biochem unit 1

Foundations of Biochemistry

• Biochemistry studies the structure, organization, and functions of organisms at a molecular level. The properties of living organisms arise from thousands of different molecules.
• Structural Biochemistry covers the study of the structures of biological molecules.
• Metabolic Biochemistry looks at energy extraction, transformation, and use from the environment.
• Molecular Biology studies self-replication.
• Diverse living organisms share collective chemical traits through gradual development.
• Foundational biochemical principles discovered in E. coli are applicable to elephants as well, explaining "Biochemical unity".
• Cells serve as the structural and functional units in all living organisms.
• An E. coli consists of 70% water, 15% proteins, 6% RNA, 3% polysaccharides, 2% lipids, 2% monomeric subunits and intermediates, and 1% inorganic ions.
• The structural hierarchy in molecular organization of cells goes from monomeric units, to macromolecules, to supramolecular complexes, to the cell and its organelles

Chemical Foundations: Bioelements

• Primary bioelements consist of H, O, C, and N.
• Carbon constitutes 61.7% of the dry weight in bioelements

Carbon Bonding

• Biomolecules are compounds of carbon with a variety of functional groups and it can form covalent single, double, and triple bonds.
• Carbon atoms exhibit a tetrahedral arrangement in their four single bonds but have free rotation around each single bond.
• Double bonds have only a limited rotation around their axis.

Common Functional Groups

• Methyl: R-CH
• Ethyl: R-C₂H
• Phenyl: R-C₆H₅
• Carbonyl (aldehyde): R-CHO
• Carbonyl (ketone): R-COR
• Carboxylate: R-COO-
• Hydroxyl (alcohol): R-OH
• Enol: R-C=C-OH
• Ether: R-O-R
• Ester: R-COO-R
• Amine: R-NH₂
• Amido: R-C-NH₂
• Sulfhydryl: R-SH
• Disulfide: R-S-S-R
• Thioester: R-C-S-R
• Phosphoryl: R-O-PO₃H₂
• Phosphoanhydride: R-O-P-O-P-O-R

Hydrocarbons

• Alkanes, also known as saturated hydrocarbons, lack double bonds.
• Alkenes possess one double bond and are termed unsaturated.
• Alkynes have a triple bond and are also unsaturated.

Nomenclature

• Methane has one carbon
• Ethane has two carbons
• Propane has 3 carbons
• Butane has 4 carbons
• Pentane has 5 carbons
• Hexane has 6 carbons
• Heptane has 7 carbons
• Octane has 8 carbons
• Nonane has 9 carbons
• Decane has 10 carbons.
• Alcohols are named with the suffix -ol to the parent alkane: Methanol, ethanol, propanol.

Functional groups in organic molecules

Nomenclature

• Aldehydes suffix is -al
• Ketones suffix is -one
• Carboxylic acid suffix is -oic
• If deprotonated, suffix is -ate.

Oxidation and reduction

• Oxidation is the loss of electrons
• Reduction is the gain of electrons.
• Oxidation represents the gain of oxygen and reduction is the loss of oxygen.
• Ether bond: Two organic radicals are linked through an oxygen atom.
• Ester bond: Formed when a carboxylic acid group reacts with an alcohol
• Amide bond: Formed when a carboxylic acid group reacts with an amine
• Sulfhydryl: S bound to H is a Sulfhydryl or thiol group.
• Two thiol groups can react and be bound through a Disulfide bond.
• Carboxylic group and a thiol group can react forming a thioester bond.

3D Structure: Configuration & Conformation

• Configuration: A fixed spatial arrangement of atoms.
• Stereoisomers: Molecules with identical chemical bonds and formulas.
• Interconversion between stereoisomers necessitates breaking covalent bonds.

Configurations of Geometric Isomers

• Geometric isomers, also known as cis-trans isomers, differ in substituent arrangement around a double bond.

