Download UNIT 2 Bio 1 H Living organisms are composed of about 25

UNIT 2
Bio 1 H
Living organisms are composed of about 25 chemical elements.
Approximately 25 elements are required by living organisms. Four (oxygen, carbon,
hydrogen, and nitrogen) are particularly abundant, making up 96.3% of the human
body.
Trace elements are common additives to food and water.
Trace elements are important for proper function, particularly as catalysts and
enzyme cofactors.
Radioactive isotopes can help or harm us.
Isotopes of the same element behave the same way chemically. Therefore,
organisms are indiscriminate as to the
isotopes they use.
Radioactive isotopes can function as “markers” or tracers for their nonradioactive
counterparts. Researchers use
radioactive markers to study the fate of elements and molecules in living
systems
(see Module 7.3 for an example).
Radioactive elements are also used in diagnostic medical procedures. The release
of the radioactive decay is monitored
by sophisticated instruments and assists in the diagnosis of diseases such as
cancer and kidney failure. Radiation can also be used as a treatment. (Cancer
patients receive radiation to kill the cancer cells, and hyperthyroid patients
receive radioactive iodine to reduce the activity of the thyroid gland.)
Long-term exposure or exposure to high-energy radiation can cause diseases such
as cancer. Organisms can develop
cancer by exposure to radioactive material if the exposure is long term. For
example, radon contamination in a house causes lung cancer. Radioactive
exposure from the explosion of the nuclear reactor in Chernobyl, Ukraine,
caused an increase in cancer as well as the death of 30 people in weeks.
Unequal electron sharing creates polar molecules.
In polar molecules (H2O), the electrons around the atoms are not equally shared
because the different atoms have
different attractions for electrons. This results in one part of the molecule
being slightly positive (usually where the hydrogen atoms are) and another
part being slightly negative. The oxygen in water is slightly negative, and the
two hydrogen atoms are slightly positive.
Hydrogen bonds are weak bonds important in the chemistry of life.
The attraction of these slightly positive and negative charges between different
molecules (or different parts of the
same molecule in some cases) results in weak hydrogen bonds. Hydrogen
from a water molecule binds weakly with the oxygen atom of another water
molecule (Figure 2.10A).
Hydrogen bonding occurs in other biologically important compounds such as
proteins and DNA. The saying “There is
strength in numbers” applies to hydrogen bonds. Hydrogen bonds are weak,
but they are numerous and hold molecules together.
Hydrogen bonds make liquid water cohesive.
Cohesion is the tendency of water molecules to stick together.
Cohesion between water molecules allows them to form drops and be transported
through the tissues of plants.
Surface tension results from the cohesion of water molecules to each other so
that a small aquatic insect such as a water
strider can walk across the top of a pond without sinking.
Water’s hydrogen bonds moderate temperature.
Breaking hydrogen bonds requires a large amount of energy; therefore, as water
is heated, it takes a large amount of
energy to observe an increase in the temperature of the water. The
temperature of water rises more slowly when heated than does the
temperature of nonpolar liquids because water has so many hydrogen bonds.
The opposite is true of water as it cools; formation of hydrogen bonds causes the
temperature of water to lower more
slowly when cooled because heat is released as the hydrogen bonds are
formed.
Ice is less dense than liquid water (Figure 2.13).
Hydrogen bonds in ice result in an extremely stable, three-dimensional structure.
A given volume of ice has fewer water molecules than an equal volume of liquid
water and is therefore less dense.
Water is the solvent of life.
A solution is a homogeneous mixture of a liquid solvent and one or more solutes
(solid or liquid compounds that dissolve in the solvent).
Because water is a polar molecule, it readily forms solutions with a wide variety of
other polar compounds
(for example, sugar) and with the charged ions of ionic compounds such as
sodium chloride.
The chemistry of life is sensitive to acidic and basic conditions (Figure 2.15).
Another property of aqueous solutions important to living things is the pH
(potential hydrogen) of the solution
(a measure of acidity or basicity).
pH expresses the tendency of water to ionize, dissociating into OH- (hydroxide
ions) and H+ (hydrogen ions).
