It can be quite correctly argued that life exists on Earth because of the abundant liquid water. Other planets have water, but they either have it as a gas (Venus) or ice (Mars). This relationship is shown in Figure 1. Recent studies of Mars reveal the presence sometime in the past of running fluid, possibly water. The chemical nature of water is thus one we must examine as it permeates living systems: water is a universal solvent, and can be too much of a good thing for some cells to deal with.
Water is polar covalently bonded within the molecule. This unequal sharing of the electrons results in a slightly positive and a slightly negative side of the molecule. Other molecules, such as Ethane, are nonpolar, having neither a positive nor a negative side, as shown in Figure 2.
Figure 2. The difference between a polar (water) and nonpolar (ethane) molecule is due to the unequal sharing of electrons within the polar molecule. Nonpolar molecules have electrons equally shared within their covalent bonds.
These
link up by the hydrogen bond discussed earlier. Consequently, water has a great
interconnectivity of individual molecules, which is caused by the individually
weak hydrogen bonds, shown in Figure 3,
that can be quite strong when taken by the billions.
Figure 3. Formation of a hydrogen bond between the
hydrogen side of one water molecule and the oxygen side of another water
molecule.
Water has been referred
to as the universal solvent. Living things are composed of atoms and molecules within
aqueous solutions (solutions that have materials dissolved in water). Solutions
are uniform mixtures of the molecules of two or more substances. The solvent is
usually the substance present in the greatest amount (and is usually also a
liquid). The substances of lesser amounts are the solutes.
The solubility of many
molecules is determined by their molecular structure. You are familiar with the
phrase "mixing like oil and water." The biochemical basis for this
phrase is that the organic macromolecules known as lipids (of which fats are an
important, although often troublesome, group) have areas that lack polar
covalent bonds. The polar covalently bonded water molecules act to exclude
nonpolar molecules, causing the fats to clump together. The structure of many
molecules can greatly influence their solubility. Sugars, such as glucose, have
many hydroxyl (OH) groups, which tend to increase the solubility of the
molecule. This aspect of water is illustrated in Figure 4.
Figure 4. Dissolution of an ionically bonded
compound, sodium chloride, by water molecules.
used with permission.
Water
tends to disassociate into H+ and OH- ions. In this
disassociation, the oxygen retains the electrons and only one of the hydrogens,
becoming a negatively charged ion known as hydroxide. Pure water has the same
number (or concentration) of H+ as OH- ions. Acidic solutions have more H+ ions than OH- ions. Basic solutions have the
opposite.The pH of several common solutions is shown in Figure 5. An acid
causes an increase in the numbers of H+ ions and a base causes
an increase in the numbers of OH- ions.
Figure 5. pH of some common items.
The pH scale is a logarithmic Figure 5. pH of some common items. scale
representing the concentration of H+ ions in a solution. Remember
that as the H+concentration increases the OH- concentration decreases and vice versa . If we have a solution with
one in every ten molecules being H+, we refer to the concentration
of H+ ions
as 1/10. Remember from algebra that we can write a fraction as a negative
exponent, thus 1/10 becomes 10-1. Conversely 1/100 becomes 10-2 , 1/1000 becomes 10-3,
etc. Logarithms are exponents to which a number (usually 10) has been raised.
For example log 10 (pronounced "the log of 10") = 1 (since 10 may be
written as 101). The log 1/10 (or 10-1) = -1. pH, a
measure of the concentration of H+ ions, is the negative log of
the H+ ion
concentration. If the pH of water is 7, then the concentration of H+ ions is 10-7, or
1/10,000,000. In the case of strong acids, such as hydrochloric acid (HCl), an
acid secreted by the lining of your stomach, [H+] (the concentration
of H+ ions,
written in a chemical shorthand) is 10-1; therefore the pH is 1.
