Chemical Level of Organization Notes

Chemical Level of Organization

Human DNA is a double helix organized into 46 chromosomes.

Chapter Objectives

Describe the fundamental composition of matter.
Identify the three subatomic particles: protons, neutrons, and electrons.
Identify the four most abundant elements in the body: oxygen, carbon, hydrogen, and nitrogen.
Explain the relationship between an atom's number of electrons and its relative stability.
Distinguish between ionic bonds, covalent bonds, and hydrogen bonds.
Explain how energy is invested, stored, and released via chemical reactions.
Explain the importance of inorganic compounds: water, salts, acids, and bases.
Compare and contrast the four classes of organic compounds: proteins, carbohydrates, lipids, and nucleic acids.

Introduction

Chemicals called nucleotide bases are the foundation of the genetic code.
There are about three billion base pairs in human DNA.
Human chemistry includes organic molecules (carbon-based) and biochemicals (produced by the body).
Life cannot exist without elements such as phosphorus, carbon, sodium, and calcium, which originated in stars.
These elements form inorganic and organic chemical compounds like water, glucose, and proteins.

Chemical Bonds

Explain the relationship between molecules and compounds.
Distinguish between ions, cations, and anions.
Identify the key difference between ionic and covalent bonds.
Distinguish between nonpolar and polar covalent bonds.
Explain how water molecules link via hydrogen bonds.
Atoms must come close enough for their valence shells to interact to form chemical bonds.
A chemical bond is a weak or strong electrical attraction that holds atoms together.
A molecule is a stable grouping of two or more atoms held together by chemical bonds (e.g., $H_2$ ).
A chemical compound is a molecule made up of two or more atoms of different elements (e.g., $H<em>2O$ , $CH</em>4$ ).
Three types of chemical bonds are important in human physiology: ionic bonds, covalent bonds, and hydrogen bonds.

Ions and Ionic Bonds

An atom with the same number of protons and electrons is electrically neutral.
An ion is an atom that has an electrical charge (positive or negative) due to the donation or acceptance of one or more electrons.
Potassium (K) has an atomic number of 19 and one electron in its valence shell, making it likely to donate one electron to achieve a full valence shell and become a positive ion.
A potassium ion ( $K^+$ ) has lost a single electron and is positively charged; it is called a cation.
Fluorine (F) has an atomic number of nine and seven electrons in its valence shell, making it likely to accept one electron to achieve a full valence shell and become a negative ion.
The ionized form of fluorine is called fluoride ( $F^-$ ) and is negatively charged; it is called an anion.
Ions with multiple electrons to donate or accept have stronger positive or negative charges (e.g., Magnesium: $Mg^{2+}$ , Selenium: $Se^{2-}$ .
An ionic bond is an ongoing, close association between ions of opposite charge.
Sodium chloride (table salt) is an example of ionic bonding, where sodium donates an electron to chlorine, forming $Na^+$ and $Cl^-$ .

Covalent Bonds

Involve the sharing of electrons in a mutually stabilizing relationship, where atoms do not lose or gain electrons permanently.
Covalent bonds are stronger than ionic bonds due to the close sharing of electron pairs.

Nonpolar Covalent Bonds

Electrons in the outermost valence shell are shared to fill the valence shells of both atoms, stabilizing them.
In a single covalent bond, a single electron is shared; in a double bond, two pairs of electrons are shared; triple bonds also exist.
Covalently bonded molecules that are electrically balanced are described as nonpolar.

Polar Covalent Bonds

Involve unequal sharing of electrons, creating regions with opposite electrical charges.
A polar molecule contains regions that have opposite electrical charges.
Water ( $H_2O$ ) is a polar molecule because the oxygen atom attracts electrons more strongly than the hydrogen atoms.
The oxygen region has a slightly negative charge, and the hydrogen regions have a slightly positive charge, denoted using the Greek letter delta ( $\delta$ ) and plus (+) or minus (–) signs.
These charges are called partial charges because their strength is less than that of a full electron.
The shape of a molecule, like water, can contribute to its polarity, forming a dipole.

