Cells: The Fundamental Units of Life

Chapters 1 and 15: Cells: The Fundamental Units of Life

The Cell: Basic Unit of Life

• A cell is defined as the smallest unit capable of carrying out all activities associated with life.

  • Examples of single-celled organisms include prokaryotes, protists, and fungi.

  • Plants and animals are multicellular, composed of millions of cells.

• Despite the enormous diversity of cells across the planet, they share basic structures and components.

Cell Theory: A Unifying Concept

• This scientific theory was proposed in the 1850s.

• It is supported by three basic tenets:

  • All living organisms are made up of cells.

  • The cell is the basic unit of structure and organization in organisms.

  • Cells arise from pre-existing cells.

Key Features of Cells

• Enclosed by plasma membrane: This acts as a selective barrier, controlling the entry and exit of substances.

  • It allows the cell to accumulate necessary substances for biochemical reactions.

• Cytoplasm: This consists of organelles and the cytosol (the fluid component).

• Organelles: These are internal cellular structures specialized to carry out specific cellular activities, and are usually membrane-bound.

Why are Cells Small? (Surface Area to Volume Ratio)

• Cells maintain a high surface area to volume (SA:V) ratio for efficient function.

• Formulas:

  • Surface Area (SA) = $6a^2$

  • Volume (V) = $a^3$

  • Where $a$ equals the length of each side of a cube.

• Example:

  • A $1 ext{ mm} imes 1 ext{ mm} imes 1 ext{ mm}$ cube has an SA:V ratio of $6:1$.

  • A $2 ext{ mm} imes 2 ext{ mm} imes 2 ext{ mm}$ cube has an SA:V ratio of $3:1$.

• Implications of size:

  • As a cell gets bigger, its SA:V ratio gets smaller (more volume, less membrane surface area).

  • This makes it difficult for gases and nutrients to diffuse across membranes efficiently (due to concentration gradients).

  • It also becomes harder to transport materials to different locations within the cell due to the increased distance.

Prokaryotic Cells

• Organisms: Bacteria and Archaea.

• Size: Very small, approximately $1/10$ the size of eukaryotic cells.

• Common Shapes:

  • Cocci (spherical)

  • Bacilli (rod-shaped)

  • Spirochete (spiral-shaped)

• Key Characteristics:

  • Most have cell walls outside the plasma membrane.

  • Many possess flagella for movement.

  • The interior contains ribosomes and inclusions (storage granules).

  • DNA is located in a nucleoid region, not enclosed by a membrane.

  • No membrane-enclosed internal organelles.

Structure of Prokaryotic Cells

• Cell Wall:

  • A tough, fibrous protective layer that gives the cell its shape.

  • Composed of peptidoglycan (PG), which consists of long chains of amino sugars connected by peptide bridges.

  • Differences in Cell Wall Structure: Gram-Positive vs. Gram-Negative Bacteria

    • Distinguished by a staining procedure, crucial for treating diseases.

    • Gram-positive bacteria: Possess a thick PG layer and absorb and retain crystal violet stain.

    • Gram-negative bacteria: Have a thin PG layer and an outer membrane containing polysaccharides and lipoprotein, and thus do not absorb and retain crystal violet stain.

• Capsule:

  • A polysaccharide layer surrounding the cell wall.

  • Not found on all prokaryotes.

  • Helps cells adhere to surfaces and protects bacteria from elimination by immune cells.

• Fimbriae:

  • Numerous hair-like projections primarily used for adherence to surfaces.

• Pilus:

  • Longer and less numerous than fimbriae.

  • Also plays a role in adherence.

  • The F pilus (or sex pilus) is involved in the transfer of DNA between bacteria.

• Flagellum (plural: flagella):

  • May or may not be present.

  • Motility structures that project outward from the cell.

  • Spin like a propeller, with the direction determining 'run' or 'tumble' movement.

  • Bacterial Flagellum Parts:

    • Basal Body: Anchors the flagellum to the cell wall and plasma membrane; contains a motor that uses energy from ATP.

    • Hook: Connects the basal body to the filament.

