Biological Molecules

Molecules of Living Organisms
One of the themes of biology is the unity of life: all organisms, from bacteria to Douglas fir trees to humans share a common molecular structure.

The cells and tissues of virtually all organisms are made up of the same basic molecules. Many of these are substances with which we are familiar: our carbohydrates, lipids, proteins and the nucleic acids.

These molecules are all compounds with a "backbone" of carbon, or more specifically carbonذhydrogen molecules, which are called hydrocarbons. The incredible versatility of carbon accounts for the multitude of different organic molecules, built from the common backbones, which are found in different kinds of organisms. In chemistry, molecules with a backbone of carbon that also contain hydrogen are called organic molecules. The other atoms and molecules necessary for life are inorganic. Besides carbohydrates, proteins, lipids and nucleic acids, our vitamins are considered to be organic. (Water, oxygen, carbon dioxide and the minerals needed to sustain life are inorganic.)

These groups of compounds are responsible for such things as:

Fuel (energy to do cell work and keep us alive)

Structure

Metabolism

Fuel Storage

Genetic Information

Before understanding the structure of the major groups of compounds of living organisms, we should first study the element, carbon , what a hydrocarbon is , and also study the molecules called functional groups , which bond to hydrocarbons, altering the chemical nature of the resulting compound.

Properties of Carbon

Carbon is one of the atoms (elements) that forms covalent bonds (joins with other atoms) to become stable. Each carbon atom makes 4 bonds
Carbon may make bonds with other carbon atoms forming chains, branching chains or rings of linked carbon atoms. Ring compounds are common in living organisms. BR>
Carbon may also bond to different kinds of atoms, most notably hydrogen. In fact, the basic carbon compound is a hydrocarbon , formed from carbon and hydrogen.

                     H                         H H H
                     |                         | | |
                   H-C-H	             H-C-C-C-H
                     |                         | | |
                     H                         H H H

Properties of Hydrocarbons

Hydrocarbons, like carbon, typically vary in:

The number of carbons on the chain
Straight, branching chains or ring compounds
What is attached to the carbon chain

Most hydrocarbons have very similar properties. For example the C--H bond is energy rich ; so hydrocarbons make good fuels (methane, propane, butane, methanol, alcohol)

Hydrocarbon variations that differ only in the arrangement of atoms are called isomers . Isomers are very important in biology, and we shall see many examples of isomers.

Hydrocarbons can also have variations in bonding. Carbon may make double or triple bonds as well as single bonds. The resulting compounds will be different in shape and often function.

Carbon ring componds are common in living organisms. The shape of the ring compound is important to its properties. The covalent bond angles in the ring determine the molecule's shape. Two common ring shapes are the "chair" and the "boat"

The major compounds of living organisms are modifications of hydrocarbons with something (very precise) added. These atoms or molecules are called functional groups, because they change how the hydrocarbon functions and gives it properties of a carbohydrate, or lipid or protein, etc.

Functional Groups
The functional groups are molecular fragments which, when substituted for one or more hydrogen atoms in a hydrocarbon, confer particular chemical properties to the new compound. The functional group can be said to determine the "behavior" of the molecule. Once you have learned the properties of some functional groups, the major compounds of living organisms are easy!
Some Functional Groups Important in Biological Molecules
(See alsoTable 3-1 in your textbook)

Functional Group Name Structural Formula
Type of Compound
Example

Hydrogen
.....-H Alkane H
|
H-C-H
|
H

Hydroxyl
.....-OH Alcohol H
|
..H-C-OH
|
H

Carbonyl .....=O Aldehyde .......H..H..H
.........|...|..|
....H-C-C-C=O
.........|..|
........H.H..

Carbonyl .....=O Ketone H....H
|...|
H-C-C-C-H
|.."..|
H..O..H

Carboxyl ....-C=O
.. ...|
... ..OH Organic Acid ........H
.........|
.....H-C-C=O
.........|...|
........H..OH

Amino ....H
.....|
...-N-H Amine .. ..H.H
.. ...|. .|
..H-C-N-H
......|
.....H.

