Mr. kousen is … Water Man.

Hi. Thanks for stoppin' by. This area of my "biology help pages" is about biochemistry, an area that many students find pretty challenging (difficult). While the ideas are abstract, much of the material boils down to memorization.  Memorization boils down to studying. Studying boils down to work. Work boils down to effort.  So, put your best effort forward & let's get to work !

Organic vs Inorganic compounds:

Now where have you seen that before ? That is 1/3 of the cell theory, right ? The chemical compounds that make up the structures in cells are a mixture of organic compounds and inorganic compounds. To keep it simple, remember it this way : organic compounds always contain carbon and hydrogen (and maybe some other elements), inorganic compounds do not contain carbon and hydrogen together.

Organic compounds are found in living things, their wastes, and their remains.

Examples of organic compounds : carbohydrates (sugars, starches), lipids (fats & waxes), proteins, nucleic acids (DNA & RNA).

Examples of inorganic compounds : water, carbon dioxide.

The elements (atoms) in organic compounds are held together by covalent bonds, which form as a result of the sharing of two electrons between two atoms.

For now, let's save any other nitty-gritty chemistry details for chemistry, OK ?

Chemical Formulas :

There are three kinds of chemical formulas we should understand.  The simplest is the "molecular formula", which tells you the number of atoms of each element present in a compound. An "empirical formula" is basically a molecular formula with the numbers of atoms shown in the smallest possible ratio. A structural formula is like a diagram of the compound.  It shows the atoms present and how they are arranged and bonded together in the compound.

Here are the molecular, empirical, & structural formulas for one compound that we will all learn to love --- GLUCOSE.

Molecular Formula	Empirical Formula	Structural Formula
C6H12O6	CH2O

• The molecular formula tells us that there are 6 carbon atoms, 12 hydrogen atoms, & 6 oxygen atoms in one single glucose molecule.
• Notice that if you look at the structural formula & tally up each letter (element) you get the molecular formula.
• Each line (dash) represents the covalent bond holding the atoms together.
• The ratio of the elements in the molecular formula is 6:12:6, which reduces to 1:2:1 (the number expressed in the empirical formula : CH₂O --- we don't bother writing the "1"s).

Understanding the formulas is very important --- they are like vocabulary in this chapter, if you don't know 'em, it'll be like trying to read & understand this : capt bio for president !

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Dehydration Synthesis vs Hydrolysis :

All of the organic compounds we will study are examples of polymers. A polymer is a large chemical compound composed of smaller repeating units --- over & over & over again. Like a long choo-choo train is made up of smaller connected, repeating, choo-choo cars.

The chemical process that connectsthe smaller subunits to form large organic compounds is called dehydration synthesis.  Remember "synthesis" from chapter 1 ? It still means the same thing : build. The "dehydration" part of the term refers to the fact that water is lost during the chemical process that bonds the subunits together. We will "see" this in a minute when we get more specific.

Hydrolysis is the process that breaks large organic compounds into their smaller subunits. It is the opposite of dehydration synthesis. In HYDROlysis, water (hydro) is added and the large compounds are split ("lysis" means split). The process of hydrolysis is involved in digestion --- when food is broken down into nutrients.

So, to summarize :

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1. Which is an example of an organic compound ?

a)C₁₇H₃₅COOH b) (NH₄)₃PO₄ c) H₂O d) NaCl

a) molecular b) empirical c) structural

CO₂ + H₂O + sunlight ---> C₆H₁₂O₆ + O₂

C₁₂H₂₂O₁₁ + H₂O --->  C₆H₁₂O₆ + C₆H₁₂O₆

CARBOHYDRATES:
 

NOTES:
 
• The 2:1 ratio of hydrogen to oxygen atoms in all carbohydrates is a very important identifying characteristic.
• Another clue to identifying carbohydrates is their structure. Monosaccharides have a ring-like structure, kind of like a hexagon. So if you are looking at structural formulas and you see "rings", it's probably a carbohydrate; especially if only carbon, hydrogen, & oxygen are present in the molecule. Want to see what I mean ?

