having troubole understanding the relationship of trans and cis when dealing with isomerism

A search for answers on our site about isomers leads me to think that we need something more comprehensive about just what sorts of isomers there are.

First, an isomer is another, different structure that has the same molecular formula as the reference structure. For example, benzene and prismane are isomers; they both have the formula C₆H₆.

There are two types of isomers: constitutional isomers and stereoisomers.

• Constitutional isomers have the constituent atoms linked differently; examples are benzene and prismane, not to mention 1-butene and 2-butene.
  CH₂=CHCH₂CH₃ vs. CH₃CH=CHCH₃
• Stereoisomers have identical connectivity but the connections are differently arranged in space. This is a much harder concept, as you have found: cis/trans isomers are stereoisomers.

Let's talk specifically about cis/trans isomers for a moment. cis and trans refer to the direction things point around some reference center. For example, suppose Daunte Culpepper is sacked by Corey Williams and Cullen Jenkins. If they both tackle him from the same side, they're cis to each other; if they hit Culpepper from opposite sides, they're trans (particularly if one hits high and the other hits low...)

In the same way, two methyl groups around a common central portion of a molecule can be cis or trans to each other:

    CH3               CH3   CH3
    |                 |     |
    =======           =======
          |
          CH3

Incidentally, there are two kinds of stereoisomers:

• Enantiomers are stereoisomers that are also mirror images of each other. A particular molecular structure can have no more than one enantiomer.
• Diastereomers are stereoisomers that are not mirror images of each other. A particular molecular structure may have any number of possible diastereomers. cis/trans isomers are diastereomers.

There's also another kind of easily-defined stereoisomeric relationship besides cis/trans. That's the sort that involves chiral centers, and since this answer is already pretty long I won't go into it here.

You may notice that I have cleverly not answered your main question. You should be able to do that now.