i. Naturally occurring elements
H2 Hydrogen gas (H-H)
O2 Oxygen gas (O-O)
Note: Inert gases are also naturally occurring elements but occur as single atoms.
ii. Compounds
H20 Water (H-O-H)
CO2 Carbon dioxide (O-C-O)
NaCl Sodium Chloride (Table salt)
def. Naturally occurring element: A substance with only one element in which the relative proportions never vary.
def. Compound: A substance with more than one element in which the relative proportions never vary.
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3.15 Chemical Reactions
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Molecules interact and rearrange their chemical bonds in chemical reactions.
Life depends on these chemical reactions!
Types of chemical reactions:
reactants product(s)
i. Synthesis (put together): A + B -----> AB
-- e.g., sucrose (table sugar) synthesis in plants
ii. Decomposition (break down): AB -----> A + B
-- e.g., digestion of sucrose (table sugar) in the human body
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3.16 Chemical Bonds
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Chemical bond is a union between the electron structures of two or more atoms or ions -- attractions that hold molecules together.
Ionic Bond
def. Ionic bond: Bond formed by the force between ions of opposite charge.
-- one atom attracts the electrons more than the other atom
one atom gains one or more electrons positively charged
one atom loses one or more electrons negatively charged
-- opposite charged ions positive & negative attract each other bond
-- strong bonds in crystal form (salt crystals hard as rock)
-- weak bonds in water (salt crystals dissolve in water)
Covalent Bond
def. Covalent bond: Bond formed by the sharing of one or more electrons between atoms or group of atoms.
-- both atoms attract the electrons equally
-- always strong bonds
e.g.,
-- water H2O
-- many organic compounds
i. nonpolar covalent bonds
-- atoms share the electrons equally, e.g., oils.
ii. polar covalent bonds
-- atoms share electrons unequally slight difference in charge between the two poles of the molecule, e.g., water.
Hydrogen Bond
def. Hydrogen bond: Bond formed by the weak charged attractions when an electropositive hydrogen atom in a polar covalent bond is attracted to a neighboring electronegative atom, and therefore interacts weakly with this neighboring atom.
-- bond between a slightly positive hydrogen atom & another slightly negative atom in a POLAR COVALENT BOND
-- weak bonds
-- biologically important:
-- properties of water, e.g., surface tension
-- shape and function of proteins: allow the protein molecule to twist and bend
-- shape and function of DNA: strong enough to allow the DNA molecule to twist and weak enough to split
-- chemical signaling of hormones: allow hormones to temporarily attach to other molecules
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3.2 WATER CHEMISTRY
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LECTURE OBJECTIVES:
1. Discuss why water is important.
2. List and describe the unique properties of water that make the molecule indispensable to living systems.
3. Explain the difference between an acid, a base, a salt and a buffer, and recognize that it is important that pH remains within natural limits (explain how these properties are related to hydrogen bonding).
4. List potential damage caused by acid precipitation, and recognize that changes in natural pH impacts natural ecosystems.
5. Define selected key terms.
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Key Terms
def. Acid: A substance having a sour taste that releases H+ ions in water (having the ability to turn litmus red, and the ability to react with bases to form salts).
def. Acid rain: The falling to earth of rain, snow or fog, that is more acidic than pH 5.6, that contains sulfur (S)
and nitrogen (N) oxides. (Also called acid precipitation, or wet acid deposition.)
def. Base: A substance having a bitter taste that releases OH- ions in water (having the ability to turn litmus blue, and the ability to react with acids to form salts).
def. Neutralization: the chemical process when an acid and a base is mixed, forming water and a salt.
def. pH: A measure of how acidic or basic (alkaline) a solution of water is (numerically equal to 7 for neutral solutions).
def. pH scale: A scale used to indicate the strength of an acid or a base (to measure the concentration of hydrogen ions in water solutions)
def. Salt: An inorganic compound formed when an acid reacts with a base.
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3.21 Importance of Water
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Many chemical reactions in living things require water (as a reactant).
