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INTRODUCTION

Gene expression is the process by which inheritable information from a gene

(A gene is the basic unit ofheredity in a living organism), such as the DNA sequence,

is made into a functional gene product. A gene product is the biochemical material,

either RNA orprotein, resulting from expression of a gene. A measurement of the

amount of gene product is sometimes used to infer how active a gene is. Abnormal

amounts of gene product can be correlated with disease-causing alleles, such as the

overactivity ofoncogenes which can causecancer, such asprotein orRNA.

Several steps in the gene expression process may be modulated, including the

transcription step and translation step and the post-translational modification of aprotein. Gene regulation gives the cellcontrol over structure and function, and is the

basis forcellular differentiation, morphogenesis and the versatility and adaptability of

any organism. Gene regulation may also serve as a substrate for evolutionary change,

since control of the timing, location, and amount of gene expression can have a

profound effect on the functions (actions) of the gene in the organism. Non-protein

coding genes (e.g. rRNA genes, tRNA genes) are transcribed, but not translated into

protein. Genes are expressed by being transcribed into RNA, and this transcript may

then be translated into protein.

Proteins are organic compounds made of amino acids arranged in a linear

chain and joined together bypeptide bonds between the carboxyl and amino groups of

adjacent amino acid residues. The sequence of amino acids in a protein is defined by

the sequence of a gene, which is encoded in the genetic code.[1] In general, the genetic

code specifies 20 standard amino acids, however in certain organisms the genetic

code can include selenocysteine - and in certain archaea -pyrrolysine. The residues in

a protein are often observed to be chemically modified by post-translational

modification, which can happen either before the protein is used in the cell, or as part

of control mechanisms. Proteins can also work together to achieve a particular

function, and they often associate to form stable complexes.

Like other biological macromolecules such as polysaccharides and nucleic

acids, proteins are essential parts of organisms and participate in every process within

cells. Many proteins are enzymes that catalyzebiochemical reactions and are vital to

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http://en.wikipedia.org/wiki/Genehttp://en.wikipedia.org/wiki/Heredityhttp://en.wikipedia.org/wiki/Organismhttp://en.wikipedia.org/wiki/DNA_sequencehttp://en.wikipedia.org/wiki/DNA_sequencehttp://en.wikipedia.org/wiki/Gene_producthttp://en.wikipedia.org/wiki/Gene_producthttp://en.wikipedia.org/wiki/RNAhttp://en.wikipedia.org/wiki/RNAhttp://en.wikipedia.org/wiki/Proteinhttp://en.wikipedia.org/wiki/Proteinhttp://en.wikipedia.org/wiki/Gene_expressionhttp://en.wikipedia.org/wiki/Gene_expressionhttp://en.wikipedia.org/wiki/Genehttp://en.wikipedia.org/wiki/Genehttp://en.wikipedia.org/wiki/Genehttp://en.wikipedia.org/wiki/Diseasehttp://en.wikipedia.org/wiki/Allelehttp://en.wikipedia.org/wiki/Oncogenehttp://en.wikipedia.org/wiki/Carcinogenesishttp://en.wikipedia.org/wiki/Cancerhttp://en.wikipedia.org/wiki/Cancerhttp://en.wikipedia.org/wiki/Proteinhttp://en.wikipedia.org/wiki/RNAhttp://en.wikipedia.org/wiki/RNAhttp://en.wikipedia.org/wiki/Transcription_(genetics)http://en.wikipedia.org/wiki/Translation_(biology)http://en.wikipedia.org/wiki/Post-translational_modificationhttp://en.wikipedia.org/wiki/Post-translational_modificationhttp://en.wikipedia.org/wiki/Cell_(biology)http://en.wikipedia.org/wiki/Cell_(biology)http://en.wikipedia.org/wiki/Cellular_differentiationhttp://en.wikipedia.org/wiki/Cellular_differentiationhttp://en.wikipedia.org/wiki/Morphogenesishttp://en.wikipedia.org/wiki/Organismhttp://en.wikipedia.org/wiki/RRNAhttp://en.wikipedia.org/wiki/TRNAhttp://en.wikipedia.org/wiki/Translation_(genetics)http://en.wikipedia.org/wiki/Organic_compoundhttp://en.wikipedia.org/wiki/Amino_acidhttp://en.wikipedia.org/wiki/Peptide_bondhttp://en.wikipedia.org/wiki/Carboxylhttp://en.wikipedia.org/wiki/Aminohttp://en.wikipedia.org/wiki/Residue_(chemistry)http://en.wikipedia.org/wiki/DNA_sequencehttp://en.wikipedia.org/wiki/Genehttp://en.wikipedia.org/wiki/Genetic_codehttp://en.wikipedia.org/wiki/Protein#cite_note-0http://en.wikipedia.org/wiki/Protein#cite_note-0http://en.wikipedia.org/wiki/Selenocysteinehttp://en.wikipedia.org/wiki/Archaeahttp://en.wikipedia.org/wiki/Pyrrolysinehttp://en.wikipedia.org/wiki/Post-translational_modificationhttp://en.wikipedia.org/wiki/Post-translational_modificationhttp://en.wikipedia.org/wiki/Cell_(biology)http://en.wikipedia.org/wiki/Protein_complexhttp://en.wikipedia.org/wiki/Macromoleculeshttp://en.wikipedia.org/wiki/Polysaccharidehttp://en.wikipedia.org/wiki/Nucleic_acidhttp://en.wikipedia.org/wiki/Nucleic_acidhttp://en.wikipedia.org/wiki/Cell_(biology)http://en.wikipedia.org/wiki/Enzymehttp://en.wikipedia.org/wiki/Catalysishttp://en.wikipedia.org/wiki/Genehttp://en.wikipedia.org/wiki/Heredityhttp://en.wikipedia.org/wiki/Organismhttp://en.wikipedia.org/wiki/DNA_sequencehttp://en.wikipedia.org/wiki/Gene_producthttp://en.wikipedia.org/wiki/RNAhttp://en.wikipedia.org/wiki/Proteinhttp://en.wikipedia.org/wiki/Gene_expressionhttp://en.wikipedia.org/wiki/Genehttp://en.wikipedia.org/wiki/Diseasehttp://en.wikipedia.org/wiki/Allelehttp://en.wikipedia.org/wiki/Oncogenehttp://en.wikipedia.org/wiki/Carcinogenesishttp://en.wikipedia.org/wiki/Cancerhttp://en.wikipedia.org/wiki/Proteinhttp://en.wikipedia.org/wiki/RNAhttp://en.wikipedia.org/wiki/Transcription_(genetics)http://en.wikipedia.org/wiki/Translation_(biology)http://en.wikipedia.org/wiki/Post-translational_modificationhttp://en.wikipedia.org/wiki/Cell_(biology)http://en.wikipedia.org/wiki/Cellular_differentiationhttp://en.wikipedia.org/wiki/Morphogenesishttp://en.wikipedia.org/wiki/Organismhttp://en.wikipedia.org/wiki/RRNAhttp://en.wikipedia.org/wiki/TRNAhttp://en.wikipedia.org/wiki/Translation_(genetics)http://en.wikipedia.org/wiki/Organic_compoundhttp://en.wikipedia.org/wiki/Amino_acidhttp://en.wikipedia.org/wiki/Peptide_bondhttp://en.wikipedia.org/wiki/Carboxylhttp://en.wikipedia.org/wiki/Aminohttp://en.wikipedia.org/wiki/Residue_(chemistry)http://en.wikipedia.org/wiki/DNA_sequencehttp://en.wikipedia.org/wiki/Genehttp://en.wikipedia.org/wiki/Genetic_codehttp://en.wikipedia.org/wiki/Protein#cite_note-0http://en.wikipedia.org/wiki/Selenocysteinehttp://en.wikipedia.org/wiki/Archaeahttp://en.wikipedia.org/wiki/Pyrrolysinehttp://en.wikipedia.org/wiki/Post-translational_modificationhttp://en.wikipedia.org/wiki/Post-translational_modificationhttp://en.wikipedia.org/wiki/Cell_(biology)http://en.wikipedia.org/wiki/Protein_complexhttp://en.wikipedia.org/wiki/Macromoleculeshttp://en.wikipedia.org/wiki/Polysaccharidehttp://en.wikipedia.org/wiki/Nucleic_acidhttp://en.wikipedia.org/wiki/Nucleic_acidhttp://en.wikipedia.org/wiki/Cell_(biology)http://en.wikipedia.org/wiki/Enzymehttp://en.wikipedia.org/wiki/Catalysis