    • Filament: Composed of a protein called flagellin.

  • Functions: Motility (e.g., chemotaxis), adherence, and biofilm formation.

• Ribosome:

  • Complexes of RNA and protein, serving as the site of protein synthesis.

  • They are smaller than eukaryotic ribosomes and have different RNA and protein compositions.

• Inclusion/Storage Granule:

  • Areas within the cell where nutrients (e.g., glycogen, lipids, phosphate) are stored.

Eukaryotic Cells

• Compartmentalization: A defining feature where the cell is divided into various membrane-enclosed compartments (organelles).

  • This localizes substrates, increasing the efficiency of reactions.

  • Allows multiple reactions to occur simultaneously.

  • Some organelles are present only in specific cell types.

  • The larger size of eukaryotic cells makes compartmentalization necessary for efficient molecular diffusion.

Nucleus

• Contains most of the cell's DNA, which is complexed with proteins to form chromatin and tightly packaged into chromosomes.

• It is the site of DNA and RNA synthesis.

• Nuclear Envelope:

  • Inner membrane: Contains binding sites for chromosomes and the nuclear lamina, a meshwork of protein filaments that provides structural support.

  • Outer membrane: Continuous with the endoplasmic reticulum (ER) membrane.

• Nuclear Pores:

  • Large protein complexes that control the entry and exit of molecules to and from the nucleus.

  • Proteins are imported, while RNA and ribosomal subunits are exported.

  • Ions and small molecules can pass freely.

  • Large macromolecules must contain a Nuclear Localization Signal (NLS) to enter.

  • Each nucleus typically contains $3000-4000$ pores.

• Nuclear Import Mechanism:

  • Importins bind proteins containing an NLS, forming a 'cargo complex'.

  • Importins with cargo bind to select repetitive sequences on cytosolic fibrils extending from the nuclear pore complex.

  • They move from one repeat to the next through a gel-like meshwork to deliver the cargo.

  • Importins then return to the cytosol.

• Typical Signal Sequences (Examples from Table 15-3):

  • Import into ER: Starts with $ext{H}_3 ext{N}$-Met-Met-Ser-Phe-Val-Ser-Leu-Leu-Leu-Val-Gly-Ile-Leu-Phe-Trp-Ala-Thr-Glu-Ala-Glu-Gln-Leu-Thr-Lys-Cys-Glu-Val-Phe-Gln-

  • Retention in lumen of ER: -Lys-Asp-Glu-Leu-COO-

  • Import into mitochondria: $ext{H}_3 ext{N}$-Met-Leu-Ser-Leu-Arg-Gln-Ser-Ile-Arg-Phe-Phe-Lys-Pro-Ala-Thr-Arg-Thr-Leu-Cys-Ser-Ser-Arg-Tyr-

  • Import into nucleus: -Pro-Pro-Lys-Lys-Lys-Arg-Lys-Val- (rich in positively charged amino acids)

  • Export from nucleus: -Met-Glu-Glu-Leu-Ser-Gln-Ala-Leu-Ala-Ser-Ser-Phe-Leu-Leu-

  • Import into peroxisomes: -Ser-Lys-Leu-

    • Note: $ext{H}_3 ext{N}$ indicates the N-terminus; COO- indicates the C-terminus. Positively charged amino acids are often red, negatively charged blue, and important hydrophobic ones green. (As depicted in original context table).

Nucleolus

• A compact structure within the nucleus (can have one or more).

• Not enclosed by a membrane.

• Produced by the aggregation of DNA, RNA, and proteins.

• Site of ribosomal RNA (rRNA) synthesis and the assembly of ribosomes.

Ribosome

• Particles composed of proteins and rRNA.

• Consist of a large and small subunit, which differ between prokaryotes and eukaryotes.

• May be attached to certain membranes (e.g., ER) or be free in the cytoplasm.

• The primary site of protein synthesis.

Endoplasmic Reticulum (ER)

• A network surrounding the nucleus and extending into the cytoplasm.

• Connects to the nuclear envelope.