Organisms on Earth are made mostly of water:
- adult human 40-60% of body weight
- infant human 75% of body weight
Water is a polar molecule (Oxygen slightly more electronegative than hydrogen)
[
-- forms Hydrogen bonds
[
IMPORTANT PROPERTIES OF WATER
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3.22 Important Properties of Water
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1. Solvent Properties
-- many imp. chemicals in the body dissolved in water -- polar molecules)
-- life on Earth rely on water
2. Temperature Properties
(temperature buffer) Example: continent vs. sea climate
-- because of hydrogen bond water needs to be heated up substantially before its temperature increases measurably
-- below 0°C hydrogen bonds resist breaking -- ICE
3. Cohesion Properties
(water molecules attracted to each other)
-- surface tension
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3.23 Acids and Bases
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def. Acid: A substance having a sour taste that releases H+ ions in water (having the ability to turn litmus red, and the ability to react with bases to form salts).
def. Base: A substance having a bitter taste that releases OH- ions in water (having the ability to turn litmus blue, and the ability to react with acids to form salts).
def. Neutralization: the chemical process when an acid and a base is mixed, forming water and a salt.
def. pH: A measure of how acidic or basic (alkaline) a solution of water is (numerically equal to 7 for neutral solutions).
def. pH scale: A scale used to indicate the strength of an acid or a base (to measure the concentration of hydrogen ions in water solutions)
def. Salt: An inorganic compound formed when an acid reacts with a base.
Acids and bases -- biologically important compounds
-- acids and bases destroy proteins (denature) -- important for living systems
-- acids and bases are corrosive (esp. strong acids and bases) -- environmental implications
-- acid - corrosive, e.g., Hydrochloric acid, HCl
-- base - caustic, e.g., Lye, NaOH, Sodium hydroxide
pH Scale
The degree to which a solution is acidic or basic is measured by a quantity called the
-- pH
-- pH is a number that can be measured
-- Ranges from 0 (acidic) 7 (neutral) 14 (basic)
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14
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HCl H2O NaOH
Low pH High pH
Tooth enamel dissolves at pH 5.5
pH of some solutions (many are highly variable!)
pH value Solutions
0 HCl
<1 battery acid
1 gastric juice (HCl + enzymes)
2.3 lemon juice
3 carbonated drinks, vinegar (sour wine), some acid rain, orange juice, beer
4 tomato juice, banana, grapes
5 black coffee
5.5 tooth decay start
5.6 normal rain
6 (5 - 7) urine
6.6 milk
6.2 - 7.4 saliva
---
7 pure water
---
7.35 - 7.45 blood
7.8 - 8.3 sea water
9 baking soda
9.5 tums
10 soap
10.5 milk of magnesia
11 Household ammonia
12.5 hair removers
13.5 oven cleaner
14 NaOH "lye"
Neutralization Reaction
def. Salt: An inorganic compound formed when an acid reacts with a base.
reactants product(s)
A + B -----> C + D
Acid + Base -----> Salt + Water
HCl + NaOH -----> NaCl + H2O
pH 1 pH 14 solid pH 7
-- cannot measure pH in solids
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3.24 Acid Precipitation (Acid Rain)
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def. Acid rain: The falling to earth of rain, snow or fog, that is more acidic than pH 5.6, that contains sulfur (S)
and nitrogen (N) oxides. (Also called acid precipitation, or wet acid deposition.)
pH tolerance of organisms vary
-- normal pH for most organisms is around pH 7
-- acidophiles (lactic acid bacteria, most yeasts, most molds, Thiobacillus, Sulfolobus)
-- alkaliphiles (Vibrio cholerae)
Normal rainwater has few impurities (polluted rainwater may have several)
1. burning of fossil fuels (oil, coal, natural gas)
2. industrial gases, NO, NO2, and SO2, in the atmosphere
3. gases dissolve in rainwater forming acids H2SO4 (sulfuric acid) & HNO2 (nitric acid)
4. rain
5. acid damage foliage
6. acid runoff into lakes and rivers
7. lower pH in lakes and water
Damage caused by acid rain
a. Forest damage (acidification may eliminate sensitive species)
b. Soil damage
c. Aquatic damage
d. Building damage
e. Visibility damage
Acidification can spread to relatively non-industrialized areas
or industrial areas with good environmental policies.
