BioMolecules

Carbohydrates
Carbohydrates (glycans) have the following
basic composition: I
(CH2O)n or H - C - OH
I
 Monosaccharides - simple sugars with multiple OH
groups. Based on number of carbons (3, 4, 5, 6), a
monosaccharide is a triose, tetrose, pentose or
hexose.
 Disaccharides - 2 monosaccharides covalently
linked.
 Oligosaccharides - a few monosaccharides
covalently linked.
 Polysaccharides - polymers consisting of chains of
monosaccharide or disaccharide units.
 Monosaccharides

Aldoses (e.g., glucose) have Ketoses (e.g., fructose) have

an aldehyde group at one a keto group, usually at C2.
end.
H O
C CH2OH

H C OH C O

HO C H HO C H

H C OH H C OH

H C OH H C OH

CH2OH CH2OH

D-glucose D-fructose
Preparation of glucose
 Properties of glucose
Reduction

Reax of CHO

Oxid of CHO
Acylation

Oxidation
 Structure of Glucose

Close Structure Open Structure

Fructose
 Disaccharides
1.

2.
3.
 Polysaccharides

Amylose

Amylopectin
Cellulose :
 D vs L Designation

CHO CHO
D & L designations
are based on the H C OH HO C H
configuration about CH2OH CH2OH
the single
asymmetric C in D-glyceraldehyde L-glyceraldehyde
glyceraldehyde. CHO CHO

The lower H C OH HO C H
representations are CH2OH CH2OH
Fischer Projections.
D-glyceraldehyde L-glyceraldehyde
 Sugar Nomenclature

O H O H
For sugars with more C C

than one chiral center,

H – C – OH
HO – C – H
HO – C – H
H – C – OH
D or L refers to the H – C – OH HO – C – H
H – C – OH HO – C – H
asymmetric C farthest CH OH 2 CH2OH

from the aldehyde or -glucose

D L-glucose

keto group.
Most naturally
occurring sugars are D
isomers.
D & L sugars are mirror O H O H
images of one another.
C C
They have the same H – C – OH HO – C – H
name, e.g., D-glucose HO – C – H H – C – OH
& L-glucose.
H – C – OH HO – C – H
Other stereoisomers H – C – OH HO – C – H
have unique names,
CH2OH CH2OH
e.g., glucose, mannose,
galactose, etc. D-glucose L-glucose

The number of stereoisomers is 2n, where n is

the number of asymmetric centers.
The 6-C aldoses have 4 asymmetric centers. Thus
there are 16 stereoisomers (8 D-sugars and 8 L-
sugars).
Hemiacetal & hemiketal formation

H H
An aldehyde
can react with C O + R' OH R' O C OH
an alcohol to R R
form a aldehyde alcohol hemiacetal
hemiacetal.
R R
A ketone can
react with an C O + "R OH "R O C OH
alcohol to form R' R'
a hemiketal. ketone alcohol hemiketal
 CHO
Pentoses and 1

hexoses can H
2
C OH
cyclize as the HO C H D-glucose
ketone or aldehyde 3
H C OH (linear form)
reacts with a 4
distal OH. H C OH
5
Glucose forms an CH2OH
6
intra-molecular
hemiacetal, as the 6 CH2OH 6 CH2OH

C1 aldehyde & H
5 O H H
5 O OH
C5 OH react, to H H
1
4 1 4
form a 6-member OH H OH H

pyranose ring, OH
3 2
OH OH
3 2
H
named after H OH H OH
pyran. -D-glucose -D-glucose

These representations of the cyclic sugars are called

Haworth projections.
 1
CH2OH

2C O

HO C H
1 CH2OH
3 HOH2C 6 O
H C OH
4 5 H HO 2

H C OH H 4 3 OH
5
OH H
6
CH2OH

D-fructose (linear) -D-fructofuranose

Fructose forms either

 a 6-member pyranose ring, by reaction of the C2
keto group with the OH on C6, or
 a 5-member furanose ring, by reaction of the C2
keto group with the OH on C5.
 6 CH2OH 6 CH2OH
5 O 5 O
H H H OH
H H
4 H 1 4 H 1
OH OH
OH OH OH H
3 2 3 2
H OH H OH
-D-glucose -D-glucose

