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Overview: The Molecules of Life
• All living things are made up of four classes of large biological molecules:
1. Carbohydrates2. lipids3. Proteins4. nucleic acids
• Within cells, small organic molecules are joined together to form larger molecules
• Macromolecules are large molecules composed of thousands of covalently connected atoms
• Molecular structure and function are inseparable
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Many Important Biomolecules are Polymers
p ro te in com plex
p ro te in su b un it
a m ino ac id
m em b rane
p ho sp ho lip id
fa tty a c id
ce ll w a ll
ce llu lo se
g lu co se
ch ro m o som e
D N A
n uc leo tidemonomer
polymer
supramolecularstructure
lipids proteins carbo nucleic acids
• A condensation reaction or more specifically a dehydration reaction occurs when two monomers bond together through the loss of a water molecule
• Enzymes are macromolecules that speed up the dehydration process
• Polymers are disassembled to monomers by hydrolysis, a reaction that is essentially the reverse of the dehydration reaction
The Synthesis and Breakdown of Polymers
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Fig. 5-2
Short polymer
HO 1 2 3 H HO H
Unlinked monomer
Dehydration removes a watermolecule, forming a new bond
HO
H2O
H1 2 3 4
Longer polymer
(a) Dehydration reaction in the synthesis of a polymer
HO 1 2 3 4 H
H2OHydrolysis adds a watermolecule, breaking a bond
HO HH HO1 2 3
(b) Hydrolysis of a polymer
Fig. 5-2a
Dehydration removes a watermolecule, forming a new bond
Short polymer Unlinked monomer
Longer polymer
Dehydration reaction in the synthesis of a polymer
HO
HO
HO
H2O
H
HH
4321
1 2 3
(a)
Fig. 5-2b
Hydrolysis adds a watermolecule, breaking a bond
Hydrolysis of a polymer
HO
HO HO
H2O
H
H
H321
1 2 3 4
(b)
Carbohydrates (sugars)
• Most abundant macromolecules in nature
Functions:• Energy Storage• Structure• Cellular Recognition• DNA Backbone
Classification of Sugars
• Monosaccharides simple sugars• Polyalcohols• Aldehyde, ketone• Common formula: (CH2O)n = CnH2nOn when n≥3• They contain C, H, and O
• Monosaccharides are classified by three characteristics:① The location of the carbonyl group (as aldose or ketose)
② The number of carbons in the carbon skeleton (Based on number of carbons (3, 4, 5, 6), a monosaccharide is a triose, tetrose, pentose or hexose.
③ Chiral handedness
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Disaccharides - 2 monosaccharides covalently linked.Oligosaccharides - a few monosaccharides covalently
linked. Polysaccharides - polymers consisting of chains of
monosaccharide or disaccharide units.
• Aldotriose• Ketotriose• Aldotetrose• Ketotetrose• Aldopentose• Ketopentose• ….
Aldoses
Enantiomers = mirror images
D vs L Designation enantiomers = mirror images
D & L designations are based on the configuration about the single asymmetric C in glyceraldehyde.
The lower representations are Fischer Projections.
CHO
C
CH2OH
HO H
CHO
C
CH2OH
H OH
CHO
C
CH2OH
HO H
CHO
C
CH2OH
H OH
L-glyceraldehydeD-glyceraldehyde
L-glyceraldehydeD-glyceraldehyde
Optical activity measured by polarimeter
Temperature T (given in degrees Celsius) and wavelength λ (in nanometers). If the wavelength of the light used is 589 nanometer (the sodium D line), the symbol “D” is used.
Some examples: Sucrose +66.47°Lactose +52.3°Cholesterol −31.5°Penicillin V +223°Fructose -92.4 degreesGlucose +52.5 degrees
D-Aldose Tree
Carbohydrates - Stereochemistry
For sugars with more than one chiral center, D or L refers to the asymmetric C farthest from the aldehyde or keto group.
Most naturally occurring sugars are D isomers.
• put most oxidized carbon at top• continue carbon chain to bottom• non-hydrogen substituent on right=D
• The number of stereoisomers is 2n, where n is the number of asymmetric centers.
Optical activity
Racemic solution Meso compound
Simple ketoses
• Ketotetrose• Ketopentose• Ketohexoses: D-fructose
-Fructose helps add to your weight.
-Can cause you to have a chance in getting diabetes.
-Can cause blood clots
-Can damage the liver
-Weakens the immune system
Cyclic sugar structures; Haworth projections
• internal hemiacetal formationan alcohol group adds to the carbonyl
Hemiacetal & hemiketal formation
An aldehyde can react with an alcohol to form a hemiacetal.
A ketone can react with an alcohol to form a hemiketal.
O C
H
R
OH
O C
R
R'
OHC
R
R'
O
aldehyde alcohol hemiacetal
ketone alcohol hemiketal
C
H
R
O R'R' OH
"R OH "R
+
+
Hemiacetal formation (mechanism)
Cyclization of glucose produces a new asymmetric center at C1. The 2 stereoisomers are called anomers, a & b.
Haworth projections represent the cyclic sugars as having essentially planar rings, with the OH at the anomeric C1:
a (OH below the ring) b (OH above the ring).
H O
OH
H
OHH
OH
CH2OH
H
-D-glucose
OH
H H O
OH
H
OHH
OH
CH2OH
H
H
OH
-D-glucose
23
4
5
6
1 1
6
5
4
3 2
furanose: a 5-membered ring pyranose: a 6-membered ring
Because of the tetrahedral nature of carbon bonds, pyranose sugars actually assume a "chair" or "boat" configuration, depending on the sugar.
The representation above reflects the chair configuration of the glucopyranose ring more accurately than the Haworth projection.
