Table of Contents
Advanced Molecular Biology .......................................................................................... 10
INTRODUCTION .............................................................................................................. 10
GENES ................................................................................................................................... 10
MOLECULAR BIOLOGY ............................................................................................................ 10
GENE EXPRESSION ................................................................................................................. 11
THE DIFFERENCES IN THE REGULATION OF GENE EXPRESSION BETWEEN PROKARYOTES AND
EUKARYOTES ......................................................................................................................... 11
THE TRP OPERON REGULATION .............................................................................................. 11
THE LAC REPRESSOR............................................................................................................... 12
TYPES OF VACCINES ............................................................................................................... 13
DIFFERENT VACCINE PLATFORMS IN DEVELOPMENT AGAINST COVID-19 ................................. 13
VACCINE PLATFORMS TECHNOLOGIES .................................................................................... 14
DNA AND RNA VACCINES ....................................................................................................... 14
VIRUS BASED VACCINES ......................................................................................................... 14
RNA VACCINE......................................................................................................................... 15
RNA VACCINE DELIVERY ......................................................................................................... 16
VIRAL VECTOR-BASED VACCINES ............................................................................................ 16
CORONA VIRUS ...................................................................................................................... 16
SARA-COV-2........................................................................................................................... 18
IT CAUSES COVID-19............................................................................................................... 18
GENE THERAPY ...................................................................................................................... 19
THE PROCESS OF INSERTING VECTOR IN GENE THERAPY ......................................................... 20
CAHALLANGES IN GENE THERAPY ........................................................................................... 21
CRISPR-CAS9 .......................................................................................................................... 22
MOLECULAR MECHANISM OF DNA REPLICATION ............................................................ 24
PROKARYOTES VS EUKARYOTES ............................................................................................. 24
CELL ORGANELLES .................................................................................................................. 24
NUCLEUS ............................................................................................................................... 25
RIBOSOME ............................................................................................................................. 26
PROKARYOTIC DNA ................................................................................................................ 27
PLASMIDS .............................................................................................................................. 27
EUKARUOTIC DNA.................................................................................................................. 27
CHROMATIN .......................................................................................................................... 28
1
, HISTONES .............................................................................................................................. 28
NUCLEOSOME ........................................................................................................................ 29
SUPERCOILING IN PROKARYOTIC GENOMS ............................................................................. 29
TOPOISOMERASES ................................................................................................................. 30
CLASSICAL MODELS FOR DNA REPLICATION ............................................................................ 30
THREE IMPORTANT EXPERIMENTS SUPPORT THAT DNA REPLICATION IS SEMI-CONSERVATIVE 31
MESELSON AND STAHL EXPERIMENT PROVED DNA REPLICATES IN A SEMI-CONSERVATIVE
MANNER ............................................................................................................................... 31
PROKARYOTIC DNA REPLICATION ........................................................................................... 31
THREE STAGES OF DNA REPLICATION...................................................................................... 32
DNA POLYMERASE ................................................................................................................. 32
INITIATION................................................................................................................................................... 32
ELONGATION ............................................................................................................................................... 33
REPLICATION FORK ................................................................................................................ 34
TERMINATION ............................................................................................................................................. 34
THE ENZYMES IN PROKARYOTIC DNA REPLICATION ................................................................ 35
SUMMARY OF THE PROCESS OF DNA REPLICATION ................................................................. 35
PROKARYOTES VS EUKARYOTES ............................................................................................. 36
EUKARYOTES DNA REPLICATION............................................................................................. 36
PRE-REPLICATION COMPLEX PROKARYOTES ........................................................................... 37
PRE-REPLICATION COMPLEX (PRE-RC), EUKARYOTIC PRE-RC ................................................... 37
REPLISOME ............................................................................................................................ 37
INITIATION ............................................................................................................................ 38