Cyclization of glucose produces a new asymmetric

center at C1. The 2 stereoisomers are called anomers,
 & .
Haworth projections represent the cyclic sugars as
having essentially planar rings, with the OH at the
anomeric C1:
  (OH below the ring)
  (OH above the ring).
 Sugar derivatives
COOH CHO
CH2OH
H C OH H C OH
H C OH
HO C H HO C H
H C OH
H C OH H C OH
H C OH
H C OH H C OH
CH2OH
CH2OH COOH
D-ribitol
D-gluconic acid D-glucuronic acid

 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.
 Glycosidic Bonds
The anomeric hydroxyl and a hydroxyl of another sugar
or some other compound can join together, splitting
out water to form a glycosidic bond:
R-OH + HO-R'  R-O-R' + H2O
E.g., methanol reacts with the anomeric OH on
glucose to form methyl glucoside (methyl-
glucopyranose).

H OH H OH
H O H2 O H O
HO HO
HO H + CH3-OH HO H
H OH H OH
H OH H OCH3
-D-glucopyranose methanol methyl--D-glucopyranose
Disaccharides:
Maltose, a cleavage
product of starch 6 CH2OH 6 CH2OH

5 O 5 O H
(e.g., amylose), is a H
H
H H
H
disaccharide with an 4 OH H 1 4
OH H 1

(1 4) glycosidic OH 3 2
O
3 2
OH

link between C1 - C4 H OH maltose H OH

OH of 2 glucoses.
It is the  anomer
(C1 O points down).
Other disaccharides include:
 Sucrose, common table sugar, has a glycosidic
bond linking the anomeric hydroxyls of glucose &
fructose.
Because the configuration at the anomeric C of
glucose is  (O points down from ring), the
linkage is (12).
The full name of sucrose is -D-glucopyranosyl-
(12)--D-fructopyranose.)
 Lactose, milk sugar, is composed of galactose &
glucose, with (14) linkage from the anomeric
OH of galactose. Its full name is -D-
galactopyranosyl-(1 4)--D-glucopyranose
Disaccharides
 Sucrose is a non reducing sugar composed of alpha D
glucose and beta D fructose.
 Sucrose contain c1 alpha and c2 Beta glycosodic likage
 Maltose is a reducing sugar composed of 2 molecules
alpha D glucose linked by alpha 1,4 glycosodic linkage.
 Lactose is a reducing sugar consisting of Beta D Glucose
and B D Galactose linked by beta 1,4 glycosodic
linkage.
Polysaccharides

 All polysaccharides are non reducing

 CH2OH 6CH OH CH2OH CH2OH CH2OH
2
O 5 O H O H O H H O H
H H H H H
H H H H H
OH H 1 4 OH H 1 OH H OH H OH H
O O O O OH
OH 2
3
H OH H OH H OH H OH H OH
amylose

Polysaccharides:

Plants store glucose as amylose or amylopectin,

glucose polymers collectively called starch.
Glucose storage in polymeric form minimizes
osmotic effects.
Amylose is a glucose polymer with (14) linkages.
The end of the polysaccharide with an anomeric C1
not involved in a glycosidic bond is called the
reducing end.
Amylose is a Polysaccharide

 Amylose is water soluble form(15%) of starch

 It’s a linear polymer of alpha Glucose liked by alpha 1,4 linkage
 CH2OH CH2OH
H O H H O H amylopectin
H H
OH H OH H 1
O
OH
O
H OH H OH

CH2OH CH2OH 6 CH2 CH2OH CH2OH

H O H H O H H 5 O H H O H H O H
H H H H H
OH H OH H OH H 1 4 OH H OH H
4 O O
O O OH
OH
3 2
H OH H OH H OH H OH H OH

Amylopectin is a glucose polymer with mainly (14)

linkages, but it also has branches formed by (16)
linkages. Branches are generally longer than shown
above.
The branches produce a compact structure & provide
multiple chain ends at which enzymatic cleavage can
occur.
Amylopectin is a Polysaccharide

 Amylopectin is water insoluble form(85%) of starch

 It’s a branched polymer of alpha Glucose liked by alpha 1,4 and
alpha 1,6 linkage
 CH2OH CH2OH
H O O
glycogen
H H H
H H
OH H OH H 1
O
OH
O
H OH H OH

