Inside the Cell

Inside the Cell

Fundamental Units of Life

• Cells are recognized as the fundamental unit of life.

• Viruses are complex biological entities that exhibit some characteristics of life but do not meet the full criteria to be classified as living organisms.

Cellular Components

All cells contain:

1. Macromolecules

   • Proteins: Perform most of the cell’s functions.

   • Nucleic Acids: Store, transmit, and process genetic information.

   • Carbohydrates:

     • Provide chemical energy.

     • Serve as a carbon source, support, and identity markers.

   • Lipids:

     • Provide energy and are building blocks for cell membranes.

     • Function as signaling molecules.

2. Plasma Membrane: Serves as a selectively permeable barrier that regulates the movement of substances in and out of the cell.

3. Cytoplasm: The gel-like fluid inside the cell where the components are suspended.

4. Ribosomes: Organelles that are crucial for protein synthesis.

Cell Morphology

• Based on morphology, cells can be classified into two fundamental types:

  1. Eukaryotes: Characterized by the presence of a membrane-bounded nucleus.

  2. Prokaryotes: Lacking a membrane-bounded nucleus.

Phylogenetic Classification of Life

Based on phylogeny (or evolutionary history), life is categorized into three domains:

• Eubacteria: True bacteria; single-celled organisms.

• Archaea: Extremophiles; similar to bacteria but genetically distinct.

• Eukarya: Includes organisms with complex cells, such as animals (Animalia), fungi, plants (Plantae), and protists.

Comparison of Prokaryotes and Eukaryotes

Characteristics of Eukaryotes

• Eukaryotes can range in size from very small to large.

• They can be either multicellular or unicellular.

• Size comparison suggests that eukaryotic cells are generally larger than prokaryotic cells.

• Eukaryotic chromosomes are enclosed within a nucleus.

Compartmentalization of Eukaryotic Cells

• The relatively large size of eukaryotic cells poses a challenge for molecular diffusion. This issue is mitigated by:

  • Compartmentalization: The cell volume is divided into smaller membrane-bound organelles, offering advantages such as:

  1. Separation of incompatible chemical reactions.

  2. Increased efficiency of chemical reactions.

General Features of Eukaryotic Cells

Animal Cells

• Components include:

  • Plasma Membrane

  • Extracellular Matrix

  • Centrioles (animal-specific)

  • Lysosome (animal-specific)

  • Nuclear Envelope

  • Chromosomes

  • Nucleolus

  • Mitochondrion

  • Peroxisome

  • Rough and Smooth Endoplasmic Reticulum

  • Golgi Apparatus

• On average, prokaryotic cells are about 10 times smaller than eukaryotes in diameter and about 1000 times smaller in volume.

Plant Cells

• Components unique to plant cells include:

  • Vacuole

  • Chloroplast

  • Cell Wall

The Nucleus

• Structure:

  • The nucleus is a large and highly organized organelle surrounded by a double-membrane nuclear envelope with pores.

  • Contains a distinct region called the nucleolus, where:

  • Ribosomal RNA is synthesized.

  • Ribosomal subunits are assembled.

• Functions:

  • Acts as the storage and processing center for genetic information.

  • Contains chromosomes:

  • Euchromatin: Lighter areas, containing actively transcribed genes.

  • Heterochromatin: Darker areas, containing inactive portions of the genome.

Ribosomes

• Ribosomes are complex molecular machines that manufacture proteins and are found in all prokaryotic and eukaryotic cells, except mature red blood cells.

• Structure consists of:

  • A small ribosomal subunit.

  • A large ribosomal subunit, both containing rRNA and ribosomal proteins.

Endoplasmic Reticulum (ER)

• The endoplasmic reticulum is an organelle that extends from the nuclear envelope and is classified into two types:

  1. Rough Endoplasmic Reticulum (RER): Studded with ribosomes; responsible for protein synthesis and folding. Proteins produced are targeted for:

  • Cytoplasm

  • Mitochondria

  • Peroxisomes

  • Chloroplasts

  • Nucleus

  1. Smooth Endoplasmic Reticulum (SER): Lacks ribosomes; functions include:

  • Lipid synthesis, including phospholipids and steroids.