DIFFERENCE BETWEEN PROKARYOTIC AND EUKARYOTIC DNA REPLICATION............................ 39
SUMMARY OF EUKARYOTIC DNA POLYMERASE FUNCTIONS ................................................... 39
TELOMERES ........................................................................................................................... 40
TELOMERASE ......................................................................................................................... 40
TELOMERE REPLICATION ........................................................................................................ 41
TERMINATION ....................................................................................................................... 41
DNA TRANSCRIPTION, COMPOSITION BETWEEN PROKARUOTES AND EUKARUOTES ........ 43
DNA TRANSCRIPTION ............................................................................................................. 43
NUCLEUS AND NUCLEOTIDES.................................................................................................. 43
FUNCTIONS OF NUCLEOLUS.................................................................................................... 43
PRODUCTS OF RNA POL ......................................................................................................... 44
RNA POLYMERASE ................................................................................................................. 45
TRANSCRIPTION..................................................................................................................... 45
DNA OR RNA STRAND HAS DIRECFTIONALITY ......................................................................... 46
2
,TRANSCRIPTION OF A GENE TAKES PLACE IN THREE STAGES.................................................... 47
INITIATION ............................................................................................................................ 47
TRANSCRIPTION (INITIATION SITE) ......................................................................................... 48
PROMOTER ............................................................................................................................ 48
PROKARYOTIC PROMOTERS ................................................................................................... 49
PROKARYOTIC RNA POLYMERASE........................................................................................... 50
PROKARYOTIC RNA POLYMERASE (RNAP) ............................................................................... 51
FUNCTIONS OF THE SYBUNIT .................................................................................................. 51
SUBUNIT ............................................................................................................................. 51
ELONGATION IN PROKARYOTES ............................................................................................. 51
TWO KINDS OF TERMINATION SIGNALS .................................................................................. 52
RHO FACTOR.......................................................................................................................... 52
RNA-BASED TERMINATION SIGNAL......................................................................................... 53
RHO INDEPENDENT TERMINATION ......................................................................................... 53
BPROTEIN-BASE TERMINATION SIGNALS ................................................................................ 53
RHO DEPENDANT TERMINATION ............................................................................................ 53
EUKARRYOTIC PROMOTERS ................................................................................................... 53
EUKARYOTIC PROMOTERS...................................................................................................... 54
THE PROXIMAL PROMOTER .................................................................................................... 55
DISTAL PROMOTER ................................................................................................................ 55
TARNSCRIPTION FACTOR (TF) ................................................................................................. 56
GENERAL TRANSCRIPTION FACRORS (GTFs) ............................................................................ 56
TRANSCRIPTION INNITIATION COMPLEX................................................................................. 57
GENERAL TYRANSCRIPTION FACTORS (GTFs)........................................................................... 58
CIS-REGULATORY ELEMENTS (CREs) AND TRANS-REGULATORY ELEMENTS (TREs) .................... 59
CIS-REGULATORY ELEMRNTS (CREs)........................................................................................ 59
INSULATOR- CIS-REGULATORY ELEMENT ................................................................................ 59
TRANS-REGULATORY ELEMENTS (TRE) .................................................................................... 60
DIFRERENCE BETWEEN CIS REGULATORY ELEMENTS AND TRANS REGULATORY ELEMENTS ...... 61
THE THREE EUKARYOTIC RNA POLYMERASES (RNAPs)............................................................. 61
THREE RNA POLYMERASES ..................................................................................................... 62
RNA POLYMERASE I ..................................................................................................................................... 62
RNA POLYMERASE II .................................................................................................................................... 62
RNA POLYMERASE III ................................................................................................................................... 62
INITIATION OF TRANSCRIPTION IN EUKARYOTES..................................................................... 62
MEDIATOR............................................................................................................................. 63
ELONGATION ......................................................................................................................... 63
3
, ELONGATION IN EUKARYOTES ................................................................................................ 63
TERMINATION ....................................................................................................................... 64
Transcribed by RNA Polymerase I ........................................................................................... 64
Transcribed by RNA Polymerase II .......................................................................................... 64
TRANSCRIBED BY RNA POLYMERASE III................................................................................... 64
SIMILARITIES BETWEEN PROKARYOTIC AND EUKARYOTIC TRANSCRIPTION ............................. 65
COPARISON OF TRANSCRIPTION IN PROKARYOTES AND EUKARYOTES .................................... 65
