Core Biological Principles: DNA, Photosynthesis, Tissues, and Circulation

Posted on Aug 7, 2025 in Biology

DNA Fundamentals

HIND II was discovered by Smith, Wilcox, and Kelley. Its recognition sequence is 5′ GT (pyrimidine: T or C) / Purine (A or G) AC 3′.

Recombinant DNA Synthesis

1. Cut two different DNA molecules with the same restriction enzyme.
2. Mix DNA pieces together, allowing for sticky ends to form weak hydrogen bonds.
3. Seal the DNA fragments with ligase.

Plasmids are double-stranded DNA molecules where DNA fragments are inserted for cloning or expression.

Gel Electrophoresis Principles

Electrophoresis uses an electrical current to separate charged molecules based on their charge and size.

• Molecules move through a porous matrix, which also separates them based on size.
• DNA moves toward the positive electrode because DNA is negatively charged.
• The density of the matrix (e.g., agarose) determines the migration speed of DNA.
  • Smaller DNA fragments move through the gel faster than larger fragments. Larger fragments remain closer to the top of the gel.
  • The size of a DNA band can be determined by comparing it to a DNA ladder (known sizes of DNA fragments).
• A higher percentage of agarose results in slower migration of DNA fragments through the gel. (The gel contains the same concentrations of salts as the electrophoresis buffer.)
• Purpose of salts: Salts allow electrical current to flow through the gel, decreasing electrical resistance.
• DNA must be stained to be visible (e.g., using SYBR Safe DNA gel stain).

What is the purpose of the loading dye? It indicates how far the fragments have moved during electrophoresis.

• What happens if you turn off the power supply too early? The bands will not separate properly.
• How can you tell that the power supply is on? The buffer will start to bubble because oxygen is formed at the anode and hydrogen is formed at the cathode.
• What would you need to do if your DNA bands fall outside of your standard curve and you need to know their sizes? Use a different marker (DNA ladder) that has a different range of base pairs, fitting within the base pair length of your samples.

Photosynthesis: The Light Reaction

Equation: CO₂ + H₂O + (light energy) → (CH₂O)_n + O₂

Types of Photosynthetic Reactions

• Light Reaction:
  • Where? Thylakoid membrane.
  • Generates high-energy electrons with reducing potential.
  • Water splits into oxygen and hydrogen, forming reduced compounds (NADPH and ATP).
• Dark Reaction (Light-Independent Reactions / Calvin Cycle):
  • Where? Stroma.
  • Utilizes NADPH and ATP from the light reaction to synthesize glucose and other carbohydrates from CO₂ (also known as carbon fixation).
  • Carbon fixation continues to occur in the absence of light as long as the products of the light reaction (NADPH and ATP) are present.

Light Capture and Pigments

For the light reaction to proceed, plants must effectively capture light energy, which is accomplished by the presence of pigments.

These pigments are located within the thylakoid membranes of chloroplasts and are organized into photosystems.

Each photosystem contains a reaction center, where a protein-chlorophyll A complex converts light energy into chemical energy through a series of electron transfers during the light reactions.

Other pigments are arranged in antenna complexes that capture light energy and transfer this energy to the reaction center.

The absorption of light by plant pigments is the initial step in photosynthesis.

• Chlorophyll-A: The primary pigment in photosynthesis.
• Carotenes and Chlorophyll-B: These perform a secondary role by absorbing light at different wavelengths than chlorophyll-A and then transferring that energy to chlorophyll-A.

Leaf Color and Pigment Function

Why do leaves appear green? Leaves appear green due to the abundance of chlorophylls, which impart the green color and absorb most of the energy used in photosynthesis. Chlorophylls primarily absorb light in the blue and red wavelength ranges, thus reflecting green light.

Example: Green cellophane transmits green light and absorbs red and blue light.

Function of Accessory Pigments: Accessory pigments are typically yellow-red in color and absorb light at different wavelengths, transferring this additional energy to chlorophyll-A. These pigments broaden the range of light wavelengths that can drive photosynthesis, thereby increasing the efficiency of energy capture.

Chloroplasts prefer blue and red light, but chlorophyll alone cannot process all wavelengths. Accessory pigments enable chloroplasts to absorb more light energy, compensating for the gaps that chlorophyll cannot cover.

Why do leaves change color in the fall? The dramatic colors seen in tree leaves during fall are produced by accessory pigments. Normally, chlorophyll masks these accessory pigments. However, due to environmental changes, chlorophyll degrades, and the colors of the accessory pigments are no longer masked.