2. Organic molecules
Organic
molecules are those that: 1) formed by the actions of living things; and/or 2)
have a carbon backbone. Methane (CH4) is an example of this. If we
remove the H from one of the methane units below, and begin linking them up,
while removing other H units, we begin to form an organic molecule. (NOTE: Not
all methane is organically derived, methane is a major component of the
atmosphere of Jupiter, which we think is devoid of life). When two methanes are
combined, the resultant molecule is Ethane, which has a chemical formula C2H6.
Molecules made up of H and C are known as hydrocarbons. The formulas and
structural representations of several simple organic molecules are shown in
Figure 6.
Figure 6. Types of hydrocarbon compounds and their
structure.
Scientists eventually
realized that specific chemical properties were a result of the presence of
particular functional groups. Functional groups are clusters of atoms with
characteristic structure and functions. Polar molecules (with +/- charges) are
attracted to water molecules and are hydrophilic. Nonpolar molecules are
repelled by water and do not dissolve in water; are hydrophobic. Hydrocarbon is
hydrophobic except when it has an attached ionized functional group such as
carboxyl (acid) (COOH), then molecule is hydrophilic. Since cells are 70-90%
water, the degree to which organic molecules interact with water affects their
function. One of the most common groups is the -OH (hydroxyl) group. Its
presence will enable a molecule to be water soluble.
Figure 7. Functional groups in organic molecules.
Carbon has four
electrons in outer shell, and can bond with up to four other atoms (usually H,
O, N, or another C). Since carbon can make covalent bonds with another carbon
atom, carbon chains and rings that serve as the backbones of organic molecules
are possible.
Chemical bonds store
energy. The C-C covalent bond has 83.1 Kcal (kilocalories) per mole, while the
C=C double covalent bond has 147 Kcal/mole. Energy is in two forms: kinetic, or energy in
use/motion; and potential, or energy at rest or in storage. Chemical bonds are
potential energy, until they are converted into another form of energy, kinetic
energy (according to the two laws of thermodynamics).
Each organic molecule
group has small molecules (monomers) that are linked to form a larger organic
molecule (macromolecule). Monomers can be jouined together to form polymers
that are the large macromolecules made of three to millions of monomer
subunits.
Macromolecules are
constructed by covalently bonding monomers by condensation reactions where
water is removed from functional groups on the monomers. Cellular enzymes carry
out condensation (and the reversal of the reaction, hydrolysis of polymers).
Condensation involves a dehydration synthesis because a water is removed
(dehydration) and a bond is made (synthesis). When two monomers join, a
hydroxyl (OH) group is removed from one monomer and a hydrogen (H) is removed
from the other. This produces the water given off during a condensation
reaction. Hydrolysis (hydration) reactions break down polymers in reverse of
condensation; a hydroxyl (OH) group from water attaches to one monomer and
hydrogen (H) attaches to the other.
There are four classes
of macromolecules (polysaccharides, triglycerides, polypeptides, nucleic
acids). These classes perform a variety of functions in cells.
2.1 Carbohydrates have the general formula [CH2O]n where n is a number between 3 and 6. Note the
different CH2O units in Figure 8. Carbohydrates function in
short-term energy storage (such as sugar); as intermediate-term energy storage
(starch for plants and glycogen for animals); and as structural components in
cells (cellulose in the cell walls of plants and many protists), and chitin in the
exoskeleton of insects and other arthropods.
Sugars are structurally the
simplest carbohydrates. They are the structural unit which makes up the other
types of carbohydrates. Monosaccharides are single (mono=one) sugars.
Important monosaccharides include ribose (C5H10O5),
glucose (C6H12O6), and fructose (same formula
but different structure than glucose).
Figure 8. The chain (left) and ring (center and
right) method of representing carbohydrates. We
classify monosaccharides by the number of carbon atoms and the types of
functional groups present in the sugar. For example, glucose and fructose,
illustrated in Figure 9, have the same chemical formula (C6H12O6),
but a different structure: glucose having an aldehyde (internal hydroxyl shown
as: -OH) and fructose having a keto group (internal double-bond O, shown as:
=O). This functional group difference, as small as it seems, accounts for the
greater sweetness of fructose as compared to glucose.
