Download CHEMISTRY OF LIFE

CHEMISTRY OF LIFE
NATURE OF MATTER
ATOMS
Chemistry will help you learn about biology because organisms are chemical machines.
All matter consists of atoms.
Atom = the smallest unit of matter that cannot be broken down by chemical means.
Scientists have developed models (due to the small size of atoms) to explain the structure
and properties of atoms.
Atoms consist of 3 kinds of particles: electrons, protons, and neutrons.
Protons and Neutrons make up the nucleus of the atom.
Electrons are found in the electron cloud surrounding the nucleus.
Electrons are negatively charged.
Protons are positively charged.
Neutrons have a neutral charge.
Since protons and neutrons are both found in the nucleus, this leaves the nucleus with a
positive charge.
Because protons and electrons are oppositely charged, they attract one another.
Atoms typically have one electron for each proton leaving the atom with a neutral charge.
Elements:
Element = a pure substance made of only one kind of atom.
There are more than 100 known elements.
Each element is represented by a letter/s symbol (Hydrogen = H, Carbon = C, etc.).
Elements differ in the number of protons their atoms contain.
Hydrogen contains one proton and one electron.
Oxygen contains eight protons and eight electrons.
The number of neutrons in the atom is often but not always equal to the number of
protons in the atom.
CHEMICAL BONDING
Atoms can form with other atoms to form stable substances.
Chemical bond = a force the joins atoms.
Compound = a substance made of the joined atoms of two or more different elements.
Sodium (Na) bonds with Chlorine (Cl) to form Sodium Chloride (NaCl) also known as
table salt.
NaCl consists of one Na atom for every Cl atom.
Covalent Bonds:
Covalent bonds form when two or more atoms share electrons to form a molecule.
Molecule = a group of atoms held together by covalent bonds.
“Water molecules” = H2O
Because the number of protons is equal to the number of electrons in a molecule, the
molecule has no net electrical charge.
Carbon dioxide (CO2) and Oxygen gas (O2).
The arrangement of their electrons determines how atoms bond together.
Electrons are grouped into different levels (energy shells).
The levels closest to the nucleus have less energy than the levels farther from the nucleus.
Each level can hold a limited number of electrons.
The outer electron levels of H and He can hold up to two electrons.
All other atoms have outer electron levels that can hold up to eight electrons.
An atom becomes stable when its outer electron level is full.
If the outer electron level is not full, an atom will react readily with atoms that can
provide electrons to fill its outer level.
H2O forms when an oxygen atom (6 outer electrons) combines with 2 hydrogen atoms (1
outer electron each).
Hydrogen Bonds:
The electrons in a water molecule are shared by oxygen and hydrogen atoms.
However, the shared electrons are attracted more strongly by the oxygen nucleus.
The water molecule therefore has partially positive and negative ends, or poles.
The partially positive end of one water molecule is attracted to the negative end of
another water molecule.
Polar molecules = molecules with an unequal distribution of electrical charge.
Hydrogen bond = a weak chemical attraction between polar molecules.
Ionic Bonds:
Ion = an atom or molecule that has gained or lost one or more electrons.
Ions have an electrical charge because they contain an unequal number of electrons and
protons.
An atom that has lost an electron is positively charged.
One that has gained an electron is negatively charged.
Sodium is unstable because it has only one electron in its outer level.
Sodium readily gives up this electron to become a stable, positively charged sodium ion
(Na+).
Chlorine is unstable because it has seven electrons in its outer level.
Chlorine readily accepts an electron to become a stable, negatively charged chloride ion
(Cl-).
The negative charge of a chloride ion is attracted to the positive charge of a sodium ion.
Thus, sodium atoms and chlorine atoms readily form an ionic bond to become sodium
chloride (NaCl).
WATER AND SOLUTIONS
WATER IN LIVING THINGS
Nearly 70% of your body is made of water.
About two-thirds of the molecules in your body are water molecules.
Your body’s cells are filled with water and water is the medium in which most cellular
events take place.
Your cells are also surrounded by water, and water helps move nutrients and other
substances into and out of your cells.
Storage of Energy:
Water absorbs heat more slowly and retains the energy longer than many other
substances do.
Many organisms release excess heat through water evaporation (sweating) = homeostasis.
Cohesion and Adhesion:
The hydrogen bonds between water molecules cause the cohesion of liquid water.
Cohesion = an attraction between substances of the same kind.
Surface Tension = caused by hydrogen bonds and prevents the surface of water from
stretching or breaking easily.
Adhesion = an attraction between different substances.
Capillary action (water being attracted to the stem of a plant) allows water to move
“upward” through a plant.
AQUEOUS SOLUTIONS
Many substances dissolve in water (salt, sugar, etc.).
Solution = a mixture in which one or more substances are evenly distributed in another
substance.
Many important substances in the body have been dissolved in blood or other aqueous
fluids.
This allows substances to move within and between cells.
Polarity:
The polarity of water enables many substances to dissolve in water.
