2.1 The Structure of Atoms

An atom is the smallest component of a substance, and it cannot be subdivided into smaller substances without losing its properties.
The science of the interaction between atoms and molecules is called chemistry.
Every atom has a centrally located nucleus and negatively charged particles called electrons that move around the nucleus in regions called electron shells.
The nucleus is made up of positively charged particles called protons and uncharged particles called neutrons.
Atoms are often listed by their atomic number, which is the number of protons in the nucleus.
All atoms with the same number of protons behave the same way chemically and are classified as the same chemical element.
Most elements have several isotopes, which are atoms with different numbers of neutrons in their nuclei.
In an atom, electrons are arranged in electron shells, which are regions corresponding to different energy levels.
- The arrangement is called an electronic configuration.
Shells are adhered outward from the nucleus, and each shell can hold a characteristic maximum number of electrons.
- Two electrons in the innermost shell (lowest energy level), eight electrons in the second shell, and eight electrons in the third shell, if it is the atom’s outermost (valence) shell.
An atom can give up, accept, or share electrons with other atoms to fill the outermost shell.
When an atom’s outermost electron shell is only partially filled, the atom is chemically unstable.

2.2 How Atoms Form Molecules: Chemical Bonds

The valence, or combining capacity, of an atom is the number of extra or missing electrons in its outermost electron shell.
Atoms achieve the full complement of electrons in their outermost energy shells by combining to form molecules, which are made up of atoms of one or more elements.
A molecule that contains at least two different kinds of atoms is called a compound.
Molecules hold together because the valence electrons of the combining atoms form attractive forces, called chemical bonds, between the atomic nuclei.
When atoms have gained or lost outer electrons, the chemical bond is called an ionic bond.
- An ionic bond is an attraction between ions of opposite charge that holds them together to form a stable molecule.
An atom whose outer electron shell is less than half-filled will lose electrons and form positively charged ions, called cations.
When an atom’s outer electron shell is more than half-filled, the atom will gain electrons and form negatively charged ions, called anions.
A covalent bond is a chemical bond formed by two atoms sharing one or more pairs of electrons.
A hydrogen bond is where a hydrogen atom is covalently bonded to one oxygen or nitrogen atom and it is attracted to another oxygen or nitrogen.
- Hydrogen bond are considerably weaker than either ionic or covalent bonds; they have only about 5% of the strength of covalent bonds.
The molecular mass of a molecule is the sum of the atomic masses of all its atoms.
One mole of a substance is its molecular mass expressed in grams.
The unit of molecules mass is a dalton (da).

2.3 Chemical Reactions

Chemical reactions involve the making or breaking of bonds between atoms.
A chemical reaction that absorbs more energy than it releases is called an endergonic reaction (endo = within).
A chemical reaction that releases more energy than it absorbs is called exergonic reaction (exo = out), meaning that energy is directed outward.
When two or more atoms, ions, or molecules combine to form new and larger molecules, the reaction is called a synthesis reaction.
Pathways of synthesis reaction in living organisms are called anabolic reaction or anabolism.
The reverse of a synthesis reaction is a decomposition reaction.
- Decomposition reactions split large molecules into smaller molecules, ions, or atoms.
- Decomposition reactions that occur in living organisms are called catabolic reactions or catabolism.
Many reactions, such as exchange reactions, are actually part synthesis and part decomposition.
A chemical reaction that the end product can revert to the original molecule is termed a reversible reaction.

2.4 Inorganic Compounds

Inorganic compounds are defined as molecules, usually small and structurally simple, which typically lack carbon and in which ionic bonds may play an important role.
Organic compounds always contain carbon and hydrogen and typically are structurally complex.
Any molecule having such an unequal distribution of charges is called a polar molecule.
The polarity of water makes it an excellent dissolving medium, or solvent.
Many polar substances undergo dissociation, or separation, into individual molecules in water where they dissolve.
The negative part of the water molecules is attracted to the positive part of the molecules in the solute, or dissolving substance, and the positive part of the water molecule is attracted to the negative part of the solute molecules.
Ionization or dissociation, where they break apart into ions.
An acid is a substance that dissociates into one or more hydrogen ions and one or more negative ions.
- An acid can also be defined as a proton donor.
A base dissociates into one or more negatively charged hydroxide ions that can accept, or combine with, protons, and one or more positive ions.
A salt is a substance that dissociates in water into cations and anions, neither of which is H+ or OH-.
It is convenient to express the amount of H+ in a solution by a logarithmic pH scale, which ranges from 0 to 14.
- The term pH means the potential of hydrogen.
- One logarithmic scale, a change of one whole number represents a tenfold change from the previous concentration.
Organisms possess natural pH buffers, compounds that help keep the pH from changing drastically.

