Cells and molecules (biomembranes, nucleic acids, cytoskeleton)

Introduction: Welcome to the Microscopic World of the Cell!

When you start studying Biology, you encounter countless detailed names of molecules and cell parts, and you might feel anxious, thinking, "Memorizing all of this looks overwhelming..."
Don't worry! Instead of memorizing biological phenomena in isolated pieces, focusing on the relationship between structure and function makes everything much simpler to understand.
In this unit, let's build a solid foundation by learning about biological membranes, nucleic acids, and the cytoskeleton—the essential components that shape cells and sustain life processes from the ground up!

1. Substances That Compose Cells (Biomolecules)

Our bodies and cells are composed of an assortment of chemical substances. To understand life phenomena at the molecular level, let's first review the big picture of what substances are present.

Major Components of the Cell

The substances that make up living organisms can be broadly classified into the following:
・Water: The most abundant component in living organisms (about 60–70% in animals). It is polar and functions as a solvent that dissolves many substances.
・Proteins: Composed of many linked amino acids. They act as the primary players in life activities, functioning as enzymes, components of biological membranes, the cytoskeleton, and more.
・Lipids: Substances that are poorly soluble in water but soluble in organic solvents. They serve as energy reserves and main components of biological membranes (such as phospholipids).
・Carbohydrates: Include glucose, starch, glycogen, etc. They serve as energy sources for cellular activities and structural components of cell walls (cellulose).
・Nucleic Acids: Include DNA and RNA. They are involved in storing, transmitting, and expressing genetic information.
・Inorganic Salts (Minerals): Sodium ions, potassium ions, calcium ions, etc. They help maintain osmotic pressure and pH in body fluids, and participate in nerve impulse conduction.

[Chemistry Mini-Tip] Hydrophilic vs. Hydrophobic
The property of interacting favorably with water molecules is called hydrophilic (water-soluble), whereas having an aversion to water and readily dissolving in oils is called hydrophobic (lipid-soluble). This difference in properties plays a crucial role in the structure of biological membranes, which we'll cover next!

2. Structure and Properties of Biological Membranes

The cell membrane (plasma membrane) enclosing the cell, as well as the membranes enclosing organelles like the nucleus, mitochondria, and chloroplasts, are collectively called biological membranes. Biological membranes are not just passive barriers; they are sophisticated systems that strictly control the entry and exit of substances.

The Phospholipid Bilayer

The basic framework of a biological membrane is a phospholipid bilayer, made of two layers of lipids called phospholipids.
A single phospholipid molecule has two distinct regions with different properties:
・Head: Contains a phosphate group and is hydrophilic (water-loving).
・Tails: Consist of fatty acids and are hydrophobic (water-fearing / oil-loving).
In an aqueous solution, the hydrophobic tails face each other inward to avoid water molecules, while the hydrophilic heads face outward toward the water. Because of this, a stable bilayer forms spontaneously!

The Fluid Mosaic Model

The structure of a biological membrane is not a rigid, fixed sheet.
Various membrane proteins are embedded in a mosaic pattern within the phospholipid bilayer, and both phospholipids and proteins can move (diffuse) laterally within the plane of the membrane. This structural model is called the fluid mosaic model (proposed by Singer and Nicolson).
*Some membrane proteins span the membrane (transmembrane proteins), while others are attached to the membrane surface (peripheral proteins).

Selective Permeability of Biological Membranes

Biological membranes do not let just any substance pass through freely. The property whereby the membrane allows certain substances to pass more easily than others is called selective permeability.
・Substances that pass easily: Small, nonpolar molecules such as oxygen (\(O_2\)) and carbon dioxide (\(CO_2\)), as well as highly lipid-soluble substances.
・Substances that do not pass easily: Large hydrophilic molecules such as glucose and amino acids, and charged ions such as sodium ions (\(Na^+\)) and potassium ions (\(K^+\)).
Hydrophilic substances and ions that cannot easily pass through rely on membrane proteins (channels, transporters, pumps, etc.) to cross the membrane.

[Key Concept] Passive Transport vs. Active Transport
・Passive Transport: The movement of substances down their concentration gradient, from an area of higher concentration to lower concentration. It does not require energy (ATP) (e.g., movement of ions through channels).
・Active Transport: The transport of substances against their concentration gradient, from lower concentration to higher concentration. It consumes energy from ATP (e.g., the sodium-potassium pump).

[Common Mistake]
It's easy to mistakenly picture the cell membrane as a rigid wall. While the cell wall (found in plants, bacteria, etc.) is indeed rigid and sturdy, the cell membrane (plasma membrane) present in animal cells as well is a fluid, flexible structure like a thin film of oil. Make sure you don't confuse the two!

3. Structure and Characteristics of Nucleic Acids

Nucleic acids are critically important molecules that store an organism's genetic information and direct protein synthesis. There are two main types of nucleic acids: DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).

The Basic Unit: Nucleotide

Nucleic acids are polymers (polynucleotides) made of many repeating basic units called nucleotides.
A nucleotide is formed by three components bonded in a \(1 : 1 : 1\) ratio:
Phosphate group + Sugar (a five-carbon pentose sugar) + Nitrogenous base (an organic compound containing nitrogen)

Thorough Comparison: DNA vs. RNA

The differences between DNA and RNA are extremely high-yield topics frequently tested on the Common Test! Focus on the differences in their sugars, bases, and 3D structures.

1. Differences in Sugar
・DNA: Deoxyribose (a sugar with one fewer oxygen atom compared to ribose)
・RNA: Ribose

2. Differences in Nitrogenous Bases
・DNA: Four types—Adenine (A), Thymine (T), Guanine (G), Cytosine (C)
・RNA: Four types—Adenine (A), Uracil (U), Guanine (G), Cytosine (C)
*Notice that Thymine (T) in DNA is replaced by Uracil (U) in RNA!

