Download Summary/Reflection of Dan Freedman`s article, Science Education

UNIT 1—Biochemistry
I. Atoms, Molecules, Ions, and Bonds
A. Nucleus
1. Proton—positive charge
2. Neutron—neutral charge
B. Shells outside nucleus
1. Electron—negative charge
2. Arrangement of electrons determine reactions with other atoms and the nature of the chemical
bonds.
C. Ionic bonds
1. One or more electrons are completely transferred from one atom to another
2. Atom that gains electron has an overall negative charge
3. Atom that donates electron has an overall positive charge
4. Ions = Atoms with either a positive or negative charge
5. The attraction between positive and negative ions creates the ionic bond.
6. e.g. Sodium (Na+) and chlorine (Cl-) form an ionic bond to create sodium chloride (NaCl)
D. Covalent bonds
1. Electrons between atoms are shared
2. Single covalent bond = two shared electrons
3. Double covalent bond = four shared electrons
4. Triple covalent bond = six shared electrons
5. Nonpolar covalent bond = two atoms sharing the electrons are exactly the same (e.g. O2)
6. Polar covalent bond = atoms sharing electrons are different (e.g. H2O)
a. Larger nucleus exerts a stronger pull on the shared electrons
b. Creates charged areas within the molecule (i.e. negative or positive poles)
E. Hydrogen bonds
1. Weak bonds between positively charged hydrogen atom in one covalently bonded molecule and the
negatively charged area of another covalently bonded molecule.
2. e.g. Water forms hydrogen bonds between molecules
UNIT 1—Biochemistry
II. Properties of Water
A. Special properties due to hydrogen bonds among water molecules
B. Water is an excellent solvent
1. Ionic substances are soluble in water because the poles of the polar water molecules interact with
the charged substances and separate them into ions.
2. Polar covalent substances dissolve because they share the same hydrogen bonding with water as
water shares with itself.
a. Polar covalent substances are called hydrophilic (i.e. water loving)
3. Nonpolar covalent substances do not dissolve in water because they lack charged poles
a. Nonpolar covalent substances are called hydrophobic (i.e. water fearing)
C. Water molecules have a high degree of cohesion because they are held together by hydrogen bonds.
1. Water has strong surface tension
2. Water has strong capillary action
3. These properties contribute to the movement of water through plant vessels and animal capillaries
D. The temperature of water is very stable
1. Relatively large amount of energy to warm (and boil) or to cool (and freeze)
2. This accounts for the removal of a lot of heat when perspiration evaporates
3. This is also why oceans provide a very temperature-constant environment
UNIT 1—Biochemistry
III. Organic Molecules
A. Carbon atoms have four electrons that are available to form bonds with other atoms
H
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B. In methane (CH4 or H—C—H), carbon forms covalent bonds with four hydrogen atoms.
|
H
C. Each bond shares two electrons
D. Complex molecules are formed by stringing carbon atoms together
1. Straight lines
2. Rings
3. Other atoms add variety (nitrogen, oxygen, etc.)
E. Study of the variety and complexity of carbon molecules is called organic chemistry
1. Molecules with similar structural or chemical properties are grouped together
2. Many organic molecules share similar properties because they have similar clusters of atoms, called
functional groups
3. Each functional group gives the molecule a particular property, such as acidity or polarity.
a. hydroxyl (—OH) is polar and hydrophilic
b. carboxyl (—C==O) is a weak acid
\
OH
c. amino (—N—H ) is a weak base
\
H
O
||
d. organic phosphate (—P—O-) is an acid
|
OH
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e. methyl ( —C—H) is hydrophobic
|
H
\
f. ketone ( C==O) is polar
/
H
|
g. aldehyde (—C==O) is polar
UNIT 1—Biochemistry
IV. Carbohydrates are classified into three groups according to the number of sugar (or saccharide) molecules
present.
A. Monosaccharides are the simplest kinds of carbohydrates.
1. Consist of a single sugar molecule.
2. Sugar molecules have the formula (CH2O)n, where n is any number from 3 to 8
3. Fructose—n is 6 C6H12O6
4. Glucose—n is 6 C6H12O6 also, but with different configuration of carbon atoms
a. Two forms of -glucose and -glucose differ by reversing the H and the OH on the first carbon.
5. Very small changes in the position of certain atoms can dramatically change the chemistry of the
molecule.
B. Disaccharides consist of two linked sugar molecules.
1. Glucose and fructose link to form sucrose
C. Polysaccharides consist of a series of connected monosaccharides
1. Any molecule that consists of a repeating molecular unit is called a polymer.
a. Thus, a polysaccharide is a monosaccharide polymer.
