Physical Biochemistry

What are the energy converting processes in biological systems?

• Organisms use energy obtained from the environment to maintain homeostatic conditions that are far from equilibrium; reaching equilibrium with the environment is equivalent to death.

• Solar energy is converted to chemical energy through the processes of photosynthesis and carbon fixation; chemical energy is converted by cells into useful work (osmotic work, chemical work, and mechanical work).

• The primary energy conversion processes in cells are oxidation–reduction (redox) reactions that involve the transfer of electrons between molecules.

• All biological processes follow the laws of thermodynamics. The first law of thermodynamics states that energy cannot be created or destroyed, only converted from one form to another. The second law of thermodynamics states that entropy (S), or the dispersion of energy, in the universe is always increasing.

• The delta G°’ value for a reaction is a constant and corresponds to the amount of energy needed to go from the biochemical standard condition, where all reactants and products are present initially at 1 M concentrations, to the condition at which all reactants

What are the properties of H2O that make it so critical for life?

● Water has three properties that make it essential for life on Earth: (1) the solid form of water is less dense than the liquid form, which is why ice floats; (2) water is liquid over a wide range of temperatures; and (3) water is an excellent solvent because of its hydrogen-bonding abilities and polar properties.

● The molecular structure of H2O gives rise to a separation of charge, with two partial negative charges on the oxygen atom and one partial positive charge on each of the hydrogens (δ1 and δ1).

● Extensive hydrogen bonding between H2O molecules gives water its unusually high viscosity, boiling point, and melting point compared to those of other molecules of a similar molecular mass.

● Biochemical processes depend on weak noncovalent interactions, which permit structures to exist for short periods of time. The four basic types of weak noncovalent interactions in nature are hydrogen bonds, ionic interactions, van der Waals interactions, and hydrophobic effects.

What are definitions of pH and pKa with regard to the ionization of H2O?

● The ionization of water gives rise to hydrogen ions, H+, which are protons, and hydroxyl ions, OH. Protons do not exist free in solution, but instead combine with H2O to generate hydronium ions, H3O+.

● The pH scale runs from 0 to 14 and is a convenient method to describe H+ concentration in aqueous solutions, using the expression pH = -log[H+]. Solutions with pH<6.5 are considered acidic ([H+]> [OH]), solutions with pH >7.5 are basic ([H+] < [OH]), and neutral solutions have a pH in the range of 6.5–7.5 ([H+] = [OH-]).

● Acids are proton donors, whereas bases are proton acceptors. The ionization reaction of an acid–base conjugate pair can be written as HA <=> H+ + A.

● The acid dissociation constant, Ka, is derived from the ionization reaction of an acid and can be defined as pKa = -log Ka. Acid–base conjugate pairs with low pKa values are able to dissociate protons at low pH, whereas acid–base conjugate pairs with high pKa values dissociate protons at high pH.

● The Henderson–Hasselbalch equation relates pH and pKa and can be used to determine the ratio of A (proton acceptor) to HA (proton donor) at a given pH if the pKa is known.

What are the structures and functions of cell membranes in living cells?

● Separation of aqueous compartments by hydrophobic lipid bilayers permits regulation and specialization of biochemical processes. Selective exchange of nutrients and toxic waste products across cell membranes requires transmembrane proteins.

● The major components of cellular membranes are phospholipids, which are amphipathic molecules that contain both hydrophobic (water-fearing) and hydrophilic (water-loving) chemical groups. Phospholipids form lipid monolayers at the air–water interface or, upon vigorous mixing, generate lipid bilayers, micelles, and liposomes.

● Eukaryotic cells contain three major membrane types: (1) a plasma membrane that surrounds the entire cell; (2) an endomembrane system of cytoplasmic membrane structures; and (3) organelle membranes in mitochondria and chloroplasts that function in energy conversion processes.

● The endomembrane system is a network of lipid bilayers that includes the nuclear envelope, the smooth and rough endoplasmic reticulum, the Golgi apparatus, and vesicles carrying catabolic enzymes (lysosomes and peroxisomes).

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