  • Breakdown of lipids and harmful molecules, such as alcohol and drugs.

  • Storage reservoir for Ca$^{2+}$ ions.

Golgi Apparatus

• Structure:

  • Composed of a series of stacked flat membranous sacs called cisternae.

• Function:

  • Modifies proteins and lipids synthesized in the ER and prepares them for export outside the cell or for transport to other cellular locations.

  • Membranous vesicles transport materials to and from the Golgi apparatus.

  • Prominent in cells that synthesize and secrete large quantities of substances, such as B cells and neurons.

Lysosomes

• Function as recycling centers, more common in animal cells than in plants.

• Contain approximately 40 different enzymes including acid hydrolases, which work best at acidic pH (5.0) maintained by proton pumps in the membrane.

• Responsible for hydrolyzing macromolecules and exporting monomers to the cytosol.

• A deficiency in any of the enzymes can cause disease, such as Tay-Sachs disease, due to the build-up of certain lipids.

Endomembrane System

• Comprises lysosomes, Golgi apparatus, and ER.

• Functions include:

  1. Synthesizing proteins and lipids in the ER.

  2. Processing in the Golgi apparatus.

  3. Transporting materials to their designated cellular locations.

How Do Proteins Reach Their Destinations?

1. Molecular Tags: Each protein leaving the Golgi apparatus has a unique molecular tag (signal sequence) on its N- or C- terminus that directs it to its particular type of transport vesicle.

   • Example: An ER signal sequence for proteins destined for the ER.

2. Transport Vesicles: Each transport vesicle has its own tag for correct routing.

3. Exocytosis: Proteins can be secreted from a cell through this process.

Recycling Material in the Lysosome

• Large molecules are digested by lysosomes before their monomers can be utilized by cells.

• Materials enter the cell via endocytosis (an active transport mechanism) which can occur in three forms:

  1. Phagocytosis: Cellular eating.

  2. Pinocytosis: Cellular drinking.

  3. Receptor-mediated endocytosis: Specific uptake of molecules.

Additional Functions of Lysosomes

• Autophagy: A process where lysosomes digest large cellular structures and organelles in the cytoplasm, encapsulating portions of the cytoplasm into an autophagosome that fuses with a lysosome for digestion.

Vacuoles

• Structure: Large membrane-bound structures found in plants and fungi.

• Functions include:

  • Storage of water and ions to maintain normal cell volume (turgor pressure).

  • Protein storage within seeds.

  • Pigment storage in flower petals and fruits (e.g., anthocyanin).

  • Storage of noxious compounds to deter herbivores.

Peroxisomes

• Globular organelles found in all eukaryotic cells that originate from empty vesicles loaded with enzymes from the cytosol.

• Serve as centers for redox reactions and detoxifying substances like alcohol and formaldehyde, making materials more water-soluble for easier excretion.

Mitochondria

• Organelles supplying most of the cell’s ATP through cellular respiration.

• Structure:

  • Consists of two membranes; the inner one is folded into cristae, surrounding the mitochondrial matrix.

  • Has its own mitochondrial DNA (mtDNA) and ribosomes.

Chloroplasts

• Present in most plant and algal cells, where photosynthesis occurs.

• Structure:

  • Contains three membranes, featuring thylakoids (arranged in stacks called grana) and a surrounding stroma.

  • Also have their own DNA and ribosomes.

Endosymbiosis Theory

• Suggests that chloroplasts and mitochondria may have originated from free-living bacteria that were engulfed, resulting in a mutually beneficial relationship.

• Evidence supporting this theory includes:

  • The presence of DNA within mitochondria and chloroplasts that resembles prokaryotic DNA.

  • Their ability to synthesize small ribosomes.

  • Their capability of independent growth and division.

Cytoskeleton

• Structure: Composed of protein fibers providing shape and structural stability to the cell.

• Functions include:

  • Organizing organelles and cellular structures into a coherent system.

  • Facilitating cell movement.

  • Aiding in the transportation of materials within the cell.

Eukaryotic Cell Wall

• Found in fungi, algae, and plants; provides structural support.

• Composed of carbohydrate rods or fibers running through a rigid matrix of polysaccharides and proteins.

Summary Table of Eukaryotic Cell Components