General Biology: Atomic Structure, Macromolecules, Membranes, and Cellular Processes

Atomic Structure and Chemical Bonding

The Structure of Atoms

Atoms are the fundamental units of matter, composed of protons, neutrons, and electrons. The arrangement of electrons in shells and orbitals determines the chemical properties of an element.

• Energy Shells: Electrons occupy energy levels or shells around the nucleus. The first, innermost energy shell is called the 1s orbital and can hold a maximum of 2 electrons.

• Atomic Number: The atomic number of an atom is defined as the number of protons in its nucleus. This determines the element's identity.

• Electron Configuration and Bonding: The number of electrons in the outer shell (valence electrons) influences how many bonds an atom can form. For example, nitrogen has 7 electrons and can form a maximum of 3 covalent bonds to complete its octet.

Example: Nitrogen (atomic number 7) has the electron configuration 1s2 2s2 2p3, with 5 valence electrons, allowing it to form three bonds (e.g., in ammonia, NH3).

Biological Macromolecules: Polysaccharides

Starch and Cellulose

Starch and cellulose are both polysaccharides composed of glucose monomers, but they differ in structure and function.

• Starch: A storage polysaccharide in plants, composed of α-glucose units. It has some branching (amylopectin) and is poorly soluble, making it suitable for energy storage.

• Cellulose: A structural polysaccharide in plant cell walls, composed of β-glucose units. It is unbranched, insoluble, and very stable, providing rigidity to plant cells.

Comparison Table:

Property	Starch	Cellulose
Monomer	α-glucose	β-glucose
Branching	Some (amylopectin)	None
Solubility	Poorly soluble	Insoluble
Function	Energy storage	Structural support

Membrane Structure and Transport

Osmosis and Diffusion

Cell membranes are selectively permeable, allowing certain substances to pass while restricting others. Osmosis is the movement of water across a membrane, while diffusion refers to the movement of solutes.

• Semi-permeable Membranes: Allow some molecules (e.g., galactose, mannose) to pass, but not others (e.g., maltose).

• Osmotic Effects: If a bag containing certain solutes is placed in a solution with different concentrations, water and permeable solutes will move to balance concentrations, affecting turgidity (firmness) of the bag.

• Entropy: The movement of solutes and water increases the entropy (disorder) of the system.

Membrane Transport Mechanisms

• Simple Diffusion: Small, nonpolar molecules (e.g., O2, CO2) diffuse across the lipid bilayer without assistance.

• Facilitated Diffusion: Ions (e.g., Na+) and polar molecules require transport proteins to cross the membrane.

• Active Transport: Movement of substances against their concentration gradient requires energy (usually ATP).

Example: Sodium ions (Na+) are transported across membranes by proteins such as the sodium-potassium pump.

Phospholipids and Membrane Structure

• Phospholipids: Amphipathic molecules with a hydrophilic (polar) phosphate head and hydrophobic (nonpolar) fatty acid tails. This dual nature allows them to form bilayers, the basis of cell membranes.

• Liposomes: Artificially created vesicles with a phospholipid bilayer, used to study membrane properties.

Energy Requirements for Transport

• Active Transport: Always requires energy when moving solutes from low to high concentration (against the gradient).

• Passive Transport: Does not require energy; includes diffusion and facilitated diffusion.

Biological Calculations: Toxicology Example

LD50 and Dosage Calculations

LD50 (Lethal Dose, 50%) is the amount of a substance required to kill 50% of a test population. It is commonly used in toxicology to assess the safety of chemicals.

• Formula: $\text{Number of drinks} = \frac{\text{LD}_{50} \times \text{body weight}}{\text{amount per drink}}$

• Example: For caffeine, if LD50 is 170 mg/kg, body weight is 54 kg, and each drink contains 221 mg caffeine:

$\text{Number of drinks} = \frac{170 \times 54}{221} \approx 41.5$

Additional info: In practice, rounding and safety factors are applied in real toxicology assessments.

Enzymes and Metabolic Regulation

Enzyme Kinetics

Enzymes are biological catalysts that speed up chemical reactions. Their activity depends on substrate concentration and enzyme affinity.

• Vmax: The maximum rate of reaction when the enzyme is saturated with substrate.

• Km: The substrate concentration at which the reaction rate is half of Vmax. Lower Km indicates higher affinity.

• Regulation: Enzymes with very high affinity (very low Km) would always be saturated, making regulation by substrate concentration difficult.

Michaelis-Menten Equation:

$v = \frac{V_{max}[S]}{K_m + [S]}$

Protein-Protein Interactions

• Specificity: Highly specific protein-protein interactions are crucial for processes such as enzyme catalysis and cell signaling (e.g., receptor-ligand binding).

Cellular Respiration and Energy Production

ATP Synthesis

• Electron Transport Chain (ETC): Located in the inner mitochondrial membrane, the ETC pumps protons to create a proton gradient.

• Chemiosmosis: The flow of protons back into the mitochondrial matrix through ATP synthase drives the production of ATP.

• Substrate-Level Phosphorylation: Direct transfer of a phosphate group to ADP to form ATP, occurs in glycolysis and the citric acid cycle.

Equation for Chemiosmosis:

$\text{ADP} + P_i + H^+_{\text{gradient}} \rightarrow \text{ATP}$

Metabolic Pathways

• Glycolysis: Occurs in the cytosol; breaks down glucose to pyruvate, producing ATP and NADH.

• Krebs Cycle (Citric Acid Cycle): Occurs in the mitochondrial matrix; oxidizes acetyl-CoA to CO2, generating NADH and FADH2.

• Electron Transport Chain: Uses NADH and FADH2 to produce ATP via oxidative phosphorylation.

Metabolic Flexibility

• When glucose is unavailable, proteins can be broken down into amino acids, which are deaminated and converted into intermediates that enter glycolysis or the Krebs cycle.

Summary Table: Key Concepts

Concept	Key Points
Atomic Structure	1s orbital holds 2 electrons; atomic number = protons
Polysaccharides	Starch (branched, storage), Cellulose (unbranched, structural)
Membrane Transport	Passive (diffusion), Facilitated (proteins), Active (energy required)
Enzyme Kinetics	Vmax, Km, regulation by substrate concentration
ATP Production	Chemiosmosis, substrate-level phosphorylation, ETC

Additional info: These notes cover foundational topics in general biology, including atomic structure, macromolecules, membrane transport, enzyme kinetics, and cellular energy production, as reflected in the quiz questions.