Biology 2404

Molecules are made up of elements, the simplest chemicals. There are 92 naturally occurring elements in the world and information about all elements (naturally and man-made) form the periodic table of elements. An element is a substance made up of only one type of atom. Four types of elements make up 96% of matter found in organisms today. These four are Carbon – C, Hydrogen – H, Nitrogen – N, and Oxygen – O.

If Phosphorus –P, Calcium- Ca, and Sulfur – S are included in the reference to the human body chemical makeup, then these seven atoms make up 99% of the human body.

Other elements in the human body include: Fluorine - F, Sodium - Na, Magnesium - Mg, Chlorine -Cl, Potassium -K, Manganese -Mn, Iron- Fe, Cobalt - Co, Copper - Cu, Zinc- Zn, and Iodine - I. Most of these elements are in very low (0.1- 1.5%) or trace amounts.

Each element has a standard chemical symbol that is based on its Latin or English name. For example, Potassium’s Latin word part is Kali-, therefore its chemical symbol is K, not P. Another example is Sodium whose Latin word part is Natri-, therefore its chemical symbol is Na, not S. Not all symbols require knowledge of Latin. Phosphorus has the chemical symbol P, Sulfur has the chemical symbol S, and Magnesium has the chemical symbol Mg. Chemical symbols are frequently used in hospital records, laboratory reports, and medical articles. Elements are arranged in a sequence by increasing atomic number (number of protons the atom has) in a chart called the periodic table of the elements.

An atom is the smallest particle of an element that still retains the properties of that element. Atoms are made up of three major particles: protons in the nucleus, neutrons in the nucleus, and electrons in outer energy shells or orbitals. Protons are positively charged, neutrons are neutral in charge, and electrons are negatively charged. The number of protons gives the element its atomic number. The atomic weight of an element is based on protons and neutrons. The weight of electrons is minimal, and therefore does not provide a major influence the atomic weight.

The chemical reactivity of an atom is based on the number of electrons in the outer most shell or energy level. Those electrons in inside full or stable shells do not react in any further chemical processes. Each energy level or shell has a maximum number of electrons it can “hold.” The first energy shell or level can only contain 2 electrons, while the second energy level can hold a maximum of 8 electrons. Atoms are always in search of a full or stable outer energy shell and will combine in certain chemical reactions to obtain needed electrons. Atoms that need more than two electrons to complete their outer shell will usually share electrons with other atoms. Those atoms that only need one or two electrons will “take” or “give” their electrons to other atoms. If these electrons are lost or gained, the atom becomes a charged particle or ion. Chemical bonds are based on the reactions between outer valence electrons.

Drawing of an atom

Electrons can be shared equally, shared unequally, gained, or lost. These reactions allow for the outer shell to become full or stable and in turn give the atom its chemical or physiological properties. Types of chemical bonds seen are:

Covalent equal sharing of valence electrons

Polar Covalent unequal sharing of valence electrons which causes a slightly polarized or

charged ends

Ionic gain or loss of valence electrons, + or - charges that interact to form bonds

Hydrogen bonds formed with Hydrogen atoms based on weak charges caused by

Polar Covalent reactions

All physical objects are made of matter and can be in a solid, liquid, or gaseous state. Matter is therefore defined as anything that takes up space and has mass.

Chemical analysis of matter shows that matter is made up of elements. Elements are the basic building blocks of more complex forms, but cannot be converted to less complex substances by chemical reactions. The particles or elements of matter are always in motion and can account for all of the observed properties or behaviors of gases, liquids, and solids.

Gases consist of molecules moving rapidly in random patterns with vast empty spaces separating them.

The average speed of the molecules is directly related to its temperature. Gaseous molecules

crash against other molecules and their confining walls, thus these molecules produce the

pressures of that gas.

Liquids consist of molecules that also move in random patterns, but are more closely in contact with one

another. In contrast to gas, a liquid had a definite volume, but resists further compression.

