Important Biological Molecules

Important Biological molecules.

After doing this material and reading Chapter 3 in your text you should be able to:

  • Define organic molecule as used by chemists.
  • Explain why carbon is so useful for cells.
  • Define polymer and monomer and give examples.
  • Recognise and give the basic functions of nucleic acids
  • Give the basic functions of proteins in cells.
  • List and discuss the 4 levels of protein structure.
  • Recognize and give the functions of the following carbohydrates:
    • Simple sugars
    • Polysaccharides:  Starch, cellulose and chitin.
  • Define lipid and recognize the following types of lipids and their functions:
    • Triglycerides
    • Sterols and Steroids
    • phospholipids

Where possible I have given  links to pages using a molecular viewer called jMol (J stands for Java).  jMol allows you to rotate view the molecule in three dimensions. In fact there are even options for viewing them using certain types of “3D” glasses. So play with the links as well as just looking at the pictures. In jMol you can change the way the molecule is viewed and when you  go to one of the pages that uses jMol the molecule may not be presented in the same way as it appears in my snapshot of the molecule. So play with the settings.

Note: Unfortunately jMol does not work if you view the jMol links with tablets since  jMol requires JAVA..

Organic compounds

BIG THINGS ABOUT ORGANIC COMPOUNDS:

  • Don’t confuse the use of the word organic as used by biologists with the everyday meaning of organic as being “natural”. When you see the term organic molecule or or organic compound, “organic” means that the molecule has a skeleton of carbon atoms covalently bonded together along with hydrogens often atoms of other elements.
  • Organic molecules with just hydrogen and carbon are called hydrocarbons. The more like a hydrocarbon an organic molecule is the less attracted it is to water. Compounds that are not attracted to water such as fats and oils are called hydrophobic “water fearing”.
  • Cells can make many different types of organic molecules because each carbon atom can four covalent bonds allowing carbon atoms to form complex three dimensional structures.
  • Some organic molecules are relatively small and simple. For example Glucose is a simple sugar with the molecular formula C6H12O6.
  • Some organic molecules are huge molecules made of many smaller molecules linked together. Such molecules are called macromolecules or more precisely, polymers. For example starch and cellulose are both made from many thousands of glucose molecules linked together by covalent bonds. The individual simple molecules that make up the polymer are called monomers.

 

Why is life based on carbon?

Science Fiction is full of speculation that maybe life elsewhere could be based on other elements than carbon. A commonly used element in fiction is silicon. Silicon is the element just below carbon in the periodic table. See figure 2.5. It also can produce four covalent bonds like carbon and shares many chemical an physical properties. Why is life on our planet at any rate NOT based on silicon?

Carbon does occur by itself sometimes.

The three common natural forms are:

  • Diamond
  • Graphite
  • Fullerine

Diamond(Left), Graphite (top right), Fullerine (bottom rifght)


Functional groups

Organic molecules have a wide range of properties, some such as sugar are solids, others such as many lipids and hydrocarbons are liquids, a few such as methane or ethane are gasses under normal conditions. Also some organic molecules such as hydrocarbons are hydrophobic (not attracted to water), others such as sugars are hydrophilic (attracted to water and may dissolve in water). Some are acids, some are bases. This diversity of properties depends on the types of functional group that are attached to the molecule. Functional groups are small groups of atoms that when attached to the carbons of an organic molecule change the chemical and physical properties of the molecule.

Make sure you can recognise these main functional groups: Hydroxyl, Carboxyl, Amino, Phosphate and Methyl. The first four are hydrophilic the methyl group is hydrophobic!

 EXAMPLES OF HOW FUNCTIONAL GROUPS AFFECT THE PROPERTIES OF ORGANIC MOLECULES:

Ethane C2H6 is a hydrocarbon. It is a gas and not attracted to water molecules. So ethylene is hydrophobic. As a rule of thumb organic molecules which consist of carbon and hydrogen are hydrophilic. The more oxygen atoms and hydrophilic functional groups the molecule has, the more hydrophilic the molecule is.

Ethanol or ethyl alcohol C2H5OH has a hydroxyl group in place of one of the hydrogens in ethane. Ethanol is a liquid and attracted to water molecules (Hydrophilic).  Ethanol of course is drinking alcohol that hopefully you use in moderation.