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metabolism. Proteins also have structural or mechanical functions, such as actin and

myosin in muscle and the proteins in the cytoskeleton, which form a system of

scaffolding that maintains cell shape. Other proteins are important in cell signaling,

immune responses, cell adhesion, and the cell cycle. Proteins are also necessary in

animals' diets, since animals cannot synthesize all the amino acids they need and must

obtain essential amino acids from food. Through the process of digestion, animals

break down ingested protein into free amino acids that are then used in metabolism.

The wordprotein comes from the Greekword (proteios) "primary".

Proteins were first described and named by the Swedish chemist Jns Jakob Berzelius

in 1838. However, the central role of proteins in living organisms was not fully

appreciated until 1926, whenJames B. Sumnershowed that the enzymeureasewas a

protein.[3] The first protein to be sequenced was insulin, by Frederick Sanger, who

won the Nobel Prize for this achievement in 1958. The first protein structures to be

solved were hemoglobin and myoglobin, by Max Perutz and Sir John Cowdery

Kendrew, respectively, in 1958.[4][5] The three-dimensional structures of both proteins

were first determined by x-ray diffraction analysis; Perutz and Kendrew shared the

1962Nobel Prize in Chemistryfor these discoveries.

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http://en.wikipedia.org/wiki/Metabolismhttp://en.wikipedia.org/wiki/Actinhttp://en.wikipedia.org/wiki/Myosinhttp://en.wikipedia.org/wiki/Cytoskeletonhttp://en.wikipedia.org/wiki/Scaffoldinghttp://en.wikipedia.org/wiki/Cell_signalinghttp://en.wikipedia.org/wiki/Antibodyhttp://en.wikipedia.org/wiki/Cell_adhesionhttp://en.wikipedia.org/wiki/Cell_cyclehttp://en.wikipedia.org/wiki/Essential_amino_acidhttp://en.wikipedia.org/wiki/Digestionhttp://en.wikipedia.org/wiki/Greek_languagehttp://en.wikipedia.org/wiki/Greek_languagehttp://en.wikipedia.org/wiki/J%C3%B6ns_Jakob_Berzeliushttp://en.wikipedia.org/wiki/James_B._Sumnerhttp://en.wikipedia.org/wiki/James_B._Sumnerhttp://en.wikipedia.org/wiki/James_B._Sumnerhttp://en.wikipedia.org/wiki/Ureasehttp://en.wikipedia.org/wiki/Ureasehttp://en.wikipedia.org/wiki/Ureasehttp://en.wikipedia.org/wiki/Protein#cite_note-2http://en.wikipedia.org/wiki/Insulinhttp://en.wikipedia.org/wiki/Frederick_Sangerhttp://en.wikipedia.org/wiki/Frederick_Sangerhttp://en.wikipedia.org/wiki/Hemoglobinhttp://en.wikipedia.org/wiki/Myoglobinhttp://en.wikipedia.org/wiki/Myoglobinhttp://en.wikipedia.org/wiki/Max_Perutzhttp://en.wikipedia.org/wiki/Max_Perutzhttp://en.wikipedia.org/wiki/John_Kendrewhttp://en.wikipedia.org/wiki/John_Kendrewhttp://en.wikipedia.org/wiki/Protein#cite_note-3http://en.wikipedia.org/wiki/Protein#cite_note-4http://en.wikipedia.org/wiki/Nobel_Prize_in_Chemistryhttp://en.wikipedia.org/wiki/Nobel_Prize_in_Chemistryhttp://en.wikipedia.org/wiki/Metabolismhttp://en.wikipedia.org/wiki/Actinhttp://en.wikipedia.org/wiki/Myosinhttp://en.wikipedia.org/wiki/Cytoskeletonhttp://en.wikipedia.org/wiki/Scaffoldinghttp://en.wikipedia.org/wiki/Cell_signalinghttp://en.wikipedia.org/wiki/Antibodyhttp://en.wikipedia.org/wiki/Cell_adhesionhttp://en.wikipedia.org/wiki/Cell_cyclehttp://en.wikipedia.org/wiki/Essential_amino_acidhttp://en.wikipedia.org/wiki/Digestionhttp://en.wikipedia.org/wiki/Greek_languagehttp://en.wikipedia.org/wiki/J%C3%B6ns_Jakob_Berzeliushttp://en.wikipedia.org/wiki/James_B._Sumnerhttp://en.wikipedia.org/wiki/Ureasehttp://en.wikipedia.org/wiki/Protein#cite_note-2http://en.wikipedia.org/wiki/Insulinhttp://en.wikipedia.org/wiki/Frederick_Sangerhttp://en.wikipedia.org/wiki/Hemoglobinhttp://en.wikipedia.org/wiki/Myoglobinhttp://en.wikipedia.org/wiki/Max_Perutzhttp://en.wikipedia.org/wiki/John_Kendrewhttp://en.wikipedia.org/wiki/John_Kendrewhttp://en.wikipedia.org/wiki/Protein#cite_note-3http://en.wikipedia.org/wiki/Protein#cite_note-4http://en.wikipedia.org/wiki/Nobel_Prize_in_Chemistry


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CONTENT

1.) Measurement

The expression of many genes is regulated after transcription (i.e., by

microRNAs or ubiquitin ligases), so an increase in mRNA concentration need not

always increase expression. In fact, mRNA concentration has been shown to be a poor

predictor of resultant protein abundance.[1][2] Nevertheless, mRNA levels can be

quantitatively measured byNorthern blotting, a process in which a sample of RNA is

separated on an agarose gel and hybridized to a radio-labeled RNA probe that is

complementary to the target sequence. Northern blotting requires the use of

radioactive reagents and can have lower data quality than more modern methods (dueto the fact that quantification is done by measuring band strength in an image of a

gel), but it is still often used. It does, for example, offer the benefit of allowing the

discrimination of alternately spliced transcripts.

A more modern low-throughput approach for measuring mRNA abundance is

real-time polymerase chain reaction (The term RT-PCR is used to refer to both

reverse transcription PCR as well as real-time PCR, which is also known as

quantitative RT-PCR or quantitative PCR (qPCR). With a carefully constructed

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http://en.wikipedia.org/wiki/MicroRNAhttp://en.wikipedia.org/wiki/Ubiquitin_ligasehttp://en.wikipedia.org/wiki/Gene_expression#cite_note-Correlation_between_Protein_and_mRNA_Abundance_in_Yeast-0http://en.wikipedia.org/wiki/Gene_expression#cite_note-Comparing_protein_abundance_and_mRNA_expression_levels_on_a_genomic_scale-1http://en.wikipedia.org/wiki/Northern_blottinghttp://en.wikipedia.org/wiki/Agarose_gelhttp://en.wikipedia.org/wiki/Real-time_polymerase_chain_reactionhttp://en.wikipedia.org/wiki/QPCRhttp://en.wikipedia.org/wiki/MicroRNAhttp://en.wikipedia.org/wiki/Ubiquitin_ligasehttp://en.wikipedia.org/wiki/Gene_expression#cite_note-Correlation_between_Protein_and_mRNA_Abundance_in_Yeast-0http://en.wikipedia.org/wiki/Gene_expression#cite_note-Comparing_protein_abundance_and_mRNA_expression_levels_on_a_genomic_scale-1http://en.wikipedia.org/wiki/Northern_blottinghttp://en.wikipedia.org/wiki/Agarose_gelhttp://en.wikipedia.org/wiki/Real-time_polymerase_chain_reactionhttp://en.wikipedia.org/wiki/QPCR


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standard curve qPCR can produce an absolute measurement such as number of copies

of mRNA per nanolitre of homogenized tissue. The lower level of noise in data

obtained via qPCR often makes this the method of choice, but the price of the

required equipment and reagents can be prohibitive.

A DNA sequence or genetic sequence is a succession of letters representing

the primary structure of a real or hypothetical DNA molecule or strand, with the

capacity to carry information as described by the central dogma of molecular biology.

The possible letters areA, C, G, and T, representing the fournucleotidebases

of a DNA strand adenine, cytosine, guanine, thymine covalently linked to a

phosphodiesterbackbone. In the typical case, the sequences are printed abutting oneanother without gaps, as in the sequence AAAGTCTGAC, read left to right in the 5'

to 3' direction. Short sequences of nucleotides are referred to as oligonucleotides and

are used in a range of laboratory applications in molecular biology. With regard to

biological function, a DNA sequence may be consideredsense orantisense, and either

coding ornoncoding. DNA sequences can also contain "junk DNA."

