Molecular Biology Genes to Proteins, 3rd Edition. B. E. Tropp, Jones and Bartlett Publishers, Sudbury,. Massachusetts, USA, , pp., ISBN Request PDF on ResearchGate | On Jul 1, , Qiuyu Wang and others published Molecular biology genes to proteins, 3rd edition by B. E. Tropp. Chapter 2 (PDF file) · Chapter 1 (PDF file). OVERVIEW. The Third Edition of Molecular Biology: Genes to Proteins is a comprehensive guide through the basic.
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Then, it was found that genes contain digitally encoded instructions that direct the synthesis of proteins. The crucial insight of molecular biology is that hereditary. Introduction to Molecular Biology. Genes. Proteins. Function. Bi h. i t. Biochemistry. ➢ The study of chemical and physical structure of macromolecule was first. Genetic information is encoded by DNA Proteins work together with other proteins or nucleic acids as "molecular problems arising in molecular genetics.
Reddit Tropp, B. The first two editions of Molecular biology, published in and , were written by that splendid author, David Freifelder.
RNA and protein synthesis
Unfortunately he is no longer alive to chronicle the advances in the discipline. The writing of this edition, with its slightly modified title, was the responsibility of a new author, who obviously had a lot to live up to.
Much has happened in molecular biology and in the storing, accessing, and presentation of biological information since This has necessitated a complete revision of the earlier edition s. Chapter 1 describes molecular biology in general terms. This chapter is essentially a history lesson and sets the scene for the subsequent material.
Thus we learn of Weaver's first use of the term molecular biology, the revolutionary breeding experiments of Mendel, Miescher's isolation of DNA, and Levene's identification of its bases.
Other historical studies, such as those of Garrod lamentably, they were largely ignored , Beadle and Tatum, Todd, Griffiths, Avery and so many other brilliant scientists, are also summarized. Additionally, the extensive use of the Internet and the applications of information technology in molecular biology are highlighted. This mode of writing has enabled the author to introduce basic ideas and concepts, together with a fair amount of the bio chemistry, on which molecular biology depends, to be introduced in an engaging and reader friendly fashion.
This RNA polymerase is formed from four different subunits, indicated by different colors right.
How do the signals in the DNA termination signals stop the elongating polymerase? As the polymerase transcribes across a terminator , the hairpin may help to wedge open the movable flap on the RNA polymerase and release the RNA transcript from the exit tunnel.
At the same time, the DNA-RNA hybrid in the active site , which is held together predominantly by U-A base pairs which are less stable than G -C base pairs because they form two rather than three hydrogen bonds per base pair , is not sufficiently strong enough to hold the RNA in place, and it dissociates causing the release of the polymerase from the DNA, perhaps by forcing open its jaws. Thus, in some respects, transcription termination seems to involve a reversal of the structural transitions that happen during initiation.
The process of termination also is an example of a common theme in this chapter: the ability of RNA to fold into specific structures figures prominantly in many aspects of decoding the genome.
It is perhaps not surprising that the signals encoded in DNA that specify these transitions are difficult for researchers to recognize.
Indeed, a comparison of many different bacterial promoters reveals that they are heterogeneous in DNA sequence. These common features are often summarized in the form of a consensus sequence Figure In general, a consensus nucleotide sequence is derived by comparing many sequences with the same basic function and tallying up the most common nucleotide found at each position.
Figure Consensus sequence for the major class of E. A The promoters are characterized by two hexameric DNA sequences, the sequence and the sequence named for their approximate location relative to the start point of transcription designated more One reason that individual bacterial promoters differ in DNA sequence is that the precise sequence determines the strength or number of initiation events per unit time of the promoter.
Evolutionary processes have thus fine-tuned each promoter to initiate as often as necessary and have created a wide spectrum of promoters. Promoters for genes that code for abundant proteins are much stronger than those associated with genes that encode rare proteins, and their nucleotide sequences are responsible for these differences.