Liquid molecules can obtain higher speeds of motion and can leave the liquid as a gas. This

process is called evaporation. Likewise, when a gas is cooled, the molecules are slowed and

attracted to one another. This process is called condensation. Temperature changes affect the

rate of evaporation and condensation.

Solids are molecules in motion as well, but they touch each other to form three dimensional patterns so

that each molecule can only move in the space bounded by its neighbors. Solids are able to keep

their shape and are essentially incompressible. Temperature changes, such as melting, cause the

complete breakdown of the ordered pattern of the solid. When a solid dissolves into a liquid,

the molecules (or ions) begin to move throughout the solution.

As discussed above, the states of matter can change in a physical process by temperature changes and the spreading out or diffusion of the particles. Physical changes do not destroy the original substance or form new substances. Often this substance seems to disappear, but if there has been no other change, it is recoverable.

Chemical changes of matter are also possible as seen in the examples of cooking food, milk souring, food digestion, and gasoline burning. In chemical changes, new substances are formed that have properties completely different than the starting materials. Therefore, in all cases of a chemical change, substances disappear and new ones appear.

When a chemical change has occurred, what is really meant is that a chemical reaction has taken place. The original substances (reactants) have interacted (reacted) to form new substances (products). Chemical reactions are usually seen written as an equation, employing the use of the chemical symbols of the elements or molecules involved. In a chemical equation, the reactants are on the left, products on the right, and an arrow that indicates which way the reaction proceeds. An example of a generic chemical equation would be: A+B -> C or even AB+CD ->AC+BD.

An actual equation would be H2+Cl2 ->2HCl.

Atoms combine with other atoms in many different ways to form molecules. Atoms in molecules are held together by attractive forces called bonds. In a chemical reaction, the original substance is dismantled in order to reassemble the atoms in a different way to form new molecules. Bonds are broken and then reformed to allow for this chemical change. Breaking bonds requires energy and energy is released when bonds are formed. Therefore, chemical bonds contain or store energy, which is the ability to do work or supply heat. All chemical reactions are characterized by a gain or loss of energy. Those reactions that give off heat energy are said to be exothermic, and those that require (absorb) heat are said to be endothermic. When table sugar (sucrose) is taken into the body it undergoes a series of complicated reactions to produce the energy needed for mechanical motion, body heat, and even thinking. The overall reaction is C12H22O11 + 12 O2 -> 11 H2O + 12 CO2. In the metabolic reactions in the cells, many bonds are broken (sugar and oxygen molecules come apart) and new bonds are formed (water and carbon dioxide). More energy is released in the new bond formation than that required for bond breaking, so the exothermic reaction gives us energy for cell functions.

Chemical reactions that form or break chemical bonds can be:

Synthesis chemical bonds are formed, energy is stored

Decomposition chemical bonds are broken, energy is released

Exchange bonds break and reform creating new molecules

or compounds. Usually one way reactions.

Reversible bonds break and reform creating new molecules

or compounds. Reaction can run both ways.

Chemical reactions can be shown as one way or reversible. Some reactions seem to go entirely to completion whereas other reactions seem to go part of the way and stop. Many reactions actually proceed less than 1% or more than 99%. A great many reactions stop short of completion because the products formed react with each other to re-form the reactants. In other words, the reaction occurs in the reverse direction, known as a reversible reaction. Eventually, reversible reactions have both forward and reverse processes occurring at the same rate at the same time so that no further net change in concentration is observed. The reaction is then said to be in a dynamic equilibrium. This chemical equilibrium can be affected or disturbed to cause a shift toward the left with the addition of more reactants or a shift to the right with an addition of more products. Disturbances can be additions of reactants or products, removals of reactants or products, or a change in temperature or pressure. The equilibrium shift after a disturbance is an attempt to establish another balance within the chemical reaction.

Compounds and Molecules:

Atoms of two or more different elements combine to form compounds.

Combinations of atoms of two of the same elements are called molecules.

A molecule

Oxygen O2 covalent bond

Hydrogen gas H2 covalent bond

Nitrogen gas N2 covalent bond

A compound

Table salt Na+Cl- ionic bond

Water H2O polar covalent bond

Carbon dioxide CO2 covalent bond

Ammonia NH3 covalent bond

Nitric Oxide NO covalent bond

Chemical Models (Kit)

The following photos are taken using the chemical model kit.

