MICROBIOLOGY 101/102 INTERNET TEXT

CHAPTER V: THE CHEMISTRY OF LIFE.

Updated: 09/10/99

GLOSSARIES

GENETICS | BASIC CHEMISTRY | ADVANCED CHEMISTRY | A VIRTUAL CHEMISTRY CLASSROOM  

MICROBIOLOGY TODAY

http://www.intelihealth.com/enews?240835; House flies carrying disease
http://www.intelihealth.com/enews?240826; NY out break of E. coli 0157:H7
http://www.intelihealth.com/enews?240832; Drug to treat alcoholism by blocking receptor.

TABLE OF CONTENTS

SOME CHEMISTRY OF LIFE

Elements & Atoms
Figure 1. Cartoon of the atoms of hydrogen and oxygen. The elements of hydrogen and oxygen have 1 and 6 electrons in their respective OUTERMOST ORBITS. Since these orbits can hold 2 and 8 electrons, they are UNSTABLE and can be thought of as seeking to FILL their outermost electron orbits. How elements do this is discussed below.

The study of the chemistry of living organisms is called BIOCHEMISTRY (bio = life). All atoms are composed of three components, NEUTRONS, PROTONS and ELECTRONS. The first two reside in the nucleus of the atoms, and are indicated in the figure above as the red and brown balls. Electrons (blue balls) orbit around the nucleus much as earth orbits around the sun. The electrons are always located in SPECIFIC ORBITS or ELECTRON SHELLS around the nucleus. The maximum number of electrons in each orbit is a UNIVERSAL CONSTANT. The number of electrons in the outermost orbit of an atom determines its CHEMICAL CHARACTERISTICS. For the chemistry of living organisms, we are mostly concerned with 2 & 8-electron orbits. An atom is most STABLE when its outermost orbit is filled to capacity. For example, if the orbit around an atom is a 2 electron-orbit, but only has ONE electron in it, it is UNSTABLE and SEEKS to fill its orbit with another electron.

molecule.gif (977 bytes)
Figure 2. The water molecule.

When two or more atoms form a stable union they are called a COMPOUND or MOLECULE. The two terms can be used interchangeably; i.e., all molecules are compounds and all compounds are molecules. A compound/molecule may be composed of atoms of the same element or of atoms of different elements; as in the case of two hydrogen or nitrogen atoms joining to forming H2 & N2 gas respectively, but the majority of molecules involve the bonding of different atoms together. The association between atoms that gives them stability are called BONDS. Every molecule has certain unique chemical characteristics that differentiate it from all other molecules. Any change in a given molecule converts it into another molecule with a different, and unique, set of characteristics. The following examples illustrate this:

I. BONDS MAKE ALL THE DIFFERENCE

  1. Cells store glucose by bonding the glucose molecule together by covalent bonds to form long chains composed of 1,000s of glucose molecules. These long polymers are called polysaccharides. There are different sugar-to-sugar covalent bonds.
  2. If a glucose polysaccharide contains only a 1,4 bonds it is a starch molecule.
  3. If a glucose polysaccharide contains both a 1,4 and a 1,6 bonds it is glycogen molecule.
  4. If a glucose polysaccharide contains b 1,4 bonds it is cellulose molecule.
  5. The different bonds impose on each polysaccharide a unique chemical and physical character. An analogy is bricks vs. a building. The same bricks (glucose) may be used to construct very different structures depending on how the bricks are put together. For example, a house (starch), a school building (glycogen) or a train station (cellulose); each design has it’s own unique character.
  6. If you break any of these molecules up into shorter chains of glucose molecules they are no longer "starch/glycogen/cellulose" because they no longer have the chemical and physical characteristics that defined each of the polysaccharides.
  7. There is a gray area here; who can tell me what it is?

    Glucose & Fructose Molecules (3242 bytes)
    Moving 2 hydrogen atoms from the #2 carbon of glucose to the #1 carbon completely changes the chemical and physical character of the sugar molecules.

