The Chemistry of Life

In order to understand the biology life, it is essential to understand the chemistry of life too.

What is matter?

Matter is anything that takes up space and has mass.

What does all matter have in common?

*All matter is made up of atoms.

*Atoms are the smallest unit of matter that cannot be broken down by chemical means.

*Atoms consist of 3 kinds of subatomic particles:

1. Neutrons – Neutral (no charge*) particles (Neutrons and protons are in the nucleus, the center, of atoms.)

2. Protons – Positively charged* particles (Protons are also found in the nucleus of atoms.)

3. Electrons – Occupy the area around the nucleus. They are constantly in motion. They have a negative charge*.

*Atoms usually have the same number of protons as electrons, so there is usually no net charge to an atom.*Subatomic particles are too small to see, but these are the relative sizes of them in comparison to each other.

Atoms are so small and dynamic that it is difficult to illustrate their structure, but this is a common representation of how they would look if you could see them.

nucleusElectrons

circle the

nucleus

An element is pure substance made of only one kind of atom. (“pure gold”)

There are more than 100 known elements.

They are listed on the periodic table.

Each element is represented by a one, two or three letter abbreviation.

For example, Hydrogen is represented by H

Carbon is represented by C

Oxygen is represented with O

Elements differ in the number of protons their atoms contain.

Atoms of Oxygen contain eight protons.

Hydrogen atoms only contain one proton, though.

The number of neutrons also usually equals the number of protons, but there are exceptions.

Atoms of an element that contain different numbers of neutrons are called isotopes.

For example, there are several forms of carbon atoms: Carbon 12, carbon 13, and Carbon 14:

Carbon 12 has 6 neutrons and 6 protons (12).

Carbon 13 has 7 neutrons and 6 protons (13).

Carbon 14 contains 8 neutrons and 6 protons (14).

Chemical Bonding:Atoms can join with other atoms in a process called bonding in order to form stable substances.

A compound is what we call a substances made of the joined atoms of two or more different elements.

This compound is called water.

For example, when sodium (Na) atoms bond with

chlorine atoms (Cl), the compound sodium chloride (table salt) forms.

We represent this compound with a chemical formula:

NaCl. This formula shows that there is one atom ofsodium for every one atom of chlorine.

3 Kinds of chemical bonds:

1. Covalent – these bonds form when two or more atoms share electrons to form a molecule.

2. Hydrogen Bonds are formed when there is a weak chemical attraction between polar molecules.

An example of a molecule with hydrogen bonds is water.

The electrons in a water molecule are shared by the oxygen and the hydrogen atoms, but the negatively charged electrons are attracted more strongly by the oxygen atom’s larger positive nucleus than by the hydrogen atom’s smaller nucleus. Therefore, the electrons are shared unequally.

This causes the water molecule to become polar. The ends (poles) of the molecule are partially charged. Each molecule’s poles are weakly attracted* to the poles with the opposite charge. This attraction is called hydrogen bonding.

*(This is also why water is liquid.)

O

H

H

H

H

O

Slightly polar ends

3. Ionic bonds are bonds between oppositely charged particles (ions).

Ions are atoms or molecules that have gained or lostelectrons.

Since most atoms contain the same number of protons as electrons, there is usually no net charge to the atom.

Ions have different numbers of electrons and protons,so they will have a positive or negative charge,depending upon whether there are more protons

(+)

or more electrons (-).

Ions of opposite charge (+/-) may interact to form an ionic bond. (“Opposites attract…”)

An example of an ionic bond is Sodium Chloride. (remember…table salt?)

Sodium atoms are unstable, because they only have one Electron in their outer level. Atoms with full outer shellsare more stable.

Chlorine atoms are unstable, because the have only seven electrons in the outer level.

(Atoms are most stable when their outermost shell is full. In this case, there would be 8 electrons.)

8

12

3

4

56

7

Sodium readily gives up its lone electron, because its next innermost shell will then be full, and it becomes more stable. It also makes the ion positively charged. (It has lost one of its electrons, so there are now more positively charged protons in the nucleus than there are negatively charged electrons, leaving a net positive charge.)