Hydrogen Bonds

Form when a weakly positive hydrogen atom bonded to one electronegative atom is attracted to another electronegative atom from another molecule.
Always include hydrogen that is already part of a polar molecule.
Hydrogen bonding occurs between water molecules, where the weakly negative oxygen atom in one water molecule is attracted to the weakly positive hydrogen atoms of other water molecules.
Hydrogen bonds are relatively weak and are indicated with a dotted line.
Water molecules also attract other types of charged molecules and ions, such as sodium ( $Na^+$ ) and chloride ( $Cl^-$ ) ions in table salt.
Water molecules repel molecules with nonpolar covalent bonds, like fats, lipids, and oils.
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Chemical Reactions

Distinguish between kinetic and potential energy, and between exergonic and endergonic chemical reactions
Identify four forms of energy important in human functioning
Describe the three basic types of chemical reactions
Identify several factors influencing the rate of chemical reactions
Metabolism is the sum total of all chemical reactions that maintain an organism’s health and life.
Anabolic reactions form larger molecules from smaller ones.
Catabolic reactions break bonds between components of larger molecules, releasing smaller molecules or atoms.
Both types of reaction involve exchanges of matter and energy.

The Role of Energy in Chemical Reactions

Chemical reactions require sufficient energy to cause matter to collide with enough precision and force to break old chemical bonds and form new ones.
Kinetic energy is the energy powering matter in motion.
Potential energy is the energy of position or the energy matter possesses because of the positioning or structure of its components.
Chemical energy is a form of potential energystored in chemical bonds.
Chemical energy is invested when bonds are formed and released when they break.
Chemical energy is neither created nor destroyed but converted from one form to another.
Exergonic reactions release more energy than they absorb. Catabolism is an example.
Endergonic reactions absorb more energy than they release. These reactions require energy input.

Forms of Energy Important in Human Functioning

Chemical energy is absorbed, stored, and released by chemical bonds.
Mechanical energy, stored in physical systems like machines, engines, or the human body, directly powers the movement of matter.
Radiant energy is energy emitted and transmitted as waves (e.g., ultraviolet energy of sunlight converts a compound in skin cells to vitamin D).
Electrical energy, supplied by electrolytes in cells and body fluids, contributes to voltage changes that help transmit impulses in nerve and muscle cells.

Characteristics of Chemical Reactions

All chemical reactions begin with reactants, which enter into the reaction.
The substances produced are called the product.
In chemical reactions, the components of the reactants are all present in the products; governed by the law of conservation of mass.
Chemical equations show how reactants become products (e.g., $N + 3H \rightarrow NH<em>3$ or $NH</em>3 \rightarrow N + 3H$ ).

Synthesis Reactions

Anabolic reactions that require energy and result in the joining of components that were formerly separate.
General equation: $A + B \rightarrow AB$ .

Decomposition Reactions

Catabolic reactions that break down something larger into its constituent parts, releasing potential energy.
General equation: $AB \rightarrow A + B$ .

Exchange Reactions

Chemical reactions in which both synthesis and decomposition occur, where chemical bonds are both formed and broken, and chemical energy is absorbed, stored, and released.
Simplest form: $A + BC \rightarrow AB + C$ .
More complex form: $AB + CD \rightarrow AC + BD$ or $AB + CD \rightarrow AD + BC$ .
In theory, any chemical reaction can proceed in either direction under the right conditions (reactants may synthesize into a product that is later decomposed).
Reversibility is indicated with a double arrow: $A + BC \rightleftharpoons AB + C$ .
In the human body, many chemical reactions proceed in a predictable direction (one way or the other).

Factors Influencing the Rate of Chemical Reactions

Properties of the Reactants

The greater the surface area of the reactants, the more readily they will interact.
Gases tend to react faster than liquids or solids.
Reactions involving smaller molecules, with fewer total bonds, proceed faster.
Reactions involving highly reactive elements (like hydrogen) proceed more quickly than reactions involving less reactive elements (like helium).

Temperature

Chemical reactions occur at a faster rate at higher temperatures.
The kinetic energy of subatomic particles increases with thermal energy.
The higher the temperature, the faster the particles move, and the more likely they are to come in contact and react.

Concentration and Pressure

The more particles present within a given space, the more likely those particles are to bump into one another.
Chemists can speed up chemical reactions by increasing the concentration of particles or decreasing the volume of the space, which increases the pressure.

Enzymes and Other Catalysts

A catalyst increases the rate of a chemical reaction without itself undergoing any change.
Enzymes are the most important catalysts in the human body and are composed of protein or ribonucleic acid (RNA).
Enzymes lower the activation energy needed for a chemical reaction.
Activation energy is the