Biochemistry

Index
Protons, Neutrons, Electrons | Atom | Elements | Isotopes | Bonding
Mixtures | Solutions | Acids and Bases | Formulas
Organic Compounds | Polymers | Condensation Animated
Hydrolysis Animated | Carbohydrates | Lipids | Proteins
Enzymes | Enzyme Hydrolysis | Enzyme Condensation | Nucleic Acid
Glucose Condensation | Polypeptide Hydrolysis | Quiz

Copyright © Steve Kuensting, 2004, All Rights Reserved.
This web tutorial may not be distributed by any means
without the expressed permission of the author!



Protons, Neutrons, Electrons
All substances on this planet and in the entire universe is made of tiny little bits of matter called Atoms. Atoms are too small to see, but experimentation indicates that they are made up of even smaller pieces of matter --- protons, neutrons, and electrons. These tiny bits of matter can have "charge". A proton has a +1 charge, an electron has a -1 charge, and a neutron has no charge.





Atom
Atoms are supposed to be structured (remember - we can't see them) with the protons and neutrons in the center - the nucleus, and electrons in high speed orbits around the central nucleus. In a neutral atom, the number of protons = the number of electrons.





Elements
The most important characteristic of an atom is its number of protons -- the proton number determines all of the chemical behaviors of an atom. There are 92 naturally occurring different types of atoms on earth. They all differ by the number of protons they have -- from 1 to 92.
Phosphorus - 15 protons
Sulfur - 16 protons
Chlorine - 17 protons
Calcium - 20 protons
Iron - 26 protons
Hydrogen - 1 proton
Carbon - 6 protons
Nitrogen - 7 protons
Oxygen - 8 protons
Sodium - 11 protons

(each has different color, texture, melting point, etc.
because of their different proton numbers.)



Elements
Each of the elements is represented by symbols. The common elements are listed below and their symbols are listed. You should note these symbols and associated them with their names!

H = Hydrogen
C = Carbon
N = Nitrogen
O = Oxygen
Na = Sodium
P = Phosphorus
S = Sulfur
Cl = Chlorine
Ca = Calcium



Isotopes
Not all atoms of an element are exactly alike. While all atoms of the same element have the same number of protons, they may have different numbers of neutrons. These atoms are called isotopes. Three isotopes of carbon are carbon-12 (6 neutrons), carbon-13 (7 neutrons), and carbon-14 (8 neutrons). Some isotopes are radioactive and release energy, damaging atoms/substances around them. Some of the radioactive isotopes (radioisotopes) are used in medicine, to trace the path of subtances in the body or selectively destroy a tumor.





Bonding
Fortunately for us, atoms "like" to bond to one another to form compounds. Both ionic and covalent bonds make possible the structure of a car , the human body, or this computer. Without this bonding, most of the universe would be dust -- no complex structure would be possible.





Bonding
The driving force behind bonding is the need for atoms to fill or empty their partially filled energy levels. The energy levels of atoms are the areas that electrons can exist around the nucleus. The first can maximally hold only 2, the second can hold 8, and the third can hold 18. Atoms will bond to one another to either fill or empty these energy levels.





Ionic Bonds
Ionic bonds result from the attraction of opposite charge - much like two oppositely polarized magnets. Ionic bonds form when atoms lose or gain electrons. Ionic bonds generally form between metals and nonmetals. Whey ionic compounds are mixed with water, they often dissociate into individual ions and float freely among the water molecules.





Covalent Bonds
Covalent bonds form when atoms share electrons. A molecule is a number (2 or more) of atoms held together by covalent bonds. Molecules that are polar (such as alcohol) will mix with water while molecules that are nonpolar (such as gasoline) will not.





Reasons for Bonding
In the formation of both covalent and ionic bonds, atoms gain stability by either filling or emptying their outer partially filled energy levels. In the covalent bond, atoms use each other's electrons to fill this purpose. In the ionic bond one atom takes electrons from another, so one atom fills its outer energy level while another atom empties its outer energy level.





Ionic and Covalent Bonds
When covalent bonds and ionic bonds are represented, the nuclei are not usually drawn since they do not directly participate in the bond. The symbol of the atom/ion is used instead. The electrons are not drawn either. A line is used to represent a single covalent bond (or shared pair of electrons) between atoms while charges (+ or -) are used to represent ionic bonds. Examples are shown below. Note that some atoms bind with multiple covalent bonds - double and triple bonds.