Atoms are color coated and represent particular elements within a molecule.

Chemical bonds are represented by linear joining pieces.

White = Hydrogen

Black = Carbon

Red = Oxygen

Blue = Nitrogen

Green = Chloride

Purple = Iodine

Orange = Sodium

Sort length white joining pieces represent ionic bonds

Medium length gray joining pieces represent single covalent bonds

Long length gray joining pieces represent double covalent bonds

Chemical Models

H20	HCl	CO2
NH3	O2	H2
NaCl	NH4

Substances of Living Systems

I. Inorganic Molecules and Compounds

A. Water: universal solvent, makes up 2/3 of the body, involved with chemical process of hydrolysis and dehydration synthesis

B. Carbon Dioxide: respiratory gas that is given off as an end product of respiration

C. Oxygen: respiratory gas that is transported to the tissues for aerobic respiration

D. Ammonia: end product of protein metabolism, must be converted to urea

E. Nitric Oxide: byproduct of chemical processes, a very potent vasodilator

F. Salts: ionic compounds that are formed when an acid and base react

G. Acids : donate a H+ ion to the solution. Considered sour tasting. Examples are lemon juice and vinegar

H. Bases : accept OH- ion from the solution. Bitter tasting

I. Buffers: is a mixture of a weak acid and weak base that stabilize the pH of a solution.

II. Organic Compounds (Macromolecules)

A. Carbohydrates

1. Monosaccharides

2. Disaccharides

3. Polysaccharides

B. Fats

1. fatty acids

2. monoglycerides, diglycerides, triglycerides

3. phospholipids

4. glycolipids

5. eiconosoids

6. Cholesterol

C. Proteins

1. Fibrous

2. Globular

D. Nucleic Acids

1. DNA

2. RNA

3. High Energy Compounds

All organic compounds are based on the element carbon (C). Organic compounds form most of the dry weight of all living organisms. Organic compounds vary greatly in size and structure and are therefore well suited to provide the complexity required in living systems. The great variety of structures found in organic chemistry occurs because carbon forms four covalent bonds.

Carbon can bond to itself and to many other elements.

Hydrocarbons are organic compounds that contain only the elements hydrogen and carbon. Hydrocarbons are nonpolar molecules and are therefore hydrophobic or water fearing.

Most hydrocarbons are seen in the lipid classes.

Alcohols have a hydroxyl (-OH) group in place of a hydrogen. Most often compounds end in -ol such as ethanol. Carbohydrates have several alcohol groups

An oxygen linked to a carbon with a double bond is called a carbonyl. Aldehydes and ketones are two organic functional groups that contain a carbonyl. Carbohydrates have this structure as well.

Carboxylic Acids are organic compounds that contain the carboxyl group composed of the atoms –COOH bonded with the oxygen double bonded to the carbon and the hydroxyl group on the carbon. The acidic properties come from the tendency for the hydrogen to dissociate as H+. Examples include citric acid, acetic acid (vinegar). Proteins have a carboxylic acid portion to their structure.

Esters are Carbon to Oxygen to Carbon groups, with one of the carbons double bonded to a second oxygen. Esters are formed from the reaction of a carboxylic acid and an alcohol. Fats and waxes contain ester groups.

Organic compounds that contain the amino group –NH2 called the amine. The nitrogen atom in the amine group can function as a base by accepting a hydrogen ion (H+). Proteins have amines as part of their structure.

The phosphate group is a derivative of phosphoric acid, H3PO4. Hydrogen dissociates so the phosphate groups are considered acidic.

Phosphate groups are seen with the nucleic acids, high energy compounds, and lipids.

Recall that water is the most prevalent compound in cells and organisms. The dry weight of an organism is the matter that remains after water is removed.

Analysis of the dry weight shows a composition of primarily organic compounds.

The organic compounds can be classified into four major categories: carbohydrates, lipids, proteins, and nucleic acids.

