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My Pages On Different Subjects which Hyperlinked to all my Blog Posts

Tuesday, 4 September 2012

Genetics : Lactose Operon, Mogan Studies of Inheritance,Linkage and Amino Acids



3D Picture of All Stages of Lactose Operon




LACTOSE OPERON:
Many years ago Francois Jacob and Jacques Monod demonstrated that the bacterial genes coding for Lactose-metabolizing enzymes are expressed only when lactose is present .When E.coli cells were grown on a lactose free medium, they did not produce the enzymes, but they did so within  minutes after being placed on a lactose-enriched medium.Today we know that a region of E.coli DNA includes a promoter, an operator, and three adjacent genes associated with lactose metabolism. Any gene(or group of genes), together with its promoter and operator sequence, is called an operon. The one  we are describing here is the lactose operon.

3D Picture of First Stage of Lactose Operon
               
The regulator gene elsewhere in the DNA codes for a repressor protein that can inhibit transcription of the Lactose operon. The particular repressor binds with the operator whenever lactose concentration are low.Being a rather large molecule, the repressor overlaps the promoter and  so blocks RNA polymerase`s access to the genes.Through the negative control mechanism, Lactose metabolizing enzymes are not produced when they are not needed.

3D Picture of Second Stage of Lactose Operon
              
When lactose is present, however, it binds to and alters the shape of the repressor protein.In its altersthe shape of the repressor protein.In its altered shape, the repressor cannot bind to the operator, so RNA polymerase is free to initiate transcription. 

3D Picture of Third Stage of Lactose Operon



3D Picture of Fourth Stage of Lactose Operon


video

                                                                                    3D animation Showing The Lactose-Operon Stages

When lactose concentrations are high, nearly all the repressor molecules are activated;transcription proceeds rapidly and the Lactose-degrading enzymes are synthesized.

3D Picture of A Bacteriophage : is any one of a number of viruses that infect bacteria created by me (Manash Kundu)

LYTIC AND LYSOGENIC PATHWAY:
Replication cycle of Lambda bacteriophage.Depending on environmental factors, infection proceeds by way of either the lytic pathway or the lysogenic pathway.

Bacteriophage Lytic Cycle: The lytic cycle is typically considered the main method of viral replication, since it results in the destruction of the infected cell
       
In the lysogenic pathway. The Bacterophage enters a latent state in which the viral DNA becomes integrated into the host DNA, then remains functionally inactive during successive DNA replications and cell divisions.

Bacteriophage lysogenic Cycle : Lysogeny is characterized by integration of the Bacteriophage nucleic acid into the host bacterium's genome. The newly integrated genetic material, called a prophage can be transmitted to daughter cells at each subsequent cell division,

video

                                                                                 3D Animation Showing Lytic And Lysogenic Cycle of Bacteriophage Virus


Specific environmental agents activate the viral DNA and cause it to leave the host DNA molecule.When it does, the lytic pathway is followed

MORGAN`S STUDIES OF INHERITANCE: Drosophila Fly


MORGAN`S STUDIES OF INHERITANCE:

Thomas Hunt Morgan (1866-1945)

For his studies of inheritance, Morgan relied on the fruit fly Drosophila melanogaster rather than on the plants and animals that had been commonly used for breeding experiments.These small flies can be grown in bottles on a little bit of cornmeal, molasses and agar. A female lays hundreds of eggs in a few days, and her offspring reach reproductive age in less than two weeks. Thus Morgan could track hereditary traits through nearly 30 generations of thousands of flies in a year`s time; Before long, his laboratory was filled with bottles of busy fruit flies.

3D Picture of Normal Drosphila Fly and its Chromosomes created by Me (Manash Kundu)

3D Picture of Mutated Drosophila Fly (White Eyed) and its Chromosomes created by Me (Manash Kundu)


Drosophila eye color turned out to be a most informative trait. At first all the flies Morgan raised were wild type for eye color; they had brick-red eyes. In 1910, a white-eyed male cropped up in a laboratory bottle. Apparently the variant form arose through a spontaneous mutation in a gene controlling eye color.

White-eyed males were mated with true-breeding (Homozygous) red-eyed females
                 
Morgan established true-breeding strains of white-eyed males and females. Then he did a series of reciprocal crosses.(In the first of a pair of crosses, one parent displays the trait in question; in the second cross, the other parent displays the trait.) White-eyed males were mated with true-breeding (Homozygous) red-eyed females. In the reciprocal cross, white eyed males.The phenotypic outcomes for the paired crosses were not the same.

n the reciprocal cross, white eyed males.The phenotypic outcomes for the paired crosses were not the same.
                  
Clearly the gene controlling eye color was related to gender, and it probably was located on one of the sex chromosomes. but which one? Since females (XX) could be white eyed, the recessive allele would have to be on one of their X-chromosomes.Now suppose white eyed males (XY) also carry the recessive allele on their X-chromosome and that there is no corrosponding eye-colored gene on their Y-chromosome. Those males would have white eyes beacuse the recessive allele would be the only eye-color gene they had.
                   
The results that can be expected when the idea of an X-linked gene is combined with Mendel`s concept of segregation. By proposing that a specific gene occurs on the X but not the Y chromosome,Morgan was able to explain the seemingly odd outcome of his reciprocal crosses. The results of the experiments matched the predicted outcomes.

Drosophila Page in my Bio-World software


video
               
                                                                                          3D Animation of Drosophila Fly

LINKAGE:
During their Drosophila studies , Morgan and his co-workers found evidence that many traits are inherited as a group from one parent or the other.Their studies of an X-linked gene supported the hypothesis that each gene is located on a specific chromosome, and it seemed likely that several genes located on the same chromosome might stay physically linked together during meiosis and ens up in the same gamete.
               