Chiral and Achiral Molecules

• Chiral centers refer to asymmetric carbons.
• A molecule can have 2^n stereoisomers, where n is the number of chiral carbons.
• Enantiomers: Stereoisomers that are mirror images.
• Diastereomers are stereoisomers that are not mirror images of one another.
• Enantiomers have identical chemical reactivities, differing only in optical activity.
• A racemic mixture, containing equal amounts of two enantiomers, shows no optical rotation.
• Interconversion between stereoisomers requires breaking covalent bonds.
• Typically, only one enantiomer is present in nature, like D-monosaccharides and L-amino acids.
• Stereospecificity denotes the ability to differentiate between stereoisomers.
• Conformation is the spatial arrangement of substituent groups that freely assume different positions in space

Water and Hydrogen Bonding

• Water has a higher melting point, boiling point, and heat of vaporization than most other common solvents.
• Hydrogen bond refers to the electrostatic attraction between the oxygen of one water molecule and the hydrogen of another.
• Water consists of 2 electric dipoles.
• In liquid, each H₂O makes hydrogen bonds with 3.4 other water molecules on average.
• A hydrogen bond in liquid is 23 kJ/mol and covalent bond costs 470 kJ/mol
• In ice, each H₂O molecule forms 4 hydrogen bonds
• Hydrogen bonds are not unique to water but occur between a hydrogen-bond donor and acceptor

The Nature of Hydrogen Bonds

• Some biologically important hydrogen bonds exist between the hydroxyl group of an alcohol and water, between the carbonyl group of a ketone and water, between peptide groups in polypeptides and or between complementary bases of DNA
• Stronger hydrogen bonds are directional.
• Noncovalent interactions are weaker than covalent bonds, and they are continually forming and breaking

Properties of Water as a Solvent

• Hydrophilic substances dissolve in water.
• Hydrophobic molecules are nonpolar and do not dissolve in water.
• Amphipathic molecules have both polar and nonpolar regions.
• Water dissolves salts and charged biomolecules by screening electrostatic interactions

Behavior of Gases in Water Based on Polarity

• Nonpolar gases are poorly soluble in water, reducing entropy.
• Polar, hydrophilic regions interact positively with water
• Nonpolar, hydrophobic regions tend to avoid contact with water and cluster together.

Hydrophobic Effect

• The hydrophobic effect is when nonpolar compounds cluster together and polar regions maximize interactions with each other and the solvent.
• Micelles have thermodynamically stable structures of amphipathic compounds in water.

Structures formed by phospholipids

• Phospholipids spontaneously assemble via multiple noncovalent interactions to form structures such as micelles, liposomes, and bilayer sheets in aqueous solutions.
• Solutes alter physical properties of the solvent, water: Vapor pressure, boiling and melting points, and osmotic pressure.
• Cells generally exhibit greater osmolarity than their environment.
• Osmolarity depends on the dissolved particle concentration, not their mass.

Ionization of Water, pH, & Buffering Systems

• Pure water is slightly ionized into H+ and OH- ions.
• The ion product of water (Kw) is constant.
• The pH scale indicates H+ and OH⁻ concentrations and the pH and pOH always add up to 14.
• An acid donates a proton, and a base accepts a proton.
• Conjugate acid-base pairs consist of a proton donor/proton acceptor.
• Acids & Bases: Weak acids/bases are not fully ionized when dissolved in water.
• Ionization Constants: The tendency of an acid (HA) to lose a proton and form its conjugate base (A-) is quantified by the equilibrium constant (Keq), expressed as Ka
• pKa is analogous to pH, and a smaller pKa indicates a stronger acid.
• The titration curve of acetic acid plateaus at the midpoint where [CH₃COOH] = [CH₃COO⁻].
• A weak acid and its conjugate anion act as a buffer.
• Buffers: Mixtures of Weak Acids and conjugate bases that resist pH changes upon addition of acid or base.
• The Henderson-Hasselbalch equation relates pH to pKa and buffer concentration, describing titration curve shapes for any weak acid.
• Weak acids or bases buffer cells and tissues against pH changes.
• The phosphate buffer system, found in the cytoplasm, uses H₂PO₄⁻ and HPO₄²⁻ to maintain a pH of 5.9-7.9.
• The Bicarbonate Buffer System controls the equilibrium to keep the blood pH nearly constant and hyperventilation raises blood pH