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3.3 ORGANIC CHEMISTRY
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LECTURE OBJECTIVES:
1. Recognize the difference between inorganic and organic molecules, and understand the importance of four valence electrons in a carbon atom.
2. List the major functional groups found in organic molecules.
3. List and describe the structure and function of the four major groups of organic molecules.
4. List the major groups of molecules within each of the four major groups of organic molecules, and give examples of each.
5. Recognize the importance of structure in organic molecules (e.g., molecular formula vs. structural formulas, importance of functional groups, importance of hydrogen bonds, primary, secondary, tertiary, and quaternary structures of proteins, and helical structure of DNA)
6. Define selected key terms.
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Key Terms
def. ATP (Adenosine triphosphate): The main energy carrying molecule in cells, made from a nucleotide (composed of adenine, 3 phosphate functional groups, and ribose sugar).
def. Amino acid: Small organic molecule with both amino & carboxyl groups; subunit (building block) of proteins.
def. Carbohydrates: Organic compound, a simple sugar or large molecule composed of sugar units, including sugars and starches.
def. Disaccharides: A type of carbohydrate with two sugar units (monosaccharides) covalently bonded (e.g., sucrose, lactose, maltose).
def. DNA (Deoxyribonucleic acid): For all cells the molecule of inheritance.
def. Enzyme: A class of proteins serving as catalysts, chemical agents that speed up chemical reactions without being consumed by the reaction.
def. Fat: A lipid with a glycerol head and three fatty acid tails. Also called a triglyceride.
def. Fossil fuel: Coal, petroleum, and natural gas, nonrenewable source of energy derived from the bodies of partly decomposed prehistoric organisms.
def. Fructose: A very sweet sugar, occurring in many fruits and honey and used as a preservative for foodstuffs and as an intravenous nutrient.
Def. Functional group: A specific configuration of atoms commonly attached to the carbon skeletons of organic molecules and usually involved in chemical reactions.
def. Galactose: A monosaccharide found in milk, forms lactose together with glucose.
def. Gene: A unit of information about a heritable trait that passes on from parents to offspring.
def. Glucose: A monosaccharide a digestive breakdown product (together with maltose a disaccharide) of polysaccharides (in part dextrose)
def. Hemoglobin: An iron containing protein in red blood cells.
def. Insulin: Protein hormone that lowers blood glucose levels.
def. Lactose: A disaccharide made from whey (the watery part of milk) and used in pharmaceuticals, infant foods, bakery products, and confections; milksugar (galactos and glucose)
def. Lipids: A greasy or oily compound of mostly carbon an hydrogen that shows little tendency to dissolve in water, including oils, fats, phospholipids, steroids, and waxes.
def. Maltose: A disaccharide a digestive breakdown product (together with glucose a monosaccharide) of polysaccharides; malt sugar.
def. Monosaccharides: The simplest carbohydrate, with only one sugar unit (e.g., glucose, fructose, galactose, ribose, deoxyribose).
def. Nucleic acid: Complex molecules, a long, single- or double-stranded chain of four different kinds of nucleotides, that store and transfer information.
def. Nucleotide: The structural unit (building block) of nucleic acids, and ATP
def. Organic chemistry: The study of carbon compounds (organic compounds).
def. Organic compound: Compound with a carbon backbone (carbon chain) found in "living" things.
def. Peptides: Short organic chains of at least two amino acids.
def. Peptide bond: The covalent bond between two amino acid subunits.
def. Phospholipid: A type of lipid that is the main structural component of cell membranes, a hydrophobic tail of two fatty acids and a hydrophilic head that incorporates glycerol and a phosphate group.