Figure 9. Models of glucose and fructose.
In
an aqueous solution, glucose tends to have two structures, a (alpha) and b (beta), with an intermediate
straight-chain form (shown in Figure 10). The a form and b form differ in the
location of one -OH group, as shown in Figure 9. Glucose is a common hexose,
six carbon sugar, in plants. The products of photosynthesis are assembled to form
glucose. Energy from sunlight is converted into and stored as C-C covalent bond
energy. This energy is released in living organisms in such a way that not
enough heat is generated at once to incinerate the organisms. One mole of glucose yields 673
Kcal of energy. (A calorie is the amount of heat needed to raise one gram of
water one degree C. A Kcal has 1000 times as much energy as a cal.). Glucose is
also the form of sugar measured in the human bloodstream.
Figure 10. D-Glucose in various views (stick and
space-filling).
Disaccharides are formed when two
monosaccharides are chemically bonded together. Sucrose, a common plant
disaccharide is composed of the monosaccharides glucose and fructose. Lactose,
milk sugar, is a disaccharide composed of glucose and the monosaccharide
galactose. The maltose that flavors a malted milkshake (and other items) is
also a disaccharide made of two glose molecules bonded together as shown in
Figure 11.
Figure 11. Formation of a disaccharide (top) by
condensation and structure of two common disaccharides.
Polysaccharides are large molecules
composed of individual monosaccharide units. A common plant polysaccharide is
starch (shown in Figure 12), which is made up of many glucoses (in a
polypeptide these are referred to as glucans). Two forms of polysaccharide,
amylose and amylopectin makeup what we commonly call starch. The formation of
the ester bond by condensation (the removal of water from a molecule) allows
the linking of monosaccharides into disaccharides and polysaccharides. Glycogen
(see Figure 12) is an animal storage product that accumulates in the vertebrate
liver.
Figure 12. Images of starch (top), glycogen
(middle), and cellulose (bottom).
Cellulose,
illustrated in Figure 13 and 14, is a polysaccharide found in plant cell walls.
Cellulose forms the fibrous part of the plant cell wall. In terms of human
diets, cellulose is indigestible, and thus forms an important, easily obtained
part of dietary fiber. As compared to starch and glycogen, which are each made
up of mixtures of a and b glucoses, cellulose (and the animal structural polysaccharide
chitin) are made up of only b glucoses. The
three-dimensional structure of these polysaccharides is thus constrained into
straight microfibrils by the uniform nature of the glucoses, which resist the
actions ofenzymes (such as amylase) that
breakdown storage polysaccharides (such a starch).
Figure 13. Structure of cellulose as it occurs in a
plant cell wall.
Figure 14. Cellulose Fibers from Print Paper (SEM
x1,080).
2.2 Lipids are involved mainly with long-term energy
storage. They are generally insoluble in polar substances such as water.
Secondary functions of lipids include structural components (as in the case of phospholipids that are the major building block in cell
membranes) and "messengers" (hormones) that play roles in
communications within and between cells. Lipids are composed of three fatty
acids (usually) covalently bonded to a 3-carbon glycerol. The fatty acids are
composed of CH2 units, and are
hydrophobic/not water soluble. Some examples of fatty acids are shown in Figure
15.
Fatty acids can be saturated
(meaning they have as many hydrogens bonded to their carbons as possible) or
unsaturated (with one or more double bonds connecting their carbons, hence
fewer hydrogens). A fat is solid at room temperature, while an oil is a liquid
under the same conditions. The fatty acids in oils are mostly unsaturated,
while those in fats are mostly saturated.
Figure 15. Saturated (top and middle) and
unsaturated (bottom) fatty acids. The term staurated refers to the
"saturation" of the molecule by hydrogen atoms. The presence of a
double C=C covalent bond reduces the number of hydrogens that can bond to the
carbon chain, hence the application of therm "unsaturated".
Fats and oils function in long-term energy storage. Animals
convert excess sugars (beyond their glycogen storage capacities) into fats.