These organic compounds are extremely large and are therefore called macromolecules.

Macromolecules are assembled by linking building block molecules into long chains.

Molecules that are used as building blocks are called monomers and a long chain of linked monomers is called a polymer.

Group Monomer Polymer___________

Proteins Amino Acids Peptides and proteins

Carbohydrates Sugars Starch and cellulose

Nucleic Acids nucleotides DNA, RNA

Lipids Fatty Acids and glycerol triglycerides

Amino acids are linked together to form peptide bonds by reacting the hydrogen of the amine group on one amino acid and the carboxyl group of the carboxylic acid group on the other amino acid. The amino acids that link together can from peptides (short chains) and proteins (long chains). The primary structure of a protein or peptide is the sequence of amino acids within it.

The primary structure is specific and unique to each protein. Each primary structure is controlled by a gene, a section of DNA that codes for a protein.

As the polypeptide molecules interact, the chains fold, coil and bend. Each polypeptide or protein develops a shape that is unique to that protein and is essential to its function.

The shape of a particular protein is determined by its primary structure. Alterations of pH, temperature, or solvent around a protein may cause it to unfold, thus destroying its normal shape.

Protein unfolding is called denaturation and destroys the function of the protein.

Carbohydrate examples include sugars, starched, and cellulose. Simple sugars contain the atoms C:H:O in a ratio of 1:2:1.

Starch and cellulose are polymers that are formed by linking many glucose units. Monosaccharides examples include ribose, glucose, and fructose.

Each sugar contains a carbon backbone, several alcohol groups, and either an aldehyde or ketone group.

Glucose that dissolves in water usually forms a ring that can polymerize to form various disaccharides and polysaccharides.

Lipids include a variety of compounds that are fatty, oily, or waxy. Lipids are composed mostly of hydrocarbons and are hydrophobic.

Fats and oils are also called neutral fats or triglycerides. Each fat molecule contains three fatty acids linked to one glycerol molecule.

Other fats have a series of hydrocarbons with reactive groups such as the carbonyl, alcohol, or carboxylic acid groups.

Nucleic acids include two closely related classes of molecules, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Each is built as a series of nucleotides.

Nucleotides are a sugar + phosphate+ nitrogen base. High energy compounds are built using nitrogen bases and phosphate groups.

More discussion about inorganic and organic molecules will be found in the metabolism portion of the digestive system.

Study the chemical nature of these structures now to help in your understanding of digestive processes later.

DNA PCR

Macromolecule Experiments

In order to test for the presence of certain macromolecules and substances, reagents are used to show a reaction that will signify a postive result. See the chart below for the reagents and results. These tests
will be done in the cell exercise to show diffusion of a substance through a permeable membrane.

Solution	Reagent	Positive Result	Negative Result
Starch	Iodine	black	no color change
Dextrose	Benedicts	green-orange-red	original blue color of reagent
Protein	Biuret	blue - purple	no color change
Salt	Silver Nitrate	white precipitate	no color change

Other Processes of Chemical Systems

Energy exchange

Stored energy is potential energy, while energy of motion is kinetic energy. Molecules are constantly in motion and this molecular kinetic energy is called thermal energy. The temperature of an object is dependent on its thermal energy. Higher temperatures mean that the molecules are moving faster while lower temperatures mean that the molecules are moving slower. When thermal energy is exchanged between molecules or compounds with different temperatures, the transferred energy is called heat. Heat exchange will occur with the environment to help maintain internal body temperature homeostasis.

Ions

Defined as charged atoms resulting from gaining or losing valence electrons.

Ions form ionic bonds that are easily broken. Most ionic bonds create salts, which come apart or dissociate in solutions.

These ions which come from salts in solution are called electrolytes and their movements can create electrical events in the body.

Means the power of Hydrogen ion.. It is also the amount of hydrogen ion (H+) in solution.

Mathematically, pH = -log base 10 [H+]

The pH scale ranges from 0-10.

All pH related calculations and scales are based on water.