3. Differences in 3D Structure
・DNA: A double helix structure composed of two antiparallel polynucleotide strands twisted around each other (elucidated by Watson and Crick).
・RNA: Typically single-stranded (though it can fold back on itself to form localized base pairs).

Complementary Base Pairing and Hydrogen Bonds

Between the two strands of DNA, specific pairs of bases attract each other via weak bonds called hydrogen bonds.
・Adenine (A) always pairs with Thymine (T) (via 2 hydrogen bonds).
・Guanine (G) always pairs with Cytosine (C) (via 3 hydrogen bonds).
This specific pairing preference is known as complementary base pairing (complementarity). Thanks to this rule, Chargaff's rules hold true (in any organism's DNA, the ratio of \(A\) to \(T\) and the ratio of \(G\) to \(C\) are approximately equal).

[Fun Fact] The Secret Behind the Names DNA and RNA
"Deoxy" means "without oxygen" (de- = remove, oxy- = oxygen). In other words, because it contains a nucleic acid with a sugar that has lost one oxygen atom compared to ribose, it was named "deoxyribonucleic acid." Knowing the etymology makes remembering scientific terms so much easier!

4. Cytoskeleton and Its Functions

A cell is far more than just a "soft water balloon filled with cytoplasm." Inside, a network of filamentous proteins crisscrosses the interior like an intricate scaffold, maintaining cell shape and acting as tracks for intracellular transport. This dynamic network is called the cytoskeleton.
There are three main types of cytoskeletal elements, differing in diameter and protein composition. Let's break down each one!

(1) Microtubules (Thickest: Diameter ~\(25\text{ nm}\))

・Protein Subunit: Tubulin (globular proteins polymerized into hollow cylindrical tubes)
・Key Functions and Locations:
1. Maintaining cell shape.
2. Forming the spindle apparatus (spindle fibers) during cell division to pull chromosomes to opposite poles.
3. Structural framework of the centrosome (the main microtubule-organizing center in animal cells) and of flagella and cilia (motile cell structures).
4. Serving as "tracks" for transporting organelles and vesicles.

(2) Intermediate Filaments (Medium Thickness: Diameter ~\(10\text{ nm}\))

・Protein Subunit: Keratin and others (varies depending on cell type)
・Key Functions and Locations:
1. Highly resistant to tensile stress (pulling forces), providing mechanical strength to maintain cell shape.
2. Anchoring the nucleus and organelles in place.
*Unlike microtubules and actin filaments, they do not directly participate in cell motility as transport tracks.

(3) Actin Filaments / Microfilaments (Thinnest: Diameter ~\(7\text{ nm}\))

・Protein Subunit: Actin (thin fibers composed of globular actin monomers linked into chains)
・Key Functions and Locations:
1. Concentrated just beneath the plasma membrane to support and alter cell shape.
2. Muscle contraction (interacts with myosin in muscle cells to shorten fibers).
3. Cytoplasmic streaming observed in plant cells and other organisms.
4. Amoeboid movement and formation of the contractile ring during animal cell cytokinesis (division of cytoplasm).

Cooperation with Motor Proteins

Microtubules and actin filaments make intracellular transport possible by serving as tracks. The proteins that travel along these tracks powered by ATP energy are called motor proteins.
・Motor proteins moving along microtubules: Kinesin (mostly transports cargo from the center of the cell toward the periphery) and Dynein (mostly transports from the periphery toward the center; also drives the bending motion of flagella and cilia).
・Motor proteins moving along actin filaments: Myosin (involved in muscle contraction and cytoplasmic streaming).

[Memory Tip] Remembering Cytoskeletal Diameters
From thickest to thinnest:
Microtubules (~\(25\text{ nm}\)) > Intermediate filaments (~\(10\text{ nm}\)) > Actin filaments (~\(7\text{ nm}\))
Even though it has "micro" in its name, microtubules are actually the thickest—a classic trap on exams! Remember that "intermediate" means middle thickness, and you won't get confused.

[Common Mistake]
A frequent incorrect statement in tests is: "Microtubules form the contractile ring during cell division."
Remember: The spindle fibers (spindle apparatus) that pull chromosomes are microtubules, but the contractile ring that pinches animal cells during cytokinesis is made of actin filaments. Be sure to keep them distinct!

5. Summary & Review Checklist

To wrap up, let's review the most critical points with this quick checklist!

・Biological membranes follow the fluid mosaic model, where proteins are embedded within and move freely across a phospholipid bilayer.
・Biological membranes exhibit selective permeability: small nonpolar molecules like oxygen and carbon dioxide pass easily, while ions and large hydrophilic molecules require the help of membrane proteins.
・The basic building block of nucleic acids is the nucleotide (phosphate group + sugar + nitrogenous base).
・DNA contains deoxyribose and bases A, T, G, C in a double helix. RNA contains ribose and bases A, U, G, C, usually as a single strand.
・There are 3 types of cytoskeletal elements:
　1. Microtubules: Made of tubulin; thickest. Form the spindle apparatus, centrosomes, and flagella. Motor proteins: kinesin and dynein.
　2. Intermediate filaments: Made of keratin, etc.; high tensile strength. Maintain cellular shape.
　3. Actin filaments: Made of actin; thinnest. Involved in muscle contraction, cytoplasmic streaming, and the contractile ring. Motor protein: myosin.

*Note: Detailed mechanisms of ATP synthesis across biological membranes, cellular respiration, photosynthesis, as well as specific protein functions and enzymatic reactions will be explored in detail in other sections of this unit ("Life Phenomena and Substances"). For now, make sure you have mastered these basic membrane and molecular architectures!