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Purdue BIOL 10200 - Focus Questions #3 (Gene Expression)

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1. What is the significance of the “Central Dogma”? How does this relate to the functioning ofcells? How has this changed over time? How does it relate to the process of geneexpression?The Central Dogma dictates the flow of all genetic information in cells: DNA is the initialsource of information, it is copied and transcribed into RNA, and that transcribed informationis then translated to create proteins. The proteins made here are needed for the cell tofunction.Over time, we started to realize that certain viruses called “retro-viruses” can actually copyinformation from RNA into DNA instead of the other way around, in a process called “reversetranscription.”This relates to gene expression because the genetic material written on DNA is eventuallyexpressed in proteins. However, the specific way that it is expressed can vary tremendouslybecause of “splicing.” In essence, some bits of DNA are called “introns” and others are called“exons,” and after it is transcribed into RNA, the RNA removes some of these introns andkeeps the exons to make “mature RNA.” Depending on which introns were removed andwhich exons were kept, several different mature RNAs (corresponding to several differentproteins and several different gene expressions) can come from a single strand of DNA.2. What is the relationship between genes and proteins? What did Beadle and Tatumcontribute to understanding this?Beadle and Tatum took several mutations of Neurospora mold that all had a “conversionchain,” where they converted various substances into one another: glutamate precursor →ornithine → citrulline → arginine. The different mutations (which were all one gene apart)only ever lacked the enzyme to make just one of these substances. Thus, they concludedthat one gene = one protein. (Enzymes are proteins.)Now, we know it’s more like one gene = one polypeptide.3. What is the genetic code? How many bases are the minimum needed to specify all aminoacids? Why?The genetic code is the sequence of nucleotide bases: A, C, G and T in DNA; A, C, G and Uin RNA. These nucleotides appear in segments of 3 called “codons.” We know this becausethere are 20 amino acids, and there needs to be enough nucleotides to produce 20 or moreunique combinations. 3 is the number we settled on, as 4^3 = 64, which is more thanenough.4. How was the code “broken”? What are the general features of this code?This code is nearly universal, redundant, has 1 START codon and 3 STOP codons, and hasno other punctuation. Plus, as I mentioned above, there are 3 nucleotides, corresponding toone codon which corresponds to one amino acid. While one amino acid can have multiplecodons, no codon can have multiple amino acids. Without punctuation, the code is brokenwith the STOP codons.5. What are the different kinds of RNA and what are their roles in gene expression? What arethe stages in gene expression and how do these relate to the different kinds of RNA?The two main stages in gene expression are transcription (where DNA is converted into thesimpler mRNA) and translation (where mRNA acts as a blueprint for rRNA to put together theamino acids that tRNA brought in).mRNA is the direct product of transcription, copied from the template/antisense strand ofDNA to resemble the coding/sense strand. It is an intermediate form of DNA sent to thecytoplasm, providing information for how proteins are constructed.rRNA is a necessary component of both the small and large ribosomal units. In addition, itcreates the enzyme peptidyl transferase, which is the enzyme that makes the peptide bondbetween initiator tRNA’s carboxyl group (in the P-site) and charged tRNA’s amino acid (in theA-site)tRNA interacts with both mRNA and amino acids, and is crucial to translation:● Charged tRNA is a combination of tRNA and a specific amino acid. This combination iscreated by the enzyme aminoacyl-tRNA synthetase, which has to be specific to boththe amino acid and the anticodon on the tRNA. Eventually, once the charged tRNA getsto the ribosome in the cytoskeleton, it arrives at the A-site. It’s anticodon has to matchthe mRNA’s codon so the chain can be assembled● Initiator tRNA is paired with either methionine (eukaryotes) or N-formylmethionine(prokaryotes), and it’s presence at the P-site initiates translation. Specifically, it carriesthe anticodon UAC, which corresponds to AUG, the START codon.snRNA is involved in the modification of primary transcripts into proper mRNA. When pairedwith proteins, it creates something called snRNPs. These snRNPs are at intron-exon splicejunctions, indicating the end of an intron; and they also make up the spliceosome. Theirpresence at the splice junctions tells the spliceosome where to cut during splicing.miRNA and siRNA interfere in certain messages in DNA that they don’t want expressed.Specifically, miRNA silences while siRNA cleaves the mRNA.6. What is the basic enzymatic activity of prokaryotic RNA Pol? Does it exist in differentforms, and if so what distinguishes them? What are the requirements for the transcriptionreaction?The basic enzymatic activity of RNA POL is the successive addition of amino acids onto eachother to form a chain.RNA polymerase does not exist in specific forms in prokaryotes. After the sigma factorrecognizes the promoter on the DNA, the basic enzymatic activity happens: the corepolymerase adds matching nucleotides to whatever code is on the template/antisense strand.The transcription reaction requires a promoter (which the holoenzyme recognizes), a startsite (where core polymerase attaches and begins transcription) and a terminator (wheretranscription ends).7. How does transcription in eukaryotes differ from prokaryotes? How does the polymeraseused for transcription differ?Eukaryotic transcription is quite similar, with the same basic parts of RNA Polymerase (sigmafactor, core polymerase) and the same basic requirements (promoter, start site, terminator).However, it differs in a few major ways.● It’s transcription and translation are not coupled.● The 3’ end is not the end of transcription. Instead, a couple hundred A bases are addedto make the 3’-poly-A tail.● Splicing occurs, transforming it into a different final product.● The biggest change is that there are three different forms of RNA Polymerase creatingthree different things, and all of these forms have their own promoters. RNA PolymeraseI makes rRNA, Polymerase II makes mRNA and Polymerase III makes

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