Cellular Organization, Membrane Structure, and Genetic Expression

Cellular Hierarchy and Definition of the Cell

• Levels of Biological Organization:

  • Cell
  • Tissue
  • Organ
  • Organ System

• Definition of the Cell:

  • The cell is defined as the smallest structural unit capable of life.
  • Etymology: The word originates from the Latin word cellula, which translates to "small room".
  • Historical Discovery: The term "cell" was coined by Robert Hooke in his publication Micrographia in the year $1664$.

• Extracellular Fluid (ECF):

  • A cell is perpetually surrounded by a watery medium termed the extracellular fluid (ECF).
  • In the vast majority of tissues, this fluid is specifically designated as interstitial fluid.

• Plasma Membrane:

  • Also referred to as the cell membrane.
  • Serves the fundamental physical function of separating the internal cellular cytoplasm from the external extracellular fluid.

Classes of Human Cells

Human cells are categorized into two primary physiological classes:

• 1. Sex Cells (Gametes):

  • Also known as reproductive cells.
  • Responsible for reproductive processes and carrying genetic traits to offspring.
  • Male sex cells are sperm.
  • Female sex cells are eggs (ova).
  • Contain a total of $23$ individual chromosomes.

• 2. Somatic Cells:

  • Derived from the Greek word soma, meaning "body".
  • Encompasses all functional cells within the human body with the explicit exception of sex cells.
  • Contain a total of $46$ chromosomes, arranged into $23$ matching pairs.

Cancerous Cellular Pathologies

• Definition of Cancer:

  • Cancer is a disease state characterized by cells that divide uncontrollably when they should not, accompanied by the pathological ability to invade adjacent tissue structures and spread elsewhere in the body.

• Tumor Classifications:

  • Benign:
  • Non-cancerous in nature.
  • The localized tumor mass has no invasive effect on surrounding tissue.
  • Malignant:
  • Actively cancerous.
  • The tumor actively invades surrounding tissue.
  • Metastatic:
  • Advanced cancerous state.
  • The cancerous cells metastasize, spreading away from the primary site to establish secondary tumors elsewhere in the body.

The Plasma Membrane: Structure and Composition

The cell (plasma) membrane is composed of three essential structural biomolecules: Lipids, Proteins, and Carbohydrates.

Membrane Lipids

• Phospholipid Bilayer:
  • Formed by a continuous double layer of phospholipid molecules arranged in a full circle surrounding the cell.
  • Hydrophilic Heads: The "water-loving" heads direct themselves outward toward the watery extracellular fluid on the outside and the watery environment on the inside.
  • Hydrophobic Tails: The "water-fearing" fatty-acid tails direct themselves inward, forming an isolated core inside the membrane interior.
  • Functional Importance: Isolating the internal cytoplasm from the external environment is vital for maintaining cellular homeostasis.
• Cholesterol:
  • Interspersed within the phospholipid bilayer.
  • Functions to "stiffen" the cell membrane structure, rendering it less fluid and less permeable.
  • Essential and beneficial for membrane construction.

Membrane Proteins

Membrane proteins are divided into two distinct structural classes:

• 1. Integral Proteins (Transmembrane Proteins):

  • Reside within the structural matrix of the membrane, passing completely through from one side of the membrane to the other.

• 2. Peripheral Proteins:

  • Bound exclusively to either the inner or outer surface of the membrane without spanning its core.

• Functional Roles of Membrane Proteins:

  • Recognition: Acting as cellular identification markers.
  • Carriers: Transporting specific solutes across the plasma membrane.
  • Receptors: Binding to and responding to specific extracellular signaling molecules known as ligands (functioning analogously to wide receivers catching incoming molecules).

Membrane Carbohydrates and the Glycocalyx

• Types: Include proteoglycans, glycoproteins, and glycolipids.
• Localization: Extend outward beyond the external perimeter of the cell membrane.
• The Glycocalyx:
  • Together, these surface carbohydrates form a sticky outer coat designated as the glycocalyx ("sugar coat").
  • Primary Functions of the Glycocalyx:
  • Lubrication: Provides a lubricated surface boundary.
  • Anchoring: Helps anchor the cell to adjacent structures.

