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Ebook Interdisciplinary applied mathematics: Part 2

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Ebook Interdisciplinary applied mathematics: Part 2

CHAPTER 10Regulation of Cell FunctionIn all cells, the information necessary tor the regulation ot cell function is contained in strands of deoxyribos

Ebook Interdisciplinary applied mathematics: Part 2se nucleic acid, or DNA. rhe nucleic acids arc large polymers of smaller molecular subunits called nucleotides, which themselves are composed of three

basic molecular groups: a nitrogenous base, which is an organic ring containing nitrogen; a 5-carbon (pentose) sugar, cither ribose or deoxyribose', Ebook Interdisciplinary applied mathematics: Part 2

an inorganic phosphate group. Nucleotides may differ in the first two of these components, and consequently there are two specific types of nucleic ac

Ebook Interdisciplinary applied mathematics: Part 2

ids: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).There may be any one of five different nitrogenous bases present in the nucleotides: adeni

CHAPTER 10Regulation of Cell FunctionIn all cells, the information necessary tor the regulation ot cell function is contained in strands of deoxyribos

Ebook Interdisciplinary applied mathematics: Part 2ll names.The DNA molecule is a long double strand of nucleotide bases, which can be thought of as a twisted, or helical, ladder. The backbone (or side

s of the ladder) is composed of alternating sugar and phosphate molecules, the sugar, deoxyribose, having one fewer oxygen atom than ribose. The "rung Ebook Interdisciplinary applied mathematics: Part 2

s" of the ladder are complementary pairs of nitrogenous bases, with G always paired with c, and A always paired with T. The bond between pairs is a we

Ebook Interdisciplinary applied mathematics: Part 2

ak hydrogen bond that is easily broken and restored during the replication process. In eukaryotic cells (cells that have a nucleus), the DNA is contai

CHAPTER 10Regulation of Cell FunctionIn all cells, the information necessary tor the regulation ot cell function is contained in strands of deoxyribos

Ebook Interdisciplinary applied mathematics: Part 2mbols from the four-letter alphabet of A, c, G, and T that controls all cellular biochemical functions. The nucleotide sequence is organized into code

triplets, called codons, which code for amino acids as well as other signals, such as “start manufacture of a protein molecule” and “stop manufacture Ebook Interdisciplinary applied mathematics: Part 2

of a protein molecule.” Segments of DNA that code for a particular product are called genes, of42810: Regulation of Cell Functionwhich there are abou

Ebook Interdisciplinary applied mathematics: Part 2

t 30,000 in human DNA. Typically, a gene contains start and stop codons as well as the code for the gene product, and can include large segments of DN

CHAPTER 10Regulation of Cell FunctionIn all cells, the information necessary tor the regulation ot cell function is contained in strands of deoxyribos

Ebook Interdisciplinary applied mathematics: Part 2, although not its structure, was first discovered in the late nineteenth century, and by 1943 it had been shown (although not widely accepted) that i

t is also the carrier of genetic information. How (approximately) it accomplishes this, and the structure of the molecule, was not established until t Ebook Interdisciplinary applied mathematics: Part 2

he work of Maurice Wilkins and Rosalind Franklin at King's College in London, and James Watson and Francis Crick in Cambridge. Watson, Crick, and Wilk

Ebook Interdisciplinary applied mathematics: Part 2

ins received the 1962 Nobel Prize in Physiology or Medicine, Franklin having died tragically young some years previously, in 1958.In recent years, the

CHAPTER 10Regulation of Cell FunctionIn all cells, the information necessary tor the regulation ot cell function is contained in strands of deoxyribos

Ebook Interdisciplinary applied mathematics: Part 2enetrated deeply into practically all aspects of life, from research and education to business and forensics. Mathematicians and statisticians have no

t been slow to join these advances. Departments and institutes of bioinforrnatics arc springing up in all sorts of places, and there are few mathemati Ebook Interdisciplinary applied mathematics: Part 2

cs or statistics departments that do not have connections (some more extensive than others, of course) with molecular biologists. It is well beyond th

Ebook Interdisciplinary applied mathematics: Part 2

e scope of this book to provide even a cursory overview of this vast held. An excellent introduction to molecular biology is the book by Alberts et al

CHAPTER 10Regulation of Cell FunctionIn all cells, the information necessary tor the regulation ot cell function is contained in strands of deoxyribos

Ebook Interdisciplinary applied mathematics: Part 2) and Krane and Raymer (2003) are good introductory bioinformatics texts, while tor those who are more mathematically or statistically oriented there

arc Deonicr cl al. (2004), Ewens and (Irani (2005), and Durrett (2002).10.1 Regulation of Gene ExpressionAn RNA molecule is a single strand of nucleot Ebook Interdisciplinary applied mathematics: Part 2

ides. It is different from DNA in that the sugar in the backbone is ribose, and the base IJ is substituted for T. Cells generally contain two to eight

Ebook Interdisciplinary applied mathematics: Part 2

times as much RNA as DNA. There arc three types of RNA, each of which plays a major role in cell physiology: For our purposes here, messenger RNA (mR