RNA PROCESSING AND TRANSLATION COMPARISON BETWEEN PROKARYOTES AND
EUKARYOTES .................................................................................................................. 66
GENE ................................................................................................................................... 66
EUKARYOTIC GENE STRUCTURE .............................................................................................. 67
CISTRON ................................................................................................................................ 67
DIFFERENCE BETWEEN GENE AND CISTRON ............................................................................ 67
MONOCISTRONIC AND POLYCISTRONIC mRNA ....................................................................... 68
KEY DIFFERENCE BETWEEN MONOCISTRONIC AND POLYCISTRONIC mRNA .............................. 68
THE STRUCTURE OF A PROKARYOTIC OPERON OF PROTEIN-CODING GENES ............................ 68
DIFFERENCE BETWEEN MONOCISTRONIC AND POLYCISTRONIC mRNA .................................... 69
INTRONS................................................................................................................................ 69
INTRONS AND EXTRONS ......................................................................................................... 69
INTRON FUNCTION ................................................................................................................ 69
DNA PROCESSING .................................................................................................................. 71
RNA PROCESSING IN EUKARYOTES ......................................................................................... 71
RNA BINDING PROTEINS (RBPs) .............................................................................................. 71
mRNA MODIFICATIONS IN EUKARYOTES................................................................................. 72
5’ CAPPING ............................................................................................................................ 72
POLYADENYLATION................................................................................................................ 73
3’ POLY-A TAIL ....................................................................................................................... 74
PRE-mRNA SPLICING .............................................................................................................. 74
SPLICING................................................................................................................................ 74
ALTERNATIVE SPLICING .......................................................................................................... 75
RIBOSOMES ........................................................................................................................... 75
RIBOSOMAL RNA (rRNA) ........................................................................................................ 76
PROKARYOTIK RIBOSOME ...................................................................................................... 76
EUKARYOTIC RIBOSOME ........................................................................................................ 77
rRNA IN EUKARYOTES ............................................................................................................ 77
rRNA IN PROKARYOTES .......................................................................................................... 77
4
Advanced Molecular Biology .......................................................................................... 10
INTRODUCTION .............................................................................................................. 10
GENES ................................................................................................................................... 10
MOLECULAR BIOLOGY ............................................................................................................ 10
GENE EXPRESSION ................................................................................................................. 11
THE DIFFERENCES IN THE REGULATION OF GENE EXPRESSION BETWEEN PROKARYOTES AND
EUKARYOTES ......................................................................................................................... 11
THE TRP OPERON REGULATION .............................................................................................. 11
THE LAC REPRESSOR............................................................................................................... 12
TYPES OF VACCINES ............................................................................................................... 13
DIFFERENT VACCINE PLATFORMS IN DEVELOPMENT AGAINST COVID-19 ................................. 13
VACCINE PLATFORMS TECHNOLOGIES .................................................................................... 14
DNA AND RNA VACCINES ....................................................................................................... 14
VIRUS BASED VACCINES ......................................................................................................... 14
RNA VACCINE......................................................................................................................... 15
RNA VACCINE DELIVERY ......................................................................................................... 16
VIRAL VECTOR-BASED VACCINES ............................................................................................ 16
CORONA VIRUS ...................................................................................................................... 16
SARA-COV-2........................................................................................................................... 18
IT CAUSES COVID-19............................................................................................................... 18
GENE THERAPY ...................................................................................................................... 19
THE PROCESS OF INSERTING VECTOR IN GENE THERAPY ......................................................... 20
CAHALLANGES IN GENE THERAPY ........................................................................................... 21
CRISPR-CAS9 .......................................................................................................................... 22
MOLECULAR MECHANISM OF DNA REPLICATION ............................................................ 24
PROKARYOTES VS EUKARYOTES ............................................................................................. 24
CELL ORGANELLES .................................................................................................................. 24
NUCLEUS ............................................................................................................................... 25
