CHAPTER
2 – INTRODUCTORY CHEMISTRY & BIOCHEMISTRY
INTRODUCTORY
CHEMISTRY
Why
is it necessary to study chemistry? Living
things are made of matter (anything that
occupies space & has mass) & matter follows the laws of chemistry. Even the characteristics we consider to be unique
to living things are the result of chemical reactions (ex. movement as a result of muscle
contractions).
I. THE ATOM
A. Atom - smallest unit of matter unique to a
particular element.
B. Element - A substance made up of only one kind of
atom - ex. carbon contains only carbon atoms. Elements
can't be broken down into other substances by ordinary chemical means. Each element displays unique properties (ex. some
are gases, some are solids, some are metals, etc.). About 92 elements occur naturally
(there are also some man-made elements). Some
of the elements important to our study of living systems are carbon, oxygen, hydrogen,
nitrogen, sodium, chlorine, phosphorus, and potassium.
You may also be familiar with the elements lead, iron, iodine, gold, silver, and
copper, nickel, and platinum.
C. Some Important Things to Know about Atoms &
Elements:
1. An atom consists of 2 basic parts:
a. nucleus
- the nucleus contains protons & neutrons:
1.) protons
- positively charged; all atoms have protons; protons give the nucleus a positive charge.
2.) neutrons
- neutral in charge; fxn.: "stabilizers"; all atoms except hydrogen have one or
more neutrons.
b. electrons – negatively charged; occupy orbit
energy levels or shells around the nucleus; attracted to the positive charge of the nucleus;
in an atom, the number of electrons always equals the number of protons, so the atom,
as a whole, has no charge; electrons determine the chemical properties of elements (ex.
whether they are a liquid, solid, or gas, etc.).
2. atomic number = number of protons (or number of
electrons); in an atom, the number of protons always equals the number of electrons; this
number differs for each element.
3. atomic mass number = number of protons + number of neutrons;
the number of electrons is not included in the mass number due to their insignificant
mass.
4. The 6 elements important for building
organic molecules like carbohydrates, lipids, proteins, and nucleotides are: carbon,
hydrogen, oxygen, sulfur, nitrogen, & phosphorus.
II.
CHEMICAL REACTIONS
A. More about Electrons
1. Electrons orbit around the nucleus at
different energy levels or shells the 1st shell (k shell) can hold no more than 2
electrons; the next shell (l shell) can hold 8 electrons, 2 electrons in each of 4
orbitals; the next shell (m shell) also holds 8 electrons. These will be the only shells
that we will deal with in this class.
2. An atom is the most stable when all of its
shells are completely filled (the k shell fills first, then the l shell, then the m shell,
& so on).
3. The atoms of many elements have partially
filled outer shells, therefore they are not very stable; these atoms tend to react with
other atoms to completely fill their outer shells &, in doing so, they form chemical
bonds; it is important to remember that it's the electrons of an atom that
participate in the chemical bonds that form between atoms.
Molecules are formed when 2 or more
atoms are joined together by interactions between the electrons of their outer electron
shells.
B.
Chemical Bonds
1. Ionic bonds
a. definition - in ionic bonds electrons are transferred to other atoms to completely fill
outer shells; atoms are electrically neutral, but when they gain or lose electrons in
combining with other atoms, they are called ions (charged
atoms) & they take on a positive or negative charge; in other words, the transfer of
electrons upsets the balance of protons & electrons in an atom; atoms that lose
electrons are positively charged, atoms that gain electrons are negatively charged; ionic bonds involve the attractions between these
oppositely charged ions. So, before you can
have an ionic bond, you have got to have oppositely charged ions, & to create ions you
have got to transfer electrons.
b. example: NaCl
(sodium chloride- table salt); Na (at. # 11) has one electron in its outer m shell - it
needs 7 electrons to fill this shell - it is easier for Na just to give this electron
away, & eliminate the m shell entirely. Cl
(at. # 17) has 7 electrons in its outer m shell - it only needs 1 electron to fill its
outer shell. Therefore, when Na & Cl
atoms react, Na gives up its outer electron to Cl. Because
Na gives up an electron, it now has 11 protons & 10 electrons, resulting in a
positively charged atom. Cl now has 17
protons & 18 electrons, resulting in a negatively charged atom. Na+ & Cl- ions are
attracted to each other because of their opposite charges & an ionic bond is formed. The attraction is the ionic bond! Only the electron # changes when ions are formed!