Hydrogen Bonds
A weak but very significant type of bond BETWEEN MOLECULES is the hydrogen bond. It occurs when hydrogen that is covalently bonded to oxygen or nitrogen is attracted to the nitrogen or oxygen atoms in another molecule, which themselves are covalently bonded to a different hydrogen atom. This type of bond attracts molecules to one another and is important to holding the structures of cells, tissues, and organs together. Water's polarity makes it capable of hydrogen bonding, which causes its high boiling point, low melting point, high surface tension, and high specific heat. Surface tension is the ability of a surface to resist penetration, and specific heat describes the amount of energy needed to raise a substance 1 degree celsius in temperature. Water is thus an excellent evaporative coolant and resists temperature changes in organisms.





Water
Water's polarity is caused by unequal sharing of electrons. In water, oxygen pulls the electrons of hydrogen towards itself so that it becomes partially negative, while hydrogen becomes partially positive. As a result, water molecules behave like tiny "magnets" and stick together much more strongly than they otherwise could - by hydrogen bonding. It is the intermolecular attraction that causes water to have its unusual properties.





Compounds and Mixtures
It is rare to find an element on earth -- a pure substance consisting of only one type of atom. Even a gold ring is not an element -- it is not pure (not usually). Much more common are COMPOUNDS -- substances that are made of molecules or ions. And even more common are MIXTURES -- substances that are the combination of two or more compounds.

Elements:
hydrogen gas
carbon
oxygen gas
nitrogen gas

Compounds:
water
alcohol
sugar
carbon dioxide gas

Mixtures:
pond water
ocean water
soil
air



Mixture
In a mixture, the combined substances retain their original chemical properties. They do not combine chemically together. Thus the chemicals of a mixture can usually be separated from one another in their pure form. One example is salt water - which can be separated by boiling the water away and collecting the salt that remains.





Solutions
A SOLUTION is a type of mixture where the chemicals are mixed thoroughly. Salt water, blood, and soda are all examples of aqueous solutions because their chemical solutes are uniformly distributed. The chemical in highest concentration in a solution is called the SOLVENT. Any chemical in lesser concentration than the solvent is called a SOLUTE. Example: the solvent in saltwater is water and the solutes is salt. All solutions which have water as the solvent are called AQUEOUS SOLUTIONS.





Water as a Solvent
Water's high polarity makes it compatible with all polar substances, and ionic compounds. Many salts are very water soluble because water is highly attracted to the charges of ions. Water can thus dissolve an amazing number of solutes because of its polarity. But, its polarity prevents all nonpolar substances from becoming aqueous solutes - like fats, waxes, steroids, and oils.





Acids and Bases
Aqueous solutions are generally either acidic or basic. Water molecules dissociate in aqueous solutions due to impacts with other water molecules. The dissociation of a water molecule produces two ions: a hydrogen ion and a hydroxide ion. The hydrogen ion has a positive charge and the hydroxide ion has a negative charge.





Hydrogen and Hydroxide Ions
In pure water, the concentration of hydrogen ion and hydroxide ion is equal because the dissociation of each water molecule produces one of each. The concentrations of each ion do not continually increase because the ions will randomly meet each other (a hydrogen ion meets a hydroxide ion) in the solution and rejoin to make water.





Hydrogen and Hydroxide Ions
An acid is an aqueous solution of water and solutes where the hydrogen ions outnumber the hydroxide ions. A base is an aqueous solution of water and solutes where the hydroxide ions outnumbers the hydrogen ions. These are caused by the interaction of solutes with the water, hydrogen ions, and hydroxide ions in the solution.





pH
A solution of pure water with an equal number of hydrogen and hydroxide ions is neutral. pH is used to measure the acidity and basicity of solutions. The pH scale ranges from 1 to 14. 7 is neutral. Acids have pH's between 1 and 7, bases have pH's between 7 and 14. Strong acids have pH's near 1; strong bases have pH's near 14.





The pH Scale
Write down some of the examples listed below of acidic and basic fluids. Notice that different parts of the body have different pH values.





