From the Genome to 
    the Proteome
The Next Step: 
    Functional Genomics
Human Genome  
    Project FAQ
   ข้อสงสัยที่ถามกันบ่อย
 Benefits and
    Implications of 
    Genome Research
What's a genome?   
    Why is it important?

Stem Cells: A Primer
 ความรู้เบื้องต้นเกี่ยวกับเซลแม่
 แบบ ต้นกำเนิดร่างกายมนุษย์

เซลต้นกำเนิด 
   ข้อมูลเพิ่มเติมเกี่ยวกับเซลต้น
   กำเนิดหรือเซลแม่แบบ
   Stem Cells: A Primer

โครโมโซม
    Chromosomes
ออโตโซม
    autosomes
โครโมโซมเพศ
   Sex chromosomes

การโคลนตัวอ่อนมนุษย์เพื่อ
    การศึกษารูปแบบการนำเอา
    เซลต้นแบบมาใช้ในการรักษา
    ทางการแพทย์
    Using cloned human 
    embryos for research

Lysosomal Storage 
   Disorders (LSD)
ความผิดปรกติโครโมโซม
   คู่ที่ 5 
   Cri du chat syndrome

	Health Navigation

สนใจรายละเอียดเพิ่มเติม
กรุณาแจ้งให้ทึมงานเพื่อ
จัดเตรียมหาสาระให้



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From the Genome to the Proteome
 

Cells are the fundamental working units of every living system. All the instructions needed to direct their activities are contained within the chemical DNA (deoxyribonucleic acid).  The genome is an organism's complete set of DNA. Genomes vary widely in size: the smallest known genome for a free-living organism (a bacterium) contains about 600,000 DNA base pairs, while human and mouse genomes have some 3 billion. Except for mature red blood cells, all human cells contain a complete genome. DNA from all organisms is made up of the same chemical and physical components. The DNA sequence is the particular side-by-side arrangement of bases along the DNA strand (e.g., ATTCCGGA). This order spells out the exact instructions required to create a particular organism with its own unique traits.

In humans, as in other higher organisms, a DNA molecule consists of two strands that wrap around each other to resemble a twisted ladder whose sides, made of sugar and phosphate molecules, are connected by rungs of nitrogen-containing chemicals called bases. Each strand is a linear arrangement of repeating similar units called nucleotides, which are each composed of one sugar, one phosphate, and a nitrogenous base. Four different bases are present in DNA: adenine (A), thymine (T), cytosine (C), and guanine (G).  The particular order of the bases arranged along the sugar-phosphate backbone is called the DNA sequence; the sequence specifies the exact genetic instructions required to create a particular organism with its own unique traits.

The two DNA strands are held together by weak bonds between the bases on each strand, forming base pairs (bp). Genome size is usually stated as the total number of base pairs; the human genome contains roughly 3 billion bp.

If unwound and tied together, the strands of human DNA would stretch more than 5 feet but would be only 50 trillionths of an inch wide. For each organism, the components of these slender threads encode all the information necessary for building and maintaining life, from simple bacteria to remarkably complex human beings. Understanding how DNA performs this function requires some knowledge of its structure and organization.

Each time a cell divides into two daughter cells, its full genome is duplicated; for humans and other complex organisms, this duplication occurs in the nucleus. During cell division the DNA molecule unwinds and the weak bonds between the base pairs break, allowing the strands to separate. Each strand directs the synthesis of a complementary new strand, with free nucleotides matching up with their complementary bases on each of the separated strands. Strict base-pairing rules are adhered to; adenine will pair only with thymine (an A-T pair) and cytosine with guanine (a C-G pair). Each daughter cell receives one old and one new DNA strand. The cells' adherence to these base-pairing rules ensures that the new strand is an exact copy of the old one. This minimizes the incidence of errors (mutations) that may greatly affect the resulting organism or its offspring.

DNA in the human genome is arranged into 24 distinct chromosomes--physically separate molecules that range in length from about 50 million to 250 million base pairs. All genes are arranged linearly along the chromosomes. The nucleus of most human cells contains two sets of chromosomes, one set given by each parent. Each set has 23 single chromosomes--22 autosomes and an X or Y sex chromosome. (A normal female will have a pair of X chromosomes; a male will have an X and Y pair.) Chromosomes contain roughly equal parts of protein and DNA; chromosomal DNA contains an average of 150 million bases. DNA molecules are among the largest molecules now known.  Chromosomes can be seen under a light microscope and, when stained with certain dyes, reveal a pattern of light and dark bands reflecting regional variations in the amounts of A and T vs G and C. Differences in size and banding pattern allow the 24 chromosomes to be distinguished from each other, an analysis called a karyotype. A few types of major chromosomal abnormalities, including missing or extra copies or gross breaks and rejoinings (translocations), can be detected by microscopic examination; Down's syndrome, in which an individual's cells contain a third copy of chromosome 21, is diagnosed by karyotype analysis.  Most changes in DNA, however, are too subtle to be detected by this technique and require molecular analysis. These subtle DNA abnormalities (mutations) are responsible for many inherited diseases such as cystic fibrosis and sickle cell anemia or may predispose an individual to cancer, major psychiatric illnesses, and other complex diseases.