2. Covalent bonds - more common in the human body
& are more stable.
a. definition - Electrons are not transferred, but are shared. The
shared electrons spend part of their time around the nucleus of one atom & part of
their time around the other. Each pair of
electrons shared equals one covalent bond (if 2 pair of electrons are shared between 2
atoms, a double covalent bond is formed, a triple covalent bond occurs when 3 pr. of
electrons are shared). We only discuss single
covalent bonds.
b. example: methane
(CH4); a carbon atom can form four
covalent bonds - it has 4 electrons in its outer shell, therefore it needs 4 more
electrons to fill its outer shell; hydrogen has one electron in its outer shell, therefore
it needs one electron to fill its outer shell. Rather
than give 4 electrons away or accept 4 electrons, carbon shares its 4 electrons in its
outer shell with 4 Hydrogen atoms.
c. polar vs. nonpolar - covalent bonds can be polar or nonpolar; if
both atoms exert the same pull on the shared electrons (equal sharing), the bond is
nonpolar (example: methane); if there is unequal sharing of electrons, the bond is polar;
in molecules with polar covalent bonds, there is an atom that has a much larger nucleus
(more protons) than the other atoms in the molecule; the atom with the most protons is
more attractive to the shared electrons, so the electrons spend most of their time
around this atom's nucleus; all of these electrons spending most of their time
around a particular nucleus gives this part of the molecule a partial negative
charge; the other atom(s) in the molecule acquire a partial positive charge,
because the shared electrons are not spending much time around them. Shared electrons in polar covalent bonds are not
spending all of their time around a particular nucleus - if this were the case then
we would be talking about electrons being transferred (as in ionic bonds).
4. Hydrogen bonds - These bonds result from polar covalent
bonds; they form between molecules
& occur between the slightly negative atom of one molecule & the slightly positive
atom of another molecule. These bonds can
occur between hydrogen & oxygen & between hydrogen & nitrogen. Hydrogen bonds are weaker than ionic &
covalent bonds, because the charges on the molecules are "partial" or weak
charges.
C. Chemical Reactions - A chemical reaction when atoms or
molecules (called reactants) collide and are transformed into different combinations of
the same atoms or molecules (called products). In
this process, chemical bonds break and new ones form.
In living systems special proteins called enzymes catalyze these chemical reactions
(they make them “go”). We'll talk
more about enzymes later.
1. A single water molecule is made up of one
oxygen atom & two hydrogen atoms (H2O).
2. Oxygen has 8 protons, while each hydrogen
has only one proton. Oxygen forms a covalent
bond with each hydrogen so that the outer shells of each atom are complete.
3. Because the oxygen atom has more protons
(positives) than the hydrogen nuclei, the shared electrons have a greater attraction to
the oxygen nucleus & spend more time around it than they do around the hydrogen nuclei
(unequal sharing of electrons). The oxygen
atom therefore has 10 electrons (8 of its own & 1 from each hydrogen) spending most of
their time around its nucleus of 8 protons - this gives the oxygen end of the water
molecule a partially negative charge. Since
the hydrogen electrons are spending most of their time around the oxygen atom, the
hydrogen atoms, which have one proton each, take on a partially positive charge. This results in a polar molecule (a molecule that has partially
positive & negative regions). Their
polarity allows water molecules to interact with one another, forming hydrogen bonds.
The same type of interaction is possible between water & many other polar
substances. Polar substances are hydrophilic (water-loving) & nonpolar
substances are hydrophobic (water-fearing).
B. PROPERTIES OF WATER - Hydrophilic
& hydrophobic interactions underlie several properties of water that are biologically
important.
1. Temperature-Stabilizing Effects:
Note: The temperature
of a substance is a measure of how fast its molecules are moving; the higher the
temperature of a substance, the faster its molecules are moving.
a.) heating
water - It takes considerable heat to raise the temperature of water because the
hydrogen bonds between the water molecules restrict the movement of the molecules; in
order for the temperature of water to rise, a number of H bonds must be broken - this
takes a lot of energy. This resistance to
temperature change helps living cells to maintain a relatively constant temperature; this
is important because biochemical reactions take place within a narrow temperature range
(this has to do with the action of enzymes). This
resistance to temperature change also helps organisms that live in aquatic or marine
environments.
2. Water As a Solvent - the polarity of water is also responsible
for water's capacity as a solvent (something
that dissolves something else); water is an excellent solvent for ions & other polar
molecules (solutes) in cells.
C. ACIDS AND BASES
When molecules of inorganic acids, bases, or
salts dissolve in water of body cells, they undergo ionization
or dissociation (they break apart into their
individual ions).
1. Acids & Bases Generally Defined
Acid - Defined as a solute that releases H+
ions in a solution
[ex. HCl - hydrochloric acid dissociates
into H+ ions & Cl- ions]
Base
- Defined as a solute
that removes H+ ions from a solution; many release OH- ions in this
process.
