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3
BIOLOGICAL MOLECULES: THE CARBON COMPOUNDS
OF LIFE
Chapter Outline
3.1 CARBON BONDING
Carbon chains and rings form the backbones of all biological molecules
3.2 FUNCTIONAL GROUPS IN BIOLOGICAL MOLECULES
The hydroxyl group is a key component of alcohols
The carbonyl group is the reactive part of aldehydes and ketones
The carboxyl group forms organic acids
The amino group acts as an organic base
The phosphate group is a reactive jack-of-all-trades
The sulfhydryl group works as a molecular fastener
3.3 CARBOHYDRATES
Monosaccharides are the structural units of carbohydrates
Two monosaccharides link to form a disaccharide
Monosaccharides link in longer chains to form polysaccharides
3.4 LIPIDS
Neutral lipids are familiar fats and oils
Phospholipids provide the framework of biological membranes
Steroids contribute to membrane structure and work as hormones
3.5 PROTEINS
Cells assemble 20 kinds of amino acids into proteins by forming peptide bonds
Proteins have as many as four levels of structure
Primary structure is the fundamental determinant of protein form and function
Twists and other arrangements of the amino acid chain form the secondary structure of a protein
The tertiary structure of a protein is its overall three-dimensional conformation
Multiple amino acid chains form quaternary structure
Combinations of secondary, tertiary, and quaternary structure form functional domains in many proteins
Proteins combine with units derived from other classes of biological molecules
3.6 NUCLEOTIDES AND NUCLEIC ACIDS
Nucleotides consist of a nitrogenous base, a five-carbon sugar, and one or more phosphate groups
Nucleic acids DNA and RNA are the informational molecules of all organisms
DNA molecules consist of two nucleotide chains wound together
RNA molecules are usually single nucleotide chains
Learning Objectives
After reading the chapter, you should be able to:
1.
Understand the difference between organic molecules and hydrocarbons.
2.
Explain the difference between a dehydration reaction and hydrolysis.
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3.
Illustrate how carboxyl groups, amino groups, and phosphate groups act as acids or bases in biological reactions.
4.
Understand the structural complexity of mono-, di-, and polysaccharides.
5.
Explain how lipids are important to biological systems.
6.
Differentiate between polar and nonpolar amino acids and how those amino acids may affect different levels of
protein structure.
7.
Discriminate between DNA and RNA.
Key Terms
organic molecules
cellulose
phospholipids
chaperonins
inorganic molecules
monosaccharides
steroids
domains
hydrocarbons
polysaccharides
sterols
motifs
functional groups
isomers
cholesterol
leucine zipper
dehydration synthesis
reaction
enantiomers
phytosterols
helix-turn-helix motif
optical isomers
enzymes
condensation reaction
glycosidic bonds
amino acid
deoxyribonucleic acid
(DNA)
hydrolysis
macromolecule
peptide bond
ribonucleic acid (RNA)
hydroxyl group
polymerization
N-terminal end
nucleotide
alcohols
monomers
C-terminal end
nitrogenous base
carbonyl group
polymer
polypeptide
pyrimidines
aldehyde
neutral lipids
primary structure
purines
ketone
oils
secondary structure
deoxyribose
carboxyl group
fats
tertiary structure
ribose
organic acids
fatty acid
quaternary structure
phosphodiester bond
amino group
saturated
alpha helix
double helix
phosphate group
unsaturated
beta sheet
complementary
sulfhydryl group
monounsaturated
random coil
template
disulfide linkage
polyunsaturated
conformation
starch
triglyceride
denaturation
glycogen
waxes
chaperone proteins
Lecture Outline
A. Coniferous trees wake in spring and increase CO2 uptake through their needles.
1. Plants use sunlight and water combined with CO2 to make sugars.
2. Most organisms rely on photosynthesis in some manner.
B. Carbon dioxide concentration in the atmosphere is critical.
1. Scientists have found that CO2 levels shift seasonally.
2. Levels decrease in the spring and summer.
3. Carbon dioxide enters from forest fires and burning of fossil fuels.
4. It is critical to food production and can have effects on global environments.
3.1 Carbon Bonding
A. A wide variety of chemical bonds are all known as organic.
1. Carbon can covalently bond to other carbon.
2. Carbon chiefly binds to hydrogen, oxygen, nitrogen, and sulfur.
3. Carbons only bound to hydrogen are hydrocarbons.
4. The simplest hydrocarbon is methane.
5. Linear, branched, and ring hydrocarbons form.
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B. More complex forms can develop with double and triple carbon bonds.