Sequences can be derived from the biological raw material through a process

called DNA sequencing. In some special cases, letters besides A, T, C, and G are

present in a sequence. These letters represent ambiguity. Of all the molecules

sampled, there is more than one kind of nucleotide at that position. The rules of the

International Union of Pure and Applied Chemistry (IUPAC) are as follows:

A = adenine

C = cytosine

G = guanine

T = thymine

R = G A (purine)

Y = T C (pyrimidine)

K = G T (keto)

M = A C (amino)

S = G C (strong bonds)

W = A T (weak bonds)

B = G T C (all but A)

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http://en.wikipedia.org/wiki/Primary_structurehttp://en.wikipedia.org/wiki/DNAhttp://en.wikipedia.org/wiki/Moleculehttp://en.wikipedia.org/wiki/Informationhttp://en.wikipedia.org/wiki/Central_dogma_of_molecular_biologyhttp://en.wikipedia.org/wiki/Nucleotidehttp://en.wikipedia.org/wiki/Nucleobasehttp://en.wikipedia.org/wiki/Adeninehttp://en.wikipedia.org/wiki/Cytosinehttp://en.wikipedia.org/wiki/Guaninehttp://en.wikipedia.org/wiki/Thyminehttp://en.wikipedia.org/wiki/Covalenthttp://en.wikipedia.org/wiki/Phosphodiester_bondhttp://en.wikipedia.org/wiki/Directionality_(molecular_biology)http://en.wikipedia.org/wiki/Directionality_(molecular_biology)http://en.wikipedia.org/wiki/Oligonucleotidehttp://en.wikipedia.org/wiki/Molecular_biologyhttp://en.wikipedia.org/wiki/Sense_(molecular_biology)http://en.wikipedia.org/wiki/Sense_(molecular_biology)http://en.wikipedia.org/wiki/Sense_(molecular_biology)http://en.wikipedia.org/wiki/Sense_(molecular_biology)http://en.wikipedia.org/wiki/Coding_strandhttp://en.wikipedia.org/wiki/Noncoding_DNAhttp://en.wikipedia.org/wiki/Junk_DNAhttp://en.wikipedia.org/wiki/DNA_sequencinghttp://en.wikipedia.org/wiki/DNA_sequencinghttp://en.wikipedia.org/wiki/IUPAChttp://en.wikipedia.org/wiki/Primary_structurehttp://en.wikipedia.org/wiki/DNAhttp://en.wikipedia.org/wiki/Moleculehttp://en.wikipedia.org/wiki/Informationhttp://en.wikipedia.org/wiki/Central_dogma_of_molecular_biologyhttp://en.wikipedia.org/wiki/Nucleotidehttp://en.wikipedia.org/wiki/Nucleobasehttp://en.wikipedia.org/wiki/Adeninehttp://en.wikipedia.org/wiki/Cytosinehttp://en.wikipedia.org/wiki/Guaninehttp://en.wikipedia.org/wiki/Thyminehttp://en.wikipedia.org/wiki/Covalenthttp://en.wikipedia.org/wiki/Phosphodiester_bondhttp://en.wikipedia.org/wiki/Directionality_(molecular_biology)http://en.wikipedia.org/wiki/Directionality_(molecular_biology)http://en.wikipedia.org/wiki/Oligonucleotidehttp://en.wikipedia.org/wiki/Molecular_biologyhttp://en.wikipedia.org/wiki/Sense_(molecular_biology)http://en.wikipedia.org/wiki/Coding_strandhttp://en.wikipedia.org/wiki/Noncoding_DNAhttp://en.wikipedia.org/wiki/Junk_DNAhttp://en.wikipedia.org/wiki/DNA_sequencinghttp://en.wikipedia.org/wiki/IUPAC


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D = G A T (all but C)

H = A C T (all but G)

V = G C A (all but T)

N = A G C T (any)

In addition to low-throughput methods, transcript levels for many genes at

once (expression profiling) can be measured with DNA microarray technology or "tag

based" technologies like Serial analysis of gene expression (SAGE) or the more

advanced version SuperSAGE, which can provide a relative measure of the cellular

concentration of different messenger RNAs. Recent advances in microarray

technology allow for the quantification, on a single array, of transcript levels for every

known gene in the human genome. The great advantage of tag-based methods is the

"open architecture", allowing for the exact measurement of any transcript, known or

unknown. Especially SuperSAGE recommends itself therefore also for studying

organisms with unknown genomes.

Protein levels themselves can be estimated by a number of means. The most

commonly used method is to perform a Western blot against the protein of interest,

whereby cellularlysate is separated on apolyacrylamide gel and then probed with an

antibody to the protein of interest. The antibody can either be conjugated to a

fluorophore or to horseradish peroxidase for imaging or quantification. Another

commonly used method for assaying the amount of a particular protein in a cell is to

fuse a copy of the protein to a reporter gene such as Green fluorescent protein, which

can be directly imaged using a fluorescent microscope. Because it is very difficult to

clone a GFP-fused protein into its native location in the genome, however, this

method often cannot be used to measure endogenous regulatory mechanisms (GFP-

fusions are therefore most often expressed on extra-genomic DNA such as an

expression vector). Fusing a target protein to a reporter can also change the protein's

behavior, including its cellular localization and expression level.

The pattern of detection of a gene or gene product may be described using

terms such as facultative, constitutive, circadian, cyclic, housekeeping, or inducible.

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http://en.wikipedia.org/wiki/Expression_profilinghttp://en.wikipedia.org/wiki/DNA_microarrayhttp://en.wikipedia.org/wiki/Serial_analysis_of_gene_expressionhttp://en.wikipedia.org/wiki/Serial_analysis_of_gene_expressionhttp://en.wikipedia.org/wiki/SuperSAGEhttp://en.wikipedia.org/wiki/Concentrationhttp://en.wikipedia.org/wiki/Concentrationhttp://en.wikipedia.org/wiki/Messenger_RNAhttp://en.wikipedia.org/wiki/Western_blothttp://en.wikipedia.org/wiki/Lysatehttp://en.wikipedia.org/wiki/Polyacrylamide_gelhttp://en.wikipedia.org/wiki/Fluorophorehttp://en.wikipedia.org/wiki/Horseradish_peroxidasehttp://en.wikipedia.org/wiki/Green_fluorescent_proteinhttp://en.wikipedia.org/wiki/Expression_vectorhttp://en.wikipedia.org/wiki/Expression_profilinghttp://en.wikipedia.org/wiki/DNA_microarrayhttp://en.wikipedia.org/wiki/Serial_analysis_of_gene_expressionhttp://en.wikipedia.org/wiki/SuperSAGEhttp://en.wikipedia.org/wiki/Concentrationhttp://en.wikipedia.org/wiki/Messenger_RNAhttp://en.wikipedia.org/wiki/Western_blothttp://en.wikipedia.org/wiki/Lysatehttp://en.wikipedia.org/wiki/Polyacrylamide_gelhttp://en.wikipedia.org/wiki/Fluorophorehttp://en.wikipedia.org/wiki/Horseradish_peroxidasehttp://en.wikipedia.org/wiki/Green_fluorescent_proteinhttp://en.wikipedia.org/wiki/Expression_vector


