Theory of Intelligent Design, the best explanation of Origins

This is my personal virtual library, where i collect information, which leads in my view to Intelligent Design as the best explanation of the origin of the physical Universe, life, and biodiversity

You are not connected. Please login or register

Theory of Intelligent Design, the best explanation of Origins » Molecular biology of the cell » The hierarchical layout of the cell

The hierarchical layout of the cell

View previous topic View next topic Go down  Message [Page 1 of 1]

1 The hierarchical layout of the cell on Sat Jan 30, 2016 5:25 am


The hierarchical layout of the cell

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. 1 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.

Development, Genetic Control of 2

Development is the process through which a multicellular organism arises from a single cell. During development, cells become specialized, or differentiated, taking on different functions and forms. The organism develops a characteristic three-dimensional shape, the parts of which (such as limbs and organs) continue to maintain the same relationship to each other even as the organism grows. How the genes in a single fertilized egg dictate the creation of a complex multicellular creature is the central question in the genetic control of development.
While we are often most curious about human developmental processes, very little is known about the genetics of human development specifically, because experimentation on human embryos is forbidden by law and ethics. Instead, the details of genetic control are best understood in several model organisms, including the roundworm (Caenorhabditis elegans ), the fruit fly (Drosophila melanogaster ), the zebrafish, and the mouse. Each organism differs in the details, and in some cases the overall logic, of genetic control. The understanding of developmental control is not complete for any of these organisms, but scientists have come to understand several mechanisms that contribute to, but do not entirely explain, development.

The Importance of Transcription Factors

With few exceptions, every cell in a multicellular organism contains the same set of genes as every other cell. Despite this genetic equivalence, cells differ greatly in form, function, longevity, and many other characteristics. These differences are due to the differential expression of genes within each cell type. Thus, a nerve cell will express a certain subset of the entire genome , while a gut cell will express a different subset. (To express a gene means to use it to create its encoded product, usually a protein.) Cells become different from one another, therefore, by expressing different sets of genes. Thus, the problem of development can be addressed by understanding how initially identical cells come to express different sets of genes.
The beginning of the answer to this question lies in understanding gene transcription and transcription factors. Transcription is the process in which an enzyme called RNA polymerase binds to a gene to make an RNA copy; this is the first step in expressing the gene. Transcription factors are proteins that bind to regulatory regions of the gene, thereby influencing how easily RNA polymerase attaches to it. Different genes require different sets of transcription factors, and when these factors are in low supply, expression of that gene is slowed or stopped.
Since transcription factors are proteins, they are encoded by their own genes, which are regulated by yet other transcription factors. As we will see, many of the "master" genes that control development encode transcription factors that are expressed early in development. The sequential activation of these genes, in a domino-like fashion, is one way that the overall developmental program is carried out.

The European Way and the American Way

A central question in development is whether a particular cell is predestined to become a specific cell type from the moment of its creation, or whether its fate is less determinate, depending on a variety of cues it receives from its local environment as development proceeds. The developmental geneticist Sydney Brenner dubbed these two alternatives the European way (what matters is who your ancestors are) and the American way (what matters is what your environment is and who your neighbors are). While no multicellular organism displays either alternative exclusively, the roundworm C. elegans operates primarily according to the European plan, with each of its exactly 959 cells largely following a set developmental path, and with few decisions made through interaction with neighboring cells. Drosophila, and mammals such as mice and humans, largely develop according to the American plan, with most cells only gradually taking on a final identity, through repeated communication and competition with neighboring cells.
The difference can be seen in transplant experiments, in which cells of the early embryo are moved from one region to another. In the roundworm, the transplanted cell generally follows its original developmental plan, regardless of the environment in which it finds itself. In fruit flies and mammals, the transplanted cell generally takes on the identity of the region into which it is transplanted, switching from one developmental pathway to another, such as from bone cell to gut cell. This change is not absolute and, most importantly, it is time-dependent. Cells transplanted later in development tend to remain committed to the pathway they were on, despite their new surroundings, leading to the aberrant development of bone cells in the gut, for instance.

Morphogens and Gradients

One problem has intrigued embryologists for many decades: In the absence of strictly defined developmental fates, how does a cell "know" where it is in an embryo, in order to know what to become? An early suggestion, which has been borne out by experiments, is based on the concept of a concentration gradienta variation in concentration of a substance across a region of space.
A concentration gradient is formed whenever a substance is created in one place and moves outward by diffusion. When this occurs, there will be a high concentration of the substance near its point of origin, and increasingly lower concentrations further away. This provides positional information to a cell anywhere along the gradient. Cells pick up this chemical signal, and its strength (concentration) determines the cell's response. Typically, the signal is a transcription factor, and the response is a change in gene transcription.
Because such a signalling substance helps to give form to the embryo, it is termed a morphogen ("morph-" meaning "form," "-gen" meaning "to give rise to"). Morphogen gradients are a key means by which originally identical cells are exposed to different environments and thus sent along different developmental paths. In humans and other mammals, one morphogen that acts early in development is retinoic acid, a relative of vitamin A.