 

THE DEHYDRATION SYNTHESIS OF MALTOSE FROM TWO GLUCOSE MOLECULES

LOOK ... RINGS !!!
• The ring-thing is a big deal. It will help you. Memorize it.
• What we have in the equation above is two single rings (monosaccharides) on the left becoming chemically combined to form the two-ringed molecule on the right (a disaccharide). It is a synthesis reaction --- the product is bigger than the individual reactants.
• In order to combine the two glucose molecules, bonds must become available.  This is accomplished by removing a hydrogen ion (H⁺) from one glucose & a hydroxyl ion (OH^-) from the other (the dashed box in the equation illustrates this point). These ions bond to form the water molecule that appears on the far right.  This happens in every dehydration synthesis reaction --- water is lost as a waste product.
• If we were to turn the arrow in the equation around & read from right to left, we would be looking at the HYDROLYSIS of maltose. In the hydrolysis of maltose, water would be added to the disaccharide (maltose) causing it to split into its smaller subunits --- the two monosaccharides (glucose molecules).
• Not to beat a dead horse, but the fact that only C, H, & O are in the molecules, and that the molecules have a ring-like structure should make you very confident in identifying them as carbohydrates.
• Getting back to the carbohydrate table, chitin and cellulose are examples of carbohydrates with structural functions. Chitin is the material that makes up the exoskeletons of all arthropods (insects, spiders, lobsters, etc.). Cellulose is what the cell wall in plant cells is made of.
• Starch is the form by which plants store extra carbohydrates.  Glycogen (sometimes referred to as "animal starch") is the form by which animals store extra carbohydrates.  We store glycogen in our livers.

 

PROTEINS:

Allow me to make my first point about proteiNs by writing "proteiN" like this : proteiN. "N" stands for nitrogen.  There is an "N" in the word proteiN.  The element nitrogen is always present in proteiNs. This will help you. Memorize it. :)

Elements Present	Used by organisms for ...	Related Terms & Info
carbon hydrogen oxygen NITROGEN (always those 4) phosphorus sulfer (possibly)	structure & movement (muscles) enzymes antibodies hormones pigments	peptide bond = the bond that holds amino acids together in protein molecules dipeptide = two connected amino acids polypeptide = 3 or more connected amino acids
Building Block of Proteins:	amino acids

• Well, where to start.  Did you notice the "N" in the amiNo group ? Since big proteiN molecules (which we call polypeptides) are long chains of amino acids, every (every) proteiN has nitrogen in it. Always.
• You are responsible for recognizing & identifying the smaller parts of an amino acid. The NH₂ on the left is the amino group, the COOH on the right is called a carboxyl group. The carboxyl group is responsible for giving the amino acids its "acid" properties.
• The "R" is not an individual atom or element. Instead, the "R" spot is the location at which one of a number of groups of atoms connect to the rest of the amino acid. They are called "variable groups". There are 20 different variable groups --- so there are 20 different amino acids.  So what I am trying to say is that the basic structure of all amino acids is the same except for the variable group ("R") spot.  And whichever of the 20 variable groups you have bonded there determines which of the 20 amino acids you're dealing with.  Let me illustrate with an example:

alanine "R" group = CH3

glycine "R" group = H

• Both of these are amino acids because they have an amino group (NH₂) on the left & a carboxyl group (COOH) on the right. They are two different amino acids because they have different atoms bonded at the "R" group spot.  See ? That's not so bad, is it ?

• Now, tell me something. By what process are individual amino acids combined to from larger proteiNs ? Very very good ... dehydration synthesis. This is THE process by which ANY small organic molecules are combined to form BIG organic molecules. The dehydration synthesis of a protein is typically illustrated like so:

• There are two clues that what you are looking at in the above equation is dehydration synthesis. The first is that water is at the end --- a waste product in this process ("dehydration" = loss of water !).  The 2nd clue is that the one molecule on the right (the dipeptide) is bigger than the individual reactants (amino acids) on the left (synthesis = build).
• Now, just like with putting 2 monosaccarides together, we can't combine the two amino acids until we have freed some bonds up.  This is accomplished by removing an OH from one amino acid & an H from the other. These atoms bond & live happily ever after as H₂O (water). The yellow in the diagram above is my attempt to emphasize this idear. The removal of OH's & H's & the formation of water as a waste product happens in EVERY dehydration synthesis reaction --- whether it involves carbohydrates, proteins, or lipids.
• Notice please that the bonds "freed up" after the removal of water form the "peptide bond".
• "Dipeptide" is just a word for two amino acids that are bonded together. If we continued to add more & more amino acids to the dipeptide we would then call the molecule a POLYpeptide.
• If you haven't noticed already, "peptide" is a protein word. Dipeptide, polypeptide, peptide bond, --- all protein stuff.
• The hydrolysis (breakdown) of a dipeptide could be summarized like this:

Notice that water is added at the beginning in hydrolysis, & that our products are smaller than the molecule we start with.

