IB Biology B1 and B2 Exhaustive Study Guide

The Carbon Backbone: Carbon is the structural foundation of all organic molecules, which are the building blocks of living organisms.

Atomic Structure of Carbon:

• Carbon typically possesses $6$ protons, $6$ neutrons, and $6$ electrons.

• Electron configuration: Carbon has $2$ electrons in its innermost shell and $4$ electrons in its outer (valence) shell.

• Stability requirements: The innermost shell is stable with $2$ electrons, while outer shells require $8$ electrons for stability.

• Bonding capacity: To achieve a stable octet, carbon seeks to form $4$ covalent bonds, which is the maximum number of bonds possible for an atom in that shell.

Molecular Geometry: A carbon atom bonded to four other atoms, such as in methane ($CH_4$), forms a tetrahedral shape, though it is often represented two-dimensionally for simplicity.

Carbohydrates: Sugars and Polymers

• Saccharide Nomenclature: Carbohydrates are composed of sugars, often identified by the suffix "-ose" (e.g., glucose).

• Classification of Sugars:
    - Monomer: An individual subunit, such as a monosaccharide.
    - Dimer: Two subunits joined together, specifically a disaccharide.
    - Polymer: Multiple subunits joined to form a polysaccharide.

• Examples of Saccharides:
    - Monosaccharides: Glucose ($C_6H_{12}O_6$) and Fructose.
    - Disaccharides: Maltose (glucose + glucose) and Sucrose (glucose + fructose).
    - Polysaccharides: Glycogen, starch, and cellulose.

• Bonding and Reactions:
    - Condensation Reaction: A process where a hydrogen ($H$) and a hydroxyl group ($OH$) are removed from two monomers to form water ($H_2O$), resulting in a glycosidic bond (specifically a $C-O-C$ bond).
    - Hydrolysis: The reversible process of "lysis" or splitting a polymer into monomers by the addition of water.

• The Metric System: Students must be familiar with the International System of Units (SI) for biological measurements.

Storage and Structural Polysaccharides

• Starch in Plants: Excess carbohydrates are stored as starch in two forms:
    - Amylose: A linear chain of glucose molecules joined by $1-4$ glycosidic bonds. It typically assumes a helical shape.
    - Amylopectin: Consists mostly of $1-4$ bonds but features occasional $1-6$ glycosidic bonds, which serve as branching points.

• Glucose Isomers:
    - Alpha-D-Glucose: The hydroxyl group on carbon $1$ points down. Used in starches (amylose and amylopectin).
    - Beta-D-Glucose: The hydroxyl group on carbon $1$ points up. Following the pattern: up-down-up-down.

• Glycogen in Animals: Used for medium-term energy storage in livers and muscles. It is similar to amylopectin but contains significantly more $1-6$ branching, making it more compact and easier to hydrolyze quickly.

• Cellulose in Plants:
    - Composed of beta-glucose chains.
    - Structural arrangement: Because it uses beta-glucose, every other glucose molecule in the chain is inverted ($180^{ extcirc}$ rotation).
    - This inversion allows for hydrogen bonding between adjacent chains, forming microfibrils with high tensile strength.
    - It is the primary component of plant cell walls and is indigestible to humans.

Glycoproteins and Cell Recognition

• Structure: Consist of an oligosaccharide (a chain of a few sugars) covalently bonded to a protein embedded in the cell membrane.

• Function: Principal role in cell-to-cell recognition.

• Example: Human blood types ($A$, $B$, $AB$, $O$) are determined by the specific glycoproteins present on the surface of red blood cells.

Lipids: Fats, Oils, and Steroids

• Characteristics: Lipids are non-polar, hydrophobic biomolecules. They lack the $1:2:1$ ratio of $C:H:O$ found in carbohydrates, possessing far fewer oxygen atoms relative to carbon.

• Categories of Lipids:
    - Oils: Low melting point; liquid at room temperature.
    - Fats: Solid at room temperature but liquid at body temperature ($37^{ extcirc}C$).
    - Waxes: High melting point; solid at room temperature.
    - Steroids: Characterized by a skeleton of four fused carbon rings.