Amino + Carboxyl Amino Acid ........H
.........|
.....H-C-C=O
.........|...|
.....H-N.OH
.........|
........H

Note the central alpha carbon to which both amino and carboxyl groups attach to form the amino acid

Methyl
H
|
.....-C-H
|
H Backbone of Hydrocarbon Chains .......H..H..H
........|...|...|
....H-C-C-C-H
........|...|...|
.......H..H..H

Phosphate .......O-H
....... |
...-O-P=O
....... |
.......O-H Phospholipids
Nucleic Acids

Before discussing the specifics of the molecules of living organisms, we should also be familiar with the chemical processes by which the large molecules (macromolecules or polymers) are built from smaller molecules (often called monomers or subunits), that have a common structure.

Most of our biological molecules are assembled or broken down using the same type of chemical reaction, one which involves adding or removing water molecules. Polymers are formed from their subunits by removing molecules of water (a hydrogen (H-) from one subunit and the hydroxyl (-OH) from the second subunit) to join the subunits together. This is called a dehydration synthesis or condensation . When larger molecules are broken down, such as in digestion, water molecules are added in to break the polymers into their subunits, a process called hydrolysis.

Another common set of chemical reactions in living organisms is the oxidation and reduction. An oxidation is the loss of one or more electrons. A reduction is the gain of one or more electrons. Oxidations and reductions are always coupled. A substance that can cause a reduction is called a reducing agent, and one that can cause an oxidation is an oxidizing agent. A substance that prevents something from being oxidized is called an anti-oxidant. Vitamin C and vitamin E both function as anti-oxidants in our cells and tissues. (An anti-oxidant works by being so easily oxidized itself that the oxidizing substance oxidizes the anti-oxidant rather than the "target" molecule that needs "protection".)

We are now ready to discuss in detail the major compounds of living organisms. We shall look at the four groups of compounds: Carbohydrates, Lipids, Proteins and Nucleic Acids. (See Table 3-2 in your text for a general overview)

Carbohydrates

Functions

Basic energy source (fuel) for virtually all living organisms

Structural molecules, especially of plants

Fuel reserve molecules (e.g., starch, glycogen)

There are three groups of carbohydrates

Monosaccharides or simple sugars
Disaccharides also simple sugars
Polysaccharides complex carbohydrates, including starches and fiber

All carbohydrates are composed of one or more monosaccharides. The simple sugars are formed from one or two monosaccharides, and the complex carbohydrates (polymers) are formed from long, sometimes branching, chains of monosaccharides, formed by dehydration synthesis reactions.

Structure of the monosaccharide
Chemically, monosaccharides contain:

Carbon
Hydrogen
Oxygen

The ratio of atoms in a monosaccharide is: (CH₂O)

C_n(H₂O)_n
C₆H₁₂O₆
C₃H₆O

The functional groups of monosaccharides are:

-OH (Hydroxyl)
=O (Carbonyl)

However the arrangement of atoms in the monosaccharide is important. Each monosaccharide is constructed with the following rules:

Make a carbon chain
Attach the carbonyl group to 1 of the carbon atoms
Attach hydroxyl groups to the remaining carbon atoms
All remaining open carbon bonds will have hydrogen atoms attached

Given the rules, there are many variations possible with monosaccharides. Many isomers are possible and common.


	H - C = O
	    |
	H - C - OH
	    |			    
	H - C - OH
	    |                note: Hydroxyls (alcohol)
	H - C - OH
	    |
	    H                note: Carbonyl (aldehyde or ketone)

The common monosaccharides of living organisms are:

C₆H₁₂O₆ (glucose, galactose, fructose)
Some 5 carbon (ribose, deoxyribose, ribulose, xylose)

Note: Although we show monosaccharides and other carbohydrates in the chain structure, the carbohydrates in living organisms are found in a ring shape. Your text has some good illustrations of the ring forms of some common sugars.

