11

Introduction To Molecular

BiologyBy

Salwa Hassan Teama (M.D)

22

Molecular BiologyMolecular Biology

Molecular biologyMolecular biology;; thethe study of study of biologybiology at the at the molecularmolecular level. level.

Molecular biologyMolecular biology;; thethe study of study of gene gene structure structure and functions at the and functions at the molecular levelmolecular level to understand the to understand the molecular basis of hereditary, genetic variation, and the molecular basis of hereditary, genetic variation, and the expression patterns of genes. expression patterns of genes.

The Molecular biologyThe Molecular biology field overlaps with field overlaps with

other areas, particularly genetics and biochemistryother areas, particularly genetics and biochemistry..

33

The GenomeThe Genome

The genomeThe genome of an of an organismorganism is the totality of genetic is the totality of genetic information and is encoded in the information and is encoded in the DNADNA (or, for some (or, for some viruses, viruses, RNARNA).).

commons.wikimedia.org/wiki/Image:Genome.jpg

44

Genome DatabaseGenome Database

The database is organized in six major organism groups: Eukaryotes, Bacteria, Archaea, Viruses, Viroids and Plasmids.

55

All living things are grouped into three domain:

Eukaryotes; Prokaryotes and Archaea.

Three Domain of Life

66

The CellThe Cell

The cellThe cell is the is the smallest living unit, the smallest living unit, the basic structural and basic structural and functional unit of all living functional unit of all living things. Some organisms, things. Some organisms, such as mostsuch as most bacteria bacteria, , are are unicellular unicellular (consist of (consist of a single cell). Other a single cell). Other organisms, such as organisms, such as humanshumans, are, are multicellular.multicellular.

77

The CellThe Cell

CellsCells are stacked are stacked together to make up together to make up structures, tissues and structures, tissues and organs. Most cells have organs. Most cells have got the same information got the same information and resources and the and resources and the same basic material. same basic material. CellsCells can take many can take many shapes depending on shapes depending on their function.their function.

Function of cellsFunction of cells Secretion (Produce Secretion (Produce

enzymes). enzymes). Store sugars or fat. Store sugars or fat. Brain cells for memory Brain cells for memory

and intelligence. and intelligence. Muscle cells to contract. Muscle cells to contract. Skin cell to perform a Skin cell to perform a

protective coating.protective coating. Defense, such as white Defense, such as white

blood cells. blood cells.

88

Eukaryotic CellEukaryotic Cell

EukaryotesEukaryotes are generally more advanced than are generally more advanced than prokaryotesprokaryotes. . There are many unicellular organisms which There are many unicellular organisms which are eukaryotic, but all cells in multicellular organisms are are eukaryotic, but all cells in multicellular organisms are eukaryotic. eukaryotic.

EukaryoticEukaryotic cells are found in animals; plants; fungi and cells are found in animals; plants; fungi and protists cell.protists cell.

99

Eukaryotic CellEukaryotic Cell

CellCell with a with a true nucleustrue nucleus,, where the genetic material is where the genetic material is surrounded by a membrane; surrounded by a membrane;

EukaryoticEukaryotic genomegenome is is more more complexcomplex than that of than that of prokaryotes and distributed prokaryotes and distributed among multiple chromosomes; among multiple chromosomes;

EukaryoticEukaryotic DNADNA is linearis linear;; EukaryoticEukaryotic DNADNA is is

complexedcomplexed with proteins called with proteins called ""histones;histones;

Numerous membraneNumerous membrane--bound bound organelles;organelles;

Complex internal structure;Complex internal structure; Cell division by Cell division by mitosis.mitosis.

1010

Prokaryotic CellProkaryotic Cell

Unicellular Unicellular organisms, found in organisms, found in all environmentsall environments. . These These include include bacteria and archaea.bacteria and archaea.

Without a nucleusWithout a nucleus; no nuclear ; no nuclear membrane membrane ((genetic material genetic material dispersed throughout dispersed throughout cytoplasmcytoplasm ;;

No membraneNo membrane--bound bound organellesorganelles;;

Cell contains only Cell contains only one circular one circular DNA moleculeDNA molecule contained in the contained in the cytoplasm; cytoplasm;

DNA is nakedDNA is naked (no histone); (no histone); Simple internal structureSimple internal structure; and; and Cell division by Cell division by simple binary simple binary

fissionfission..

1111

ArchaeaArchaea

ArchaeaArchaea are are prokaryotes; organisms prokaryotes; organisms without nucleuswithout nucleus but some but some aspect of their molecular aspect of their molecular biology are more similar biology are more similar to those of eukaryotes.to those of eukaryotes.

