Fundamental Macromolecules and Concepts - Biochemistry

Biomolecules contain carbon as their key element, and they mostly contain nonmetallic elements. For example, the human body is about 65% oxygen, 20% carbon, 10% hydrogen, and 3% nitrogen - the remaining major elements that make up the human body are calcium, phosphorous, magnesium, sulfur, potassium, sodium, chlorine, and other trace elements like iron and copper. Ionic bonds are rare in biomolecules, as most biomolecules are bound via covalent bonds. Also, to create a specific biomolecule, many of the bonds must be in specific orientations-specific stereoisomers are important, especially with enzymes.

In , each bond is polar, as oxygen is much more electronegative than carbon. However, these dipole moments are equal in charge and this molecule is linear with carbon in the middle, so the entire molecule is nonpolar.

In water, oxygen is more electronegative than hydrogen; thus, electrons are pulled toward the oxygen atoms more than towards hydrogen atoms. This gives oxygen a partial negative charge and hydrogen a partial positive charge. The entire molecule is polar since water's molecular geometry is bent.

Methane includes a carbon with a hydrogen attached to each of its four bonds. Electrons are distributed relatively equally across each bond since the electronegativities of hydrogen and carbon are comparable, and the entire molecule is tetrahedral. Thus, neither the individual bonds nor the entire molecule are polar.

In , nitrogen is left with a lone pair of electrons after it bonds with three hydrogen atoms. Because of this lone pair, the molecular geometry is trigonal pyramidal and the entire molecule is polar with the nitrogen atom being slightly negative (high electronegativity) and the hydrogen atoms being slightly positive.

While the peptide bond in a polypeptide chain is locked and unable to rotate, the amino nitrogen-alpha carbon bond can rotate. Additionally, the alpha carbon-carboxyl carbon can rotate as well.

However, like in many other molecules, the cis conformation is energetically unfavorable due to steric hindrance. This steric hindrance occurs when the side chains of two residues are right next to each other within the polypeptide. This is unfavorable, and the trans conformation is therefore preferred.

An amphiphile is a molecule that contains both polar and nonpolar groups. Two tailed amphiphiles form bilayer vesicles, whereas one tailed amphiphiles in high concentrations form micelles.

Free floating is surrounded by water molecules which stabilize its positive charge. However, once these water molecules are shed due to movement through the potassium channel, something else must stabilize the positively charged ion. This is accomplished via an amino acid stretch with negatively charged residues. The amino acid stretch responsible for the stabilization is Thr-Val-Gly-Tyr-Gly.

Enantiomers have the same chemical bonds in different configurations that are non-superimposable mirror images of each other. They differ in their configuration at all chiral centers.

van der Walls interactions are weak attractive interactions that occur between any two atoms in close enough proximity for their electron clouds to interact.

Ammonia, NH3, will be the most soluble in water simply because polar substances dissolve in polar solvents. This follows the principle that "like dissolves like." Ammonia and water are both polar due to the presence of lone pairs of electrons combined with a lack of geometrical symmetry (water is bent and ammonia is trigonal pyramidal).

Carbon dioxide and nitrogen are linear, negating any potential polarity. Methane is tetrahedral, and lacks any polarized bonds. Carbon trioxide is tigonal planar, negating polar interactions due to symmetry.

Electrolytes readily dissolve and ionize in water. The term "electrolyte" refers to a molecule that will produce ions in solution, and can be synonymous with "salt" in certain contexts, as well as acidic and basic compounds.

When dealing with solutions, it is helpful to remember that solubility depends on polarity and that "like dissolves like." Polar solutes (ionic salts) dissolve well in polar solvents (water); the same goes for nonpolar solutes and solvents.

Hydrophobic interactions are driven by the increase in entropy (not enthalpy) that water molecules achieve by excluding a nonpolar solute. In the hydrophobic effect, water initially forms cage-like structures called clathrates around the nonpolar solute, which is entropically unfavorable. However, entropy is regained when the water molecules exclude the solute and interact with each other in a disordered manner.

Cohesion is defined as attraction between the same type of molecule. Water attracts other water molecules because it is polar and has partial charges. This attraction means that water has strong intermolecular forces even at room temperature and more thermal energy is required to vaporize it. Adhesion involves the attraction of a substance with a container or surface.

The electrons around water are not symmetrically positioned; rather, they are distributed toward the oxygen atom, which is highly electronegative. Hence, water's two hydrogen atoms have a net positive charge. Nonetheless, the total charge on water is neutral, with electropositive and electronegative regions, rendering it polar. This polarity allows water molecules to hydrogen-bond with each other.

The important point here is that biological polymers are basically all condensation polymers. In the case of proteins, polysaccharides (carbohydrates), and nucleic acids (like DNA and RNA), synthesis occurs via a loss of a water molecule. Non-biological molecules can also be formed via condensation, such as nylon, which also often has water as its by-product. Polystyrene is an addition polymer; upon formation, monomers do not lose any molecules. Bonds are only rearranged. Although it may seem counterintuitive, the fact is that in nature, polymers do not typically form this way.

Hypotonic solutions have a low solute concentration, and hypertonic solutions have high solute concentration. By the rules of osmosis, water moves in and out of cells along a concentration gradient, because membranes are only slightly permeable to water. Hence in a hypotonic solution, water will enter cells, causing them to swell and possibly break, while in a hypertonic solution, cells will lose water and shrink. Aquaporins are water channels that encourage osmosis, rather than hinder it.

A molecule of water is polar with the two hydrogen atoms being partially posistive and the oxygen atom being partially negative. The two hydrogens can therefore each act as a donor which accounts for two net hyrdogen bonds made by water. The oxygen contains a partial negative charge and two lone electrons pairs can each act as acceptors and from two more hydrogen bonds, making a total of 4.

Osmosis states that a solvent will move from a region of high concentration to a region of relatively lower concentration. In this case the solvent is water. The concentration of water inside the dialysis bag is higher than the concentration of water in the beaker because this water also contains 1 molar glucose. Therefore the water in the dialysis bag will flow out into the beaker to bring the concentration of water in both spaces toward equilibrium

Water is polar for all of these reasons. First, oxygen is more electronegative than hydrogen. This means that oxygen attracts electrons more strongly than hydrogen does. Thus, in the hydrogen-oxygen bond of water, the electrons will be distributed asymmetrically--they will be oriented more towards oxygen than hydrogen. The molecular geometry of the water molecule (bent) results from oxygen containing a steric number of four with two lone pairs, thus the molecule has a slightly positive end and a slightly negative end.

Interstitial water is the fluid on the outside of cells, and surrounds the cells of the human body. While estimates vary, the best answer is that 15% of the entire human body is composed of interstitial water. Overall, about 60% of the body (42L) is composed of water. Additionally, about two-thirds of the total body water is intracellular water. Finally, about 5% of the entire body is composed of plasma.

Remember that these percentages are estimates, and vary by individual. Sex and muscle mass are two factors that can significantly alter these estimates.