Trends in Biotechnology

150402 TB 10 DNA from the Beginning - Genetic Organization and

Control

Concept 29 - DNA is packaged in a chromosome.Work on cytology in the late 1800s had shown that each living thing has a characteristic set of chromosomes in the nucleus of each cell. During the same period, biochemical studies indicated that the nuclear materials that make up the chromosomes are composed of DNA and proteins. In the first four decades of the 20th century, many scientists believed that protein carried the genetic code, and DNA was merely a supporting "scaffold."

Just the opposite proved to be true. Work by Avery and Hershey, in the 1940s and 1950s, proved that DNA is the genetic molecule. Work done in the 1960s and 1970s showed that each chromosome is essentially a package for one very long, continuous strand of the DNA. In higher organisms, structural proteins, some of which are histones, provide a scaffold upon which DNA is built into a compact chromosome. The DNA strand is wound around histone cores, which, in turn, are looped and fixed to specific regions of the chromosome.

• Animation at http://www.dnaftb.org/29/animation.html

• The review problem is at http://www.dnaftb.org/29/problem.html

Photo of chromatin digested by nuclease, from Hewish and Burgoyne's 1973 experiment.

Electron micrograph of the 10-nm fiber.

Electron micrograph of the 30-nm fiber

Electron micrograph of the DNA and the protein scaffold left over from one chromosome (insert) with all the histone stripped out.

• Living things have a characteristic set of chromosomes in the nucleus of each cell.

• Biochemical studies indicated that the nuclear materials that make up the chromosomes are composed of DNA and proteins.

• Each chromosome is a package for one very long, continuous strand of the DNA.

• In higher organisms, structural proteins, some of which are histones, provide a scaffold upon which DNA is built into a compact chromosome.

• The DNA strand is wound around histone cores, which, in turn, are looped and fixed to specific regions of the chromosome.

Concept 30 - Higher cells have an ancient chromosome.In addition to the set of chromosomes found in the nucleus, a different type of chromosome is found in the energy-generating organelles of the cytoplasm, the mitochondria. The mitochondrial (mt) chromosome contains genes involved in the process of oxidative phosphorylation — the production and storage of energy.

There is evidence that mitochondria once existed as free-living bacteria, which were taken up by primitive ancestors of eukaryotic cells. The primitive host cell provided a ready source of energy-rich nutrients, and the mitochondrion provided a means to extract energy using oxygen. This symbiotic relationship became key to survival, as oxygen accumulated in the primitive atmosphere.

Mitochondria are physically similar in size to bacteria, and the mt genome retains bacteria-like features. Like bacterial chromosomes, the mt genome is a circular molecule. Also, very few introns are found in mt genes. Plants contain an additional ancient chromosome in the chloroplasts, which were also absorbed as symbionts.

•Animation at http://www.dnaftb.org/30/animation.html •The review problem is at http://www.dnaftb.org/30/problem.html

Concept 31 - Most DNA does not encode protein.In most cases when DNA is extracted from living cells, the proteins (including histones) are dissolved away. This results in long strands of naked DNA, which retain their genetic information. So it is useful to visualize a chromosome as a continuous strand of DNA. Arrayed along the DNA strand are the genes, specific regions whose sequences carry the genetic code for making specific proteins.

The genes of bacteria are tightly packed together; virtually all the DNA encodes proteins. However, experiments done in the 1960s, showed that a large proportion of eukaryotic DNA is composed of repeated sequences that do not encode proteins. Long non-coding sequences — or intergenic regions — separate relatively infrequent "islands" of genes.

Research in the 1970s showed that numerous non-coding sequences — introns — are also found within genes, interrupting the protein-coding regions, or exons. It is estimated that only about five percent of human DNA encodes protein.

•Animation at http://www.dnaftb.org/31/animation.html •The review problem is at http://www.dnaftb.org/31/problem.html

Concept 32 - Some DNA can jump.In the 1950s, Barbara McClintock showed that certain DNA fragments, termed transposons, can be activated to transpose ("jump") from one position on a chromosome to another. She hypothesized that transposition provides a means to rapidly reorganize genes in response to environmental stress.

McClintock's work was remarkable, not only because it went against prevailing ideas, but also because it was based entirely on observation of chromosomes and genetic crosses. Confirmation of her ideas had to await the discovery of the modern tools of DNA analysis. This work paved the way for the modern concept of chromosomes as dynamic, changing structures.

