Basic Chemistry III - Bio molecules

Biomolecules

Macromolecule

Macromolecules are large molecules consisting of many thousands of atoms. Many of the important molecules found in living things are macromolecules. Examples are large carbohydrates called polysaccharides such as starch and cellulose, Proteins, and Nucleic acids such as DNA and RNA. Curiously macromolecules in living things are all constructed by taking simple molecules and chemically linking them together to make long chains analogous to box cars on a train. Macromolecules may have a complex three dimensional structure. This is especially true for proteins. The three dimensional structure typically relates to the function of the macromolecule.

Monomer

The term monomer refers to the simple molecular building blocks that can be put together in long chains to form macromolecules. Examples of common monomers in biological molecules are glucose, amino acids and nucleotides.

Polymer

The term polymer refers to a large molecule made by stringing together many repeating monomers. Polysaccharides, Proteins and Nucleic acids are important polymers.

Carbon: The Three Main Forms of the Element

Carbon is important in biology because carbon forms the "back-bone" of just about all biologically important molecules. This is because carbon forms long and sometimes complex covalently bonded structures and also because carbon compounds vary greatly in the type of interactions they have with water. For example some carbon compounds, such as most lipids, have strictly hydrophobic interactions with water, others such as sugars are hydrophilic. Still others such as proteins and phospholipids are partly hydrophobic and partly hydrophilic.

Diamond

Diamonds are formed deep in the earth under extreme pressure and heat. A diamond is essentially one large covalently bonded molecule as shown here.

Graphite

The "lead" in pencils is actually largely the second form of carbon, which is called graphite. Graphite is soft but consists of many small flat crystals consisting of covalently bonded carbon molecules. It's the sliding of these crystals past each other that makes graphite soft and slippery.

Fullerene

Imagine scientist's surprise when they found this form of carbon in soot! Fullerene gets its name because it resembles the geodesic domes developed by Buckminster Fuller. More informally these shapes are called "Bucky balls". Fullerene also occurs in large balls and tubular fullerene structures have been made in the laboratory.

Lipid

Lipids are nonpolar, hydrophobic compounds consisting mainly of a carbon skeleton with hydrogen’s attached. They typically dissolve in non polar organic solvents such as benzene or ether but tend to dissolve poorly, if at all in water.

Beyond that lipids fall into a number of not closely related groups of chemicals, some of which are familiar and some not so familiar.

Below is the diagram depicting different types of lipid.

Steroids

Steroids are important hormones and structural components of cell membranes. Steroids can be recognized by a characteristic four ring backbone as in this example, cholesterol shown in both ball and stick and stick representations. Note the 4 rings characteristic of steroids.

Terpenes

Terpenes are hydrocarbon chains of alternating double and single bonded carbon atoms. Many are important plant defensive compounds. For example, the smell of pine trees and the sticky sap that pine trees give off are largely mixtures of terpenes. Steroids are built of

simple three carbon terpene units called isoprene units.

Organic and "fatty" acids

Organic acids

Organic acids are very important compounds in living things. They are important components of structural molecules such as phospholipids and also are an important source of energy.Organic acids have a carboxyl group and long a chain of carbons attached to it.

This diagram shows formic acid, the simplest organic acid. The name formic comes from the Latin word (Formica) for ant. This acid is an important alarm and defensive compound for many ants.

Acetic acid, the acid in vinegar, has one more carbon than formic acid.

Fatty acids

Fatty acids are organic acids which have a long chain of carbon and hydrogen's attached to the carboxyl group. Oleic Acid is a common saturated fatty acid. Actually the bend in the carbon chain suggests that oleic acid is not completely saturated.

Tri-glycerides

Triglycerides are lipids made with three fatty acids and a glycerol molecule.

Glycerol

Glycerol (or glycerin) is a three carbon alcohol with a hydroxyl (OH) group coming from each carbon. The fatty acids are joined to the glycerol by a dehydration synthesis as shown in the diagram here.

Saturated means that the carbon skeleton has all the available bonding sites taken up by

hydrogen's.

Fats vs oils

Tri-glycerides with unsaturated fatty acids are termed 'oils' in every day speech because they are liquid at room temperature. Tri-glycerides with saturated fatty acids tend to have a higher melting point and are solid at room temperature. We typically call these fats. Note: oil that comes out of the ground is basically a series of hydrocarbons, not tri-glycerides, so don't confuse these different uses of the word oil! The difference in physical properties of fats and oils is due to the nature of saturated vs unsaturated bonds in the carbon skeleton of the fatty acids. Saturated tri-glycerides are considered bad because they cause the body to produce excess cholesterol.

Saturated vs Unsaturated bonds

Diagram illustrating the concept of saturated vs. unsaturated bonds.