Formation of Disaccharides and polysaccharides
Disaccharides
Disaccharides are 2 monosaccharides joined by a dehydration synthesis, or condensation , which is the removal of a water molecule. The "H" is taken from one monosaccharide and the "OH" from the second. The two molecules are then joined by a C--C bond.
Examples of common disaccharides are sucrose, lactose, and maltose

Polysaccharides
Polysaccharides are formed by joining several monosaccharides, each to the next by a dehydration synthesis.
The common polysaccharides are:

Starch (alpha 1-4 linkage) (boat)

Glycogen

Both starch and glycogen are polysaccharides of glucose. Starch is a very long coiled, unbranched or branching chain, with about 1000 glucose molecules in any branch. Glycogen branches frequently (about every 10 or so glucose units) and is more easily broken down.
Starch and glycogen are important fuel storage molecules.

Cellulose (beta 1-4 linkage) (chair)

Long chains of glucose
Cellulose is for most living organisms, non-digestible. Few organisms have the enzyme needed to break down cellulose. Cellulose and related compounds form most of what we call fiber .

Chitin

Long modified glucose chains, in which a nitrogen-containing functional group replaces one of the hydroxyl groups on each glucose subunit.
Chitin forms the exoskeleton of many invertebrate animals (mostly arthropods)

Disaccharides and polysaccharides can be digested or broken down by hydrolysis . (Appropriate enzymes are required for both dehydration synthesis and for hydrolysis)

In addition to the "pure" carbohydrates, glycoproteins, common in plasma membranes, contain carbohydrate, as do protective mucus layers and all nucleic acids.

Lipids

Many of our common substances are lipids, which include fats, oils, and waxes along with a variety of related substances.

Lipid Functions

Fuel reserve molecules (Lipids are energy rich)
Structure of cell membranes
Protective surface coatings and insulation
Many hormones (regulatory chemicals)

Major types of Lipids

Triglycerides commonly known as the fats and oils
Waxes (very similar to triglycerides)
Phospholipids
Sterols (or steroids)
Terpenes

Lipid Characteristics

Most lipids are strictly nonpolar and hydrophobic, so they dissolve in nonpolar substances, but not in water.
Most lipids feel "greasy"
Lipids contain large regions of just carbon and hydrogen, as carbon-carbon bonds and carbon-hydrogen bonds

Structure of Lipids
Lipids contain:

carbon
hydrogen
oxygen

However the proportion of oxygen is low, so lipids are mostly hydrocarbons
The chemical structure of our fats and oils, the most commmon lipids, is based on fatty acid building blocks and an alcohol, glycerol
The terms fats and oils are terms of convention
- Fats are "hard" or solid at room temperature
- Oils are liquids at room temperature

Structure of Fats and Oils (the Triglycerides)
One molecule of the alcohol, glycerol

Attached to the glycerol (by dehydration synthesis) are 3 fatty acids. The fatty acids determine the characteristics or properties of the fat. The bond formed between the ذOHs of the alcohol and the ذOHs of the fatty acid is an ester bond.

Fatty acids are chains of hydrocarbons 4--22 carbons long with the carboxyl functional (acid) group at end

                  --C=O
                    |
                    OH

Each carbon within the chain has 2 spots for bonds with hydrogen
If each carbon has 2 hydrogens the fatty acid is saturated

                                                 H H H H H H H       
                                             O=C-C-C-C-C-C-C-C-H     
                                              HO H H H H H H H

If two carbon atoms are double bonded, so that there is less hydrogen in the fatty acid, it is unsaturated (monounsaturated):

                                                 H H     H H H
                                             O=C-C-C-C=C-C-C-C-H
                                              HO H H H H H H H

If more than 2 carbon atoms are unsaturated, the fatty acid is polyunsaturated :

                                               H H     H     H H H H
                                             O=C-C-C=C-C-C=C-C-C-C-C-H
                                              HO H     H     H H H H

Let's look at ways that fatty acids are different:

1. Length of chain in fatty acid

4 - 22 carbons long
Usually an even number
- Short chains are more soluble
- Short chains are more easily broken down
- Short chains oxidize more easily (process by which fats become "rancid")

