The Chemical Level of Organization

Introduction
Since chemicals compose your body and all body activities are chemical in nature, it is important to become familiar with the language and fundamental concepts of chemistry.

Matter and Energy

All living and non-living things consist of MATTER, which is anything that occupies space and has mass.
3 states of matter - solid, liquid, gas

The amount of matter in any object is its MASS. On earth, WEIGHT is the force of gravity acting on MATTER.

Matter and Energy

ENERGY - the capacity to do WORK.
Principle of CONSERVATION of ENERGY - energy can neither be created or destroyed, but one form of energy can be converted into another.

How Matter is Organized

Chemical Elements
All forms of matter are composed of chemical elements which are substances that cannot be split into simpler substances by ordinary chemical means. Elements are given letter abbreviations called chemical symbols. Trace elements are present in tiny amounts

2.1

Figure 2.1

Chemical Elements
118 (?) recognized elements, 92 occurring naturally:
Four elements comprise about 96% of total body mass:
Oxygen (65%), Carbon (18.5%), Hydrogen (9.5%), and Nitrogen (3.2%).

These make up about 3.9% of total body mass: Calcium, Phosphorus, Potassium, Sulfur, Sodium, Chlorine, Magnesium, Iodine, and Iron. Remaining 0.1% of total body mass is composed of TRACE ELEMENTS

Structure of Atoms
Units of matter of all chemical elements are called atoms. An element is a quantity of matter composed of atoms of the same type. Atoms contain:
Nucleus: protons (p+) & neutrons (neutral charge) Electrons (e-) surround the nucleus as a cloud (electron shells are designated regions of the cloud)

2 Representations of the Structure of an Atom

Atomic Number and Mass Number

Atomic number is number of protons in the nucleus. Mass number is the sum of its protons and neutrons.

Ions, Molecules, & Compounds

Ions
An atom that gave up or gained an electron Written with its chemical symbol and (+) or (-)

Molecule
Atoms share electrons Written as molecular formula showing the number of atoms of each element (H2O)

Chemical Bonds
The atoms of a molecule are held together by forces of attraction called chemical bonds. The likelihood that an atom will form a chemical bond with another atom depends on the number of electrons in its outermost shell, also called the valence shell.

Chemical Reactions
Electrons orbiting around the nucleus tend to spend most of their time in specific regions called ELECTRON SHELLS. Each electron shell can hold a maximum number of electrons.
Ex. First shell - nearest the nucleus can hold no more than 2 e-.
Second shell - no more than 8 e Third shell - no more than 18 e-, although in some, stability can be reached with 8 e- in third shell.

Chemical Reactions
To reach stability, atoms tend to either EMPTY or FILL their outermost shell to its maximum. They may either give up, accept, or share electrons with other atoms.

Chemical Reactions
Chlorine Example
In a chlorine atom, the outermost shell has 7 e-. One stable form of chlorine can be reached with only 8 e- in the 3rd shell.
So, chlorine tends to try to GAIN another electron that another atom has lost.

Sodium has only one electron in its outer shell and it is much easier for sodium to give up this electron rather than try to gain 7 to fill its outer shell.

Chemical Reactions
Atoms of a few elements have completely FILLED outer shells and do not tend to gain or lose electrons.
Such elements are called INERT ELEMENTS and Participate in NO chemical reactions. Ex. Helium and Neon

2.1

Figure 2.1

Ionic Bonds
When an atom loses or gains a valence electron, ions are formed.
Positively and negatively charged ions are attracted to one another. Cations are positively charged ions that have given up one or more electrons (they are electron donors). Anions are negatively charged ions that have picked up one or more electrons that another atom has lost (they are electron acceptors).

The Ionic Bond Formation

 Covalent bonds are formed by the atoms of molecules

Covalent Bonds

sharing one, two, or three pairs of their valence electrons.

Covalent bonds are common and are the strongest chemical bonds in the body. Single, double, or triple covalent bonds are formed by sharing one,two, or three pairs of electrons, respectively.

Covalent bonds may be nonpolar or polar. In a nonpolar covalent bond, atoms share the electrons
equally; one atom does not attract the shared electrons more strongly than the other atom

Polar Covalent Bonds

Unequal sharing of electrons between atoms. In a water molecule, oxygen attracts the hydrogen electrons more strongly
Oxygen has greater electronegativity as indicated by the negative Greek delta sign.

Hydrogen Bonds
Approximately 5% as strong as covalent bonds Useful in establishing links between molecules or between distant parts of a very large molecule Large 3-D molecules are often held together by a large number of hydrogen bonds.

Hydrogen Bonds
Are weak intermolecular bonds; they serve as links between molecules. Help determine threedimensional shape Give water considerable cohesion which creates a very high surface tension

Hydrogen Bonds
A single large molecule may contain hundreds of hydrogen bonds and these bonds help STABILIZE molecules.

