Post on 18-Dec-2015
FUNDAMENTALS OF FUNDAMENTALS OF MOLECULAR BIOLOGYMOLECULAR BIOLOGY
• Introduction
-Molecular Biology, Cell, Molecule, Chemical Bonding
• Macromolecule
-Class
-Chemical structure
-Forms
• Important techniques in macromolecule study: centrifugation, electrophoresis, electron microscopy
MOLECULAR BIOLOGYMOLECULAR 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
CELLCELL
• 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 BONDSCHEMICAL 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 BONDSCHEMICAL BONDSWeak bonds
-Van der Waals interaction: bonds interaction that results from close contact between two chemical groups
CHEMICAL BONDSCHEMICAL 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)
SMALL MOLECULESSMALL 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 )
MACROMOLECULEMACROMOLECULE
• Macromolecule classes
1) Polysaccharides, glycogen,
oligosaccharides
2) Phospholipid, triglyceride, steroid
3) Protein: polypeptide
4) Nucleic Asid : DNA and RNA
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)
BASIC STRUCTURE
• Nucleoside = Base + Sugar
Nucleotide = Base + Sugar + Phosphate
BASE NUCLEOSIDE ABBREVIATION
Adenine Deoxyadenosin AGuanine Deoxyguanosin GCytosine Deoxysitidin CUracil Uridine UThymine Deoxythymidine T
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
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
CONCLUSIONCONCLUSION
• Nucleic acids are
• Nucleic acids are built up of
• Nucleic acid sequences functions in
DNA and RNA
nucleotide
coding/storing genetic information
PROTEINPROTEIN
• Basic molecule is amino acid
H
H2N C COOH
R
R IS ONE OF THE 20 DIFFERENT SIDE CHAINS. AT pH 7, BOTH AMINO GROUP AND CARBOXYL WILL
BE IONISED
AMINO ACID CLASSESAMINO ACID CLASSES
• NEUTRAL & HYDROPHOBIC-
ALA, VAL, LEU, ILE, PRO, TRP, PHE, MET• NEUTRAL AND POLAR-
GLY, SER, THR, TYR, CYS, ASN, GLN• ACIDIC-
ASP, GLU• BASIC-
LYS, ARG, HIS
PROTEIN CONFORMATIONPROTEIN 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 STRUCTUREPRIMARY 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
SECONDARYSECONDARY STRUCTURESTRUCTURE• 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-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-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-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 STRUCTURETERTIARY 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 STRUCTUREMULTIMERIC 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 PROTEINCHEMICAL 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