Biological

Macromolecules
Structure & Function of macromolecules

Nucleic Acids (DNA and RNA)

Proteins
Carbohydrates

Macromolecules
Biotechnology often concerned with
isolation, separation and
manipulation of the macromolecules
contained within living cells.

DNA
RNA
Proteins

Nucleic Acid

Biologically important macromolecules are

polymers of smaller subunits
Created through condensation reactions
Macromolecule

Carbohydrates
Lipids
Proteins
Nucleic acids

Subunit

:
:
:
:

Simple sugars
CH2 units
amino acids
nucleotides

C, O, H, N, P, S and a few other trace elements (Fe, Mg, Mn, Co etc)

1. Nucleic Acids
1a. DNA Deoxyribo nucleic acid
1b. RNA Ribo nucleic acid
DNA and RNA are polymers of nucleotides

DNA is a polymer of dNTP (deoxyribo nucleotides)

RNA is a polymer of rNTP (ribo nucleotides)

1. Nucleic Acids: DNA deoxyribo nucleic acid

Function:
Nucleic acids are linear, unbranched polymers of nucleotides.
Nucleotides are joined by Phosphodiester bond
Nucleotides = Nucleoside + Phosphate

Nucleotides = Base + Sugar + Phosphate

1.

Nucleic Acids: DNA deoxyribo nucleic acid

DNA has four kinds of bases A, T, C, and G

Thymine (T)

Cytosine (C)

Pyrimidines

Adenine (A)

Guanine (G)
Purines

1. Nucleic Acids: DNA deoxyribo nucleic acid

DNA has sugar = Deoxyribose sugar

1.

Nucleic Acids: DNA deoxyribo nucleic acid

Phosphate
group
Nitrogenous
base
Sugar
Phosphate
group

Nitrogenous base
(A, G, C, or T)

Nucleotide
Thymine (T)

Sugar
(deoxyribose)
DNA nucleotide
Polynucleotide

Sugar-phosphate backbone

1.

Nucleic Acids: DNA deoxyribo nucleic acid

Double stranded helix

Hydrogen bond (Base pairs)

Partial chemical structure

Ribbon model

Computer model

Single stand DNA (ssDNA).break H bond

DNA Primary Structure

Backbone (sugar+phophate with
phosphate ester bonds) and base

1. Nucleic Acids: DNA deoxyribo nucleic acid

20 Angstrom

1. Nucleic Acids: DNA deoxyribo nucleic acid

Base paring by Hydrogen bonding :
2 H-bonds : A T
3 H-bonds : C G

1. Nucleic Acids: DNA deoxyribo nucleic acid

DNA strands are antiparallel
5 end

3 end

5end
3 end

1. Nucleic Acids: DNA deoxyribo nucleic acid

DNA sequence (unique)

1
61
121
181
241
301
361
421

atgatgagtg gcacaggaaa cgtttcctcg atgctccaca gctatagcgc caacatacag

cacaacgatg gctctccgga cttggattta ctagaatcag aattactgga tattgctctg
ctcaactctg ggtcctctct gcaagaccct ggtttattga gtctgaacca agagaaaatg
ataacagcag gtactactac accaggtaag gaagatgaag gggagctcag ggatgacatc
gcatctttgc aaggattgct tgatcgacac gttcaatttg gcagaaagct acctctgagg
acgccatacg cgaatccact ggattttatc aacattaacc cgcagtccct tccattgtct
ctagaaatta ttgggttgcc gaaggtttct agggtggaaa ctcagatgaa gctgagtttt
cggattagaa acgcacatgc aagaaaaaac ttctttattc atctgccctc tgattgtata

Because of the base pairing rules (complementary), if we

know nucleotide sequence of one strand we also know what the
other strand is.
Convention is to right from 5 to 3 with 5 on the left.

