Chemical Constituents of Cells
This chapter covers basic chemical principles. These principles are important for understanding physiology since body functions result from chemical reactions that take place within cells.
Matter is anything that takes up space and has weight. Liquids, solids, and gases are all matter. What are some examples of matter around you right now? How about air? The chair you are sitting in? The components of your body? These are all examples of matter!
An element is defined as a pure chemical substance with only one type of atom. Think of an atom as a group of atoms that are alike but are not bonded together. For example, if you have in a container a bunch of neon atoms you have the element neon. The four most common elements in the body are carbon (C), hydrogen (H), oxygen (O) and nitrogen (N).
Atoms are tiny particles that make up elements. Atoms of one element will be different from the atoms of a different element. For example, a carbon atom is smaller and weighs less than an oxygen atom. Most atoms in this world will bind to other atoms to make molecules.
An atom is made of three types of subatomic particles called protons, neutrons, and electrons. Protons carry positive charges and are located in the nucleus or center of an atom. Neutrons carry no electrical charge and they are also located in the nucleus of an atom. Electrons carry negative charges and they are located outside the nucleus. Electrons constantly orbit the nucleus in pathways called electron orbits which are also called electron shells.
The atomic number of an element tells you the number of protons in one atom of that element. For example, the element carbon has an atomic number of 6. Therefore, one carbon atom has 6 protons in its nucleus. The number of protons of an element is also equal to the number of electrons. However, an atom can gain or lose electrons but it will never gain or lose protons.
That atomic weight of an element tells you the number of protons and neutrons in one atom of that element. For example, Lithium has an atomic number of 7. Therefore the total number of protons and neutrons together in the nucleus of one lithium atom is 7.
If you know the atomic number and the atomic weight of an element you can figure out how many protons, neutrons and electrons are in one atom of that element. For example, Lithium has an atomic number of 3 and an atomic weight of 7. How many protons does one atom of lithium have? Look at the atomic number to find your answer. The answer is 3. How many neutrons does one atom of lithium have? Subtract the number of protons from the atomic weight. 7 - 3 is 4. The number of neutrons in one atom of lithium is 4. How many electrons does one atom of lithium have? Look at the number of protons to find your answer. The answer is 3.
Click here to see the structure of the lithium atom
Click here to see the structures of other atoms
Most atoms in nature are unstable and they are constantly looking for ways to become stable! One way an atom can become stable is by becoming an ion. An atom becomes an ion when it gains are loses one or more electrons. Another way an atom can become stable is by forming a chemical bond with another atom.
We will first look at how an atom becomes stable by becoming an ion. Remember that if an atom has 7 protons it also has 7 electrons (i.e. the number of protons equals the number of electrons). You know where the protons of the atom stay - in the nucleus. Now you must learn where the electrons of an atom are placed.
Electrons orbit around the nucleus of an atom in pathways called shells. The first shell of an atom is the one closest to the nucleus and it can only hold 2 electrons. The second shell of an atom can hold up to 8 electrons and the third shell of an atom can hold up to 8 electrons. In this class we will not look at atoms with more than three shells. Let's look at the lithium atom. Lithium has an atomic number of 3. Therefore we know that lithium has 3 protons and 3 electrons. Two of the electrons will be placed in the first shell of the atom. That only leaves 1 atom to go in the second shell of the atom. And the third shell does not even exist as there are no electrons are in it. So, the second shell of lithium is the outermost shell and it is not full because it does not hold 8 electrons.
It is important to know whether or not the outermost shell of an atom is full as this determines whether it is stable or not! If the outermost shell is not full then the atom is not stable and the atom will react will another atom. So, is the lithium atom stable? No!
Let's look at the neon atom. Neon has an atomic number of 10. Therefore, it has 10 protons and 10 electrons. Two electrons will be in the first shell of the neon atom so how many electrons are left to go into the second shell? Eight is the answer. Are there any electrons to go into the third shell? No. So, the second shell is the outermost shell. Is it full? Yes! It has 8 electrons it in which is the maximum it can hold. Therefore the neon atom is stable. It will not react with other atoms.
