Molecular Interactions

Which one of the following terms describes a positive and negative charge, which are separated in space within a molecule? a) Salt bridge b) Polar bond c) Dipole d) van der Waals interaction

(c) Dipole -The separation of charge - where a positive charge and a negative charge lie at opposite ends of a bond, for example - is called a dipole, and leads to the generation of a dipole moment. The dipole moment is the difference in charge between the two ends of the dipole.

What is a disulfide bond?

-A disulfide bond, also called an S-S bond, or disulfide bridge, is a covalent bond derived from two thiol groups. -a covalent bond between two sulfur atoms of two amino acids (strong) -referred to as bridges because they create strong links between the polypeptide chain or multiple polypeptides by binding 2 sulfides together -The most common way of creating this bond is by the oxidation of sulfhydryl groups. Note: A thiol group is a functional group containing a sulfur atom bonded to a hydrogen atom. General formula: -SH

Describe the structure of alpha-keratin. How do hydrogen bonds and london dispersion forces (kind of van der waal force) stabilize its structure?

-Coiled-coil protein -Each helix stabilized by intramolecular H-bonding to form a slightly distorted alpha-helix (3.5 residues / turn) -"heptad repeats" (a group or set of seven) of hydrophobic residues and disulfur linkages are important in keeping the helices together.

Intermolecular forces

-Intermolecular forces are forces of attraction between molecules -There are several types of attractive intermolecular forces: *Dipole-dipole forces, *London dispersion forces, *Hydrogen bonding *Induced-dipole forces -The first three forces (dipole-dipole, london dispersion & hydrogen) are also collectively called van der Waals forces. -All molecular and intermolecular attractive forces are electrostatic in nature. That means they involve attractions between positive and negative species. -The strengths of these attractive forces vary widely, although usually the intermolecular forces between small molecules are weak compared to the intramolecular forces that bond atoms together within a molecule.

Hydrophobicity and drug design

-Many drugs have both hydrophobic and hydrophilic parts ("amphipathic") e.g. paracetamol -Drugs must be sufficiently hydrophobic to cross cell membranes and sufficiently polar not to stay there!

What type of interactions do molecules tend to form?

Molecular interactions are mostly non-covalent interactions. They are primarily electrostatic (unlike charges attract, like charges repel) Biologically-important molecular interactions are individually weak but specific. -- molecular recognition and nanoscale machines.

Are all heteroatomic molecules polar?

No! -Depends on the shape of the molecule -In highly symmetrical molecules, dipoles may point in opposite directions and cancel out

Do many polar molecules form hydrogen bonds?

No, many polar molecules do not form hydrogen bonds. -They do interact electrostatically, but much weaker than H-bonds -Non H-bonding compounds tend to be gases or volatile liquids at room temperature, pressure and they have low solubilities in water.

What is the name of the process when a solid immediately turns into a gas?

Sublimation

What is the minimum number of hydrogen bonds that operate between base pairs in DNA?

The base pairs that exist in DNA are joined by either two or three hydrogen bonds: C and G are joined by three hydrogen bonds, while A and T are joined by two.

When will two interacting species experience the greatest force of attraction?

The key concept to remember here is that two species will interact most strongly when this interaction is at its most stable. Remember that stability equates to low energy, so two interacting species will experience the greatest force of attraction when energy is at its lowest.

Tertiary structure

The third level of protein structure; the overall, three-dimensional shape of a polypeptide due to interactions of the R groups of the amino acids making up the chain.

Condensation, the transition from gas to liquid, is associated with an increase in intermolecular forces. True or false?

True. -Recall that the interaction between atoms or molecules of a liquid is more extensive than the interaction between atoms or molecules of a gas. This means that atoms or molecules in a liquid are held together more tightly than atoms or molecules in a gas.

Non-polar molecules can contain polar bonds. True or false?

True. -Don't be tricked into thinking that non-polar molecules can only contain non-polar bonds. Non-polar molecules can have polar bonds - but the polar bonds must be arranged in such a way that they cancel each other out (that is, they must be arranged symmetrically).

Name the typical energies of bonds and interactions for the following interaction types; (1) Covalent bond (2) Ionic bond (3) Hydrogen bond (4) Dispersion force (5) Dipole-dipole (dipolar) interaction

Units are expressed in kJ mol-1 (1) 150-1000 (2) 250 (3) 20 (4) 2 (5) 2

Pure covalent bonding only when difference in electronegativity = (?)

when difference in electronegativity = 0 e.g. isolated H2(g), N2(g), O2(g)

Describe the structure of a polypeptide alpha-helix. How do hydrogen bonds stabilise this structure?

-The alpha helix is a common motif in the secondary structure of proteins and is a coiled structure in which every backbone N−H group donates a hydrogen bond to the backbone C=O group of the amino acid located three or four residues earlier along the protein sequence. -The alpha helix is a helical structure held together by hydrogen bonds between the backbone N-H and C=O groups. The hydrogen bonds are formed within the backbone and the sidechains do not participate. -Alpha-helices have 3.6 amino acid residues per turn. -The separation of residues along the helix axis is 5.4/3.6 or 1.5 Angstroms Note: -Secondary structures are short regions of ordered structure arising from folding of the protein chain. The structures are stabilized by hydrogen bonding within the backbone. The two major types of secondary structure are the alpha-helix and the beta-pleated sheet. -The beta-pleated sheet (or beta sheet) is similar to the alpha-helix in that it is held together by hydrogen bonding between groups in the backbone. The backbone loops around several times to form the beta-pleated sheet and the strands run anti-parallel (in opposite directions) to each other. -A single protein chain can contain both alpha helices and beta sheets. The intervening protein sequences connecting different secondary structures are called random coils. -The manner in which all of the secondary structures of a single protein chain are arranged to from the overall structure is called tertiary structure.