1. Nucleic Acids: DNA deoxyribo nucleic acid

Transfer of information (coding)

DNA
Reverse
Transcription
(HIV)
RNA

1. Nucleic Acids: DNA deoxyribo nucleic acid

A specific gene specifies/encodes a polypeptide
The DNA is transcribed into RNA, which is translated into the
polypeptide (polypeptide)

DNA

TRANSCRIPTION

DNA
RNA

TRANSLATION

Protein
Figure 10.6A

1. Nucleic Acids: DNA deoxyribo nucleic acid

Gene 1

Gene 3

DNA molecule

Gene 2

DNA strand

TRANSCRIPTION

mRNA
Codon
TRANSLATION

Polypeptide
Amino acid

1. Nucleic Acids: DNA deoxyribo nucleic acid

Everyone's DNA is unique

Unique sequence of DNA base pairs

1. Nucleic Acids: RNA Ribo nucleic acid

RNA is a single stranded nucleic acid

RNA has a slightly different sugar
RNA has U instead of T
Nitrogenous base
(A, G, C, or U)
Phosphate
group

Uracil (U)

Sugar
(ribose)

Base paring (if any)

A=U
G=C

1. Nucleic Acids: RNA Ribo nucleic acid

RNA 3 major types

mRNA (messenger RNA)
tRNA (transfer RNA)
rRNA (ribosomal RNA)

1. Nucleic Acids: RNA Ribo nucleic acid

RNA function

mRNA:
transfers information from DNA to ribosome (site
where proteins are made)
Contains codons

tRNA
decodes genetic code in mRNA,
transfers amino acid from cytoplasm to ribosomes
during protein synthesis.
Contains anticodon and reads codon on mRNA

rRNA-structural component of ribosome

1. Nucleic Acids: RNA Ribo nucleic acid

mRNA contains codons which code for

amino acids.
Codon consists of three bases each.
Each codon encodes for a specific amino acid
Except three stop codons used for termination of
protein synthesis.

 Specific DNA sequences code for specific amino

acids
Transcribed strand

DNA

Transcription

RNA

Start
codon

Polypeptide

Translation

Stop
codon

Figure 10.8B

1. Nucleic Acids: RNA Ribo nucleic acid

Genetic code
The rules by which the
base sequences of
deoxyribonucleic acid
(DNA) are translated into
the amino acid sequences
of proteins.

Consists of 64 codons

Carbohydrates
Carbohydrates Contain the Elements:

Carbon
Hydrogen
Oxygen
They Are Split Into Three Groups Known
As:

Monosaccharides (Monomers)
Disaccharides (Dimers)
Polsaccharides (Polymers)

2. Carbohydrates
All have general formula CnH2nOn
Example C6H12O6 = glucose
Hydrates (H2O) of carbon (CH2O)n

2. Carbohydrates

Functions of carbohydrates in the cell

1. Large cross-linked carbohydrates make up the
rigid cell wall of plants, bacteria, and insects
2. In animal cells carbohydrates on the exterior
surface of the cell serve a recognition and
identification function. [Cell-cell interaction,
Glycolipid or glycoprotein (attached to lipid and
protein molecules in the plasma membrane)]
3. A central function is energy storage (starch in
plants and glycogen in animals) and energy
production (mitochondria: ATP)!

2. Carbohydrates

Cell structure: Cellulose, LPS, Chitin

Cellulose in plant
cell walls

Lipopolysaccharides
(LPS)
in bacterial cell wall

Chitin in
exoskeleton

Types of Carbohydrate
Saccharide is a term derived from the Latin for sugar

Carbohydrates classified according to the number of

saccharide units or sugar molecules they contain.
A monosaccharide contains a single carbohydrate,
over 200 different monosaccharides are known.
(Glucose, Ribose, Fructose)
A disaccharide gives two carbohydrate units on
hydrolysis.
Table sugar (Sucrose = Glucose + Fructose)
Milk sugar (Lactose = Glucose + Galactose)
Brewing industry (Maltose = Glucose + Glucose)
An oligosaccharide gives a "few" carbohydrate
units on hydrolysis, usually 3 to 10.
A polysaccharide gives many carbohydrates on
hydrolysis, examples are starch and cellulose.

Polysaccharide
Polymers of monosaccharides
Linked by glycosidic linkage/bond
Also called complex carbohydrates

Examples:
Cellulose (Cell Wall of plants)
Starch (Energy storage in plants)
Glycogen (Energy storage in animals)
All three are polymers of glucose molecules
Differences in glycosidic bonds, type of glucose
and branching.