• Orange = Carotene
• Yellow = Xanthophyll
• Red and purple colors = Anthocyanin
• Brown colors = Tannin

DCIP Assay for Light Reaction Activity

DCIP (Dichlorophenolindophenol) is utilized as a dye in photosynthesis experiments.

DCIP receives an electron from NADPH and becomes reduced, diverting the electron from the dark reaction pathway.

When DCIP is reduced, a decreased absorbance is observed in the spectrophotometer. A decrease in absorbance indicates that DCIP was reduced, which in turn means that NADPH was produced, confirming that the light reaction is occurring.

Experimental Controls

• Negative Controls: Aluminum foil (no light), no chloroplasts, no DCIP.
• Positive Controls: Cellophane (experimental condition with light), active light reaction.

Histology: Tissue Structures

Epithelial Tissues

• Simple Cuboidal: Functions in secretion and absorption. Cells appear square-shaped.
• Simple Columnar: Functions in absorption and secretion of mucus.
• Simple Squamous: Allows for the passage of materials.
• Stratified Squamous: Protects underlying tissues.
• Pseudostratified Columnar: Functions in secretion, particularly mucus (e.g., in the trachea).

Cell Shapes in Epithelium

• Squamous: Flat cells.
• Simple Squamous: Found in blood vessels.
• Stratified Squamous: Found in the epidermis of skin, mouth, and esophagus (protective function).
  • Highly differentiated surface cells towards the top.
• Cuboidal: Square cells, typically with a central nucleus. Found in kidney tubules and around the lumen of tubules.
• Columnar: Tall cells. Found in the digestive tract (secretion and absorptive function).
• Pseudostratified: Found in the respiratory tract and male urethra (protective function).

Connective Tissues

Types of Connective Tissue: Connective Tissue Proper, Cartilage, Bone, Blood.

Cell Types in Connective Tissue

• Fibroblasts: Produce most of the extracellular components.
• Adipose Cells: Synthesize and store fat.
• Mast Cells: Participate in inflammatory responses.
• Macrophages: Phagocytose debris and foreign invaders.

Functions of Connective Tissue

• Structural support.
• Medium for metabolic exchange.
• Defense and protection of the body.
• Storage site for fat.

Main Types of Connective Tissue Proper

• Loose Connective Tissue (e.g., Lamina Propria):
  • Characterized by loosely packed extracellular fibers.
  • Fills body spaces below and surrounds blood vessels and glands.
  • Contains a large amount of ground substance.
• Dense Connective Tissue:
  • Characterized by densely packed extracellular fibers.
  • Separated into Dense Irregular and Dense Regular types.

• Dense Irregular Connective Tissue: Fibers are oriented in all directions.
• Dense Regular Connective Tissue: Collagen fibers are organized into parallel bundles.

Cartilage

Cartilage is a weight-bearing connective tissue.

• Perichondrium:
  • Immature fibrous tissue that surrounds mature cartilage.
  • Contains vasculature.
  • Serves as a proliferative source for new cells.

Chondroblasts undergo differentiation to become mature chondrocytes.

• Chondrocytes:
  • Secrete ground substance and fibers.
  • Present in lacunae (small cavities).
  • Constitute mature cartilage, which lacks blood vessels.
  • Nutrition reaches chondrocytes by diffusion.
  • Differentiated chondrocytes typically divide 1-2 times.

Types of Cartilage

• Hyaline Cartilage:
  • Forms the embryonic skeleton, which is eventually replaced by bone.
  • Forms important rings in the trachea and bronchi of the lungs.
  • Mature hyaline cartilage has a glassy appearance.
• Elastic Cartilage:
  • Contains an extensive network of elastic fibers throughout the matrix.

Bone

Similarities Between Cartilage and Bone

In both cartilage and bone:

• Cells reside in lacunae.
• Covered on the surface by progenitor tissue.
• Contain high amounts of collagen.

Differences in Bone

Bone is different from cartilage because:

• It is calcified, making it much harder.
• It contains canaliculi: nutrients cannot diffuse to osteocytes, which require a direct blood supply.

Bone primarily serves structural support and protective functions.

