Essential Concepts in Cellular Biology and Genetics

Posted on Sep 11, 2025 in Biology

Characteristics of Life

  • Metabolism: Organisms acquire and use energy to stockpile, break down, build, and eliminate materials.
  • Development: A series of changes in form, function, and behavior.
  • Homeostasis: Maintenance of a constant internal environment despite external changes.
  • DNA/RNA: Information storage and genetic inheritance. (RNA acts as a messenger; it contains ribose, a pentose sugar).
  • Evolution: A major unifying principle of biology.
  • Natural Selection: A key mechanism of evolution.

Organization of Organisms

Organisms are classified into Kingdoms: Monera, Protista, Fungi, Plants, and Animals.

Examples of Organisms and Their Characteristics

  • Bacteria: Prokaryotic cells.
  • Cyanobacteria: Obtain energy through photosynthesis, belong to the Monera domain, often called blue-green algae, release oxygen, and were crucial for the development of life on Earth.
  • Ciliates: Protozoans with hair-like organelles called cilia, common in water, belong to the Protista domain.
  • T4 Virus: Viruses are parasitic, infecting host cells. This virus causes E. coli infections.
  • Ebola Virus: A single-stranded RNA virus.
  • Sea Urchin: Known for free reproduction, easy to obtain gametes, and transparent eggs, making them ideal for developmental studies.
  • Yeast: Fungi that can reproduce by budding or by breaking in half.
  • Aspergillus: A fungus important for gene regulation studies, commonly present in the air.
  • Drosophila Melanogaster (Fruit Fly): Excellent for genetic studies due to similarities to humans, a short life cycle, and ease of maintenance.
  • C. Elegans: A nematode known for self-consistency, highly regulated development, transparency, and the ability to be frozen and revived.
  • Jellyfish: Exhibit interesting healing and self-defense mechanisms.
  • Octopus: Highly intelligent with a complex nervous system.
  • Mollusks (e.g., Hermissenda): Useful for neuroscience research, with species that are easy to discriminate.

Key Differences: Plant vs. Animal Cells

Plant cells differ from animal cells primarily by the presence of:

  • Chloroplasts: Sites of photosynthesis.
  • Cell Wall: Provides structural support and protection.
  • Large Central Vacuole: Stores water, nutrients, and waste products.

The Cytoskeleton: Cell Shape and Movement

The cytoskeleton is a dynamic network of protein filaments that gives cells their shape, provides mechanical support, and enables cell movement and division. It is made up of:

  • Microtubules
  • Actin Filaments
  • Intermediate Filaments

Cellular Building Blocks: Macromolecules of Life

The fundamental building blocks of cells and their corresponding macromolecules are:

  • Sugars → Polysaccharides: Units of metabolism and energy storage. Monosaccharides condense to form polysaccharides.
  • Fatty Acids → Fats, Lipids: Primarily for storing energy and forming cell membranes.
  • Amino Acids → Proteins: Create structure and catalyze reactions (enzymes).
  • Nucleotides → Nucleic Acids: Source of energy and genetic information.

Key Cellular Components

  • Phospholipid: A class of lipid that is a major component of cell membranes, characterized by a hydrophilic head and two hydrophobic fatty acid tails.
  • ATP (Adenosine Triphosphate): The primary energy carrier in our cells, a type of nucleotide composed of triphosphate, ribose, and adenine.

DNA Structure and Replication Fundamentals

DNA is composed of four nucleotides: Guanine (G), Cytosine (C), Adenine (A), and Thymine (T). Subtle differences exist in their chemical structure and reactions.

Building a DNA Strand

  1. Phosphate + Sugar = Sugar-Phosphate backbone
  2. Sugar-Phosphate + Base = Nucleotide
  3. Many Nucleotides = DNA Strand
  4. Two Strands Join = Double-Stranded DNA Helix

Double-stranded DNA is much more stable. C-G pairs form three hydrogen bonds, making them more stable than A-T pairs, which form two. A single-stranded DNA molecule, often found in viruses, indicates an uneven number of strands.

DNA Replication and Genetic Code

The genetic code uses bases G, A, C, and U (in RNA, U replaces T). One gene typically codes for one protein, and proteins determine specific traits in an organism. During RNA synthesis, Thymine (T) in DNA is replaced by Uracil (U) in RNA.

Proteins: Structure, Folding, and Function

Proteins are essential macromolecules, with 20 different amino acids serving as their building blocks. The human genome contains approximately 20,000 protein-encoding genes.

Polypeptides and Proteins

Polypeptides are chains of amino acids. One or more polypeptides fold into specific three-dimensional structures to form functional proteins.

Protein Folding and Stability

Protein folding is driven by weak, non-covalent bonds, including:

  • Ionic Bonds: Electrostatic attraction between charged groups.
  • Hydrogen Bonds: Electrostatic attraction between two polar groups.
  • Van der Waals Forces: Distance-dependent interactions between atoms.