Gradients Determine the Axes of the Fruit Fly Embryo

We can see how such a morphogen acts by considering the development of the anterior-posterior axis in the fruit fly embryo. In the fly egg case, the oocyte, or fertilized egg, is accompanied by "nurse cells" at what will become the head end of the fly. This is called the anterior end; the tail end is posterior. Nurse cells create messenger RNA for a protein called bicoid, which they transport to the oocyte. Because these mRNAs originate in the anterior end, their concentration is highest there, and is lower towards the posterior end. Once the oocyte begins to divide, the mRNA is translated, and the bicoid protein is synthesized. Anterior cells have more of it than posterior cells, and the difference in concentration sets each cell group down its own developmental pathway, with anterior cells developing head structures, and posterior cells tail structures. Note that, in keeping with the "American plan," the fate of each cell is determined not by its ancestry, but by the environment it is in.
The effect of bicoid can be seen in transgenic flies, which have too many or too few copies of the gene. With extra bicoid, a higher-than-normal concentration exists further back in the oocyte, and anterior structures develop further back on the fly. With no bicoid, the anterior structures don't develop at all.
As we might expect, the bicoid protein is a transcription factor , which helps regulate expression of other genes. Other gradients of other transcription factors also exist at this stage, and together, these overlapping gradients establish the dorsal-ventral (back-belly) axis and map out the body segments that characterize all insects. While the details are complex, the fundamental idea is that of combinatorial control: At each position, it is the combination of transcription factors and their concentrations that determines which genes will be expressed, and therefore what the identity of the cells will be.
As segmentation becomes more firmly established and segments begin to take on their unique identities, gradients become less important. Instead, local gene control and cell to cell interactions create the increasingly fine level of spatial patterning.

Homeotic Genes and Segment Identity

Once segmentation is established, another important and remarkable set of genes turns on: the homeotic selector genes. These genes control development within each segment. For instance, the thorax region of the fly contains three segments, each with one pair of legs (the reason insects are six-legged). The homeotic selector gene antennapedia is normally expressed only in the thoracic segments, leading to the creation of a pair of legs.
Note that antennapedia does not itself "code for" legs. Instead, its protein product is a transcription factor. By regulating expression of many other genes, it sets off a cascade of events that results in the creation of legs. Remarkably, however, this single gene is sufficient by itself to turn on the leg-producing program, and its absence keeps the program silent. It can even turn it on in other segments. For instance, when antennapedia is mutated to allow it to be expressed in head segments, a pair of legs develops in place of the normal appendages, antennae (hence the gene name, which means "antenna foot").
Intriguingly, the sequence of homeotic selector genes along the fly chromosome matches the order of segments in which each is expressed. That is, the genes expressed in head segments come first, followed by those expressed in thoracic segments, then the abdomen, then the tail. The way in which this correspondence is exploited during development is still unknown, but the arrangement is clearly not accidental. Related genes have been found in vertebrates, including humans, and the same pattern holds: Genes expressed more anteriorly precede those expressed toward the posterior.

Homeotic Genes in Other Species

Homeotic genes also control development in other species, from yeast to humans, although the details are not as clear as they are for the fruit fly. Homeotic genes, called Hox genes, control the development of segments in the mammalian hindbrain, for example, and help establish the anterior-posterior and dorsal-ventral axes in the limbs. Vertebrates have duplicate copies of the Hox genes on several chromosomes, all of which function together to specify, for example, limb development. The multiple copies provide a redundancy not found in the fruit fly, thus making the effect of individual genes harder to detect. Nonetheless, by "knocking out" multiple versions of a particular Hox gene, researchers have shown their dramatic effects. For example, mice that are missing two copies of Hox 11 have no forelimbs, and the wrist is fused directly to the elbow.

The Homeobox

As transcription factors, the homeotic gene products must bind to DNA. Sequence analysis of both gene and protein has revealed that all share a 180-nucleotide DNA stretch, termed the homeobox, the sequence of which has remained almost unchanged over many millions of years of evolution. It codes for a 60-amino acid long DNA binding region, called the homeodomain. The homeodomain sequence of antennapedia and the mouse homeotic gene Hox B-7 differ by only two amino acids, despite having diverged several hundred million years ago.

Programmed Cell Death: Apoptosis

Development of a multicellular creature requires not only cell differentiation, but in some cases, cell death. Apoptosis helps create the spaces between the fingers, for instance. During brain development, nerve connections are sculpted through the apoptotic death of billions of cells. In C. elegans, exactly 131 cells die by apoptosis.
Cells can be directed to the apoptotic pathway if they fail to receive appropriate signals from their neighbors. In this way, it is thought that cells in the wrong locationa bone cell in the gut, for instancemight be terminated to prevent damage to the organism. The death program itself is carried out within the cell by activation of specific genes that ultimately trigger proteases, which are enzymes that break down cell contents, including the chromosomes


View user profile

View previous topic View next topic Back to top  Message [Page 1 of 1]

Permissions in this forum:
You cannot reply to topics in this forum