Organelles: Mitochondria and ATP Production

Mitochondrial Structure

• Mitochondria:
  • Plural: Mitochondria; Singular: Mitochondrion.
  • Organelle bounded by an outer membrane and an inner membrane featuring numerous functional folds (cristae).
  • Function: Produces energy storage molecules of adenosine triphosphate ($ATP$).

Pathways of ATP Production

• Metabolic Energy Analogy:

  • Glucose operates like a financial check; the cell must "cash in" glucose through metabolic breakdown to obtain direct cash in the form of usable $ATP$ molecules.

• Step 1: Glycolysis:

  • Etymology: Derived from glycos (meaning sugar) and lysis (meaning a loosening or splitting); translates literally to "sugar splitting".
  • Subcellular Location: Occurs within the cytosol of the cell.
  • Chemical Transformation: $1 \text{ glucose (6 carbons)} \rightarrow 2 \text{ pyruvate / pyruvic acid (2 } \times \text{ 3 carbons)}$.
  • Energy Yield: Generates a small quantity ("few") of $ATP$ molecules.

• Step 2: Aerobic Metabolism (Cellular Respiration):

  • Requirement: Requires molecular oxygen ($O_2$) to proceed.
  • Subcellular Location: Occurs inside the mitochondria after pyruvate is absorbed from the cytosol.
  • Process Steps:
  • Carbon dioxide ($CO_2$) is removed from pyruvate.
  • Molecular oxygen ($O_2$) is consumed directly during the process.
  • Water ($H_2O$) is produced as a chemical byproduct.
  • Energy Yield: Generates approximately $95\%$ of the total $ATP$ required to keep cells alive.

Organelles: The Nucleus and Genetic Storage

Nuclear Structure and Cellular Exceptions

• The Nucleus:
  • Represents the largest single organelle in the cell.
  • Functions as the control center of the cell by storing genetic instructions ($DNA$).
  • Metaphor: $DNA$ functions like a master cookbook or recipe book containing full instructions to manufacture every protein in the body.
• Cellular Quantities and Exceptions:
  • Baseline: Most cells possess exactly $1$ nucleus per cell.
  • Exception 1: Skeletal muscle cells contain multiple nuclei per cell.
  • Exception 2: Mature Red Blood Cells contain zero ($0$) nuclei in the human body.
• Structural Components:
  • Nuclear Envelope: A membrane structure that physically separates nuclear contents from the cytoplasm.
  • Nuclear Pores: Communication passages spanning the envelope to allow regulated transport.

Chromatin and Chromosomes

The storage state of nuclear $DNA$ depends directly on whether the cell is actively dividing:

• Chromatin:
  • Loosely coiled $DNA$ structure.
  • Present when cells are in a non-dividing state.
• Chromosomes:
  • Tightly coiled, organized $DNA$ structures.
  • Present when cells are actively dividing.
  • Quantity in somatic cells: $46$ total chromosomes, organized as $23$ pairs.
  • Quantity in sex cells (gametes): $23$ total chromosomes.

The Genetic Code and Triplet Code

• The Genetic Code:
  • Represents the chemical language of $DNA$ instructions.
  • Defined by the linear sequence of four nitrogenous bases within the $DNA$ molecule:
  • Adenine ($A$)
  • Thymine ($T$)
  • Cytosine ($C$)
  • Guanine ($G$)
• The Triplet Code:
  • A sequence of $3$ consecutive nitrogenous bases that specifies $1$ amino acid.
  • Redundancy Example: Both base triplets $TGC$ and $TGT$ code for the exact same amino acid, cysteine.
  • Representative sequences include base combinations such as ITGGAT and TAAGGTAACCTA.

Protein Synthesis and Central Dogma

• Subcellular Compartmental Constraints:

  • Master $DNA$ molecules are stuck inside the nucleus.
  • $RNA$ molecules have the chemical capacity to leave the nucleus.

• The Central Dogma Flow:

  • The directional pathway of genetic expression proceeds as follows:     $\text{DNA} \rightarrow \text{RNA} \rightarrow \text{Protein}$

• Two Main Stages of Protein Synthesis:

  • 1. Transcription:
  • The process of creating an $RNA$ molecule from a $DNA$ template inside the nucleus.
  • $\text{DNA} \rightarrow \text{RNA}$
  • 2. Translation:
  • The process where $RNA$ is translated into a functional protein sequence outside the nucleus.
  • $\text{RNA} \rightarrow \text{Protein}$