BIOLOGICAL

MACROMOLECULES

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 BIOLOGICAL MACROMOLECULES

• DNA

• RNA

• PROTEIN

• CARBOHYDRATE

• SUPRAMOLECULES: GLUCO-PROTEIN, NUCLEO-

PROTEIN, LIPO-PROTEIN

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 DNA, RNA, PROTEIN
• FORMATION

• STRUCTURE

• FUNCTION

• MOLECULAR INTERACTION

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 BIOLOGICAL PROCESSES
v DNA replication

v Transcription

v Translation

v Enzyme-substrate interaction

v Molecular signalling

v Intracellular transport

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v ……..
 DNA: BRIEF HISTORY

1. Miescher (1868): nuclein

2. Frederick Griffith (1928): genetic
material pass through bacterial
generations
3. Rosalind Franklin (1952): X-ray photo
of DNA
4. Watson and Crick (1953): double
helix structure of DNA
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 DNA
• Deoxyribonucleic acid

• Being present in the nucleus of

all organisms. The main
constituent of the chromosome

• DNA controls all cell life activities

• Cell type / type of organism is

regulated by DNA

• Suitable for storing biological

information

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 DNA

• Biological polymer.

• The monomer components

(nucleotides) include: Adenine,
Thymine, Cytosine, Guanine.

• The structure consists of two

complementary strands that
create a double helix structure.

• Monomers bind together with the

phosphodiester bonds.

• The two DNA strands are linked

by hydrogen bonds.

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 Nucleotide composition
• A deoxyribose sugar
• A phosphate group
• A nitrogenous base of purine or pyrimidine

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Nucleotide composition

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 DNA structure
• Links between nucleotides on a DNA strand
àphosphodiester bond

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 DNA structre
• Link between nucleotides on two DNA strands
à hydrogen bond

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 DNA structure
5’ 3’

3’ 5’

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genomic DNA in prokaryote

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Genomic DNA in eukaryote

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DNA denaturation and renaturation

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 RNA
• Ribonucleic acid

• Synthesized from DNA

template

• Presence mainly in cytoplasm

• The role of RNA varies,

including

Ø Transmission of genetic
information
Ø Structure
Ø Transport
Ø Catalysis
Ø Gene regulation
Ø Storing genetic information

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 RNA
• Biological polymer

• The monomer ingredients include adenine, uracil, guanine, cytosine

• Monomers are connected by phosphodiester bonds

• RNA structure is usually a single strand

• This single strand usually has secondary structures because the monomer
components are interconnected

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 Types of RNA
1. mRNA
2. rRNA
3. tRNA
4. snRNA
5. miRNA
6. hnRNA

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 mRNA
• Accounts for 5% of total RNA
• The structure is very diverse in size and
sequence
• Intermediate to carry genetic information from
DNA to protein

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 mRNA
• mRNA is synthesized
from the corresponding
DNA template
• The nucleotide
sequence of mRNA is
complementary to the
nucleotide sequence of
the DNA template
• The nucleotide
sequence of mRNA is
usually presented as a
codon
• A codon consists of 3
nucleotides
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mRNA structure

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rRNA

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tRNA

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 tRNA structure
• tRNA nucleotide
sequence defines the
secondary structure of
tRNA.

• Secondary structure: the

nucleotides are linked by
hydrogen bonds to create
a secondary structure.

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 Secondary structure of tRNA
Includes 5 main parts
called "arm" or "loop" as
follows:
• Acceptor arm
• Anticodon arm
• DHU arm
• TΨC arm
• Extra arm

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 Secondary structure of tRNA
Acceptor arm

• Located at the 3 'end of the RNA

strand.

• There is a final sequence of CCA

that does not pair with mRNA.

• Head 3’OH of Adenine will bind to

the carboxyl group of the amino
acid.

• The tRNA and amino acid complex

is called aminoacyl-tRNA.

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 Secondary structure of tRNA
Anticodon arm

• Located opposite of the arm

acceptor, 5 nucleotides
long.

• Identify the codon on the

mRNA, so its sequence is
complementary to the
mRNA codon.