1212

Eukaryotic Cell CycleEukaryotic Cell Cycle Eukaryotic Cell Eukaryotic Cell

Cycle Cycle :: defined as the defined as the sequence of events that sequence of events that occurs during the lifetime of a occurs during the lifetime of a cell and is traditionally divided cell and is traditionally divided into four phases: into four phases:

G1 = Growth and preparation G1 = Growth and preparation of the chromosomes for of the chromosomes for replication replication

S = Synthesis of DNA S = Synthesis of DNA G2 = Preparation for mitosis G2 = Preparation for mitosis M = M = MitosisMitosis

1313

Central Dogma of Molecular Biology

http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookPROTSYn.html

The flow of genetic information as follows:The flow of genetic information as follows:

1414

Deoxyribonucleic Acid (DNA)Deoxyribonucleic Acid (DNA)

Deoxyribonucleic Deoxyribonucleic Acid (DNA),Acid (DNA), the the genetic material of all genetic material of all cellular organisms and cellular organisms and most viruses, the gigantic most viruses, the gigantic molecule which is used to molecule which is used to encode genetic encode genetic information for all life on information for all life on Earth.Earth.

1515

Eukaryotic CellEukaryotic Cell

1616

http://genome.gsc.riken.go.jp/hgmis/graphics/slides/01-0085jpg.html U.S. Department of Energy Human Genome Program, http://www.ornl.gov/hgmis.

1717

Thread like structure. Thread like structure. Located in the cell Located in the cell

nucleus.nucleus. The storage place for all The storage place for all

genetic information. genetic information. The number of The number of

chromosomes varies from chromosomes varies from one species to another. one species to another.

The ChromosomeThe Chromosome

1818

In In normal human normal human cell DNAcell DNA contained in contained in the nucleus, arranged in the nucleus, arranged in 23 pairs of 23 pairs of chromosomes ; 22 pairs chromosomes ; 22 pairs of chromosomes of chromosomes (autosomes) ; the 23 (autosomes) ; the 23 chromosome pair chromosome pair determines the sex of determines the sex of individual and is individual and is composed of either two composed of either two (x) chromosomes (x) chromosomes (female) or an (x) and (y) (female) or an (x) and (y) chromosome (male).chromosome (male).

The ChromosomeThe Chromosome

1919

The basic units ofThe basic units of inheritance;inheritance; itit is a is a segment within a very segment within a very long strand of long strand of DNADNA with with specific instruction for the specific instruction for the production of one specific production of one specific protein. Genes located protein. Genes located on chromosome on it's on chromosome on it's place or place or locuslocus. .

The GeneThe Gene

2020

DNADNA and and RNARNA are long are long chain polymers of small chain polymers of small compound called compound called nucleotides. Each nucleotides. Each nucleotide is composed of nucleotide is composed of a a basebase; ; sugarsugar (ribose in (ribose in RNARNA or deoxyribose in or deoxyribose in DNADNA) and a ) and a phosphate phosphate groupgroup. . The phosphate The phosphate joins the sugars in a DNA joins the sugars in a DNA or RNA chain through their or RNA chain through their 5` and 3` hydroxyl group 5` and 3` hydroxyl group by phosphodiester bonds.by phosphodiester bonds.

General Structure of Nucleic AcidGeneral Structure of Nucleic Acid

2121

The structure of The structure of DNADNA was described by British Scientists was described by British Scientists Watson and CrickWatson and Crick as as long double helixlong double helix shaped with its shaped with its sugar phosphate backbone on the outside and its bases sugar phosphate backbone on the outside and its bases on inside; the two strand of helix run in opposite direction on inside; the two strand of helix run in opposite direction and are anti-parallel to each other. The DNA double helix and are anti-parallel to each other. The DNA double helix is stabilized by is stabilized by hydrogen bonds hydrogen bonds between the bases.between the bases.

This structure explains how genes engage in replication, This structure explains how genes engage in replication, carrying information and acquiring mutation.carrying information and acquiring mutation.

The The G+CG+C content of a natural content of a natural DNADNA can vary from 22- can vary from 22-73% and this can have a strong effect on the physical 73% and this can have a strong effect on the physical properties of properties of DNADNA, particularly its melting temperature. , particularly its melting temperature.

2222

There are four different types ofThere are four different types of nucleotidesnucleotides found in found in DNADNA,, differing only in thediffering only in the nitrogenous basenitrogenous base: : AA is for is for adenineadenine; ; GG is for guanine;is for guanine; CC is for cytosine andis for cytosine and TT is for is for thymine.thymine.

These bases are classified based on their chemical These bases are classified based on their chemical structuresstructures into two groups:into two groups: adenine and guanineadenine and guanine are double ringed structureare double ringed structure termedtermed purinepurine , , thymine thymine and cytosineand cytosine are single ring structuresare single ring structures termed termed pyrimidinepyrimidine. .