Summary
All organisms contain mixtures of chemicals within them. Blood is an example of one such mixture. Blood contains chemicals such as glucose, water, salt, and protein. Each of the chemicals glucose, water, salt, and protein are in turn made of atoms - mainly carbon, hydrogen, oxygen, and nitrogen. Most of the chemicals found in organisms are made of only these four atoms.





Formulas
Chemical formulas are used to represent the atomic composition of a compound. There are two types of chemical formulas - Simple and Structural. Simple tell only the number and type of atoms in a compound. Structural show number, type, and arrangement of atoms in a compound. Atoms are represented with letters: H for hydrogen, O for oxygen, N for nitrogen, etc., no protons, neutrons, or electrons are drawn. (too difficult)





Organic Compounds
The most important compounds to life are a type of molecular compounds, those consisting of molecules that contain the atom carbon. All compounds containing carbon are called ORGANIC COMPOUNDS. Carbon is unique in that every carbon atom can bond to 4 other atoms at the same time, making it possible to form huge molecules consisting of thousands of atoms.





Polymers
Many of the large organic molecules found in living things actually consist of chains of smaller molecules, much like a necklace may consist of many small links or pearls. These large organic molecules are called POLYMERS and the smaller molecules they are made of are called MONOMERS. One example of a polymer not found in living things is PVC (polyvinyl chloride). It is used to make plastic pipe. The monomer that forms PVC pipe is vinyl chloride. It is structurally represented below.





In living things, monomers are linked together in order to store small monomer molecules, to form large thread-like molecules for structure, or to form molecules that can store information. Monomers are linked together in a reaction called condensation, where water is formed in the process. Polymers can just as easily be broken down into their monomer parts by a process called hydrolysis, which uses water as it occurs.





Condensation Animated
These next links animate the process of condensation, using the previous shapes. Special molecules called enzymes make this process possible. Enzymes will be discussed later.


Condensation Animation

Download/Play Simple Gif Animation: Slow | Regular | Fast

The animations are Copyright © 1989, Steve Kuensting, All Rights Reserved.



In the condensation process, the water molecules are produced because of the atoms that are left over in the monomer bonding process. The enzyme is necessary to help form the bonds between the monomers. Eleven monomers were bonded together to form 1 polymer and 10 water molecules. In a chemical equation, it would look like the following:





Hydrolysis Animated
Hydrolysis is the reverse of condensation, where a large polymer molecule is broken down into its monomer components with the use of water. Enzymes are also needed for this process to occur.



Hydrolysis Animation

Download/Play Simple Gif Animation: Slow | Regular | Fast

The animations are Copyright © 1989, Steve Kuensting, All Rights Reserved.



In the hydrolysis process, the water molecules are used because of the exposed bonds left after the monomers are unbonded from one another. The enzyme is necessary to help break the bonds between the monomers. One polymer was broken down and 5 water molecules were used to form 6 monomers. In a chemical equation, it would look like the following:





There are 4 major groups of organic compounds that are found in living things - in a bacteria, an oak tree, or a bird. They are:
Carbohydrates, Lipids, Proteins, Nucleic acids. Each group is used differently by a living thing. Below are discussions detailing each of the groups.



Carbohydrates
Carbohydrates contain the atoms carbon, hydrogen, and oxygen. The hydrogen to oxygen atom ratio is usually 2:1, the number of carbon atoms can vary. All carbohydrates are used primarily for fuel use or storage, although one type provides structure to plants. In the carbohydrate group, there are 3 types of molecules: Monosaccharides, Disaccharides, and Polysaccharides.





Carbohydrates
Monosaccharides are also known as SIMPLE SUGARS. The most
common simple sugar is GLUCOSE. It is found in human blood,plant leaves, and many other places. It is made by plants in photosynthesis and used by animals for fuel.




Carbohydrates
There are actually three types of simple sugars: Glucose, Galactose, and Fructose. There structures are shown below. Notice that they all have the same simple formula, but different structural formula. Compounds with this characteristic are called ISOMERS. Glucose, fructose, and galactose all taste differently than one another because of their different molecular shapes.
Glucose, Fructose, and Galactose





Carbohydrates
Organisms often condense two monosaccharides together to form a disaccharide or "double sugar". The most common and sweetest tasting of all disaccharides is sucrose. It is composed of a fructose and a glucose molecule bonded together. Two less common disaccharides are lactose (milk sugar) and maltose (malt sugar). All three are isomers. The simple and structural formulas of sucrose are shown below.