def. Polysaccharides: A type of carbohydrate with many, usually hundreds or thousands of covalently linked sugar units in straight or branched chains (e.g., glycogen, starch, cellulose, chitin).
def. Proteins: Large organic compound composed of one or more chains of amino acids held together with peptide bonds.
def. RNA (Ribonucleic acid): A category of nucleic acids that function in the process by which genetic instructions are used to build proteins.
def. Steroid: (‰ Sterol) A lipids consisting of a carbon backbone (carbon skeleton) of four carbon rings with various functional groups attached.
def. Sucrose: A disaccharide found in many plants, especially sugar cane and sugar beet, and widely used as sweetener, preservative, and in the manufacture of plastics and cellulose; table sugar (two glucose molecules)
def. Wax: A lipids with long hydrophobic fatty acid chains linked to long-chain alcohols or carbon rings.
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3.31 Carbon Chemistry
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In this chapter we will discuss the four macromolecules important for living organisms: Carbohydrates, Lipids, Proteins, and Nucleic Acids. First, however, we need to discuss the carbon atom, which make up the skeleton of all these macromolecules.
Chemicals can be divided into two groups
1. Inorganic -- chemistry of inorganic molecules
-- molecules with none or at the most one carbon atom (e.g., water, carbon dioxide)
2. Organic -- chemistry of organic molecules
-- molecules containing one, or more carbon atoms (e.g., proteins)
one carbon atom
-- Carbon dioxide, CO2 (by some inorganic, by some organic)
-- Urea, CO(NH2)2
many carbon atoms -- bonded with covalent bonds
-- short chains: Simple sugar
e.g., glucose, C6H12O6, C-C-C-C-C-C
-- long chains: Hemoglobin, (C738H1166FeN203O208S2)4
def. Organic chemistry: The study of carbon compounds (organic compounds).
def. Organic compound: Compound with a carbon backbone (carbon chain) found in "living" things.
def. Fossil fuel: Coal, petroleum, and natural gas, nonrenewable source of energy derived from the bodies of partly decomposed prehistoric organisms.
The carbon atom is unique
1. Carbon can bind 4 other molecules
2. Carbon can form long chains (the "skeleton" of organic molecules)
C-C-C-C-C-C (C6H12O6).
This "skeleton" can vary a great deal
-- variation important for living organisms
-- Variations in carbon skeletons:
i. Length
ii. Branching (branched or unbranched)
iii. Bonding (double bonds -- vary in location)
iv. Rings (carbon skeleton arranged in rings)
v. Other elements (bonded to the skeleton) -- FUNCTIONAL GROUPS
Def. Functional group: A specific configuration of atoms commonly attached to the carbon skeletons of organic molecules and usually involved in chemical reactions.
3. Carbon source for living organisms
CO2 in the atmosphere
+++ more about this in chapter 5: PHOTOSYNTHESIS
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3.32 Carbohydrates
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def. Carbohydrates: Organic compound, a simple sugar or large molecule composed of sugar units, including sugars and starches.
def. Monosaccharides: The simplest carbohydrate, with only one sugar unit (e.g., glucose, fructose, galactose, ribose, deoxyribose).
def. Fructose: A very sweet monosaccharide, occurring in many fruits and honey and used as a preservative for foodstuffs and as an intravenous nutrient.
def. Galactose: A monosaccharide found in milk, forms lactose together with glucose.
def. Glucose: A monosaccharide a digestive breakdown product (together with maltose a disaccharide) of polysaccharides (in part dextrose)
def. Disaccharides: A type of carbohydrate with two sugar units (monosaccharides) covalently bonded (e.g., sucrose, lactose, maltose).
def. Lactose: A disaccharide made from whey (the watery part of milk) and used in pharmaceuticals, infant foods, bakery products, and confections; milksugar (galactos and glucose)
def. Maltose: A disaccharide a digestive breakdown product (together with glucose a monosaccharide) of polysaccharides; malt sugar.
def. Sucrose: A disaccharide found in many plants, especially sugar cane and sugar beet, and widely used as sweetener, preservative, and in the manufacture of plastics and cellulose; table sugar (two glucose molecules)
def. Polysaccharides: A type of carbohydrate with many, usually hundreds or thousands of covalently linked sugar units in straight or branched chains (e.g., glycogen, starch, cellulose, chitin).