2. Degree of saturation

Saturated
Monounsaturated
Polyunsaturated
- Most plant fats tend to be unsaturated but fats from tropical plants tend to be very saturated
- Fish oils tend to be unsaturated (from cold water and salt water fish). Other animal fats tend to be saturated

3. Liquid vs solid

Short chains and unsaturated chains are liquid at room temperature (molecules are smaller and less dense (the double bonds distort the molecules so they don't fit close together)
Saturated chains are solid (denser) because chains fit together better

Synthetic Fat
Olestra is a synthetic fat, marketed under the trade name of Olean. It mimics the texture and properties of triglycerides, is fat soluble, but not digestible or absorbed into the body, so all Olestra consumed passes through the digestive tract. Hence, it is considered to be calorie-free. Olestra is a sucrose polyester, composed of fatty acids attached to sucrose rather than glycerol. Six to eight fatty acids are attached to the sucrose molecule so the lipase digestive enzymes can't function to hydrolyze the ester bonds.

Waxes
Waxes are similar to triglycerides except they are highly saturated and have an alcohol component that is different from glycerol. They have a rigid, solid structure at "normal" temperatures on earth. Waxes form protective layers on surfaces of many organisms, provide water-resistance, and in some cases, structure.

Phospholipids
Phospholipids are structural molecules forming the major component of all membranes of cells
Structure of phospholipid:
Glycerol molecule with:

            C--fatty acid
            |
            C--fatty acid
            |
            C--phosphate portion

The benefit of the phospholipid structure is that the phosphate region makes the molecule highly amphipathic, ideal for the cell membrane structure

Hydrophilic portion in the phosphate region.
Hydrophobic portion in the fatty acid tails

The most common phospholipid is lecithin

Phospholipids also make excellent emulsifiers and are used in a number of food and household products.

Sterols (Steroids)
All steroids are composed of hydrocarbon chains with four interconnected rings. They are synthesized from saturated fatty acids.

Steroids are used in organims for a variety of purposes.

Vitamins A & D
Hormones (adrenal cortex & sex hormones)
Cholesterol
- Precursor to most steroid hormones and vitamin D
- Necessary for structure of nerve system cells
- Component of animal cell membranes not found in plants

Terpenes
Terpenes are found in plants, and include some important pigments such as the carotenoid pigments that are responsible for the orange, red and yellow colors of many plants. There are over 22,000 different terpenes in plants. Many of the aromatic oils found in plants are terpenes. Taxol, an extract from yew, is used to treat ovarian cancer, and digitalin is a cardiac medicine. Two plant hormones are also terpenes, as are two important electron transfer molecules. Economicaly, rubber is an important terpene. Terpenes are lipid soluble and hydrophobic.

Amino Acids and Proteins
Proteins are very large molecules composed of combinations of 20 different amino acids. The precise physical shape of a protein is very important for its function. There are many, many different proteins essential for the functioning of each cell in a living organism (A cell may have 10,000 different proteins or more)

Functions of Protein
1. Structural

Component of all cell membranes
Component of cytoplasm "cytoskeleton"
Component of movement or contractile structures, such as muscle, cilia and flagella microtubules contractile properties
Component of hair, nails horns, etc. (Keratin is the main protein of these substances)

2. Metabolic molecules

Hormones regulatory chemicals
Energy transfer molecules for cell respiration (cytochromes)
Oxygen carrier in circulation (hemoglobin)
Antibodies
Enzymes
Probably most "famous"
Facilitate rate of chemical reaction

Protein Structure
All proteins are composed exclusively of subunits of amino acids, which consist of:
Very specifically arranged carbon fragments (chains) each with:

NH₂ Amino functional group
COOH Carboxyl functional group
Both functional groups attach to a specific carbon, the alpha (a) carbon, of the carbon chain. The third bonding site of the alpha carbon is typically Hydrogen.
The alpha carbon will have at its fourth bonding site a side chain, or R group which gives the amino acid its unique structure
Amino acids are joined together by a dehydration synthesis of amino/carboxyl groups forming a peptide bond.