Like bacterial promoters, transcription terminators also include a wide range of sequences, with the potential to form a simple RNA structure being the most important common feature. Since an almost unlimited number of nucleotide sequences have this potential, terminator sequences are much more heterogeneous than those of promoters. We have discussed bacterial promoters and terminators in some detail to illustrate an important point regarding the analysis of genome sequences.
Although we know a great deal about bacterial promoters and terminators and can develop consensus sequences that summarize their most salient features, their variation in nucleotide sequence makes it difficult for researchers even when aided by powerful computers to definitively locate them simply by inspection of the nucleotide sequence of a genome.
When we encounter analogous types of sequences in eucaryotes, the problem of locating them is even more difficult.
Often, additional information, some of it from direct experimentation, is needed to accurately locate the short DNA signals contained in genomes.
Promoter sequences are asymmetric see Figure , and this feature has important consequences for their arrangement in genomes. However a gene typically has only a single promoter , and because the nucleotide sequences of bacterial as well as eucaryotic promoters are asymmetric the polymerase can bind in only one orientation.
The choice of template strand for each gene is therefore determined by the location and orientation of the promoter.
Figure The importance of RNA polymerase orientation. Figure Directions of transcription along a short portion of a bacterial chromosome. Some genes are transcribed using one DNA strand as a template, while others are transcribed using the other DNA strand.
The direction of transcription is determined by the promoter more Having considered transcription in bacteria, we now turn to the situation in eucaryotes, where the synthesis of RNA molecules is a much more elaborate affair.
The three polymerases are structurally similar to one another and to the bacterial enzyme. They share some common subunits and many structural features, but they transcribe different types of genes Table RNA polymerase II transcribes the vast majority of genes, including all those that encode proteins, and our subsequent discussion therefore focuses on this enzyme.
Although eucaryotic RNA polymerase II has many structural similarities to bacterial RNA polymerase Figure , there are several important differences in the way in which the bacterial and eucaryotic enzymes function, two of which concern us immediately.
Regions of the two RNA polymerases that have similar structures are indicated in green.
The eucaryotic polymerase is larger than the bacterial enzyme 12 subunits more Broken into six sections, topics are strategically arranged to cover basic information that is necessary in understanding the more advanced topics focused on in later sections. Section 1 and 2, Protein Structure and Function and Nucleic Acids and Nucleoproteins provide the information required to understand the chemical basis of molecular biology. Section 3, Genetics and Virology provides information required to understand the biological basis of molecular biology.
Section 6, Protein Synthesis describes the structure and function of the bacterial protein synthetic machinery in bacteria, eukaryotes and archaeons.
Gene Expression and Regulation
The book is typically used in a one-semester course that may be taught in the fall or the spring. However, the book contains sufficient information so that it could be used for a full year course.
It is appropriate for juniors and seniors or first year graduate students. Section 2: Nucleic Acids and Nucleoproteins 4. Deoxyribonucleic Acid Structure 5.
Nucleic Acid Technology 6. Chromosome Structure. Section 3: Genetics and Virology 7. Genetic Analysis in Molecular Biology 8. Viruses in Molecular Biology. Section 4: DNA Metabolism 9.Transcription factors bind to specific nucleotide sequences in the promoter region and assist in the binding of RNA polymerases.
Perceived disadvantages of Northern blotting are that large quantities of RNA are required and that quantification may not be completely accurate, as it involves measuring band strength in an image of a gel.
Section 4: In Rho-independent termination, a loop forms at the end of the RNA molecule, causing it to detach itself.
Eucaryotic transcription initiation must deal with the packing of DNA into nucleosomes and higher order forms of chromatin structure, features absent from bacterial chromosomes.
Much has happened in molecular biology and in the storing, accessing, and presentation of biological information since Since AUG also codes for the amino acid methionine, methionine is the first amino acid incorporated into a protein — if it is not actually needed, it will be removed later Xiao et al, Among all regulatory motifs within the 3'-UTRs e.