LIPIDS : (Fats, Oils, & Waxes)

Lipids are our 3rd group of organic compounds.  Again, organic just means the compound contains carbon & hydrogen together.  In the case of lipids, the compounds contain C, H, & O, and that's it. No other elements in lipid molecules. Nada, none, zippo, zilch. Just those 3. OK?

Do you recall another group of organic compounds that are also built with those same 3 elements ?
Yes, carbohydrates. So how do we keep from confusing our lipids & carbohydrates? No need to panic, it's quite simple. Carbohydrates always have twice as many hydrogen atoms as oxygen atoms (H:O ratio = 2:1). Lipids never do.  Also, the structural formulas of carbohydrates have the "ring thing" (remember?) and lipids do not.

Here is a summary of Lipid stuff:
 

Elements  Present	Used by Organisms for ...	Related Terms & Info
Carbon Hydrogen Oxygen ONLY ! There is no specific H:O ratio.	Stored Energy Structure  (important part of cell membranes)	saturated fat = C-C bonds are all single bonds unsaturated fat = contain at least one double or triple C-C bond
Building Blocks of Lipids	fatty acid : glycerol :

• A fatty acid is nothing more than a long C-H chain with a carboxyl group (COOH) on the end. The 3 "dots" in the diagram above illustrate that the chain is very long.
• Remember the carboxyl group from amino acids? The carboxyl group gives a molecule an acidic property. Both of the organic acids you need to remember (fatty ACIDS & amino ACIDS) have carboxyl groups .
• Glycerol is classified as an alcohol (due to the OH's). It always looks the same: 3 C's with 3 OH's and everything else H's.
• To build one lipid molecule, we combine 3 fatty acids with 1 glycerol by the process of ... DEHYDRATION SYNTHESIS !

• Like other dehydration synthesis reactions, we must free some bonds before we combine the 3 fatty acids & glycerol. And like before, this is accomplished by removing water molecules.  We remove 3 waters in this reaction because we are bonding 3 fatty acids to the glycerol (we need 3 free bonds).
• Notice that there is no Nitrogen anywhere, so this is definately not a proteiN reaction.
• Notice also that there  are no ring-shaped molecules, so we are not dealing with carbohydrates either.
• The hydrolysis (digestion) of a lipid could be summarized like so:

NUCLEIC ACIDS: DNA & RNA

We will save the nitty gritty details of DNA & RNA for later in the year (Genetics).  But for now, you should know there functions & basic structure, and how DNA compares to RNA.
 

• DNA & RNA (like proteins, carbohydrates, & lipids) are polymers --- long chains of smaller repeating units.  The repeating unit in nucleic acids is called a nucleotide.
• Every nucleotide has the same basic structure:

• the phosphate is a PO₄
• the sugar (see the ring?) has 5 carbons (one at each corner)
• the N-base is one of four possibilities (more on that in a second ...)

• so DNA & RNA are alike in that they are both nucleic acids composed of nucleotides
• their differences lie in their funcstions and structure
• the main structural differences are the number of strands in the molecule, the sugar structure, and one of the N-bases (thymine in DNA, uracil in RNA)

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QUESTIONS :Organic Comp., Formulas, Dehydration Synth. & Hydrolysis

1. Which is an example of an organic compound ?

a)C₁₇H₃₅COOH b) (NH₄)₃PO₄ c) H₂O d) NaCl
* Organic compounds must have both carbon (C) & hydrogen (H) in them.

a) molecular b) empirical c) structural
* the structural give you number & types of atoms & their arrangement

CO₂ + H₂O + sunlight ---> C₆H₁₂O₆ + O₂
* Organic compounds must have both C & H in them. Anything else is inorganic.

C₁₂H₂₂O₁₁ + H₂O --->  C₆H₁₂O₆ + C₆H₁₂O₆

* hydrolysis.  we know for two reasons : 1) the two molecules we end up with (on the right) are smaller than the one on the left; & 2) water is added