Functions
a. Source of energy (to keep us alive)
b. Provide structural support (building material)
Classification
a. Monosaccharides (Simple Sugars)
-- Building blocks: One single carbon chain or ring
Example: 6C -- glucose, fructose, galactose -- HEXOSES
--- same molecular formula, C6H12O6 (different structural formulas)
--- wh. dissolved in water (as when inside cells) they circle up in a ring form.
GLUCOSE
GALACTOSE
FRUCTOSE
--- building block in RNA, and DNA
RIBOSE --- molecular formula, C5H10O5
DEOXYRIBOSE --- molecular formula, C5H10O4
b. Disaccharides
-- Building blocks: 2 monosaccharides
Example: sucrose, lactose, and maltose
-- same molecular formula, C12H22O11
SUCROSE: table sugar (Glucose + Fructose)
LACTOSE: milk sugar (Glucose + Galactose)
MALTOSE: malt sugar (Glucose + Glucose)
c. Polysaccharides
-- Building blocks: many glucose units "linked" (in ring forms).
GLYCOGEN: Animal polysaccharide
--- energy storage (carbohydrate storage molecule in animals)
--- usually in the liver & the muscles
STARCH: Plant polysaccharide (glucose subunits -- same side up)
--- energy storage (carbohydrate storage molecule in plants)
--- usually in roots & seeds
CELLULOSE: Plant polysaccharide
--- structural material (= of plants -- in cell walls) :
--- cannot be digested by most animals
--- fibers (addition to our diet, we cannot digest):
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3.33 Lipids
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def. Lipids: A greasy or oily compound of mostly carbon an hydrogen that shows little tendency to dissolve in water, including oils, fats, phospholipids, steroids, and waxes.
def. Fat: A lipid with a glycerol head and three fatty acid tails. Also called a triglyceride.
def. Phospholipid: A type of lipid that is the main structural component of cell membranes, a hydrophobic tail of two fatty acids and a hydrophilic head that incorporates glycerol and a phosphate group.
def. Steroid: (‰ Sterol) A lipids consisting of a carbon backbone (carbon skeleton) of four carbon rings with various functional groups attached.
def. Wax: A lipids with long hydrophobic fatty acid chains linked to long-chain alcohols or carbon rings.
Functions
a. can be stored in adipose tissue (= fat tissue)
b. give high amount of energy
c. heat insulator
d. cushion
e. waterproofing (inability to dissolve in water)
f. component in cell membranes
g. vitamin D
Classification
a. Triglycerides (fats & oils)
--- Building blocks: Glycerol + 3 fatty acids
b. Phospholipids
--- Building blocks: Phosphate group + Glycerol + 2 fatty acids
major component in cell membranes
c. Steroids
--- Building blocks: 4 carbon rings (but no fatty acids)
cholesterol (necessary for prod. of vitamin D react w. UV light)
vitamin D
some hormones e.g., testosterone
d. Waxes
--- Building blocks: varies
bee wax, ear wax
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3.34 Protein
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def. Amino acid: Small organic molecule with both amino & carboxyl groups; subunit (building block) of proteins.
def. Enzyme: A class of proteins serving as catalysts, chemical agents that speed up chemical reactions without being consumed by the reaction.
def. Peptides: Short organic chains of at least two amino acids.
def. Peptide bond: The covalent bond between two amino acid subunits.
def. Proteins: Large organic compound composed of one or more chains of amino acids held together with peptide bonds.
