Introduction to Molecular and Cell Biology, Biol. 220 Lecture 2: Bonds
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The elements of life

The major elements found in biological material can be remembered with the acronym SPONCH.

Covalent Bonds

Covalent Bond Angles and Lengths

Covalent bonds form when two atoms come close together and share their electrons. In a single bond one electron from each atoms is shared. In a double bond two electrons from each atoms are shared. Covalent bonds have a strength of 90 kcal/mole both in a vacuum and in water.

The SPONCH elements are shown in typical bonding states (Fig. M.). Methane (CH4), ammonia (NH3), Water (H2O), Sulfuric Acid (H2SO4), and Phosphoric Acid (H3PO4).

M. Bond structures of common elements

Note that each of these molecules displays bond angles close to those found in a tetrahedron (109.5 degree)(Fig.N.).

N. Element Bond Angles

Element	Bond Angle (°)
x-C-x x-N-x x-O-x	109.5 107.3 104.5

The unshared pairs of electrons in ammonia and water serve to complete the vertices of the tetrahedral structure. Interactive molecules.

Sulfates and phosphates also show tetrahedral structure (Fig. M.). H2S however has a bond angle of 92 degrees.

Bond lengths are the distance between nuclei of bonded atoms. By adding the covalent radius (Fig. O) of the atoms participating in the bond the covalent bond length can be determined.

O. Elemental Covalent Bond Radius

Element	Covalent radius (nm)
H C N O P S	0.030 0.077 0.070 0.066 0.110 0.104

For example a C-C bond has a length of 0.15 nm while a C-O bond has a length of 0.143 nm.

Introductory chemistry review questions.

Disulfide bonds

The oxidation of adjacent free sulfhydryl (SH) groups will form disulfide (S-S) bonds.

A.Disulfide Bonds

Sulfhydryl (SH) groups are found in cysteine residues.

The endoplasmic reticulum ER has oxidizing enzymes that form disulfide bonds.

The cytoplasm has a reducing environment.

Disulfide bonds are covalent in nature and therefore have a bonding strength of 90 kcal/mole both in a vacuum and in water.

Double Bonds

The effects of double bonds

Double bonds fix molecules into planar structures as illustrated for Ethylene (plane) Fig. 2.3

Double bonds also constrain rotations between the two carbon bonds.

Fig. 2.3  Planar structure of ethylene.

In long carbon chains, such as those for fatty acids, like Palmitate and Oleate Fig. 2.18 , double bonds can greatly change the shape of the molecule.

Fig. 2.18  The impact of introducing a double bond into a fatty acid.


Q: What would be the effect of two double bonds?

Stereoisomers

Stereoisomers of molecules exist when a central atom has four non-identical atoms attached to it. These central atoms are called chiral centers. Stereoisomers have an identical chemical formula but exist in two different orientations similar to your hands. Just like your hands, two isomers are mirror images of each other. Biological systems usually have a preference for only one stereoisomer.

Biological systems use L amino acids Fig 2.6

Fig. 2.6  Stereoisomers of alanine.

Biological systems use D sugars Fig 2.7

Fig. 2.7  Folding structures of glucose.

Q: What would the L-isomer of glucose look like?

Non-covalent bonds

Hydrogen Bonds

Electronegative atoms such as N, O, F, and Cl (Fig. 2.4.) pull the distribution of electrons away from other less electronegative atoms bound to them through covalent bonds (Fig. P.).

Fig. 2.4  Periodic table of electronegativity.

P. Polarized Bonds

This creates slightly positive polar atoms which are attracted to the slightly negative unshared pairs of electrons found in N and O. This +-attraction forms the basis of hydrogen bonding (Fig.Q.).

Q. Hydrogen Bonding of Water

Hydrogen bonds are weak bonds, ~1/20 of covalent bonds, that are sensitive to increases in temperature. Hydrogen bonds have a strength of 4 kcal/mole in a vacuum and 1 kcal/mole in water.

The bond length between the hydrogen and the electronegative O or N to which it is covalently bound is about 0.1 nm (Fig. Q.). The bond between the H and the O or N contributing the unshared pair of electrons is about 0.2 nm.

Q: Could two formaldehyde molecules, H2C=O, hydrogen bond to each other? To water?

Water

• Water is the basic solvent of life.

• If water did not hydrogen bond (Fig. R.), it would be a gas at room temperature.
  R.Two Water Molecules Hydrogen Bonding
  
  

• At room temperature, 5 to 7 water molecules will be hydrogen bonded at any one instant. Such bonds are continually being formed and broken due to the thermal motion of the molecules.

• As water temperatures drop, the thermal motion that disrupts hydrogen bonding is decreased and more water molecules will be momentarily bound together.

• As water freezes all the molecules are bound together in a hydrogen bonded lattice that we call ice.