If an atom has an outermost shell that is almost full it can gain electrons to fill the shell. Remember a full outermost shell makes it stable. Also, if an atom has an outermost shell that is almost empty it can lose the electrons in the outermost shell to empty it. Once the shell is empty it disappears leaving a shell that is full.
Let's look at an example of an atom that loses an electron to become stable. Sodium has an atomic number of 11. Therefore, how many electrons are in its outermost shell? To figure this out you would have reasoned that sodium has 11 electrons. Two electrons in the first shell, 8 electrons in the second shell, leaving 1 electron to go into the third shell. The outermost shell (the third shell in this example) is almost empty. It only has 1 electron in it but it needs 8 to be stable. This atom will lose the electron in the third shell; the third shell disappears since it has no electrons in it and now the second shell is the outermost shell. Is the second shell full? Yes! This makes the atom stable now. Remember, it an atom has an outermost shell that is almost empty it will lose electron(s) to become stable. When an atom loses electrons, the atom becomes positively charged. We now call this positively charged atom an ion.
Now let's look at an example of an atom that gains an electron in order to become stable. The chlorine atom has an atomic number of 17. How many electrons are in its outermost shell? You should have come up with 7. This outermost shell is almost full. It only needs one more electron! So, this atom will gain an electron to become stable. When the electron is added to the outermost shell, the shell has 8 electrons and is now full and stable. Remember that if an atom has an outermost shell that is almost full it will gain electron(s) to become stable. When an atom gains electrons, the atom becomes negatively charged. We now call this negatively charged atom an ion. In other words, any charged atom (positive or negative) is called an ion.
Now that you understand how ions are formed, you can understand the ionic bond. We say an ionic bond is formed when an electron or electrons are transferred from one atom to another. When one atom loses an electron it becomes a positively charged ion and the atom that gains the electron becomes a negatively charged ion. Opposites attract! The positive ion is now attracted to the negative ion and they form an ionic bond. Sodium and chloride atoms form ionic bonds with each other very readily. Remember sodium likes to lose an electron to become stable (therefore positively charged) and chloride likes to gain an electron to become stable (therefore negatively charged). So sodium simply transfers one electron to chloride; they form oppositely charged ions and they electrically attract each other to form an ionic bond called sodium chloride (table salt).
Click here to see a figure showing the formation of an ionic bond
Atoms may also become stable by sharing electrons with other atoms. When this happens we say the atoms have formed a covalent bond. One hydrogen atom will easily form a covalent bond with another hydrogen atom. Let's look at why this occurs.
Hydrogen has an atomic number of 1. Therefore it only has 1 electron. It's first shell, which turns out to be its outermost shell, needs 1 more electron to become full. Remember the first shell of an atom can only hold 2 electrons. One hydrogen atom will find another hydrogen atom and they will share their electrons. The 2 electrons will orbit around the nucleus of one hydrogen atom and then they will orbit around the nucleus of the other hydrogen atom. They are sharing one pair of electrons which makes them both stable. The sharing of one pair of electrons forms a single covalent bond.
If two atoms share two pairs of electrons, they have formed a double covalent bond and if they share three pairs of electrons, they have formed a triple covalent bond. Covalent bonds are much stronger than ionic bonds.
Click here to see a figure showing the formation of a covalent bond
Molecules are formed when two or more atoms bond. When two hydrogen atoms bond together we get a molecule of hydrogen. When two hydrogen atoms bond to an oxygen atom, we get the molecule water. When atoms of different elements bond we get molecules that make up compounds. For example, the molecule hydrogen is not a compound because it only contains atoms of one element. Water is a compound because its molecules are made up of atoms of two different elements (hydrogen and oxygen).
Molecules can be represented by molecular formulas and structural formulas. A molecular formula indicates the types of atoms and the number of each atom in the molecule. For example, H2O is the molecular formula for water. This formula tells you that one molecule of water contains 2 hydrogen atoms and 1 water atom.
Structural formulas give you a little more information that molecular formulas. A structural formula tells you the types of atoms, the number of each atom and how the atoms are bonded together.
For examples of structural formulas click here
The structural formula of water shows you that two hydrogen atoms are covalently bonded to the same oxygen atom. A solid line between 2 atomic symbols represents a covalent bond. Two solid lines between two atomic symbols represents a double covalent bond. For example, double covalent bonds hold oxygen atoms to a carbon atom in the molecule carbon dioxide.