Alu is an example of a so-called "jumping gene" - a transposable DNA sequence that "reproduces" by copying itself and inserting into new chromosome locations.http://www.dnalc.org/resources/animations/alu.html

•Animation at http://www.dnaftb.org/32/animation.html •The review problem is at http://www.dnaftb.org/32/problem.html

•Animation and quiz •http://highered.mcgraw-hill.com/sites/0072995246/student_view0/chapter23/mechanism_of_transposition.html

•http://highered.mcgraw-hill.com/sites/0072995246/student_view0/chapter23/simple_transposition.html

•http://highered.mcgraw-hill.com/sites/0072995246/student_view0/chapter23/transposons__shifting_segments_of_the_genome.html

Concept 33 - Genes can be turned on and off.As researchers studied the genetic code and the structure of genes in the 1950s and 60s, they began to see genes as a collection of plans, one plan for each protein. • But genes do not produce their proteins all

the time -> Organisms can regulate gene expression.

• French researchers studied gene regulation using bacteria.

When lactose is available, E. coli turn on a set of genes to metabolize the sugar. Lactose removes an inhibitor from the DNA. Removing the inhibitor turns on gene production.

The gene that produces the inhibitor is a regulatory gene. Cells not only have genetic plans for structural proteins within their DNA, they also have a genetic regulatory program for expressing those plans.

•Animation and quiz at www.sumanasinc.com/webcontent/animations/content/lacoperon.html •http://highered.mcgraw-hill.com/sites/0072556781/student_view0/chapter12/animation_quiz_4.html

•Animation at http://www.dnaftb.org/33/animation.html •The review problem is at http://www.dnaftb.org/33/problem.html

Concept 34 - Genes can be moved between species.

• The genetic code is universal.• The polymerases of one organism can

accurately transcribe a gene from another organism.

• For example, different species of bacteria obtain antibiotic resistance genes by exchanging small chromosomes called plasmids.

• 1970s - researchers used this type of gene exchange to move a "recombinant" DNA molecule between two different species.

• 1980s, other scientists adapted the technique and spliced a human gene into E. coli to make recombinant human insulin and growth hormone.

• Recombinant DNA technology — genetic engineering — lets us see how genes work.

• In cases where it is impractical to test gene function using animal models, genes can first be expressed in bacteria or cell cultures.

• Similarly, the phenotypes of gene mutations and the efficacy of drugs and other agents can be tested using recombinant systems.

Cohen and Boyer's recombinant DNA technique "created" the biotech industry. In 1974, the technique was submitted for patenting, and in 1976, the first biotech company, Genentech Inc., was established based on recombinant DNA technology.

•Animation and quiz•http://highered.mcgraw-hill.com/sites/0072995246/student_view0/chapter4/early_genetic_engineering_experiment.html

•Animation at http://www.dnaftb.org/34/animation.html •The review problem is at http://www.dnaftb.org/34/problem.html

Concept 35 - DNA responds to signals from outside the cell.• Growth and development require that cells

communicate with each other and react to signals that come from other parts of the body.

• Chemicals, eg. hormones released by various glands travel throughout the body to stimulate the growth of certain cell types.

• Cells capable of being stimulated by a particular hormone possess a specific receptor anchored in the cell membrane.

• The binding of a hormone to its receptor initiates a series of molecular transformations, called signal transduction, that relay the growth signal through the cell.

First, the receptor transduces the signal through the cell membrane to the internal membrane surface, where it activates protein "messengers." These messengers are part of and initiate a cascade of chemical reactions, often involving the addition of phosphate groups.

This cascade signal passes through the cytoplasm and into the nucleus. In the final step of signal transduction, DNA binding proteins attach to regulatory sequences and start DNA replication or transcription.

•Animation at http://www.dnaftb.org/35/animation.html •The review problem is at http://www.dnaftb.org/35/problem.html

Concept 36 - Different genes are active in different kinds of cells.Most living things are composed of different kinds of cells specialized to perform different functions. A liver cell, for example, does not have the same biochemical duties as a nerve cell. Yet every cell of an organism has the same set of genetic instructions, so how can different types of cells have such different structures and biochemical functions?

Since biochemical function is determined largely by specific enzymes (proteins), different sets of genes must be turned on and off in the various cell types. This is how cells differentiate.

This notion of cell-specific expression of genes is upheld by hybridization experiments that can identify the unique mRNAs in a cell type. More recently, DNA arrays and gene chips offer the opportunity to rapidly screen all gene activity of an organism. Co-expression of genes in response to external factors can thus be explored and tested.

•Animation at http://www.dnaftb.org/36/animation.html •The review problem is at http://www.dnaftb.org/36/problem.html

Other animations and quizzes https://highered.mcgraw-hill.com/sites/0072995246/student_view0/chapter24/microarrays.htmlhttps://highered.mcgraw-hill.com/sites/0072995246/student_view0/chapter24/using_a_dna_microarray.html

Concept 37 - Master genes control basic body plans.The development of an organism — from a fertilized egg, through embryonic and juvenile stages, to adulthood — requires the coordinated expression of sets of genes at the proper times and in the proper places.

