Biology 1: Cell Structure and Organelles University Study Notes

Course Overview and Learning Objectives

• Course Identification: BIOLOGY 1 (RNMR_2026).
• Instructor: Rusydatul Nabila Mahmad Rusli, PhD Medical Science (UPM), Master Medical Science (UniKL RCMP), Bach. in Clinical Lab Science (Hons) (UniKL Mestech).
• Course Learning Outcome (CLO 1): Describe biological principles related to cell structure and function, genetics, growth development, and ecology.
• Topical Outcomes: By the end of the lesson, students should be able to:
  • Elaborate on the cell theories with examples.
  • Identify different components of prokaryotic and eukaryotic cells.
  • Compare prokaryotic and eukaryotic cells.
  • Describe various structures and functions of organelles.

The Cell Theory

• Fundamental Tenets:
  • All living things consist of cells.
  • All cells come from other cells.
  • Cells are the smallest living things and represent the basic units of organization of all organisms.
  • The ability of cells to divide and form new cells is the basis for all reproduction and for the growth and repair of multicellular organisms.
  • All cells are enclosed by a membrane.
  • Every cell, at some stage in its life, contains DNA.
• Taxonomic Classification: The two major kinds of cells are prokaryotic cells and eukaryotic cells.

Historical Contributors to Cell Discovery

• Hooke: The first to identify cells and was responsible for naming them after observing cork.
• Leeuwenhoek: Made better lenses and observed cells in greater detail; first to observe "animalcules."
• Schleiden: The first to note that plants were made up of cells.
• Schwann: Concluded that all living things were made up of cells; responsible for cell theory.
• Virchow: Proposed that all cells come from other cells.
• Additional Note: Schleiden and Schwann are collectively credited with the responsibility for the formal cell theory.

Specific Components of Cell Types

• Prokaryotic cell components:
  • Capsule.
  • Pilus.
  • Cell wall.
  • Plasma membrane.
  • Nucleoid (DNA).
  • Cytoplasm.
  • Ribosomes.
  • Flagellum.
• Eukaryotic cell components:
  • Nucleus and Nucleolus.
  • Cytosol and Cytoplasm.
  • Ribosomes.
  • Cytoskeleton.
  • Mitochondrion.
  • Peroxisome.
  • Golgi body.
  • Plasma membrane.
  • Lysosome.
  • Endoplasmic reticulum (Smooth and Rough).

Comparison of Prokaryotic and Eukaryotic Cells

Cell Ultrastructure: Architecture and Overview

• Cell Architecture: A cell is a tiny, three-dimensional sac consisting of three main parts:
  • Cell membrane: The outer layer (and cell wall in plant cells).
  • Cytoplasm: Includes the cytosol and the membranous organelles suspended within it.
  • Nucleus: The location where information for growth, development, and reproduction is situated.
• Classification of Organelles:
  • Membranous Organelles: Nucleus, endoplasmic reticulum, mitochondria, chloroplasts, and Golgi apparatus.
  • Non-membranous Organelles: Ribosomes and centrioles.
• Note: All cell organelles, apart from the nucleus, are considered part of the cytoplasm.

Cell Wall Structure and Gram Staining

• Prokaryotic Cell Walls: Most bacteria are encased by a strong wall composed of peptidoglycan (a carbohydrate).
• Eukaryotic Cell Walls: Plants, fungi, and protists have cell walls made from cellulose or chitin.
• Gram Stain Classification (Bacteria):
  • Gram-positive: Characterized by a thick, single-layered cell wall. Produces a purple color after staining. Typical example: Micrococcus luteus.
  • Gram-negative: Characterized by a multilayered cell wall with an outer membrane. Exhibits a red color after staining. Typical example: Escherichia coli.
• Gram-negative components: Porin, phospholipid, polysaccharide, lipid protein, and an outer membrane.
• Gram-positive components: Lipoteichoic acid and membrane protein.
• Functions of the Cell Wall:
  • Protects the cell.
  • Maintains cell shape.
  • Prevents excessive uptake of water.