Saturated bonds are when each of the carbons has four single bonds as in the top figure. Unsaturated carbons have one or more double or triple bonds. Note the kinky or pleated shape of the unsaturated carbon skeleton. This spaces the chains allowing them to slide around. This is the main reason unsaturated tri-glycerides tend to be liquid at room temperatures: That is, oils rather than fats.

Phospholipids

Phospholipids are like tri-glycerides except that the first hydroxyl of the glycerine molecule has a polar phosphate containing group in place of the fatty acid. This means that phospholipids have a hydrophilic head and hydrophobic tail and this is important because phospholipids self assemble in water into a bi-layer. The Biochemical Gallery's opening illustration is of a phospholipid bi-layer forming because of the interaction between the phospholipids and water. This tendency to form bi-layers is the basis of the cell membrane characteristic of all living things at least on earth and is an example of self assembly.

Diagrammatic view of a phospholipid

Note that one part of the molecule is hydrophobic (the carbon backbones from the two organic acids) and the other part, the head is hydrophilic. This is important in phospholipids to organize themselves into bi layers when placed in water.

Phospholipid bilayer structure of a plasma membrane

Carbohydrates

Carbohydrates are organic compounds that usually contain carbon hydrogen and oxygen in the ratios: 1 Carbon: 2 Hydrogen's: 1 Oxygen.

There are four classes of carbohydrates that are of general interest. Monosaccharide's,

Disaccharides, Oligosaccharides and Polysaccarides.

Monosaccharide's (simple sugars) have a carbon skeleton of 3 or more carbon atoms depending on the monosaccharide. The most familiar monosaccharide is Glucose (C6 H12 O6). A ball and stick model of glucose is shown here in its ring form, which is the form it takes in water. As a solid, glucose has a straight chain form.

Isomers of Glucose

Galactose is another monosaccharide with six carbons. Galacotse is a component of a disaccharide called lactose.

A. Glucose, a six-membered ring monosaccharide. B. Fructose, a five-membered ring monosaccharide. C. Sucrose, a disaccharide containing glucose and fructose. D. Molecular representation of starch illustrating the alpha-glycosidic linkages joining monosaccharides to form the polysaccharide structure.

Amino acids

Amino acids

Amino acids have an amino group consisting of nitrogen and hydrogen's at one end of the molecule and an organic acid or carboxyl group at the other end. In addition, the first carbon of the amino acid can attach any one of a number of different functional groups. These give each type of amino acid distinct chemical and physical properties. The amino acids shown in the three dimensional models were selected to illustrate the major kinds of amino acids.

Amino acids are important for several reasons. First, they are the monomers or building blocks from which proteins are made. Second, many amino acids are the precursors for important neurotransmitters and other signaling molecules in the body such as the hormone melatonin.

 

Glycine

Glycine is the simplest amino acid. On the right side is a carboxyl or organic acid group consisting of a carbon double (gray) bonded to an oxygen (red) and single bonded to a hydroxyl group (OH). On left side is nitrogen (blue) bonded to three hydrogen's and to the second carbon. This amino group is basic.

Valine

Valine is a somewhat more complex amino acid. Notice the small side chain consisting of three carbons bonded to hydrogen's. Each amino acid differs in what functional group it has hanging from the second carbon.

Tryptophan

Tryptophan is the starting material for serotonin, an important neurotransmitter and for melatonin, a hormone produced by the pineal gland.

Phenylalanine

Phenylalanine is a good example of an amino acid with a non polar (hydrophobic) side group.

Aspartic acid

Aspartic acid (Aspartate) is an example of an amino acid with a functional group that ionizes in solution.

Cysteine

Cysteine is an example of amino acid containing sulfur. These are important structural amino acids because two sulfurs from distant amino acids in a polypeptide can link together to form covalent bonds that help to stabilize the structure of the polypeptide.

Peptides

The word 'peptide' refers to two or more amino acids joined together by peptide bonds. Peptides can contain more than two amino acids as in this peptide composed of four amino acids trptophan, methionine, aspartime and phenylalanine.

Peptide Bonds

Two or more amino acids can be linked together by a dehydration synthesis to form a peptide. The characteristic chemical bond is called a peptide bond. This picture shows two amino acids joined together by the carboxyl group of one and the amine group of the second. Notice that a water molecule is removed in the process.

Polypeptides

Longer chains of amino acids strung together are called polypeptides, more commonly referred to as proteins. Proteins have a complex three dimensional structure as shown in these RasMol models.

Insulin: Stick Model

Insulin: Cartoon model showing the arrangement of amino acids into sheets and coils in the insulin molecule.

Protein from cobra venom: Stick Model

Protein structure

Proteins have a complex three dimensional structure which is important because the function of a protein is closely tied to its three dimensional structure. The nature of this structure is usually explained in terms of a structural hierarchy, from primary to quaternary.