1. Ethane, ethene, and ethyne (single, double, and triple bonds)
2. Double bonds in rings
3. Polysaccharides are long chains of carbon rings.
C. Carbon and hydrocarbon and other elements—organic
3.2 Functional Groups in Biological Molecules
A. Four main types of biological molecules are made and destroyed in the cell.
1. Carbohydrates
2. Lipids
3. Proteins
4. Nucleic Acids
B. Functional groups are located so their covalent bonds form and break easily.
1. Hydroxyl
2. Carbonyl
3. Carboxyl
4. Amino
5. Phosphate
6. Sulfhydryl
7. Double bonds have two pairs of shared electrons (e.g., C = O).
8. Dehydration is the removal of OH and H to form H2O.
9. Hydrolysis uses water to place an OH and H on molecules.
C. The hydroxyl group is key to alcohols.
1. —OH = hydroxyl groups are polar
2. R-OH; R = carbon
3. Ethanol used to precipitate DNA
D. Carbonyl groups are in aldehydes and ketones.
1. Carbonyl—carbon with a double bond to oxygen is highly reactive with bases.
2. Aldehydes and ketones are important in energy molecules.
E. The carboxyl group forms organic acids.
1. —COOH or carboxylic acid
2. Acid due to OH, which releases H+ ions (e.g., acetic acid)
3. Dehydration synthesis
F. The amino group acts as an organic base.
1. —NH2
2. Readily accepts H+ like a base
G. The phosphate group is a reactive jack-of-all-trades.
1. —PO4
a. Two links bind —OH to central phosphate.
b. One formed by a double bond to oxygen off the central phosphate.
c. One binds the central phosphate to oxygen, which also binds carbon.
2. Acts as a weak acid due to —OH groups
3. Can form a chemical bridge to link two organic blocks (e.g., DNA)
H. The sulfhydryl group works as a molecular fastener.
1. Forms covalent linkages
2. Disulfide linkages (S-S)
3.3 Carbohydrates
A. Characteristics
1. Most abundant biological molecule
2. Major chemical fuel energy for cells
3. Stored as starch in plants
4. Stored as glycogen in animals
5. Chains of carbohydrates can form structural components (e.g., cellulose).
B. C, H, O—1:2:1 ratio (CH2O)
1. Monosaccharides: (glucose—C6H12O6)
2. Disaccharide: two monosaccharides (sucrose)
3. Polysaccharides: more than ten monosaccharides
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C. Monosaccharides are structural units.
1. Water-soluble and sweet
2. Three common monosaccharides:
a. Trioses: 3-carbon
b. Pentoses: 5-carbon
c. Hexoses: 6-carbon
3. Linear and ring forms
a. When linear, all carbons except one have both OH and H.
b. Last carbon has carbonyl.
1. Aldehyde position on end
2. Ketone position on an inside carbon
c. Monosaccharides with five or more C can form rings.
D. Isomers of the monosaccharides
1. Asymmetric carbons: link to four different chemical groups
2. Can form isomers (e.g., D-Glyceraldehyde and L-Glyceraldehyde)
a. L-form (Laevus = left): hydroxyl to the left
b. D-form (Dexter = right): hydroxyl to the right
c. Enantiomers are “mirror images”.
1. D-form is most common in biological systems.
2. Amino acids form enantiomers, and L-form is most common.
d. Ring forms asymmetrically (two forms).
1. Hydroxyl pointing below plane of ring = alpha glucose
2. Hydroxyl pointing above plane of ring = beta glucose
3. Gives polysaccharides different properties
a. Starch: with α-linked glucose, which is easy to digest
b. Cellulose: with β-linked glucose, which is almost indigestible
E. Monosaccharides link to form disaccharides.
1. Form by dehydration synthesis
2. Maltose forms from 2-α glucose.
a. Oxygen bridge between # 1 carbon of one glucose and # 4 of the second
b. Glycosidic bonds (1 4)
c. 1  3 and 1  6 links are also common.
d. α or β depending on hydroxyl on the carbon that forms the bond
e. Sucrose (one glucose and one fructose) is most common in nature.
f. Lactose (one glucose and one galactose) is common in milk.
F. Monosaccharides link to form polysaccharides.
1. Polymerization forms polysaccharides from monomers.
a. Linear: unbranched
b. Branched: with side chains
2. Amylopectin is easily built or broken down to store/release glucose.
3. Cellulose: structural polysaccharide found in plants; strong and tough
4. Chitin: structural polysaccharide found in exoskeletons of insects, crabs, and some fungi
5. Surface polysaccharides bind protein and lipid.
a. Hold cells together
b. Recognition receptors on cell surface
3.4 Lipids
A. Water insoluble, nonpolar, and mostly hydrocarbon
B. Dissolve in nonpolar solvents (acetone and chloroform)
C. From cell membranes and serve as energy and as hormones
1. Neutral lipids: energy storage as oils and fats
2. Phospholipids: carboxyl
3. Steroids
D. Saturated fatty acids (FAs) have only H bonds on the carbons.
E. Unsaturated FAs have double bonds, reducing the number of H bonds.
1. Monounsaturated
2. Polyunsaturated
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3. Kink forms a bend
4. The more kinks, the lower the melting point.
F. Glycerol and triglyceride formation
1. Three carbon molecules with three hydroxyl groups
2. FAs: three for triglyceride
3. FAs: the more saturated, the less fluid
4. Shorter chains remain liquid at lower temperatures.
5. Gram for gram, glycerides weigh less than carbohydrates.
6. Unsaturated is considered healthier than saturated.
7. Waxes: FAs with long-chain alcohols or hydrocarbons
G. Phospholipids and biological membranes
1. Phosphate binds one carbon in glycerol.
2. FAs bind remaining two positions.
3. Phosphate head is hydrophilic.
4. FAs are hydrophobic.
5. Form bilayer
H. Steroids in membrane structure and as hormones
1. Four carbon rings
2. Side groups determine type.
3. Sterols are most abundant and have one polar hydroxyl group.
4. Mostly hydrophobic with hydroxyl giving slight hydrophobic property
a. Cholesterol: found in membranes to stabilize the membrane fluidity
b. Steroid hormones: control development, behavior, and more
c. Sex hormones are steroids.
d. Male and female sex hormones are similar except for one hydrogen.
5. Other lipid types: chlorophylls and carotenoids
Applied Research: Fats, Cholesterol, and Coronary Artery Disease
A. Butter, Bacon, eggs, ice cream, and cheesecake. Irresistible or off limits?
1. Animal fats and cholesterol
2. Hardening of the arteries (a.k.a. artherosclerosis).
a. Deposits of lipids
b. Deposits of fibrous “plaque”
c. Reduces diameter of arteries
d. Reduces bloodflow
1. Blocks O2 blood from heart muscle
2. Results in damaged heart and heart attack
B. Different kinds of cholesterol are both good and bad.
1. All the cholesterol is made by your liver.
a. LDL: low density lipoprotein = “BAD”
b. HDL: high density lipoprotein = “GOOD”
1. Higher levels of HDL reduce heart disease.
2. HDL removes excess cholesterol from plaques.
3. HDL + cholesterol is transported to the liver where it is broken down.
2. Fats in foods
a. Diets high in saturated fats increase LDL.
b. HDL levels are not affected by these diets.
c. Animal foods contain saturated fats.
d. Foods of plants contain unsaturated fats.
3. The food industry takes unsaturated vegetable oils and saturates them (solidifies the oil).
a. Partial dehydrogenation
b. Removes unsaturated sites
c. Eliminating double bonds causes trans fatty acids (FAs).
1. Usually hydrogens are on the same side.
2. Trans means across (one on top and one on bottom).
3. Trans FAs are found in vegetable shortening, margarine, cookies, etc.
4. Trans FAs raise LDL and lower HDL.
5. Trans FAs increase coronary heart disease.
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d.
Many cultures consume animal fats.
1. Masai people of Africa almost totally drink milk and eat cheese and have low heart disease
incidence.
2. French people eat lots of dairy, but they say it is the wine that keeps them healthy!
3.5 Proteins
A. Structural: framework of cells
B. Enzymes: alter rate of chemical reactions
C. Motile molecules: allow cells to move
D. Transporters: move substances across membrane
E. Regulate activity of other proteins and DNA
F. Proteins are polymers made of amino acids.
1. Amino groups
2. Carboxyl groups
3. Range from 3–50,000 amino acids
G. Amino acids—20 different kinds
1. Central carbon with one (NH2), one (COOH), and one (H +) atom
2. Remaining bond is occupied by 1 of 19 different side groups.
3. Acts as acid or base
a. Amino can accept H+.
b. Carboxyl can produce H+.
4. Different sides give different properties.
a. —SH allows crosslinks, locking peptides together.
b. Proline ring causes turns in the proteins.
5. Amino acids form peptide bonds.
a. Peptide bonds form by a dehydration synthesis between NH2 and COOH of two amino acids.
b. NH2: called N-terminal end
c. COOH: called C-terminal end
d. Amino acids added to the C-terminal end
e. Called polypeptide (many peptides)
f. Different folds give different properties.