Chemical reactions occurs when bonds are made or broken between atoms and molecules. In some chemical reactions, bonds are broken and made. One type of chemical reaction is called the synthesis reaction. In a synthesis reaction, bonds are made. Also, in a synthesis reaction, the product is always larger than the reactants. The product of a reaction is the substance you end up with. The reactants of a reaction are the substances you start out with. A synthesis reaction can be represented like this:
A + B --> AB
The reactants are A and B. The product is AB. In this reaction a bond was made between the two reactants and the product is larger than the starting reactants.
Another type of chemical reaction is the decomposition reaction. In a decomposition reaction bonds are broken so the product of the reaction is smaller than the reactants. A decomposition reaction can be represented like this:
AB --> A + B
In this reaction the bond in AB is broken to give us A and B. Notice that a decomposition reaction is the opposite of a synthesis reaction.
Another type of chemical reaction is the exchange reaction. An exchange reaction is a decomposition reaction followed by a synthesis reaction. It can be represented like this:
AB + CD --> AD + CB
In this reaction, the bond in AB is broken and the bond in CD is broken which represents the decomposition portion of the reaction. Then a bond is formed between A and D and another bond is formed between B and C; the forming of these bonds represents the synthesis part of the reaction.
Many chemical reactions are reversible. In other words, the products of the chemical reaction can be changed back into the reactants. A reversible reaction is represented by a double arrow.
A + B <--> AB
In a reversible reaction if the product is more stable than the reactants, then the product will be formed. However, if the reactants are more stable than the product then the reactants will be formed.
Some substances release ions when put into water. These substances are called electrolytes. For example, NaCl (sodium chloride) is an electrolyte. When you put NaCl in water, it releases the sodium ion (Na+) and the chloride ion (Cl-). Acids and bases are types of electrolytes.
Acids are defined as electrolytes that release hydrogen ions (H+) in water. For example, hydrochloric acid (HCl) will release hydrogen ions and chloride ions when you put it in water. Therefore, it is acidic. It is also an electrolyte because is releases ions.
Bases are defined as electrolytes that will release ions that will combine with hydrogen ions when put in water. Many bases release the hydroxyl ion (OH-) in water. The hydroxyl ion will combine with the hydrogen ion bond to form water. Sodium hydroxide (NaOH) is an example of a base. In water, sodium hydroxide releases the sodium ion (Na+) and the hydroxyl ion (OH-).
pH measures the concentration of hydrogen ions. The pH scale runs from 0 to 14. If a solution has a pH of 7, the solution is neutral. If a solution has a pH less than 7, the solution is acidic. If a solution has a pH greater than 7, it is basic or alkaline. The more acidic a solution is, the higher the concentration of hydrogen ions it has. Therefore, if solution A has a pH of 3 and solution B has a pH of 5, solution A is more acidic and solution A has a higher concentration of hydrogen ions. Therefore, as pH goes down, the concentration of hydrogen ions goes up!
Click here to see the pH scale and pHs of various substances
Cells are made up of matter. Matter can be divided into two large categories, organic matter and inorganic matter. Organic matter contains carbon and hydrogen. Inorganic matter does not contain carbon and hydrogen. Organic molecules tend to be large while inorganic molecules tend to be small.
Examples of inorganic substances are water, oxygen, carbon dioxide and salts such as sodium chloride.
Water is the most abundant inorganic compound in the body. It accounts for about 70% of your body weight. Most chemical reactions in the body take place in water. Water is the major component of all body fluids (blood, urine, cytoplasm, etc). Water also plays an important role in maintaining body temperature as it carries a large amount of heat from muscles in the body to the body surface where heat can be lost.
Molecular oxygen is another important inorganic substance in the body. Molecules of oxygen are used by cells in the body to produce energy.
Carbon dioxide is an inorganic waste product produced by most body cells. Inorganic salts provide tissues and cells with necessary ions such as sodium (Na+), chloride (Cl-), potassium (K+), calcium (Ca2+), etc.
Click here to see a summary of important inorganic substances in the human body
Carbohydrates, lipids, proteins, and nucleic acids are examples, of organic substances found in body cells.