The bases pair in a specific way: AdenineThe bases pair in a specific way: Adenine AA with with thyminethymine TT (two hydrogen bonds) (two hydrogen bonds) and guanineand guanine GG with with cytosinecytosine C C (three hydrogen bonds).(three hydrogen bonds).

Within the structure of Within the structure of DNADNA, the number of, the number of thyminethymine is is always always equal to the number of adenine and the equal to the number of adenine and the number ofnumber of cytosinecytosine is is always equal toalways equal to guanineguanine..

In contrast to DNA; In contrast to DNA; RNA is a single strandedRNA is a single stranded, the , the pyrimidine base pyrimidine base uracil (U)uracil (U) replaces replaces thymine thymine and and ribose sugar replaces deoxyribose.ribose sugar replaces deoxyribose.

2323

2424

Genomic DNA organizationGenomic DNA organization

Eukaryotic Eukaryotic genes:genes: DNA molecules DNA molecules complexed with other complexed with other proteins especially basic proteins especially basic proteins called proteins called histoneshistones, , to form a substance to form a substance known asknown as chromatinchromatin.. A A human cell contains human cell contains about 2 meters of about 2 meters of DNADNA.. DNADNA in body could in body could stretch to the sun and stretch to the sun and back almost 100 times. back almost 100 times. So it is tightly packed.So it is tightly packed.

2525

Eukaryotic ChromatinEukaryotic Chromatin

Eukaryotic Eukaryotic chromatinchromatin is folded in is folded in several ways. The first several ways. The first order of folding involves order of folding involves structures called structures called nucleosomesnucleosomes,, which have a which have a core of histones, around core of histones, around which the which the DNADNA winds ( four winds ( four pairs of histones H2A, pairs of histones H2A, H2B,H3 and H4 in a wedge H2B,H3 and H4 in a wedge shaped disc, around it shaped disc, around it wrapped a stretch of 147 bp wrapped a stretch of 147 bp of of DNADNA).).

2626

DNA FormsDNA Forms

2727

DNA ReplicationDNA Replication

DNA Replication:DNA Replication: The The DNADNA (all gene) duplication; the (all gene) duplication; the transfer the genetic information from transfer the genetic information from a parent to a daughter cell ; the a parent to a daughter cell ; the DNADNA base sequence are precisely base sequence are precisely copied.copied.

ReplicationReplication proceeds in proceeds in a a semiconservativesemiconservative manner, each manner, each strand of the DNA helix serves as a strand of the DNA helix serves as a template for the synthesis of template for the synthesis of complementary DNA strands. This complementary DNA strands. This lead to the formation of two lead to the formation of two complete copies of the DNA complete copies of the DNA molecule, each consisting of one molecule, each consisting of one strand derived from the parent DNA strand derived from the parent DNA molecule and one newly molecule and one newly synthesized complementary strand. synthesized complementary strand.

2828

Mitochondrial DNAMitochondrial DNA

MitochondriaMitochondria is a membrane- is a membrane-enclosed enclosed organelleorganelle found in most found in most eukaryotic cellseukaryotic cells.These organelles .These organelles range from 1–10 micrometers (range from 1–10 micrometers (μmμm) ) in size. in size.

MitochondriaMitochondria generate most of generate most of the cell's supply of the cell's supply of adenosineadenosine triphosphatetriphosphate (ATP). (ATP).

MitochondriaMitochondria are involved in are involved in a range of other processes, such as a range of other processes, such as signaling,signaling, cellular differentiation,cellular differentiation, cell cell death,death, as well as the control of the as well as the control of the cell cyclecell cycle and and cell growthcell growth..

MitochondriaMitochondria have been have been implicated in several human implicated in several human diseases, including diseases, including mental mental disordersdisorders,cardiac dysfunction,,cardiac dysfunction,[and and may play a role in the may play a role in the aging process.aging process.

MitochondriaMitochondria has its own has its own DNA.DNA.

2929

Mitochondrial DNAMitochondrial DNA

Mitochondrial DNAMitochondrial DNA contains 37 genes, all of contains 37 genes, all of which are essential for normal mitochondrial functionwhich are essential for normal mitochondrial function. . Thirteen of these genes provide instructions for making Thirteen of these genes provide instructions for making enzymes involved in oxidative phosphorylationenzymes involved in oxidative phosphorylation. .

Oxidative phosphorylation is a process that uses oxygen Oxidative phosphorylation is a process that uses oxygen and simple sugars to create adenosine triphosphate and simple sugars to create adenosine triphosphate ((ATPATP)), the cell's main energy source, the cell's main energy source. .

The remaining genes provide instructions for making The remaining genes provide instructions for making molecules called transfer RNAs molecules called transfer RNAs ((tRNAstRNAs) ) and ribosomal and ribosomal RNAs RNAs ((rRNAsrRNAs)). .

Mitochondrial genesMitochondrial genes are among the estimated are among the estimated 20,000 to 25,000 total genes in the human genome20,000 to 25,000 total genes in the human genome..

