protein.

The Cell Cycle and Interphase

• Overview: The cell cycle is a series of events involving growth and division. It consists of Interphase and the Mitotic Phase.
• Interphase: The cell grows, replicates chromosomes, and prepares for division in three specific stages:
  • Gap-1 Phase ($G_1$): The longest phase of the cell cycle (lasting $8$ to $10$ hours). During this time, there are no major microscopic changes, but the cell grows intensively and accumulates the building blocks of DNA, including nucleotides, sugar, and phosphate groups. It also accumulates DNA-associated proteins and energy resources to replenish what was lost in previous cytokinesis.
  • Synthesis Phase ($S$): Lasts $6$ to $8$ hours. This is the longest phase of interphase. Activities include the formation of sister chromatids (identical pairs of DNA), attachment of these chromatids at the centromeric region, duplication of the centrosome, and the formation of the mitotic spindle apparatus.
  • Gap-2 Phase ($G_2$): Lasts $4$ to $6$ hours. The cell prepares for the mitotic phase by replenishing energy reserves. Activities include high levels of protein synthesis, manipulation of chromosomes, duplication of various organelles, and the dismantling of the cytoskeleton to provide resources for mitosis.
• Resting State ($G_0$): Some cells exit the cycle after the M phase and enter $G_0$. In this state, the cell is not preparing to divide but is performing its standard biological functions. This can be permanent or temporary depending on external signals.

Regulation of the Cell Cycle

• Checkpoints: Control mechanisms that ensure the proper progression and completion of phases. Each serves as a potential termination point.
• The Three Major Checkpoints:
  1. $G_1$ Checkpoint (Start/Restriction/Major Checkpoint): Ensures the cell is ready for DNA synthesis.
  2. $G_2/M$ Checkpoint: Ensures everything is ready to enter the Mitosis (M) phase.
  3. Metaphase-to-Anaphase Transition (Spindle Checkpoint): Confirms the cell is ready to complete division.

Cell Division: Mitosis and Cytokinesis

• Mitosis: The process of dividing DNA into two identical sets, occurring after interphase. It consists of four main phases:
  • Prophase:
    • Early Prophase: Chromatin coils to form chromosomes, the nuclear membrane disappears, and centrioles migrate to opposite poles.
    • Middle Prophase: Spindle fibers (microtubules) develop. Polar fibers extend from centriole to centriole; kinetochore fibers extend from centromeres to centrioles.
    • Late Prophase (Prometaphase): Protein fibers called asters radiate from centrioles in animal cells.
  • Metaphase: Kinetochore fibers move chromosomes to align at the equator (metaphase plate) of the cell.
  • Anaphase: The centromere of each chromatid pair divides. Chromatids separate and are pushed to opposite poles in one quick motion by spindle fibers.
  • Telophase: Spindle fibers disappear, chromatids unwind back into chromatin, and a nuclear membrane forms around each mass of chromatin.
• Cytokinesis: The division of the parent cell's cytoplasm. The cell pinches together at the center (cleavage furrow formed by microfilaments). While DNA sets are identical, cytoplasm and organelles are shared only roughly equally.

The Human Genome and Genetics

• Genome Definition: All DNA contained in an organism or cell, including nuclear chromosomes and mitochondrial DNA. In plants, this also includes chloroplast DNA.
• Comparative Omics:
  • Genomics: Study of the Genome (all DNA in a cell).
  • Transcriptomics: Study of the Transcriptome (all RNA transcripts: mRNA, tRNA, rRNA, non-coding RNA).
  • Proteomics: Study of the Proteome (all proteins expressed at any given time).
• Human Genome Composition:
  • DNA Scale: Each cell contains $2$ meters of DNA made of $3$ billion chemical base pairs ($A, T, C, G$).
  • Chromosomes: Threadlike packages of genes. Humans have $23$ pairs ($46$ total). This includes $22$ pairs of autosomes ($44$ individual) and one pair of sex chromosomes ($XX$ for female, $XY$ for male).
  • Genes: Approximately $30,000$ genes code for proteins. A gene is the functional unit of heredity and a specific sequence of nucleotides in DNA or RNA.
• Study Case: CDH13 Gene Polymorphism: Research indicates that polymorphism in the CDH13 gene (encoding T-cadherin, the adiponectin receptor) is a genetic risk factor for Metabolic Syndrome. Specifically, rs3865188 in the promoter region of CDH13 is associated with metabolic traits in Asian and Caucasian populations and has been studied in Black African populations (specifically Gambian populations) as well.

The Human Genome Project (HGP)

• Background: An international research project that ran from $1990$ to $2003$.
• Primary Goals:
  • Map and sequence all genes ($30,000$) and base pairs ($3$ billion).
  • Store information in databases and improve data analysis tools.
  • Transfer technology to the private sector and address Ethical, Legal, and Social Issues (ELSI).
• General Characteristics Discovered:
  • The human genome is $99.9\%$ the same in all people.
  • Only about $2\%$ of the genome contains protein-coding genes.
  • At least $50\%$ of the genome consists of repeated sequences, formerly called "junk DNA."
  • Repeats help reshape the genome by rearranging, creating new genes, or modifying existing ones.
• Applications of Genomics:
  • Medicine: Developing rapid diagnostics, customized treatments, gene therapy, and identifying drug candidates.
  • Energy and Environment: Using microbes to clean up toxic waste, capture carbon to reduce climate change, and generate clean energy like hydrogen.
  • Bioanthropology: Understanding human lineage and exploring migration patterns.
  • Agriculture: Creating crops/livestock resistant to pests and pests, improving nutrition, and incorporating vaccines into food.
  • Forensics: Identifying kinships, catastrophe victims, or contaminants in environmental samples (air, soil, food).