[ex. Mg(OH)2 - magnesium hydroxide dissociates into OH-
ions & Mg++ ions].
2. pH Scale - Fluids are assigned a pH value (0 -14),
which refers to the hydrogen ion concentration present in the fluid. The hydrogen ion concentration is abbreviated as
[H+].
a. acid - pH below 7.0; base - pH above 7.0; neutral - pH = 7.0
b. pH = - log [ H+ ] (formula for calculating pH)
c. It is a common misconception to think that
as the [H+] increases, the pH also increases!
The rule is: As [H+] increases, pH decreases! This can be seen from the following example:
solution
A: [H +] = 1 x 10-2 or
0.01
pH = -log[1 x 10-3] = 2
solution
B: [H+ ] = 1 x 10-8 or 0.00000001 pH = -log[1 x 10-4] = 8
(A quick way to find the pH of these
solutions is to look at the exponent or count the number of decimal places in the [H+])
Solution A is more acidic than Solution B -
Solution has a higher [H+] than Solution B (0.001 > 0.0001); therefore,
Solution A has a lower pH than B.
When you think about a pH value, think that
this number is really the number of decimal places in the hydrogen ion concentration. The larger the number, the more decimal places
there are, indicating a smaller hydrogen ion concentration.
3. Buffers - help maintain a constant pH by removing
or adding H+ ions; the pH inside living systems is generally between 7.35-7.45
(exception: the hydrochloric acid in the digestive system makes the pH here 2-3); this pH
range is important, as many biochemical reactions take place only within this range;
buffers can combine with hydrogen ions &/or release them, & so help stabilize the
pH.
BIOCHEMISTRY
4
Groups of Organic Compounds Important in Living Organisms:
Carbohydrates Lipids
Proteins
Nucleotides
Organic
compound defined – A compound containing carbon (with exception of carbon
dioxide); found in all living things.
THE
CENTRAL ROLE OF CARBON
A. The Carbon Backbone - The processes of
life are primarily the result of the chemistry compounds of carbon. Because of carbon's tendency to form four covalent
bonds in four different directions, carbon can form an unbelievably large number of
different compounds of high complexity; organic compounds derive their basic shapes
from the carbon atoms; this shape helps determine the compound's function in living
systems.
B. Functional groups - The structure & behavior of organic
compounds also depends on the properties of their functional groups; functional groups are
groups of atoms (ex. hydrogen, oxygen, nitrogen, phosphorus, sulfur) attached to the
carbon backbone.
I. CARBOHYDRATES:
A.
Structure: generally made up of only three elements: carbon, hydrogen, & oxygen
B. Three
Principle Classes of Carbohydrates:
1. Monosaccharide
a. Structure - composed of single sugar molecule; the atoms
in a sugar molecule can form a straight chain or a ring (rings are more common in the
body).
b. Examples - Glucose, Ribose, Fructose,
Galactose
d. Functions - monosaccharides are important energy
molecules in living things; glucose is the primary energy source for humans & many
other animals; also important as building blocks of larger sugars.
2.
Oligosaccharides
- composed of short chains of monosaccharides; Examples:
a. Sucrose (table sugar) is a disaccharide composed of
glucose & fructose; sucrose is the form in which sugars are transported in plants.
b. Lactose (milk sugar) is a disaccharide composed of
glucose & galactose.
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Sucrose = Glucose
+ Fructose
2.
Polysaccharides - straight or branched chains of many
monosaccharide units
a. Storage Polysaccharides
1.) Starch
- sugar storage in plants.
2.) Glycogen
– “animal starch;” principle storage form for glucose in higher animals;
this energy storage is short term; lipids are used for long term energy storage.
b. Structural
Polysaccharides
1.) Cellulose
– Principal component of the plant cell wall; also found in the cell walls of
algae and fungi. Monosaccharides are bonded
together in such a way that the molecule resists breakdown by multicellular organisms. We don’t have the digestive enzymes to break
the bonds; however, some microorganisms do have these enzymes; this is why microbes are so
important in the gut of a termite, cow, etc.)
2.) Chitin
– contains nitrogen; forms the cell wall of some fungi (it’s the same stuff
insect exoskeleton’s are made of!)
II. PROTEINS
A. Protein Structure:
1. Proteins are composed of subunits called amino acids (there are 20 different amino acids
that make up proteins). Amino acids contain
carbon, hydrogen, oxygen, and nitrogen. Some
also contain sulfur. Amino acids have a
structure similar to the one below. The
R stands for some other atom or group of atoms bonded to the central carbon atom in the
molecule. The sequence of amino acids in a chain helps determine
the structure & shape of the protein & therefore the function of the protein;
there are many possible combinations of amino acids that produce the many different kinds
of proteins.
