Welcome to Membranes, Proteins, DNA, and Gene Expression!

Hello future biologists! This chapter is absolutely central to understanding how life works, especially within the context of Molecules, Diet, Transport, and Health. Think of it like this: your cells are mini-cities, and this chapter explains the city's walls (membranes), the workers (proteins), the blueprints (DNA), and how the workers read the blueprints (gene expression).

Understanding these concepts is vital because all biological processes—from absorbing nutrients in your gut to nerve signaling—rely on these molecular interactions. Don't worry if some parts seem complex; we will break them down into simple, manageable steps!

Section 1: The Cell Surface Membrane and Transport

1.1 Structure: The Fluid Mosaic Model

The cell surface membrane (or plasma membrane) is the boundary of the cell. It’s not a rigid wall; it’s a dynamic, flexible barrier described by the Fluid Mosaic Model.

Key Components Explained
  • Phospholipid Bilayer: This forms the basic structure. Phospholipids have two parts:

    Head (Hydrophilic): Water-loving, facing outwards towards the watery environment (cytosol and tissue fluid).

    Tail (Hydrophobic): Water-hating, facing inwards, sheltered from water.

    Analogy: Imagine a crowd of people standing side-by-side, holding hands, with their feet tucked inwards to avoid stepping in a puddle!

  • Proteins: Embedded within the bilayer like tiles in a mosaic. These perform most of the membrane’s functions. We distinguish between extrinsic (on the surface) and intrinsic (spanning the membrane) proteins.
  • Cholesterol: Found mainly in animal cells, cholesterol fits between the hydrophobic tails. It provides mechanical stability and regulates the fluidity of the membrane. (Think of it as the cement holding the mosaic pieces together slightly more firmly.)
  • Glycolipids and Glycoproteins: Carbohydrate chains attached to lipids (glycolipids) or proteins (glycoproteins). These are crucial for cell recognition (the cell's "ID badge") and adhesion, forming the glycocalyx.

Why is it called Fluid Mosaic?

Fluid: The phospholipids and proteins can move laterally (sideways), making the membrane flexible, not solid.

Mosaic: The proteins are scattered throughout the bilayer in an irregular pattern, like pieces of a mosaic artwork.

Quick Review: Functions of the Membrane

The membrane is partially permeable (or selectively permeable). Its main jobs include:

  • Controlling which substances enter and leave the cell.
  • Providing a boundary for organelles.
  • Serving as a site for chemical reactions (e.g., enzyme attachment).
  • Allowing cell communication and recognition.

1.2 Transport Mechanisms

Cells need to constantly move molecules—nutrients in, waste out—which they achieve using two main categories of transport: Passive and Active.

A. Passive Transport (No Energy Required)

Molecules move down the concentration gradient (from high concentration to low concentration). This movement is powered solely by the random kinetic energy of the molecules themselves.

  1. Simple Diffusion:
    Movement of small, non-polar molecules (like oxygen and carbon dioxide) directly through the phospholipid bilayer.
    Analogy: Opening a bottle of perfume—the smell spreads naturally until it fills the whole room.
  2. Facilitated Diffusion:
    Movement of large, polar, or charged molecules (like glucose or ions). They need help from carrier proteins or channel proteins embedded in the membrane.
    Note: While it requires a protein, it is still passive because it moves down the concentration gradient.
  3. Osmosis: (The Movement of Water)
    The net movement of water molecules across a selectively permeable membrane from an area of higher water potential to an area of lower water potential.
    Prerequisite Concept: Water Potential (\(\Psi\)) is the potential for water to move. Pure water has the highest potential (\(0 \text{ kPa}\)). Adding solutes lowers the water potential (makes it negative).
B. Active Transport (Energy Required)

This process moves molecules up or against the concentration gradient (from low concentration to high concentration).

  • It requires energy, usually supplied by ATP (Adenosine Triphosphate).
  • It relies on carrier proteins (often called pumps) which change shape when ATP is hydrolysed (broken down).

Analogy: Moving something heavy downhill (diffusion) is easy. Moving it uphill (active transport) requires energy (ATP) and a machine (the pump/carrier protein).

Step-by-Step Active Transport (Using a Carrier Protein):
1. The molecule to be transported binds to the specific site on the carrier protein.
2. ATP binds to the protein and is hydrolysed, releasing energy.
3. The energy causes the protein to change shape.
4. The molecule is released on the opposite side of the membrane, moving against the gradient.
5. The protein returns to its original shape.

KEY TAKEAWAY - Transport
Passive transport happens naturally (down the gradient) and requires no ATP. Active transport forces movement (up the gradient) and requires ATP and specific carrier proteins.

Section 2: Proteins – The Molecular Workers

Proteins are incredibly important—they act as enzymes, antibodies, structural components (like collagen), and, crucially for transport, membrane carriers. Their function is entirely dependent on their 3D shape.

2.1 Amino Acids and Primary Structure

Proteins are polymers made up of monomers called amino acids. There are 20 different common amino acids.

  • Amino acids link together via a condensation reaction, forming a peptide bond and releasing water.
  • A chain of amino acids is called a polypeptide.
  • The Primary Structure is simply the unique sequence of amino acids in the polypeptide chain. (Think of this as the spelling of a word; if you change one letter, the word changes meaning.)

2.2 Secondary, Tertiary, and Quaternary Structures

The chain doesn't stay straight; it folds up immediately into a complex 3D shape.

