Foundations of BioChemistry

How does biological reproduction demonstrate emergent properties beyond those of individual biomolecules?

Biological reproduction demonstrates emergent properties through:

1. Programmatic self-perpetuation: The entire collection of molecules carries out a coordinated program, resulting in reproduction of both the physical structures and the program itself.

2. Information transfer with fidelity: Organisms can create billions of identical daughter cells in short periods, each containing thousands of complex molecules arranged in precise patterns.

3. Error correction mechanisms: Living systems maintain near-perfect fidelity despite the inherent tendency toward randomness in chemical systems.

4. Adaptability with heredity: Reproduction includes mechanisms for both fidelity and controlled variation, allowing adaptation to changing environments while maintaining essential structures.

This process transcends the properties of individual biomolecules, as none can independently reproduce themselves with such complexity and precision.

What are the three universal components found in all living cells and how are they functionally distinct?

All living cells contain three fundamental components:

1. Nucleus/Nucleoid

   • Eukaryotes: Membrane-bounded nucleus
   • Bacteria: Non-membrane-bounded nucleoid
   • Function: Houses genetic material (DNA and associated proteins)

2. Plasma Membrane

   • Structure: Tough, flexible lipid bilayer
   • Properties: Selectively permeable to polar substances
   • Components: Contains membrane proteins with three key functions: • Transport of substances • Signal reception • Enzymatic activity

3. Cytoplasm

   • Composition: Aqueous cell contents with suspended particles and organelles
   • Subdivides into: • Cytosol: Concentrated solution containing enzymes, RNA, monomeric subunits, metabolites, and inorganic ions • Organelles: Specialized structures including ribosomes, storage granules, mitochondria, chloroplasts, lysosomes, and endoplasmic reticulum

Note: These components work together in an integrated system to maintain cellular function.

How do lithotrophs and organotrophs differ as subtypes of chemotrophs?

• Lithotrophs:

  • Obtain energy from inorganic chemical compounds
  • Examples include sulfur bacteria (oxidize sulfur compounds) and hydrogen bacteria
  • Still require organic carbon sources (are heterotrophic)
  • Often found in extreme environments where inorganic energy sources are abundant

• Organotrophs:

  • Obtain energy from organic chemical compounds
  • Examples include most prokaryotes and all non-photosynthetic eukaryotes (including humans)
  • Are heterotrophic (require organic carbon sources)
  • Most common metabolic strategy for animals, fungi, and many bacteria

Why do biological systems primarily utilize elements with relatively low atomic numbers?

• The lightest elements form the strongest and most stable covalent bonds

• Most abundant bioelements (H, C, N, O) can form:

  • Hydrogen: one bond
  • Carbon: four bonds
  • Nitrogen: three bonds
  • Oxygen: two bonds

• These elements:

  • Create diverse molecular structures through different bonding arrangements
  • Form stable bonds with appropriate energy requirements for biochemical reactions
  • Enable creation of macromolecules with specific three-dimensional structures
  • Allow for reversible interactions necessary for metabolism

• Higher atomic number elements are typically used in specialized roles:

  • As electron carriers in redox reactions
  • In catalytic centers of enzymes
  • For specific structural functions

How does stereochemistry manifest in molecules like alanine, and why is it critical to biochemical function?

Stereochemistry in biochemical molecules:

• Configuration: The fixed spatial arrangement of atoms that cannot be changed without breaking chemical bonds
• Stereoisomers: Molecules with identical chemical bonds but different 3D arrangements of atoms
• Chirality: In alanine, the alpha carbon is a chiral center with four different groups attached (amino group, carboxyl group, methyl group, and hydrogen)

Stereochemistry is critical to biochemical function because:

1. Stereospecificity: Biomolecular interactions (enzyme-substrate, receptor-ligand) require precise spatial complementarity
2. Biological activity: L-amino acids are used in proteins while D-amino acids generally aren't recognized by human enzymes
3. Metabolic pathways: Enzymes can distinguish between stereoisomers, often acting on only one form
4. Structural integrity: Protein folding depends on the specific stereochemistry of constituent amino acids

Example: If alanine's stereochemistry were reversed from L to D form, it could not be incorporated into proteins by ribosomes, demonstrating how molecular recognition depends on precise 3D arrangement.

