Principles of Biological Structure Notes

Principles of Biological Structure

Readings

• No specific assignment in Stryer for this lecture.
• Two PDF files posted:
  • Chapters 4 and 5 of Mark’s Basic Medical Biochemistry (Smith, C. et al., 2005).
  • Chapter 4: Basic discussion of water, acids, bases, and buffers in biological systems (review).
  • Chapter 5: Brief overview of essential organic chemistry.

Introduction to Chemistry of Human Cells

• Introduction to the chemistry of human cells.
• Types of molecules providing structural basis for cellular function.
• Basic properties of water as a solvent, and acid-base changes in an aqueous environment.

Abundance of Molecules and Ions

• Water is the most abundant molecule inside a human cell.
• Most abundant intracellular small cation: potassium.
• Intracellular anions: chloride and phosphate (H2PO4^-).
• Cells are bathed in an aqueous environment in vivo.
• Cell culture maintains physiological environment by providing extracellular ions:
  • Sodium, calcium, chloride, and bicarbonate.

Carbon-Based Life and Organic Molecules

• Life on earth is carbon-based; all organic molecules contain carbon.
• Sugars (e.g., glucose) and fatty acids (e.g., myristate, palmitate) contain carbon, hydrogen, and oxygen.
• Amino acids also contain nitrogen.
• Nucleotides contain sugars, nitrogenous bases, and phosphate.
• Small organic molecules are held together by covalent bonds (sharing electrons).
• Covalent bonds are strong and broken only during specific chemical reactions.

Macromolecules and Subunits

• Macromolecules are assembled using small organic molecules as building blocks/subunits.
• Proteins: covalently-bound chains of amino acids.
• Polysaccharides: assembled from sugar units.
• Nucleic acids (DNA and RNA): chains of nucleotides.
• Physical and functional characteristics are determined by specific subunits.
• Amino acid sequence determines protein properties.

Hydrolysis

• Hydrolysis is a common process for breaking down macromolecules into building blocks.
• Digestive enzymes catalyze hydrolysis of macromolecules.

Molecular Shapes

• Molecules have different shapes.
• DNA is usually a double helix.
• Protein molecules vary greatly in shape/size.
• Space-filling models: atoms as colored spheres.
• Ball-and-stick models: depict bonds between atoms.
• Color codes: White=H, red=O, gray=C, yellow=P, blue=N, and green=S.

Covalent vs. Non-Covalent Bonds/Forces

• Covalent bonds hold together individual organic molecules.
• Non-covalent bonds/forces affect interactions between molecules and maintain macromolecules in specific 3D structures.
• DNA molecule example: nucleotide bases are bound covalently into long chains.
• Binding of two long strands to each other and their joint formation of a double helix is mediation by hydrogen bonds, which are one type of non-covalent interaction.

Electrostatic Interactions

• Occur between charged atoms or molecules.
• Opposite charges attract; similar charges repel.
• Sodium chloride (table salt): inorganic molecule held together by an ionic bond.
• In aqueous solution, ionic bonds are weakened; ions are separated and surrounded by water molecules.
• Electrostatic interactions also occur between charged groups on larger molecules (same macromolecule or between two macromolecules).
• Example: attraction between DNA (net negative charge) and positively charged proteins (e.g., histones).

Hydrogen Bonds Between Water Molecules

• In each water (H_2O) molecule, the two H atoms are linked to the O atom by covalent bonds.
• Covalent bonds are highly polar because O has a stronger attraction for shared electrons.
• Symbols \delta+ and \delta- indicate partial charge differences.
• Hydrogen bonds form between a positively charged H from one water molecule and a negatively charged O from a second water molecule.
• Water is liquid because of the strength of hydrogen bonds.
• Hydrogen bonds: a special type of polar interaction where an electropositive hydrogen atom is partially shared by two electronegative atoms.
• Other molecules (e.g., alcohols) containing polar bonds can form hydrogen bonds with water and dissolve readily.

Water as a Solvent

• Water is good at dissolving polar molecules (e.g., inorganic salts).
• Water molecules surround each ion: negative O portions attracted to cations (positive); positive H portions attracted to anions (negative).

Hydrogen Bonds in Biological Macromolecules

• Positively charged hydrogen atoms bound in hydroxyl (–OH) or amino (–NH) bonds interact with negatively charged oxygen or nitrogen atoms.
• Hydrogen bonds between nucleotide bases provide structural basis for DNA double helix pairing.
• Important in stabilizing the secondary structure of proteins.

