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CH2210 An Introduction
to the Study of Biomolecules The Monomers
Factors to Consider in the Study of Biomolecules
What are the features of the basic building blocks ? (ex: monosaccharides, alcohols, fatty acids, amino acids)
1) General structure and functional groups 2) Polar and non-polar portions
3) Hydrogen bonding capabilities
4) Acid-Base properties
5) Optical activity
6) Other chemical properties
Factors to Consider in the Study of Biomolecules
Do the small building blocks function by themselves ?
Are the building blocks put together into larger structures ?
What are the physical properties of these larger structures ?
How are the various types of biomolecules suited for their individual functions ?
Amylase Serum albumin
Insulin Collagen
Myosin Immunoglobulins
Myoglobin
Introduction to the Study of Proteins
Introduction to the Study of Proteins
Storage proteins: Provide a reservoir of nitrogen and other nutrients, especially when external sources are low or absent.
Proteins - the most plentiful organic compounds in the body, making up more than half its dry weight
Proteins can be categorized by function.
Catalytic proteins, or enzymes: Catalyze the synthesis and utilization of proteins, carbohydrates, lipids, nucleic acids, and almost all other biomolecules.
Transport proteins: Bind and carry specific molecules from place to place.
Structural proteins: Give physical shape, and the strength to maintain it, to structures in animals.
Regulatory proteins: Control cellular activity.
Contractile proteins: Provide cells and organisms with the ability to change shape and move.
Protective proteins: Defend against invaders and prevent or minimize damage after injury.
Proteins ----------------------------> Amino AcidsHydrolysis
Mammals require all 20 amino acids for protein synthesis but can synthesize only 10 of them.
There are 10 essential amino acids that must be obtained from the diet.
Phenylalanine, Valine, Tryptophan, Threonine, Isoleucine, Methionine, Histidine, Arginine, Lysine, Leucine
Proteins are Made of α-Amino Acids
Generalized structure of an α-amino acid
R CH C
O
O HNH2
Side chain
alpha carbon
H3N HC
CH3
C
O
NH
CH
CHCH3H3C
C
O
OH H3N
CH
CHCH3H3C
C
O
OH
H3N HC
CH3
C
O
OH
hydrolysis+
Proteins ----------------------------> Amino AcidsHydrolysis
Peptide Bond Formation
H2NCH
C
O
OH
CH3
NCH
C
O
OH
CHH
H
CH3H3C
H2NCH
C
O
CH3
NCH
C
O
OH
CH
H
CH3H3C
+ H2O
How are amino acids joined together ?
Alanine Valine
Alanylvaline (Ala-Val)
The two amino acids are joined through a “dehydration
synthesis” or condensation reaction.
peptide bond
Peptides
α-Amino Acids
R
C
CO O H
H2N
Side chain
alpha carbon H
An α-amino acid An ε-amino acid
*
An α-amino acid
R
H2N C
H
COOH
R
H2N CH2 COOHCH2 CH2 CH2 CH2
R
⍺ amino acids are usually drawn in their “zwitterionic form.”
R
-
+
C
C
R
H2N H
O OH
C
C
R
H3N H
O O
Non-polar, Neutral Side Chains
Polar, Neutral Side Chains
Basic Side Chains
Acidic Side Chains
The amino acids are categorized chemically by the behavior of their
R-groups.
R
-
+
Amino Acids with Nonpolar, Uncharged Side Chains
Amino Acids with Polar, Uncharged Side Chains
Amino Acids with Polar, Charged Side Chains
Charges on Amino Acidsα-Amino Acids May Exist in a Zwitterionic Form
The actual structure of a neutral amino acid in neutral solution and in the solid is a charged molecule, containing a -COO- group and an –NH3+ group, called a zwitterion. The net charge on the molecule is zero.
The presence of the charged groups in the zwitterion result in very strong secondary forces between the positive and negative charges:
MP = 314°C
MP = 53°C
R
CH C
O
O H
H2N
R
CH C
O
O
H3N
Uncharged (nonexistent)
Zwitterion (solid and in solution)
1) Amino acids are also soluble in water due to the strong secondary forces between the zwitterionic charge centers of the amino acids and the dipolar water molecules.
2) Free amino acids exist exclusively in the zwitterionic form in the solid state.
3) In solution, amino acids assume a charged form based on the pH of the solution.
Amino Acids in Solution
+ -
How do carboxylic acids and amines behave in acidic, neutral, and basic solutions ?
R C OH
O
R C O
O
R C O
O
pH =1 pH = 7 pH = 12
R NH2R NH3R NH3
Amino Acids in Solution
The behavior of the carboxylic acid and amine functional groups DOES NOT CHANGE when they are in the same molecule.