Carbohydrates are molecules that contain carbon, hydrogen and oxygen. The hydrogen to oxygen ratio is always close to 2:1 in these molecules. For example, C6H12O6 (glucose) is a carbohydrate molecule. Notice it contains the elements, carbon, hydrogen and oxygen; also notice that it has twice as many hydrogens as oxygens (a ratio of 2:1). The building blocks of carbohydrates are molecules called monosaccharides. Glucose is the most common monosaccharide in cells. When two monosaccharides bond together they form a disaccharide. Sucrose (C12H22O11,common table sugar) is an example of a disaccharide. When many monosaccharides bond together they form a polysaccharide. Starch is an example of a polysaccharide. Starch is the carbohydrate found in many foods such as potatoes, pasta and rice. Body cells depend on carbohydrate molecules to make energy. Carbohydrates are also used by cells to build cell structures.
Click here to see the structures of a monosaccharide, disaccharide, and polysaccharide
Lipids are organic molecules that always contain carbon, hydrogen and oxygen. However unlike carbohydrate molecules, the hydrogen to oxygen ratio is never close to 2:1; the hydrogen to oxygen ratio is always much greater in lipid molecules. For example, tristearin (C57H110O6) is a lipid molecule. Notice how many hydrogens and how few oxygens are in this molecule compared to a carbohydrate molecule. Lipid molecules also often contain phosphorous. Examples of lipid molecules are triglycerides, phospholipids, and steroids.
Triglycerides are more commonly called fat molecules. The building blocks of fat molecules are fatty acids and glycerol. Each glycerol molecule binds with three fatty acid molecules to make one triglyceride molecule. The glycerol molecule of triglycerides is always the same. However, there are many different types of fatty acid molecules. Therefore, there are many different types of triglyceride molecules. Triglycerides are used to store energy for cells.
Click here to see the structure of a fatty acid and triglyceride
Phospholipids are a type of lipid made up of 1 glycerol molecule, 2 fatty acid molecules, and a phosphate molecule. Phospholipids are primarily used to make cell membranes.
Click here to see the structure of a phospholipid
Steroids are very large lipid molecules with complex of connected rings of carbon atoms. Cholesterol is an example of an important steroid for body cells. Cholesterol is used to make cell membranes. It is also used to make many hormones of the body.
Click here to see the structure of a steroid molecule and a cholesterol molecule
Proteins are organic molecules that contain carbon, hydrogen, oxygen, and nitrogen. Many proteins also contain sulfur. The building blocks of proteins are smaller molecules called amino acids. There are about 20 different amino acids that make up proteins. Proteins contain specific numbers of different amino acids joined together in a specific linear sequence called an amino acid chain or a polypeptide chain. Once an amino acid chain is formed it will twist and bend into a three-dimensional shape.
The twisting and bending of the amino acid chain is caused by the formation of hydrogen bonds along the chain. Hydrogen bonds are very weak bonds formed between hydrogen atoms and a nitrogen or oxygen atom. These hydrogen bonds help to maintain the three-dimensional shape of the protein molecule. Hydrogen bonds break easily when they are exposed to excessive heat, radiation, or pH changes. When the hydrogen bonds break, the protein loses its shape and can no longer function. A protein that loses its shape is said to be denatured.
Proteins have many functions in the body. Many proteins act as structural materials for the building of cell parts. Other proteins act as hormones, enzymes, receptors, and antibodies.
Click here to see the structures of amino acids
Click here to see the structure of a protein
Nucleic acids are organic molecules that contain carbon, hydrogen, oxygen, nitrogen and phosphorous. These large molecules form genes and participate in protein synthesis. The building blocks of nucleic acids are molecules called nucleotides. A nucleotide molecule is made of a sugar molecule, a phosphate molecule, and an organic base.
DNA and RNA are two examples of nucleic acids. DNA is made of nucleotides that contain the sugar deoxyribose. DNA stores genetic information for cells. RNA is made of nucleotides that contain the sugar ribose. RNA is used to make proteins.
Click here to see the structure of a nucleotide and a chain of nucleotides (polynucleotide)
Click here to see a summary of the organic substances found in the human body