CH2OH CH2OH 6 CH2 CH2OH CH2OH

H O H H O H H 5 O H H O H H O H
H H H H H
OH H OH H OH H 1 4 OH H OH H
4 O O
O O OH
OH 2
3
H OH H OH H OH H OH H OH

Glycogen, the glucose storage polymer in animals, is

similar in structure to amylopectin.
But glycogen has more (16) branches.
The highly branched structure permits rapid glucose
release from glycogen stores, e.g., in muscle during
exercise.
The ability to rapidly mobilize glucose is more
essential to animals than to plants.
Glycogen is a Polysaccharide

 glycogen is stored form of glucose in animal and human organ

 It’s a branched polymer of alpha Glucose liked by alpha 1,4 and
alpha 1,6 linkage
 CH2OH 6CH OH CH2OH CH2OH CH2OH
2
O 5 O O H O H O OH
H H H
H H H H H
OH H 1 O 4 OH H 1 O OH H O OH H O OH H
OH H H H
H 2 H
3
H OH H OH H OH H OH H OH
cellulose

Cellulose, a major constituent of plant cell walls,

consists of long linear chains of glucose with (14)
linkages.
Every other glucose is flipped over, due to  linkages.
This promotes intra-chain and inter-chain H-bonds and
.
Cellulose is a Polysaccharide

 Cellulose is structural material of plant cell wall.

 It’s a linear polymer of Beta Glucose liked by Beta 1-4 glycosodic
linkage
Question
Which of the following is D sugars.

A. B.

C. D.
Question
Which of the following is D sugars.

A. B.

C. D.

Ans. (A,C)
 Functions of Proteins
 Structural Collagen; bones, tendons, cartilage
Keratin; hair, skin, wool, nails, feathers
 Movement Myosin & Actin; muscle contractions

 Transport Hemoglobin; transports O2

Lipoproteins; transports lipids
 Storage Casein; in milk. Albumin; in eggs

 Hormone Insulin; regulates blood glucose

Growth hormone; regulates growth
 Protection Immunoglobulins; stimulate immunity
Snake venom; plant toxins;
Sucrase; catalyzes sucrose hydrolysis
 Enzymes Pepsin; catalyzes protein hydrolysis
 16.2 Amino Acids

Amino acids
 Are the building blocks of proteins.
 Contain a carboxylic acid group and an amino group on the alpha ()
carbon.
 Are ionized in solution.
 Each contain a different side group (R).

R R
│ + │
H2N—C —COOH H3N—C —COO−
│ │
H H
ionized form
 16.2 Amino Acids
There are 20 amino acid used by
our body for proper functioning.

 There are 8 essential amino which

can not be synthesized by our body.

 There are 12 amino acid which can

be synthesized by our body they are
non essential amino acid.
Examples of Amino Acids

H
+ │
H3N—C—COO−
│
H glycine

CH3
+ │
H3N—C—COO−
│
H alanine
 Types of Amino Acids

Amino acids are classified as

Nonpolar
 Nonpolar (hydrophobic) with
hydrocarbon side chains.
Polar
 Polar (hydrophilic) with polar or
ionic side chains.
 OH/SH/SR/delocalized
Nitrgen(Tryptophan)/CONH2/PhOH
etc Acidic Basic
 Acidic (hydrophilic) with acidic side
COOH group chains.
 Basic (hydrophilic) with
–NH2 ,Imidazole, Guanidine etc

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 Nonpolar Amino Acids

A nonpolar amino acid has

 An R group that is H, an alkyl group, or aromatic.

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 Polar Amino Acids

A polar amino acid has

 An R group that is an alcohol, thiol, or amide.

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 Acidic and Basic Amino Acids

An amino acid is
 Acidic with a carboxyl R group (COO−).
 Basic with an amino R group (NH3+).

Basic Amino Acids

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Learning Check

Identify each as (P) polar or (NP) nonpolar.

+
A. H3N–CH2–COO− (Glycine)

CH3
|
CH–OH
+ │
B. H3N–CH–COO− (Threonine)
 Solution

Identify each as (P) polar or (NP) nonpolar.

+
A. H3N–CH2–COO− (Glycine) (NP) nonpolar

CH3
|
CH–OH
+ │
B. H3N–CH–COO− (Threonine) (P) polar
Fischer Projections of Amino Acids

Amino acids
 Are chiral except for glycine.
 Have Fischer projections that are stereoisomers.
 That are L are used in proteins.