• Because of the polar nature of water molecules they will tend to cluster around ions. The electronegative domain or water will be attracted to the positive ions and the electropositive domain the negative ions (Fig. S.).
  
  S.Water Ion Interactions
  
  

• Molecules that can hydrogen bond to water tend to be more soluble in aqueous solutions than those that do not hydrogen bond (Fig. T.).
• T.Water Hydrogen Bonding to Organics
  

• Molecules that can interact with water are called hydrophillic (water loving).

• Nonpolar molecules do not interact with water and are considered hydrophobic (water fearing). Hydrogen bonded water molecules tend to for ice-like cages, called "clathrate structures" around such molecules (Fig. G.).
  
  G.Water and Hydrophobic Interfaces
  
  

Q: A water soluble protein orients it's molecules such that hydrophobic groups are buried within the protein and hydrophillic groups are exposed to the aqueous (water) environment. What would happen to this protein if it were placed into a non-polar solvent (hydrophobic)?

Ionic Bonds

• Ionic interactions occur between either fully or partially negative and positive groups.

• The force of attractions between two charges i+ and i- is:
  force = (i+) (i-)/(r^2D)

  where D = dielectric constant (1 for vacuum and 80 for water)
  and r = distance of separation of (i+) and (i-).

• In the absence of water ionic bonds are very strong but water masks the charges (Fig. H.) and therefore in aqueous solutions this type of bonding is quite weak. Ionic bonds have a strength of 80 kcal/mole in a vacuum but only 3 kcal/mole in water.
  
  H.Water Ion Interactions
  
  

  
  

• Ionic bonds are further weakened in the presence of salts which easily dissociate into their ionic forms and compete in the bonding process (Fig. I.).
  

I. Salts and Hydrogen Bonding to Organics

Q: During the process of purification of a protein, it begins to aggregate and precipitate. What can you add to make the protein soluble again?

van der Waals Forces

• As two atoms come into close proximity they show a weak bonding interaction due to their fluctuating electrical charges. This force is known as van der Waals attraction (Fig. K.). van der Waals attraction (per atom) is 0.1 kcal/mole both in a vacuum and in water.

  K.Energy vs Distance
  
  
  
  

• If two atoms come to close to each other they will be strongly repelled (Fig. A.).

• The most effective distance between atoms can be calculated by adding the van der Waals radius of the two interacting atoms (Fig. L.).

  L.van der Waal's radius
  

  Element	van der Waal's radius (nm)
  H C N O P S	0.12 0.16 0.15 0.145 0.19 0.185

  Q: Which shape combinations would form the most stable combinations due to van der Waals interactions?    OO, ((, ||
  
  

Hydrophobic Interactions

Molecules or parts of molecules that have low or no affinity for water are called hydrophobic. These are usually composed of hydrocarbons that lack O or N or other polar groups and therefore cannot hydrogen bond or interact easily with water.

• Water forces hydrophobic groups together in order to minimize their disruptive impact on the hydrogen-bonded aqueous network. This is often referred to as hydrophobic bonding although it is not bonding but merely an exclusionary force. This force, however, is one of the major driving factors in the initial stages of protein folding.

• The water molecules adjacent to hydrophobic domains form icelike cages that surround the hydrophobic region (Fig. G.).

Structure stability from Ring Stacking

• Many components in nucleic acids and some in proteins have planar hydrocarbon rings that may carry localized weak charges.

• These charges are sufficient to maintain solubility in aqueous solutions but the poorly soluble organic rings tend to cluster as stacks with their faces adjacent to each other (Fig. J.).
  
  J.Ring Stacking
  
  
• Interaction between molecules carrying pi electrons stabilizes conjugated ring structures and is known as pi bonding.

Q: Which of the following can participate in ring stacking? Cyclohexane, Benzene

Factors influencing the strength of interactions

Number of interactions

Fig. 2.11  Strength of molecular association is proportional to the number of interactions.

Strength of individual interactions

Hydrogen Bonds = 1 kcal/mole in water, 4 kcal/mole without water

Ionic Bonds = 3 kcal/mole

van der Waals = 0.1 kcal/mole

Hydrophobic Interactions = ? (initial driving force in the folding of proteins)

Ring Stacking = ?

Disulfide Bonds = 90 kcal/mole (same as covalent)

Availability of solvent

Fig. 2.13  Structural changes in a protein may occur in dehydrated environments.

Structure of components

Fig. 2.19  Fatty acids can be associated with hydrophilic structures through ester bonds between the carboxyl group and the hydroxyl groups of glycerol.

Fig. 2.20 Micelles form from fatty-acids but liposomes form with derivatives of diacylglycerol.

Combinations of individual interactions

Fig. 2.17  Macromolecules associate through multiple molecular interactions.

In-class assignment