II. SMALL ATOMIC CHANGES MAKE LARGE DIFFERENCES

  1. The change of location of 2 hydrogen atoms in the molecule glucose (formula = C6H12O6), can convert it into fructose (ALSO = C6H12O6), a different molecule.
  2. Our taste-buds can distinguish between this change via the ligand/receptor system.

 

 

III. THE REASON OUR GENES ARE MADE OF DNA

Ribose Molecules (2760 bytes)

The loss of an oxygen atom from the #2 carbon of ribose, forming deoxyribose, significantly changes the chemical nature of the pentose sugar.

  1. The two pentose sugars in DNA & RNA differ only in the presence of an oxygen atom at one position. RNA contains ribose, which has that oxygen whereas DNA uses deoxyribose which lacks that oxygen.
  2. Since deoxyribose is more stable than ribose, nature uses it for the majority of life’s genomic material.

 

 

 

 

Water Molecule (7564 bytes)
Figure 3. Covalent bonds in water. In covalent bonds one electron spends part of its time orbiting around one atom and the rest of its time orbiting around the other atom in the compound. Biological molecules like proteins, nucleic acids and lipids are held together mostly by covalent bonds. In the water molecule shown above, note that the two types of atoms SHARE their electrons (yellow oval) so that both fill their outermost orbits to the maximum numbers of 2 & 8 respectively.

Bonds differ in strength in that there are WEAK BONDS and STRONG BONDS. Strong bonds are VERY STABLE and it takes a considerable amount of energy to break them. Strong bonds are required in living organisms to give them the STABILITY OF STRUCTURE to exist in a chaotic world. For example the microbes that live in boiling springs are subject to the destructive forces of heat and to survive these cells must have bonds that are not destroyed by the temperature of their environment. However, for cells to grow and to carry out the diverse processes of life they must be FLEXIBLE. Strong bonds limit flexibility, so weak bonds are important in the chemistry of life. The most common strong bonds are COVALENT BONDS (CB) that occur when atoms SHARE electrons so as to FILL each other outer electron orbits to the optimum level

 

 

 

Ionic Bond (7472 bytes)
Figure 4. Ionic bonds. The sodium atom on the left has only one electron (blue) in its outermost orbit so it is unstable. To achieve a stable electron shell, sodium atoms like to GIVE AWAY or DONATE its outermost electron to other atoms. Chlorine has seven electrons in its outermost orbit and only needs ONE to achieve stability. When sodium donates its electron to chlorine, both achieve orbital bliss and stability. However, since electrons carry a negative charge, the sodium atom becomes POSITIVELY charged when it donates an electron and chlorine becomes NEGATIVELY charged upon gaining an electron. The two charged atoms are now called IONS and they strongly attract each other forming the compound SALT or NaCl.

 

 

In cases where atoms DONATE ELECTRONS TO OTHER ATOMS to achieve the optimum number of electrons in the outer orbits + and - ions are formed which attract each other much like the poles of magnets. The bonds formed by these attractions are called IONIC BONDS. Ionic bonds are not as strong as covalent bonds, but they play an important role in biochemistry.

Another type of association between molecules, which is not a TRUE BOND, is called the HYDROPHOBIC ASSOCIATIONS. The hydrophobic associations form between molecules that are hydrophobic (hydro=water; phobic=dislike). Since water molecules love each other so much they refuse to associate with the hydrophobic molecules. That is water is a hydrophobic bigot.

Lipid Bilayer
Figure 5. Hydrophobic association.

The result is that the water molecules force or push the hydrophobic molecules together. Molecules that love to associate with water are said to be HYDROPHILIC and they are always surrounded by a shell or covering of water molecules. For example, the central core of many proteins is rich in hydrophobic associations because the TERRIBLE HYDROPHILIC MOLECULES along with their associating water molecules have pushed the hydrophobic molecules into the center. A common molecule associated with these types of associations are phospholipids (click on the "phospholipid" box) that are often found in cell membranes; note the long hydrophobic tails (gray & white balls) and the hydrophilic phosphate end (orange ball) and how water lies on the outer surface of the membrane. Other molecules that form hydrophilic associations are the common fats that we are warned to cut back on like oleic and palmitic acid and cholesterol. A detailed picture of a membrane and membrane components using Chime can be viewed at this site.