Chemical Reactions
New bonds form and/or old bonds are broken. Metabolism is the sum of all the chemical reactions in the body. Law of conservation of energy
The total mass of reactants equals the total mass of the products.

Forms of Energy and Chemical Reactions

Energy is the capacity to do work. Kinetic energy is the energy associated with matter in motion. Potential energy is energy stored by matter due to its position.

Energy Transfer in Chemical Reactions

An exergonic reaction is one in which the bond being broken has more energy than the one formed so that extra energy is released, usually as heat (occurs during catabolism of food molecules).

An endergonic reaction is just the opposite and thus requires that energy be added, usually from a molecule called ATP, to form a bond, as in bonding amino acid molecules together to form proteins.

Activation Energy

Chemical Reactions
Thousands of chemical reactions are going on in the body simultaneously and atoms, ions, and molecules are constantly moving and colliding. It takes a sufficiently forceful collision to disrupt electrons and break a chemical bond or form a new one.

Chemical Reactions
The energy needed for a specific chemical reaction to occur is called ACTIVATION ENERGY.
This is the amount of energy needed to disrupt the STABLE electronic configuration of a specific molecule so that electrons can be REARRANGED.

Catalysts and chemical reactions

Factors that Cause a Collision and Chemical Reaction

Concentration Temperature Catalysts are chemical compounds that speed up chemical reactions by lowering the activation energy needed for a reaction to occur. A catalyst does not alter the difference in potential energy between the reactants and products. It only lowers the amount of energy needed to get the reaction started. A catalyst helps to properly orient the colliding particles of matter so that a reaction can occur at a lower collision speed. The catalyst itself is unchanged at the end of the reaction; it is often reused many times.

Catalysts and chemical reactions

Chemical Reactions
Some types of chemical reactions:
SYNTHESIS DECOMPOSITION EXCHANGE REVERSIBLE OXIDATION-REDUCTION

Chemical Reactions
Synthesis Reactions
A + B ---> AB All of the synthesis reactions in your body are collectively called ANABOLISM. A good example is combining amino acids to form proteins.
AA + AA + AA + AA -----> Protein

Chemical Reactions
Decomposition Reactions
AB -----> A + B In a decomposition reaction, a substance is broken down into smaller parts. All of the decomposition reactions in the body are collectively referred to as CATABOLISM. Ex. Breaking down of glucose to its smaller components, such as pyruvic acid or breaking down a protein to its component amino acids.

Chemical Reactions
Exchange Reactions
AB + CD -----> AD + BC Part synthesis and part decomposition. Chemical bonds between AB and CD are broken, but new bonds are formed between AD and BC.

Chemical Reactions
Reversible Reactions
AB <-----> A + B This is a type of reaction where the products can revert back to the original reactants. Ex. ATP <-----> ADP + P + energy

Chemical Reactions
OXIDATION-REDUCTION REACTIONS
Also called REDOX reactions. OXIDATION - REMOVAL of electrons from a molecule.
This results in a DECREASE in the energy content of the molecule.

REDUCTION - Opposite of Oxidation. ADDITION of electrons to a molecule.

Results in an INCREASE in the energy content of the molecule.

Inorganic vs. Organic

Usually INORGANIC COMPOUNDS lack CARBON - water, many salts, acids, bases, CO2.
Many contain IONIC bonds.

ORGANIC COMPOUNDS always CONTAIN carbon.

Carbon chains are the backbone for many substances of living cells. Usually organic compounds are held together with COVALENT bonds.

Inorganic Compounds
When molecules of inorganic acids, bases, or salts dissolve in water, they undergo IONIZATION or DISSOCIATION.
They separate into IONS.

ACID - a substance that dissociates into one or more HYDROGEN IONS (H+) and one or more ANIONS (negative ions).

Inorganic Compounds
BASE - dissociates into one or more HYDROXIDE IONS (OH-) and one or more CATIONS (positive ions). SALT - dissolves into cations and anions, neither of which is H+ or OH-.
NaCl ----> Na+ + Cl-

Inorganic Compounds
WATER - the most abundant inorganic substance in all living systems. In our body fluids, water is the SOLVENT. A SOLVENT is a liquid or gas in which some other material (solid, liquid, or gas), called a SOLUTE, has been dissolved.
The combination of SOLVENT plus SOLUTE is called a SOLUTION.

Acid-Base Balance
To maintain our body HOMEOSTASIS, intracellular and extracellular fluids must contain almost equal amounts of acids and bases.
If you have more H+ ions in a solution, the more ACIDIC it is. Conversely, the more OH- ions in a solution, the more BASIC (ALKALINE) a solution is.