O
H
HO
H
HO
H
OH
OHHH
OH
O
H
HO
H
HO
H
H
OHHOH
OH
-D-glucopyranose -D-glucopyranose
1
6
5
4
32
β-D-Glucopyranose = +19α-D-Glucopyranose = +112At equilibrium = +52°
Mutarotation of glucose
• the two stereoisomers at the hemiacetal (anomeric) carbon
• alpha anomer: OH group is down (Haworth)
• beta anomer: OH group is up (Haworth)anomers are diastereomers (different physical properties)
Fructose forms eithera 6-member pyranose ring, by reaction of the C2 keto group with the OH on C6, ora 5-member furanose ring, by reaction of the C2 keto group with the OH on C5.
CH2OH
C O
C HHO
C OHH
C OHH
CH2OH
HOH2C
OH
CH2OH
HOH H
H HO
O
1
6
5
4
3
2
6
5
4 3
2
1
D-fructose (linear) -D-fructofuranose
GlycosylationGlycosidic bond• a glycosidic bond is a type ofcovalent bond that joins a carbohydrate (sugar) molecule to another group, which may or may not be another carbohydrate
Methyl α-D-glucopyranoside
O-glycoside
N-glycoside
Glycosylation of hemoglobin
Sugar derivatives
sugar alcohol - lacks an aldehyde or ketone; e.g., ribitol.sugar acid - the aldehyde at C1, or OH at C6, is oxidized to a carboxylic acid; e.g., gluconic acid, glucuronic acid.
CH2OH
C
C
C
CH2OH
H OH
H OH
H OH
D-ribitol
COOH
C
C
C
C
H OH
HO H
H OH
D-gluconic acid D-glucuronic acid
CH2OH
OHH
CHO
C
C
C
C
H OH
HO H
H OH
COOH
OHH
Sugar derivatives
Reduction of Aldehyde or ketone
Oxidation of alcohol at C-6
Oxidation of aldehyde group
Oxidation at both ends
Deoxy sugars
L-Rhamnose
Amino sugars
amino sugar - an amino group substitutes for a hydroxyl. An example is glucosamine. The amino group may be acetylated, as in N-acetylglucosamine.
H O
OH
H
OH
H
NH2H
OH
CH2OH
H
-D-glucosamine
H O
OH
H
OH
H
NH
OH
CH2OH
H
-D-N-acetylglucosamine
C CH3
O
H
N-acetylneuraminate (N-acetylneuraminic acid, also called sialic acid) is often found as a terminal residue of oligosaccharide chains of glycoproteins.
Sialic acid imparts negative charge to glycoproteins, because its carboxyl group tends to dissociate a proton at physiological pH, as shown here.
NH O
H
COO
OH
H
HOH
H
H
RCH3C
O
HC
HC
CH2OH
OH
OH
N-acetylneuraminate (sialic acid)
R =
Sialic acid
• Metastatic cancer cells often express a high density of sialic acid-rich glycoproteins. This overexpression of sialic acid on surfaces creates a negative charge on cell membranes. This creates repulsion between cells (cell opposition) and helps these late-stage cancer cells enter the blood stream.
Phosphate ester derivative
Sulfate esters
D-Galactose 4-sulfate sodium salt
Glycosaminoglycans (GAGs) or MucopolysaccharidesHeteropolysaccharides
• long unbranched heteropolysaccharides• Consist of a repeating disaccharide unit• Repeating disaccharide unit = a hexose (or hexouronic acid linked to a hexosamine.
• In the Golgi apparatus, GAG disaccharides are added to protein cores to yield proteoglycans except hyaluronan
Hyaluronic acid
1T3 glycosidic bonds in b configuration
The repeating disaccharides are linked by 1T4 linkages in b
configuration
IdoUAβ1-3'GalNAcβ1-4
-Gal(6S)β1-4GlcNAc(6S)β1-3
GlcUAβ1-3'GalNAcβ1-4
Chondroitin Sulfate
GlcUAβ1-3'GalNAcβ1-4
D-glucuronic acid (GlcA) and N-acetyl-D-galactosamine (GalNAc).
Types of chondroitin sulfate
"Chondroitin sulfate B" is an old name for dermatan sulfate, and it is no longer classified as a form
of chondroitin sulfate.
Dermatan sulfate• Dermatan sulfate is a glycosaminoglycan• Distinguished from chondroitin sulfate by the presence of iduronic
acid• It was called a mucopolysaccharide• Is found mostly in skin, also in blood vessels, heart valves, tendons,
and lungs• May have roles in coagulation, cardiovascular disease,
carcinogenesis, infection, wound repair, and fibrosis
IdoUAβ1-3'GalNAcβ1-4
Keratan sulfate• Keratan sulfate (KS), also called keratosulfate• any of several glycosaminoglycans (structural carbohydrates) that have
been found in the cornea, cartilage, and bones• It is also synthesized in the central nervous system • Participate both in development and in the glial scar formation after
injury• Are highly hydrated molecules which in joints can act as a cushion to
absorb mechanical shock• The basic repeating disaccharide unit within keratan sulfate is -3Galβ1-
4GlcNAcβ1-• Keratan sulfate occurs as aproteoglycan (PG) in which the chains are
attached to cell-surface proteoglycan (PG) in which KS chains are attached to extracellular matrix proteins, termed core proteins
-Gal(6S)β1-4GlcNAc(6S)β1-3
Heparin
• a highly sulfated glycosaminoglycan
• widely used as an injectable anticoagulant
• Highest negative charged density of any known biological molecule
• One unit of heparin (the "Howell Unit") is an amount approximately equivalent to 0.002 mg of pure heparin, which is the quantity required to keep 1 mL of cat's blood fluid for 24 hours at 0 °C
-IdoUA(2S)α1-4GlcNS(6S)α1-
Proteoglycan
Cellulose