Sodium becomes + Potassium becomes -

Chloride readily accepts the new electron from sodium, because this electron completes the required eight electron it needs to fill its outer shell. This makes itmore stable. It also becomes negatively charged. ( It has gained an extra electron. Therefore, the ion has more negatively charged electrons than there are positively charged protons. Thus, the ion has a net negative charge.)

Water and Solutions

There is water in all living things. You may not realize it,

but nearly 70% of your body is water. (Almost two thirds of the molecules in your body are water molecules.)

Your body’s cells are filled with water, and water is the solution in which most chemical reactions within the cells take place.

There is also water outside of your cells. The water that surrounds our cells also helps with moving substances into and out of our cells.

Properties of water that make it an important substance for life:

1. Storage of energy – water absorbs heat more slowly and retains this energy longer than many other substances do. (ex. boiling water “a watched pot never boils”…takes forever to boil, etc…; ex. sweat this is evaporative cooling it works, because water retains heat and carries heat from the inside of the body to the outside of the body with the water.)

2. Cohesion and Adhesion – Hydrogen bonds between water molecules also cause cohesion of water molecules and cause H20 to be liquid water.

Cohesion is an attraction between substances of the same

kind. (Because of cohesion, water molecules stick to each

other and form thin films and drops, like in the case ofdew.) “Co” = cooperate 2 similar substances stick together.

Adhesion is an attraction between different substances. Because of adhesion some substances get wet. Adhesion powers a process called capillary action. (straws and stems/roots of plants: water sticks to the insides of the tubes and is transported throughout the plant.)

“Add” 1 substance + 1 other substance = 2 different substances

Aqueous solutions – many substances dissolve in water. This is called an aqueous solution. (Ex. salt water)

Many substances in the body are dissolved in water or blood, which allows them to travel within and between the cells. (Ex. sugar)

Polarity – the polarity of water enables many substances to dissolve in water.

Because of their charge, ions dissolve best in water. Whenions are dissolved in water, the resulting solution is full of ions surrounded by water molecules.

Nonpolar molecules do not dissolve well in water. When nonpolar substances are put in water, the water molecules are more attracted to each other than they are the nonpolar substance. This causes the nonpolar substances to clump together. This explains why oil forms clumps orbeads in water. (Ex. cell membranes)

Acids and Bases

While the bonds in water molecules are strong, at any given time, a tiny fraction of those bonds might break, forming hydrogen ions (H+) and hydroxide ions (OH-).

H2O H+ + OH-

As a result, pure water always has a low concentration of hydrogen ions and hydroxide ions, which are present in equal numbers.

Acids – compounds that form hydrogen ions, when dissolved in water, are called acids.

Bases – compounds that reduce the concentration of hydrogen ions are called bases. Many bases also form hydroxide ions in water. The hydroxide ions in these bases react with the hydrogen ions to form more water molecules.

pH Scale – is based on the concentration of hydrogen ions in a solution. All solutions have a value between 0 and 14. Pure water has a value of 7, which is neutral.

Acids have a pH value below 7. These are called acidic.

Bases have a pH value above 7. These are called basic or alkaline.

pH Scale

Each whole number on the pH scale represents a factor of ten on the scale. For example, A solution with a pH of 5 has 10 times as many hydrogen ions as a solution with a pH of value 6.

Carbon compounds – compounds in the human body are organic. Organic compounds are those containing carbon atoms covalently bonded to other elements – typicallyhydrogen, oxygen, and other carbon atoms.

4 Macromolecules

• There are 4 classes of macromolecules in living organisms. The word macromolecule stands for macro = big + molecule = more than one atom bonded together.

• The 4 macromolecules are: carbohydrates, lipids, proteins and nucleic acids.

1.Carbohydrates – organic compounds made up of carbon, hydrogen, and oxygen atoms in a 1:2:1 ratio. These are a common source of energy found in food such as fruits, vegetables, and grains.

Monosaccharides – The building blocks of carbohydrates are simple sugars called monosaccharides. (mono = one = single sugar)

Disaccharides – (Di = two = double) Double sugars formed when two monosaccharides are joined.

Polysaccharides – are chains of three or more monosaccharides. A polysaccharide is an example of a macromolecule.

