Grade 12 Biology: Unit 1 - Biochemistry and Chemical Bonding

Introduction to Biology and biochemistry

• Definition of Biology: Biology is defined as the study of living things.

• Branches of Grade 12 Biology: The curriculum for Grade 12 Biology is divided into several major branches:

  • Biochemistry

  • Metabolic Processes

  • Molecular Genetics

  • Homeostasis

  • Population Dynamics

• Definition of Biochemistry: Often referred to as the "Chemistry of Life," biochemistry is the study of chemical substances and the specific chemical processes that occur within living organisms.

Elemental Composition of the Human Body

• Major Elements (96%): Approximately $96\%$ of the human body mass is composed of four primary elements:

  • Oxygen ($O$)

  • Carbon ($C$)

  • Hydrogen ($H$)

  • Nitrogen ($N$)

• Minor Elements (4%): Approximately $4\%$ of the human body mass consists of:

  • Calcium ($Ca$)

  • Phosphorus ($P$)

  • Potassium ($K$)

  • Sulfur ($S$)

  • Sodium ($Na$)

  • Chlorine ($Cl$)

  • Magnesium ($Mg$)

• Trace Elements (<0.01%): Minerals present in extremely small amounts (< 0.01\% of body mass) are called trace elements. Examples include:

  • Iron ($Fe$)

  • Iodine ($I$)

Types of Macromolecules

• The four main types of macromolecules essential to life are:

  • Carbohydrates: Primary energy sources.

  • Proteins: Structural and functional units (e.g., enzymes, antibodies).

  • Nucleic Acids: Information storage (DNA and RNA).

  • Lipids: Fats and oils used for energy storage and membranes.

Chemical Bonding in Biological Systems

• Ionic Bonding:

  • Defined as the electrostatic attraction between a cation (positively charged ion) and an anion (negatively charged ion).

  • Biological Context: Ionic bonds are rarely found in the human body because the abundance of water causes them to dissociate into individual ions.

  • Exceptions:

    • The interior of large proteins may contain ionic bonds if the environment is strictly water-free (hydrophobic).

    • Binding between proteins and DNA: The negative charges on the phosphate backbone of DNA attract the positively charged amino acids lysine and arginine found in histone proteins.

• Covalent Bonding:

  • The electrostatic attraction between shared bonding electrons and the positive nucleus.

  • Can form between atoms of the same element or different elements.

  • Electronegativity ($EN$): The ability of an atom to attract electrons in a covalent bond.

  • Pure Covalent Bonds: Occur when electrons are shared equally ($\Delta EN = 0$). Examples: $H_2$, $O_2$.

  • Polar Covalent Bonds: Occur when electrons are shared unequally due to differences in electronegativity (\Delta EN > 0 but below ionic thresholds).

    • Leads to partial charges: partial positive ($\delta +$) and partial negative ($\delta -$).

    • Example ($H_2O$): Oxygen is more electronegative than hydrogen ($EN \text{ of } O = 3.44$, $EN \text{ of } H = 2.20$, $\Delta EN = 1.24$). Oxygen pulls electrons closer, resulting in a $\delta -$ on oxygen and a $\delta +$ on hydrogens.

• Molecular Bonding (Intermolecular Forces):

  • Hydrogen Bonds: Occur when a hydrogen atom is covalently bonded to a highly electronegative atom (Fluorine, Oxygen, or Nitrogen: $F$, $O$, $N$). The partial positive hydrogen is attracted to the partial negative atom of a neighboring molecule. Represented by dotted or dashed lines.

  • London (Dispersion) Forces: Arise from electrostatic interactions between temporary dipoles induced by the constant movement of electrons. They exist in all atoms and molecules but are the only force present between nonpolar molecules.

  • Hydrophobic Interactions: Occur between nonpolar functional groups (e.g., Methyl groups $-CH_3$). Because these groups cannot form hydrogen bonds, they interact with each other via London dispersion forces to avoid polar water environments.

Functional Groups: Properties and Biological Roles

• Hydroxyl Group ($-OH$):

  • Properties: Polar; high boiling point; highly soluble in water.