2.5 Organic Compounds

The chain of carbon atoms in an organic molecule is called the carbon skeleton, a huge number of combinations is possible for carbon skeletons.
The bonding of other elements with carbon and hydrogen forms characteristic functional groups, specific groups of atoms that are most commonly involved in chemical reactions and are responsible for most of the characteristic chemical properties of a particular organic compound.
Small organic molecules can be combined into very large molecules called macromolecules.
- Macromolecules are usually polymers, which are formed by covalent bonding of many repeating small molecules called monomers.
In a dehydration synthesis, also known as a condensation synthesis, a molecule of water is released.
Carbohydrates are a large and diverse group of organic compounds that includes sugars and starch.
- Carbohydrates are made up of carbon, hydrogen, and oxygen atoms.
Simple sugars are called monosaccharides; each molecule contains three to seven carbon atoms.
Disaccharides are formed when two monosaccharides bond in a dehydration synthesis reaction.
Polysaccharides consist of tens or hundred of monosaccharides joined through dehydration synthesis.
Lipids are composed of atoms of carbon, hydrogen, and oxygen atoms.
- Most lipids are insoluble in water but dissolve readily in nonpolar solvents.
- Lipids provide structure of membranes and some cell walls and functions in energy storage.
Complex lipids contain elements such as phosphorus, iatrogenic and sulfur and carbon.
Proteins are organic molecules that contain carbon, hydrogen, oxygen, and nitrogen. Some also contain sulfur.
Enzymes are the proteins that speed up biochemical reactions.
Amino acids are the building blocks of proteins.
The bonds between amino acids are called peptide bonds.
- Peptide bonds are formed by dehydration synthesis.
Deoxyribonucleic acid (DNA) is the substance of which genes are made.
DNA and another substance called ribonucleic acid (RNA) are together referred to as nucleic acids because they were first discovered in the nuclei cells.
Each nucleotide has three parts: a nitrogen-containing base, a pentose sugar, and a phosphate group.
A and G are double-ring structures called purines, whereas T, C, and U are single-ring structures referred to as pyrimidines.
The term nucleoside refers to the combination of purine or pyrimidine plus a pentose sugar; it does not contain a phosphate group.
According to the model proposed by Watson and Crick, a DNA molecule consists of two long strands wrapped around each other to form a double helix.
Adenosine triphosphate (ATP) is the principle energy-carrying molecule of all cells and is indispensable to the life of the cell.
- ATP is called a high-energy molecule because it releases a larger amount of usable energy when the third phosphate group is hydrolyzed to become adenosine diphosphate (ADP).

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Chapter 2: Chemical Principles

2.1 The Structure of Atoms

An atom is the smallest component of a substance, and it cannot be subdivided into smaller substances without losing its properties.
The science of the interaction between atoms and molecules is called chemistry.
Every atom has a centrally located nucleus and negatively charged particles called electrons that move around the nucleus in regions called electron shells.
The nucleus is made up of positively charged particles called protons and uncharged particles called neutrons.
Atoms are often listed by their atomic number, which is the number of protons in the nucleus.
All atoms with the same number of protons behave the same way chemically and are classified as the same chemical element.
Most elements have several isotopes, which are atoms with different numbers of neutrons in their nuclei.
In an atom, electrons are arranged in electron shells, which are regions corresponding to different energy levels.
- The arrangement is called an electronic configuration.
Shells are adhered outward from the nucleus, and each shell can hold a characteristic maximum number of electrons.
- Two electrons in the innermost shell (lowest energy level), eight electrons in the second shell, and eight electrons in the third shell, if it is the atom’s outermost (valence) shell.
An atom can give up, accept, or share electrons with other atoms to fill the outermost shell.
When an atom’s outermost electron shell is only partially filled, the atom is chemically unstable.

2.2 How Atoms Form Molecules: Chemical Bonds

The valence, or combining capacity, of an atom is the number of extra or missing electrons in its outermost electron shell.
Atoms achieve the full complement of electrons in their outermost energy shells by combining to form molecules, which are made up of atoms of one or more elements.
A molecule that contains at least two different kinds of atoms is called a compound.
Molecules hold together because the valence electrons of the combining atoms form attractive forces, called chemical bonds, between the atomic nuclei.
When atoms have gained or lost outer electrons, the chemical bond is called an ionic bond.
- An ionic bond is an attraction between ions of opposite charge that holds them together to form a stable molecule.
An atom whose outer electron shell is less than half-filled will lose electrons and form positively charged ions, called cations.
When an atom’s outer electron shell is more than half-filled, the atom will gain electrons and form negatively charged ions, called anions.
A covalent bond is a chemical bond formed by two atoms sharing one or more pairs of electrons.
A hydrogen bond is where a hydrogen atom is covalently bonded to one oxygen or nitrogen atom and it is attracted to another oxygen or nitrogen.
- Hydrogen bond are considerably weaker than either ionic or covalent bonds; they have only about 5% of the strength of covalent bonds.
The molecular mass of a molecule is the sum of the atomic masses of all its atoms.
One mole of a substance is its molecular mass expressed in grams.
The unit of molecules mass is a dalton (da).