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2.) Regulation of gene expression

Regulation of gene expression is the cellular control of the amount and timing

of appearance of the functional product of a gene. Any step of gene expression may

be modulated, from the DNA-RNA transcription step to post-translational

modification of a protein. Gene regulation gives the cell control over structure and

function, and is the basis forcellular differentiation,morphogenesis and the versatility

and adaptability of any organism.

In developmental biology, cellular differentiation is the process by which a

less specialized cell becomes a more specialized cell type. Differentiation occurs

numerous times during the development of a multicellular organism as the organismchanges from a single zygote to a complex system of tissues and cell types.

Differentiation is a common process in adults as well: adult stem cells divide and

create fully-differentiated daughter cells during tissue repair and during normal cell

turnover. Differentiation dramatically changes a cell's size, shape, membrane

potential, metabolic activity, and responsiveness to signals. These changes are largely

due to highly-controlled modifications in gene expression. With a few exceptions,

cellular differentiation almost never involves a change in the DNA sequence itself.

Thus, different cells can have very different physical characteristics despite having the

same genome.

A cell that is able to differentiate into many cell types is known as pluripotent.

Such cells are called stem cells in animals and meristematic cells in higher plants. A

cell that is able to differentiate into all cell types is known as totipotent. In mammals,

only the zygote and early embryonic cells are totipotent, while in plants many

differentiated cells can become totipotent with simple laboratory techniques. In

cytopathology, the level of cellular differentiation is used as a measure of cancer

progression. "Grade" is a marker of how differentiated a cell in a tumor is.

3.) Expression system

An expression system consists, minimally, of a source of DNA and the

molecular machinery required to transcribe the DNA into mRNA and translate the

mRNA intoprotein using the nutrients and fuel provided. In the broadest sense, this

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http://en.wikipedia.org/wiki/Transcription_(genetics)http://en.wikipedia.org/wiki/Post-translational_modificationhttp://en.wikipedia.org/wiki/Post-translational_modificationhttp://en.wikipedia.org/wiki/Post-translational_modificationhttp://en.wikipedia.org/wiki/Cellular_differentiationhttp://en.wikipedia.org/wiki/Cellular_differentiationhttp://en.wikipedia.org/wiki/Cellular_differentiationhttp://en.wikipedia.org/wiki/Morphogenesishttp://en.wikipedia.org/wiki/Organismhttp://en.wikipedia.org/wiki/Developmental_biologyhttp://en.wikipedia.org/wiki/Cell_(biology)http://en.wikipedia.org/wiki/Cell_typehttp://en.wikipedia.org/wiki/Multicellular_organismhttp://en.wikipedia.org/wiki/Zygotehttp://en.wikipedia.org/wiki/Tissue_(biology)http://en.wikipedia.org/wiki/Adult_stem_cellhttp://en.wikipedia.org/wiki/Cell_divisionhttp://en.wikipedia.org/wiki/Membrane_potentialhttp://en.wikipedia.org/wiki/Membrane_potentialhttp://en.wikipedia.org/wiki/Metabolismhttp://en.wikipedia.org/wiki/Gene_expressionhttp://en.wikipedia.org/wiki/DNAhttp://en.wikipedia.org/wiki/Genomehttp://en.wikipedia.org/wiki/Pluripotenthttp://en.wikipedia.org/wiki/Stem_cellhttp://en.wikipedia.org/wiki/Meristemhttp://en.wikipedia.org/wiki/Cell_typehttp://en.wikipedia.org/wiki/Totipotenthttp://en.wikipedia.org/wiki/Embryohttp://en.wikipedia.org/wiki/Cytopathologyhttp://en.wikipedia.org/wiki/Cancerhttp://en.wikipedia.org/wiki/Grading_(tumors)http://en.wikipedia.org/wiki/DNAhttp://en.wikipedia.org/wiki/Molecular_machineryhttp://en.wikipedia.org/wiki/Transcription_(genetics)http://en.wikipedia.org/wiki/MRNAhttp://en.wikipedia.org/wiki/Translatehttp://en.wikipedia.org/wiki/Proteinhttp://en.wikipedia.org/wiki/Transcription_(genetics)http://en.wikipedia.org/wiki/Post-translational_modificationhttp://en.wikipedia.org/wiki/Post-translational_modificationhttp://en.wikipedia.org/wiki/Cellular_differentiationhttp://en.wikipedia.org/wiki/Morphogenesishttp://en.wikipedia.org/wiki/Organismhttp://en.wikipedia.org/wiki/Developmental_biologyhttp://en.wikipedia.org/wiki/Cell_(biology)http://en.wikipedia.org/wiki/Cell_typehttp://en.wikipedia.org/wiki/Multicellular_organismhttp://en.wikipedia.org/wiki/Zygotehttp://en.wikipedia.org/wiki/Tissue_(biology)http://en.wikipedia.org/wiki/Adult_stem_cellhttp://en.wikipedia.org/wiki/Cell_divisionhttp://en.wikipedia.org/wiki/Membrane_potentialhttp://en.wikipedia.org/wiki/Membrane_potentialhttp://en.wikipedia.org/wiki/Metabolismhttp://en.wikipedia.org/wiki/Gene_expressionhttp://en.wikipedia.org/wiki/DNAhttp://en.wikipedia.org/wiki/Genomehttp://en.wikipedia.org/wiki/Pluripotenthttp://en.wikipedia.org/wiki/Stem_cellhttp://en.wikipedia.org/wiki/Meristemhttp://en.wikipedia.org/wiki/Cell_typehttp://en.wikipedia.org/wiki/Totipotenthttp://en.wikipedia.org/wiki/Embryohttp://en.wikipedia.org/wiki/Cytopathologyhttp://en.wikipedia.org/wiki/Cancerhttp://en.wikipedia.org/wiki/Grading_(tumors)http://en.wikipedia.org/wiki/DNAhttp://en.wikipedia.org/wiki/Molecular_machineryhttp://en.wikipedia.org/wiki/Transcription_(genetics)http://en.wikipedia.org/wiki/MRNAhttp://en.wikipedia.org/wiki/Translatehttp://en.wikipedia.org/wiki/Protein