HYDROGEN BONDS

Polar Water Molecule (5057 bytes)
Figure 6. Polar molecules. In a water molecule the oxygen atom is attached, ASYMMETRICALLY to two hydrogen atoms by covalent bonds. The oxygen nucleus attracts the hydrogen electrons more strongly than the hydrogen nucleus, thus the negatively charged electrons hang around the oxygen nucleus more, giving it a more NEGATIVE charge and the hydrogen atoms a more POSITIVE charge. The water molecules bind together (figure below) through the weak + & - associations forming a film on the surface of water that is STRONG enough for some insects to walk on it.

H-bonds of water (7365 bytes)
Figure 7. Hydrogen bonds. By binding together the water molecules form a film on the surface. To learn more about water click here.

When two atoms that differ in their attraction for electrons form a covalent bond a POLAR molecule forms because the electrons are unequally distributed; being closer to one of the atoms than to the other. That is, the distribution of elections is ASYMMETRICAL. Since the electrons are negatively charged the atom that attracts electrons the most strongly take on a small NEGATIVE charge. The atom at the other end of the asymmetrical molecule has a DEFICIENCY of electrons and takes on a slight POSITIVE charge. Thus one POLE of the molecule is partly negative and the other is partly positive. Hydrogen forms polar molecules with oxygen and nitrogen, but not with carbon. Water is one such POLAR molecule; the hydrogen has a positive charge and the oxygen a negative charge. The positive hydrogen in polar molecules forms weak bonds with the negative poles of other polar molecules. These weak bonds are called HYDROGEN BONDS and are very important in biological molecules.

WEAK BONDS are crucial to the processes of life. Their role are illustrated in #DNA. The large molecules of DNA which carry the genetic information of every organism (except a few viruses) have a problem. On the one hand it must be STABLE or the genetic message become garbled and lost, but it must be "READ" easily both to be #REPLICATED or COPIED for the next generation and to provided the information to make the tools of life for the cell it currently resides in. HYDROGEN BONDS solve this problem. Hydrogen bonds are very weak; so weak in fact that the heat from our own bodies is enough to cause single hydrogen bonds to break. But in very large molecules like proteins, and nucleic acids there can be many hydrogen bonds. The SUM of the hydrogen bonds in a protein or nucleic acid polymer, provides stability. Yet within these molecules, small numbers of hydrogen bonds are EASILY BROKEN when required; the overall molecule remaining stable because of the many other hydrogen bonds. Hydrogen bonds are like buttons in a shirt; individual buttons are easily opened when it is necessary to get into the shirt, but the other buttons retain the basic shape of the shirt even while one or two buttons are opened.

COMMON COMPONENTS IN CELLS

Click here to view the Klotho site which shows almost any biochemical molecule. However, first you must load the HELPER applications, RasMol & kinemage by following the instructions at this site. You should also load the helper Chime.

  1. Type in the name of the molecule you want to see like "glucose" or "adenine" or "alanine" in the window or click on the "Compound listing" and choose the molecule you want to see by name-go to step #3.
  2. Click the "Search Klotho". You will see a list of molecules related to what you have types.
  3. Click on one of them. On the page that comes up you will see a stick version at the top of the page.
  4. Scroll down until you come to : "The compound's PDB file can be seen in three ways". If you have loaded RasMol, click on "Interactive Viewer" to bring up a picture of the molecule.
  5. Using the mouse, hold down the left button and move the molecule around for viewing from different angles. To change the viewing form of the molecule click the right button and chose from the menu that appears.
  6. If you don't have RasMol, click on "Static Image" at step #4.

The major molecules in #all life are:

CARBOHYDRATES and SUGARS, like glucose, sucrose and fructose, and their polymer, POLYSACCHARIDES (like the starch in bread or the cellulose in paper). To see the structure of individual sugars click here. Click here for another set of pictures of carbohydrates in the ring form and here for a discussion of the role of sugars in biological systems.