Acetic acid has a carboxyl group (COOH). Carboxyl groups are sometimes called organic acid groups because compounds with carboxyl groups donate hydrogen ions to a solution. Typically these are weak acids rather than strong acids like hydrochloric acid. Acetic acid is the acid in vinegar so there is nothing exotic about this compound either!

Glycine is an amino acid that has both an amino group and a carboxyl group attached to the carbon. The amino group (NH3) acts like a base and the carboxyl group like an acid. So Glycine is an amino acid. Glycine like other amino acids is a solid at room temperature.

So this example starting with ethane which is a gas and ending with glycine an amino acid shows how adding different functional groups to an organic molecule can change the physical and chemical properties of the molecule.

Ethane(top left), Ethanol (top right), Acetic Acid (lower left), Glycine(lower right)

 

Polymers and monomers.

One big theme for cells is that the great big molecules made by cells such as proteins or nucleic acids are polymers. Polymers are huge molecules made out of many smaller molecules called monomers. For example starch is a polymer made out of many thousands of glucose molecules joined together by covalent bonds. We will briefly survey the main types of polymers and their monomers starting with polysaccharides. We also look at lipids which are medium sized molecules, that while they are NOT polymers, are extremely important for cells.

Making polymers.

Cells make polymers by a process called dehydration synthesis or dehydration reaction. For instance as a plant cell makes starch every time a glucose molecule is added, a water is removed enabling the glucose to join with the others. The same idea-joining a monomer to a polymer by removing a water is used to join amino acids during protein synthesis and to join nucleotides together to make nucleic acids.

Digesting Polymers.

When organisms break down polymers when they are no longer needed or during digestion, the covalent bonds between the monomers is broken apart but adding water. This is the reverse of the dehydration synthesis and is called hydrolysis. So when you eat beef or some other protein rich food the proteins are broken down during digestion by enzymes. The result of this hydrolysis is the amino acids. The amino acids are absorbed into the blood stream by the small intestine. The amino acids are taken onto our cells from the blood stream and the cells use them to make just the proteins they need.

Polysccacharides

Polysaccarides are polymers made out of many simple sugars. Most commonly the sugar used to make polysaccharides is glucose. There are lots of different types simple sugars and they combine to form larger carbohydrates. For example common table sugar is called sucrose and it is made out of a glucose molecule covalently bonded to another simple sugar called fructose.

Glucose is found in two forms. An open form on the left and a closed form with a six sided ring on the right.

 

 

 

Glucose though is the monomer used to make the following familiar polysccharides.

 

 

 

 

 

 

Here is a summary of the main polysaccahrides and their monomers that you should know.

 

Nucleic acids

DNA and tRNA are nucleic acids-sometimes also referred to as polynucleotides because these are polymers made of of many nucleotides.

DNA double Helix rendered with jMol

DNA double Helix rendered with jMol

 

 

 

 

 

 

 

 

DNA Double Helix

RNA’s are nucleic acids related to DNA. In cells, RNA’s are involved in protein synthesis either carrying instructions for making a protein to the ribosome where the protein is made, or carrying amino acids to the ribosome for assembly into the protein. Today we understand that RNA’s have a number of other functions in the cell in terms of regulating gene expression. Also some viruses use RNA as genetic material rather than DNA.

This picture shows a transfer RNA which carries a specific amino acid to the ribosome during protein synthesis.

 

tRNA

A jMol rendering of tRNA. This particular transfer RNA carries an amino acid called phenylalanine to the ribosome.

 

 

 

 

 

 

 

 

 

tRNA

Here is a summary of the major Nucleic acids and their nucleotide monomers.

Proteins

Proteins have many functions in the body. Catalase is one of a number of protein based enzymes that cells have that break down hydrogen peroxide into water and oxygen gas. Cells have these enzymes because peroxide like compounds are  produced as a bi-product of metabolism. These compounds are strong oxidizing agents and destroy covalent bonds in organic molecules.

Catalase showing secondary structure.

A jMol rendering of the catalase protein showing different folding arrangements found in the protein’s secondary structure

 

This catalase is from beef liver and in lab we will meet a catalase produced by potatoes. By the way these enzymes today are referred to as peroxidases.

 

 

 

 

Catalase from Beef Liver

 

Four Levels of Protein Structure

As is so common elsewhere in biology form and function go together in protein chemistry. Proteins typical have a complex form related to their function and changes in environmental factors such as temperature, pH, presence or absence of various trace elements and organic cofactors such as vitamins can have a profound effect of the ability of a protein to function.