Carbohydrates
Organisms often condense many monosaccharides together to form polysaccharides - a carbohydrate made of 3 or more simple sugars. The only simple sugar that is ever polymerized to form polysaccharides is glucose. There are three common polysaccharides - starch, glycogen, and cellulose. Each consists of long chains of glucose molecules like beads on a string. They differ in how the glucose molecules are strung together. Below is a simple representation of a starch molecule where glucose is represented as a hexagon instead of showing all of the atoms.





Carbohydrates
Starch is found in plants, most often in roots. It is produced by plants to store glucose made in photosynthesis. Cellulose provides support to a plant and is found only in plants. Glycogen is found in animals, in muscle and liver primarily. It is produced as a means of storing glucose temporarily, until needed.




Carbohydrates
This concludes our discussion of the carbohydrates. Below is an outline of the carbohydrates.




Lipids
Lipids are compound containing the atoms carbon, hydrogen, and oxygen, and the hydrogen to oxygen atom ratio is usually much greater than 2:1. Lipids are primarily used to store energy in living things and are much more commonly found in animals than in plants. There are basically four types of lipids: fatty acids, triglycerides, waxes, and steroids.





Lipids
Fatty acids are the simplest lipids. A fatty acid molecule consists of a long chain of carbon atoms with a special group of atoms at one end --- the carboxyl group. Several fatty acids are drawn below, with the carboxyl groups labeled. Notice that each differs in the length of the carbon chain and the number of hydrogen atoms, they each have the same number of oxygen atoms. Find the carboxyl groups on the structural formulas below.





Lipids
Fatty acids that are saturated contain the maximum amount of hydrogen atoms that their carbon atoms can hold. They are often found within fats. Unsaturated fatty acids contain double bonds between one or more carbon atoms and they contain less hydrogen. Unsaturated fatty acids are often found within oils. Fatty acids are chemicals that store energy in cells.





Lipids
Triglycerides are molecules made of two smaller types of molecules that are bonded together. These two smaller molecules are glycerol and fatty acids. There is only one type of glycerol molecule which is represented below, but there are many types of fatty acids and a simple one is represented below.




Lipids
A triglyceride molecule is made of 1 glycerol molecule bonded to 3 fatty acid molecules. The fatty acids are usually quite large, consisting of chains of carbon atoms that can be up to 16 carbon atoms long. The fatty acids store the energy that is contained in a fat molecule. Triglycerides serve as energy storage molecules or as heat insulators in animals. One triglyceride is shown below, where each fatty acid it contains is only 4 carbons long.





Lipids
There are two main types of triglycerides. Those that are liquids at room temperature are called oils and those that are solids at room temperature are called fats. The oils are unsaturated or polyunsatured because their fatty acid chains contain double bonds. The fats are saturated and their fatty acids contain no double bonds. Animals usually contain the fats (fat on a steak), whereas plants usually contain the oils (corn oil).

Fats - found in animals = hamburger grease, steak fat, human fat
Oils - found in plants, corn oil, coconut oil, peanut oils



Lipids
Waxes are lipids that consist of a long fatty acid which is bonded to a long alcohol molecule. Waxes are used in plants to waterproof root, stem, and leaf parts. In animals, waxes are often found on skin layers, such as the ear, to keep microbes out.






Lipids
Steroids differ radically from the other lipids in that they contain no fatty acids. Steroids are only considered to be lipids because they do not dissolve in water. All steroids consist of 4 carbon rings. They are often used as hormones in living things, such as testosterone -- the male sex hormone. Other examples are cholesterol and estrogen. A steroid is drawn below.





Lipids
This concludes our discussion of lipids. Below is an outline of the lipids.





Proteins
Proteins contain the atoms carbon, hydrogen, oxygen, and NITROGEN. Proteins are used for structure in living things, such as in muscles or tendons. Proteins also serve as hormones - chemical messengers transported in the blood, and enzymes - chemicals capable of speeding up ordinarily slow chemical reactions in an organism. It is the proteins of an organism that make it unique from all other organisms.