Biological pH ranges from 1 (stomach acid, high concentration of H+) to 9
(seawater, low concentration of H+).
A pH of 7 = neutral, [H+] = [OH-]; lower pH = acid, increased [H+]; higher pH =
basic, increased [OH-].
Biological fluids contain buffers, substances that resist changes in pH by reacting
with, and neutralizing, H+ or OH- ions.
Acid precipitation threatens the environment.
Compounds of sulfur and nitrogen are part of air pollutants released from the
combustion of fossil fuels. These
compounds react with atmospheric water to form acidic compounds (sulfuric
and nitric acid).
Low pH associated with acid rain can be harmful to organisms adapted to neutral
pH.
Acid rains harm aquatic environments and likely cause various imbalances in
terrestrial environments such as forests.
The capacity to withstand changes in pH (buffering) is naturally a characteristic
of some areas
(for example, limestone buffers acid rain).
In recent decades, in the United States, Canada, and Europe, levels of acid
precipitation have declined.
Chemical reactions change the composition of matter.
The general form of a chemical reaction is: Reactants = Products.
The reactants are the starting material, and the products are the result.
For example, 2 H2 + O2 = 2 H2O. Notice that the number of atoms is the same on
each side of the equation.
I. Introduction
Module 3.1 Life’s molecular diversity is based on the properties of carbon.
A. Organic compounds contain at least one carbon atom (Figure 3.1).
B. Carbon has 4 electrons in the outer shell; therefore carbon has a
strong tendency to fill the shell to 8 by forming covalent bonds with other atoms,
particularly hydrogen, oxygen, and nitrogen. The 4 electrons in the outermost
shell of carbon allow it to form complex structures (e.g., long, branched chains,
ring structures). This is a major reason carbon is the structural backbone of
organic compounds. A compound composed only of carbon and hydrogen is called a
hydrocarbon, which is generally nonpolar. A series of covalently attached carbons
in a molecule form the backbone, or carbon skeleton.
C. Point out the double bond in Figure 3.1, explaining that it
represents 4 shared electrons.
D. The way bonding occurs among atoms in molecules determines the
overall shape of the molecule.
E. Isomers are molecules with the same numbers of each atom but
with different structural arrangements of the atoms.
Module 3.2 Functional groups help determine the properties of organic
compounds.
A. Functional groups are generally attached to or part of the carbon
skeleton of different molecules and exhibit predictable chemical properties.
B. Functional groups are the atoms of an organic compound directly
participating in chemical reactions. The sex hormones testosterone and estradiol
illustrate the power of functional groups (Figure 3.2).
C. Figure 3.2 illustrates five functional groups important to life,
discussing a few of the examples.
D. All of these functional groups have polar characteristics.
Therefore, most of the molecules on which they are found are polar molecules.
Module 3.3 Cells make a huge number of large molecules from a small set of small
molecules.
A. Monomers are the fundamental molecular unit. Polymers are
macromolecules made by linking many of the same kind of fundamental units.
B. Types of reactions (note that water is involved in both; Figure
3.3A, B): dehydration reaction—molecules synthesized by loss of a water molecule
between reacting monomers, the most common way organic polymers are
synthesized; hydrolysis—literally, “breaking apart with water”—the most common
way organic polymers are degraded.
C. The study of molecular reactions in living systems is a broad topic
that will be a theme throughout the course. The two reactions reviewed in this
module are ones involved in the formation of molecular structures introduced in
the remaining modules.
D. Lactose intolerance results from the inability to hydrolyze lactose
due to the absence of the enzyme lactase, thus illustrating the need to be able to
perform the correct chemical reactions.
II. Carbohydrates
Module 3.4 Monosaccharides are the simplest carbohydrates.
A. Show examples of the isomers glucose and fructose (Figure 3.4B).
B. The suffix “-ose” indicates that the molecule is a sugar.
C. In solution, many monosaccharides form ring-shaped molecules
(Figure 3.4C).