Here is a video using the jMol at the Protein Data-base website to explain the levels of protein structure. Make sure that you read about protein structure in chapter 3 of your text and can identify what these levels are due to.

The four levels of protein structure to explain are:

  • Primary structure
  • Secondary Structure
  • Teritiary Structure
  • Quaternary Structure
One remark about the video is that tertiary structure is affected by the solution that the protein is in-not just water but also the ions and other other substances in the protein’s aqueous environment. The shape and hence the function of enzymes and other proteins is affected by many factors in the environment including temperature and pH.

Denaturation.

If a protein is exposed to extreme conditions beyond what it is adapted for, say boiling water or extremely high or low pH the protein’s three dimensional structure as altered to the point where it can no longer return to its original shape and function. This is called denaturation. You are familiar with this if you have boiled an egg. The egg white is denatured albumin protein that has become denatured by the boiling water.

Here is a summary with examples of proteins.  There is almost an infinite number of proteins that are possible. For instance a small protein might have 50 amino acids. But the mumber of hypothetically possible proteins just 50 amino acids long is 20^50 (20 raised to the 50th power) which is a huge number. You might try to work it out.  Remember that proteins have complex three dimensional shapes which are related to their function.

 

Lipids.

Lipids are a diverse group of medium sized molecules. Commonly lipids include sterols and steroids, waxes and fats and oils. Most lipids consist mainly of hydrogen and carbons and so they tend to be non polar which makes them generally hydrophobic- not attracted to water. Hence the saying “oil and water don’t mix”

Steroids and sterols are lipids with a distinctive set of four carbon rings. Examples include cholesterol and various steroid hormones such as estrogen and testosterone. Cortisol  is also a steroid type hormone. Cholesterol is an important part of cell membranes and a raw material for making various hormones.

Cholesterol

Cholesterol

 

 

 

 

 

 

 

Triglycerides are what we in every day speech call fats and oils. These lipids consist of a three carbon alcohol called glycerine or glycerol to which are attached three fatty acids.   Since there are three fatty acids attached to the glycerol, fats and oils are often called triglycerides. The difference between fats and oils is that in fats the hydrocarbon chains that make up the fatty acids are saturated meaning every available space for hydrogens is taken up.  Physically the result is a solid (fat) at room temperature. These triglycerides are said to be saturated fats.  In oils there are some double bonds in these hydrocarbon chains which prevents the triglycerides of oils from packing too close and so these lipids stay liquid at room temperature.  Since these lipids could be treated to hold more hydrogen, these are said to be unsaturated.

A saturated triglyceride

A Saturated Triglyceride

 

 

 

 

 

 

From http://employees.csbsju.edu/hjakubowski/Jmol/TAG/TAG.htm

Fats and oils are generally energy storage molecules and are used when ever an organism needs a compact source of energy. Triglycerides can store 9 Food calories of energy per gram of “fat” or “oil” as opposed to only 4 Food calories per gram for proteins and carbohydrates.

One important class of lipids are phospholipids which are important in the structure of cell membranes. These lipids have a polar head which is hydrophilic. The rest of the molecule consists of two non polar and hence hydrophobic tails. When phospholipids are put in water they arrange themselves into a lipid bilayer which is also an important structural element in cell membranes.

Here is a phospholipid. The orange ball at the top of the image is the phosphate atom that is part of the polar head.

A phospholipid. The polar head with the phosphate group is near the top.

 

 

 

 

 

 

 

 

from: http://bioinformatics.org/firstglance/fgij/fg.htm?mol=http://biomodel.uah.es/en/model2/bilayer/comun/pc-oph.pdb

This is what happens when phospholipids are put in water. The areas that are red and white are the polar heads of the phospholipids that are attracted to the water. The hydrocarbon tails are in the center since they neither are attracted to water or repel each other since they are non polar.

Phsopholipid bi-layer

Red areas = polar heads attracted to the water on either side of the bi-layer.

 

http://bioinformatics.org/firstglance/fgij/fg.htm?mol=http://biomodel.uah.es/en/model2/bilayer/comun/cutf2.pdb

Here is the lipid summary with the major types of lipids and what you should know about them.

 

 

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