Most plants store excess sugars as starch, although some seeds and fruits have
energy stored as oils (e.g. corn oil, peanut oil, palm oil, canola oil, and
sunflower oil). Fats yield 9.3 Kcal/gm, while carbohydrates yield 3.79 Kcal/gm.
Fats thus store six times as much energy as glycogen.
Diets are attempts to
reduce the amount of fats present in specialized cells known as adipose cells
that accumulate in certain areas of the human body. By restricting the intakes
of carbohydrates and fats, the body is forced to draw on its own stores to
makeup the energy debt. The body responds to this by lowering its metabolic
rate, often resulting in a drop of "energy level." Successful diets
usually involve three things: decreasing the amounts of carbohydrates and fats;
exercise; and behavior modification.
Another use of fats is
as insulators and cushions. The human body naturally accumulates some fats in
the "posterior" area. Subdermal ("under the skin") fat
plays a role in insulation.
Phospholipids and glycolipids are important structural components of cell
membranes. Phospholipids, shown in Figure 16, are modified so that a phosphate group (PO4-)
is added to one of the fatty acids. The addition of this group makes a polar
"head" and two nonpolar "tails". Waxes are an important
structural component for many organisms, such as the cuticle, a waxy layer
covering the leaves and stems of many land plants; and protective coverings on
skin and fur of animals.
Figure 16. Structure of a phospholipid,
space-filling model (left) and chain model (right).
Cholesterol and steroids: Most mention of these two types of lipids in the news is usually
negative. Cholesterol, illustrated in Figure 17, has many biological uses, it
occurs in cell membranes, and its forms the sheath of some types of nerve cells.
However, excess cholesterol in the blood has been linked to atherosclerosis,
hardening of the arteries. Recent studies suggest a link between arterial
plaque deposits of cholesterol, antibodies to the pneumonia-causing form of Chlamydia, and heart attacks. The
plaque increases blood pressure, much the way blockages in plumbing cause burst
pipes in old houses.
Figure 17. Structure of four steroids. Image from Purves et al.
2.3 Proteins are very important in biological systems as
control and structural elements. Control functions of proteins are carried out
by enzymes and proteinaceous hormones. Enzymes are chemicals that act as organic
catalysts (a catalyst is a chemical that promotes but is not changed by a
chemical reaction). Click here for an illustrated page about enzymes.
Structural proteins function in the cell membrane, muscle tissue, etc.
The building block of any
protein is the amino acid, which has an amino end (NH2)
and a carboxyl end (COOH). The struucture of a generalized aminio acid as well
as the specific structures of the 20 biological amino acids are shown in Figure
18 and 19 respectively. The R indicates the variable component (R-group) of
each amino acid. Alanine and Valine, for example, are both nonpolar amino
acids, but they differ, as do all amino acids, by the composition of their
R-groups. All living things (and even viruses) use various combinations of the
same twenty amino acids. A very powerful bit of evidence for the phylogenetic connection of all living
things.
Figure 18. Structure of an amino acid.
Figure 19. Structures in the R-groups of the twenty
amino acids found in all living things.
Amino
acids are linked together by joining the amino end of one molecule to the
carboxyl end of another. Removal of water allows formation of a type of
covalent bond known as a peptide bond. This process is
illustrated in Figure 20.
Figure 20. Formation of a peptide bond between two
amino acids by the condensation (dehydration) of the amino end of one amino
acid and the acid end of the other amino acid.
Amino acids are linked
together into a polypeptide, the primary structure in the organization of proteins. The primary
structure of a protein is the sequence of amino acids, which is directly
related to the sequence of information in the RNA molecule, which in turn is a
copy of the information in the DNA molecule. Changes in the primary structure
can alter the proper functioning of the protein. Protein function is usually
tied to their three-dimensional structure. The primary structure is the sequence
of amino acids in a polypeptide..