Describe the cis-trans isomerism found in double bonds, and explain why it is biologically significant using a specific example.

Cis-Trans Isomerism:

• Occurs due to restricted rotation around double bonds
• Substituents can be arranged either:
  • Cis: Groups on the same side of the double bond
  • Trans: Groups on opposite sides of the double bond
• Conversions between cis and trans forms require breaking the π bond

Biological Significance - Example of Retinal:

• 11-cis-retinal is the light-absorbing pigment in the vertebrate retina
• When light strikes 11-cis-retinal, it absorbs energy (~250 kJ/mol)
• This energy converts 11-cis-retinal to all-trans-retinal
• This configurational change triggers a cascade of electrical signals
• Results in nerve impulse transmission to the brain, enabling vision
• The cis-trans conversion is the first crucial step in the visual process

Other examples include fatty acids (cis configuration creates kinks) and membrane lipids (affects membrane fluidity).

How do you determine R vs S configuration for a chiral carbon when using the Cahn-Ingold-Prelog priority rules?

To determine R vs S configuration:

1. Assign priorities (1-4) to the four substituents attached to the chiral carbon based on atomic number (higher = higher priority)
2. Orient the molecule with the lowest priority group (4) pointing away from you
3. Trace a path from highest to lowest priority groups (1→2→3)
4. If the path is clockwise, the configuration is R (Latin: rectus, "right")
5. If the path is counterclockwise, the configuration is S (Latin: sinister, "left")

Example: In a compound where priorities decrease clockwise (1→2→3→4) with group 4 pointing away, the configuration is R.

Note: The R/S system provides absolute stereochemical designation regardless of a compound's name.

What is the energy difference between the staggered and eclipsed conformations of ethane, and why does this energy barrier exist?

• The energy difference between staggered and eclipsed conformations of ethane is 12.1 kJ/mol
• This energy barrier exists due to:
  • Electron-electron repulsion between the C-H bonds as they pass by each other
  • Torsional strain when the electron clouds of adjacent bonds overlap
• Staggered conformations (at 60°, 180°, 300°) represent energy minima (most stable)
• Eclipsed conformations (at 0°, 120°, 240°) represent energy maxima (least stable)
• This energy barrier is sufficiently small to allow rapid interconversion at room temperature (millions of times per second)

What are the three primary inputs to cellular metabolism, their relationship to the two major types of biochemical pathways, and how are they ultimately transformed?

The three primary inputs to cellular metabolism are:

1. Stored nutrients
2. Ingested foods
3. Solar photons (for photosynthetic organisms)

Their transformation through metabolic pathways:

• These inputs enter catabolic (exergonic) reaction pathways
• Catabolic processes break them down, releasing energy that is captured as ATP
• The breakdown produces simple molecules (CO₂, NH₃, H₂O) as end products
• These simple molecules serve as precursors that can be incorporated into anabolic pathways
• Anabolic (endergonic) pathways use ATP energy to transform these precursors into:
  • Complex biomolecules (proteins, nucleic acids, polysaccharides, lipids)
  • Cellular work (mechanical, osmotic, other)

This transformation represents a continuous cycle where matter flows between complex and simple forms, while energy flows from energy-rich sources through ATP to energy-requiring processes.

Example: Glucose from food is catabolized via glycolysis and the TCA cycle to CO₂ and H₂O, generating ATP, which powers the anabolic synthesis of glycogen from glucose precursors.

How do point mutations accumulate over time to drive speciation events in the evolutionary process?

Point mutations accumulate through these mechanisms:

• Sequential nucleotide substitutions occur in DNA over generations
• Mutations branch into separate lineages when populations separate
• Each lineage continues to accumulate unique mutations independently
• When two lineages diverge significantly in their genetic makeup that they can no longer interbreed, a new species forms

Example: A gene with sequence TGAGCTA might undergo a G→A mutation, then accumulate additional distinct mutations in separate populations, eventually yielding organisms with incompatible genetic sequences that represent different species.