Biomolecules

There are 4 categories of macromolecules:

Carbohydrates
Proteins,
Lipids,
and Nucleic acids
 Carbon is the central element
• All biomolecules contain a Carbon chain or ring
• Carbon has 4 outer shell electrons (valence = 4)
• Therefore it’s bonding capacity is great
• It forms covalent bonds –hence, has strong bonds
• Once bound to other elements (or to other
Carbons), it is very stable
 CH4 =
Carbon linkages
Propane
• Single chains
• Rings = C3H8

The 4 types of biomolecules often

consist of large carbon chains
 Carbon binds to more than just
hydrogen!!
• To OH groups in sugars
• To NH2 groups in amino
acids
• To H2PO4 groups of
nucleotides of DNA,
RNA, and ATP

Amino acid

OH, NH2, PO4 are called ‘functional groups’!

Fig. 3.1

Functional groups:
 Carbohydrates
• Monosaccharides
• Oligosaccharides
• Polysaccharides
 Monosaccharides
• General formula
Cn(H2O)n
• Divided into aldoses
and ketoses
 Oligosaccharides

Disaccharides Trisaccharides
Sucrose Rhaminose
Lactose Raffinose
Maltose
Cellobiose
 Polysaccharides

Homopolysaccharide Heteropolysaccharide
Starch Hyaluronic acid
Glucogen Chondriotin 4 sulphate
Cellulose Keraton 6 sulphate
Pectin Heparin
Chitin
Insulin
 Isomers have the same molecular
formulas but different structures
• Structural isomer = difference in the C skeleton structure

• Stereoisomer = difference in location of functional groups

• .
 Enantiomers are special types of
stereoisomers
Enantiomers are mirror
images of each other
One such enantiomer
contains C bound to 4
different molecules and is
called a chiral molecule
Chiral molecules rotate
polarized light to the right
(D form) or to the left (L
form) molecules
Examples: amino acids (L
form)
sugars (D form)
 Monomers and polymers
• Monomers are made into polymers via dehydration reactions
• Polymers are broken down into monomers via hydrolysis
reactions
Carbohydrates (or sugars)
• Simple sugars
(monosaccharides)
• Only one 3-C, 5-C, 6-
C chain or ring
involved
Fig. 3.5

Examples of sugar monomers*

*Remember how C’s are counted

within the ring structures (starting
from the right side and counting
clockwise)
Carbohydrates (sugars)

• Double sugars
(disaccharides)
• Two 6-C chains or
rings bonded together
 Disaccharides

Sugar name Components with bond involved

Maltose Glucose alpha (14) Glucose alpha
Cellobiose Glucose beta(14) Glucose alpha

Lactose Galactose beta (14) Glucose alpha

Sucrose Glucose alpha (12) beta fructose

Trehalose Glucose alpha (11) Glucose alpha

 Maltose
• Formed as an
intermediate product
of the amylases on
starch
• Consist of two glucose
molecules which are
joined to each other by
alpha 14 linkage
• Reducing in nature
 Cellobiose

• Formed during the

hydrolysis of cellulose
• Consist of two glucose
molecules with
bets(14) linkage
• Reducing sugar
 Lactose

• Found in milk
• Consist of glucose and
galactose
• Galactose is in beta
form and joined with
beta (14) linkage to
C-4 of glucose
• Reducing in nature
 Sucrose

• Abundant in plant
world
• Consist of glucose and
fructose
• Also known as table
sugar
• Non reducing in
nature
• Does not go under
mutarotation
 Trehalose

• Found in the
hemolymph of many
insects
• Consist of glucose
molecules joined with
alpha (11) linkage
 Polysaccharides
Homopolysaccharide