* A monomer is a single unit * a polymer is made up of several

2.Lipids – are nonpolar molecules that are not soluble or mostly insoluble in water. They include fats, phospholipids, steroids, and waxes. Lipids are an important part of the structure and function of cell membranes. Steroids include cholesterol, which is found in animal cell membranes. Other lipids include the pigments, such as chlorophyll, found in plant cell membranes.

Fats are lipids that store energy. Typical fats have three fatty acid chains bonded to a glycerol molecule backbone.

A fatty acid is a long chain of carbon atoms, with hydrogen atoms bonded to them. Because hydrogen-carbon bonds are so rich in energy, fats can store a lot of energy.

In saturated fats, ALL of the carbon atoms in the chain are

bonded to two hydrogen atoms except the ones on the ends,

which are bonded to three hydrogen atom as well as the adjacent carbon atom. Most animal fats are saturated.Ex. fats: butter, lard, and grease from cooked meats.)Saturated fats have relatively straight molecules and are solids at room temperature.

In unsaturated fats, some of the carbon atoms are

linked with a double covalent bond, then linked with only one hydrogen atom. This produces kinks in the structure of

the molecule, which makes the fat liquid at room

temperature. The molecules don’t pack so neatly together. (Ex. vegetable oil)

Saturated Unsaturated

3. Proteins – usually a large molecule formed by linked smaller molecules called amino acids*.

* amino acids are the building blocks of proteins.

***So… is a protein a monomer or a polymer?

There are 20 different kinds of amino acids. Some amino acids are polar, and some are nonpolar. Some are charged and some are not charged.

Proteins fold into compact shapes, depending upon how their amino acids interact with water and one another.

Some proteins are enzymes and promote chemical reactions. Other proteins have important structural functions. (ex. Collagen found in the skin, ligaments, tendons, and bones. Your hair is made of the protein keratin. The fibers of a blood clot are also made of protein.)

Other proteins of the body, such as those in the immune system, help fight infections. These are called antibodies.

In the muscles, there are special proteins, which help the muscles to contract. The muscles contain the structural proteins, actin and myosin.

In your blood, a protein called hemoglobin, carries oxygen in our blood from our lungs to our body tissues.

Most foods contain a mixture of carbohydrates, proteins, and fats. The body can use these to build new structures, but it more often, it uses them as an energy source. Your cells harvest the energy from food molecules for yourmetabolism.

The energy of food molecules is measured in the metric units called kilocalories (kcal). (or “calories” for short)

The minimal rate of energy use per hour is 70 kcal/h for men and 60 kcal/h for women.

Walking uses about 200 kcal/h, and jogging uses about 600 kcal/h.

The body stores the excess kilocalories as fat, regardless of whether they were obtained from carbohydrates, proteins, or fats.

Most carbohydrates in foods come from plant products, such as fruits, grains, and vegetables.

Other sources are milk (lactose) and meats (glycogen).

About 4 kcal of energy are supplied by 1 gram of Carbohydrates.

Candy and soft drinks also contain sugars.

Primary sources of dietary proteins include legumes (dried beans), eggs, milk, fish, poultry,and meat.

Proteins also provide about 4kcal/gram.

Dietary protein is the source of amino acids as well as the raw materials for nucleic acids.

4.Nucleic Acids – all of your cells contain nucleic acids. These are a long chain of smaller molecules called nucleotides.

A nucleotide has three parts: a sugar, a nitrogenous base, and a phosphate group. This phosphate group contains phosphorus and oxygen atoms.

There are two types of nucleic acids: DNA and RNA.

DNA is also called Deoxyribonucleic acid. It consists of two strands of nucleotides that spiral around each other (double helix). Chromosomes contain long strands of DNA, which contains hereditary information.

RNA can be a single stranded or double stranded molecule. It is called ribonucleic acid. RNA plays a key role in the manufacture of proteins. RNA can also react as an enzyme,promoting the chemical reactions that link amino acids to form proteins.

RNA

5.ATP – another important biological molecule is ATP. This is called Adenosine Triphosphate. It is a single nucleotide with two extra energy storing phosphate groups. When food molecules are broken down inside cells, some of the energy is temporarily stored in ATP. Cells need a constant supply of energy in order to function. (aka. “energy currency of the cell”)

Energy and Chemical Reactions

Your are surrounded by energy. It is in the chemical bonds of your food, the motion of a speeding car, the sound waves from the strings of a guitar, and the heat energy given off by a blazing fire.