  • Role: Required for condensation reactions. Found on proteins and carbohydrates to improve solubility. Essential for DNA replication (interaction between the $3'$ hydroxyl of deoxyribose and the phosphate group).

• Carbonyl Group ($-CO$ or $-COH$):

  • Properties: Polar; high boiling point; soluble in water.

  • Role: Found in weak acids such as amino acids and citric acid. The enzyme chymotrypsin uses a carbonyl group to cleave substrate peptides.

• Carboxyl Group ($-COOH$):

  • Properties: Polar; high boiling point; water-soluble.

  • Role: Neutralization reactions; formation of peptide bonds. Found in amino acids like glutamic acid. In ATP synthase, the carboxyl group in the "c-ring" allows the protein to rotate during metabolism.

• Amino Group ($-NH_2$):

  • Properties: Polar; weak base (accepts $H^+$ to become $-NH_3^+$).

  • Role: Required for protein synthesis; forms peptide bonds. Lysine and arginine contain additional amino groups in their side chains, which attract the negative phosphate groups in DNA.

• Sulfhydryl Group ($-SH$):

  • Properties: Slightly polar; lower boiling point and lower solubility than hydroxyl groups (cannot form hydrogen bonds).

  • Role: Two sulfhydryl groups can undergo oxidation to form a disulfide bond ($-S-S-$), which stabilizes the three-dimensional structure (tertiary folding) of proteins.

• Phosphate Group ($-PO_4$):

  • Properties: Highly polar; very water-soluble; boiling point increases with more phosphate groups (e.g., ATP > ADP > AMP).

    • Boiling Point of AMP: $798.5^{\circ}C$

    • Boiling Point of ADP: $877.7^{\circ}C$

    • Boiling Point of ATP: $951.4^{\circ}C$

  • Role: Used in cell signaling (signal transduction), DNA production, phospholipids for cell membranes, and ATP for energy.

• Methyl Group ($-CH_3$):

  • Properties: Nonpolar; low water solubility; stable and rarely reactive.

  • Role: Increases hydrophobicity in lipids. Methylation of DNA or histone proteins is a critical mechanism for regulating gene expression.

Types of Chemical Linkages

• Ester Linkage: Forms between a carboxyl group and a hydroxyl group. Found in fats, triglycerides, and phospholipids.

• Ether Linkage: Forms between two hydroxyl groups. In sugars, this is specifically called a glycosidic linkage.

• Peptide Linkage: Forms between a carboxyl group and an amino group. This is the characteristic bond in proteins (polypeptides).

• Anhydride Linkage: Forms between two carboxyl groups, two phosphate groups, or a phosphate and a carboxyl group. High-energy bonds found in ATP.

• Disulfide Linkage: Forms between two sulfhydryl groups. Vital for stabilizing the tertiary structure of proteins.

Types of Biochemical Reactions

• Condensation (Dehydration Synthesis): Two molecules combine to form a larger molecule, producing a water molecule ($H_2O$) as a byproduct.

• Hydrolysis: The use of a water molecule to break a chemical bond. Example: The enzyme lactase uses water to break lactose into galactose and glucose.

• Neutralization: An acid and a base react to form a salt and water.

• Redox (Reduction-Oxidation): Involves the transfer of electrons.

  • Oxidation: Loss of electrons (electrons appear as a product).

  • Reduction: Gain of electrons (electrons appear as a reactant).

  • Example: $CO_2 + 2H_2O \rightarrow CH_2O + O_2 + H_2O$

• Phosphorylation: The addition of an inorganic phosphate ($P_i$) to a molecule. Example: Hexokinase adds a phosphate to glucose during glycolysis using $Mg^{2+}$ as a cofactor.

Carbohydrates: Structure and Classification

• General Formula: Most monosaccharides follow $(CH_2O)_n$ with a $1:2:1$ ratio of C:H:O.