Plasma Membrane and Fluid Mosaic Model

• Major Components: Phospholipids and proteins.
• Fluid Mosaic Model: Consists of two layers (a bilayer) of phospholipids with globular proteins embedded within.
• Phospholipid Dynamics: The bilayer can move laterally within the membrane.
  • Hydrophilic heads: In contact with water.
  • Hydrophobic tails: In contact with each other and kept remote from water.
• Membrane Proteins: Constitute $50\%$ of the mass of the membrane.
  • Integral Proteins: Penetrate far enough into the membrane for their hydrophobic regions to be surrounded by hydrocarbon lipid tails.
  • Peripheral Proteins: Not embedded in the lipid bilayer; they are appendages attached to the surface of the membrane.
• Cholesterol: Functions to help stabilize membrane stability.
• Additional Surface Components: Glycoproteins, glycolipids, and carbohydrates.

The Nucleus

• Conceptual Role: The "brain" of eukaryotic cells; it package genes and their controlling factors.
• Physical Structure:
  • Separated from the cytoplasm by a nuclear envelope (double-layer membrane).
  • Contains nucleoplasm and chromatin (DNA + protein).
  • Chromatin can condense to form chromosomes.
  • Contains a dark nucleolus composed of $rRNA$.
• Primary Functions:
  • Store genes on chromosomes.
  • Organize genes into chromosomes to facilitate cell division.
  • Transport regulatory factors and gene products via nuclear pores.
  • Produce messenger Ribonucleic acid ($mRNA$) that codes for protein.
  • Produce ribosomes in the nucleolus.
  • Organize the uncoiling of DNA to replicate key genes.

Chloroplasts and Mitochondria

• Chloroplast Structure and Function:
  • Convert sunlight into organic compounds using chlorophyll and other pigments.
  • Inner membrane: Consists of flattened sacs called thylakoids.
  • Grana: Stacks of thylakoids.
  • Stroma: Fluid-filled space enclosed by the inner membrane.
  • Thylakoid space: The space within the thylakoid sacs.
• Mitochondria Structure and Function:
  • Main Function: Site for cellular respiration and $ATP$ production.
  • Membrane: Double-layered; the outer layer is smooth while the inner layer is folded into sheets called cristae.
  • Intermembrane space: Formed between the inner and outer layers.
  • Matrix: Interior cavity filled with gel-like substance.
  • Enzymatic Content: Both the intermembrane space and matrix contain enzymes required for cellular respiration.

The Endoplasmic Reticulum (ER) and Golgi Apparatus

• Endoplasmic Reticulum (ER):
  • Network of membranous tubules and flattened sacs called cisternae.
  • Frequently continuous with the nuclear envelope and sometimes the cell membrane.
  • Functions: Creates passageways for material transport, contains various enzymes, and provides a structural skeleton for cell shape.
  • Rough ER: Studded with ribosomes; produces proteins for export; modifies proteins; found in cells active in protein synthesis/secretion.
  • Smooth ER: No ribosomes; synthesizes lipids, steroids, and cholesterol; involved in detoxification of alcohol and drugs.
• Golgi Apparatus:
  • Consists of $3-20$ flattened, curved saccules called cisternae.
  • Poles:
  • Cis face: Receiving side near the ER.
  • Trans face: Shipping side.
  • Functions: Modifies proteins and lipids, packages them into vesicles for secretion or exocytosis.

Ribosomes and Lysosomes

• Ribosomes:
  • Serve in protein synthesis.
  • Composed of $rRNA$ and protein molecules.
  • Consist of a large subunit and a small subunit, both of which are made in the nucleolus.
  • Locations: Free in cytoplasm or bound to the endoplasmic reticulum.
• Lysosomes:
  • Simple sacs containing hydrolytic enzymes (protease, nucleases, lipases, phospholipases, and sulphatases).
  • Membrane serves as a recognition site to ensure enzymes reach correct targets (like food vacuoles or phagosomes).
  • Key Functions:
  • Autolysis.
  • Autophagy (removal of damaged organelles).
  • Digestion of structures in other cells (e.g., gills and tails in tadpoles).
  • Fertilization (digesting the ovum membrane).

Plant-Specific Organelles: Central Vacuole

• Description: Large liquid-filled organelle found only in plant cells.
• Specifications:
  • Occupies $90\%$ of the plant cell volume.
  • Bound by a single membrane.
• Usage: Interior is used for storing nutrients or degrading unwanted substances.