3030

Function of The DNAFunction of The DNA

Deoxyribonucleic Acid (Deoxyribonucleic Acid (DNADNA),), the the gigantic molecule which is used togigantic molecule which is used to encode genetic encode genetic information for all life on Earth.information for all life on Earth.

The chemical basis ofThe chemical basis of hereditaryhereditary and genetic variationand genetic variation are related to DNA.are related to DNA.

DNADNA directs the synthesis ofdirects the synthesis of RNARNA which in turnwhich in turn directsdirects protein synthesisprotein synthesis. .

3131

The Genetic Code

The purine and pyrmidine bases of the DNA molecule The purine and pyrmidine bases of the DNA molecule are the letters or alphabet of the genetic code. All are the letters or alphabet of the genetic code. All information contained in DNA represented by four letters: information contained in DNA represented by four letters: A,T,C,G.A,T,C,G.

Three nucleotides of DNA (1st, 2nd and 3rd) form triplet Three nucleotides of DNA (1st, 2nd and 3rd) form triplet codons. A group of codons constitute the genetic code, codons. A group of codons constitute the genetic code, that can be translated into amino acid of proteins.that can be translated into amino acid of proteins.

RNA Codon tRNA Amino AcidsRNA Codon tRNA Amino Acids

3232

The Genetic Code

The sequence of codons The sequence of codons in the in the mRNAmRNA defines the defines the primary structure of the primary structure of the final protein. Since there final protein. Since there are 64 possible codons, are 64 possible codons, most amino acids have most amino acids have more than one possible more than one possible codon. Out of the 64 codon. Out of the 64 possible 3-base codons, possible 3-base codons, 61 specify amino acids; 61 specify amino acids; the other three are stop the other three are stop signals signals (UAG, UAA, or (UAG, UAA, or UGA). UGA).

3333

The RNAThe RNA

Three major classes of Three major classes of RNARNA: messenger : messenger (mRNA),(mRNA), transfer transfer (tRNA)(tRNA) and ribosomal and ribosomal (rRNA).(rRNA). Minor classes Minor classes of RNA include small nuclear RNA ; small nucleolar of RNA include small nuclear RNA ; small nucleolar RNA;………..RNA;………..

3434

The RNAThe RNA

- The concentration of The concentration of purine and pyrimidine purine and pyrimidine bases do not necessarily bases do not necessarily equal one another in RNA equal one another in RNA because RNA is single because RNA is single stranded. However, the stranded. However, the single strand of RNA is single strand of RNA is capable of folding back capable of folding back on itself like a on itself like a hairpinhairpin and and acquiring double strand acquiring double strand structure.structure.

3535

Messenger RNAMessenger RNA

mRNAmRNA molecules represent molecules represent transcripts of structural genes transcripts of structural genes that encode all the information that encode all the information necessary for the synthesis of a necessary for the synthesis of a single type polypeptide of protein.single type polypeptide of protein.

mRNAmRNA;; intermediate carrier intermediate carrier of genetic information; deliver of genetic information; deliver genetic information to the genetic information to the cytoplasm where protein cytoplasm where protein synthesis take place.synthesis take place.

The The mRNAmRNA also contains also contains regions that are not translated: in regions that are not translated: in eukaryotes this includes theeukaryotes this includes the 5' 5' untranslated region, 3' untranslated region, 3' untranslated region, 5' capand untranslated region, 5' capand poly-A tail.poly-A tail.

3636

Transfer RNA(tRNA)Transfer RNA(tRNA)

All All tRNAstRNAs share a share a common secondary common secondary structure represented by structure represented by a a coverleaf.coverleaf. They have They have four-paired stems four-paired stems defining three stem loops defining three stem loops (the D loop, anticodon (the D loop, anticodon loop, and T loop) and the loop, and T loop) and the acceptor stem to which acceptor stem to which amino acids are added in amino acids are added in the charging step.the charging step.

RNA molecules that carry RNA molecules that carry amino acids to the amino acids to the growing polypeptide. growing polypeptide.

3737

Ribosomal RNA (rRNA)Ribosomal RNA (rRNA)

Ribosomal RNA (rRNA)Ribosomal RNA (rRNA) is the central is the central component of the ribosome, the function of the rRNA is component of the ribosome, the function of the rRNA is to provide a mechanism for decoding mRNA into amino to provide a mechanism for decoding mRNA into amino acids and to interact with the tRNAs during translation by acids and to interact with the tRNAs during translation by providing peptidyl transferase activity. providing peptidyl transferase activity.