White eyes had served as an observable "marker" for tracking the inheritance of one gene, and now other mutations were used in a similar way. (By 1915 Morgan`s group has isolated more bthan eighty types of flies with distinctive mutations.) For example: a wild type fly has straight, flat wings and gray body, and the two genes for those traits were designated C and B. Some mutants had curved wings (c) and a black body (b) , and they were mated with wild type flies in dihybrid crosses. In this type of cross, remember, parents true-breeding for two traits of interest produce first-generation offspring that are heterozygous for both traits.All offspring of the CC BB * ccbb cross were CcBb.


Picture of All Major  Twenty (20) Amino Acids

Amino acids

The generic structure of an alpha amino acid in its unionized form.


are molecules containing an amine group, a carboxylic acid group, and a side-chain that is specific to each amino acid. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen. They are particularly important in biochemistry, where the term usually refers to alpha-amino acids.

An alpha-amino acid has the generic formula H2NCHRCOOH, where R is an organic substituent;the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (the α–carbon). Other types of amino acid exist when the amino group is attached to a different carbon atom; for example, in gamma-amino acids (such as gamma-amino-butyric acid) the carbon atom to which the amino group attaches is separated from the carboxylate group by two other carbon atoms. The various alpha-amino acids differ in which side-chain (R-group) is attached to their alpha carbon, and can vary in size from just one hydrogen atom in glycine to a large heterocyclic group in tryptophan.

Picture of Ten (10) Major Amino Acids


Picture of other Ten (10) Major Amino Acids

Amino acids serve as the building blocks of proteins, which are linear chains of amino acids. Amino acids can be linked together in varying sequences to form a vast variety of proteins. Twenty amino acids are naturally incorporated into polypeptides and are called proteinogenic or standard amino acids. These 20 are encoded by the universal genetic code. Nine standard amino acids are called "essential" for humans because they cannot be created from other compounds by the human body, and so must be taken in as food.

Amino acids are important in nutrition and are commonly used in nutrition supplements, fertilizers, food technology and industry. In industry, applications include the production of biodegradable plastics, drugs, and chiral catalysts.

Picture of  Major Amino Acids

Standard amino acids

Picture of  Major Amino Acids

Amino acids are the structural units that make up proteins. They join together to form short polymer chains called peptides or longer chains called either polypeptides or proteins. These polymers are linear and unbranched, with each amino acid within the chain attached to two neighboring amino acids. The process of making proteins is called translation and involves the step-by-step addition of amino acids to a growing protein chain by a ribozyme that is called a ribosome. The order in which the amino acids are added is read through the genetic code from an mRNA template, which is a RNA copy of one of the organism's genes.

Twenty-two amino acids are naturally incorporated into polypeptides and are called proteinogenic or natural amino acids.Of these, 20 are encoded by the universal genetic code. The remaining 2, selenocysteine and pyrrolysine, are incorporated into proteins by unique synthetic mechanisms. Selenocysteine is incorporated when the mRNA being translated includes a SECIS element, which causes the UGA codon to encode selenocysteine instead of a stop codon.Pyrrolysine is used by some methanogenic archaea in enzymes that they use to produce methane. It is coded for with the codon UAG, which is normally a stop codon in other organisms This UAG codon is followed by a PYLIS downstream sequence.

 Non-standard amino acids

Aside from the 22 standard amino acids, there are many other amino acids that are called non-proteinogenic or non-standard. Those either are not found in proteins (for example carnitine, GABA), or are not produced directly and in isolation by standard cellular machinery (for example, hydroxyproline and selenomethionine).

Amino Acids Page in My Bio-World Software


THE GENETIC CODE

AMINO ACIDS                                             RNA CODON

ALANINE                                                 GCA GCC GCG GCU              

ARGININE                                               AGA AGG CGA CGC CGG CGU

ASPARAGINE                                         AAC AAU                                

ASPARTIC ACID                                    GAC GAU                                

CYSTEINE                                              UGC UGU                               

GLUTAMIC ACID                                    GAA  GAG                              

GLUTAMINE                                           CAA CAG                               

GLYCINE                                                GGA GGC GGG GGU             

HISTIDINE                                              CAC CAU                               

ISOLEUCINE                                           AUA AUC AUU                       

LEUCINE                                                UUA UUG CUA CUC CUG CUU 

LYSINE                                                   AAA AAG                                

METHIONINE                                          AUG                                       

PHENYLALANINE                                   UUC UUU                                

PROLINE                                               CCA CCC CCG CCU                 

SERINE                                                 AGC AGU UCA UCC UCG UCU  

THREONINE                                          ACA ACC ACG ACU                  

TRYPTOPHAN                                       UGG                                          

TYROSINE                                             UAC UAU                                   

VALINE                                                 GUA GUC GUG GUU                  

STOP CODONS                                     UAA UAG UGA                          


Catabolism:

Degradation of an amino acid often involves deamination by moving its amino group to alpha-ketoglutarate, forming glutamate. This process involves transaminases, often the same as those used in amination during synthesis. In many vertebrates, the amino group is then removed through the urea cycle and is excreted in the form of urea. However, amino acid degradation can produce uric acid or ammonia instead. For example, serine dehydratase converts serine to pyruvate and ammonia. After removal of one or more amino groups, the remainder of the molecule can sometimes be used to synthesize new amino acids, or it can be used for energy by entering glycolysis or the citric acid cycle,


Picture of All Major Amino Acids usefull during Kreb`s Cycle : Amino Acids are written in yellow over red background



video
                                                                
                                                                                          3D Animation Showing Major Amino-Acids












































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