Ionic compounds and polar molecules dissolve best in water.
When ionic compounds are dissolved in water, the ions become surrounded by polar
water molecules.
Ions are attracted to the ends of water molecules with the opposite charge.
The resulting solution is a mixture of water molecules and ions.
A similar attraction results with polar molecules and water.
In both cases, the ions or molecules become evenly distributed in the water.
Nonpolar molecules do not dissolve well in water.
When nonpolar substances, such as oil, are placed in water: the water molecules are more
attracted to each other than to the nonpolar molecules.
As a result, the nonpolar molecules are shoved together.
The inability of nonpolar molecules to dissolve in polar molecules is important to
organisms.
The shape and function of cell membranes depend on the interaction of polar water with
nonpolar membrane molecules.
Acids and Bases:
At any given time a tiny fraction of those bonds might break, forming a hydrogen ion,
H+, and a hydroxide ion, OH-:
H2O  H+ + OHAs 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.
When an acid is added to water, the concentration of hydrogen ions in the solution is
increased above that of pure water.
Base = compounds that reduce the concentration of hydrogen ions in a solution.
Many bases form hydroxide ions when dissolved in water.
Such bases lower the concentration of hydrogen ions because hydroxide ions react with
hydrogen ions to form water molecules.
The pH scale is based on the concentration of hydrogen ions in solution.
All solutions have a pH value between 0 and 14.
Pure water has a pH value of 7.
Acidic solutions have pH values below 7 (0-6).
Basic solutions have pH values above 7 (8-14).
Each whole number represents a factor of 10 on the scale.
A solution with a pH value of 5 has 10 times as many hydrogen ions as one with a pH
value of 6.
CHEMISTRY OF CELLS
CARBON COMPOUNDS
Most matter in your body that is not water is made of organic compounds.
Organic compounds contain carbon atoms that are covalently bonded to other elements –
typically hydrogen, oxygen, and other carbon atoms.
Four principle classes of organic compounds are found in living things: carbohydrates,
lipids, proteins, and nucleic acids.
Without these, cells could not function.
Carbohydrates:
Carbohydrates = organic compounds made of carbon, hydrogen, and oxygen atoms in a
proportion of 1:2:1.
Key source of energy and are found in most foods – especially in fruits, vegetables, and
grain.
Monosaccharides = single sugars that are the building blocks of carbohydrates.
Examples: Glucose (C6H12O6) and Fructose
Major source of energy in the cell
Disaccharides = double sugars formed when two monosaccharides are joined.
Example: Sucrose (common table sugar) consists of both glucose and fructose.
Polysaccharides = chains of three or more monosaccharides.
Example: Starch
Polysaccharides are examples of macromolecules.
Macromolecule = a large molecule made of many smaller molecules.
Some polysaccharides function as storehouses of energy.
Examples: starch (made by plants) and glycogen (made by animals).
Both of these are made of hundreds of linked glucose molecules.
Cellulose is a polysaccharide that provides structural support for plants.
Humans cannot digest cellulose.
Lipids:
Lipids = nonpolar molecules that are not soluble or mostly insoluble in water.
Fats, phospholipids, steroids (cholesterol), and waxes.
Lipids are an important part of the structure and function of cell membranes.
Chlorophyll (pigment) is a lipid.
Fats and lipids store energy.
Fatty acid = a long chain of carbon atoms with hydrogen atoms bonded to them.
Most carbon atoms in a fatty acid are bonded to either one or two hydrogen atoms.
Because these bonds are rich in energy, fats can store a lot of energy.
Saturated fatty acid = all of the carbon atoms in the chain are bonded to two hydrogen
atoms (except the carbon atom on the end, which is bonded to three hydrogen atoms).
Most animal fats – such as those in butter, lard, and grease from cooked meats - contain
primarily saturated fatty acids.
Relatively straight molecules.
Generally solid at room temperature.
Unsaturated fatty acid = some of the carbon atoms are linked by a “double” covalent
bond , each with only one hydrogen atom.
This bond produces “kinks” in the molecule.
Most plant oils (olive oil) and some fish oils.
Generally liquid at room temperature.
Proteins:
Protein = usually a large molecule formed by smaller molecules called amino acids.
Amino acids = the building blocks of proteins.
Twenty different amino acids are found in proteins.
Some are polar and some nonpolar.
Some are electrically charged and others are not charged.
Proteins fold into compact shapes, determined in part by how the protein’s amino acids
interact with water and one another.
Enzymes are proteins that promote chemical reactions.
The protein collagen is found in skin, ligaments, tendons, and bones.
Hair, muscles, and bones contain protein.
Antibodies (proteins) help your body against infection.
Hemoglobin (found in red blood cells) carries oxygen.
Nucleic Acids:
All of your cells contain nucleic acids.
Nucleic acid = a long chain of smaller molecules called nucleotides.
Nucleotide is composed of three parts: a sugar, a base, and a phosphate group (contains
phosphorus and oxygen atoms).
Two types of nucleic acids – DNA and RNA.