The relative strength of these bonds (from strongest to weakest) is generally: Ionic > Covalent > Hydrogen > Van der Waals.

Common Protein Secondary Structures

  • Alpha Helix: A stiff, rigid structure stabilized by hydrogen bonds, with a pitch of 0.54 nm and a complete turn every 3.6 amino acids.
  • Beta Sheet: A pleated structure with a pitch of 0.7 nm and a repetition every 2 nm.
  • Coiled Coil: Formed when two alpha helices coil together, creating a stronger and more stable structure, commonly found in nature.

How Protein Engines Work

  1. An enzyme binds to two substrate molecules and catalyzes a reaction.
  2. The binding of the substrate to the enzyme rearranges electrons, facilitating the reaction.
  3. Bending of the enzyme induces local strain, favoring the reaction.

An allosteric mechanism can make the cycle irreversible, allowing for unidirectional movement (e.g., in molecular motors). This process, known as chromomechanical transduction, converts chemical energy into mechanical work.

Biological Research Methods and Techniques

Microscopy: Visualizing the Microscopic World

Early microscopes were developed by pioneers like Leeuwenhoek (glass microscope, 200x lens), Abbe, Schott, and Zeiss (Abbe’s advancements improved Zeiss microscopes).

Resolution in Microscopy

Resolution, the ability to distinguish two separate objects, is approximately 0.2 µm for light microscopes. It is determined by the objective lens and condenser lens, and can be calculated by the formula:

Resolution = (0.61 * wavelength) / (n * sin(theta))

Where: n = refractive index of the medium; theta = half angular width of the cone of rays collected by the objective lens.

Types of Microscopes

  • Inverted Microscope: Light comes from above, making it suitable for micromanipulation.
  • Transmission Electron Microscope (TEM): Developed by Siemens in 1964, these are digitally/electronically controlled. Specimens are chemically fixed (stabilized by killing them) and sectioned into thin slices for viewing on a copper grid covered with carbon/plastic film. High voltage TEM allows for thicker specimens, reduced specimen heating, and resolution below 200 nm. Ultra-high voltage TEM offers even greater capabilities. Light diffraction limits resolution in light microscopy.
  • Fluorescence Microscopy: The basic task is to illuminate the specimen with excitation light and then detect the much weaker emitted light to form an image.
  • Quantum Dots: Nanoscopic semiconductor crystals used as fluorescent probes.
  • Confocal Fluorescence Microscopy: Selectively collects light from a specific focal plane, rejecting out-of-focus light to create sharper images.

Cell Separation and Culture

  • Cell Sorter: Separates different cell types from a tissue sample. After cells are broken up, they pass through a laser beam, which sorts them based on specific properties.
  • Tissue Culture: A technique to grow individual cells or tissues in an artificial environment.

Chromatography: Physical Separation Methods

Chromatography is a physical method of separation.

  • Centrifuge Purification: Separates molecules based on density. Faster spinning leads to greater separation.
  • Ion Exchange Chromatography: Covalently links charged molecules (positive or negative) to a stationary phase for separation.
  • Gel-Filtration Chromatography (Size Exclusion): Separates molecules based on their size.

Polymerase Chain Reaction (PCR) Explained

PCR is a powerful application of DNA technology used to amplify a specific region of DNA, creating millions of copies. It allows for the detection of DNA at crime scenes, amplification of genes from an organism’s DNA, and genetic modification.

The PCR Process

  1. Denaturation (Melt): Heat double-stranded DNA to separate the two strands.
  2. Annealing: Primers bind to complementary sequences on the separated DNA strands.
  3. Extension: DNA polymerase synthesizes new DNA strands.

The number of DNA molecules doubles with each cycle (2^n, where n is the number of cycles).

DNA Sequencing and Electrophoresis

  • Enzymatic DNA Sequencing: Modifies DNA precursors. Deoxyribonucleotides allow for extension at the 3′ end, while dideoxyribonucleotides prevent strand elongation at the 3′ end by DNA polymerase, enabling sequence determination.
  • Electrophoresis: A technique where DNA fragments are separated by size, with the shortest lengths migrating furthest down the gel, useful for sequencing.

The Cytoskeleton and Molecular Motors

The cytoskeleton provides structure to cells, helping them maintain shape and internal organization.

Microtubules

Microtubules are hollow cylinders made of tubulin (alpha and beta subunits stacked together). They have an outer diameter (OD) of 24 nm and an inner diameter (ID) of 12 nm. The central space is called the lumen. Each microtubule typically consists of 13 protofilaments. Microtubules exhibit flexible rigidity, being stronger as a complete microtubule than as individual protofilaments.

Actin Filaments

Actin filaments are linear polymers of globular actin subunits, occurring as microfilaments in the cytoskeleton and as thin filaments in the contractile apparatus of muscle and non-muscle cells. They are smaller and thinner than microtubules, with a diameter of 5-6 nm.