H
H
O
N----C----C
H
R OH
2. Peptide bonds - linkage formed between one amino acid
& another amino acid; the name of these bonds is why chains of amino acids are called polypeptides.
3. Producing the three dimensional structure
of a protein: We have been discussing proteins as
"chains of amino acids." However,
the final structure of proteins is not a straight chain of amino acids. Proteins are very complex, three-dimensional
molecules, with numerous twists & folds. The
amino acid chain of every kind of protein is folded in a very specific way [the chain will
twist & fold itself based on the linkage of amino acids in a specific sequence &
the environmental conditions (i.e., temperature & pH)].
There are several bonds & forces which give a protein its specific 3-D
structure (i.e., hydrogen bonds, ionic bonds, etc.); these bonds link distant parts of the
molecule, forming loops, twists, etc. Destruction
of a protein's 3-D structure by extreme heat or pH is called denaturation (see
"enzymes" on the next page for how this occurs).
Analogy for protein structure: Think of a phone cord. Pull it straight (like a straight chain of a.a.),
then let it twist, then roll the twisted cord into a ball.
(Every type of protein folds and twists in a very specific way.)
B. Some
Specific Functions of Proteins:
1. Structural Proteins: collagen in connective tissue, keratin in
the skin, cytoskeleton in cells
2. Functional Proteins:
a. membrane transport proteins – transport
substances across the cell membrane
b. cell movement – ex. flagellum
c. enzymes as catalysts (enzymes speed up the
rate of chemical reactions); all life processes are primarily the result of chemical
reactions; molecules in living things require enzymes in order to react; without enzymes,
chemical reactions in living things can’t occur; see below for more information on
enzymes.
d. antibodies in the immune response
C. Enzymes – a large, globular protein molecule
that accelerates a specific chemical
reaction. Virtually all chemical reactions
that take place in cells involve enzymes!!! Most
of a cell’s proteins are enzymes.
1. Why
are enzymes needed? In order for
particular molecules to react with one another, they must be in close proximity & must
collide with sufficient force to overcome the mutual repulsion of their negatively charged
electron clouds & to break existing chemical bonds within the molecules. The force with which they collide depends on their
kinetic energy (energy of motion). Most
chemical reactions require an initial input of energy to get started, which increases the
kinetic energy of the molecules, enabling a greater number of them to collide with
sufficient force. In the chemistry lab, we
can supply this energy with heat. In a cell,
many different reactions are going on at the same time, therefore heat cannot be used as
it would be nondiscriminatory (it would affect many reactions at the same time). Cells get around this problem by using enzymes,
which serve as catalysts (they get the
chemical reactions going). The enzymes form a
temporary association with the molecules that are to react, bringing them close to one
another & weakening the existing chemical bonds, making it easier for new ones to
form.
2. Enzyme
Structure & Function - Enzymes are large, complex, globular proteins consisting of
one or more polypeptide chains. The molecules
that enzymes acts on are known as the substrates. Enzymes are folded to form a groove or pocket
(called an active site) on their surface into
which the substrate fits & where the chemical reactions take place. See diagram below:
3. Effects
of Temperature & pH on Enzyme Function
1. Temperature: As
the temperature increases, so does the rate of enzyme catalyzed reactions, but only up to
a certain point. At high temperatures, the
enzymes are denatured (due to the vibration of
molecules at high temperatures, the bonds that maintain the enzyme's structure are broken
& the protein unfolds). If denaturation is severe, the damage to the enzyme is
irreversible.
2. pH: The
shape of the enzyme depends partly on attraction between positively & negatively
charged amino acids. As the pH changes
(acidic - more H+, basic - fewer H+), these charges change, changing
the shape of the enzyme & its function. Remember: the optimum pH for most enzymes is 6-8. (exception: the
stomach which has a pH of 2)
Note:
All proteins can be denatured by heat and extreme pH.
III. PEPTIDOGLYCAN
This molecule
has both protein and polysaccharide components and it forms the cell wall of eubacteria. It may be one or several layers thick. It is an extremely strong protective covering. Glycan strands in all eubacteria are made of
alternating units of 2 modified sugars, N-acetylglucosamine (NAGA) and N-acetylmuramic
acid (NAMA). (It’s structure is similar to a chain link fence!) More later!
IV. LIPIDS
A.