Polysaccharides
Cellulose
Most abundant carbohydrate on the planet!
Component of plant cell walls
Enzyme cellulase digest/hydrolysis
Indigestible by humans
Digestible by other mammals like cow. why?
Beta Glucose molecule linked by ( 1- 4)
glycosidic bonds
It is unbranched
Cellulose chains/polymers contain
intermolecular and intramolecular H-bonding
and van der Walls interactions : Rigid structure
Function: Structural component of plant cell wall

Cellulose
Linear chains of glucose

b 1-4 glycosidic bond (OH on C1 above the plane)

Polysaccharides can be linked to other

molecules to form glyco-proteins and
glyco-lipids

Glycoproteins
Some examples

Polysaccharide component of antibodies has major

effect on antibody function

Polysaccharides attached to proteins on surface of

red blood cells (RBC) determine blood type (A,B,O)

Polysaccharides are attached to proteins in the

Golgi apparatus process called glycosylation

Proteins

Polymers of amino acids

Animo acid joined by peptide bonds
Therefore also called polypeptide
20 amino acids
The large number of amino acids allows huge
diversity in amino acid sequence
N = # of amino acids in a protein
N20 = # of possible combinations

Proteins play key roles in a living system

Three examples of protein
functions
Catalysis (Biocatalyst):
Almost all biochemical
reactions in a living cell are
catalyzed by protein
enzymes.
Transport:
Some proteins transports
various substances, such
as oxygen, ions, and so on.
Information transfer:
For example, hormones.

Alcohol
dehydrogenase
oxidizes alcohols
to aldehydes or
ketones

Haemoglobin
carries oxygen

Insulin controls
the amount of
sugar in the
blood

Protein Functions
Some more examples

Structure- form structural components of the cell including:

Cell membrane, Cytoskeleton
Lamins, collagen, keratin.

Movement - Muscle contraction, (Eg: actin, myosin)

Body defense (Antibodies are proteins:Y)

Transport-regulate transport of molecules into and out of the

cell / nucleus / organelles.
Channels (integral membrane proteins: Eg ATPase (H+
movement)

Protein

Polymers of 20 amino acids

All amino acids have a Common core

Amino end (N end)
Acid end (C end, carboxy end)
20 different side chains (R)

H
H2N

COOH

General Amino Acid Structure

Amino Acid Structure

Peptide bond between two amino acids

Polypeptide chain nomenclature

Peptide chains are numbered from the N (amino)
terminus to the C (carboxyl) terminus
Example: (N-terminal) Gly-Arg-Phe-Ala-Lys (Cterminal) (or GRFAK)
N-terminus has amino group free
C-terminus has COOH group free

Protein Structure
Four levels of protein structure

Primary Structure
Secondary Structure
Tertiary Structure

Quaternary Structure (sometimes)

Levels of Protein Structure

Primary structure
Is the linear order of amino acids in a protein
AAS DSLVEVHVFIVPPILQAVVSIATTRXD
DXDSAAASIPMVPGWVLKQV GSQAGSFL
AIVMGGGDLEVILILAGYQESSIA

Single letter code for amino acids, (also a three letter code).
Example Glycine (Gly) (G)
R= H

Protein Structure
Secondary Structure
The local conformation of polypeptide.
Common regularly repeating structures in proteins
Two types:
Alpha helix
Beta sheets (two types)
Anti-parallel
Parallel

Secondary structure
-helix

-sheet

Protein Structure
Tertiary structure
Complete 3D structure of protein (single polypeptide)
It describes the shape of the fully folded polypeptide chain

Alpha
Helix

Anti-parallel beta sheet

Parallel beta sheet

Protein Structure
Quaternary structure
Arrangement of two or more polypeptide chains into
multisubunit molecule

Not all proteins have quaternary structure

Only if they are made of multiple polypeptide chains

(a) Hemoglobin

(b) Tetramer schematic

Hierarchical nature of protein structure

Primary structure (Amino acid sequence)

Secondary structure -helix, -sheet

Tertiary structure Three-dimensional structure

formed by assembly of secondary structures

Quaternary structure Structure formed by more

than one polypeptide chains

Three-dimensional structure of
proteins

Tertiary
structure

Quaternary structure

X-ray diffraction and Computational biology