Concept of pH
pH scale runs from 0 to 14 (concentration of H+ in moles/liter) pH of 7 is neutral
(distilled water -- concentration of OH- and H+ are equal)

pH below 7 is acidic ([H+] > [OH-]). pH above 7 is alkaline ([H+] < [OH-]). pH is a logarithmic scale
Example: a change of two or three pH units pH of 1 contains 10x10=100 more H+ than pH of 3 pH of 8 contains 10x10x10=1000 more H+ than pH of 11

The pH Scale

Maintaining pH: Buffer Systems

The pH values of different parts of the body are maintained fairly constant by buffer systems, which usually consist of a weak acid and a weak base.
Convert strong acids or bases into weak acids or bases.

Organic Compounds
ALWAYS contain CARBON. Small organic molecules can combine to form very large organic molecules called MACROMOLECULES, which are usually POLYMERS of small repeating subunits called MONOMERS.

Organic Compounds
When two ORGANIC MONOMERS join together, the reaction usually involves the elimination of a molecule of water.
This type of reaction is called a DEHYDRATION SYNTHESIS reaction, because a molecule of water is released.

Organic Compounds
It is also possible for macromolecules to be BROKEN DOWN into monomers by the addition of water.
This type of reaction is called a HYDROLYSIS reaction, which means to split apart by using water. Together, the dehydration synthesis and hydrolysis reactions would be a REVERSIBLE REACTION.

Organic Compounds
Major Classes of Macromolecules
Carbohydrates Lipids Proteins Nucleic Acids

Carbohydrates
Carbohydrates provide most of the energy needed for life and include sugars, starches, glycogen, and cellulose. Some carbohydrates are converted to other substances which are used to build structures and to generate ATP. Other carbohydrates function as food reserves. Carbohydrates are divided into three major groups based on their size: monosaccharides, disaccharides, and polysaccharides

Monosaccharides

Disaccharides
Combining 2 monosaccharides by dehydration synthesis releases a water molecule.
sucrose = glucose & fructose maltose = glucose & glucose lactose = glucose & galactose (lactose intolerance)

Polysaccharides
Polysaccharides are the largest carbohydrates and may contain hundreds of monosaccharides. The principal polysaccharide in the human body is glycogen, which is stored in the liver or skeletal muscles. When blood sugar level drops, the liver hydrolyzes glycogen to yield glucose which is released from the liver into the blood

Lipids Lipids, like carbohydrates, contain carbon, hydrogen, and

hydrophobic mostly insoluble in polar solvents such as water combines with proteins (lipoproteins) for transport in blood

oxygen; but unlike carbohydrates, they do not have a 2:1 ratio of hydrogen to oxygen. They have few polar covalent bonds

Triglycerides Triglycerides are the most plentiful lipids in

the body and provide protection, insulation, and energy (both immediate and stored).
At room temperature, triglycerides may be either solid (fats) or liquid (oils). Triglycerides provide more than twice as much energy per gram as either carbohydrates or proteins. Triglyceride storage is virtually unlimited. Excess dietary carbohydrates, proteins, fats, and oils will be deposited in adipose tissue as triglycerides.

Triglycerides

Lipids
1. TRIGLYCERIDES - continued
A. SATURATED fats - have only SINGLE covalent bonds between fatty acid carbon atoms. B. MONOUNSATUARATED fats - one DOUBLE covalent bond between 2 fatty acid carbon atoms. C. POLYUNSATURATED fats - MORE than one double covalent bond between fatty acid carbon atoms.

Phospholipids
Phospholipids are important membrane components. They are amphipathic, with both polar and nonpolar regions
a polar head
a phosphate group (PO4-3) & glycerol molecule forms hydrogen bonds with water

2 nonpolar fatty acid tails

interact only with lipids

Steroids
Steroids have four rings of carbon atoms Steroids include
sex hormone bile salts some vitamins cholesterol, with cholesterol serving as an important component of cell membranes and as starting material for synthesizing other steroids.

Four Ring Structure of Steroids

Proteins
Proteins have a more complex and larger range of functions than carbohydrates or lipids In a normal, lean adult = 12-18% protein.
They may be structural, physiological, function in muscle contraction, antibodies, and hormones. Proteins always contain C, H, O, and N, and even Sulfur.

Proteins
Constructed from combinations of 20 amino acids. dipeptides formed from 2 amino acids joined by a covalent bond called a peptide bond polypeptides chains formed from 10 to 2000 amino acids.

Formation of a Dipeptide Bond

Dipeptides formed from 2 amino acids joined by a covalent bond called a peptide bond

dehydration synthesis
Polypeptides chains contain 10 to 2000 amino acids.

Formation of a Dipeptide Bond

Dipeptides formed from 2 amino acids joined by a covalent bond called a peptide bond

dehydration synthesis
Polypeptides chains contain 10 to 2000 amino acids.