COOH COOH COOH COOH

H2N H H NH2 H2N H H NH2
CH3 CH3 CH2SH CH2SH

L-alanine D-alanine L-cysteine D-cysteine

Zwitterions and Isoelectric Points

A zwitterion
• Has charged —NH3+ and COO- groups.
• Forms when both the —NH2 and the —COOH groups in an amino acid
ionize in water.
• Has equal + and − charges at the isoelectric point (pI).

O O
║ + ║
NH2—CH2—C—OH H3N—CH2—C—O–
Glycine Zwitterion of glycine
Formation of Peptides

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The Peptide Bond

A peptide bond
 Is an amide bond.
 Forms between the carboxyl group of one amino acid and the amino
group of the next amino acid.

O CH3 O
+ || + | ||
H3N—CH2—C—O– + H3N—CH—C—O–

O H CH3 O
+ || | | ||
H3N—CH2—C—N—CH—C—O– + H2O
peptide bond
 Formation of A Dipeptide

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Learning Check

Write the dipeptide Ser-Thr.

OH CH3
| |
CH2 O HCOH O
+ | ║ + | ║
H3N─CH─C─O – + H3N─CH─C─O–
Ser Thr
Solution

Write the dipeptide Ser-Thr.

OH CH3
| |
CH2 O HCOH O
+ | ║ + | ║
H3N─CH─C─O – + H3N─CH─C─O–
Ser peptide Thr
OH bond CH3
| |
CH2 O H HCOH O
+ | ║ | | ║
NH3─CH─C─N ─CH─C─O + H2O –

Ser-Thr
 Naming Dipeptides

A dipeptide is named with

 N Tterminal is always kept at left and c terminal always at right side.
 A -yl ending for the N-terminal amino acid.
 The full amino acid name of the free carboxyl group (COO-) at the C-
terminal end.

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 Dipeptide has 2 amino acid joined by 1 peptide
linkage
 Decapeptide has 10 amino acid joined by 9 peptide
linkage
Protein Structure: Primary and
Secondary Levels

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 Primary Structure of Proteins

The primary structure of a protein is

 The particular sequence of amino acids.
 The backbone of a peptide chain or protein.

CH3
CH3 S
CH CH3 SH CH2
CH3 O CH O CH2 O CH2 O
H3N CH C N CH C N CH C N CH C O-
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Ala─Leu─Cys─Met
Primary Structures

The nonapeptides oxytocin and vasopressin

 Have similar primary structures.
 Differ only in the amino acids at positions 3 and 8.

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Primary Structure
of Insulin
Insulin
 Was the first protein to have its
primary structure determined.
 Has a primary structure of two
polypeptide chains linked by
disulfide bonds.
 Has a chain A with 21 amino acids
and a chain B with 30 amino acids.

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Secondary Structure – Alpha Helix

The secondary structures of proteins indicate the

three-dimensional spatial arrangements of the
polypeptide chains.

An alpha helix has

 A coiled shape held in place by hydrogen bonds between the amide
groups and the carbonyl groups of the amino acids along the chain.
 Hydrogen bonds between the H of a –N-H group and the O of C=O
of the fourth amino acid down the chain.
Secondary Structure – Alpha Helix

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Secondary Structure – Beta Pleated Sheet

A beta-pleated sheet is a secondary structure that

 Consists of polypeptide chains arranged side by side.
 Has hydrogen bonds between chains.
 Has R groups above and below the sheet.
 Is typical of fibrous proteins such as silk.
Secondary Structure: β-Pleated Sheet

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Protein Structure: Tertiary and
Quaternary Levels

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 Essential Amino Acids

Essential amino acids

 Must be obtained from the TABLE 19.3
diet.
 Are the ten amino acids not
synthesized by the body.
 Are in meat and
diary products.
 Are missing (one or more) in
grains and vegetables.
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Tertiary Structure

The tertiary structure of a protein

 Gives a specific three dimensional shape to the polypeptide chain.
 Involves interactions and cross links between different parts of the
peptide chain.
 Is stabilized by
Hydrophobic and hydrophilic interactions. Salt bridges.
Hydrogen bonds.
Disulfide bonds.
Tertiary Structure

 The interactions of
the R groups give a
protein its specific
three-dimensional
tertiary structure.

