Monday, May 07, 2007

Pushing Electrons

 
Biochemistry, as the name implies, is concerned with the chemistry of life. The chemistry part is mostly organic chemistry and organic chemistry is mostly about pushing electrons.

Covalent bonds are formed when the nuclei of two atoms share a pair of electrons. The "bond" is actually a cloud of electrons orbiting the two nuclei. The atoms are held together because neither one is stable without the shared electrons. The reactions in organic chemistry and biochemistry can be thought of as simple rearrangements of electrons to form new covalent bonds and break apart old ones. In this sense it's all about pushing electrons from one location to another.

The best way to think about covalent bonds is to visualize the electrons in the other shell of atoms. Those are the ones that participated in bonding. The outer shell electrons are often referred to as the valence electrons. The first shell of electrons can only hold two electrons. Hydrogen atoms have a single electron so in order to form a stable compound they have to combine with something that supplies an electron that can be shared. The simplest of these compounds is a molecule of hydrogen (H2).

When two atoms of hydrogen combine to form H2 both atoms succeed in filling their outer shells with two electron by sharing electrons. The shared pair of electrons is the covalent bond. The type of structures shown in the equation are called Lewis Structures. The dots represent electrons in the outer shell of the atom.

The inner electron shell can only hold two electrons but all other shells can accommodate eight electrons. The atomic number of oxygen is 8, which means that it has two electrons in the inner shell and only six in the outer shell. It needs to combine with two other atoms in order to get enough electrons to fill the outer shell.
In this example, oxygen with six electrons in the valence shell is combining with two hydrogen atoms to form water (H2O). By sharing electrons both the hydrogen atoms and the oxygen atom will complete their outer shells of electrons—hydrogen with two electrons and oxygen with eight.

Sometimes atoms can share more than a pair of electrons. For example, when two atoms of oxygen combine to form the oxygen molecule (O2) there are four electrons shared between the two atoms. This results in a double bond between them.
Carbon has an atomic number of 6, which means that it has two electrons in the inner shell and only four electrons in the outer shell. Carbon can combine with four other atoms to fill up its outer shell with eight electrons. This ability to combine with several different atoms is one of the reasons why carbon is such a versatile atom. The structure of ethanol (CH3CH2OH, left) illustrates this versatility. Note that each atom has a complete outer shell of electrons and that each carbon atom is covalently bonded to four other atoms.

Biochemical reactions are a lot more complicated but once you understand the concept of electron pushing it becomes relatively easy to make sense of the reaction mechanisms seen in textbooks. The only additional information you need is the knowledge that some atoms can carry an extra electron and this makes them a negatively charged ion (e.g., — O-). Some stable atoms are missing an electron in their outer shell so this makes them a positively charged ion (e.g., — N+).

In many cases a proton (H+) is released from a compound leaving its electron behind. This proton has to combine with an atom that already has a pair of electrons in its outer shell (e.g., a base B:). Here's an example of the reaction mechanism for aldolase, one of the enzymes in the gluconeogenesis/glycolysis pathway.
The outline of the enzyme is shown in blue. One of the key concepts in biochemistry is that enzymes speed up reactions, in part, by supplying and storing electrons. In this case an electron withdrawing group (X) pulls electrons from oxygen and this weakens the carbon-oxygen double bond (keto group). Carbon #2, in turn, pulls an electron from carbon #3 weakening the C3-C4 bond that will be broken. (Aldolase cleaves a six-carbon compound into two three-carbon compounds as shown here. It also preforms the reverse reaction where two three-carbon compounds are combined to form a six-carbon compound.)

A basic residue in the protein (B) removes a proton from the -OH (hydroxyl) group to form a B-H covalent bond. This leaves an additional electron on the oxygen and it combines with one left on C4 to from a double bond. The red arrows show the movement of electrons in these reaction mechanisms.

The key point here is that biochemical reactions are just like those of all chemical reactions. They involve the movement of electrons to break and form covalent bonds.

4 comments :

  1. I found this quite valuable. I'm taking a biochemistry course without any organic chem background, and need a jumpstart understanding of these reactions. I'd like to see some more simple examples of electron pushing. Any more you can add on some tricky examples would be appreciated.

    Also, I think it would be better to replace the sentence: "It needs to combine with two other atoms in order to get enough electrons to fill the outer shell." "It would need to combine with two other hydrogen atoms in order to get enough electrons to fill the outer shell."

    Thanks,

    -SB

    ReplyDelete
  2. Re: "A basic residue in the protein (B) removes a proton from the -OH (hydroxyl) group to form a B-H covalent bond. This leaves an additional electron on the oxygen and it combines with one left on C4 to from a double bond. The red arrows show the movement of electrons in these reaction mechanisms."

    Would you call the B-H bond a "coordinate" bond? I have seen that term when one of the atoms supplies all the electrons.

    Also, is there a positive charge at the B-H location? If so, I think you should show/state that, even if obvious to experienced chemists. Any detail left takes away corroborating info that is valuable when you are first making sense of a concept.

    Thanks,

    -SB

    ReplyDelete
  3. minor gripe: if you try to print this page, tons of extraneous pages come out. Needs a "printable view" of the main article.

    Regards,

    -SB

    ReplyDelete
  4. anonymous says,

    minor gripe: if you try to print this page, tons of extraneous pages come out. Needs a "printable view" of the main article.

    Major gripe. I wish there was an easy way to do that.

    What I usually do on other blogs is to use Snagit (or something similar) to capture the page image then print it.

    ReplyDelete