Proteins
Amino Acids
These are the building blocks of proteins. There are 20 different amino acids in the body. Each amino acid has 3 important groups attached to a central carbon atom.
1. Amino Group (-NH2) 2. Carboxyl Group (-COOH) 3. Side Chain (R group) - gives each amino acid its identity.

Formation of a Dipeptide Bond

Dipeptides formed from 2 amino acids joined by a covalent bond called a peptide bond

dehydration synthesis
Polypeptides chains contain 10 to 2000 amino acids.

Levels of Structural Organization

Levels of structural organization include primary secondary tertiary quaternary The resulting shape of the protein greatly influences its ability to recognize and bind to other molecules.

Denaturation of a protein by a hostile environment causes

loss of its characteristic shape and function.
Breaking down amino acid Change in temperature, increasing or decreaing acid or base

Proteins
Levels of Protein Structural Organization
Much of a proteins ability to function is determined by what their shape or CONFORMATION is.
1. PRIMARY STRUCTURE - refers to the unique SEQUENCE of amino acids making up a polypeptide strand.

Proteins
Levels of Protein Structural Organization
2. SECONDARY STRUCTURE - refers to the repeated twisting or folding of neighboring amino acids in the polypeptide chain.

Alpha helices Beta pleated sheets

Proteins
Levels of Protein Structural Organization 3. TERTIARY STRUCTURE - refers to the 3-dimensional shape of a polypeptide chain. 4. QUATERNARY STRUCTURE - when a protein contains more than one polypeptide chain.

Enzymes
All kinds of reactions are continually occurring in your body. In your basic chemistry class, what did you normally do to get a chemical reaction going?
YOU ADDED HEAT.

The bodys general temperature is too low for chemical reactions to occur at a rate fast enough to sustain life.

Enzymes
To deal with this, the body has ENZYMES (a type of protein) which speed up chemical reactions without killing or disrupting the cell.
A substance that speeds up a chemical reaction in this way is called a CATALYST and in living cells, ENZYMES function as catalysts.

Enzymes
In an enzymatic reaction:
1. The enzyme comes together with the molecule which it acts on (SUBSTRATE) to form an enzymesubstrate complex. 2. The substrate portion is transformed by breaking down and rearrangement of chemical bonds.
Transformed molecules are called PRODUCTS of the reaction.

Enzymes
In an enzymatic reaction:
3. The products move away from the enzyme and the unchanged enzyme is now capable of attaching to another molecule and performing the reaction AGAIN.

Enzymes
The names of enzymes usually end in -ASE.
For example, oxidases add oxygen, kinases add phosphate, dehydrogenases remove hydrogen.

DNA and RNA

Nucleic acids are huge organic molecules that contain carbon, hydrogen, oxygen, nitrogen, and phosphorus. Deoxyribonucleic acid (DNA) forms the genetic code inside each cell and thereby regulates most of the activities that take place in our cells throughout a lifetime. Ribonucleic acid (RNA) relays instructions from the genes in the cells nucleus to guide each cells assembly of amino acids into proteins by the ribosomes. The basic units of nucleic acids are nucleotides, composed of a

nitrogenous base, a pentose, sugar, and a phosphate group.

Nucleic Acids :46 chromosome

The monomers of nucleic acids are called NUCLEOTIDES:
Components of a nucleotide:
1. BASE (Nitrogenous Base) - Nitrogen containing structures. In DNA, the bases are ADENINE (A), THYMINE (T), CYTOSINE (C), and GUANINE (G). A pairs with T, T with A, C with G, and G with C.

Nucleic Acids
2. PENTOSE SUGAR meaning it has 5 carbons, called DEOXYRIBOSE. 3. PHOSPHATE GROUP DNA is arranged in a double-helix.

RNA Structure
Differs from DNA
single stranded ribose sugar not deoxyribose sugar uracil nitrogenous base replaces thymine

Types of RNA within the cell, each with a specific function

messenger RNA ribosomal RNA transfer RNA

RNA Structure

Nucleic Acids
Pairing Example
Strand of:
DNA - ATTAGGCCA Complementary strand of DNA - TAATCCGGT Complementary strand of RNA - UAAUCCGGU

Nucleic Acids
Pairing Example
Strand of:
DNA - ATTAGGCCA Complementary strand of DNA - TAATCCGGT Complementary strand of RNA - UAAUCCGGU

RNA Structure

Adenosine Triphosphate (ATP)

Temporary molecular storage of energy as it is being transferred from exergonic catabolic reactions to cellular activities

Formation & Usage of ATP

Hydrolysis of ATP (removal of terminal phosphate group by enzyme -- ATPase)
releases energy leaves ADP (adenosine diphosphate)

Synthesis of ATP
enzyme ATP synthase catalyzes the addition of the terminal phosphate group to ADP energy from 1 glucose molecule is used during both anaerobic and aerobic respiration to create 36 to 38 molecules of ATP