Starch : Amylose and amylopectin

Glycogen: apha (14) and (16) bonding is present between glucose
molecules
Cellulose : beta (14) linkage is present between glucose molecules
Pectin: alpha (14) linkage is present between galactouronic acid
Chitin: beta (14) linkage between N-acetyl glucosamine
Dextran: alpha (14) , alpha (16), alpha (13), alpha (12) between glucose
molecules
 Starch : Amylose
• Consist of long
unbranched chain of
glucose molecules
connected by alpha
(14) linkage
• Chain varies in
molecular weight from
few thousand to more
than a million
• Not soluble in water
 Amylopectin
• Highly branched
• Chain consist of
glucose molecules
joined by alpha
(14) linkage with
alpha (16)
branching at every 24-
30 residues
• On hydrolysis
releases Glucose and
Maltose
 Glycogen:
• Main storage polysaccharides of animal cell
where as starch in plant cell
• Abundant in liver
• Structure similar to amylopectin but highly
branched
 Cellulose
• Structural polysaccharide of cell wall
• Linear polymer of d-glucose in beta (14) linkage
• Major component of wood and thus paper and cotton
• On complete hydrolysis yeilds d-glucose and partial hydrolysis yeilds
the reducing sugar cellobiose.
• Enzyme capable of digestic cellulose is cellulase which is secreated
by the digestive track of most mammals.
 Pectin
• Component of higher
plants.
• Polysaccharide of
alpha-d-glactoyoronic
acid is linked by alpha
(14) linkages.
• COOH groups of
pectin are either
partially or completely
esterified with methyl
alcohol
 Chitin
• Monomer of N-acetyl glucosamine, having beta
(14) linkage
• Form the linear fiblres and make exoskeleton of
anthropods and also in fungi
 Heteropolysaccharide:
Hyaluronic acid
• Straight chain polymer
of d-glucuronic acid
and N-acetyl d-
glucosamine
alternating chain
• Two linkages are
involved i.e. Beta
(13) and beta (14)
• Found in higher
animalsas component
of various tissues.
 Chondriotin 4 sulphate
• Similar in strutcture to hyaluronic acid axcept it has
N-acetyl galactose amine 4 sulphate in space of N-
acetyl glucosamine.
• Joined by beta (13) linkage
• Contributes to the tensile strength by cartilage,
tendons and ligaments.
 Keratin 6 sulphate
• Consist of d-galactose in place of glucuronic acid.
• Second unit is N-acetyl glucosamine 6 sulphate,
joined by beta(14) linkage however beta(13) is
present between dimeric unit.
• Its present in cartilage, bone, horny structure like
horn, hair, nail.
 Heparin
• Has glucuronic acid
easterified at C-2
which is attached to
N-sulphate.
• Joined by alpha(14)
linkage
• Help in blood
coagulation and
therefore acts as an
anticoagulant.
 Carbohydrates (sugars)
• Complex carbo’s
(polysaccharides)
– Starch
– Cellulose
– Glycogen
– Chitin

Glycogen to glucose
in animals
Fig. 3.9
Polysaccharides
Starch structure vs Glycogen structure
Fig. 3.10

Polysaccharides: Cellulose structure

Proteins
• Composed of chains
of amino acids

• 20 amino acids exist

• Amino acids contain

– Central Carbon
– Amine group
– Carboxyl group
– R group
Fig. 3.20

The 20 Amino Acids

All differ with respect
to their R group
 Non-polar aliphatic
compounds(GAVLIMP)
• 7 amino acids in this category
• These are non-polar and hydrophobic in
nature.
• Although glycine is non-polar but its small
side chain generally makes no contribution
to hydrophobic interaction
Polar amino acids: Aliphatic
Uncharged(SCTAG)
 Polar charged amino acids:
positively and negatively
• Positively charged are called as basic amino
acids.
• These include: Lysine, Arginine, Histidine.
• Negatively charged are called as acidic
amino acids.
• These include: Aspartate and glutamate.
 Peptide bonds occur between amino acids
• The COOH group of 1
amino acid binds to
the NH2 group of
another amino acid

• Forms a peptide bond!

Fig. 3.21

The chain (polymer) of amino acids forms a variety of

loops, coils, and folded sheets from an assortment of
bonds and attractions between amino acids within the
chain(s)
 There are at least 7 functions of proteins

• Enzyme catalysts – specific for 1 reaction

• Defense – antibody proteins, other proteins
• Transport- Hgb, Mgb, transferrins, etc
• Support – keratin, fibrin, collagen
• Motion – actin/myosin, cytoskeletal fibers
• Regulation- some hormones, regulatory proteins
on DNA, cell receptors
• Storage – Ca and Fe attached to storage proteins
There are four levels of protein
structure
• Primary = sequence of
aa’s
• Secondary = forms
pleated sheet, helix, or
coil
• Tertiary = entire
length of aa’s folded
into a shape
• Quaternary = several
aa sequences linked
together
Primary structure of proteins
 Secondary structure of proteins
• Refers to the regular folding pattern of
polypeptide chain.
• The most prominent secondary structures
are alpha-helix, beta sheet and beta turn
Beta-sheet
Fig. 3.23