2. Starch is a polysaccharide made up of a thousand or more -glucose molecules
a. Used in plants for energy storage
b. Easily broken down (digested) by humans and other animals
3. Cellulose is polysaccharide made of -glucose
a. Used for structural components
b. Major ingredient in wood
c. Only specialized organisms, like bacteria and protozoa in the guts of termites, can break down
cellulose.
4. The -glucose in starch and the -glucose in cellulose illustrate the dramatic chemical changes that
can arise from subtle molecular changes.
UNIT 1—Biochemistry
V. Lipids are a class of substances that are insoluble in water (and other polar solvents) but are soluble in
nonpolar substances (like ether or chloroform).
A. Many lipids (e.g. fats, oils, and waxes) have three fatty acids attached to a glycerol molecule.
1. Fatty acids are hydrocarbons (chains of covalently bonded carbons and hydrogens) with a carboxyl
group at one end of the chain.
2. A saturated fatty acid has a single covalent bond between each pair of carbon atoms, and each
carbon has two hydrogen atoms bonded to it.
a. “Saturated” with hydrogen
3. An unsaturated fatty acid occurs when a double covalent bond replaces the single covalent bond
and two hydrogen atoms.
4. Polyunsaturated fatty acids have many of these double bonds.
5. Fatty acids differ by the number and placement of double bonds and by the length of the
hydrocarbon chain.
B. Phospholipids look just like lipids, except that one of the fatty acid chains is replaced by a phosphate
group.
1. Additional chemical groups are usually attached to the phosphate group.
2. Fatty acid “tails” of phospholipids are nonpolar and hydrophobic
3. Glycerol and phosphate “heads” are polar and hydrophilic.
4. Phospholipids are often found oriented in sandwich-like formations with the hydrophobic tails
grouped together on the inside of the sandwich and the hydrophilic heads oriented toward the
outside.
5. Phospholipids are the structural foundation of cell membranes.
C. Steroids are characterized by a backbone of four linked carbon rings.
1. Cholesterol (a component of cell membranes)
2. Certain hormones, including testosterone and estrogen
UNIT 1—Biochemistry
VI. Proteins represent a class of molecules that has varied functions.
A. Eggs, muscles, antibodies, silk, fingernails, and many hormones are proteins
B. Enzymes are proteins that catalyze (speed up) the chemical activities in living systems.
C. Although the functions of these different proteins are diverse, their structures are similar.
1. All proteins are polymers of amino acids, that is they consist of a chain of amino acids covalently
bonded.
a. The bonds between amino acids are called peptide bonds.
b. The chain is a polypeptide, or peptide.
2. Proteins differ by the number and arrangement of the twenty different amino acids.
a. The general structural formula for an amino acid consists of a central carbon bonded to an
amino group (NH2), a carboxyl group (COOH), and a hydrogen atom.
b. The fourth bond to the central carbon group is an atom or a group of atoms that varies from one
kind of amino acid to another, symbolized with the letter R.
1) Glycine is the simplest amino acid (i.e. R = a hydrogen atom)
2) Serine (R = CH2OH)
3) Cysteine (R = sulfur)
4) Phenylalanine (R = a carbon ring)
D. There are four levels that describe the structure of a protein:
1. The primary structure of a protein describes the order of the amino acids.
a. The antidiuretic hormone (ADH) contains the amino acids cysteine, tyrosine, phenylalanine,
glutamic acid, asparagine, cysteine, proline, arginine, and glycine.
b. Using the three letters representative of the amino acid’s name, the primary structure for ADH
can be written as cys-tyr-phe-glu-asn-cys-pro-arg-gly.
2. The secondary structure of a protein is a three-dimensional shape that results from hydrogen
bonding between amino acids.
a. Two patterns may emerge.
b. The first, an alpha helix (“alpha” because it was the first to be identified), is a spiral (helix).
c. The second pattern, a beta pleated sheet, is a folded plane that looks much like the pleats on a
skirt.
d. Proteins whose shape is dominated by these patterns often form fibrous proteins.
3. The tertiary structure of a protein included additional three-dimensional shaping that results from
interactions among R groups.
a. Hydrophobic R groups tend to clump toward the inside of the protein.
b. Hydrophilic R groups clump toward the outside of the protein.
c. These interactions, as well as amino acids with large R groups, distort the hydrogen bonding in
the secondary structure.
d. Additional three-dimensional shaping occurs when the amino acid cysteine bonds to another
cysteine across a disulfide bond. This causes the protein to twist around the bond.
e. Proteins whose shape is dominated by tertiary structure interactions are often globular proteins.