Protein Structure
The protein structure is critical for its function. Each protein has a unique shape or conformation. However, all proteins are composed exclusively of subunits of amino acids, which join together in long chains called polypeptides which fold or coil into the unique shape of the functional protein.

To discuss protein one must

Discuss amino acids
Discuss formation of protein from amino acid

Amino Acids
Amino Acids Contain

Carbon, Hydrogen, Oxygen, Nitrogen, and sometimes Sulfur
Amino acids have two function groups (both of which are typically in the ionized form)
- NH₂ Amino functional group
- COOH Carboxyl functional group
Both functional groups attach to a specific carbon, the alpha (a) carbon, of the carbon chain. The third bonding site of the alpha carbon is typically Hydrogen.
The alpha carbon will have at its fourth bonding site a side chain, or R group which gives the amino acid its unique structure
There are 20 + different amino acids in protein. All have a common structure except for the R group.
Some amino acids have R groups that are polar (so they are hydrophilic), some R groups are nonpolar (and hydrophobic), some have acidic side chains (generally with a negative charge) and some are basic. Cysteine , contains sulfur in the R group, so cysteines can form disulfide bonds (Disulfide bridges)
Amino acids are joined together by a dehydration synthesis of amino/carboxyl groups forming a peptide bond.

     H
     |
  R--C--C=O
     |  |
  H--N  O--H            HO--C=0	= carboxyl (acid) functional group
     |  
     H		
                        H--N--H	= amino functional group
				           |

                        R = symbol for side chain, or variable group 
                        (what makes each kind of amino acid different)

How do amino acids join to make a protein?

A protein starts as a chain of amino acids, called a polypeptide
Amino acids are joined by the peptide bond, via dehydration synthesis to form the polypeptide
The polypeptide chain is referred to as the primary structure of the protein.
The specific amino acids in the polypeptide chain will determine its ultimate conformation, or shape, and hence, its function. Even one amino acid substitution in the bonding sequence of a polypeptide can dramatically alter the final protein's shape and ability to function.

The peptide bond is shown below:

    H  R               H  R              H  R          H  R
    |  |               |  |              |  |          |  |
 H--N--C--C--OH  +  H--N--C--C--OH  ---> H--N--C--C--N--C--C--OH    + H2O
       |  "               |  "              |  "          |  "
       H  O               H  O              H  O          H  O


                             Note the peptide bond (between nitrogen and carbon)

How do polypeptides vary?
1. Number of amino acids in the chain: 50--1000 or so
2. Which kind of amino acids are in the chain (of the 20 types)
3. How many of each kind of amino acid
4. The bonding order or sequence of amino acids

Protein shape and structure
The polypeptide chain is just the beginning of a protein. Functional proteins undergo further processing to obtain a final functional shape. Some proteins are composed of more than one polypeptide. The surface structure of the protein is critical for its function.

The function of many proteins depends on a specific region of the protein that binds to another molecule. Antibodies, critical to the immune system, function by binding to specific regions of the antigen molecules, to deactivate them. An enzyme binds to the substrate (the reactants) at a specific active site on the enzyme.

Secondary and tertiary structures that form from the polypeptide determine the ultimate shape of each protein. As peptide bonds are formed, aligning the amino acids, hydrogen bonds form between different amino acids in the chain.

This bonding coils the polypeptide into the secondary structure of the protein, most commonly the alpha helix, discovered by Linus Pauling. The alpha helix coils at every 4th amino acid.

Some regions of the polypeptide have portions that lie parallel to each other (still held by hydrogen bonds) instead of in the alpha helix, in which the amino acids' hydrogen bonds form a pleated structure. Fibrous proteins have significant pleated structures.

Following the secondary shape, openings for bonding along the side chains (the R groups) of amino acids causes more folding or twisting to obtain a final, three-dimensional functional protein, called the tertiary structure. Disulfide bonds (which are strong covalent bonds) between nearby cysteine molecules are important to the tertiary structure as well, as are hydrogen bonds, some ionic bonds between charged R-groups and van der Waals interactions. The final shape for most proteins is a globular shape.

