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 (H 2 O)

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 BASENUCLEOSIDEABBREVIATION AdenineDeoxyadenosinA GuanineDeoxyguanosinG CytosineDeoxysitidinC UracilUridineU ThymineDeoxythymidineT

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

COVALENT BOND N-GLYCOSIDIC BOND PHOSPHODIESTER BOND CHEMICAL BONDS

BONDS BETWEEN 2 BASES

DNA CHAIN Nucleotide sequence is read in the 5’ to 3’ direction- Sequence- 5’ TGCA 3’

DNA DOUBLE CHAIN

DNA CHAIN VS RNA CHAIN DNA Chain RNA Chain SUGAR DeoxyriboseRibose BASEA, G, C, TA, 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 Nucleic acids are built up of Nucleic acid sequences functions in DNA and RNA nucleotide coding/storing genetic information

PROTEIN Basic molecule is amino acid H H 2 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 & 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

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) ValLeu SerTyrPro 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  -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