Amino Acids in Solution
CH C OH
O
CH3
NH3
CH C O
O
CH3
NH3
CH C O
O
CH3
NH2
pH =1 pH = 7 pH = 12
How does the amino acid alanine behave in acidic, basic, and neutral solutions ?
At low pH, the functional groups have accepted all of the protons possible, and at high pH, the functional groups have
donated all of the protons possible.
CH C OH
O
CH3
NH2
1) Each amino acid has a pH at which almost all of the molecules are present in a neutral form (0 net charge), called the isoelectric point.
2) At a pH below that of the isoelectric point, the cation concentration increases (net positive charge).
3) At a pH above that of the isoelectric point, the anion concentration increases (net negative charge).
4) Most neutral amino acids have isoelectric points in the range 5 - 6.
5) “Neutral” amino acids include 15 of the 20 common amino acids.
Amino Acids in Solution
CH C OH
O
CH3
NH3
CH C O
O
CH3
NH3
CH C O
O
CH3
NH2
pH =1 pH = 7 pH = 12
Alanine as an Example
pH = 6
Amino Acids in Solution
Compounds with the ability to both release protons (acids) and absorb protons (bases) are called
amphoteric compounds*.
Amino acids are least soluble in their zwitterionic form, although even this form is fairly soluble.
*Is there a common chemical application for such compounds??
Carbohydrates Introduction
A. Polyhydroxy Aldehydes or Ketones
B. Serve a variety of functions
1. Energy storage (Glucose, Glycogen, Starch) 2. Structural Support (Cellulose, Chitin) 3. Biochemical Control (DNA, Glycoproteins)
C. “Hydrates of Carbon” - General formula: Cn(H2O)n, n=1,2,3....
D. “Saccharides” - from Latin saccharum (sugar)
1. Monosaccharides - “simple” sugars 2. Disaccharides, trisaccharides, tetrasaccharides,... 3. Oligosaccharides 4. Polysaccharides
Carbohydrates - General Description
CARBON CHAIN C
OHO OH
HO OH CARBON CHAIN
OH OH
HO OH
CARBON CHAIN C
O
H
HO OH
HO OH
Carbohydrates - General Nomenclature
A. “-OSE” ending - Glucose, Galactose, Sucrose, Cellulose
B. Classification by Number of Carbons
1. C3H6O3 - Tri + ose = Triose 2. C4H8O4 - Tetra + ose = Tetrose 3. C5H10O5 - Penta + ose = Pentose
C. Classification by Functional Groups
1. Aldoses contain the aldehyde functional group. 2. Ketoses contain the ketone functional group.
D. Combining “A”, “B”, and “C”
an aldopentose a ketohexose
HO
H2C
HCCH
HCC
O
HOH
OH
OH
H2CCH H
CC H
CCH2
O OH
OHOH
OH
OH
A. Simple Monosaccharide Structures
D-Glyceraldehyde Dihydroxyacetone (A simple aldose) (A simple ketose)
B. Note: Glyceraldehyde exists in two “enantiomeric” forms
Carbohydrates - Simple Structures
“D”
HOOHH OH
CHO
CH2OH
A. Simple Monosaccharide Structures
D-Glyceraldehyde Dihydroxyacetone (A simple aldose) (A simple ketose)
B. Note: Glyceraldehyde exists in two “enantiomeric” forms
Carbohydrates - Simple Structures
“D” “L”
Stereochemistry - “Handedness” in Organic Compounds
Enantiomers - compounds that have the following characteristics:
1) Molecules of two compounds are mirror images of each other.
2) Molecules of two compounds are nonsuperimposable.
The characteristics of enantiomers are often the
result of a single “chiral” carbon atom.
Chirality and Optical Activity
Chiral compounds exhibit a property called optical activity and are said to be optically active.
Achiral molecules are optically inactive.
Optical activity is the ability of a compound to rotate the plane of plane-polarized light.
Chirality and Optical Activity
A chiral compound rotates the plane of plane-polarized light.
Chirality and Optical Activity
A sample tube containing an optically active compound is placed between the observer
and plane-polarized light.
An analyzing filter allows the observer to quantitate
the degree to which the plane-polarized light is
rotated.
Optical Activity - The Polarimeter
Optical Activity of Enantiomers
Optical activity is the only property that distinguishes one enantiomer from the other. All other properties (MP, BP, solubility, etc.) are the same.