• Due to supplementation,
hydrogen bonding between
anticodon arm and mRNA
can be formed at the codon
site.

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 Secondary structure of tRNA
DHU arm
• There are 3-4
nucleotides in length.
• A place to recognize
the enzyme aminoacyl-
tRNA synthetase

TΨC arm
• Located opposite DHU
arm.
• Contains pseudo
uridine and is involved
in the binding of tRNA
to ribosome.

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 Secondary structure of tRNA
• Extra arm/variable arm

• 75% tRNA contains extra arm.

• If extra arm has 3-5 nucleotide

size, it belongs to class 1.

• If extra arm has a size of 13-21

nucleotides, it belongs to class 2.

• The extra arm function is not well

understood.

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 Tertiary structure of tRNA
• The tertiary structure of
tRNA is formed by the
additional coiled secondary
structure with the formation
of a hydrogen bond
between the DHU arm and
TΨC arm.

• The tertiary structure of

tRNA helps tRNA bind to
positions P and A on
ribosome.

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 PROTEIN
• Takes up to 15% of the total cell volume

• A macromolecule composed of 1 or
more biological polymers bound
together

• A polymer (polypeptide chain) consists

of monomer connected together. The
monomer is the amino acid.

• There are 20 different types of amino

acid. The amino acids join together in
the polypepide chain with peptide
bonds

• Proteins have a major role in cell / body

activities

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 Roles of protein
• Catalysis
• Structure
• Transport
• Motor
• Signal
• Receptor
• Regulation
• Special functions

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 Amino acid composition
• Is an important organic
compound.

• The structure consists of

an amino group (NH2)
and a carboxylic acid
group (COOH) on both
sides of the carbon base
attached to the subgroup
R.

• R subgroups differ in
different amino acids.

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 Protein structure
• Primary structure

• Secondary structure

• Tertiary structure

• Quaternary structure

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 Primary structure
• Amino acids are joined by
peptide bonds.

• The amino acid sequence

of the primary structure
determines the secondary
structure of the protein

• Polarized amino acids

turn outward, non-polar
amino acids turn inward.

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 Secondary structure
• The polypeptide chain is not in a straight form but is twisted due to
hydrogen bonds between amino acids.

• There are two main twisting structures: alpha helix and beta pleating

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 Tertiary structure
• The alpha helix and beta pleating twisted together to form each
region (domain) specific to each type of protein.
• Domains determine the activity and function of proteins.
• The tertiary structure is formed by various links: disulfur, hydrophilic
bonding, hydrophobic bonding, hydrogen bonding, electrostatic
bonding ...

MIL1 protein B domain kinase C protein 38

 Quaternary structure
• The polypeptide (subunit) chains are linked together by weak bonds
such as hydrogen bonding, electrostatic bonding, ionic bonding.
• Subunites bind together to create an active protein.

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 Protein structures

Primary

Tertiary
Secondary

Quaternary 40
Chemical bonds in the living system
• Chemical bonding: attraction between chemical
components together.

• Linking force: the energy needed to break the bond.

• There are two types of links: covalent bonds and weak

chemical bonds.

• Covalent bond: to bind the component units of a

molecule. Large energy needs to break the bond.

• Weak bonds: bind molecules to form a functional

complex. Small energy needs to break the bonds.
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Chemical bonds in the living system
• Covalent bond

• Hydrogen bond

• Ionic bond

• Hydrophobic bond

• Van de Waals force

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 Roles of weak bonds
• Enzyme-substrate interaction

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 Roles of weak bonds
• The spatial structure of molecules /
macromolecules

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 Roles of weak bonds
• Ensuring connection between
macromolecules

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 Summary of Chemical Interactions
Bond: Covalent Hydrogen Ionic Van der Hydro-
Waals phobic
Energy forces
~3 ~5 ~1 ~3
needed to ~100
break: kcal/mole

Comments: Electrons Water-water; Full charge Fluctuating Not a bond

shared Organic-water; transfer; induced per se;
Organic- Can attract dipole; Entropy
organic H-bond; Close range driven;
Strong in only Only works
Strength crystal in water
class- strong
weak weak weak weak
ification:

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