Download Molekul - Universiti Kebangsaan Malaysia

FUNDAMENTALS OF
MOLECULAR BIOLOGY
• Introduction
-Molecular Biology, Cell, Molecule, Chemical
Bonding
• Macromolecule
-Class
-Chemical structure
-Forms
• Important techniques in macromolecule study:
centrifugation, electrophoresis, electron
microscopy
MOLECULAR BIOLOGY
• Study on the molecular level about the
fundamentals of life
• Study from the biochemical view and
molecular structure of molecules such as
DNA, RNA, protein and the function of
compartments in living cells
• The knowledge in molecular biology
enables manipulations to be done for
example in biotechnology
• Implications: CGAT, BioValley, Human
Genome Project
CELL
• Living cells are made up of small molecules
and macromolecule that are formed from 4
fundamental elements:
C (carbon)
H (hydrogen)
O (oxygen)
N (nitrogen)
P (phosphorus) and others
CHEMICAL BONDS
- weak bonds (non covalent)
Hydrogen bond, Van der Waals interaction,
hydrophobic interaction, ionic bonding (in
aqueous solution)
- strong bonds
covalent bond, ionic bonding (in the
absence of water), peptide bond
CHEMICAL BONDS
Weak bonds
-Hydrogen bond-e.g..water (H2O)
CHEMICAL BONDS
Weak bonds
-Van der Waals interaction: bonds
interaction that results from close contact
between two chemical groups
CHEMICAL BONDS
No covalent bonds (weak)
-hydrophobic interaction: the non-polar
groups such as hydrocarbon chains pulling
each other in aqueous condition
(analogy-oil in water)
CHEMICAL BONDS
• Strong bonds: Covalent bonds
Principle: Electron sharing
CHEMICAL BONDS
• Strong bonds: Ionic bond
SMALL MOLECULES
• Cell uses 4 forms of small molecules:
- sugar (food molecule/energy)
- fatty acid (cell membrane component/
energy storage)
- amino acid (structure protein and
enzyme)
-nucleotide (nucleic acid subunit )
MACROMOLECULE
• Macromolecule classes
1) Polysaccharides, glycogen,
oligosaccharides
2) Phospholipid, triglyceride, steroid
3) Protein: polypeptide
4) Nucleic Asid : DNA and RNA
NUCLEIC ACID
• WHAT IS NUCLEIC ACID
• BASIC STRUCTURE
• THE DIFFERENCES
BETWEEN DNA DAN RNA
• FUNCTION
WHAT IS NUCLEIC ACID
• DNA- Deoxyribonucleic acid
• RNA- Ribonucleic acid
• Made up of nucleotides containing 3 basic
component:
-Base (Purine and Pirimidine)
-Phosphate
-Sugar :
{-D-Ribose (RNA) or
 -D-Deoxyribose (DNA)
NUCLEOTIDES
OH
H
BASIC STRUCTURE
• Nucleoside = Base + Sugar
Nucleotide = Base + Sugar + Phosphate
BASE
NUCLEOSIDE ABBREVIATION
Adenine
Guanine
Cytosine
Uracil
Thymine
Deoxyadenosin
Deoxyguanosin
Deoxysitidin
Uridine
Deoxythymidine
A
G
C
U
T
BASIC STRUCTURE-BASE
BASIC STRUCTURE CHEMICAL BONDS
• Covalent bond-between P, O, H and C
• N-glycosidic bond- sugar and base
• Phosphodiester bond- 5’C and 3’C of
sugar
• Hydrogen bond- between 2 bases
• Hydrophobic interaction- between 2 base
pairs
CHEMICAL BONDS
COVALENT BOND
N-GLYCOSIDIC BOND
PHOSPHODIESTER BOND
BONDS BETWEEN 2 BASES
DNA CHAIN