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includes every living cell capable of producing protein from DNA. However, an

expression system more specifically refers to a laboratory tool, often artificial in some

manner, used for assembling the product of a specific gene or genes. It is defined as

the "combination of an expression vector, its cloned DNA, and the host for the vector

that provide a context to allow foreign gene function in a host cell, that is, produce

proteins at a high level".

In addition to these biological tools, certain naturally observed configurations

of DNA (genes, promoters, enhancers, repressors) and the associated machinery itself

are referred to as an expression system, as in the simple repressor 'switch' expression

system in Lambda phage. It is these natural expression systems that inspire artificial

expression systems, (such as the Tet-on and Tet-offexpression systems).

Each expression system has distinct advantages and liabilities, and may be

named after the host, the DNA source or the delivery mechanism for the genetic

material. For example, common expression systems include bacteria (such as E.coli,

B. subtilis), yeast (such as S.cerevisiae),plasmid, artificial chromosomes,phage (such

as lambda), cell lines, orvirus(such asbaculovirus,retrovirus, adenovirus).

4.) Overexpression

In the laboratory, the protein encoded by a gene is sometimes expressed in

increased quantity. This can come about by increasing the number of copies of the

gene or increasing the binding strength of the promoter region.

Often, the DNA sequence for a protein of interest will be cloned orsubcloned

into a plasmid containing the lac promoter, which is then transformed into the

bacteriumEscherichia coli. Addition ofIPTG (a lactose analog) causes the bacteria to

express the protein of interest. However, this strategy does not always yield functional

protein, in which case, otherorganisms ortissue cultures may be more effective. For

example, the yeast Saccharomyces cerevisiae is often preferred to bacteria for

proteins that undergo extensive posttranslational modification. Nonetheless, bacterial

expression has the advantage of easily producing large amounts of protein, which is

required for X-ray crystallography or nuclear magnetic resonance experiments for

structure determination.

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http://en.wikipedia.org/wiki/Artificialhttp://en.wikipedia.org/wiki/Expression_vectorhttp://en.wikipedia.org/wiki/Lambda_phagehttp://en.wikipedia.org/wiki/Tetracycline_controlled_transcriptional_activationhttp://en.wikipedia.org/wiki/Tetracycline_controlled_transcriptional_activationhttp://en.wikipedia.org/wiki/Host_(biology)http://en.wikipedia.org/wiki/Bacteriahttp://en.wikipedia.org/wiki/Escherichia_colihttp://en.wikipedia.org/wiki/Escherichia_colihttp://en.wikipedia.org/wiki/B._subtilishttp://en.wikipedia.org/wiki/Yeasthttp://en.wikipedia.org/wiki/Saccharomyces_cerevisiaehttp://en.wikipedia.org/wiki/Plasmidhttp://en.wikipedia.org/wiki/Artificial_chromosomeshttp://en.wikipedia.org/wiki/Artificial_chromosomeshttp://en.wikipedia.org/wiki/Phagehttp://en.wikipedia.org/wiki/Lambda_phagehttp://en.wikipedia.org/wiki/Cell_lineshttp://en.wikipedia.org/wiki/Cell_lineshttp://en.wikipedia.org/wiki/Virushttp://en.wikipedia.org/wiki/Virushttp://en.wikipedia.org/wiki/Baculovirushttp://en.wikipedia.org/wiki/Baculovirushttp://en.wikipedia.org/wiki/Retrovirushttp://en.wikipedia.org/wiki/Adenovirushttp://en.wikipedia.org/wiki/Cloning#Cloning_in_biologyhttp://en.wikipedia.org/wiki/Subcloninghttp://en.wikipedia.org/wiki/Plasmidhttp://en.wikipedia.org/wiki/Lac_operonhttp://en.wikipedia.org/wiki/Transformation_(genetics)http://en.wikipedia.org/wiki/Escherichia_colihttp://en.wikipedia.org/wiki/IPTGhttp://en.wikipedia.org/wiki/Lactosehttp://en.wikipedia.org/wiki/Organismhttp://en.wikipedia.org/wiki/Tissue_culturehttp://en.wikipedia.org/wiki/Yeasthttp://en.wikipedia.org/wiki/Yeasthttp://en.wikipedia.org/wiki/Saccharomyces_cerevisiaehttp://en.wikipedia.org/wiki/Posttranslational_modificationhttp://en.wikipedia.org/wiki/X-ray_crystallographyhttp://en.wikipedia.org/wiki/Nuclear_magnetic_resonancehttp://en.wikipedia.org/wiki/Artificialhttp://en.wikipedia.org/wiki/Expression_vectorhttp://en.wikipedia.org/wiki/Lambda_phagehttp://en.wikipedia.org/wiki/Tetracycline_controlled_transcriptional_activationhttp://en.wikipedia.org/wiki/Host_(biology)http://en.wikipedia.org/wiki/Bacteriahttp://en.wikipedia.org/wiki/Escherichia_colihttp://en.wikipedia.org/wiki/B._subtilishttp://en.wikipedia.org/wiki/Yeasthttp://en.wikipedia.org/wiki/Saccharomyces_cerevisiaehttp://en.wikipedia.org/wiki/Plasmidhttp://en.wikipedia.org/wiki/Artificial_chromosomeshttp://en.wikipedia.org/wiki/Phagehttp://en.wikipedia.org/wiki/Lambda_phagehttp://en.wikipedia.org/wiki/Cell_lineshttp://en.wikipedia.org/wiki/Virushttp://en.wikipedia.org/wiki/Baculovirushttp://en.wikipedia.org/wiki/Retrovirushttp://en.wikipedia.org/wiki/Adenovirushttp://en.wikipedia.org/wiki/Cloning#Cloning_in_biologyhttp://en.wikipedia.org/wiki/Subcloninghttp://en.wikipedia.org/wiki/Plasmidhttp://en.wikipedia.org/wiki/Lac_operonhttp://en.wikipedia.org/wiki/Transformation_(genetics)http://en.wikipedia.org/wiki/Escherichia_colihttp://en.wikipedia.org/wiki/IPTGhttp://en.wikipedia.org/wiki/Lactosehttp://en.wikipedia.org/wiki/Organismhttp://en.wikipedia.org/wiki/Tissue_culturehttp://en.wikipedia.org/wiki/Yeasthttp://en.wikipedia.org/wiki/Saccharomyces_cerevisiaehttp://en.wikipedia.org/wiki/Posttranslational_modificationhttp://en.wikipedia.org/wiki/X-ray_crystallographyhttp://en.wikipedia.org/wiki/Nuclear_magnetic_resonance