If two or more polypeptide chains join in aggregates, they form a quaternary structure, such as in the protein molecule, hemoglobin. Often quaternary proteins are complexed with a different molecule, often a mineral. Hemoglobin contains iron, for example.

Protein Stability
As we have seen, the physical shape of a protein is maintained by weak bonds. Many of these bonds are hydrogen bonds formed from the polarity of the amino acids and their "R" groups. If these weak bonds are broken, the protein structure is destroyed and the molecule can no longer function. This process is called denaturation.

Things that can denature protein:

Heat (as low as 110 F, many @ 130 F)
Heavy metals (e.g., silver, mercury)
pH changes
Salts
Alcohols (Ethyl alcohol least toxic)
Many proteins will denature if placed in a non-polar substance
Other chemicals

Enzymes are seriously affected by denaturation ذ but other proteins of body can also be denatured. Although in most cases, a denatured protein loses its function permanently, in some cases, re-naturation can occur if the substance which promotes the denaturation is removed from the protein. This is more true of chemical denaturants and particularly in experimental environments.

Nucleotides and Nucleic Acids
Nucleic acids are our information carrying compounds -- our genetic molecules. As with many of our other compounds, the nucleic acids are composed of subunits of nucleotides. Nucleotides, in addition have independent functions.

Functions of Nucleotides

Components of nucleic acids (which are long chains of nucleotides)
Energy carrier molecules (ATP)
Energy transport coenzymes (NAD+, NADP+)
Chemical intracellular messengers

Functions of Nucleic Acids

Storage of genetic information (DNA)
Transmit genetic information from generation to generation (DNA)
Transmit genetic information for cell use (RNA)

Most of the information on nucleotides and nucleic acids will be discussed when we discuss genetics and energy relationships of cells. For now we shall just present the basic structure of the nucleotides...

Nucleotide Structure

5 carbon sugar component
Phosphate group
Nitrogen Base component
Arrangement of a Nucleotide:
S-N
|
P
Nucleic acids (polynucleotides) are formed when S P covalent phosphodiesterlinkages form long chains.
```
						S - N
						|
						P
						|
						S - N
						|
						P
						S - N
						|	 
						P	
                                              etc. 
```
In DNA, a double chain is formed when 2 nitrogen bases hydrogen bond.
```
					   S N ^ N S
					   |       |
					   P       P
```
RNA molecules are single chains.
Genes (specific regions of DNA molecules) contain the hereditary information of an organism. The linear sequence of nitrogen bases of the nucleotides determines the amino acid sequence for proteins in the cells and tissues. As with all of biology, the processes of evolution are validated in DNA information. Organisms more closely related evolutionarily, have more similar DNA.

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Functional Group Name	Structural Formula	Type of Compound	Example
Hydrogen	.....-H	Alkane	H \| H-C-H \| H
Hydroxyl	.....-OH	Alcohol	H \| ..H-C-OH \| H
Carbonyl	.....=O	Aldehyde	.......H..H..H .........\|...\|..\| ....H-C-C-C=O .........\|..\| ........H.H..
Carbonyl	.....=O	Ketone	H....H \|...\| H-C-C-C-H \|.."..\| H..O..H
Carboxyl	....-C=O .. ...\| ... ..OH	Organic Acid	........H .........\| .....H-C-C=O .........\|...\| ........H..OH
Amino	....H .....\| ...-N-H	Amine	.. ..H.H .. ...\|. .\| ..H-C-N-H ......\| .....H.
Amino + Carboxyl		Amino Acid	........H .........\| .....H-C-C=O .........\|...\| .....H-N.OH .........\| ........H
Note the central alpha carbon to which both amino and carboxyl groups attach to form the amino acid
Methyl	H \| .....-C-H \| H	Backbone of Hydrocarbon Chains	.......H..H..H ........\|...\|...\| ....H-C-C-C-H ........\|...\|...\| .......H..H..H
Phosphate	.......O-H ....... \| ...-O-P=O ....... \| .......O-H		Phospholipids Nucleic Acids