RIBOSOME ............................................................................................................................. 26
PROKARYOTIC DNA ................................................................................................................ 27
PLASMIDS .............................................................................................................................. 27
EUKARUOTIC DNA.................................................................................................................. 27
CHROMATIN .......................................................................................................................... 28
1
, HISTONES .............................................................................................................................. 28
NUCLEOSOME ........................................................................................................................ 29
SUPERCOILING IN PROKARYOTIC GENOMS ............................................................................. 29
TOPOISOMERASES ................................................................................................................. 30
CLASSICAL MODELS FOR DNA REPLICATION ............................................................................ 30
THREE IMPORTANT EXPERIMENTS SUPPORT THAT DNA REPLICATION IS SEMI-CONSERVATIVE 31
MESELSON AND STAHL EXPERIMENT PROVED DNA REPLICATES IN A SEMI-CONSERVATIVE
MANNER ............................................................................................................................... 31
PROKARYOTIC DNA REPLICATION ........................................................................................... 31
THREE STAGES OF DNA REPLICATION...................................................................................... 32
DNA POLYMERASE ................................................................................................................. 32
INITIATION................................................................................................................................................... 32
ELONGATION ............................................................................................................................................... 33
REPLICATION FORK ................................................................................................................ 34
TERMINATION ............................................................................................................................................. 34
THE ENZYMES IN PROKARYOTIC DNA REPLICATION ................................................................ 35
SUMMARY OF THE PROCESS OF DNA REPLICATION ................................................................. 35
PROKARYOTES VS EUKARYOTES ............................................................................................. 36
EUKARYOTES DNA REPLICATION............................................................................................. 36
PRE-REPLICATION COMPLEX PROKARYOTES ........................................................................... 37
PRE-REPLICATION COMPLEX (PRE-RC), EUKARYOTIC PRE-RC ................................................... 37
REPLISOME ............................................................................................................................ 37
INITIATION ............................................................................................................................ 38
DIFFERENCE BETWEEN PROKARYOTIC AND EUKARYOTIC DNA REPLICATION............................ 39
SUMMARY OF EUKARYOTIC DNA POLYMERASE FUNCTIONS ................................................... 39
TELOMERES ........................................................................................................................... 40
TELOMERASE ......................................................................................................................... 40
TELOMERE REPLICATION ........................................................................................................ 41
TERMINATION ....................................................................................................................... 41
DNA TRANSCRIPTION, COMPOSITION BETWEEN PROKARUOTES AND EUKARUOTES ........ 43
DNA TRANSCRIPTION ............................................................................................................. 43
NUCLEUS AND NUCLEOTIDES.................................................................................................. 43
FUNCTIONS OF NUCLEOLUS.................................................................................................... 43
PRODUCTS OF RNA POL ......................................................................................................... 44
RNA POLYMERASE ................................................................................................................. 45
TRANSCRIPTION..................................................................................................................... 45
DNA OR RNA STRAND HAS DIRECFTIONALITY ......................................................................... 46
2
,TRANSCRIPTION OF A GENE TAKES PLACE IN THREE STAGES.................................................... 47
INITIATION ............................................................................................................................ 47
TRANSCRIPTION (INITIATION SITE) ......................................................................................... 48
PROMOTER ............................................................................................................................ 48
PROKARYOTIC PROMOTERS ................................................................................................... 49
PROKARYOTIC RNA POLYMERASE........................................................................................... 50
PROKARYOTIC RNA POLYMERASE (RNAP) ............................................................................... 51
FUNCTIONS OF THE SYBUNIT .................................................................................................. 51
SUBUNIT ............................................................................................................................. 51
ELONGATION IN PROKARYOTES ............................................................................................. 51
TWO KINDS OF TERMINATION SIGNALS .................................................................................. 52
RHO FACTOR.......................................................................................................................... 52
RNA-BASED TERMINATION SIGNAL......................................................................................... 53
RHO INDEPENDENT TERMINATION ......................................................................................... 53
BPROTEIN-BASE TERMINATION SIGNALS ................................................................................ 53