Hydrophobic Effect

-The hydrophobic effect describes the energetic preference of nonpolar molecular surfaces to interact with other nonpolar molecular surfaces and thereby to displace water molecules from the interacting surfaces. The hydrophobic effect is due to both enthalpic and entropic effects. -The hydrophobic effect is the tendency of non-polar molecules and molecular segments in an aqueous solution to avoid the contact with water molecules -When a hydrophobe is dropped in an aqueous medium, hydrogen bonds between water molecules will be broken to make room for the hydrophobe; however, water molecules do not react with hydrophobe. This is considered an endothermic reaction, because when bonds are broken heat is put into the system. Water molecules that are distorted by the presence of the hydrophobe will make new hydrogen bonds and form an ice-like cage structure called a clathrate cage around the hydrophobe. This orientation makes the system (hydrophobe) more structured with an decrease of the total entropy of the system; therefore ΔS<0 . -The change in enthalpy ( ΔH ) of the system can be negative, zero, or positive because the new hydrogen bonds can partially, completely, or over compensate for the hydrogen bonds broken by the entrance of the hydrophobe. The change in enthalpy, however, is insignificant in determining the spontaneity of the reaction (mixing of hydrophobic molecules and water) because the change in entropy ( ΔS ) is large. The mixing hydrophobes and water molecules is not spontaneous; however, hydrophobic interactions between hydrophobes are spontaneous. When hydropobes come together and interact with each other, enthalpy increases ( ΔH is positive) because some of hydrogen bonds that form the clathrate cage will be broken. Tearing down a portion of the clathrate cage will cause the entropy to increase ( ΔS is positive), since forming it decreases the entropy.

Salt Bridge

-a salt bridge is the name for the interaction that occurs between two oppositely-charged amino acid side chains in a polypeptide

Give two examples of biomolecules that are charged.

-e.g. DNA backbone contains negatively-charged phosphate linkages. - e.g. Some amino acid side-chains are charged at pH 7 NOTE: These charges never exist in isolation

Hydrogen bonds are directional

-require some overlap of atomic orbitals (slightly covalent) -strongest H-bonds are linear

Van Arkel-Ketelaar Triangle

Bond triangles or van Arkel-Ketelaar triangles (named after Anton Eduard van Arkel and J. A. A. Ketelaar) are triangles used for showing different compounds in varying degrees of ionic, metallic and covalent bonding. The bond triangle shows that chemical bonds are not just particular bonds of a specific type. Rather, bond types are interconnected and different compounds have varying degrees of different bonding character (for example, covalent bonds with significant ionic character are called polar covalent bonds). Different compounds that obey the octet rule (sp-elements) and hydrogen can be placed on the triangle. Unfortunately, d-elements cannot be analysed using van Arkel-Ketelaar triangle, as their electronegativity is so high that it is taken as a constant. Using electronegativity - two compound average electronegativity on x-axis and electronegativity difference on y-axis, we can rate the dominant bond between the compounds. Example is here On the right side (from ionic to covalent) should be compounds with varying difference in electronegativity. The compounds with equal electronegativity, such as Cl2 (chlorine) are placed in the covalent corner , while the ionic corner has compounds with large electronegativity difference, such as NaCl (table salt). The bottom side (from metallic to covalent) contains compounds with varying degree of directionality in the bond. At one extreme is metallic bonds with delocalized bonding and the other are covalent bonds in which the orbitals overlap in a particular direction. The left side (from ionic to metallic) is meant for delocalized bonds with varying electronegativity difference.

Discuss CO2 interaction with water

CO2 can form hydrogen bonds with water, but its linear shape makes it a non-polar molecule. This means that carbon dioxide is less soluble in water than polar molecules are. The solubility of carbon dioxide is increased when the water is cold, and decreased greatly when the water is warm. Note: Similarly, O2 has a double bond between the two atoms of oxygen. It is also a linear molecule (O=O) which makes it non-polar and insoluble in water.

What is the name of the process when a gas immediately turns into a solid?

Deposition

Most biologically important molecules are heteroatomic!

Heteroatomic is a molecule in which two or more kinds of atoms are present. -Non-identical atoms covalently bound together -Bonds have difference in electronegativity ≠ 0 -Bonding is partially ionic

Heteroatoms

In chemistry, a heteroatom is, strictly, any atom that is not carbon or hydrogen. In practice, the term is usually used more specifically, to indicate that non-carbon atoms have replaced carbon in the backbone of the molecular structure.

What is the difference between intramolecular and intermolecular interactions?

Intramolecular forces are the forces that hold atoms together within a molecule. Intermolecular forces are forces that exist between molecules. Note: dotted lines for all intermolecular interactions