Energy is the ability to move or change matter.

Energy exists in many forms: light, heat, chemical, mechanical, and electrical energy.

Energy can be converted from one form to another. (ex. kicking a ball, cooking an egg, a bioluminescent beetle)

Energy can be stored or released by chemical reactions. A reaction is a process during which chemical bonds between atoms are broken and new ones are formed, producing new substances.

At this very moment thousands of chemical reactions are occurring in every cell of your body .

The starting materials of a chemical reaction are called the reactants.

The newly formed materials or resulting materials are called the products.

The standard form of a chemical equation is written:

Reactants Products

The arrow is read as “changes to” or “forms.”

ex. Dissolving sodium chloride in water causes the following reaction:

NaCl Na+ + Cl-

NaCl is the reactant.

Na+ is a product.

Cl- is also a product.

Energy in Chemical Reactions

The chemical energy in chemical reactions is released when chemical bonds are broken and stored when new bonds are formed.

stored energy: ex. Light energy from the sun is captured by plants and stored in the chemical bonds in the sugar that they make.

released energy: ex. The original energy from sunlight is released again when the body breaks the chemical bondsbetween the atoms of sugar molecules during digestion.

Metabolism is the sum total of all chemical reactions in the body.

Your body gets most of the energy needed for metabolism from the food you eat.

As food is digested, chemical reactions convert energy in food molecules into a form of energy that can be used by the cells to do work. (ATP)

Activation Energy

This is the energy needed to start a chemical reaction.

Ex. Rolling a boulder down a hill…

Activation energy is that little “chemical push” at the start of the reaction which gets it started.

Ex. Chemical food energy, bicyclist, mechanical energy + thermal energy (Bike moves)

Enzymes

These are substances that increase the speed of chemical reactions. The chemical reactions in the cell are able to occur rapidly and at relatively low temperature, because of enzymes.

Most enzymes are proteins.

Enzymes are catalysts, which means they reduce the activation energy needed for a reaction to start.

Enzymes help organisms maintain homeostasis.

Without enzymes, most chemical reactions would not occur quickly enough to maintain life.

Ex. Blood carries carbon dioxide (CO2) to your lungs,

where it is eliminated when you breathe.

In the blood, carbon dioxide reacts with water (H2O)

to form carbonic acid (H

2CO

3) in the reaction shown

below:

CO2

+ H2O ----- H

2CO

3

*Remember which ones are the reactants and which ones are the products?

In the lungs, the reverse reaction occurs convertingcarbonic acid back into carbon dioxide and water vapor, which can both be breathed out (exhaled).

Without an enzyme, this reaction occurs very slowly. Only about 2,000 molecules of carbonic acid are produced in an hour!

This reaction is not fast enough for your blood to carry away the carbon dioxide released by millions of cells.

With the enzyme carbonic anhydrase, which is present in the blood, there are about 600,000 molecules of carbonic acid formed per SECOND!

The enzyme increases the reaction rate about one million times!

Enzyme Specificity

A substance upon which an enzyme reacts is known as a substrate. Enzymes can only act upon specific substrates.

This is because enzymes are shaped to fit the substrate.

Typically, enzymes have deep folds called active sites.

The enzyme acts only when the correct substrate fits into the active site. (like a lock and a key)

Enzyme Action

Factors in Enzyme Activity

Any factor that can change an enzyme’s shape can change it’s effectiveness.

For example, enzymes react most efficiently within a certain temperature range (native conformation v. denatured proteins = change of shape)

Enzymes also react within a certain pH range. (Remember the % of hydrogen content?)

Temperature or pH changes outside the acceptable range can cause chemical bonds in enzymes to weaken or even break, thus changing the shape and effectiveness ofenzyme action.

The enzymes which are active in a cell determine what happens in the cell.

The body’s cells contain many different enzymes, and each catalyzes a different chemical reaction.

For example, as you read this slide, the chemical reactions occurring in the nerve cells in your eyes are different from the chemical reactions occurring in your blood.

THE END