Molecular Bonds and Forces - Biochemistry

Covalent bonding is too strong to allow for the enzyme to subsequently release the substrate or product (depending on if the initial substrate or eventual product does the covalent bonding). Thus, it permanently inhibits the enzyme active site and prevents it from continuing its activity. All of the other interactions are much weaker and allow the enzyme to release the product. They are all ways in which active sites interact with their substrates.

The substituents of a chiral center are arranged in a specific manner that cannot be superimposed on its mirror image. An example is a carbon atom with four unique substituent groups.

Oxygen is more electronegative than hydrogen. This results in the electrons to spend more time with the oxygen atom making it negatively chared and the hydrogen atoms to be positively charged. The charged water molecule is then able to form hydrogen bonds with polar molecules.

Phospholipids are amphipathic - in other words they are simultaneously hydrophobic and hydrophilic. They have hydrophobic carbon tails and hydrophilic head groups. Because the carbon chains are repulsed by water, phospholipids come together so that their carbon tails are touching and the polar heads face out in either direction. These hydrophobic interactions ultimately form a phospholipid bilayer.

Hydrophobic molecules are nonpolar molecules - from the Greek "hydro-" water and "phobic" fearing. Examples of hydrophobic molecules are lipids.

A polar molecule has both positive and negative ends. This dipole can interact in many ways with other molecules, both polar and non-polar. If it interacts with a neighboring nonpolar molecule, there is an induced dipole within that neighbor resulting in a dipole-induced dipole force.

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.

Hydrogen bonding occurs when a molecule contains a hydrogen atom bonded to fluorine, oxygen, or nitrogen. This hydrogen becomes partially positive in charge, while the attached atom becomes partially negative. This is due to unequal electronegativity causing increased electron density for the more electronegative atom, and therefore a more negative charge. The partially positive charge then forms an electrostatic attraction to another partially negative atom nearby.

In the double-helix structure of DNA, there are 2 hydrogen bonds between adenine and thymine, and 3 hydrogen bonds between cytosine and guanine. Phosphodiester bonds are covalent bonds between the 5-C sugar and phosphate group of nucleotides (and are much stronger than the hydrogen bonds between complementary bases).

In a solution of water, the outside of a folded protein is going to be in direct contact with water. Therefore, polar or ionic attractions are most favored on the outside of a protein in a solution of water since these can form attractions. The only amino acid listed that can form either polar or ionic attractions is glutamic acid.

Hydrogen bonds are found in primary structure of protein, as well as between the bases in DNA structure. Hydrogen bonds are only found between hydrogens attached to oxygen, nitrogen, or fluorine. They increase the attraction between water molecules, therefore are harder to break in large numbers, causing an increase in boiling point.

An example of strong intermolecular bond is a hydrogen bond. A hydrogen bond occurs between a hydrogen atom on a molecule and an either nitrogen, oxygen, or fluorine atom on an adjacent molecule. The question states that there are bonds between molecule A and molecule B. We can assume that these are hydrogen bonds. This means that molecule A can have hydrogen atom and/or nitrogen, oxygen, or fluorine atoms. Similarly, molecule B can also have hydrogen atom and/or nitrogen, oxygen, or fluorine atoms.

Molecule C doesn’t form hydrogen bonds with either of the other two molecules. This means it cannot have hydrogen and/or nitrogen, oxygen, or fluorine atoms. This is because if molecule C had any of these atoms then it would interact with at least one of the other molecules and form hydrogen bonds (because molecule A and molecule B have these other atoms).

Covalent bonds occur between atoms within (or intra) molecules. This means that covalent bonds are intramolecular bonds. Hydrogen bonds, on the other hand, occur between hydrogen atoms of one molecule and either a nitrogen, an oxygen, or a fluorine atom in another molecule. Since hydrogen bonds occur between molecules, they are classified as intermolecular bonds. There are some situations in which hydrogen bonds may be formed intramolecularly, but these are special cases.

Hydrogen bonds occur between a hydrogen atom in one molecule and either nitrogen, oxygen, or fluorine atom in another molecule. It only involves nitrogen, oxygen, or fluorine atoms because these atoms have high electronegativity. Since they have very high electronegativity, these three atoms can easily attract the electron found in the hydrogen atom and form hydrogen bonds. Chlorine doesn’t have high enough electronegativity to form hydrogen bonds.

An atom's state of matter does not determine whether an atom can form hydrogen bonds. Fluorine, just like chlorine, is a halogen and it can form hydrogen bonds.

Hydrogen bonds can occur between two molecules (intermolecular) and within parts of a single molecule (intramolecular). They are weaker than covalent bonds but are stronger than a Van der Waals interaction, and this strength is determined by a number of factors including bond angle.

For a hydrogen bond to occur, the atom to which the hydrogen is bonded has to have a high relative Pauling electronegativity. Only oxygen, nitrogen, and fluorine, in the upper right corner of the periodic table, have these electronegativities. Neon, argon, and xenon are, of course, inert noble gases, although xenon is sometimes assigned a high electronegativity. This is due, however, to rare bonding events -- certainly not regular hydrogen bonding. Sodium, magnesium and aluminum often form positively charged ions, so they would not tend to attract a hydrogen nucleus.

Hydrogen can form hydrogen bonds with nitrogen, oxygen, and fluorine. A water molecule consists of an oxygen atom bonded to two hydrogen atoms. Each hydrogen atom can form a hydrogen bond with a nitrogen, fluorine, or oxygen atom. Also, the oxygen, which has two lone pairs of electrons, can form two hydrogen bonds with hydrogen atoms. This sums to four hydrogen bonds per water molecule.

Only nitrogen, oxygen, and fluorine can form hydrogen bonds since these three elements are very electronegative. Thus, their partial negative charge (and the presence of a lone pair of electrons) attracts a partially positive hydrogen atom. Carbon, on the other hand, is not very electronegative and thus cannot form hydrogen bonds.

Uracil is not a base in DNA, so A-U can be ruled out as an answer. Moreover, C-G and A-T are the correct base pairs, so the other combinations can be ruled out as well. C-G requires more energy to break because there are three hydrogen bonds between these bases, while A-T has only two hydrogen bonds holding them together.

Bond strengths are measured in kilojoules/mole. Hydrogen bonds can have a strength of . Ionic bonds can have a strength of . This makes hydrogen bonds much weaker than ionic bonds.