  • Secondary Structure: Folding due to hydrogen bonds forming between the C=O group of one amino acid and the N-H group of another. The two most common forms are the alpha (α) helix (spiral) and the beta (β) pleated sheet.
  • Tertiary Structure: The final, complex 3D shape achieved when the secondary structure folds upon itself. This structure is held together by various bonds between the R-groups (side chains) of the amino acids:
    • Hydrogen bonds (weak, numerous)
    • Ionic bonds (stronger, between charged groups)
    • Disulfide bridges (strong covalent bonds, only between cysteine R-groups)
    • Hydrophobic interactions (R-groups moving away from water)

    This tertiary structure dictates the function of the protein—the precise shape of an enzyme’s active site or a transport protein’s binding site.

  • Quaternary Structure: Exists only if the functional protein is made up of two or more polypeptide chains working together (e.g., haemoglobin, which has four chains).
Did you know?

If a protein loses its specific 3D shape (tertiary structure) due to high heat, extreme pH, or high solute concentration, it is denatured. A denatured enzyme or transport protein cannot function, which is why maintaining homeostasis (stable internal conditions) is vital for life.

KEY TAKEAWAY - Proteins
Proteins are polymers of amino acids. Their final, functional shape (tertiary structure) is determined by the sequence of amino acids (primary structure) and is held together by R-group interactions. Shape equals function!

Section 3: DNA and Gene Expression

If proteins are the workers (enzymes, carriers), where do the instructions come from? They come from the Deoxyribonucleic Acid (DNA)—the genetic blueprint stored in the nucleus.

3.1 The Structure of DNA

DNA is a double-stranded molecule twisted into a double helix. It is a polymer made up of monomers called nucleotides.

Structure of a Nucleotide

Each DNA nucleotide has three components:

  1. A Phosphate group
  2. A Deoxyribose Sugar (a pentose sugar)
  3. An organic Nitrogenous Base

There are four bases in DNA: Adenine (A), Thymine (T), Cytosine (C), and Guanine (G).

Forming the Double Helix
  • The Phosphate and Sugar groups alternate to form the strong sugar-phosphate backbone of each strand.
  • The two strands are held together by hydrogen bonds between the bases.
  • Bases pair specifically (Complementary Base Pairing): A always pairs with T (2 hydrogen bonds) and C always pairs with G (3 hydrogen bonds).
  • The strands are antiparallel, meaning they run in opposite directions (one runs 5' to 3', the other runs 3' to 5').

3.2 The Genetic Code

A gene is a section of DNA that codes for the production of a specific polypeptide.

The instructions are read in sets of three bases, called a triplet on DNA or a codon on mRNA. Each codon specifies a single amino acid.

  • The code is universal (almost all organisms use the same code).
  • The code is non-overlapping (each base is read only once).
  • The code is degenerate (most amino acids are coded for by more than one codon).

3.3 Gene Expression: Making a Protein

Gene expression is the process of synthesizing a protein from the instructions in a gene. It involves two main stages: Transcription and Translation.

Stage 1: Transcription (Making a messenger copy)

This occurs in the nucleus. The goal is to make a mobile copy of the gene called messenger RNA (mRNA), which can leave the nucleus.

  1. The specific gene section of the DNA unwinds and the two strands separate (by breaking hydrogen bonds).
  2. The enzyme RNA polymerase moves along the template strand of the DNA.
  3. It lines up free RNA nucleotides (A, U, C, G) according to complementary base pairing (Note: RNA uses Uracil (U) instead of Thymine (T)).
  4. A single strand of mRNA is synthesized, carrying the genetic message.
  5. The mRNA detaches and leaves the nucleus through a nuclear pore, heading towards the ribosomes.

Memory Aid: T-RAN-scription involves making the RNA transcript.

Stage 2: Translation (Building the protein)

This occurs on the ribosomes in the cytoplasm.

  1. The mRNA molecule attaches to a ribosome.
  2. Transfer RNA (tRNA) molecules, each carrying a specific amino acid, move to the ribosome.
  3. Each tRNA has an anticodon (a triplet of bases) that is complementary to a codon on the mRNA.
  4. As the ribosome moves along the mRNA, the tRNA molecules line up, depositing their amino acids in the correct sequence.
  5. Peptide bonds form between the adjacent amino acids, creating the polypeptide chain.
  6. The process continues until a 'stop' codon is reached, and the polypeptide chain detaches.

The newly formed polypeptide then folds immediately into its functional secondary and tertiary structure (often helped by other proteins) to become a functional protein, such as an enzyme or a membrane transport carrier!

KEY TAKEAWAY - Gene Expression
DNA holds the code. Transcription creates an mRNA copy in the nucleus. Translation uses that mRNA copy and tRNA (carrying amino acids) to build the functional protein on the ribosome.

Final Summary: Connecting the Concepts

This entire chapter is connected:

  • DNA contains the instructions (genes).
  • Gene Expression (Transcription and Translation) uses those instructions to build Proteins.
  • These Proteins become functional components—like enzymes for digestion (Diet/Health) or channel/carrier proteins embedded in the Membrane.
  • The Membrane uses these proteins to control Transport, ensuring the cell can absorb nutrients and maintain healthy internal conditions (Homeostasis).

Well done! You have covered some of the most fundamental concepts in Molecular Biology. Keep reviewing these steps, and remember: function always follows structure!