Each chromosome contains many genes, the basic physical and functional units of heredity. Genes are specific sequences of bases that encode instructions on how to make proteins, the molecules that perform most life functions and even make up the majority of cellular structures. Genes comprise only about 2% of the human genome; the remainder consists of noncoding regions, whose functions may include providing chromosomal structural integrity and regulating where, when, and in what quantity proteins are made. The human genome is estimated to contain 30,000 to 40,000 genes.

Human genes vary widely in length, often extending over thousands of bases, but only about 10% of the genome is known to include the protein-coding sequences (exons) of genes. Interspersed with many genes are intron sequences, which have no coding function. The balance of the genome is thought to consist of other noncoding regions (such as control sequences and intergenic regions), whose functions are obscure.
 

Although genes get a lot of attention, it's the proteins that perform most life functions. Proteins are large, complex molecules made up of smaller subunits called amino acids. Twenty different kinds of amino acids are usually found in proteins. Within the gene, each specific sequence of three DNA bases (codons) directs the cells' protein-synthesizing machinery to add specific amino acids. For example, the base sequence ATG codes for the amino acid methionine. Since 3 bases code for 1 amino acid, the protein coded by an average-sized gene (3000 bp) will contain 1000 amino acids. The genetic code is thus a series of codons that specify which amino acids are required to make up specific proteins. Chemical properties that distinguish the 20 different amino acids cause the protein chains to fold up into specific three-dimensional structures that define their particular functions in the cell.

The constellation of all proteins in a cell is called its proteome. Unlike the relatively unchanging genome, the dynamic proteome changes from moment to moment in response to tens of thousands of intra- and extracellular environmental signals. A protein's chemistry and behavior is specified by the gene sequence and by the number and identities of other proteins made in the same cell at the same time and with which it associates and reacts. Studies to explore protein structure and their activities, known as proteomics, will be the focus of much research for decades to come and will help elucidate the molecular basis of health and disease.  The protein-coding instructions from the genes are transmitted indirectly through messenger ribonucleic acid (mRNA), a transient intermediary molecule similar to a single strand of DNA. For the information within a gene to be expressed, a complementary RNA strand is produced (a process called transcription) from the DNA template in the nucleus. This mRNA is moved from the nucleus to the cellular cytoplasm, where it serves as the template for protein synthesis. The cells' protein-synthesizing machinery then translates the codons into a string of amino acids that will constitute the protein molecule for which it codes. In the laboratory, the mRNA molecule can be isolated and used as a template to synthesize a complementary DNA (cDNA) strand, which can then be used to locate the corresponding genes on a chromosome map.

In June of 2000, HGP leaders, Craig Venter of the private company Celera Genomics, and President Clinton announced the completion of a "working draft" DNA sequence of the human genome.

In February 2001, HGP and Celera Genomics scientists published the long-awaited details of the working-draft DNA sequence achieved less than a year before. Although the draft is filled with mysteries, the first panoramic view of the human genetic landscape has revealed a wealth of information and some early surprises. Papers describing research observations in the journals Nature (Feb. 15, 2001) and Science (Feb. 16, 2001) are freely accessible via the Web.

Although clearly not a Holy Grail or Rosetta Stone for deciphering all of biology two early metaphors commonly used to describe the coveted prize the sequence is a magnificent and unprecedented resource that will serve as a basis for research and discovery throughout this century and beyond. It will have diverse practical applications and a profound impact upon how we view ourselves and our place in the tapestry of life around us.

One insight already gleaned from the sequence is that, even on the molecular level, we are more than the sum of our 35,000 or so genes. Surprisingly, this newly estimated number of genes is only one-third as great as previously thought and is only twice as many as those of a tiny transparent worm, although the numbers may be revised as more computational and experimental analyses are performed. At once humbled and intrigued by this finding, scientists suggest that the genetic key to human complexity lies not in the number of genes but in how gene parts are used to build different products in a process called alternative splicing. Other sources of added complexity are the thousands of post-translational chemical modifications made to proteins and the repertoire of regulatory mechanisms controlling these processes.

The draft encompasses 90% of the human genome's euchromatic portion, which contains the most genes. In constructing the working draft, the 16 genome sequencing centers produced over 22.1 billion bases of raw sequence data, comprising overlapping fragments totaling 3.9 billion bases and providing sevenfold coverage (sequenced seven times) of the human genome. Over 30% is high-quality, finished sequence, with eight- to tenfold coverage, 99.99% accuracy, and few gaps. All data are freely available via the Web.

The entire working draft will be finished to high quality by 2003. Coincidentally, that year also will be the 50th anniversary of Watson and Crick's publication of DNA structure that launched the era of molecular genetics (www.nature.com/genomics/human/watson-crick). Much will remain to be deciphered even then. Some highlights from Nature, Science, and The Wellcome Trust follow.

What Does the Draft Human Genome Sequence Tell Us?