General Structure - all lipids are mostly nonpolar
(hydrophobic) & are insoluble in polar solvents such as water; lipid structure varies
greatly & is discussed below for each type.
B.
Some General Functions:
1. long term energy storage (example: glycerides); energy is stored in the chemical
bonds; excess carbohydrates, proteins or fats are converted to triglycerides & are
stored in adipose (fat) tissue.
2. structural (example: phospholipids make up the cell membrane of cells)
C. Types of Lipids:
1. Lipids with Fatty Acids – Glycerides &
Phospholipids:
a. Glycerides
1.)
Structure: classified
as mono-, di-, & triglycerides, depending on the number of fatty
acids attached a single glycerol molecule; glycerol has 3 carbon atoms & 3 hydroxyl
(OH) groups; fatty acids are long, nonpolar
chains composed of hydrogen & 4 to 24 carbon atoms, with a carboxyl (COOH) group at
one end.
a.) Saturated fatty acids - all carbons in the
fatty acid tails are joined together by single
carbon to carbon bonds & as many hydrogen atoms as possible are linked to the carbons
(the carbons are said to be "saturated" with hydrogens); triglycerides with many
saturated fatty acids are solid at room temperature; occur mostly in animal tissues, but
also in a few plant products; examples: butter, lard, cocoa butter, palm oil, coconut oil;
the liver produces cholesterol from some breakdown products of saturated fats.
b.) Unsaturated
fatty acids - one or more double bonds
occur between carbon atoms in the fatty acid tails; this cuts down on the number of
hydrogen atoms that can bond to the carbons; liquids at room temperature; the double bonds
create a kink in the shape of the molecule prevent the fatty acids from packing close
together & becoming solidified; unsaturated fatty acids are more common in plants; monounsaturated fatty acids are better for you
that the polyunsaturated ones; the poly’s
can produce compounds called trans fatty acids,
which increase the risk of heart disease.
A
triglyceride molecule:
H--C---O---C--C—C--C--C--C—C—C—C—C--C—H
saturated f.a.
O H
H H H
H H H
H H H
H H
H H H
H H H
H H
H--C---O---C--C—C--C--C--C--C—C—C—C—C--H saturated f.a.
O H H
H H H
H H H
H H
H H H
H H H
H H H
H
H—C---O---C—C—C—C==C—C—C—C—C—C—C---H unsaturated
f.a.
H
O H H
H H H
H H H
2.) Functions of Glycerides
a.) Energy
- For most organisms and cellular microorganisms, sugars in excess of what can be stored
as glycogen are converted into fats for more permanent storage; this is not the case in
bacteria!
b. Phospholipids
1.) Structure
- 2 fatty acids & 1 phosphate group are linked to a glycerol molecule; a small polar
group is linked to the phosphate group; this results in a molecule with a dual nature -
the molecule has a nonpolar, hydrophobic end & a polar, hydrophilic end.
2.) Function: Structural. The
phosphate end of the molecule & its polar group are called the "head" of the
molecule; the two fatty acids are called the "tails" of the molecule; the head
is hydrophilic ("water-loving"), while the 2 fatty acid "tails" are
hydrophobic ("water-fearing"). This
arrangement forms the structural basis of cellular membranes & is called the phospholipid bilayer.
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2 Fatty AcidTails (nonpolar)
V
2. Lipids without Fatty Acids: Steroids
a. Structure - different from other lipids; they consist
of 4 interlocking carbon rings with numerous hydrogens attached; while they have no fatty
acids, they are still nonpolar & hydrophobic, so they are classified as lipids.
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b. Some
Examples:
1.) cholesterol
- important component in eukaryotic cell membranes & serves as the starting
material for the synthesis of other steroids. Not
found in the cell membranes of bacteria with the exception of the Mycoplasms.
V. NUCLEOTIDES
A. Structure:
nucleotide = phosphate(s) + monosaccharide + a nitrogen-containing compound (called
a base); it’s the bases that spell out the genetic message in DNA & RNA).
B. Functions:
1. Nucleotides are the basic subunits of nucleic acids such as
a. DNA (deoxyribonucleic nucleic acid) - carrier of the genetic message - makes up
chromosomes in the nucleus of the cell.
b. RNA (ribonucleic
acid) - transcribes genetic message present in DNA & produces proteins from it.
2. Nucleotides also make up the adenosine phosphates (ex. ATP - adenosine triphosphate – used for energy
molecule in the cell).
3. Nucleotides make up some coenzymes (ex. NAD & FAD);
these molecules function as electron carriers in some biochemical reactions; they are
called the cell’s “reducing power.” We’ll
talk about this more in the metabolism chapter.