  • Glucose: $C_6H_{12}O_6$

  • Exceptions: Deoxyribose ($C_5H_{10}O_4$), disaccharides (e.g., Maltose $C_{12}H_{22}O_{11}$), and polysaccharides do not strictly follow the $1:2:1$ ratio due to the loss of oxygen or water during formation.

• Classifications:

  • Monomer: A small molecule (e.g., monosaccharides, amino acids, nucleotides).

  • Polymer: A large molecule made of multiple repeating monomers linked by covalent bonds.

• Monosaccharides:

  • Glucose: Main energy source; used for cellular respiration to generate ATP.

  • Galactose: Found in milk sugars.

  • Fructose: Found in fruit sugars.

  • Forms of Glucose: Exists in chain and ring forms. Ring form is designated as $\alpha$-glucose or $\beta$-glucose based on the orientation of the $-OH$ group on Carbon 1 ($C1$).

• Disaccharides: Formed by two monosaccharides via condensation (glycosidic bond).

  • Maltose: Glucose + Glucose (found in malted grains).

  • Lactose: Glucose + Galactose (found in milk).

  • Sucrose: Glucose + Fructose (table sugar).

  • Mnemonic for memorization: "Super Glowing Frogs Leave Gardens Glowing" ($S=G+F$, $L=G+Ga$).

• Polysaccharides:

  • Starch: Plant energy storage. Composed of:

    • Amylose: Unbranched chains with $\alpha$-1,4 glycosidic linkages.

    • Amylopectin: Branched chains with $\alpha$-1,4 and $\alpha$-1,6 glycosidic linkages. Cleaved by the enzyme amylase.

  • Glycogen: Animal energy storage (found in liver and muscle). Highly branched with $\alpha$-1,4 and $\alpha$-1,6 linkages.

  • Cellulose: Plant structural support. Linear, fibrous chains with $\beta$-1,4 glycosidic linkages. Humans cannot digest cellulose because we lack the enzyme to break the $\beta$-1,4 bond.

Biological Benefits of Carbohydrates

• Energy Production: Glucose is the primary fuel for ATP generation.

• Brain Function: The brain relies on glucose as its primary energy source.

• Energy Storage: Starch (plants) and Glycogen (animals).

• Digestive Health: Cellulose (fiber) provides bulk, helps maintain volume in the intestinal tract, and promotes a feeling of fullness.

Questions & Discussion

• Checkpoint: Identifying Bonding in Polypeptides: Students are asked to analyze shaded regions of a given polypeptide to identify types of bonding present (e.g., hydrogen bonds, disulfide bridges, hydrophobic interactions).

• Checkpoint: Functional Groups in Acetyl-CoA: Determine the names and numbers of various functional groups in the Acetyl-CoA molecule (includes amide, hydroxyl, phosphate, sulfhydryl, and amino groups).

• Checkpoint: Phosphatidylcholine Linkages: Identify which lipids in the cell membrane use ester linkages vs. ether linkages.

• Checkpoint: Disulfide Bonds in Antibodies: Determine the count of disulfide bonds and predict the effect of DTT (a reagent that breaks disulfide bonds). If DTT is added to human antibodies, the structural stability of the protein would be lost as the bonds holding the chains together are broken.

• Checkpoint: Duodenum Reactions: When chyme enters the duodenum, the pancreas releases bicarbonate ($HCO_3^-$) and proteases. The resulting reactions are Neutralization (bicarbonate neutralizing stomach acid) and Hydrolysis (proteases breaking down proteins).

• Checkpoint: Molecule Identification: Identify which molecules are NOT carbohydrates. For example, a fatty acid is a hydrocarbon with a carboxyl group, not a carbohydrate. Glycine is an amino acid.

• Checkpoint: Locations of Molecules: Predict where specific polysaccharides are found (e.g., Liver/cow = Glycogen; Celery = Cellulose).

• Checkpoint: Ketogenic Diet: Predict side effects of the Keto diet ($5\%$ carbs, $25\%$ protein, $70\%$ fat). Potential issues include lack of fiber from cellulose, decreased glucose for brain function, and shifts in metabolic processes due to extreme reductions in the recommended carbohydrate range ($45-65\%$).