By the Numbers

• The human genome contains 3164.7 million chemical nucleotide bases (A, C, T, and G).
• The average gene consists of 3000 bases, but sizes vary greatly, with the largest known human gene being dystrophin at 2.4 million bases.
• The total number of genes is estimated at 30,000 to 35,000 much lower than previous estimates of 80,000 to 140,000 that had been based on extrapolations from gene-rich areas as opposed to a composite of gene-rich and gene-poor areas.
• Almost all (99.9%) nucleotide bases are exactly the same in all people.
• The functions are unknown for over 50% of discovered genes.

• Less than 2% of the genome codes for proteins.
• Repeated sequences that do not code for proteins ("junk DNA") make up at least 50% of the human genome.
• Repetitive sequences are thought to have no direct functions, but they shed light on chromosome structure and dynamics. Over time, these repeats reshape the genome by rearranging it, creating entirely new genes, and modifying and reshuffling existing genes.
• During the past 50 million years, a dramatic decrease seems to have occurred in the rate of accumulation of repeats in the human genome.

• The human genome's gene-dense "urban centers" are predominantly composed of the DNA building blocks G and C.
• In contrast, the gene-poor "deserts" are rich in the DNA building blocks A and T. GC- and AT-rich regions usually can be seen through a microscope as light and dark bands on chromosomes.
• Genes appear to be concentrated in random areas along the genome, with vast expanses of noncoding DNA between.
• Stretches of up to 30,000 C and G bases repeating over and over often occur adjacent to gene-rich areas, forming a barrier between the genes and the "junk DNA." These CpG islands are believed to help regulate gene activity.
• Chromosome 1 has the most genes (2968), and the Y chromosome has the fewest (231).

• Unlike the human's seemingly random distribution of gene-rich areas, many other organisms' genomes are more uniform, with genes evenly spaced throughout.
• Humans have on average three times as many kinds of proteins as the fly or worm because of mRNA transcript "alternative splicing" and chemical modifications to the proteins. This process can yield different protein products from the same gene.
• Humans share most of the same protein families with worms, flies, and plants, but the number of gene family members has expanded in humans, especially in proteins involved in development and immunity.
• The human genome has a much greater portion (50%) of repeat sequences than the mustard weed (11%), the worm (7%), and the fly (3%).
• Although humans appear to have stopped accumulating repeated DNA over 50 million years ago, there seems to be no such decline in rodents. This may account for some of the fundamental differences between hominids and rodents, although gene estimates are similar in these species. Scientists have proposed many theories to explain evolutionary contrasts between humans and other organisms, including those of life span, litter sizes, inbreeding, and genetic drift.

• Scientists have identified about 1.4 million locations where single-base DNA differences (SNPs) occur in humans. This information promises to revolutionize the processes of finding chromosomal locations for disease-associated sequences and tracing human history.
• The ratio of germline (sperm or egg cell) mutations is 2:1 in males vs females. Researchers point to several reasons for the higher mutation rate in the male germline, including the greater number of cell divisions required for sperm formation than for eggs.

The draft sequence already is having an impact on finding genes associated with disease. Over 30 genes have been pinpointed and associated with breast cancer, muscle disease, deafness, and blindness. Additionally, finding the DNA sequences underlying such common diseases as cardiovascular disease, diabetes, arthritis, and cancers is being aided by the human variation maps (SNPs) generated in the HGP in cooperation with the private sector. These genes and SNPs provide focused targets for the development of effective new therapies.

One of the greatest impacts of having the sequence may well be in enabling an entirely new approach to biological research. In the past, researchers studied one or a few genes at a time. With whole-genome sequences and new high-throughput technologies, they can approach questions systematically and on a grand scale. They can study all the genes in a genome, for example, or all the transcripts in a particular tissue or organ or tumor, or how tens of thousands of genes and proteins work together in interconnected networks to orchestrate the chemistry of life. 

The Next Step: Functional Genomics

The words of Winston Churchill, spoken in 1942 after 3 years of war, capture well the HGP era: "Now this is not the end. It is not even the beginning of the end. But it is, perhaps, the end of the beginning."

The avalanche of genome data grows daily. The new challenge will be to use this vast reservoir of data to explore how DNA and proteins work with each other and the environment to create complex, dynamic living systems. Systematic studies of function on a grand scale-functional genomics-will be the focus of biological explorations in this century and beyond. These explorations will encompass studies in transcriptomics, proteomics, structural genomics, new experimental methodologies, and comparative genomics.

• Transcriptomics involves large-scale analysis of messenger RNAs transcribed from active genes to follow when, where, and under what conditions genes are expressed.
• Studying protein expression and function--or proteomics--can bring researchers closer to what's actually happening in the cell than gene-expression studies. This capability has applications to drug design.
• Structural genomics initiatives are being launched worldwide to generate the 3-D structures of one or more proteins from each protein family, thus offering clues to function and biological targets for drug design.
• Experimental methods for understanding the function of DNA sequences and the proteins they encode include knockout studies to inactivate genes in living organisms and monitor any changes that could reveal their functions.
• Comparative genomics--analyzing DNA sequence patterns of humans and well-studied model organisms side-by-side-has become one of the most powerful strategies for identifying human genes and interpreting their function.