Unit 1 Biochemistry Study Notes

Overview of Biochemistry

• Definition of Biochemistry:

  • Biochemistry is the quantitative and structural study of the chemical substances, pathways, and molecular transformations occurring within living organisms.

  • It serves as the fundamental bridge between physical chemistry, organic chemistry, molecular genetics, and cellular biology.

• Primary Core Objectives:

  • Elucidate how inanimate chemical constituents assemble and interact to execute life processes such as growth, metabolism, response to stimuli, and reproduction.

  • Characterize the three-dimensional structures, chemical reactivities, and non-covalent interactions of biological macromolecules.

  • Map metabolic pathways to understand how energy is captured, transduced, stored, and utilized by cellular systems.

Chemical Foundations of Life

• Essential Biological Elements:

  • Living systems are predominantly constructed from six bulk chemical elements: Carbon ($\text{C}$), Hydrogen ($\text{H}$), Nitrogen ($\text{N}$), Oxygen ($\text{O}$), Phosphorus ($\text{P}$), and Sulfur ($\text{S}$).

  • Carbon ($\text{C}$) forms the structural backbone of organic molecules due to its tetravalent nature, enabling the formation of up to four single covalent bonds, as well as stable double and triple bonds.

• Key Functional Groups in Biomolecules:

  • Hydroxyl Group ($-\text{OH}$): Promotes solubility in aqueous environments by forming hydrogen bonds; characteristic of alcohols and carbohydrates.

  • Carbonyl Group ($-\text{C=O}$): Polar group found in aldehydes and ketones; serves as an electrophilic center during metabolic carbon-carbon bond formation and cleavage.

  • Carboxyl Group ($-\text{COOH}$): Functions as an acid by donating a proton ($\text{H}^+$) to form a negatively charged carboxylate ion ($-\text{COO}^-$); found in amino acids and fatty acids.

  • Amino Group ($-\text{NH}_2$): Functions as a base by accepting a proton ($\text{H}^+$) to form a positively charged ammonium ion ($-\text{NH}_3^+$); essential component of amino acids and nitrogenous bases.

  • Phosphate Group ($-\text{PO}_4^{2-}$): Imparts significant negative charge and high transfer potential; essential component of Adenosine Triphosphate ($\text{ATP}$), nucleic acids, and phospholipids.

  • Sulfhydryl Group ($-\text{SH}$): Present in the amino acid cysteine; undergoes oxidation to form covalent disulfide linkages ($-\text{S-S}-$) critical for protein structural stabilization.

Water and Aqueous Chemistry

• Physico-Chemical Properties of Water:

  • Water ($\text{H}_2\text{O}$) constitutes approximately $70\%$ to $90\%$ of total cellular mass and acts as the universal biological solvent.

  • Structure: Features a bent geometry with a bond angle of approximately $104.5^\circ$, creating a permanent electrical dipole moment due to oxygen's high electronegativity.

  • Hydrogen Bonding: Each water molecule can participate in up to four directional hydrogen bonds, producing high specific heat capacity, high heat of vaporization, and cohesive surface tension.

• Water Ionization and $\text{pH}$ Dynamics:

  • Water undergoes auto-ionization according to the equilibrium:     $\text{H}_2\text{O}_{(l)} \rightleftharpoons \text{H}^+_{(aq)} + \text{OH}^-_{(aq)}$

  • Ion product constant of water ($K_w$) at $25^\circ\text{C}$:     $K_w = [\text{H}^+][\text{OH}^-] = 1.0 \times 10^{-14}\,\text{M}^2$

  • Definition of $\text{pH}$:     $\text{pH} = -\log_{10}([\text{H}^+])$

  • The Henderson-Hasselbalch Equation for biological buffers:     $\text{pH} = \text{p}K_a + \log_{10}\left(\frac{[\text{A}^-]}{[\text{HA}]}\right)$

Macromolecular Classes and Architecture

• Four Major Classes of Biological Macromolecules:

  • Proteins: Monomeric units are amino acids joined via covalent peptide bonds ($-\text{CO-NH}-$). Functions include enzymatic catalysis, structural architecture, cellular transport, and signal transduction.

  • Nucleic Acids: Monomeric units are nucleotides (comprising a nitrogenous base, a pentose sugar, and a phosphate group) linked by phosphodiester bonds. Responsibilities include genetic storage ($\text{DNA}$) and gene expression/catalysis ($\text{RNA}$).

  • Carbohydrates: Monomeric units are monosaccharides with general chemical formula $\text{C}_n(\text{H}_2\text{O})_n$ joined by glycosidic bonds. Functions include structural integrity (e.g., cellulose) and energy storage (e.g., glycogen and starch).

  • Lipids: Non-polymeric hydrophobic or amphipathic molecules including triacylglycerols, phospholipids, and steroids. Functions include membrane bilayer composition, biological signaling, and dense energy storage.

Bioenergetics and Thermodynamics

• Fundamental Thermodynamic Laws in Cells:

  • First Law of Thermodynamics: Energy cannot be created or destroyed, only transformed from one form into another.

  • Second Law of Thermodynamics: Every natural process spontaneously increases the total entropy of the universe ($\Delta S_{\text{univ}} > 0$).

• Gibbs Free Energy ($\Delta G$):

  • Governs reaction spontaneity and directionality:     $\Delta G = \Delta H - T\Delta S$

  • Exergonic Reactions: $\Delta G < 0$ (spontaneous process that releases energy available to do biological work).

  • Endergonic Reactions: $\Delta G > 0$ (non-spontaneous process requiring energy input).

  • Relationship to Equilibrium Constant ($K_{\text{eq}}^{\prime}$) under standard biochemical conditions ($T = 298.15\,\text{K}$, $P = 1\,\text{atm}$, $\text{pH} = 7.0$, $[\text{H}_2\text{O}] = 55.5\,\text{M}$):     $\Delta G^{\circ \prime} = -R T \ln(K_{\text{eq}}^{\prime})$     where $R = 8.314\,\text{J}\,\text{mol}^{-1}\,\text{K}^{-1}$.