Each has 4 kinds of nucleotides.
DNA (deoxyribonucleic acid) consists of two strands of nucleotides that spiral around
each other.
Chromosomes contain long strands of DNA involved in heredity.
RNA (ribonucleic acid) may consist of a single strand of nucleotides or a based-paired
nucleotides.
RNA plays a key role in the manufacture of proteins.
RNA can also act as an enzyme, promoting the chemical reactions that link amino acids
to form proteins.
ENERGY AND CHEMICAL REACTIONS
ENERGY FOR LIFE PROCESSES
Energy is everywhere.
Food, speeding car, sound, and warmth.
Energy = the ability to move or change matter.
Energy exists in many forms – including light, heat, chemical energy, mechanical energy,
and electrical energy.
It can be converted from one form to another
Energy can be stored or released by chemical reactions.
Chemical reaction = a process during which chemical bonds between atoms are broken
and new ones are formed, producing one or more different substances.
Thousands of chemical reactions are happening all the time in any cell.
Reactants = the starting materials for chemical reactions.
Products = the newly formed substances.
Chemical equations = summarize chemical reactions
Reactants  Products
The arrow is read as “changes to” or “forms”.
NaCl  Na+ + ClEnergy in Chemical Reactions:
In chemical reactions, energy is absorbed or released when chemical bonds are broken
and new ones are formed.
Metabolism = all of the chemical reactions that occur within an organism.
Your cells get most of the energy needed for metabolism from the food you eat.
As food is digested, chemical reactions convert the chemical energy in food molecules to
forms of energy that can be used by cells.
Activation Energy:
Activation energy = the energy needed to start a chemical reaction.
Activation energy is simply a chemical “push” (like pushing a rock) that starts a chemical
reaction.
Enzymes:
Cells consume fuel because they need energy to function.
Most biochemical reactions – chemical reactions that occur in cells – require activation
energy to begin.
The chemical reactions in cells occur quickly and at relatively low temperatures because
of enzymes.
Enzymes = substances that increase the speed of chemical reactions.
Most enzymes are proteins.
Enzymes are catalysts.
Catalysts = substances that reduce the activation energy of a chemical reaction.
An enzyme increases the speed of a chemical reaction by reducing the activation energy
of the reaction.
Enzymes help organisms maintain homeostasis.
Without enzymes, chemical reactions would not occur quickly enough to sustain life.
For example, consider a reaction that takes place in your blood.
Blood carries carbon dioxide, CO2, (a waste product made by cells) to your lungs, where
it is eliminated as you breathe out.
In the lungs, carbon dioxide reacts with water, H2O, to form carbonic acid, H2CO3:
CO2 + H2O  H2CO3
Assisted by carbonic anhydrase
The reverse reaction occurs in your lungs, converting carbonic acid back to carbon
dioxide and water.
CO2 + H2O  H2CO3
Assisted by carbonic anhydrase
Most enzyme-assisted reactions are reversible, meaning they can proceed in the opposite
direction.
Without an enzyme, the reaction that produces carbonic acid is very slow (2000/hour).
This rate is not fast enough for your blood to carry away the carbon dioxide.
Blood contains the enzyme “carbonic anhydrase”.
Allows 600,000 carbonic acid molecules per second.
Increases the reaction rate about one million times enabling your body to eliminate
carbon dioxide efficiently.
Enzyme Specificity:
Substrate = a substance on which an enzyme acts during a chemical reaction.
Enzymes act only on specific substrates.
For example: The enzyme amylase assists in the breakdown of starch to glucose.
Starch  Glucose
with the aid of amylase
Starch  Glucose
with the aid of amylase
Starch is amylase’s substrate.
Catalase assists in the breakdown of hydrogen peroxide (H2O2) which is a toxin formed
in cells.
2H2O2  2H2O + O2 with the aid of catalase (Reversible also)
Hydrogen peroxide is catalase’s substrate.
An enzyme’s shape determines its activity.
Typically, an enzyme is a large protein with one or more deep folds on its surface.
Active site = the fold/pocket where an enzyme’s substrate fits into.
An enzyme acts only on a specific substrate because only that substrate fits into its active
site.
Three steps of enzyme activity:
1. A substrate attaches to an enzyme’s active site.
2. The enzyme reduces the activation energy of the reaction.
3. New products are formed. The enzyme is not changed by the reaction and free to
catalyze further reactions.
Factors in Enzyme Activity:
Any factor that changes the shape of an enzyme can affect the enzyme’s activity.
For example, enzymes operate most efficiently within a certain range of temperatures.
Temperature outside this range can either break or strengthen some of the enzyme’s
bonds, changing its shape.
Enzymes also operate best within a certain range of pH values.
A pH value outside this range can cause bonds in an enzyme to break, reducing the
enzyme’s effectiveness.
The enzymes that are active at any one time in a cell determine what happens in that cell.
Your body’s cells contain many different enzymes, and each enzyme catalyzes a different
chemical reaction.
Different kinds of cells contain different collections of enzymes.