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5.) Gene networks and expression

Genes have sometimes been regarded as nodes in a network, with inputs being

proteins such as transcription factors, and outputs being the level of gene expression.

The node itself performs a function, and the operation of these functions have been

interpreted as performing a kind of information processing within cell and determine

cellular behaviour.

6.) Techniques and tools

The following experimental techniques are used to measure gene expression and

are listed in roughly chronological order, starting with the older, more established

technologies. They are divided into two groups based on their degree ofmultiplexity.

Low-to-mid-plex techniques:

o Expression vector

o Reporter gene

o Northern blot

o Fluorescent in situ hybridization

o Real-time PCR

o Multiplex PCR

o RACE

Higher-plex techniques:

o SAGE

o DNA microarray

o Tiling arrayo ChIP-Seq

o mRNA-Seq

CONCLUSION

Gene expression is the process by which inheritable information from a gene,

such as the DNA sequence, is made into a functional gene product, such asprotein or

RNA.

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http://en.wikipedia.org/wiki/Transcription_factorhttp://en.wikipedia.org/wiki/Information_processinghttp://en.wikipedia.org/wiki/Multiplex_(assay)http://en.wikipedia.org/wiki/Expression_vectorhttp://en.wikipedia.org/wiki/Reporter_genehttp://en.wikipedia.org/wiki/Northern_blothttp://en.wikipedia.org/wiki/Fluorescent_in_situ_hybridizationhttp://en.wikipedia.org/wiki/Real-time_PCRhttp://en.wikipedia.org/wiki/Variants_of_PCRhttp://en.wikipedia.org/wiki/Rapid_Amplification_of_cDNA_Endshttp://en.wikipedia.org/wiki/Serial_analysis_of_gene_expressionhttp://en.wikipedia.org/wiki/DNA_microarrayhttp://en.wikipedia.org/wiki/Tiling_arrayhttp://en.wikipedia.org/wiki/Chip-Sequencinghttp://en.wikipedia.org/w/index.php?title=MRNA-Sequencing&action=edit&redlink=1http://en.wikipedia.org/wiki/Genehttp://en.wikipedia.org/wiki/DNA_sequencehttp://en.wikipedia.org/wiki/Gene_producthttp://en.wikipedia.org/wiki/Proteinhttp://en.wikipedia.org/wiki/RNAhttp://en.wikipedia.org/wiki/Transcription_factorhttp://en.wikipedia.org/wiki/Information_processinghttp://en.wikipedia.org/wiki/Multiplex_(assay)http://en.wikipedia.org/wiki/Expression_vectorhttp://en.wikipedia.org/wiki/Reporter_genehttp://en.wikipedia.org/wiki/Northern_blothttp://en.wikipedia.org/wiki/Fluorescent_in_situ_hybridizationhttp://en.wikipedia.org/wiki/Real-time_PCRhttp://en.wikipedia.org/wiki/Variants_of_PCRhttp://en.wikipedia.org/wiki/Rapid_Amplification_of_cDNA_Endshttp://en.wikipedia.org/wiki/Serial_analysis_of_gene_expressionhttp://en.wikipedia.org/wiki/DNA_microarrayhttp://en.wikipedia.org/wiki/Tiling_arrayhttp://en.wikipedia.org/wiki/Chip-Sequencinghttp://en.wikipedia.org/w/index.php?title=MRNA-Sequencing&action=edit&redlink=1http://en.wikipedia.org/wiki/Genehttp://en.wikipedia.org/wiki/DNA_sequencehttp://en.wikipedia.org/wiki/Gene_producthttp://en.wikipedia.org/wiki/Proteinhttp://en.wikipedia.org/wiki/RNA


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Several steps in the gene expression process may be modulated, including the

transcription step and translation step and the post-translational modification of a

protein. Gene regulation gives the cellcontrol over structure and function, and is the

basis forcellular differentiation, morphogenesis and the versatility and adaptability of

any organism. Gene regulation may also serve as a substrate for evolutionary change,

since control of the timing, location, and amount of gene expression can have a

profound effect on the functions (actions) of the gene in the organism. Non-protein

coding genes (e.g. rRNA genes, tRNA genes) are transcribed, but not translated into

protein.