AMINO ACIDS and their polymers, #PROTEIN . Click here for a view of amino acids, however you must use the RasMol helper application. From this URL you should learn what "Side Chains" on amino acids are. Click here for basic material on amino acids and proteins. As you will learn in Chap 7, proteins are the "tools" of life in that they make things work in a cell. If DNA is the "blueprint or plans" of life,proteins are the "hammers, nails, glue, and screw drivers" etc. of life. One such protein is hemoglobin which makes our blood red and carries the oxygen we aerobes need to live. Another protein, one in our tears, is lysozyme, which dissolves many types of bacteria; does it make sense to you that our tears should contain such a protein?

#NUCLEIC ACIDS and NUCLEIC ACID POLYMERS.

Nucleic acids (NA) are the building blocks of the genetic material (genes) of living organisms. View this site for a look at the major NA that are required for life. When individual NA are strung together in long, #large molecules, they are called polynucleotides or NUCLEIC ACID POLYMERS. In later chapters you will learn how certain of these polymers hold the code of life.

FATS/lipids. This site shows you the structure of three common fats found in many living organisms. Click here and here for additional information on fats and lipids and look at the section on the cytoplasmic membrane in #Chap 3. Fats and lipids are important components of cell membranes, without which cells could not exist. Lipid membranes separate the ordered material and processes inside the cell from the chaos that exists outside the cell. In Eukaryotic cells lipid membranes separate the organelles within these cells from the other material in the cytoplasm which increases the efficiency of whatever the organelle does for the cell. Lipid cell membranes usually exist as LIPID BILAYERS. Click here to see a lipid bilayer. The cell membranes are fluid, something like a soap bubble, and within them are proteins that carry (transport) various molecules selectively into and out of the cytoplasm. For a description of this process click here.

Various MINERALS; iron, magnesium, phosphorus, zinc, copper etc. How many of you have tried Zn to see if it helps your colds?

Small organic molecules we commonly call VITAMINS such as folic acid, pantothenic acid, vitamin C etc. How many of you have tried vitamin C for your colds?

Sugar Polymer
Figure 8. Sugar polymer. In this molecule, sugar monomers (e.g. glucose; red hexagons) are fastened together with covalent bonds (black lines) to form a larger molecule called a POLYMER. All biopolymers can be represented in a similar fashion. Click here for a 3D view of sugars.

Living organisms are mostly composed of POLYMERIC molecules, which are large molecules composed of repeating subunits of smaller molecules, called MONOMERS, strung together in various arrangements. Common biopolymers are proteins, starch, cellulose, fats and nucleic acids. In this course you will not be concerned with the detailed chemical structures of these polymers or the monomers that they are made of. Rather, you will responsible for learning the BASIC PRINCIPLES of their compositions and functions in living organisms.

There is a SIMPLE TERMINOLOGY that, once learned, allows one to easily describe the general size & composition of biomolecules. The size of biomolecules. is described in general terms by their PREFIXES:

POLY means MANY or LOTS;

MONO means one, which is the basic SUBUNIT of a polymer;

BI, & DI, TRI, TETRA, PENTA and HEX mean two, three, four, five and six subunits bonded together to form a larger molecule.

OLIGO means something larger than ~6 subunits but not as many as POLYMER.

SUFFIXES are often used to describe the general molecular type of a biomolecule:

The suffix "OSE", refers to mono sugars like glucOSE, fructOSE, sucrOSE etc.;

The suffix "SACCHARIDE" refers to sugar; i.e., a POLYSACCHARIDE is a large molecule composed of many sugar subunits (Fig. 8). A polysaccharide may be composed of ONLY ONE TYPE of sugar (starch has only glucose in it) or MANY DIFFERENT SUGARS (lipopolysaccharide = #LPS), plus other molecules.