4. The quaternary structure describes a protein that is assembled from two or more separate peptide
chains.
a. The globular protein, hemoglobin, consists of four peptide chains that are held together by
hydrogen bonding, interactions among R groups, and disulfide bonds.
UNIT 1—Biochemistry
VII.
Chemical Reactions in Metabolic Processes
A. In order for a chemical reaction to take place, the reacting molecules (or atoms) must first collide and
then have sufficient energy (activation energy) to trigger the formation of new bonds.
1. Many reactions occur spontaneously.
2. The presence of a catalyst accelerates the rate of the reaction because it lowers the activation
energy required for the reaction to take place.
3. A catalyst is any substance that accelerates a reaction but does not undergo a chemical change itself.
a. Since the catalyst is not changed by the reaction, it can be used over and over again.
B. Chemical reactions that occur in biological systems are referred to as metabolism.
1. Metabolism includes the breakdown of substances (catabolism),
2. the formation of new products (synthesis or anabolism), or
3. the transferring of energy from one substance to another
C. Metabolic processes have the following characteristics in common:
1. The net direction of metabolic reactions—whether the overall reaction proceeds in the forward or
reverse direction—is determined by the concentration of the reactants and the end products.
a. Chemical equilibrium describes the condition where the rate of reaction in the forward
direction equals the rate in the reverse direction, as a result there is no net production of
reactants or products.
2. Enzymes act as catalysts for metabolic reactions.
a. Enzymes are globular proteins that are specific for particular reactions.
b. Amylase catalyzes the reaction that breaks the -glucose bond in starch but cannot break the glucose bond in cellulose.
c. The standard suffix for enzymes is “ase,” so it is easy to identify enzymes that use this ending
(some do not).
d. The substances on which the enzyme acts is called the substrate.
1) The enzyme, amylase, catalyzes the breakdown of the substrate, amylose (starch).
e. The induced-fit model describes how enzymes work.
1) Within the protein (the enzyme), there is an active site with which the reactants readily
interact because of the shape, polarity, or other characteristics of the active site.
2) The interaction of the reactants (substrate) and the enzyme causes the enzyme to change
shape.
3) The new position places the substrate molecules into a position favorable to their reaction.
f. The operation of an enzyme is optimal at a specific temperature.
1) The human body, for example, is maintained at a temperature of 98.6 F, near the optimal
temperature for most human enzymes.
2) Above 104 F, these enzymes begin to lose their ability to catalyze reactions as they
become denatured; that is, they lose their three-dimensional shape as hydrogen bonds and
peptide bonds begin to break down.
g. Enzymes are also optimal at specific levels of pH (a measure of acidity/alkalinity).
1) The enzyme, pepsinogen, which digests proteins in the stomach, becomes active only at a
low pH (very acidic).
3. ATP (adenosine triphosphate) is a common source of activation energy for metabolic reactions.
a. The last two phosphate groups are high-energy bonds.
b. When ATP supplies energy to a reaction, it is usually the energy in the last bond that is
delivered to the reaction.
c. In the process of giving up this energy, the last phosphate bond is broken and the ATP molecule
is converted to ADP (adenosine diphosphate) and a phosphate group (Pi).
d. New ATP molecules are assembled by phosphorylation when ADP combines with a phosphate
group using energy obtained from some energy-rich molecule (like glucose).
4. Cofactors are nonprotein molecules that assist enzymes.
a. Organic cofactors are called coenzymes.
UNIT 1—Biochemistry
1) Their function is usually to donate or accept some component of a reaction, often electrons.
2) Vitamins are often coenzymes or components of coenzymes.
b. Inorganic cofactors are often metal ions, like Fe++.
D. Living systems often regulate chemical reactions (i.e. start and shut off reactions) by regulating its
enzyme.
1. Allosteric enzymes have two kinds of binding sites.
a. One for the substrate molecules
b. One for the allosteric effector
2. The presence (or absence) of the allosteric effector in the binding site either activates or inhibits the
enzyme’s ability to catalyze a reaction.
3. In feedback inhibition, an end product of a series of reactions acts as an allosteric effector, shutting
down one of the enzymes catalyzing the reaction series.
4. In competitive inhibition, a substance inhibits an enzyme by occupying the active site, thus
displacing the substrate.