2.3 Chemical Reactions

Chemical reactions involve the making or breaking of bonds between atoms.
A chemical reaction that absorbs more energy than it releases is called an endergonic reaction (endo = within).
A chemical reaction that releases more energy than it absorbs is called exergonic reaction (exo = out), meaning that energy is directed outward.
When two or more atoms, ions, or molecules combine to form new and larger molecules, the reaction is called a synthesis reaction.
Pathways of synthesis reaction in living organisms are called anabolic reaction or anabolism.
The reverse of a synthesis reaction is a decomposition reaction.
- Decomposition reactions split large molecules into smaller molecules, ions, or atoms.
- Decomposition reactions that occur in living organisms are called catabolic reactions or catabolism.
Many reactions, such as exchange reactions, are actually part synthesis and part decomposition.
A chemical reaction that the end product can revert to the original molecule is termed a reversible reaction.

2.4 Inorganic Compounds

Inorganic compounds are defined as molecules, usually small and structurally simple, which typically lack carbon and in which ionic bonds may play an important role.
Organic compounds always contain carbon and hydrogen and typically are structurally complex.
Any molecule having such an unequal distribution of charges is called a polar molecule.
The polarity of water makes it an excellent dissolving medium, or solvent.
Many polar substances undergo dissociation, or separation, into individual molecules in water where they dissolve.
The negative part of the water molecules is attracted to the positive part of the molecules in the solute, or dissolving substance, and the positive part of the water molecule is attracted to the negative part of the solute molecules.
Ionization or dissociation, where they break apart into ions.
An acid is a substance that dissociates into one or more hydrogen ions and one or more negative ions.
- An acid can also be defined as a proton donor.
A base dissociates into one or more negatively charged hydroxide ions that can accept, or combine with, protons, and one or more positive ions.
A salt is a substance that dissociates in water into cations and anions, neither of which is H+ or OH-.
It is convenient to express the amount of H+ in a solution by a logarithmic pH scale, which ranges from 0 to 14.
- The term pH means the potential of hydrogen.
- One logarithmic scale, a change of one whole number represents a tenfold change from the previous concentration.
Organisms possess natural pH buffers, compounds that help keep the pH from changing drastically.

2.5 Organic Compounds

The chain of carbon atoms in an organic molecule is called the carbon skeleton, a huge number of combinations is possible for carbon skeletons.
The bonding of other elements with carbon and hydrogen forms characteristic functional groups, specific groups of atoms that are most commonly involved in chemical reactions and are responsible for most of the characteristic chemical properties of a particular organic compound.
Small organic molecules can be combined into very large molecules called macromolecules.
- Macromolecules are usually polymers, which are formed by covalent bonding of many repeating small molecules called monomers.
In a dehydration synthesis, also known as a condensation synthesis, a molecule of water is released.
Carbohydrates are a large and diverse group of organic compounds that includes sugars and starch.
- Carbohydrates are made up of carbon, hydrogen, and oxygen atoms.
Simple sugars are called monosaccharides; each molecule contains three to seven carbon atoms.
Disaccharides are formed when two monosaccharides bond in a dehydration synthesis reaction.
Polysaccharides consist of tens or hundred of monosaccharides joined through dehydration synthesis.
Lipids are composed of atoms of carbon, hydrogen, and oxygen atoms.
- Most lipids are insoluble in water but dissolve readily in nonpolar solvents.
- Lipids provide structure of membranes and some cell walls and functions in energy storage.
Complex lipids contain elements such as phosphorus, iatrogenic and sulfur and carbon.
Proteins are organic molecules that contain carbon, hydrogen, oxygen, and nitrogen. Some also contain sulfur.
Enzymes are the proteins that speed up biochemical reactions.
Amino acids are the building blocks of proteins.
The bonds between amino acids are called peptide bonds.
- Peptide bonds are formed by dehydration synthesis.
Deoxyribonucleic acid (DNA) is the substance of which genes are made.
DNA and another substance called ribonucleic acid (RNA) are together referred to as nucleic acids because they were first discovered in the nuclei cells.
Each nucleotide has three parts: a nitrogen-containing base, a pentose sugar, and a phosphate group.
A and G are double-ring structures called purines, whereas T, C, and U are single-ring structures referred to as pyrimidines.
The term nucleoside refers to the combination of purine or pyrimidine plus a pentose sugar; it does not contain a phosphate group.
According to the model proposed by Watson and Crick, a DNA molecule consists of two long strands wrapped around each other to form a double helix.
Adenosine triphosphate (ATP) is the principle energy-carrying molecule of all cells and is indispensable to the life of the cell.
- ATP is called a high-energy molecule because it releases a larger amount of usable energy when the third phosphate group is hydrolyzed to become adenosine diphosphate (ADP).