3838

RibosomesRibosomes

Ribosomes ;Ribosomes ; Factory Factory for protein synthesis; for protein synthesis; are are composed of composed of ribosomal ribosomal RNARNA and ribosomal and ribosomal proteins (known as a proteins (known as a Ribonucleoproteinor Ribonucleoproteinor RNP). They translate RNP). They translate messenger RNA (mRNA) messenger RNA (mRNA) toto build polypeptide build polypeptide chains using amino acids chains using amino acids delivered by delivered by transfer RNA transfer RNA (tRNA)(tRNA)..

3939

RibosomesRibosomes

Eukaryotic ribosomesEukaryotic ribosomes are larger.are larger. They consist They consist of two subunits; a 60S subunit holds (three rRNAs of two subunits; a 60S subunit holds (three rRNAs 5S,5S, 5.8S5.8S, 28S and about 40 proteins) and a 40S subunit , 28S and about 40 proteins) and a 40S subunit contains (an18S rRNA and about 30 proteins) , which contains (an18S rRNA and about 30 proteins) , which come together to form an 80S particle compared with come together to form an 80S particle compared with prokaryotic 70S ribosomeprokaryotic 70S ribosome

4040

Most mRNA are Most mRNA are translated by more than translated by more than one ribosome at a time; one ribosome at a time; the result, a structure in the result, a structure in which many ribosomes which many ribosomes translate an mRNA in translate an mRNA in tandem, is called a tandem, is called a polysomes.polysomes.

PolysomesPolysomes

4141

The ProteinThe Protein

ProteinsProteins are the basic building materials of a cell, made by are the basic building materials of a cell, made by cell itself; cell itself; the final product of most genes.the final product of most genes.

ProteinsProteins are chain like polymers of a few or many thousands are chain like polymers of a few or many thousands of amino acids. Amino acids are represented by codons, which are of amino acids. Amino acids are represented by codons, which are 3-nucleotide RNA sequences. Amino acids joined together by 3-nucleotide RNA sequences. Amino acids joined together by peptide bonds peptide bonds ((polypeptide)polypeptide).. Proteins can be composed of one or Proteins can be composed of one or more polypeptide chains.more polypeptide chains.

ProteinsProteins have many functions: provide structure that help have many functions: provide structure that help cells integrity and shape (e.g. collagen in bone); serve as enzymes cells integrity and shape (e.g. collagen in bone); serve as enzymes and hormones; bind and carry substance and control of activities of and hormones; bind and carry substance and control of activities of genes….genes….

4242

Four levels of a protein's Four levels of a protein's structurestructure::

Primary structure:Primary structure: Formed by joining the amino Formed by joining the amino acid sequence into a polypeptideacid sequence into a polypeptide. .

Secondary structure:Secondary structure: Different conformation Different conformation that can be taken by the polypeptide: alpha helix and that can be taken by the polypeptide: alpha helix and strands of beta sheet. strands of beta sheet.

Tertiary structure :Tertiary structure : Result from folding the Result from folding the secondary structure components of the polypeptide into secondary structure components of the polypeptide into three-dimensional configuration.three-dimensional configuration.

Quaternary structure :Quaternary structure : complex of several complex of several protein molecules or polypeptide chains, usually called protein molecules or polypeptide chains, usually called protein subunits, which function as part of the larger protein subunits, which function as part of the larger assembly or protein complex.assembly or protein complex.

4343

Protein Structure

4444

Gene ExpressionGene Expression

Gene expressionGene expression process by which a gene process by which a gene product (an RNA or polypeptide ) is made.product (an RNA or polypeptide ) is made.

InIn transcription stepstranscription steps,, RNA polymerase RNA polymerase make a copy of information in the gene (complementary make a copy of information in the gene (complementary RNA) RNA) (mRNA)(mRNA) complementary to one strands of DNA. complementary to one strands of DNA.

In In translation steptranslation step,, ribosomes read a ribosomes read a messenger RNA and make protein according to its messenger RNA and make protein according to its instruction. Thus any change in gene sequence may instruction. Thus any change in gene sequence may lead to change in the protein product.lead to change in the protein product.

4545

Types of control in EukaryotesTypes of control in Eukaryotes

Transcriptional,Transcriptional, prevent transcription, prevent prevent transcription, prevent mRNA from being synthesized.mRNA from being synthesized.

PosttranscriptionPosttranscriptional,al, control mRNA after it has control mRNA after it has been produced.been produced.

Translational,Translational, prevent translation; involve prevent translation; involve protein factors needed for protein factors needed for translation.translation.

PosttranslationalPosttranslational,, after the protein has been after the protein has been produced.produced.

4646

MutationMutation

MutationMutation includeinclude both gross alteration of chromosome both gross alteration of chromosome and more subtle alteration to specific gene sequence. and more subtle alteration to specific gene sequence.

Gross chromosomal aberrations include: large deletions; Gross chromosomal aberrations include: large deletions; addition and translocation (reciprocal and nonreciprocal).addition and translocation (reciprocal and nonreciprocal).