D-Lactic Acid L-Lactic Acid
m.p. 53 oC m.p. 53 oC
Very soluble in water Very soluble in water
[α] = - 2.6 o [α] = +2.6 o
Naming Chiral Compounds
1) The two enantiomers of a pair of enantiomers rotate the plane of plane-polarized light the same number of degrees but in opposite directions.
2) Rotation in the clockwise direction is called dextrorotatory (“+”) and in the anticlockwise direction, levorotary (“-”).
3)“D-” and “L-” are not directly related to (+) and (-), but are designations developed in carbohydrate chemistry to indicate a certain relationship between hydroxy groups.
4) When both the configuration and the optical rotation are known for a compound, both are indicated in the name:
D-(+)-glyceraldehyde D-(-)-fructose
5) “R-” and “S-” designate specific relationship between atoms attached to a “chiral” carbon atom and are based on priority rules discussed in more detail in you text.
Carbohydrates - Simple Structures
Important Aldopentoses
C
C
C
OHH
OHH
C
CH2OH
OHH
O HC
C
C
HH
OHH
C
CH2OH
OHH
O H
D-ribose 2-deoxy-D-ribose
Glucose and Galactose are epimers
Important Aldohexoses
D-glucose D-galactose
C
C
C
OHH
HHO
C
C
HHO
O H
CH2OH
OHH
C
C
C
OHH
HHO
C
C
OHH
O H
CH2OH
OHH
Carbohydrates - Simple Structures
An Important Ketohexose
D-fructose
CH2OH
C
C
O
HHO
C
C
OHH
CH2OH
OHH D-glucoseD-fructose
Comparison of the structures of D-fructose and D-glucose
CH2OH
C
C
O
HHO
C
C
OHH
CH2OH
OHH
C
C
C
OHH
HHO
C
C
OHH
O H
CH2OH
OHH
Carbohydrates - Simple Structures
How to remember them
D-galactoseD-glucose
CHO
CH2OH
OHH
HHO
OHH
OHH
D-fructose
CH2OH
C
C
O
HHO
C
C
OHH
CH2OH
OHH
C
C
C
OHH
HHO
C
C
OHH
O H
CH2OH
OHH
D-glucose
C
C
C
OHH
HHO
C
C
OHH
O H
CH2OH
OHH
D-glucose
C
C
C
OHH
HHO
C
C
HHO
O H
CH2OH
OHH
1
2
3
4
5
6
Emil Fischer (1852-1919)
1902 Nobel Prize
in Chemistry
Fischer Projections
H3C
H3CH2C
H
Cl
H
BrOH
CH3
CH3
ClH
BrH
CH3HO
CH2CH3
CH3
ClH
BrH
CH3HO
CH2CH3
CHO
C
C
C
C
CH2OH
OH
OH
OH
OH
H
H
H
H
CHO
C
C
C
C
CH2OH
HO
OH
OH
OH
H
H
H
H
CHO
C
C
C
C
CH2OH
OH
HO
OH
OH
H
H
H
H
CHO
C
C
C
C
CH2OH
HO
HO
OH
OH
H
H
H
H
CHO
C
C
C
C
CH2OH
OH
OH
OH
H
H
H
H
HO
CHO
C
C
C
C
CH2OH
HO
OH
OH
H
H
H
H
HO
CHO
C
C
C
C
CH2OH
OH
HO
HO
OH
H
H
H
H
CHO
C
C
C
C
CH2OH
HO
HO
HO
OH
H
H
H
H
CHO
C
C
CH2OH
HO
OH
H
H
CHO
C
C
CH2OH
OH
OH
H
H
CHO
C
CH2OH
OHH
Absolute Configurations of the D-Aldoses
D-allose D-altrose D-glucose D-mannose D-gulose D-idose D-galactose D-talose
D-ribose D-arabinose D-xylose D-lyxose
D-erythrose D-threoseD-glyceraldehyde
CHO
C
C
C
CH2OH
OH
OH
OH
H
H
H
CHO
C
C
C
CH2OH
HO
OH
OH
H
H
H
CHO
C
C
C
CH2OH
OH
HO
OH
H
H
H
CHO
C
C
C
CH2OH
HO
HO
OH
H
H
H
Introduction to the Study of Lipids
Lipids
Classification of a compound as a lipid is based on its solubility behavior rather than the
presence of a common functional group.
Lipids are compounds which dissolve in nonpolar or low
polarity solvents such as toluene, dioxane, or carbon tetrachloride.
Lipids
Note:
Other than triacylglycerols, most lipids are actually amphipathic:
One part of the molecule is hydrophobic. One part of the molecule is hydrophilic.
However, the hydrophobic part of a lipid molecule is usually much larger than the hydrophilic part. Therefore,
most lipids are insoluble (or very slightly soluble) in water.