Module 3.5 Cells link two single sugars to form disaccharides.
A. Two monosaccharides are put together to form a disaccharide via
a glycosidic bond (Figure 3.5). Combining two glucose molecules with the removal
of water makes maltose.
B. Disaccharide formation is an example of a dehydration reaction
(Module 3.3).
C. The most common disaccharide is sucrose (table sugar), which is
composed of glucose and fructose.
Module 3.6 Connection: How sweet is sweet?
A. There are five taste receptors on the tongue: bitter, salty, sour,
sweet, and umami (tastes like chicken!).
B. Humans perceive a sweet taste when a chemical binds to the
sweet receptor on the tongue. The chemical can be a sugar or other chemicals
such as aspartame.
C. The stronger the binding by a chemical to the sweet receptor,
the sweeter the chemical is perceived to be. Fructose is considered 4 times
sweeter than sucrose.
E. Some artificial sweeteners bind to other receptors like bitter,
thus the familiar bitter aftertaste.
Module 3.7 Polysaccharides are long chains of sugar units.
A. Different organisms use monosaccharides, such as glucose, to
build several different polymers or polysaccharides: starch, glycogen, and
cellulose (Figure 3.7).
B. Each of these molecules is synthesized by dehydration synthesis,
but there are subtle differences in the covalent bonds that lead to different
overall structures and functions.
C. Starch is used for long-term energy storage only in plants.
Starch molecules are helical and may be either unbranched or branched. Animals
can hydrolyze this polymer to obtain glucose.
D. Glycogen has the same kind of bond between monomers as starch,
but it is highly branched. Glycogen also is used for long-term energy storage, but
only in animals. Animals can hydrolyze this polymer to obtain glucose.
E. Cellulose has a different kind of bond between monomers,
forming linear polymers that are cross-linked by hydrogen bonds with other linear
chains. Cellulose is the principal structural molecule in the cell walls of plants and
algae. Animals cannot hydrolyze this polymer to obtain glucose without the help of
intestinal bacteria (only certain bacteria, protozoa, and fungi can hydrolyze
cellulose); therefore, it is referred to as fiber.
III. Lipids
Module 3.8 Fats are lipids that are mostly energy-storage molecules.
A. In lipids, carbon and hydrogen predominate; there is very little
oxygen, which makes them more or less hydrophobic. General molecular formula
for fatty acid: (CH2)n.
B. Diverse types of lipids have different roles, including energy
storage and structural and metabolic functions.
C. Fats are polymers of fatty acids (usually three) and one glycerol
molecule, formed by dehydration reactions, and are called triglycerides (Figure
3.8B, C). Fats are tremendous sources of energy and can store approximately 2
times the equivalent of polysaccharides.
D. Saturated fatty acids have no double bonds between carbons (the
carbons are “saturated” with hydrogen atoms). The molecular backbones are
flexible and tend to ball up into tight globules. Saturated fats, such as butter and
lard, are solid at room temperature.
E. Unsaturated fats may include several double bonds between
carbons. This causes the molecules to be less flexible, and they do not pack into
solid globules. Unsaturated fats, such as olive oil and corn oil, are liquid at room
temperature.
F. Most plant fats are unsaturated, whereas animal fats are richer
in saturated fats.
Module 3.9 Phospholipids, waxes, and steroids are lipids with a variety of
functions.
A. Phospholipids are a major component of cell membranes. They
have two fatty acid molecules (instead of three) and a phosphate group.
B. Waxes are effective hydrophobic coatings formed by many
organisms (insects, plants, and humans) to ward off water. They consist of a single
fatty acid linked to an alcohol.
C. Steroids are lipids with backbones bent into rings. Cholesterol is
an important steroid formed by animals (Figure 3.9; notice that the diagram omits
carbons and hydrogens at each intersection in the rings and shows just the
backbone shape). Among other things, cholesterol is the precursor to bile acids
that function in the digestion of fats and is the starting material for the
synthesis of female and male sex hormones (see Figure 3.2).