MutationMutation in a gene's DNA sequence can alter the in a gene's DNA sequence can alter the amino acid sequence of the protein encoded by the gene. amino acid sequence of the protein encoded by the gene. Point mutations are the result of the substitution of a single Point mutations are the result of the substitution of a single base. Frame-shift mutations occur when the reading frame base. Frame-shift mutations occur when the reading frame of the gene is shifted by addition or deletion of one or more of the gene is shifted by addition or deletion of one or more bases. bases.

4747

MutationMutation

Mutations can have harmful, Mutations can have harmful, beneficial, neutral, or uncertain beneficial, neutral, or uncertain effects on health and may be effects on health and may be inherited asinherited as autosomal autosomal dominant, autosomal dominant, autosomal recessive,recessive, or Xor X--linked traitslinked traits.. Mutations that cause serious Mutations that cause serious disability early in life are disability early in life are usually rare because of their usually rare because of their adverse effect on life adverse effect on life expectancy and reproductionexpectancy and reproduction..

4848

Common Tools in Molecular Common Tools in Molecular BiologyBiology

Nucleic acid fractionationNucleic acid fractionation Polymerase chain reactionPolymerase chain reaction Probes, Hybridization Probes, Hybridization Vector, Molecular cloningVector, Molecular cloning Nucleic acid enzymesNucleic acid enzymes MicroarrayMicroarray DNA sequencingDNA sequencing Electrophoretic separation of nucleic acidElectrophoretic separation of nucleic acid Detection of genes:Detection of genes: *DNA:*DNA: Southern blotting; inSitu hybridization; FISH Southern blotting; inSitu hybridization; FISH

TechniqueTechnique *RNA:*RNA: Northern blotting Northern blotting *Protein:*Protein: Western blotting, immunohistochemistry Western blotting, immunohistochemistry

4949

Human Genome ProjectHuman Genome Project

GoalsGoals Identify all the approximately 20,000-25,000 genes in Identify all the approximately 20,000-25,000 genes in

human DNA, human DNA, Determine the sequences of the 3 billion chemical base Determine the sequences of the 3 billion chemical base

pairs that make up human DNA, store this information in pairs that make up human DNA, store this information in databases, databases,

Improve tools for data analysis, Improve tools for data analysis, transfer related technologies to the private sector, and transfer related technologies to the private sector, and

Address the ethical, legal, and social issues (ELSI) that may Address the ethical, legal, and social issues (ELSI) that may arise from the project.arise from the project.

5050

Molecular Biology : UsesMolecular Biology : Uses

Various methods in molecular biology diagnose the Various methods in molecular biology diagnose the different human diseases; diagnosis of an infectious different human diseases; diagnosis of an infectious agent, in malignancy, the presence of the genetic agent, in malignancy, the presence of the genetic disease and in transplantation, paternity and forensic disease and in transplantation, paternity and forensic analysis.analysis.

The Most Recent Applied TechnologiesThe Most Recent Applied Technologies Genetic engineeringGenetic engineering DNA finger-printing in the social and forensic science. DNA finger-printing in the social and forensic science. Pre and postnatal diagnosis of inherited diseases. Pre and postnatal diagnosis of inherited diseases. Gene therapy. Gene therapy. Drug Design.Drug Design.

5151

Molecular biology is Molecular biology is facilitating research in facilitating research in many field including many field including biochemistry, biochemistry, microbiology, microbiology, immunology and immunology and genetics,genetics,…………………………………………

Molecular biology Molecular biology allows the laboratory to allows the laboratory to be predictive in nature, be predictive in nature, it gives information that it gives information that the patients may be at the patients may be at risk for disease (future).risk for disease (future).

5252

GlossaryGlossary Alleles Alleles are forms of the same gene with small differences in their sequence of DNA bases.are forms of the same gene with small differences in their sequence of DNA bases. Exon (Coding DNA):Exon (Coding DNA): A gene sequence contains protein coding information.A gene sequence contains protein coding information. Introns Introns ((intervening sequence) (A noncoding DNA sequence ): Intervening stretches of DNA that separate exons. intervening sequence) (A noncoding DNA sequence ): Intervening stretches of DNA that separate exons. Primary transcript:Primary transcript: The initial production of gene transcription in the nucleus; an RNA containing copies of all exons and introns.The initial production of gene transcription in the nucleus; an RNA containing copies of all exons and introns. RNA gene or non-coding RNA geneRNA gene or non-coding RNA gene: : RNA molecule that is notRNA molecule that is not translated translated into a protein. Noncoding RNA genes produce transcripts that into a protein. Noncoding RNA genes produce transcripts that

exert their function without ever producing proteins. Non-coding RNA genes include transfer RNA exert their function without ever producing proteins. Non-coding RNA genes include transfer RNA (tRNA)(tRNA) and and ribosomal RNA (rRNA),ribosomal RNA (rRNA), small RNAs such as small RNAs such as snoRNAs, microRNAs, siRNAssnoRNAs, microRNAs, siRNAsand and piRNAs piRNAs and lastly long and lastly long ncRNAs.ncRNAs.