Key Bone Structures

• Canaliculi
• Haversian Canals
• Osteocyte Lacunae
• Concentric rings of lacunae with osteocytes

Blood

• Blood Cells: Red Blood Cells (RBCs), White Blood Cells (WBCs), and Platelets.
• Extracellular Matrix: Plasma.
• Fiber: Present in an inactive form (fibrinogen).

• RBCs: Primarily involved in gas exchange.
• WBCs: Defend the body against foreign substances.
• Platelets: Originate from megakaryocytes in bone marrow.
  • Blood Clots: Formed by the aggregation of platelets to create fibrin clots.

Muscle Tissue

Muscle Functions

• Generate force and contraction (used for locomotion).
• Connective tissue components provide:
  • Blood supply (due to high metabolic rate).
  • An anchor through which force is generated.

Types of Muscle Tissue

There are three types of muscle tissue, each with distinct contractile properties:

• Skeletal Muscle
• Cardiac Muscle
• Smooth Muscle

All muscle types contain Desmin as an intermediate filament protein.

Skeletal Muscle

• Highly organized.
• Responsible for voluntary movement.
• Contains contractile units called sarcomeres.
• The arrangement of sarcomeres along the length gives a striated appearance (A and I bands).

Smooth Muscle

• Surrounds blood vessels.
• Lacks striations.
• Found in the walls of the digestive tract, arteries, and urinary bladder.
• Cells are spindle-shaped.
• Exhibits involuntary activity.

Cardiac Muscle

• Specialized for the contraction of the heart.
• Cells are branched.
• Presence of intercalated discs.

Polyspermy Prevention Mechanisms

Temporary Fast Block to Polyspermy

• In the egg, Na⁺ channels open in the plasma membrane (located below the jelly coat/vitelline layer).
• Normally, Na⁺ concentration is higher outside than inside, so sodium enters the cell, causing the plasma membrane to depolarize.
• Depolarization triggers voltage-sensitive calcium channels to open in the endoplasmic reticulum (ER).

Permanent Slow Block to Polyspermy

• Calcium channel activation also stimulates a Na⁺/H⁺ exchanger, which pumps H⁺ out of the cell, increasing intracellular pH.
• These pH changes cause the polymerization of actin subunits into microfilament cables that thrust acrosomal processes toward the egg plasma membrane.
• An increase in intracellular calcium causes water to enter the cell, increasing hydrostatic pressure.
• Calcium also leads to the fusion of cortical vesicles with the egg plasma membrane, releasing their contents into the space surrounding the egg. This process inactivates the Bindin protein.
• Additional sperm are released from the vitelline membrane, preventing further binding.

Consequences of Polyspermy

The fate of polyspermic eggs includes:

• Formation of extra mitotic spindles.
• Incorrect chromosome assortment.
• Arrested development.

Cortical Granule Contents

Cortical granules contain various substances:

• Proteases: Cleave Bindin receptors and the binding between the vitelline membrane and the egg plasma membrane.
• Mucopolysaccharides: Increase osmotic pressure, leading to water influx and the lifting of the vitelline membrane, which forms the fertilization membrane.
• Peroxidase: Hardens the fertilization membrane, making it impermeable to sperm.
• Hyalin: Forms a protective coat around the embryo.

Note: These granules are released during the slow block to polyspermy.

The Vascular System

The vascular system supports blood flow, which is maintained by heart contractions.

• Blood Flow Pathway: Heart → Arteries → Capillaries → Veins → Heart.

The Lymphatic System

The lymphatic system functions in the passive drainage of interstitial fluid (lymph) back to the heart.

Heart Anatomy

• Endocardium: The innermost layer.
• Myocardium: The middle layer, which is much thicker and contains cardiac muscle.
• Epicardium: The outer layer, providing protection for the heart.
  • Pericardium: A double-layered connective tissue sac encasing the heart, which helps to minimize friction between the constantly beating heart and surrounding structures.

Blood Circulation Pathway

• The “Lub” sound is produced by the forceful closing of the AV (Atrioventricular) valves.
• The “Dub” sound is produced by the semilunar valves closing.

The semilunar valves prevent backflow into the ventricles. The transmission of the contraction signal is carried out by specialized cardiac cells that have poor contractile potential.

• Key components of the cardiac conduction system include the SA node, AV node, and Purkinje fibers within the atrioventricular bundle of His.

The SA node is the heart’s natural pacemaker.

Conduction Pathway: SA node → AV node → AV bundle → Purkinje fibers → Ventricles.