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Tertiary Structure

TABLE 19.5
Globular Proteins

Globular proteins Myoglobin

 Have compact, spherical
shapes.
 Carry out synthesis, transport,
and metabolism in the cells.
 Such as myoglobin store and
transport oxygen in muscle.

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 Fibrous Proteins

Fibrous proteins
 Consist of long, fiber-like shapes.
 Such as alpha keratins make up hair, wool, skin, and nails.
 Such as feathers contain beta keratins with large amounts of beta-
pleated sheet structures.

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Quaternary Structure

The quaternary structure

 Is the combination of two or more
hemoglobin
tertiary units.
 Is stabilized by the same interactions
found in tertiary structures.
 Of hemoglobin consists of two alpha
chains and two beta chains. The heme
group in each subunit picks up oxygen for
transport in the blood to the tissues.

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Summary of Protein Structure

TABLE 19.6

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 Summary of Protein Structures

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Protein Hydrolysis and Denaturation

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Protein Hydrolysis

Protein hydrolysis
 Splits the peptide bonds to give smaller peptides and amino acids.
 Occurs in the digestion of proteins.
 Occurs in cells when amino acids are needed to synthesize new
proteins and repair tissues.
Hydrolysis of a Dipeptide

 In the lab, the hydrolysis of a peptide requires acid or base, water

and heat.
 In the body, enzymes catalyze the hydrolysis of proteins.

OH
heat,
CH3 O CH2 O +
+ H2O, H
H3N CH C N CH C OH
H OH
CH3 O CH2 O
+ +
H3N CH COH + H3N CH C OH
Denaturation

Denaturation involves
 The disruption of highly organized tertiary structure of proten is
called denaturation .
 Heat and organic compounds that break apart H bonds and disrupt
hydrophobic interactions.
 Acids and bases that break H bonds between polar R groups and
disrupt ionic bonds.
 Heavy metal ions that react with S-S bonds to form solids.
 Agitation such as whipping that stretches peptide chains until bonds
break.
Applications of Denaturation

Denaturation of protein occurs

when
 An egg is cooked.
 The skin is wiped with alcohol.
 Heat is used to cauterize blood
vessels.
 Instruments are sterilized in
autoclaves.

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1
Carbohydrates In RNA and DNA respectively
DNA 2

DNA stands for deoxyribose nucleic acid

This chemical substance is present in the nucleus

of all cells in all living organisms

DNA controls all the chemical changes which

take place in cells

The kind of cell which is formed, (muscle, blood,

nerve etc) is controlled by DNA

The kind of organism which is produced (buttercup,

giraffe, herring, human etc) is controlled by DNA
DNA molecule 3

DNA is a very large molecule made up of a long

chain of sub-units

The sub-units are called nucleotides

Each nucleotide is made up of

a sugar called deoxyribose

a phosphate group -PO4 and

an organic base
Phosphodiester Linkage : 2 sugar molecule join together by
Phosphodiester Linkage
Ribose & deoxyribose 4

Ribose is a sugar, like glucose, but with only five

carbon atoms in its molecule

Deoxyribose is almost the same but lacks one

oxygen atom

Both molecules may be represented by the symbol

 8

In fact, the DNA usually consists of a double

strand of nucleotides

The sugar-phosphate chains are on the outside

and the strands are held together by chemical
bonds between the bases
replication 16

Before a cell divides, the DNA strands unwind

and separate

Each strand makes a new partner by adding

the appropriate nucleotides

The result is that there are now two double-stranded DNA

molecules in the nucleus

So that when the cell divides, each nucleus

contains identical DNA

This process is called replication

DNA and enzymes 23

The proteins build the cell structures

They also make enzymes

The DNA controls which enzymes are made and

the enzymes determine what reactions take place

The structures and reactions in the cell determine

what sort of a cell it is and what its function is

So DNA exerts its control through the enzymes

Vitamins
Vitamins are classified into two groups depending upon
their solubility in water or fat.

(i) Fat soluble vitamins: Vitamins which are soluble in fat

(ii) and oils but insoluble in water are kept in this group.
(iii) These are vitamins A, D, E and K.
(iv) They are stored in liver and adipose (fat storing) tissues.

(ii) Water soluble vitamins: B group vitamins and vitamin C

are soluble in water so they are grouped together.
Water soluble vitamins must be supplied regularly in diet
because they are readily excreted in urine and cannot be stored
(except vitamin B12) in our body.