• Forms different shapes: tightly packed, flattened sac-like structures or highly curved and tubular networks.

• The space between its membranes is called the lumen.

• Divided into two prominent regions: smooth ER and rough ER.

• Smooth Endoplasmic Reticulum (SER):

  • Has a tubular appearance and a smooth surface.

  • Functions:

    • Synthesis of lipids, carbohydrates, and steroid hormones.

    • Detoxification in liver cells (breaks down drugs, carcinogens, alcohol).

• Rough Endoplasmic Reticulum (RER):

  • Its outer surface is studded with ribosomes, giving it a 'rough' or 'bumpy' appearance.

  • Ribosomes, not the ER itself, are the site of protein synthesis.

  • Function: Assembly and modification of proteins.

    • Includes the formation of disulfide bonds and glycosylation.

  • Protein Processing in RER:

    • As a protein is synthesized by an ER-bound ribosome, it passes through an ER pore.

    • If the protein is destined for secretion or another organelle, it enters the ER lumen.

    • Some proteins remain embedded in the ER membrane as transmembrane proteins.

    • Protein folding is aided by molecular chaperones.

    • Modification by enzymes may add lipids (forming lipoproteins) or carbohydrates (forming glycoproteins).

    • Modified proteins are then incorporated into vesicles for transport from the ER to their next destination.

Golgi Apparatus

• Consists of cisternae, which are flattened membrane-bound sacs, typically ($3-20$ per stack).

• Each Golgi stack has three functional regions:

  • cis face (entry surface): Receives vesicles from the ER.

  • Medial region: Intermediate processing area.

  • trans face (exit surface): Faces the plasma membrane, serving as the site of transport out of the Golgi to other organelles or the plasma membrane (PM).

• Functions:

  • Further modification of oligosaccharide chains that were added to proteins in the ER.

  • Protein sorting, determining destinations such as:

    • Return to the ER.

    • Exocytosis, supplying the plasma membrane with newly made lipids and proteins.

    • Secretion of proteins.

Endomembrane System and Vesicular Transport

• The endomembrane system is a network of organelles involved in vesicular transport, connecting the ER, Golgi, lysosomes, and other organelles.

• Vesicular Transport Steps:

  1. Receptors bind specific ligand/cargo and cluster in coated pits: This initiates the formation of a vesicle.

  2. Formation of coated vesicles:

     • The protein coat helps shape the membrane into a bud and captures specific molecules for onward transport.

     • Adaptins: Proteins that secure the coat to the vesicle membrane and help select specific cargo molecules.

     • Dynamin: A GTP-binding protein that assembles around the neck of the budding vesicle and pinches it off from the parent membrane.

  3. Vesicle docking and membrane fusion:

     • Vesicles are transported by motor proteins along cytoskeletal fibers.

     • Tethering: Interactions occur between Rab proteins on the vesicle and tethering proteins on the target organelle membrane.

     • Docking: Involves additional recognition by SNARE proteins.

     • Finally, the lipid bilayers fuse, and the cargo is delivered to the target compartment.

Lysosomes

• Small membrane-bound sacs containing hydrolytic enzymes (acid hydrolases), found only in animal cells.

• Acid hydrolases are transported through the ER to the Golgi, then bud off to form lysosomes.

• The lysosomal membrane contains specific transporters and proton pumps to maintain its acidic internal environment.

• Functions:

  • Digestion of food particles.

  • Breakdown of malfunctioning cellular structures (e.g., old organelles).

• Types/Processes:

  • Primary lysosomes: Formed by budding from the Golgi apparatus.

  • Secondary lysosomes: Result from the fusion of a primary lysosome with an endosome or phagosome containing material to be digested.

  • Autophagy: A process by which a cell 'eats itself', enclosing a damaged organelle within a double membrane which then fuses with a lysosome for degradation.

Vacuole

• Large membrane-bound sacs, similar to lysosomes, found only in plants, fungi, and protozoa.

• Functions:

  • Digests nutrients.

  • Stores salts, pigments, and metabolic wastes, maintaining a high solute concentration.

  • Accumulation of water creates turgor pressure, pushing on the cell wall to provide structural strength.