• Triglycerides: Formed from one glycerol molecule and three fatty acids via three condensation reactions.

• Phospholipids: Similar to triglycerides, but the third fatty acid is replaced by a phosphate group. They are amphipathic (possessing both hydrophilic and hydrophobic regions) and form the basis of cell membranes.

Fatty Acids and Health Implications

• Saturated Fatty Acids: "Saturated" with hydrogen atoms; contain no double bonds between carbon atoms in the hydrocarbon chain.

• Unsaturated Fatty Acids: Contain at least one double bond ($C=C$).
    - Monounsaturated: One double bond.
    - Polyunsaturated: More than one double bond.

• Isomerism in Unsaturated Fats:
    - Cis-fatty acids: Hydrogens are on the same side of the double bond, causing a physical bend in the chain. These are healthy, natural, and stay liquid at room temperature.
    - Trans-fatty acids: Hydrogens are on opposite sides, resulting in a straight chain. These are often artificially produced, can pack tightly together (like straight spaghetti), and are associated with cardiovascular disease. Many have been banned by the FDA.

Energy Storage and Physiological Roles of Lipids

• Storage Efficiency: Lipids release twice as much energy per gram ($37 ext{kJ}/g$) during cellular respiration compared to carbohydrates ($17 ext{kJ}/g$).

• Mass Advantage: Animals (especially flying ones like birds and bats) use lipids for long-term storage because they can store the same energy in half the body mass required for carbohydrates.

• Thermal Insulation: Lipids are poor conductors of heat, serving as blubber in marine mammals (e.g., whales, seals) or penguins.

• Protection: Act as shock absorbers for vital organs, such as the kidneys.

Proteins and Amino Acids

• Protein Synthesis: Regulated by DNA; every three bases (a codon) codes for one amino acid. Ribosomes assemble these into polypeptides.

• Amino Acid Structure:
    - Alpha Carbon: The central carbon atom.
    - Amine Group: Contains nitrogen ($NH_2$).
    - Carboxyl Group: ($COOH$).
    - R-Group: The variable side chain. There are $20$ different amino acids used in ribosomes.

• Nutritional Categories:
    - Essential Amino Acids ($9$): Cannot be synthesized by the body; must be obtained from the diet.
    - Non-essential Amino Acids ($11$): Can be synthesized by transforming other amino acids.
    - Vegan Diets: Must ensure a variety of plant sources to obtain all essential amino acids.

• Peptide Bonds: Formed between the nitrogen of one amine group and the carbon of another's carboxyl group through condensation.

Levels of Protein Structure

• Primary Structure: The specific linear sequence of amino acids coded by DNA.

• Secondary Structure: Formed by hydrogen bonds between the polar $C=O$ and $N-H$ groups of the polypeptide backbone. Common shapes include the Alpha-helix and Beta-pleated sheet.

• Tertiary Structure: The 3D folding resulting from R-group interactions:
    - Ionic bonds (charged R-groups).
    - Hydrogen bonds (polar R-groups).
    - Disulfide bridges (cysteine residues containing sulfur).
    - Hydrophobic interactions (non-polar R-groups folding inward).

• Quaternary Structure: Exists when two or more polypeptide chains join to form a functional protein (e.g., Collagen, Hemoglobin).

Denaturation of Proteins

• Definition: A permanent change in the 3D shape of a protein, rendering it non-functional.

• Causes:
    - Heat: Increases molecular vibrations, breaking intermolecular bonds. Example: Cooking an egg white (albumin).
    - pH Extremes: Change the concentration of protons ($H^+$), disrupting ionic bonds based on charge.

Cell Membrane Structure and Transport

• Fluid Mosaic Model: Phospholipid bilayer with embedded proteins and cholesterol.

• Permeability: Small, non-polar molecules (e.g., $O_2$, $CO_2$) pass freely. Polar molecules (glucose) and ions ($Cl^-$) have low permeability.

• Types of Transport:
    1. Simple Diffusion: Passive movement from high to low concentration directly through the bilayer.
    2. Facilitated Diffusion: Passive movement from high to low concentration through specific channel proteins.
    3. Osmosis: Net movement of water from low solute to high solute concentration. Aquaporins facilitate rapid movement.
    4. Active Transport: Movement against the concentration gradient (low to high) using ATP energy and protein pumps.