Varieties of Lipids
• Triacylglycerols—animal fats and plant oils— sources of energy and a storage form of energy not required for immediate use.
• Glycerophospholipids, sphingolipids, and cholesterol are the primary structural components of the membranes that surround all cells and organelles.
• Steroid hormones and other hormone-like lipids act as chemical messengers, initiating or altering activity in specific target cells.
• The lipid-soluble (fat-soluble) vitamins - required for a variety of physiological functions.
• Bile salts - needed for the digestion of lipids in the intestinal tract.
Classification of Lipids
Hydrolyzable Lipids
Non-Hydrolyzable Lipids
Contain one or more straight chain fatty acids connected to
another structure through ester, amide, or glycoside linkages.
Do not contain hydrolyzable linkages.
Classification of Lipids
Hydrolyzable lipids generally contain “Fatty Acids” as
part of their structure.
Fatty Acids
carboxylic acid functional group
long hydrocarbon
chain
RC
O
OH
Fatty Acids
CO
ONa+
Biologically Important Fatty Acids
Fatty acids may be saturated or unsaturated:
Saturated fatty acids: contain no C=C bonds. Palmitic (C-16) and stearic (C-18) acids are the most common.
Unsaturated fatty acids: contain one or more C=C bonds
(Almost all naturally occurring unsaturated fatty acids contain cis double bonds.)
(monounsaturated and polyunsaturated fatty acids).
Oleic (C-18, one C=C) - the most common.
Linoleic and linolenic acids - essential fatty acids for animals Synthesized only by plants. They must be supplied in the diet.
(The position of the double bonds in unsaturated fatty acids is sometimes indicated by an omega number (ω-). The ω-1 carbon is the methyl group farthest from the carbonyl carbon.) Linoleic and linolenic acids are ω-6 and ω-3 fatty acids.
COOH
COOH
COOH
COOH
COOH
COOH
COOH
COOH
COOH
COOH
COOH
Number of Carbons
Common Name
Systematic Name StructureMelting Point ºC
12 lauric dodecanoic 44
14 myristic tetradecanoic 58
16 palmitic hexadecanoic 63
18 stearic octadecanoic 69
20 arachidic eicosanoic 77
16 palmitoleic hexadecenoic 0
18 oleic octadecenoic 13
18 linolenic octadecadienoic -5
18 linolenic octadecatrienoic -11
20 arachidonic eicosatetraenoic -50
20 EPA eicosapentaenoic -50
Fatty Acids - Physical Properties
Fatty Acids - Structures
bp 69º bp 13º
bp -5º bp -11º
Waxes
Most waxes are fatty acid esters with long chain alcohols having only one –OH group.
The alcohols in waxes usually contain an even number of carbon atoms ranging from 14 to 36.
Beeswax Carnauba wax
Lanolins:
OCH3-(CH2)n-C-O
OCH3-(CH2)24-C-O-(CH2)29-CH3
OCH3-(CH2)14-C-O-(CH2)29-CH3
Triacylglycerols (Triglycerides)
Make up about 90% of our dietary lipid intake.
Animal Fats, Fish oils, Plant Oils
Triacylglycerols are triesters of glycerol:
hydrolyzable
Naturally occurring triacylglycerols contain a variety of fatty acid components. Any fat or oil is a mixture of many different triacylglycerols, few of which are “simple” (R1=R2=R3).
The percentage of unsaturated fatty acids varies with the source:
Animal sources other than fish: 40-60% Fish (high percentage of polyunsaturation): 75-80% Plant sources: 85-90%
Triacylglycerols Defined by Their “R” Groups
Triacylglycerols - Fatty Acid Composition
Triacylglycerols - Physical Properties
Triacylglycerols - Chemical Properties
Hydrolysis
Acidic Conditions
Basic Conditions
+
+
+-
-
-
Saponification “soap” synthesis
Triacylglycerols - Chemical PropertiesReduction
H2C
HC
H2C
O
O
O
O
O
O
H2C
HC
H2C
O
O
O
O
O
O
H2, Ni, heat, pressureHydrogenation of one or more double bonds
Unsaturated oil—————>More saturated fat
Corn oil—————>Solid Crisco
Triacylglycerols - Catalytic Hydrogenation
Catalytic hydrogenation - the addition of H2 to alkene double bonds in the presence of a metal catalyst (Ni or Pt).
This process is the basis for the conversion of plant oils into margarine and other products.
Some but not all of the double bonds in vegetable oils are hydrogenated in order to convert them into more solid, more
palatable forms.
Effectively, one can adjust the melting point of any lipid component of a food!!!
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