The secondary
structure is the tendency of the polypeptide to coil or pleat due to
H-bonding between R-groups. The tertiary
structure is controlled by bonding (or in some cases repulsion) between
R-groups. Tertiary structure of an HIV protein and its similarity to gamma
interferon are shown in Figure 22. Many proteins, such as hemoglobin, are formed from one or
more polypeptides. Such structure is termed quaternary structure. Structural proteins,
such as collagen, have regular repeated primary structures. Like the structural
carbohydrates, the components determine the final shape and ultimately
function. Collagens have a variety of functions in living things, such as the
tendons, hide, and corneas of a cow. Keratin is another structural protein. It
is found in fingernails, feathers, hair, and rhinoceros horns. Microtubules,
important in cell division and structures of flagella and cilia (among other
things), are composed of globular structural proteins.
Figure 21. HIV p17 protein and similarities of its
structure to gamma interferon.
2.4 Nucleic acids are polymers composed of monomer units known as nucleotides. There are a very few
different types of nucleotides. The main functions of nucleotides are
information storage (DNA), protein synthesis (RNA), and energy transfers (ATP
and NAD). Nucleotides, shown in Figure 22, consist of a sugar, a nitrogenous
base, and a phosphate. The sugars are either ribose or deoxyribose. They differ
by the lack of one oxygen in deoxyribose. Both are pentoses usually in a ring
form. There are five nitrogenous bases. Purines (Adenine and Guanine) are
double-ring structures, while pyrimidines (Cytosine, Thymine and Uracil) are
single-ringed.
Figure 22. Structure of two types of nucleotide.
Deoxyribonucleic
acid (better known as DNA) is the physical carrier of inheritance for
99% of living organisms. The bases in DNA are C, G, A and T, as shown in Figure
23. We will learn more about the DNA structure and function later in the course
(click here for a quick look
[actually take all the time you want!] ;)).
Figure 23. Structure of a segment of a DNA double
helix.
DNA functions in
information storage. Figure 23. Structure of a segment of a DNA double helix. The English alphabet has 26 letters that can be
variously combined to form over 50,000 words. DNA has four letters (C, G, A,
and T, the nitrogenous bases) that code for twenty words (the twenty amino acids found in all living things) that can make an
infinite variety of sentences (polypeptides). Changes in the sequences of these
basesinformation can alter the meaning of a sentence.
For example take the
sentence: I
saw Elvis. This implies certain
knowledge (that I've been out in the sun too long without a hat, etc.).
If we alter the sentence
by inverting the middle word, we get: I was Elvis (thank you, thank you
very much). Now we have greatly altered the information.
A third alteration will
change the meaning: I was Levis. Clearly the original sentence's meaning is now
greatly changed.
Changes in DNA
information will be translated into changes in the primary structure of a polypeptide, and from there to thesecondary and tertiary structures. A mutation is any change in the DNA base sequence. Most
mutations are harmful, few are neutral, and a very few are beneficial and
contribute the organism's reproductive success. Mutations are the wellspring of
variation, variation is central to Darwin and Wallace's theory of evolution by natural selection.
Ribonucleic acid (RNA), shown in Figure 24 was discovered after DNA.
DNA, with exceptions in chloroplasts and mitochondria, is restricted to the
nucleus (in eukaryotes, the nucleoid region in prokaryotes). RNA occurs in the
nucleus as well as in the cytoplasm (also remember that it occurs as part of
the ribosomes that line the rough endoplasmic reticulum).
There are three types of RNA:
Details of RNA and its role in
protein synthesis are available by clicking here.
Figure 24. Structure of the RNA molecule.
Adenosine triphosphate,
better known as ATP (Figure 25), the energy currency or coin of the cell,
transfers energy from chemical bonds to endergonic (energy absorbing) reactions
within the cell. Structurally, ATP consists of the adenine nucleotide (ribose
sugar, adenine base, and phosphate group, PO4-2) plus two
other phosphate groups.
Energy
is stored in the covalent bonds between phosphates, with the greatest amount of
energy (approximately 7 kcal/mole) in the bond between the second and third
phosphate groups. This covalent bond is known as a pyrophosphate bond.