Enhancers and silencers:Enhancers and silencers: are DNA elements that stimulate or depress the transcription of associated genes; they rely on tissue specific binding are DNA elements that stimulate or depress the transcription of associated genes; they rely on tissue specific binding proteins for their activities; sometimes a DNA elements can act either as an enhancer or silencer depending on what is bound to it.proteins for their activities; sometimes a DNA elements can act either as an enhancer or silencer depending on what is bound to it.

Activators:Activators: Additional gene-specific transcription factors that can bind to enhancer and help in transcription activationAdditional gene-specific transcription factors that can bind to enhancer and help in transcription activation . . Open reading frame Open reading frame (ORF)(ORF) :: A reading frame that is uninterrupted by translation stop codon (reading frame that contains a A reading frame that is uninterrupted by translation stop codon (reading frame that contains a start codonstart codonand the and the

subsequent translated region, but no subsequent translated region, but no stop codon).stop codon). Directionality:Directionality: in molecular biology, refers to the end-to-end chemical orientation of a single strand of nucleic acid. The chemical convention of naming carbon in molecular biology, refers to the end-to-end chemical orientation of a single strand of nucleic acid. The chemical convention of naming carbon

atoms in the nucleotide sugar-ring numerically gives rise to a atoms in the nucleotide sugar-ring numerically gives rise to a 5'5' end and a end and a 3'3' end ( "five prime end" and "three prime end"). The relative positions of structures along a end ( "five prime end" and "three prime end"). The relative positions of structures along a strand of nucleic acid, including genes, transcription factors, and polymerases are usually noted as being either strand of nucleic acid, including genes, transcription factors, and polymerases are usually noted as being either upstreamupstream (towards the 5' end) or (towards the 5' end) or downstreamdownstream (towards the 3' end).(towards the 3' end).

3' flanking region:3' flanking region: Present adjacent to 3' end of the gene; often contain sequences which affect the formation of the 3` end of the message and may Present adjacent to 3' end of the gene; often contain sequences which affect the formation of the 3` end of the message and may contain enhancers or protein binding sites. contain enhancers or protein binding sites.

5' flanking region:5' flanking region: A region adjacent to 5' end of the gene. It is not transcribed into RNA; it contains theA region adjacent to 5' end of the gene. It is not transcribed into RNA; it contains the promoter.promoter. May contain enhancers or other protein May contain enhancers or other protein binding sitesbinding sites..

3' untranslated region:3' untranslated region: The The three prime untranslated regionthree prime untranslated region (3' UTR) (3' UTR) is a particular section of messenger RNA (mRNA). It follows the coding region. It is a particular section of messenger RNA (mRNA). It follows the coding region. It is a region of the DNA which is transcribed into mRNA and becomes the 3' end or the message, Several regulatory sequences are found in the 3' UTR. The 3' is a region of the DNA which is transcribed into mRNA and becomes the 3' end or the message, Several regulatory sequences are found in the 3' UTR. The 3' untranslated region may affect the translation efficiency of the mRNA or the stability of the mRNA. It also has sequences which are required for the addition of the untranslated region may affect the translation efficiency of the mRNA or the stability of the mRNA. It also has sequences which are required for the addition of the poly(A) tail to the message (including one known as thepoly(A) tail to the message (including one known as the "hexanucleotide", AAUAAA"hexanucleotide", AAUAAA). ).

5' untranslated region:5' untranslated region: The The five prime untranslated regionfive prime untranslated region ( (5' UTR5' UTR),), also known as thealso known as the leader sequenceleader sequence, , is a particular section of messenger RNA (mRNA) and is a particular section of messenger RNA (mRNA) and the DNA that codes for it. It is a region of a gene which is transcribed into mRNA. It starts at the site (where transcription begins) and ends just before thethe DNA that codes for it. It is a region of a gene which is transcribed into mRNA. It starts at the site (where transcription begins) and ends just before the start codon start codon (usually AUG)(usually AUG) of the coding region. It usually contains a ribosome binding site (RBS), in bacteria also known as the Shine Dalgarno sequence (AGGAGGU). In of the coding region. It usually contains a ribosome binding site (RBS), in bacteria also known as the Shine Dalgarno sequence (AGGAGGU). In prokaryotic mRNA the 5' UTR is normally short. Some viruses and cellular genes have unusual long structured 5' UTRs which may have roles in gene expression. prokaryotic mRNA the 5' UTR is normally short. Some viruses and cellular genes have unusual long structured 5' UTRs which may have roles in gene expression. Several regulatory sequences may be found in the 5' UTRSeveral regulatory sequences may be found in the 5' UTR..