The expression of many genes is regulated after transcription (i.e., by

microRNAs orubiquitin ligases), so an increase in mRNA concentration need not

always increase expression. Regulation of gene expression is the cellular control of

the amount and timing of appearance of the functional product of a gene. Any step of

gene expression may be modulated, from the DNA-RNA transcription step to post-

translational modification of a protein.

An expression system consists, minimally, of a source of DNA and the

molecular machinery required to transcribe the DNA intomRNA and translate the

mRNA into proteinusing the nutrients and fuel provided. In the broadest sense, this

includes every living cell capable of producing protein from DNA.

In the laboratory, the protein encoded by a gene is sometimes expressed in

increased quantity. This can come about by increasing the number of copies of the

gene or increasing the binding strength of the promoter region. Genes have sometimes

been regarded as nodes in a network, with inputs being proteins such as transcription

factors, and outputs being the level of gene expression. The node itself performs a

function, and the operation of these functions have been interpreted as performing a

kind ofinformation processing within cell and determine cellular behaviour.

9
http://en.wikipedia.org/wiki/Transcription_(genetics)http://en.wikipedia.org/wiki/Translation_(biology)http://en.wikipedia.org/wiki/Post-translational_modificationhttp://en.wikipedia.org/wiki/Post-translational_modificationhttp://en.wikipedia.org/wiki/Cell_(biology)http://en.wikipedia.org/wiki/Cell_(biology)http://en.wikipedia.org/wiki/Cellular_differentiationhttp://en.wikipedia.org/wiki/Cellular_differentiationhttp://en.wikipedia.org/wiki/Morphogenesishttp://en.wikipedia.org/wiki/Organismhttp://en.wikipedia.org/wiki/RRNAhttp://en.wikipedia.org/wiki/TRNAhttp://en.wikipedia.org/wiki/Translation_(genetics)http://en.wikipedia.org/wiki/MicroRNAhttp://en.wikipedia.org/wiki/Ubiquitin_ligasehttp://en.wikipedia.org/wiki/Ubiquitin_ligasehttp://en.wikipedia.org/wiki/Transcription_(genetics)http://en.wikipedia.org/wiki/Post-translational_modificationhttp://en.wikipedia.org/wiki/Post-translational_modificationhttp://en.wikipedia.org/wiki/DNAhttp://en.wikipedia.org/wiki/Molecular_machineryhttp://en.wikipedia.org/wiki/Transcription_(genetics)http://en.wikipedia.org/wiki/MRNAhttp://en.wikipedia.org/wiki/MRNAhttp://en.wikipedia.org/wiki/Translatehttp://en.wikipedia.org/wiki/Proteinhttp://en.wikipedia.org/wiki/Proteinhttp://en.wikipedia.org/wiki/Transcription_factorhttp://en.wikipedia.org/wiki/Transcription_factorhttp://en.wikipedia.org/wiki/Transcription_factorhttp://en.wikipedia.org/wiki/Information_processinghttp://en.wikipedia.org/wiki/Transcription_(genetics)http://en.wikipedia.org/wiki/Translation_(biology)http://en.wikipedia.org/wiki/Post-translational_modificationhttp://en.wikipedia.org/wiki/Cell_(biology)http://en.wikipedia.org/wiki/Cellular_differentiationhttp://en.wikipedia.org/wiki/Morphogenesishttp://en.wikipedia.org/wiki/Organismhttp://en.wikipedia.org/wiki/RRNAhttp://en.wikipedia.org/wiki/TRNAhttp://en.wikipedia.org/wiki/Translation_(genetics)http://en.wikipedia.org/wiki/MicroRNAhttp://en.wikipedia.org/wiki/Ubiquitin_ligasehttp://en.wikipedia.org/wiki/Transcription_(genetics)http://en.wikipedia.org/wiki/Post-translational_modificationhttp://en.wikipedia.org/wiki/Post-translational_modificationhttp://en.wikipedia.org/wiki/DNAhttp://en.wikipedia.org/wiki/Molecular_machineryhttp://en.wikipedia.org/wiki/Transcription_(genetics)http://en.wikipedia.org/wiki/MRNAhttp://en.wikipedia.org/wiki/Translatehttp://en.wikipedia.org/wiki/Proteinhttp://en.wikipedia.org/wiki/Transcription_factorhttp://en.wikipedia.org/wiki/Transcription_factorhttp://en.wikipedia.org/wiki/Information_processing


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REFERENCES

Gygi, Steven P.; Yvan Rochon, B. Robert Franza, Ruedi Aebersold (1999).

"Correlation between Protein and mRNA Abundance in Yeast" (in English).

American Society for Microbiology. 1720-1730.

http://mcb.asm.org/cgi/reprint/19/3/1720.pdf. Retrieved on 2008-12-18.

Greenbaum, Dov; Christopher Colangelo, Kenneth Williams, Mark Gerstein (29

August 2003)."Comparing protein abundance and mRNA expression levels on

a genomic scale" (in English). Genome Biology.

http://genomebiology.com/2003/4/9/117. Retrieved on 2008-12-18.

Glossary of gene expression terms"Definition: expression system". Online

Medical Dictionary. Centre for Cancer Education, University of Newcastle upon

Tyne: Cancerweb. 1997-11-13. http://cancerweb.ncl.ac.uk/cgi-bin/omd?

expression+system. Retrieved on 2008-06-10.

"Expression system - definition". Biology Online. Biology-Online.org. 2005-10-

03. http://www.biology-online.org/dictionary/Expression_system. Retrieved on

2008-06-10.

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ASSIGMENT BLOCK 5

GENE EXPRESSION

By :

Yudi Pranata

54081001014

11


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Medical Faculty of Sriwidjaya University

2008

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tugas blok 5

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