Module 3.10 Connection: Anabolic steroids and related substances pose health
risks.
A. Anabolic steroids are synthetic and natural variants of the male
hormone testosterone, which, among other roles, causes the buildup of muscle and
bone mass during puberty in men.
IV. Proteins
Module 3.11 Proteins are essential to the structures and activities of life.
A. Proteins are constructed from monomers called amino acids.
B. The structure of the protein determines its function.
C. The seven major classes of protein are:
1. Structural: hair, cell cytoskeleton
2. Contractile: as part of muscle and other motile cells, produce
movement
3. Storage: sources of amino acids, such as egg white
4. Defense: antibodies, membrane proteins, complement proteins
5. Transport: hemoglobin, membrane proteins
6. Signaling: hormones, membrane proteins
7. Enzymatic: regulate the speed of a biochemical reaction much
like a chemical catalyst is used to speed up a reaction.
Module 3.12 Proteins are made from amino acids linked by peptide bonds.
A. Amino acids are characterized by having an alpha carbon atom
covalently bonded to one hydrogen, one amino group (NH2), one carboxyl group
(COOH), and one functional group symbolized by an R (Figure 3.12A).
B. Each naturally occurring amino acid has one of 20 functional
groups (Figure 3.12B), which determines the chemical characteristics of each
amino acid.
C. Amino acids are grouped into two categories based upon the
characteristics of the R groups. The two categories are hydrophilic (polar neutral
or charged) and hydrophobic (nonpolar).
D. Organisms use amino acids as the monomer to build polypeptides
by dehydration reactions. The bond between each amino acid is called a peptide
bond (Figure 3.12C).
E. The peptide bond can be broken by hydrolysis, to release free
amino acids.
F. Polypeptides are from several to more than a thousand amino
acids long, and the specific sequence determines the function of the protein (a
polypeptide with more than 20 amino acids is classified as a protein). To illustrate
the enormous number of proteins, compare the 20 amino acids used to make
proteins to the 26 letters of the alphabet for words.
Module 3.13 A protein’s specific shape determines its function.
A. Long polypeptide chains include numerous and various amino acids.
B. The final structure of a protein, and thus its potential role,
depends on the way these long, linear molecules fold.
C. Each sequence of amino acids spontaneously folds in a different
way (Figure 3.13A). The folding creates grooves that function as binding sites for
other molecules (Figure 3.13B).
D. Changes in heat, ionic strength, or salinity can cause proteins to
unfold and lose their functionality (this is called denaturation).
E. The four levels of structure are shown in the protein
transthyretin in Figures 3.14A, B, C, and D.
Module 3.14 A protein’s shape depends on four levels of structure.
A. Transthyretin is found in blood and is important in the transport
of a thyroid hormone and vitamin A.
B. Three-letter abbreviations represent amino acids; each amino
acid is in a precise order in the chain (Figure 3.14A).
C. In transthyretin, there are four polypeptide chains, each with
127 amino acids.
D. Changes in the primary structure of a protein (the amino acid
sequence) can affect its overall structure and, thus, its ability to function. Sickle
cell disease is an excellent example of a single amino acid defect.
E. Secondary structure is a result of hydrogen bond formation
occurring between amino and carboxyl groups of amino acids in sequence along
each polypeptide chain.
F. Depending on where the groups are relative to one another, the
secondary structure takes the shape of an alpha helix or a pleated sheet (Figure
3.14B).
G. The R groups usually do not play a role in secondary structure and
are not diagrammed.
H. Tertiary structure, which is the overall shape of the polypeptide,
results from the clustering of hydrophobic and hydrophilic R groups and bond
formation (hydrogen and ionic) between certain R groups along the coils and pleats
(Figure 3.14C). An important and often overlooked covalent bond that maintains
tertiary structure is the disulfide bond that forms between two cysteine amino
acids.
I. In transthyretin, the tertiary shape is essentially globular, not
fibrous like spider silk. The globular arrangement promotes hydrophilic amino
acids to interact with the aqueous environment and forces the hydrophobic amino
acids toward the center of the protein, sequestered from the water.