Peroxisome

• Membranous sacs formed by budding from the smooth ER.

• Functions:

  • Oxidation of fatty acids.

  • Synthesis of some phospholipids.

  • Detoxification of alcohol in liver cells.

• Generates hydrogen peroxide ($ext{H}<em>2 ext{O}</em>2$) as a by-product of oxidation reactions, which is toxic to the cell.

  • Peroxisomes possess the enzyme catalase to break down $ext{H}<em>2 ext{O}</em>2$ into harmless water ($ext{H}<em>2 ext{O}$) and oxygen ($ext{O}</em>2$).

• They are found in high numbers in cells that synthesize, store, or degrade lipids.

Mitochondria and Chloroplasts

• Share many features with bacterial ancestors, including their own DNA, ribosomes, and machinery for DNA and RNA synthesis.

• This similarity supports the Theory of Serial Endosymbiosis, which explains their origin as transformations of engulfed prokaryotes.

  • An anaerobic eukaryotic cell engulfed an aerobic bacterium, which evolved into a mitochondrion, losing its original plasma membrane and gaining a double membrane derived from the engulfing cell and its own bacterial outer membrane.

  • Later, some aerobic eukaryotic cells with mitochondria engulfed a photosynthetic bacterium, which evolved into a chloroplast, similarly gaining a double membrane structure.

Mitochondria

• The primary site of oxidative phosphorylation, the process that generates ATP.

• Enclosed by a double membrane:

  • Inner Membrane: Highly folded into structures called cristae, which increase the surface area; contains protein complexes of the electron transport chain (ETC); strictly regulates the types of molecules that pass through.

  • Outer Membrane: Smooth and allows most small molecules to pass freely.

• Intermembrane space: The region between the outer and inner membranes.

• Matrix: The fluid-filled space enclosed by the inner membrane; contains a small amount of its own DNA (approximately $1\%$ of the cell's total DNA).

Chloroplast

• Disc-shaped, double-membrane organelle found only in plants and algae.

• The site of photosynthesis, converting light energy into chemical energy.

• Contains chlorophyll (a green pigment that traps light energy) and other light-absorbing yellow and orange pigments.

• Stroma: The fluid-filled space enclosed by the inner membrane; contains enzymes to produce carbohydrates from $ext{CO}<em>2$ and $ext{H}</em>2 ext{O}$.

• Thylakoids: Flattened, disc-like sacs within the chloroplast, often stacked into grana.

  • They are the site of light-dependent reactions in photosynthesis, used to generate ATP.

  • Contain chlorophyll and other pigments.

• Granum (plural: grana): A stack of thylakoids.

Relative Volumes and Numbers of Major Membrane-Enclosed Organelles in a Liver Cell (Hepatocyte)

Cytoskeleton

• A dense network of protein fibers, including microfilaments, intermediate filaments, and microtubules.

• Provides mechanical strength, maintains cell shape, and enables cell movement.

• Functions in cell division.

• Involved in the transport of materials within the cell.

• It is highly dynamic and constantly changing.

Cilia and Flagella

• Cilia: Hair-like structures that extend from the cell surface.

  • Beat in a whip-like fashion.

  • Play roles in locomotion, collection of food particles, and the mucociliary escalator (e.g., in respiratory tracts).

• Flagellum (singular): Similar in structure to cilia but longer and less numerous.

• Structure of Cilia and Flagella:

  • The core is a $9+2$ microtubule array: $9$ fused pairs of microtubules arranged in a circle, with $2$ unfused microtubules in the center.

  • They are anchored in the cell by a basal body, which has a $9 imes3$ microtubule organization.

  • Movement is produced by the bending of the core as microtubules slide against each other, driven by motor protein Dynein.

Cell Wall

• Surrounds the cells of fungi, algae, and plants (not animal cells).

• Provides structural support and protection.

• Composed of polysaccharides and proteins.

  • In plants, it is primarily made of cellulose.

  • In fungi, it is made of chitin.

  • In algae, it is composed of cellulose and other polysaccharides.