Acids donate H+ to the solution, bases accept or tie up H+ in a solution

Buffers are solutions that contain at least a weak acid and a weak base

free radicals

Result from high energy sources breaking apart molecules by knocking away electrons from the valence shells of atoms.

The atoms that result are called free radicals. They are charged particles because they have unpaired valence electrons and are extremely unstable.

Isotopes

Defined as different atoms of the same element. The proton number does not change, but the number of neutrons will change.

Carbon 14 has six protons and six electrons like a normal carbon atom, but has eight neutrons, instead of six.

C-14 is mildly radioactive and is used in carbon dating to estimate the age of fossilized remains.

Other radioactive isotopes can be used in diagnosis and treatment.

Reduction / Oxidation

Also known as redox reactions that involves the gain or loss of electrons.

The substance that looses one or more electrons is said to be oxidized.

The substance that gains one or more electrons is said to be reduced.

Electrolytes

Electrolytes are divided into three groups: acids, bases, and salts. Acids are compounds that can release hydrogen ions in an aqueous solution.

Some common acids are HCl—hydrochloric acid, H2SO4 – sulfuric acid, HNO3—nitric acid, and H3PO4—phosphoric acid.

One group of bases (also called alkalis) includes electrolytes that can release the OH- ion (hydroxide ion) in an aqueous solution.

Four bases are NaOH—sodium hydroxide, KOH—potassium hydroxide, Ca(OH)2—calcium hydroxide, and NH4OH—ammonium hydroxide.

Salts are electrolytes that release ions other than H+ or OH- in solution. Common table salt, NaCl is one example.

Many salts are present in dissolved form in seawater, cytoplasm, and the body fluids of many organisms.

Several ions derived from salts play important roles in the biochemistry of living cells, and the internal concentrations of these ions are often carefully regulated.

Chemicals stored in chemistry closet

Medical Terms

Oxi- oxygen Hydr/o water

Calc/i calcium Kal/i potassium

Natr/i sodium Prot/o first

Glyc/o sugar Bi- two, twice

Adip/o fat Therm/o heat

Exercises/Activities

1) Write the chemical formula for

Water, Carbon Dioxide, Ammonia, Sodium Chloride, Potassium Chloride, Calcium Chloride, Hydrogen ion,

2) Read the pH of the following solutions shown in the photo and explain what pH means for each solution.

3) Read the labels of four products (or their equivalents) and identify the chemicals or elements found in

a) Cereal

b) Chicken Noodle Soup

c) Eggs

d) Margarine, butter, or oil

4) Name the functional group:

a) Apples contain malonic acid which has a –COOH group. What is this group’s classification?

b) Vanillin contains a C=O group. What is this group’s possible classification?

c) Glucose contains a C-OH group. What is this group’s classification?

d) Urea contains two –NH2 groups. What is this group’s classification?

e) The cell membrane has many C-H groups with PO4-. What are these two group classifications?

f) Rasberries contain Isobutyl formate which has a O=C-O-C group. What is this group’s classification?

5) Protein Denature: Take 2 eggs and separate the yolk from the egg white. Put one egg white in a hot pan and the second egg white in a bowl containing lemon juice. What happens to the egg whites? What substance is in egg whites that is made and used in our bodies? What types of conditions in our bodies might cause this egg white "substance" to react in a similar manner? If this happens, what will happen to our systems, organs, and tissues?

6) DNA and RNA

Give the location, structure, and function

Define related processes: replication, transcription, translation

7) DNA Extraction: Follow the handout to extract DNA. Use a small clear glass jar (jelly jar) instead of the test tube. Take a photo to include in your Lab report (if LAR is selected for a write up).

Applications

Nutrition

Physiology; Biochemistry

Blood chemistry: electrolytes, pulseoximeter

Equipment : Spectrophotometer, pH meter, chemistry lab machine

Radioactive isotope imaging

Antioxidants

Diseases / Problems

Iron deficiency, B-12 deficiency, Scurvy, Ricketts, Night Blindness

Copper storage disease

Free Radicals

Acidosis, Alkalosis