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 BONDS

Weak bonds

-Hydrogen bond-e.g..water (H2O)

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)

CHEMICAL BONDSCHEMICAL BONDS

• Strong bonds: Covalent bonds

Principle: Electron sharing

CHEMICAL BONDSCHEMICAL BONDS

• Strong bonds: Ionic bond

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

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)

NUCLEOTIDESNUCLEOTIDES

OH

H

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-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 BONDN-GLYCOSIDIC BONDPHOSPHODIESTER BOND

CHEMICAL BONDSCHEMICAL 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 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

20 AMINO ACIDS20 AMINO ACIDS

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

GENETIC CODEGENETIC CODE

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 AND -HELIX AND -SHEET-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-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

PROTEIN FEATURESPROTEIN FEATURES