The Enzyme That Unwinds a Segment of the DNA Molecule Is

○ ○ ○ ○ ○ The enzyme that unwinds a segment of the DNA molecule is a helicase. How do DNA polymerase I and DNA Polymerase III differ? DNA Polymerase III synthesizes the majority of the DNA, while DNA Polymerase I synthesizes DNA in the regions where the RNA primers were laid down on the lagging strand. The enzyme that travels along a template strand, assembling nucleotides on a growing DNA strand is DNA polymerase III, Before DNA polymerase can begin assembling DNA nucleotides to produce either the Okazaki fragments of the lagging strand or the continuous molecule of the leading strand, which of the following must occur? RNA primase constructs a short RNA primer. If DNA ligase was nonfunctional, what would be a likely consequence? DNA replication would occur, but the lagging strand would be composed of many small fragments. 12.1 Overview of Gene Expression What is meant by gene expression? In a multicellular organism, usually every cell contains the complete genome. All genes are present in every nucleus. However, in any given cell, only some of the genes are actually producing mRNA. Many of the genes are inactive and never do anything. Other genes only produce mRNA at certain points in the life of a cell or in response to certain conditions. The production of mRNA is known as gene expression. Genes that do not produce mRNA and do not contribute to the phenotype are not being expressed. ○ Transcription is like DNA to RNA. ○ Translation is like RNA to protein. ○ ○ ○ When RNA is translated to a protein it usually means gene expression’s molecules go from being information storage molecules to metabolic and structural functional molecules. If there is an error during the transcription of a gene, The final protein might not be functional. If there is an error during translation of a gene, the protein might not be functional. 12.2 Transcription mRNA Synthesis ○ The segment of the DNA molecule where messenger RNA synthesis begins is called the promoter region. ○ The complementary messenger RNA strand that would be synthesized from the DNA base sequence of 5'-CTGAC-3' would be 3'-GACUG-5' ○ The structure that causes the synthesis of RNA to cease is known as the transcription terminator. ○ What is a difference between DNA replication and RNA transcription?In DNA replication the helix is never closed after it is opened by helicase, but once RNA polymerase has finished transcribing a region, the double helix closes. ○ How do you know that the gene being transcribed in the animation is in a prokaryote? ○ The initiation of transcription involves a sigma factor. Are both strands of DNA used in making RNA? DNA is a two stranded molecule. Only one strand is used to transcribe mRNA. During transcription the two strands separate and RNA polymerase synthesizes mRNA based on the sequence of one the two strands. Then the two DNA strands join together again. Either strand may be used to produce mRNA. One strand does not exclusively code for mRNA while the other does not. But for any given mRNA strand only one of the DNA strands is used.The complementary nature of DNA would make it very unlikely that both strands could code simultaneously for functional proteins. Here is an analogy with language. Imagine that each letter in the alphabet had a complimentary letter. For example A might match with Q, B with X, and so on. If we were to write a normal English word the complementary sequence would be determined by the letters in that word and could not be changed. It is very unlikely that the complementary sequence would be a recognizable word. ○ The enzyme that accomplishes transcription is termed ○ The enzyme that accomplishes transcription is termed RNA polymerase. ○ The transcription enzyme first attaches to the promoter of the gene. ○ RNA polymerase is able to open the DNA double helix as it moves down the template. What type of enzymatic activity does this mean RNA polymerase must possess? Helicase activity. ○ Which of the following statements about a structural gene is TRUE? Transcription of structural genes requires DNA sequences that are not part of the gene itself. ○ Why are nucleotide triphosphates used to polymerize RNA? The triphosphate is a high energy molecule so that polymerization is spontaneous. How is mRNA transcribed without disrupting a DNA molecule? Just like DNA synthesis, mRNA synthesis is done along small sections of DNA that are uncoiled and the two strands separated. Once the mRNA is created from one of the DNA strands, that portion of the DNA rejoins and recoils as more DNA opens up further down. In this way a continuous strand of mRNA can be synthesized without uncoiling a long sequence of DNA and separating the two strands. Only separating a small portion of the DNA at a time reduces the probability of damage to the molecule. ○ ○ The Rho protein is involved in the termination stage of transcription. ○ Sigma factor recognizes the promoter region. ○ Formation of a holoenzyme occurs first in transcription. ○ If the sigma factor didn’t bind to the RNA polymerase, the RNA polymerase would not bind to the template DNA. ○ If the rho protein did not bind to the RNA, the RNA polymerase would not dissociate from the RNA and the template DNA. ○ Bicyclomycin is an antibiotic that is effective against many gram negative bacteria. It works by inhibiting Rho. What direct effect would this have on a bacteria? It would prevent termination of RNA transcription, causing mRNA transcripts to be abnormally long. Transcription Factors What is meant by gene activation? In a multicellular organism every cell contains every gene found in the organism. Not all genes are actually used in every cell. The specialization of cells into different types means that some genes are used in some cells and not in others. Also many genes are only used at certain times. How are genes turned on and off? There are many different mechanisms for controlling transcription of mRNA. If a gene is ‘turned on' then transcription proceeds followed by translation and production of a protein. If a gene is ‘turned off' then transcription is halted. Different kinds of cells have different patterns of transcription (known as gene expression). Gene expression also varies within a cell depending on the influence of external factors. ○ ○ ○ The basal transcription factors are essential for transcription and they cannot increase the rate of transcription by themselves. The assembly of transcription factors begins upstream from the transcription start site. A large region of a promoter has been deleted upstream of a gene. Basal transcription factors won’t bind to the template DNA, therefore RNA polymerase will not bind to the template DNA and transcription will not occur. 12.3 RNA Modification in Eukaryotes. RNA Splicing What property of RNA and DNA allows for the cutting of the molecule and removing of pieces without destroying the entire structure? Both RNA and DNA are modular structures. They consist of repeated elements: sugars and bases. Each repeated element has a 3' and a 5 ‘ end. These repeated elements link to one another in a chain, attaching the 3' end of one molecule to the 5' end of another molecule. If a section of the chain is removed the two separated sections will have exposed 3' and 5' ends. Thus the two separated sections can easily attach to one another and form a complete chain. The modular nature of DNA and RNA allow the molecules to be modified relatively easily when necessary. ○ Splicing joins together two exons.