Nucleation and Elongation of Actin

G-actin (globular actin) particles come together to form a nucleus (nucleation). Subunits can then assemble onto either end (F-actin, elongation). The filament reaches a steady state where the rate of addition of G-actin particles equals the rate of dissociation from the minus (-) end. This steady state is dependent on the concentration of monomers.

Actin Polymerization and Treadmilling

Once steady state is reached, there is no net growth, but subunits continue to add and dissociate. Treadmilling is a phenomenon observed in many cellular cytoskeletal filaments where one end of a filament grows in length while the other end shrinks, resulting in a section of the filament seemingly moving across the cytosol. GTP hydrolysis (GTP → GDP + Pi) is often involved in regulating microtubule dynamics, and various drugs can disrupt these processes.

Molecular Motors: Kinesin and Myosin

Kinesin and Fast Axonal Transport

Kinesin is a molecular motor responsible for fast axonal transport, moving vesicles towards the plus (+) end of microtubules. Its molecular organization includes a heavy chain, a coiled-coil region, and a light chain. Kinesin “walks” along microtubules. Studies (in vivo = inside the organism, in vitro = outside the organism) show that regardless of the number of kinesin molecules attached to a microtubule, it moves at the same speed. Higher ATP concentrations lead to faster microtubule movement.

Laser Trapping

This technique uses a focused laser beam to generate a force, allowing researchers to detect the location of a particle and determine the force generated and the distance a molecular motor like kinesin moves.

Myosin

Myosin is to actin what kinesin is to microtubules; it is a molecular motor that interacts with actin filaments.

Biological Motors and Stepping (Howard et al., Nature)

Research by Howard et al. demonstrated that biological motors move with regular steps. Kinesin, for example, moves with 8-nm steps, corresponding to the distance between tubulin dimers on a microtubule. The procedure involves depositing silica beads carrying single molecules of kinesin onto microtubules. If the microtubule is bound to glass, kinesin moves. A single kinesin molecule can move a microtubule, even in highly diluted solutions.

Muscle Contraction

Muscles contract through the sliding filament model within structures called sarcomeres.

Sarcomere Structure

Sarcomeres are composed of thin filaments (actin) and thick filaments (myosin). Myosin moves along actin. I bands are less dense and contain only actin. A bands contain both actin and myosin.

Sliding Filament Model

Muscle contraction involves the sliding of actin and myosin filaments past each other, shortening the sarcomere from its relaxed state to a contracted state (e.g., 2.2 µm). This process is initiated at the neuromuscular junction, where neurons transmit signals to muscles.

Neuromuscular Junction and Excitation-Contraction Coupling

Cells maintain an electric potential. A nerve impulse triggers the release of acetylcholine, leading to an influx of Na+ ions. This opens calcium channels, releasing calcium ions from the sarcoplasmic reticulum (which stores calcium) into the muscle cell. This calcium release causes muscle contraction.

  • Myofibril: A collection of mini-fibers within a muscle cell.
  • Electromechanical Coupling: The process linking electrical excitation to mechanical contraction, typically occurring within 20-30 ms, representing the body’s reaction time.
  • Twitches/Tetanus: A single twitch results from one release of calcium. Sustained contraction, like holding an object, is known as tetanus.

DNA Packaging, Replication, and Cell Division

DNA Structure and Properties

DNA is packed into chromosomes within cells. Genome sizes vary widely, from 10^5 to 10^12 base pairs. Only about 1% of genes in the human genome code for DNA. DNA is easily subject to radiation damage.

Persistence Length of Polymers

The persistence length quantifies the stiffness of a polymer, representing the length at which angles between segments are no longer correlated. DNA has a relatively short persistence length, indicating flexibility, while microtubules have a longer persistence length, making them stiffer. A persistence length 100 times its diameter indicates a very stiff polymer.

DNA Molecule Characteristics

  • Ends: The 3′ end has a hydroxyl group, and the 5′ end has a phosphate group.
  • Pitch: The DNA helix has a pitch of 0.34 nm per base pair, or 3.4 Å.

DNA encodes proteins, which confer characteristic properties to cells. DNA also serves as its own template for duplication.

DNA Replication

During replication, DNA unzips into two strands. RNA polymerase synthesizes an RNA primer, and DNA polymerase then adds nucleotides. The leading strand is synthesized continuously in the 5′ to 3′ direction, while the lagging strand is synthesized discontinuously, forming Okazaki fragments (in the 3′ to 5′ direction overall).

Mitosis and Chromosomes

Humans have 23 pairs of chromosomes (46 total), including X and Y sex chromosomes. Mitosis is the process of cell division that separates chromosomes, ensuring genetic continuity.

Key Concepts in Cell Division

  • Telomeres: Protective caps at the ends of chromosomes that can influence life expectancy.
  • Replication Origins: The human genome has approximately 46 replication origins to ensure efficient copying.
  • Anaphase: A phase of mitosis where sister chromatids separate and shorten.
  • Interphase: The period between cell divisions, after separation and before the next division.
  • Chromatin Packing: DNA wraps around histone proteins to form chromatin, allowing for compact packaging within the nucleus.