CHAPTER 10Regulation of Cell FunctionIn all cells, the information necessary tor the regulation ot cell function is contained in strands of deoxyribos

Ebook Interdisciplinary applied mathematics: Part 2nty amino acids that are to be incorporated into a protein molecule that is being produced. Finally, ribosomal RNA constitutes about 60% of the riboso

me, a structure in the cellular cytoplasm on which proteins are manufactured.The two primary functions that lake place in the nucleus are the reproduc Ebook Interdisciplinary applied mathematics: Part 2

tion of DNA and the production of RNA. RNA is formed by a process called transcription, as follows. An enzyme called polymerase (or, more precisely, a

Ebook Interdisciplinary applied mathematics: Part 2

polymerase complex, since many other proteins are also needed) attaches to some starling site on the DNA, breaks the bonds between base pairs in that

CHAPTER 10Regulation of Cell FunctionIn all cells, the information necessary tor the regulation ot cell function is contained in strands of deoxyribos

Ebook Interdisciplinary applied mathematics: Part 2 RNA polymerase moves along the DNA strand, the RNA molecule is formed, and the DNA crossbridges reform. The process stops when the RNA polymerase rea

ches a transcriptional termination site and disengages from the DNA.Proteins are manufactured employing all three RNA types. After a strand of mRNA th Ebook Interdisciplinary applied mathematics: Part 2

at codes for some protein is formed in the nucleus, it is released to the cytoplasm. There it encounters ribosomes that “read” the mRNA much like a ta

Ebook Interdisciplinary applied mathematics: Part 2

pe recording. As a particular codon is reached, it temporarily binds with the specific tRNA with the complementary codon carrying the corresponding am

CHAPTER 10Regulation of Cell FunctionIn all cells, the information necessary tor the regulation ot cell function is contained in strands of deoxyribos

Ebook Interdisciplinary applied mathematics: Part 2the DNA.Synthesis of a cellular biochemical product usually requires a scries of reactions, each of which is catalyzed by a special enzyme. In prokary

otes, formation of the necessary enzymes is often controlled by a sequence of genes located in scr ies on the DNA strand. This area of the i)N/\ stran Ebook Interdisciplinary applied mathematics: Part 2

d is called an operon, and the individual genes within the operon are called structural genes. At the beginning of the operon is a segment called a pr

Ebook Interdisciplinary applied mathematics: Part 2

omoter, which is a series of nucleotides that has a specific affinity for RNA polymerase. The polymerase must bind with this promoter before it can be

CHAPTER 10Regulation of Cell FunctionIn all cells, the information necessary tor the regulation ot cell function is contained in strands of deoxyribos

Ebook Interdisciplinary applied mathematics: Part 2atory repr essor protein can bind, preventing the attachment of RNA polymerase, thereby blocking the transcription of the genes of the opcron. Repress

or protein generally exists in two allosteric forms, one that can bind with the repressor operator- and thereby repr ess tr anscription, and one that Ebook Interdisciplinary applied mathematics: Part 2

does not bind. A substance that changes the repressor so that it breaks its bond with the operator- is called an activator, or inducer.The original co

Ebook Interdisciplinary applied mathematics: Part 2

ncept of the operon was due to Jacob et al. (I960), closely followed by mathematical studies (Goodwin, 1965; Griffith, 1968a,b; Tyson and Othmcr, 1978

CHAPTER 10Regulation of Cell FunctionIn all cells, the information necessary tor the regulation ot cell function is contained in strands of deoxyribos

Ebook Interdisciplinary applied mathematics: Part 2d of the organism or changes in the environment.10.1.1 The trp RepressorTryptophan is an essential amino acid that cannot be synthesized by humans and

therefore must be part of our diet. Try ptophan is a precursor for serotonin (a neurotransmitter), melatonin (a hormone), and niacin. Improper metabo Ebook Interdisciplinary applied mathematics: Part 2

lism of tryptophan has been implicated as a possible cause of schizophrenia, since improper metabolism creates a waste product in the brain that is to

Ebook Interdisciplinary applied mathematics: Part 2

xic, causing hallucinations and delusions. Tryptophan can, however, be synthesized by bacteria such as E. coli, and the regulation of tryptophan produ

CHAPTER 10Regulation of Cell FunctionIn all cells, the information necessary tor the regulation ot cell function is contained in strands of deoxyribos

Ebook Interdisciplinary applied mathematics: Part 2r or lesser complexity (Bliss el al., 1982; Sinha, 1988; Santillan and Mackey,43010: Regulation OF Cell Function2001 a,b; Mackey el al., 2004). Here,

we present only a highly .simplified version of these models, designed to illustrate some of the basic principles.The trp operon comprises a regulator Ebook Interdisciplinary applied mathematics: Part 2

y region and a coding region consisting of live structural genes that code for three enzymes required to convert chorismic acid into tryptophan (Fig.

Ebook Interdisciplinary applied mathematics: Part 2

10.1 A). Expression of the trp operon is regulated by the Trp repressor protein which is encoded by the trpR gene. In contrast to the lac opcron, whic

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