Proteins
All proteins are polymers made of smaller monomers called AMINO ACIDS. There are 20 different amino acids found in the proteins of living things. They are all similar in that they all have an AMINO GROUP of atoms and a CARBOXYL GROUP of atoms (also found in fatty acids). Two simple amino acids are represented below, both with simple and structural formulas. The amino and carboxyl groups are labeled.





Proteins
The twenty different amino acids all have names, not important to remember but to recognize. They are all listed below. Notice that most of their names end in "ine". Whenever a chemical name is given and it ends in "ine" it is probably the name of an amino acid.
The 20 amino acids





Proteins
Two amino acids can be condensed together to form a new molecule called a DIPEPTIDE. The special bond between the two amino acids is called a peptide bond. A dipeptide formed from 2 amino acids is shown below.





Proteins
Dipeptides are rare in nature. They usually only exist during condensation until another amino acid is linked in the chain to form a polypeptide. A polypeptide is a large molecule consisting of 3 or more amino acids. They are always formed from the condensation of amino acids. A polypeptide is represented below.





Proteins
Polypeptides are usually very long polymer chains of amino acids, up to hundreds of amino acids in length. The number, type, and sequencing of amino acids in the polypeptide determine all of the properties of the polypeptide.





Proteins
Finally, proteins are made up of two or more polypeptide chains that are usually bonded together. The polypeptide chains usually wrap around one another to form a unique shape depending on the number, type, and sequencing of amino acids in the polypeptide chains.





Enzymes
Probably the most important group of proteins are the enzymes. Enzymes are proteins that act as catalysts -- they speed up chemical reactions. All chemical reactions require heat energy to occur. The enzyme speeds up the reaction by lowering the amount of heat energy needed to cause the reaction to occur. The reaction can then occur quickly with very little heat.



Enzymes
The current model which helps to explain how an enzyme lowers the activation energy states that a specific part of an enzyme, the active site, actually fits into a particular part of a molecule -- the substrate -- which is taking part in a chemical reaction. By doing this, a covalent bond is weakened and collision with another molecule will then cause the bond to break. If the enzyme did not weaken the bond, the bond would not break. Also, the enzyme itself is not harmed, it can then move to a new substrate to weaken another bond and cause another chemical reaction. Enzymes are not used up in chemical reactions.





Enzyme Hydrolysis
To see this process in action, an enzyme is pictured below, but it is only drawn as a shape. It is actually a protein made of polypeptides. The substrate is shown also as a shape. The substrate could be a carbohydrate, lipid, protein, or nucleic acid. What you are about to see animated is hydrolysis, the breaking apart of molecules with the use of water.


Enzyme Hydrolysis Animation

Download/Play Simple Gif Animation: Slow | Regular | Fast



Enzyme Condensation
The stray molecule provided the vibrational energy needed for the enzyme-weakened bond in the substrate to break. The water molecule was used in the breaking of the substrate bond. That is why it disappeared, it became part of the products. On the next simulation condensation is shown, the bonding together of molecules, which is the reverse of hydrolysis.



Enzyme Condensation Animation

Download/Play Simple Gif Animation: Slow | Regular | Fast



Enzymes
Again, the stray molecule provided the vibrational energy needed for the substrates to bond. The water molecule was produced from extra atoms released in the forming of the bonds between the substrates. That is why it appeared at the end, being formed as a product.





Enzyme Energy Diagram
A graph depicting the energy change of a reaction will show energy change on the Y-axis and the path of the reaction on the X-axis. Below, are graphs depicting an exothermic reaction, one that releases energy. The graph on the left depicts a reaction without enzyme, the one on the right, with enzyme. Note that the activation energy (AE) is lowered in the enzyme-mediated reaction. Also note that the reactants store more energy than the products.





Enzyme Energy Diagram
Below are graphs depicting an endothermic reaction, one that absorbs energy. The graph on the left depicts a reaction without enzyme, the one on the right, with enzyme. Note that the activation energy (AE) is lowered in the enzyme-mediated reaction. Also note that the reactants store less energy than the products.





