BCEM 393 Chapter Notes - Chapter 2: Hydrogen Bond, Chemical Polarity, Protein Folding
16 May 2018
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Water, Weak Bonds, and the Generation of Order Out of
Chaos
- The four key biomolecules of life — proteins, lipids, carbohydrates, and nucleic acids — are
stable mostly because they are constructed with strong covalent bonds1
- The structure and function of the cell itself are stabilized by weak interactions that have only a
fraction of the strength of covalent bonds
- How is such stabilization possible? It is possible because many weak bonds allow transient
interactions. A substrate can bind to an enzyme, and the product can leave the enzyme. A
hormone can bind to its receptor then dissociate from the receptor after the signal has been
received. Weak bonds allow for dynamic interactions and permit energy and information to
move about the cell and organism
- Transient chemical interactions form the basis of biochemistry and life itself
- Water, as a solvent, has the capability of affecting weak bonds, making some weaker and
powering the formation of others
- Hydrophobic molecules such as fats, cannot interact with water at all. Yet, this chemical
antipathy is put to use
- The formation of membranes and intricate 3D structures of biomolecules (eg. proteins) are
powered by an energetic solution to the chemical opposition between water and hydrophobic
molecules
- The typical length of noncovalent bonds is 4 angstroms (or 0.4 nm)
2.1 THERMAL MOTIONS POWER BIOLOGICAL INTERACTIONS
- English botanist, Robert Brown observed under a microscope, pollen granules suspended in
water. He noted that the granules darted randomly about. This movement, is now referred to
as Brownian motion, and is a vital energy source for life
- The movement of the particles that Brown observed is due to the random fluctuation of the
energy content of the environment — thermal noise. The water and gas molecules of the
environment are bouncing randomly about at a rate determined only by temperature
- Brownian motion is responsible for initiating many biochemical interactions
- In the cell, water is the most common medium for thermal noise of Brownian motion
- Water is the lubricant that facilitates the flow of energy and information transformations
through Brownian motion. Enzymes find their substrates; fuels can be progressively modified
to yield energy and signal molecules can diffuse from their sites of origin to their sites of effect
2.2 BIOCHEMICAL INTERACTIONS TAKE PLACE IN AN AQUEOUS SOLUTION
- Water renders molecules mobile and permits Brownian-motion-powered interactions between
molecules
- Important properties of water are due to the fat that oxygen is an electronegative atom. That
is, although the bonds joining the hydrogen atoms to the oxygen atom are covalent, the
electrons of the bond spend more time near the oxygen atom
1 Covalent bonds are ones in which electrons are shared by the participating atoms
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- Because the charge distribution is a water molecule is not equal — oxygen atom is slightly
negatively charged and hydrogen atoms are slightly positively charged — the molecule is
said to be polar
- The partially positively charged hydrogen atoms of one molecule can interact with the partially
negatively charged oxygen atoms of another molecule — this interaction is a hydrogen bond
- Hydrogen bonds are not unique to water molecules and are common weak bonds in
biomolecules
- Liquid water has a partly ordered structure in which hydrogen bonded clusters of molecules
are continually forming and breaking apart, with each molecule of water hydrogen bonding to
approximately 3.4 neighbours. Hence, water is cohesive
- The polarity of water and its ability to form hydrogen bonds renders it a solvent for any
charged or polar molecule
2.3 WEAK INTERACTIONS ARE IMPORTANT BIOCHEMICAL PROPERTIES
- Weak, noncovalent forces play roles in the faithful replication of DNA, the folding of proteins
into elaborate 3D forms, the specific recognition of reactants by enzymes, and the detection
of molecular signals
- The 3 fundamental non covalent bonds are (1) ionic bonds, or electrostatic interactions; (2)
hydrogen bonds; and (3) van der Waals interactions. They differ in geometry, strength, and
specificity. Moreover, these bonds are greatly affected in different ways by the presence of
water
- Electrostatic Interactions Are Between Electrical Charges
- Electrostatic interactions are those between distinct electrical charges on atoms
- These interactions usually take place between atoms bearing a completely negative and
completely positive charge
- Coulomb’s law is used to determine the energy of an electrostatic interaction between two
ions
- The electrostatic interaction between two atoms bearing single opposite charges varies
inversely with the square of the distance separating them as well as with the nature of the
intervening medium
- These interactions are strongest in a vacuum, where the dielectric constant2 is 1
- The distance for the maximal bond strength is about 3 angstroms
- Due to its polar characteristics, water weakens electrostatic interactions. Conversely,
electrostatic interactions are maximized in an uncharged environment
- Water can dissolve any molecule that has sufficient partial or complete charges on the
molecule to interact with water. This ability to dissolve is very important
- Brownian motion powers collisions among the dissolved molecules, and many of the
collisions result in fleeting but productive interactions
- Hydrogen Bonds Form Between and Electronegative Atom and Hydrogen
- The unequal distribution of charges that permit hydrogen-bond formation can arise
whenever hydrogen is covalently bound to an electronegative atom
- Hydrogen bonds are much weaker and longer than covalent bonds
2 Constant which accounts for the effects of the intervening medium
find more resources at oneclass.com
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Document Summary
Water, weak bonds, and the generation of order out of. The four key biomolecules of life proteins, lipids, carbohydrates, and nucleic acids are stable mostly because they are constructed with strong covalent bonds1. The structure and function of the cell itself are stabilized by weak interactions that have only a fraction of the strength of covalent bonds. It is possible because many weak bonds allow transient interactions. A substrate can bind to an enzyme, and the product can leave the enzyme. A hormone can bind to its receptor then dissociate from the receptor after the signal has been received. Weak bonds allow for dynamic interactions and permit energy and information to move about the cell and organism. Transient chemical interactions form the basis of biochemistry and life itself. Water, as a solvent, has the capability of affecting weak bonds, making some weaker and powering the formation of others. Hydrophobic molecules such as fats, cannot interact with water at all.