Nucleotide sequence is read in the 5’ to 3’ directionSequence- 5’ TGCA 3’
DNA DOUBLE CHAIN
DNA CHAIN VS RNA CHAIN
DNA Chain
RNA Chain
SUGAR
Deoxyribose
Ribose
BASE
A, G, C, T
A, G, C, U
1) 5’ AGCTTGCTT 3’
2) 5’ UCCGAUCTT 3’
NUCLEIC ACID FUNCTION
• Storing genetic information- DNA and RNA
• Components that are involved in protein coding:
mRNA- messenger
rRNA- structure
tRNA- transport
CONCLUSION
• Nucleic acids are DNA and RNA
• Nucleic acids are built up of nucleotide
• Nucleic acid sequences functions in
coding/storing genetic
information
PROTEIN
• Basic molecule is amino acid
H
H2 N
C
COOH
R
R IS ONE OF THE 20 DIFFERENT SIDE CHAINS. AT pH 7,
BOTH AMINO GROUP AND CARBOXYL WILL
BE IONISED
20 AMINO ACIDS
AMINO ACID CLASSES
• NEUTRAL & HYDROPHOBICALA, VAL, LEU, ILE, PRO, TRP, PHE, MET
• NEUTRAL AND POLARGLY, SER, THR, TYR, CYS, ASN, GLN
• ACIDICASP, GLU
• BASICLYS, ARG, HIS
GENETIC CODE
PROTEIN CONFORMATION
• PROTEIN IS ABLE TO FOLD INTO 3
DIMENSION CONFORMATION
• THESE CONFORMATIONS ARE BUILT
FROM SEVERAL STRUCTURAL LEVELS:
PRIMARY STRUCTURE
SECONDARY STRUCTURE
TERTIARY STRUCTURE
MULTIMERIC STRUCTURE
PRIMARY STRUCTURE
• A SERIES OF AMINO ACIDS BOUND IN A
LINEAR FASHION; THE AA SERIES ARE
CODED BY THE GENETIC MATERIAL
• THE BINDING OF 2 AMINO ACIDS (5 TO
4000 aa) IS MADE UP OF AMIDES
(PEPTIDE BOND)
Val
Leu
Ser
Tyr
Pro
Peptide bond
SECONDARY STRUCTURE
• THE PRIMARY STRUCTURE FOLDS INTO
THE SECONDARY STRUCTURE TO FORM
A BACK BONE STRUCTURE
• AMINO ACIDS ARE BONDED NATURALLY
OR WITH THE AID OF OTHER PROTEINS
• -HELIX AND -SHEET/STRAND ARE THE
COMPONENTS OF THIS SECONDARY
STRUCTURE
-HELIX AND -SHEET
-HELIX
• -HELIX IS STABILISED BY THE
HYDROGEN BONDS THAT ARE
FORMED BETWEEN THE C=O
GROUP ON ONE OF THE
PEPTIDE BOND WITH THE NH
GROUP OF ANOTHER PEPTIDE
BOND WHICH IS 4 RESIDUES
AWAY IN THE POLYPEPTIDE
CHAIN
• -HELIX SEGMENTS ARE
USUALLY SHORT
-SHEET
• -SHEET IS STABILISED BY
HYDROGEN BOND BETWEEN
AMINO ACIDS ON THE SAME OR
DIFFERENT POLYPEPTIDE
CHAIN OR BETWEEN THE SAME
POLYPEPTIDE BUT IN A
DIFFERENT DIRECTION
-SHEET
• INVOLVES HYDROGEN
BOND BETWEEN THE
C=O GROUP OF ONE
PEPTIDE BOND AND NH
GROUP OF ANOTHER
PEPTIDE BOND
• CAN BE FORMED WHEN
GLYCINE AND ALANIN
RESIDUES ARE
AVAILABLE
TERTIARY STRUCTURE
• THE 3 DIMENTIONAL ORGANISATION OF
ALL ATOMS IN POLYPEPTIDE CHAIN
INCLUDING THE R GROUP AND
POLIPEPTIDE BACK BONE
• THIS LEVEL IS THE COMPLETE
STRUCTURE FOR PROTEIN WITH ONLY
ONE POLYPEPTIDE CHAIN
MULTIMERIC STRUCTURE
• THE HIGHEST FOLDING LEVEL TO FORM
MULTIMERIC PROTEIN THAT CONTAINS
AGGREGATES OF SEVERAL
POLYPEPTIDE CHAIN
• ALSO KNOWN AS QUARTENARY
STRUCTURE
• POLYPEPTIDE CHAINS THAT FORMS
MULTIMERIC PROTEIN IS KNOWN AS
SUBUNIT PROTEIN
CHEMICAL BONDS OF PROTEIN
• COVALENT BOND-DISULPHIDE BRIDGE
BETWEEN 2 CISTEINE RESIDUES TO
FORM CISTINE
(SECONDARY STRUCTURE)
• NON-KOVALEN BOND:
-IONIC BOND
-HYDROGEN BOND
-HYDROPHOBIC INTERACTION
-VAN DER WAALS INTERACTION
PROTEIN FEATURES