Gene A protein

The proteins of the viral envelope. The gene that codes for these proteins is the env gene. A protein coded by the env gene is responsible for binding the virus to the cell receptor. For HIV, there are two env proteins, gp 120 and gp 41. 

In the second and third stages of replication ( )X174 RF molecules are themselves replicated and are then used for synthesis of new viral (+) strands. At both stages a virally encoded gene A protein, which has endonuclease activity, nicks the duplex. Cutting the (+) strand it leaves a free 3-OH on DNA residue 4305, while the 5 -phospho group of residue 4306 becomes... 

Figure 29-17 Partial sequence and secondary structure model of RNA of bacteriophage MS2. The initiation and termination codons for each of the three genes (A protein, coat protein, and replicase) are enclosed in boxes as is the second stop signal that is in-frame for the A protein gene but out-of-frame for the coat protein gene. The entire coat protein gene is shown but less them one-third of the entire sequence is given. From W. Fiers and associates.499-501...

Having settled on a definition of chemoinformatics, it is time for us to reflect on the distinction between chemoinformatics and bioinformatics. The objects of interest of bioinformatics are mainly genes and proteins. But genes, DNA and RNA, and proteins are chemical compounds They are objects of high interest in chemistry, Chemists have made substantial contributions to the elucidation of the structure and function of nucleic adds and proteins. The message is dear there is no clearcut distinction between bioinfonnatics and chemoinformatics I... 

For the bioinformatician the emphasis lies on how a gene expresses a protein -an enzyme - that catalyzes a biochemical reaction (Figure 10.3-13). 

Gene A sequence of DNA at a particular position on a specific chromosome that encodes a precise functional product (usually protein)... 

Translation of the Foreign Gene. The translation of a mRNA into a protein is governed by the presence of appropriate initiation sequences that specify binding of the mRNA to the ribosome. In addition, not all the codons of the genetic code are used equally frequently by all organisms. 

Cellular Protein Biosynthesis. The process of cellular protein biosynthesis is virtually the same in all organisms. The information which defines the amino acid sequence of a protein is encoded by its corresponding sequence of DNA (the gene). The DNA is composed of two strands of polynucleotides, each comprising some arrangement (sequence) of the four nucleotide building blocks of the nucleic acids adenine (A), thymine (T),... 

Three hormones regulate turnover of calcium in the body (22). 1,25-Dihydroxycholecalciferol is a steroid derivative made by the combined action of the skin, Hver, and kidneys, or furnished by dietary factors with vitamin D activity. The apparent action of this compound is to promote the transcription of genes for proteins that faciUtate transport of calcium and phosphate ions through the plasma membrane. Parathormone (PTH) is a polypeptide hormone secreted by the parathyroid gland, in response to a fall in extracellular Ca(Il). It acts on bones and kidneys in concert with 1,25-dihydroxycholecalciferol to stimulate resorption of bone and reabsorption of calcium from the glomerular filtrate. Calcitonin, the third hormone, is a polypeptide secreted by the thyroid gland in response to a rise in blood Ca(Il) concentration. Its production leads to an increase in bone deposition, increased loss of calcium and phosphate in the urine, and inhibition of the synthesis of 1,25-dihydroxycholecalciferol. 

However, the a helices are not packed against each other in the usual way as described in Chapter 3. Instead, a helices 2 and 3, residues 15-36, form a unique helix-turn-helix arrangement that in 1981 had only been observed once, in a different bacterial DNA-binding protein, the catabolite gene-activating protein CAR... 

Weber, L, Steitz, T.A. The structure of a complex of catabo-lite gene activator protein and cyclic AMP refined at 2.S A resolution. /. Mol. Biol. 198 311-326, 1987. 

Eucaryotes have many more genes and a broader range of specific transcription factors than procaryotes and gene expression is regulated by using sets of these factors in a combinatorial way. Eucaryotes have found several different solutions to the problem of producing a three-dimensional scaffold that allows a protein to interact specifically with DNA. In the next chapter we shall discuss some of the solutions that have no counterpart in procaryotes. However, the procaryotic helix-turn-helix solution to this problem (see Chapter 8) is also exploited in eucaryotes, in homeodomain proteins and some other families of transcription factors. 

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