Amino Acids and Peptide Bonds
BUILDING BLOCKS (structural unit of proteins)
-- held together by PEPTIDE BONDS (a kind of covalent bond)
Peptide Bond: Bond between the COOH group of one AA, & the NH2 group of another AA
AA - AA - AA - AA - AA - AA - AA
DIPEPTIDE
TRIPEPTIDE
POLYPEPTIDE
PROTEIN (> 100 AA)
Functions
a. speed up chemical reactions (enzymes)
b. deliver signals (hormones)
c. transport agent (blood cells)
d. immunity (antibodies)
e. structural material
Classification
a. Structural proteins
i. in cell membranes (egg white albumin)
ii. muscle cells fibers ("meat")
iii. in blood cells (e.g. antibodies, hemoglobin)
iv. spider silk
b. Regulatory proteins
i. enzymes (lactase help digest milk, pepsin in stomach)
ii. some hormones (insulin)
def. Hemoglobin
def. Insulin
Levels of protein structure (Protein architecture)
1. PRIMARY STRUCTURE
--- Sequence of Amino Acids
2. SECONDARY STRUCTURE (superimposed on the primary structure)
--- the AA chain is coiled or pleated because of hydrogen bonds
3. TERTIARY STRUCTURE (superimposed on the secondary structure)
--- the coiled or pleated structure is folded
--- held in place by hydrogen bonds (weak)
--- If two or more polypeptide chains
4. QUATERNARY STRUCTURE
--- the single folded chain in many proteins is aggregated with other chains
e.g., Collagen (3 chains twisted), Hemoglobin (4 chains)
Denaturation
Proteins may lose their unique structure and become biologically inactive, under extreme conditions
-- pH, salt, temperature e.g., egg coagulation
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3.35 Nucleic Acids
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def. Nucleic acid: Complex molecules, a long, single- or double-stranded chain of four different kinds of nucleotides, that store and transfer information.
def. Nucleotide: The structural unit (building block) of nucleic acids, and ATP
def. ATP (Adenosine triphosphate): The main energy carrying molecule in cells, made from a nucleotide (composed of adenine, 3 phosphate functional groups, and ribose sugar).
def. DNA (Deoxyribonucleic acid): For all cells the molecule of inheritance.
def. RNA (Ribonucleic acid): A category of nucleic acids that function in the process by which genetic instructions are used to build proteins.
def. Gene: A unit of information about a heritable trait that passes on from parents to offspring.
Functions
a. DNA - store information genetic blueprint, our hereditary material
b. RNA - transfer information from DNA so it can be used
Classification
a. DNA Deoxyribonucleic Acid
-- LONG, DOUBLE stranded molecule
-- Building blocks: Nucleotides with the following composition
Deoxyribose
Phosphate group
Nitrogen base (Adenine, Thymine, Guanine, & Cytosine)
b. RNA - Ribonucleic Acid
-- SHORT, SINGLE stranded molecule
-- Building blocks: Nucleotides with the following composition
Ribose
Phosphate group
Nitrogen base (Adenine, Uracil, Guanine, & Cytosine)
ATP
def. ATP (Adenosine triphosphate): The main energy carrying molecule in cells, made from a nucleotide (composed of adenine, 3 phosphate functional groups, and ribose sugar).
The energy molecule of the body:
Building blocks: (nucleotide derivate)
Ribose
Phosphate groups
Adenine (the nitrogen base)
Web page layout and design © and intellectual property Jan A. Nilsson, 1999, 2000, 2001, 2002, 2003, 2004, 2004, 2005. Page created 08.VIII.1999, last updated 16.VII.2005, most likely during the wee hours of the morning on a G3 PowerBook owned by Jan A. Nilsson.
-- Disclaimer: "Dr. Nilsson's CyberOffice", at the time of writing located as a file under the South Texas College's (STC) web server with the general URL http://www.southtexascollege.edu/, is the intellectual property of Dr. Jan A. Nilsson, member of STC biology faculty. The content of Dr. Nilsson's CyberOffice does not necessarily reflect the opinions and beliefs of the STC faculty, staff, administration, and Board of Trustees.