Nucleic Acid
Nucleic acids are the most complex molecules found in a cell. Nucleic acids contain the atoms Carbon, Hydrogen, Oxygen, Nitrogen, and Phosphorous, the most different types of atoms of all of the biochemicals. Nucleic acids are used for the storage and processing of genetic information. There are two types of nucleic acid -- DEOXYRIBONUCLEIC ACID (DNA) and RIBONUCLEIC ACID (RNA). DNA actually stores the genetic information while RNA transfers the genetic information to areas for protein production.





Nucleic Acid
Both DNA and RNA are polymer molecules made of smaller monomers called NUCLEOTIDES. A nucleotide is itself a fairly large molecule and is made of 3 smaller molecules. The three smaller molecules are: 1) a phosphate molecule, 2) a 5 carbon sugar, and 3) a nitrogen base molecule. A nucleotide is shown below, with its smaller component molecules labeled.





Nucleic Acid
To simplify the discussion, we will only analyze DNA. There are only 4 DNA nucleotides, and each differs from the other by the type of nitrogen base it contains. With only 4 monomers with which to build DNA, it is less complex than protein. The 4 nitrogen bases are shown below with their abbreviations below. Notice that 2 of the nitrogen bases consist of only one ring, the other 2 consist of 2 rings.





Nucleic Acid
Many nucleotides strung together make up a nucleic acid molecule. A nucleic acid molecule can be thousands of nucleotides long. A small nucleic acid is shown below, consisting only of 4 nucleotides.





Nucleic Acid
DNA differs from RNA in that DNA always consists of 2 nucleotide strings woven together, whereas RNA is always only one string of nucleotides. The two are represented below.





Glucose Condensation: Starch Formation
This next animation shows the process of starch formation, by the condensation of glucose, showing the actual structural formulas.



Glucose Condensation Animation

Download/Play Simple Gif Animation: Slow | Regular | Fast

The animations are Copyright © 1989, Steve Kuensting, All Rights Reserved.



Polypeptide Hydrolysis
The next animation shows the process of amino acid liberation, by the hydrolysis of a polypeptide, showing the actual structural formulas.



Polypeptide Hydrolysis Animation

Download/Play Simple Gif Animation: Slow | Regular | Fast

The animations are Copyright © 1989, Steve Kuensting, All Rights Reserved.



Quiz

  1. List the symbols of the atoms contained by carbohydrates.

  2. List the symbols of the atoms contained by proteins.

  3. List the symbols of the atoms contained by lipids.

  4. List the symbols of the atoms contained by nucleic acids.

  5. Which of the 4 groups of biochemicals is most used for energy?

  6. Name a molecule consisting of 3 or more amino acids.

  7. Which of the 4 biochemicals is most used for structure?

  8. Which of the 4 biochemicals includes the fatty acids?

  9. Which of the 4 biochemicals is most used for energy storage and insulation?

  10. What is the name of the protein molecule that speeds up chemical reactions in an organism?

  11. What type of reaction produces polymers and water from monomers?

  12. What type of reaction produces monomers from polymers and water?

  13. What does an enzyme lower in order to speed up a chemical reaction?

  14. Which of the 4 biochemicals stores or transfers genetic or hereditary information?

  15. Does a condensation reaction produce water or use water?

  16. Which of the 4 biochemicals includes the largest molecules found in an organism?

  17. What type of lipid seals water and waterproofs a plant?

  18. What is the name of all molecules consisting of 2 simple sugars?

  19. Name the positively charged particle found in the nucleus of an atom.

  20. What polysaccharide does a plant use to store simple sugars?

  21. Name the negatively charged particle found in an atom.

  22. What is the name of the central part of an atom?

  23. What subatomic particle determines all of the chemical properties of an atom?

  24. What type of bond is formed from the attraction of oppositely charged particles.

  25. What type of bond forms when electrons are shared?

  26. What atomic structure is formed from the covalent bonding of two or more atoms?

  27. What is the general name of all chemicals containing carbon?

  28. What type of chemical formula shows the number, type, and arrangement of atoms in a molecule?

  29. What small monomer contains a carboxyl group of atoms and an amino group of atoms?

  30. A triglyceride is made of 3 ___________ and 1 ___________.


Diagram Quiz
    Identify the following structural formulas.



















    Answers