The suffix "PEPTIDE" refers to a molecule composed of 2 or more AMINO ACIDS; a DIPEPTIDE is composed of 2 amino acids, a TRIPEPTIDE of three etc. A long string of amino acids is called a POLYPEPTIDE or a PROTEIN. The amino acid monomers or subunits of peptides and proteins are fastened together with very strong covalent bonds called PEPTIDE BONDS. Click here for a brief discussion of peptide bonds.

dna1.gif (10483 bytes)
Figure 9. A molecule of DNA. The PINK balls are the phosphate groups and the 5-sided ORANGE structures are the pentose sugar, deoxyribose. These two chains of alternating sugar-phosphate molecules, make up the BACKBONE of the DNA molecule. The four bases (RED, GREEN, BLUE and ORANGE) are attached to the pentose sugar and always face each other, forming the DOUBLE STRAND. Note that an "A" always associates with a "T" and a "G" with a "C". The blue lines between the bases represent #HYDROGEN BONDS that hold the two strands together. An A-T & G-C are called BASE PAIRS. The A-T association has two hydrogen bonds, whereas the G-C association has 3. The human genome contains approximately 3 billion base pairs. The DNA molecule is the INSTRUCTION MANUAL that tells a cell how to make more of the exact same cells.

Two types of polynucleotides are present in all cells. These are DEOXYRIBONUCLEIC ACID (DNA) and RIBONUCLEIC ACID (RNA). There are two chemical differences between them. Both have a PENTOSE sugar (5-carbon atoms), but DNA contains the pentose sugar DEOXYRIBOSE and RNA contains the pentose sugar RIBOSE. Both DNA and RNA contain phosphate and four nucleotide BASES. Three of the bases are the same, GUANINE, ADENINE, CYTOSINE, however DNA contains THYMINE, while RNA contains URACIL. The bases are almost always found in pairs consisting of AT or AU and GC. Both DNA and RNA exist as long chains. The backbone of these chains are alternating sugar-phosphate units. The bases are attached to the respective sugars and stick out on one side of the chain. Usually, but not always, RNA and DNA exist as DOUBLE STRANDS. These double strands are bonded together through HYDROGEN BONDING between the BASE PAIRS. So a DNA chain has pairs of AT and GC facing each other at all points down the double strands. The AT pairs have TWO hydrogen bonds and the GC have THREE hydrogen bonds between each pair. Click here for another discussion of nucleic acids; both with excellent pictures. Visit this site for a well illustrated slide show on nucleic acids and be able to tell the difference between ribose and deoxyribose.

Detailed models of DNA can be viewed at this site by clicking here (need Chime 2.0or higher). To view a stereoscopic image (3D) at the 1st site click on the images labeled "name image # s" (the "s" stands for stereoscopic). To observe the 3D forms cross your eyes and stare at a spot midway between the two images. It will take some effort & both images need to be equally on the screen for it to work.

At the 2nd site, click on "DNA", then rotate the DNA molecule while holding down the left mouse button. Use the rt. button to bring up the view-menu and play with various views of the DNA molecule. For a 3D view of the DNA, choose "Options" on the menu; choose "Stereo Display" and click left mouse button. Use the mouse to rotate the DNA while viewing it in stereo. Note the GROOVES in the DNA; activate the HYDROGEN BONDS and look for them using the stick view (they are hard to spot).

INTERNET ADDRESSES OF POSSIBLE INTEREST

http://colossus.chem.indiana.edu/supplement.html; Great site containing a biochemistry course. It is a high-level course, but some of the figures and explanations are suitable for Micro 101 students.

http://www.nyu.edu:80/pages/mathmol/library/life/life.html; 3D views of AA, need RasMol or WebSpace helpers

http://c4.cabrillo.cc.ca.us/; Lots of models of biological compounds; need the plug-in Chime.

http://gened.emc.maricopa.edu/academics/classes/biology/index.html; Lots of the basics in this material.

Click here for a self assessment test of what you have learned.

Copyright © Dr. R. E. Hurlbert, 1999.
This material may be used for educational purposes only and may not be duplicated for commercial purposes.
SCIENCE HALL, ROOM 440CA
PHONE: 509-335-5108
FAX: 509-335-1907
E-mail address: hurlbert@wsu.edu or hurlbert@pullman.com
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