Studies of several bizarre mutations in the fruitfly, Drosophila, provided keys to understanding the molecular basis of large-scale developmental plans. Early embryonic genes express proteins that set up the orientation and define the body segments of the fly embryo. Then "homeotic" genes act on the segments to make the body parts distinct to each segment.

Sequence analysis showed that homeotic genes from Drosophila and vertebrate animals share a 180-nucleotide region, called the homeobox. These homeobox proteins have structures highly similar to the regions of regulatory proteins that bind to DNA promoters and enhancers. Thus, a homeotic protein elicits coordinated expression when the protein binds to a specific promoter or enhancer sequence shared by a number of genes involved in the development of body region or segment.

•Animation at http://www.dnaftb.org/37/animation.html •The review problem is at http://www.dnaftb.org/37/problem.html

Concept 38 - Development balances cell growth and death.Growth results from the reproduction of new cells from pre-existing ones, by the process of cell division (mitosis). Once a tissue or organ reaches an appropriate size, mitosis slows and cells enter a resting phase.

This cell cycle of growth and rest is controlled by "checkpoint" molecules first characterized in the 1980s and 1990s in yeast, and then in other eukaryotes.

Remarkably, normal development requires that some healthy cells be eliminated, killed, by a process called "apoptosis." Initial clues about the nature of apoptosis came from detailed studies of the roundworm Caenorhabditis elegans, in which development of each of the 959 cells in the adult can be traced from the fertilized egg.

Analysis of cell "fates" showed that specific cells are programmed to die at specific times during embryonic development. Disruptions in the program lead to an overabundance of cells — a hallmark of cancer.

•Animation at http://www.dnaftb.org/38/animation.html •The review problem is at http://www.dnaftb.org/38/problem.html

Concept 39 - A genome is an entire set of genes.Each organism has a defining set of chromosomes that contain all of its genetic information. The human genome, for example, is the set of genetic information encoded in 46 chromosomes found in the nucleus of each cell. The chromosomes are organized into 23 pairs — one chromosome of each pair is inherited from the mother and one from the father. One pair of chromosomes — X and Y — determine sex; the other 22 pairs are called autosomes.

So, the human genome is made up of a set of very long DNA molecules, one corresponding to each chromosome. The object of the Human Genome Project was to determine the entire nucleotide sequence of each of these DNA molecules — and the location and identity of all the estimated 35, 000 genes. It was found that the human genome contains approximately 20,000 protein-coding genes, significantly fewer than had been anticipated.

Sequencing the human genome has relied mainly on automated machines that sequence the DNA and computer programs that search and identify genes. A "working draft" DNA sequence of the human genome was completed in June 2000. Initial analyses of this working draft were published in February 2001.

Protein-coding sequences account for only a very small fraction of the genome (approximately 1.5%), and the rest is associated with non-coding RNA molecules, regulatory DNA sequences, LINEs, SINEs, introns, and sequences for which as yet no function has been found.

•Animation at http://www.dnaftb.org/39/animation.html •The review problem is at http://www.dnaftb.org/39/problem.html

Concept 40 - Living things share common genes.All living organisms store genetic information using the same molecules — DNA and RNA. Written in the genetic code of these molecules is compelling evidence of the shared ancestry of all living things. Evolution of higher life forms requires the development of new genes to support different body plans and types of nutrition. Even so, complex organisms retain many genes that govern core metabolic functions carried over from their primitive past.

Genes are maintained over an organism's evolution, however, genes can also be exchanged or "stolen" from other organisms. Bacteria can exchange plasmids carrying antibiotic resistance genes through conjugation, and viruses can insert their genes into host cells. Some mammalian genes have also been adopted by viruses and later passed onto other mammalian hosts.

Regardless of how an organism gets and retains a gene, regions essential for the correct function of the protein are always conserved. Some mutations can accumulate in non-essential regions; these mutations are an overall history of the evolutionary life of a gene.

•Animation at http://www.dnaftb.org/40/animation.html •The review problem is at http://www.dnaftb.org/40/problem.html

Concept 41 - DNA is only the beginning for understanding the human genome.Although DNA transmits genetic information through time, it basically has a passive role. Proteins encoded by DNA actually carry out the myriad cellular reactions that constitute "life." Now that the Human Genome Project has provided us with a catalog of tens of thousands of genes, we are left with the question: "What do proteins made by these genes actually do?"

Scientists have always looked to mutant organisms to provide clues about protein function. Now, specific mutants can be created at will by inserting an altered or non-functioning copy of a gene back into a living organism, then looking for changes in behavior or development.

Since mice breed quickly and share about 99% of their genes with humans, they have become the animal model of choice for large-scale functional studies. However, doing a single transgenic experiment is several orders of magnitude more difficult than sequencing the gene itself. The real work of understanding the human genome still lies ahead.

•Animation at http://www.dnaftb.org/41/animation.html •The review problem is at http://www.dnaftb.org/41/problem.html