Reverse Transcription:Reverse Transcription: Some viruses (such as Some viruses (such as HIV,HIV, the cause of the cause of AIDSAIDS), have the ability to transcribe RNA into DNA. ), have the ability to transcribe RNA into DNA.

5353

References & Online Further References & Online Further ReadingReading Robert F. Weaver. Molecular Biology. Fourth Edition. Page 600. McGraw-Hill International Edition. ISBN 978-0-07-110216-2Robert F. Weaver. Molecular Biology. Fourth Edition. Page 600. McGraw-Hill International Edition. ISBN 978-0-07-110216-2

Innis,David H. Gelfand,John J. Sninsky PCR Applications: Protocols for Functional Genomics: ISBN:0123721865 Innis,David H. Gelfand,John J. Sninsky PCR Applications: Protocols for Functional Genomics: ISBN:0123721865 Daniel H. Farkas. DNA Simplified: The Hitchhiker's Guide to DNA. Washington, DC: AACC Press, 1996, ISBN 0-915274-84-1. Daniel H. Farkas. DNA Simplified: The Hitchhiker's Guide to DNA. Washington, DC: AACC Press, 1996, ISBN 0-915274-84-1. William B. Coleman,Gregory J. Tsongalis: Molecular Diagnostics: For the Clinical Laboratorian: ISBN 1588293564... William B. Coleman,Gregory J. Tsongalis: Molecular Diagnostics: For the Clinical Laboratorian: ISBN 1588293564... Robert F. Mueller,Ian D. Young. Robert F. Mueller,Ian D. Young. EmeryEmery''ss ElementsElements of of MedicalMedical GeneticsGenetics: ISBN. : ISBN. 044307125X044307125X DanielDaniel P. P. StitesStites,Abba T. Terr. Basic Human Immunology: ISBN. ,Abba T. Terr. Basic Human Immunology: ISBN. 08385054300838505430 Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, and Peter Walter. Molecular Biology of the cell. ISBN. 9780815341055 Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, and Peter Walter. Molecular Biology of the cell. ISBN. 9780815341055 http://www.pubmedcentral.nih.gov/http://www.pubmedcentral.nih.gov/ http://www.biomedcentral.com/1471-2105/2/8/abstract. http://www.biomedcentral.com/1471-2105/2/8/abstract. Elena RivasElena Rivas and and Sean R EddySean R Eddy Noncoding RNA gene detection using comparative sequence analysisNoncoding RNA gene detection using comparative sequence analysis BMC BioinformaticsBMC Bioinformatics 2001, 2001, 2:2:8doi:10.1186/1471-2105-2-88doi:10.1186/1471-2105-2-8 www.medscape.comwww.medscape.com http://www.medterms.com/script/main/art.asp?articlekey=4026http://www.medterms.com/script/main/art.asp?articlekey=4026 www.emedicine.comwww.emedicine.com www.ebi.ac.uk/2can good introduction to bioinformatics and molecular biology www.ebi.ac.uk/2can good introduction to bioinformatics and molecular biology http://www.genomicglossaries.com/http://www.genomicglossaries.com/ http://www.gene.ucl.ac.uk/nomenclature/guidelines.html defines the nomenclature for human geneshttp://www.gene.ucl.ac.uk/nomenclature/guidelines.html defines the nomenclature for human genes http://www.accessexcellence.orghttp://www.accessexcellence.org http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/Codons.htmlhttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/Codons.html http://www.web-books.com/MoBio/http://www.web-books.com/MoBio/ http://www.expasy.orghttp://www.expasy.org http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookPROTSYn.htmlhttp://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookPROTSYn.html Cell & Molecular Biology online: http://www.cellbio.com/recommend.htmlCell & Molecular Biology online: http://www.cellbio.com/recommend.html http://www.ornl.gov/sci/techresources/Human_Genome/glossary/glossary.shtml%20http://www.ornl.gov/sci/techresources/Human_Genome/glossary/glossary.shtml%20 http://www.genome.gov/10000715http://www.genome.gov/10000715 http://www.ncbi.nlm.nih.gov/About/primer/mapping.htmlhttp://www.ncbi.nlm.nih.gov/About/primer/mapping.html http://www.lilly.com/research/discovering/targets.html http://www.lilly.com/research/discovering/targets.html http://www.informatics.jax.org/expression.shtml http://www.informatics.jax.org/expression.shtml www.wikipdia.comwww.wikipdia.com http://www.biology.arizona.edu/cell_bio/tutorials/pev/page2.htmlhttp://www.biology.arizona.edu/cell_bio/tutorials/pev/page2.html http://www.genome.ou.edu/protocol_book/protocol_index.htmlhttp://www.genome.ou.edu/protocol_book/protocol_index.html

5454

Thank You