H. Proteins have four levels of structure.
1. Primary = amino acid sequence
2. Secondary = twists and folds in a region
3. Tertiary = 3D fold in space
4. Quaternary = 2 or more polypeptides folding and working together
I. Primary structure is fundamental to form and function.
1. A single amino acid change can alter biological function.
2. Fredrick Sanger studied insulin in 1953 and determined its sequence.
J. Twists of secondary arrangement
1. Can curl into alpha helix
a. Linus Pauling and Robert Corey: CIT 1951
b. Found regular right hand twist
c. Rigid and rod like with long or short segments
2. Fold into beta strand
a. Pauling and Corey identified β-strand.
b. Zigzags in flat plain
c. Can line up with other β-strands to form β-sheets
d. Strong as with silk fibers
K. Random coil = irregular fold
L. Tertiary structure and 3D conformation
1. All the structures (α-helix, β-strand…) combine to give 3D shape.
2. Changes of side groups also contribute to final conformation.
3. Tertiary structure buries some amino acids and exposes others.
4. Charge and folds contribute to function.
5. Solubility is also determined by tertiary structure.
6. Hydrophobic and hydrophilic regions common to membrane bound proteins are important to transport.
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M. Tertiary structure of most proteins is flexible.
N. Extreme conditions (temperature, pH, etc.) can denature proteins.
1. Some proteins lose biological function after denaturation.
2. Some organisms are adapted to function in extreme conditions.
3. Denaturation can be permanent or reversible.
O. Current interest concentrates on how they fold.
1. How do they fold correctly?
2. Chaperone proteins guide the folding in some.
P. Multiple polypeptides form quaternary structure.
1. Complex proteins (e.g., hemoglobin)
2. Form active sites
3. Chaperonins are involved in correct association of some proteins.
Q. Combinations of secondary, tertiary, and quaternary work together to form functional domains.
1. Domains
2. Domains often form hinge regions.
3. Many have multiple functions (e.g., sperm surface protein).
4. Energy-releasing domains are similar in shape even in very different proteins.
5. Motifs are 3D arrangements of amino acid chains within and between domains.
a. Several types of motifs
b. Frequently cell surface proteins
R. Nucleic acids and proteins = nucleoproteins (e.g., chromosomes)
3.6 Nucleotides and Nucleic Acids
A. DNA: hereditary information for all eukaryotes and prokaryotes
B. RNA: mRNA, tRNA, and rRNA
1. Used by some viruses as hereditary material
2. mRNA carry instructions for making proteins.
3. Transport amino acids (tRNA)
4. Major component of ribosomes (rRNA) assemble proteins.
C. Nucleotides (nitrogenous bases, ribose sugar, phosphate group)
1. Nitrogenous bases C-N rings with base characteristics
a. Pyrimidines: one C:N ring (U, T, C)
b. Purines: two C:N rings (A, G)
2. Ribose sugar (5-carbon sugar)
3. 1–3 phosphate groups
D. Deoxyribose or ribose sugars
1. Carbons are numbered with prime (1′, 2′, 3′, 4′, 5′).
2. Nitrogenous bases are not written with prime number symbol.
3. Deoxyribose has an H+ at 2′ position.
4. Ribose sugar has an OH at the 2′ position.
E. Nitrogenous base + 5-carbon sugar is called a nucleoside.
1. Nucleotides are nucleoside phosphates.
2. Adenosine = adenine + ribose sugar
3. Adenosine monophosphate has one phosphate group.
4. Adenosine diphosphate has two phosphate groups.
5. Adenosine triphosphate has three phosphate groups.
6. Phosphate status is important to its function.
F. DNA and RNA are informational molecules.
1. Polynucleotide chains
2. Phosphodiester bond forms between 5′ carbon of one sugar and 3′ of another.
3. Bases extend out from the chain.
4. Each has one base.
a. A, T, G, or C for DNA
b. A, G, C, or U for RNA
G. DNA has two chains of nucleotides antiparallel.
1. Described by James D. Watson and Francis H.C. Crick
2. Maurice Wilkins and Rosalind Franklin did the research.
3. Two DNA chains wrapped around each other with nitrogenous bases serving as rungs of the ladder
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4.
5.
6.
Hydrogen bonds: two between A and T and three between G and C
One purine (A or G) and one pyrimidine (U, T, or C) bind between the polynucleotides.
Sequence of one chain determines the sequence of its partner: “complementary”.
a. Important to DNA replication: one side = template
b. Important to gene coding
H. RNA usually has single nucleotide chains.
1. mRNA: typically single strand
2. rRNA: folds into globular units
3. tRNA: folds to form specific structures
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