Motifs and Domains: Important features of 2° and 4°

structure
 Difference between motif and
domain
• Motifs are structural characteristics and domains
are functional regions (not necessarily related to
size). In a protein, a particular arrangement of
amino acids or secondary structure that can be
found in other proteins (not necessarily
evolutionarily related) can be called a motif. If
that particular arrangement is related to some
function (DNA or protein binding, catalytic, etc.)
then it is a domain. For example, the leucine
zipper motif is usually found as part of a
dimerization domain in many transcription factors.
 There are two main classes of protein
tertiary structure

• Fibrous proteins are generally composed

of long and narrow strands and have a
structural role (they are something)
• Globular proteins generally have a more
compact and rounded shape and have
functional roles (they do something)
 Quaternary structure
• When 2 or more polypeptide
chains arrange in space, it is
called as quaternary structure.
• Protein subunits mat be
identical or different.
• Subunits held together by non-
covalent interactions.
• Haemoglobin is a tetrameric
protein containing 4 subunits in
which 2 are similar known as
alpha chains and other two are
called as beta-chains.
Nucleic acids: DNA and RNA

• DNA =
deoxyribonucleic acid
• DNA is a double
polymer (chain)
• Each chain is made of
nucleotides
• The 2 chains bond
together to form a
helix
DNA nucleotides
• Each nucleotide in
DNA contains:
– 5-C sugar
(deoxyribose)
– Phosphate
– Nitrogen base
-adenine (A)
-guanine (G)
-cytosine (C)
-thymine (T)
 Nitrogen bases
These are of two types

Pyrimidine: Purine:

6-membered ring Nine membered ring

Nitrogen present in the ring at 1 and 3 Nitrogen present at 1, 3, 7 and 9

position position in the ring

They are cytosine (C), Thymine (T) and They are Adenine (A) and Guanine (G)
Uracil (U)
Phosphate group
.
Fig. 3.14

One polymer of nucleotides on one “backbone” of nucleic acid

Fig. 3.15

The DNA “double helix”

 Lipids: Hydrophobic molecules
• Biomolecules which are insoluble in water
and soluble in non-polar solvents. For eg.
Ether, benzene and chloroform.
• Structural component of cell membrane.
• Act as metabolic fuel.
• Cell surface components involved in cell-
cell recoginition.
 Fatty acids
• These are caboxylic acid with hydrocarbon
chain bringing from 4 to 36 carbon long.
• If chain is fully saturated then its called as
saturated fatty acids.
• If chain contains double bonds then it is
called as unsaturated fatty acids.
• Fatty acids are stored in the form of
triacylglycerol in the fat cells.
Glycerol and fatty acid chains

•Glycerol formed triacylglycerol by reacting with

3 molecules of RCOOH.
•When energy is required by the body TG is
hydrolysed to release the fatty acids.
 Triacylglycerol
• Fatty acid esters of the alcohol glycerol are
called as acyl glycerol.
• They are called as natural fat.
• Triacylglycerol which are solid at room
temperature are called as fat and those are
liquid are called as oil.
Saturated and unsaturated fats

The difference resides in the number of H’s attached

to C’s in the fatty acid chains; the amount of
“saturation” on the C’s
Saturated vs unsaturated fats and diet
• Saturated fats raise LDL-cholesterol levels in the
blood (animal fats, dairy, coconut oil, cocoa
butter)
• Polyunsaturated fats leave LDL-cholesterol
unchanged; but lower HDL-cholesterol (safflower
and corn oil)
• Monounsaturated fats leave LDL and HDL levels
unchanged (olive oil, canola, peanut oil, avocados)
• One variety of polyunsaturated fat (Omega-3 fatty
acids) guards against blood clot formation and
reduce fat levels in the blood (certain fish,
walnuts, almonds, and tofu)
 Phospholipids and cell membranes
• P-lipids make up the majority of cell
membranes including:
– The plasma membrane
– Nuclear envelope
– Endoplasmic reticulum (ER)
– Golgi apparatus
– Membrane-bound vesicles
Structure of single P-lipid

The 3 C’s of glycerol are bound to:

2 fatty acid chains
phosphate
Cell environment organizes P-lipid
bilayer to proper orientation

Hydrophilic (polar) “heads” of P-lipid oriented to the

exterior; hydrophobic (non-polar) “tails” oriented to
the interior