Blood Pressure Dynamics

Cardiac Output (CO) is a key determinant of blood pressure.

• CO = HR × SV
  • HR: Heart Rate (rate of contraction).
  • SV: Stroke Volume (volume of blood pumped per contraction).
• Blood Pressure (BP): The force of blood against the vessel walls. An increase in resistance or blood volume will increase BP.
• Cardiac output also represents the amount of blood pumped by a heart ventricle in one minute.

• Sphygmomanometer: A device used to measure blood pressure.
  • The cuff pressure exceeds that in the artery, stopping blood flow to the lower arm. As the cuff is loosened, blood begins to pulsate through the artery and is detected using a stethoscope.
• Korotkoff Sounds: The sounds of turbulence within the artery detected during blood pressure measurement.
• Systolic Pressure: The pressure at which the first Korotkoff sound is detected (peak pressure during contraction).
• Diastolic Pressure: The pressure at which the Korotkoff sounds disappear (minimum pressure during relaxation).

Autonomic Regulation of Blood Pressure

• Parasympathetic Nervous System: Dilates arteries and arterioles, lowering resistance and decreasing blood pressure.
• Sympathetic Nervous System: Constricts arteries and arterioles, raising resistance and increasing blood pressure.

Comparative Circulatory Systems

Fish Circulation

Fish hearts typically have four chambers in a linear orientation:

• Sinus Venosus: Receiving chamber.
• Atrium: Receiving chamber.
• Ventricle: Pumping chamber.
• Conus Arteriosus: Pumping chamber.

• After leaving the heart, blood flows through the gills for oxygenation, then is pumped through arteries to peripheral tissues before returning via veins to the sinus venosus.
• Limitation: A significant drop in blood pressure occurs after the gills and before the blood returns to the heart, which limits the efficiency of gas exchange in peripheral tissues.

Amphibian Circulation

• Limitation: Amphibians have only one ventricle, leading to the mixing of deoxygenated and oxygenated blood.
• Oxygenated blood from the lungs returns to the heart, from where it is pumped to the rest of the body.

Pulmonary Circulation: Blood flow between the heart and lungs.

Systemic Circulation: Blood flow between the heart and the rest of the body.

Mammalian Two-Cycle Pump

• Both atria fill simultaneously and contract to empty blood into the ventricles. The same amount of blood is pumped through both circulatory pathways (pulmonary and systemic) to maintain equal blood pressure and prevent conditions like edema.
• The left ventricle is significantly thicker than the right. This is necessary to overcome peripheral resistance and generate sufficient pressure to force open the aortic semilunar valve, dispersing oxygenated blood throughout the entire body, including areas further from the heart.

Blood Vessel Structure

Blood vessels are composed of three main layers:

• Tunica Intima: The innermost layer.
  • Composed of endothelium and underlying subendothelial connective tissue.
  • Contains the internal elastic lamina, a thick, convoluted layer of elastin important for vessel elasticity.
• Tunica Media: The middle layer.
  • Consists of circular layers of smooth muscle fibers, whose function is to control the diameter of the vessel.
  • Arteries typically have a thicker tunica media with more muscle and elastic fibers.
  • Large arteries also possess external elastic membranes.
• Tunica Adventitia (or Tunica Externa): The outermost layer.
  • A connective tissue layer containing collagen and elastic fibers.
  • Anchors the vessel to surrounding tissue.
  • It is typically the thickest layer in veins.
  • In larger vessels, it is thick enough to require its own blood supply, containing vasa vasorum (smaller vessels that supply oxygen and other nutrients to the cells of the vessel wall).

Types of Blood Vessels

• Capillaries:
  • Smallest vessels.
  • Connect arterioles to venules.
  • Primary site for the exchange of oxygen, carbon dioxide, nutrients, and waste products.
  • Consist of a single layer of simple squamous epithelium.
  • Contain fenestrations (small openings between cells) that facilitate exchange.
  • Exhibit the lowest velocity of blood flow, optimizing exchange.
• Arteries:
  • Have a thicker tunica media than veins.
  • Possess thicker walls and a smaller lumen compared to veins.
  • Larger arteries have many more elastic fibers in their tunica media and tunica adventitia.
• Veins:
  • Have thinner walls than arteries.
  • Possess a thicker tunica adventitia.
  • Contain valves to maintain unidirectional blood flow.
  • Have a larger lumen.
  • Often appear collapsed in cross-section due to thinner walls and lower pressure.