lecture #13 intro to biomolecules-the monomers-2019-61...

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


The behavior of the carboxylic acid and amine functional groups DOES NOT CHANGE when they are in the same molecule.


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.


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


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


“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.


A chiral compound rotates the plane of plane-polarized light.


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.


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


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


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!!!

lecture #13 intro to biomolecules-the monomers-2019-61...

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