RHO DEPENDANT TERMINATION ............................................................................................ 53
EUKARRYOTIC PROMOTERS ................................................................................................... 53
EUKARYOTIC PROMOTERS...................................................................................................... 54
THE PROXIMAL PROMOTER .................................................................................................... 55
DISTAL PROMOTER ................................................................................................................ 55
TARNSCRIPTION FACTOR (TF) ................................................................................................. 56
GENERAL TRANSCRIPTION FACRORS (GTFs) ............................................................................ 56
TRANSCRIPTION INNITIATION COMPLEX................................................................................. 57
GENERAL TYRANSCRIPTION FACTORS (GTFs)........................................................................... 58
CIS-REGULATORY ELEMENTS (CREs) AND TRANS-REGULATORY ELEMENTS (TREs) .................... 59
CIS-REGULATORY ELEMRNTS (CREs)........................................................................................ 59
INSULATOR- CIS-REGULATORY ELEMENT ................................................................................ 59
TRANS-REGULATORY ELEMENTS (TRE) .................................................................................... 60
DIFRERENCE BETWEEN CIS REGULATORY ELEMENTS AND TRANS REGULATORY ELEMENTS ...... 61
THE THREE EUKARYOTIC RNA POLYMERASES (RNAPs)............................................................. 61
THREE RNA POLYMERASES ..................................................................................................... 62
RNA POLYMERASE I ..................................................................................................................................... 62
RNA POLYMERASE II .................................................................................................................................... 62
RNA POLYMERASE III ................................................................................................................................... 62
INITIATION OF TRANSCRIPTION IN EUKARYOTES..................................................................... 62
MEDIATOR............................................................................................................................. 63
ELONGATION ......................................................................................................................... 63
3
, ELONGATION IN EUKARYOTES ................................................................................................ 63
TERMINATION ....................................................................................................................... 64
Transcribed by RNA Polymerase I ........................................................................................... 64
Transcribed by RNA Polymerase II .......................................................................................... 64
TRANSCRIBED BY RNA POLYMERASE III................................................................................... 64
SIMILARITIES BETWEEN PROKARYOTIC AND EUKARYOTIC TRANSCRIPTION ............................. 65
COPARISON OF TRANSCRIPTION IN PROKARYOTES AND EUKARYOTES .................................... 65
RNA PROCESSING AND TRANSLATION COMPARISON BETWEEN PROKARYOTES AND
EUKARYOTES .................................................................................................................. 66
GENE ................................................................................................................................... 66
EUKARYOTIC GENE STRUCTURE .............................................................................................. 67
CISTRON ................................................................................................................................ 67
DIFFERENCE BETWEEN GENE AND CISTRON ............................................................................ 67
MONOCISTRONIC AND POLYCISTRONIC mRNA ....................................................................... 68
KEY DIFFERENCE BETWEEN MONOCISTRONIC AND POLYCISTRONIC mRNA .............................. 68
THE STRUCTURE OF A PROKARYOTIC OPERON OF PROTEIN-CODING GENES ............................ 68
DIFFERENCE BETWEEN MONOCISTRONIC AND POLYCISTRONIC mRNA .................................... 69
INTRONS................................................................................................................................ 69
INTRONS AND EXTRONS ......................................................................................................... 69
INTRON FUNCTION ................................................................................................................ 69
DNA PROCESSING .................................................................................................................. 71
RNA PROCESSING IN EUKARYOTES ......................................................................................... 71
RNA BINDING PROTEINS (RBPs) .............................................................................................. 71
mRNA MODIFICATIONS IN EUKARYOTES................................................................................. 72
5’ CAPPING ............................................................................................................................ 72
POLYADENYLATION................................................................................................................ 73
3’ POLY-A TAIL ....................................................................................................................... 74
PRE-mRNA SPLICING .............................................................................................................. 74
SPLICING................................................................................................................................ 74
ALTERNATIVE SPLICING .......................................................................................................... 75
RIBOSOMES ........................................................................................................................... 75
RIBOSOMAL RNA (rRNA) ........................................................................................................ 76
PROKARYOTIK RIBOSOME ...................................................................................................... 76
EUKARYOTIC RIBOSOME ........................................................................................................ 77
rRNA IN EUKARYOTES ............................................................................................................ 77
rRNA IN PROKARYOTES .......................................................................................................... 77
4