Primary Structure

The primary structure of a polypeptide or protein is the sequence of amino acids in the protein. In the case of insulin shown here, there are two polypeptide chains in the primary structure. Each three letter abbreviation stands for one of the twenty basic amino acids found in living things:

Chain 1 GLY- ILE -VAL- GLU -GLN -CYS -CYS -THR- SER -ILE -CYS- SER -LEU - TYR -GLN -LEU -GLU -ASN -TYR -CYS -ASN

Chain 2 PHE -VAL -ASN-GLN -HIS -LEU -CYS- GLY- ASP -HIS -LEU- VAL- GLU- ALA -LEU- TYR -LEU- VAL- CYS- GLY- GLU- ARG -GLY- PHE -PHE -TYR - THR -PRO -LYS -THR

Secondary StructureSecondary structure refers to the folding of the chain of amino acids into a helix or a pleated sheet.

Fig. 1 : Example of a beta-sheet (arrows indicate the direction of the amino acid chain)

Fig. 2 : Example of an alpha-helix. A: schematic, B: molecular, C: from top, D: space filling model.

The structure is a pleated sheet formed by parallel chains of amino acids. These sheets are important in many structural proteins. Many proteins have sheets and helices. Secondary structure arises from the geometry of the bond angle between amino acids as well as hydrogen bonds between nearby amino acids.

Tertiary Structure

Tertiary structure refers to a higher level of folding in which the helices and sheets of the secondary structure fold upon themselves. This higher level folding arises for several reasons. First, different regions of the amino acid chain are hydrophilic or hydrophobic and arrange themselves accordingly in water. Second, different regions of the chain bond with each other via hydrogen bonding or disulfide linkages.

Quaternary structure

Quaternary structure arises when polypeptide chains are bound together usually by hydrogen bonds. For example hemoglobin, the oxygen carrying protein in blood has four subunits of hydrogen bonded together. Most proteins with a molecular weight of 50,000 or more are

made of such units. Sometimes quaternary structure may be very complex. For example, beef glutamate dehydrogenase is an enzyme with a molecular weight of 2,200,000. Each enzyme molecule consists of eight large subunits. In turn, each of these consists of numerous smaller units.

The interesting thing about proteins made of polypeptide subunits is that given the right solution, they self assemble into a complete and functional protein! The cell takes full advantage of this property to rapidly generate the cytoskeleton much of which consists of very long chains or helices, or tubes of protein sub-units as in the example below.

This is just a small section of a long double helix made out of thousands of small protein sub units, and illustrates the size of structures the cell can build using protein subunits.

Nucleotides and Nucleic Acids

Nucleotides

Nucleotides are monomers consisting of a phosphate group, a five carbon sugar (either ribose or deoxyribose) and a one or two ring nitrogen containing base.

Nucleotides are important for several reasons. First, the genetic material (DNA) is a polymer of four different nucleotides. The genetic information is coded in the sequence of nucleotides in a DNA molecule. Polymers of nucleotides such as DNA and the several types of RNA in the body are called nucleic acids.

Nucleotides and related compounds are also important energy carrying compounds. Among

the ones commonly encountered are ATP, and NADH.

Nitrogen bases

In nucleotides there may be any one of a number of nitrogen bases. Nitrogen bases are functional groups consisting of one or two rings containing both carbon and nitrogen. Adenine monophosphate, AMP and cytosine monophosphate, CMP illustrate the two basic types of nucleotide nitrogen bases.

Purines

Purines are nitrogen containing bases consisting of two rings. AMP's nitrogen base has two nitrogen bearing rings (Nitrogen=blue, Phosphorus=yellow, Carbon = grey, Oxygen = red) and is thus a purine called adenine. The two purines you will encounter as part of the structure of nucleotides are called adenine and guanine.

Pyrimidines

A pyrimidine is a nitrogen base with just one ring consisting of carbon and nitrogen. CMP's nitrogen bearing base has one ring and that kind of base is called a pyrimidine. The major pyrimidines found in nucleotides are cytosine (as in CMP), thymine, and uracil.

NADH

NADH is an important electron acceptor in cellular respiration. Note that it consists of a purine containing nucleotide and a pyrimidine containing nucleotide.

Nucleic acids

Nucleic acids are polymers of nucleotides joined together to make large macromolecules. The important nucleic acids are deoxyribonucleic acid (DNA) and various types of ribonucleic acid (RNA).

DNA

This model represents part of a strand of DNA, the genetic material. Notice the double helix, the backbones of which are formed by joined phosphate groups (yellow). DNA is the genetic material found in cells and contain instructions that help to determine the structure and function of cells.

RNA

Below is a type of RNA called transfer RNA. This molecule is involved in protein synthesis. It is not a double helix but actually more of a clover looped shape. In both DNA and the RNA's, hydrogen bonds are important in determining the molecule's shape.