• The Sodium-Potassium Pump ($Na^+/K^+$ Pump):**
    - Uses ATP to pump $3$ Na$^+$ out and $2$ K$^+$ in.
    - Salty Banana Metaphor: Salt ($NaCl$) is on the outside (salty); potassium ($K$) is on the inside (banana).

• Vesicular Transport:
    - Endocytosis: Cell membrane engulfs external material to form a vesicle (e.g., Paramecium feeding, white blood cells eating pathogens).
    - Exocytosis: Vesicles fuse with the plasma membrane to secrete contents (e.g., hormone release, Paramecium contractile vacuoles).

• Clathrin: A three-legged protein that forms a lattice cage around budding vesicles to assist in their formation.

Membrane Fluidity and Cholesterol

• Tail Saturation: Saturated tails make membranes more viscous; unsaturated tails (with bends) increase fluidity, especially important for organisms in cold environments (e.g., Antarctic fish).

• Cholesterol's Dual Role:
    - In Warmth: Reduces fluidity by preventing phospholipids from moving too freely (fuzzy sweater/Velcro analogy).
    - In Cold: Prevents phospholipids from packing too tightly and crystallizing/fracturing.

Organelles and Compartmentalization

• Advantages of Compartmentalization:
    - Concentration of enzymes and substrates for efficiency.
    - Sequestering of dangerous substances (e.g., digestive enzymes in lysosomes).
    - Maintenance of optimal pH for specific reactions (e.g., pH < 2 in food vacuoles).

• Mitochondria Adaptations:
    - Cristae: Infoldings of the inner membrane to increase surface area for the Electron Transport Chain (ETC).
    - Intermembrane Space: Small volume allows for rapid buildup of a proton gradient.
    - Matrix: Concentrated enzymes for the Krebs cycle.

• Chloroplast Adaptations:
    - Thylakoids: Small membrane pouches; large surface area for photosystems and ETC.
    - Thylakoid Lumen: Small space for rapid proton gradient buildup.
    - Stroma: Contains concentrated enzymes for the Calvin cycle.

• Nucleus: Double membrane with pores to allow mRNA and ribosomes out, and proteins for replication/transcription in.

Cell Specialization and Stem Cells

• Differentiation: Triggered by gradients of signaling chemicals; every cell keeps a full set of DNA, but only specific genes are expressed.

• Stem Cell Types:
    - Totipotent: Early embryo (up to $8$-cell stage); can become any cell type plus extra-embryonic tissues. Can form a whole organism.
    - Pluripotent: Later embryo; can become many cell types but not a whole organism.
    - Multipotent: Adult stem cells (e.g., bone marrow, hair follicles); can become a limited range of related cell types.

• Stem Cell Niche: Precise locations where stem cells are maintained (e.g., bone marrow).

• SA:Vol Ratio: Cells must remain small to maintain a high Surface Area to Volume ratio, ensuring short diffusion paths for nutrients and waste.

Specialized Human Cells

• Gametes:
    - Egg Cell (Ovum): Largest cell in human body; contains yolk for food reserves; haploid nucleus; Cortical Granules release enzymes to prevent polyspermy.
    - Sperm Cell: Tiny and streamlined; acrosome (enzymes to digest Zona Pellucida); midpiece packed with mitochondria for flagellar movement.

• Blood Cells:
    - Red Blood Cells (Erythrocytes): Small, indented (biconcave) to navigate capillaries; missing nuclei to maximize hemoglobin.
    - White Blood Cells (Leukocytes): Larger; immune response.

• Muscle Cells:
    - Striated Skeletal Muscle: Long, unbranched, multi-nucleated; for voluntary movement.
    - Cardiac Muscle: Shorter, branched, single nucleus; connected by intercalated discs to synchronize the heartbeat.

• Pneumocytes (Lung Cells):
    - Type 1: Extremely thin for gas exchange.
    - Type 2: Secrete surfactant to prevent alveolar collapse during exhalation.