Chapter 7: Genes and Proteins Synthesis pg : Transcription: DNA-Directed RNA Synthesis pg Initiation

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Eustace Jennings
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1 UNIT 3: Molecular Genetics Chapter 7: Genes and Proteins Synthesis pg : Transcription: DNA-Directed RNA Synthesis pg Initiation Promoter is a nucleotide sequence that lies just before a gene and allows for the binding of RNA polymerase. TATA box is a region of the promoter that enables the binding of RNA polymerase. In prokaryotes and eukaryotes RNA polymerase will bind to the DNA molecule at a promoter region just upstream from the actual gene. In eukaryotes the promoter region contains a TATA box (high concentration of A and T) that the RNA polymerase attaches, where prokaryotes contain a TATAAT sequence. Since adenine and thymine are complementary and are bonded together by two hydrogen bonds, it is easier to break these bonds as opposed to breaking the three hydrogen bonds between cytosine and guanine. RNA polymerase used less energy when unwinding and unzipping the DNA molecule. At this point the portion of the DNA molecule containing the gene to be transcribed into RNA is exposed and is called the transcriptional unit. Elongation Coding strand is the DNA strand that is not being copied but contains the same sequence as the new RNA molecule. When the DNA molecule is unzipped the process of producing a pre-mrna begins without the need of a primer. The pre-mrna molecule is produced in 5 to 3 direction, reading the template DNA strand from a 3 to 5 direction. The template strand is read, the opposite DNA strand is known as the coding strand, it will the same as the pre-mrna sequence, except the coding strand has thymine while the pre-mrna has uracil.

2 As the DNA continuous to unzip, RNA nucleotides molecules are being attached one by one. If the cell requires a particular protein, they usually need to produce thousands or even millions of copies. Instead of producing the protein one event at a time, a second RNA polymerase may follow the first, if there is room at the promoter region, and produce another pre-mrna. This can occur many times, producing many pre-mrnas. Termination Termination sequence - is a sequence of bases at the end of a gene that signals the RNA polymerase to stop transcribing. Once the RNA polymerase reaches the end of the gene, RNA polymerase recognizes a termination sequence, and transcription stops. In eukaryotes have a termination sequence identified by a string adenine bases. The new formed pre-mrna now disassociates from the DNA template strand.

3 Figure 1: Transcribing a gene into precursor mrna in eukaryotes. There are three stages: initiation, elongation, and termination. RNA polymerase moves along the gene, separating the two DNA strands to allow RNA synthesis in the 5 3 direction. The 3 5 DNA strand is used as a template.

4 Post-transcriptional Modifications Poly (A) tail is a chain of adenine nucleotides that are added to the 3 end of the pre-mrna molecule to protect it from enzymes in the cytosol. 5 cap is a sequence o seven Gs that is added to the start of a pre-mrna molecule; ribosomes recognize this site and use it as the site of initial attachment. Exon is a sequence of DNA or RNA that codes fort part of a gene. Intron is a non-coding sequence of DNA or RNA. Spliceosome is an enzyme-protein complex that removes introns from mrna. Small ribonucleoprotein (snrnp) is a protein that binds to introns and signals them for removal. Alternative splicing is a process that produces different mrnas from premrna (exons and introns), allowing more than one possible polypeptide to be made from a single gene. The newly transcribed RNA molecule (pre-mrna) or primary transcript must be modified prior to leaving the nucleus and entering the cytosol s harsh environment, where enzymes can derogate the mrna. One of the modifications is the addition of a poly (A) tail. A chain of 50 to 250 adenine nucleotides are attached to the 3 end of the pre-mrna by an enzyme called poly-a polymerase. The poly (a) tail protects the end of the mrna molecule as it enters the cytosol. A second modification is the addition of the 5 cap. The 5 cap consists of seven guanine nucleotides being attached the 5 portion of the pre-mrna. The guanines act as the initial attachment point to the ribosome and gives direction to reading the mrna.

5 The last modification is the removal of non-coding regions from the premrna, and the reattachment of coded regions, in order, to created mrna. The non-coding regions are interspersed between coding regions along the pre-mrna; non-coding regions are called introns and the coding regions are called exons. Eukaryotes contain introns in their genetic codes, but prokaryotes do not contain introns, therefore this post-transcriptional modification does not occur. Spliceosomes are enzymes responsible for splicing, removing the introns and combined the exons together. Alternative splicing can occur where the exons are resembled in a different order, creating a number and variety of proteins from one gene. From the one pre-mrna molecule, a family of proteins can be produced, which have different functions. This explains where there are approximately genes and over proteins in humans. Figure 2: The relationship between a eukaryote protein-coding gene, the pre-mrna transcribed from it, and the mrna processes from the pre-mrna.

6 Transcription in Eukaryotes versus Prokaryotes Eukaryote transcription is similar to prokaryotes but not identical. One difference is in the molecule of RNA polymerase. Prokaryotes have one type that transcribes everything, but in eukaryotes there are three types, where RNA polymerase II transcribes genes that produce proteins, Type I and III transcribes non-protein coding genes (trna and rrna). Table 1: Compare Eukaryote to Prokaryote, pg. 323 Variable Prokaryotes Eukaryotes Location - throughout the cell - in the nucleus Enzymes - one type of RNA polymerase - 3 types of RNA polymerase Elongation - 15 to 20 nucleotides per second - 5 to 8 nucleotides per second - fast - slow Promoters - less complex - more complex, found upstream Termination - proteins cleave mrna - polyuracil site, protein bind here Introns/ - no introns - introns and exons Exons Product - mrna ready to translate - pre-mrna needs to be modified

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