Figure 25. A cartoon and space-filling view of ATP.
3. Learning Objectives
- Dissolved substances are called solutes; a fluid in
which one or more substances can dissolve is called a solvent. Describe
several solutions that you use everyday in terms of what is the solvent
and what is the solute.
- Define acid and base and be able to cite an example of
each.
- The concentration of free hydrogen ions in solutions is
measured by the pH scale..
- Nearly all large biological molecules have theor
organization influenced by interactions with water. Describe this
interaction as it exists with carbohydrate molecules.
- Be able to list the three most abundant elements in
living things.
- Each carbon atom can form as many as four covalent
bonds with other carbon atoms as well as with other elements. Be able to
explain why this is so.
- Be able to list the four main groups of organic
molecules and their functions in living things.
- Enzymes are a special class of proteins that speed up
chemical reactions in cells. What about the structure of proteins allows
for the reaction specificity that occurs with most enzymes.
- Condensation reactions result in the formation of
covalent bonds between small molecules to form larger organic molecules.
Be able to describe a condensation reaction in words.
- Be able to describe what occurs during a hydrolysis
reaction.
- Be able to define carbohydrates and list their
functions.
- The simplest carbohydrates are sugar monomers, the
monosaccharides. Be able to give examples and their functions.
- A polysaccharide is a straight or branched chain of
hundreds or thousands of sugar monomers, of the same or different kinds.
Be able to give common examples and their functions.
- Be able to define lipids and to list their functions.
- Distinguish betwen a saturated fat and an unsaturated
fat. Why is such a distinction a life and death matter for many people?
- A phospholipid has two fatty acid tails attached to a
glycerol backbone. What is the importance of these molecules.
- Define steroids and describe their chemical structure. Be
able to discuss the importance of the steroids known as cholesterol and
hormones.
- Be able to describe proteins and cite their general
functions.
- Be prepared to make a sketch and name the three parts
of every amino acid.
- Describe the complex structure of a protein through its
primary, secondary, tertiary, and quaternary structure. How does this
relate to the three-dimensional structure of proteins?
- Describe the three parts of every nucleotide..
- Be able to give the general functions of DNA and RNA molecules.
Questions
1.
The chemical reaction
where water is removed during the formation of a covalent bond linking two
monomers is known as ___. a) dehydration; b) hydrolysis; c) photosynthesis; d)
protein synthesis
2.
The monomer that makes
up polysaccharides is ____. a) amino acids; b) glucose; c) fatty acids; d)
nucleotides; e) glycerol
3.
Proteins are composed of
which of these monomers? a) amino acids; b) glucose; c) fatty acids; d)
nucleotides; e) glycerol
4.
Which of these is not a
function of lipids? a) long term energy storage; b) structures in cells; c)
hormones; d) enzymes; e) sex hormones
5.
All living things use
the same ___ amino acids. a) 4; b) 20; c) 100; d) 64
6.
The sequence of ___
bases determines the ___ structure of a protein. a) RNA, secondary; b) DNA,
quaternary; c) DNA, primary; d) RNA, primary
7.
Which of these is not a
nucleotide base found in DNA? a) uracil; b) adenine; c) guanine; d) thymine; e)
cytosine
8.
Which of these
carbohydrates constitutes the bulk of dietary fiber? a) starch; b) cellulose;
c) glucose; d) fructose; e) chitin
9.
A diet high in _____ is
considered unhealthy, since this type of material is largely found in animal
tissues. a) saturated fats; b) testosterone; c) unsaturated fats; d) plant oils
10.
The form of RNA that
delivers information from DNA to be used in making a protein is ____. a)
messenger RNA; b) ribosomal RNA; c) transfer RNA; d) heterogeneous nuclear RNA
11.
The energy locked inside
an organic molecule is most readily accessible in a ___ molecule. a) fat; b)
DNA; c) glucose; d) chitin; e) enzyme
12.
Phospholipids are
important components in ____. a) cell walls; b) cytoplasm; c) DNA; d) cell
membranes; e) cholesterol
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