Question

CHEM-4340 (2018-FALL) 001 Hi Class Members, left and because I didn't give you a good review sheet in advance I narrowed down the material a bit. You will have a questions over: thesis, and the process of initiation, elongation, and/or termination of transcription. Knowing the pathways we talked about today is good, but the question might be in depth to probe your understanding of this process

Answer 1

CODON BIAS:

Codon usage bias refers to differences in the frequency of occurrence of synonymouscodons in coding DNA. A codon is a series of three nucleotides  that encodes a specific amino acid residue in a polypeptidechain or for the termination of translation.

It is generally acknowledged that codon biases reflect a balance between mutational biases and natural selection for translational optimization.

  The nature of the codon usage-tRNA optimization has been fiercely debated. It is not clear whether codon usage drives tRNA evolution or vice versa. At least one mathematical model has been developed where both codon usage and tRNA expression co-evolve in feedback fashion (i.e., codons already present in high frequencies drive up the expression of their corresponding tRNAs, and tRNAs normally expressed at high levels drive up the frequency of their corresponding codons).

Codon bias is mltiple codons for the same amino acid are not used equally. Codon bias between organism varies. Codon bias is correlated with tRNA availability.Cloned genes from one organism may not be translated by recipient organism because of codon bias.

WOBBLE HYPOTHESIS:

  The Wobble Hypothesis, by Francis Crick, states that the 3rd base in an mRNAcodon can undergo non-Watson-Crick base pairing with the 1st base of a tRNAanticodon. The mRNA codon’s first 2 bases form Hydrogen bonds with their corresponding bases on the tRNA anticodon in the usual Watson-Crick manner, in that they only form base pairs with complimentary bases. However, the formation of Hydrogen bonds between the 3rd base on the codon and the 1st base on the anticodon can potentially occur in a non-Watson-Crick manner. Therefore different base pairs to those usually seen can form at this position.

Process of transcription:

INITIATION:-

  To begin transcribing a gene, RNA polymerase binds to the DNA of the gene at a region called the promoter. Basically, the promoter tells the polymerase where to "sit down" on the DNA and begin transcribing.Each gene has its own promoter. A promoter contains DNA sequences that let RNA polymerase or its helper proteins attach to the DNA. Once the transcription bubble has formed, the polymerase can start transcribing.

ELONGATION:-

During elongation, RNA polymerase "walks" along one strand of DNA, known as the template strand, in the 3' to 5' direction. For each nucleotide in the template, RNA polymerase adds a complementary RNA nucleotide to the 3' end of the RNA strand.

TERMINATION:-

RNA polymerase will keep transcribing until it gets signals to stop. The process of ending transcription is called termination, and it happens once the polymerase transcribes a sequence of DNA known as a terminator.