J. Many (but not all) proteins consist of more than one polypeptide
chain (also known as, subunits) and have quaternary structure.
K. Transthyretin consists of four chains, each identical (Figure
3.14D). Other proteins might have all chains different or be additionally
complexed with other atoms or molecules. Another good example of a protein with
quaternary structure is hemoglobin: 4 subunits (2 1 2) and 4 heme prosthetic
groups.
V. Nucleic Acids
Module 3.16 Nucleic acids are information-rich polymers of nucleotides.
A. There are two types of nucleic acids: deoxyribonucleic acid (DNA)
and ribonucleic acid (RNA). Nucleotides are complex molecules composed of three
functional parts (Figure 3.16A, B): phosphate group, five-carbon sugar
(deoxyribose in DNA, ribose in RNA), and nitrogenous base.
B. There are five basic types of nitrogenous bases: A, T, G, and C in
DNA and A, U, G, and C in RNA (Figure 10.2B, C).
C. Nucleotide monomers join by dehydration reaction between the
nucleotide parts (phosphate to sugar) to form polynucleotides with a linear
structure of sugar-phosphate repeats (Figures 3.16A, B; Figure 10.2A).
D. Hydrogen bonding between nitrogenous bases (A to T and G to C)
causes the final structure of the nucleic acid.
E. In DNA, two linear chains are held together in an antiparallel
double helix (Figure 3.16C).
F. In RNA, one linear chain may be wrapped around itself in places,
forming one of three types of RNA: transfer RNA (tRNA), ribosomal RNA
(rRNA), or messenger RNA (mRNA). See Chapter 10 for structural details.
How Enzymes Function
Module 5.5 Enzymes speed up the cell’s chemical reactions by lowering energy
barriers.
A. Enzymes are large protein molecules that function as biological
catalysts. A catalyst is a chemical that speeds up the reaction without itself being
consumed (Figures 5.5A and B).
B. The energy of activation is the amount of energy, an “energy
barrier,” that must be put into an exergonic reaction before the reaction will
proceed (analogy of the Mexican jumping beans, Figure 5.5A; energy of activation,
Figure 5.5B).
Module 5.6 A specific enzyme catalyzes each cellular reaction.
A. The reactant in an enzyme-catalyzed reaction is the substrate.
B. One part of the enzyme binds to the substrate at the active site,
holding the substrate in a specific position that facilitates the reaction. The
interaction of the substrate with enzyme at the active site causes a
conformational change of the enzyme referred to as an induced fit and promotes
the chemical reaction (Figure 5.6).
C. At the end of the reaction, the substrate changes into the
product and is released, and the enzyme is unchanged.
Module 5.7 The cellular environment affects enzyme activity.
A. Factors such as temperature, pH, salt concentration, and the
presence of cofactors often affect the way enzymes work.
B. Organic cofactors are called coenzymes.
Module 5.8 Enzyme inhibitors block enzyme action.
A. Inhibitors work by binding with the active site (competitive
inhibitors) or some other site (noncompetitive inhibitors) on the enzyme, thus
affecting the enzyme’s ability to bind with the substrate (Figure 5.8).
B. Feedback inhibition is a type of inhibition whereby enzyme
activity is blocked by a product of the reaction catalyzed by the enzyme.
Module 5.9 Connection: Many poisons, pesticides, and drugs are enzyme inhibitors.
A. For example, cyanide inhibits the production of ATP during
respiration and the nerve gas sarin inhibits the enzyme acetylcholinesterase.
B. The pesticide malathion also inhibits the enzyme
acetylcholinesterase but is used at doses too low to be harmful to humans.
C. The antibiotic penicillin interferes with an enzyme that helps
build bacterial cell walls.
D. Pain killers such as aspirin and ibuprofen inhibit the enzyme used
to induce pain. Other therapeutic drugs used to combat HIV and cancer are also
enzyme inhibitors.