Water's Interaction with Other Molecules

• Water can form hydrogen bonds with other molecules.
• Example: hydrogen bond between carboxyl group (-C=O) and amide group (-NH) within proteins.
• Water molecules break hydrogen bonds and replace them with new bonds to the water molecule, changing macromolecule conformation.

Hydrophobic Effect

• Unlike -C=O, -N-H, and H-O-H bonds, bonds between carbon and hydrogen atoms are non-polar and do not associate with water molecules.
• Non-polar molecules (and portions of molecules) are pushed out of the hydrogen-bonded water network (hydrophobic).
• This causes non-polar molecules to be pushed together.
• Fats (triacylglycerols/triglycerides) are completely non-polar/hydrophobic.
• When mixed with water, they separate out (oil and vinegar example).

Amphipathic Molecules

• Molecules with both hydrophilic and hydrophobic portions aggregate in aqueous solutions.
• They form structures where non-polar portions are internal and polar portions are associated with the aqueous environment.
• Cellular membranes are formed by phospholipids (polar head group and two long, non-polar, hydrocarbon chains).
• Membrane: sandwich with two layers of phospholipids; non-polar chains form the inner part; polar head groups face outwards.

Biological Structure and Water Interactions

• Biological structures fold to minimize unfavorable interactions with water.
• Protein molecule example: polar and non-polar side chains.
• In native protein, non-polar chains are folded into the core; polar groups are on the surface, hydrogen bonding with water or other polar groups.
• When native folding is disrupted, the protein is denatured and loses function.

Van der Waals Attractions

• Occur because electrons around nonpolar atoms produce flickering polarization and transiently induce polarization in nearby atoms.
• Individually weak, but aggregate effect is significant when surfaces are in close contact.
• van der Waals forces attract atoms to each other until they get too close and are repelled.

Ionization of Water

• Positively charged hydrogen atoms move from one water molecule to another.
• Produces hydronium ions (H_3O^+) and hydroxyl ions (OH^-).
• Process is spontaneous and reversible.
• Ionization is in equilibrium: [H^+][OH^-] = 10^{-14}.
• Square brackets denote concentration.
• Hydronium ion (H_30^+) often written as H^+ for simplicity.

pH Scale

• When water ionizes, equal numbers of hydronium and hydroxyl ions are formed.
• Concentration of each is 10^{-7} M.
• pH scale uses the negative logarithm of the hydronium or hydrogen ion concentration.
• Pure water has a pH of 7.
• Acidic substance addition increases hydrogen ion concentration; pH values less than 7.0.
• Basic/alkaline solutions have [OH^-] > [H_3O^+]; pH values greater than 7.0; hydrogen ion concentrations less than those of acidic solutions.
• Higher pH means lower hydrogen ion concentration.

pH of Biological Fluids

• Cytoplasm (cytosol) is essentially neutral.
• Lysosomes are acid (low pH) compartments for breaking down macromolecules.
• Stomach acid provides a low pH environment for digestion.

Strong vs. Weak Acids and Bases

• Strong acids and bases are completely dissociated/ionized in aqueous solutions (e.g., HCl, H2SO4, NaOH).
• Biologically important acids/bases are “weak” and only partially ionized.
• Acetic acid is in equilibrium with acetate ion (conjugate base).
• Acid (HA) + H2O \rightleftharpoons H3O^+ + Conjugate base (A^-)
• CH3COOH + H2O \rightleftharpoons H3O^+ + CH3COO^-
• Ammonia is a weak base in equilibrium with ammonium ion (conjugate acid).

Buffering

• Weak acids and bases can accept or donate hydrogen ions (H^+), aka protons.
• They can buffer solutions and maintain a relatively constant pH.

Henderson-Hasselbalch Equation

• Expresses the quantitative equilibrium between an acid and its conjugate base.
• Usually expressed in negative log form using pKa rather than Ka.
• When pH = pK_a, concentrations of acid (HA) and conjugate base (A^-) are equal.
• Under these circumstances, the acid-conjugate base pair has the greatest capacity to accept or donate hydrogen ions, and is most effective as a buffer.

Biological Buffers

• The carbon dioxide – bicarbonate acid-base couple is an effective buffer of blood pH.
• Proteins in blood also provide significant buffering capability.
• Some culture media contain organic buffers (e.g., HEPES) to enhance buffering capacity and decrease dependence on carbon dioxide environment.
• Inorganic phosphate is a major intracellular buffer.
• Cell culture media cannot use phosphate buffers because they mimic the higher extracellular concentration of calcium.
• Calcium ions are necessary for cell adhesion and other functions.
• In the presence of millimolar concentrations of calcium, the phosphate ions form insoluble calcium phosphate complexes.