Why are changes in nucleosome spacing so important in changing gene ex.pdf

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Why are changes in nucleosome spacing so important in changing gene expression? Select one: a. Methylation of the DNA repels the nucleosomes from each other, and relaxes the conformation of the DNA. b. When DNA is methylated and histones are deacetylated, nucleosomes are relatively close together and transcription is suppressed. c. When DNA is phosphorylated or methylated and histones are acetylated, transcriptional activity is stimulated at specific DNA regions. d. Nucleosome spacing depends on parental imprinting of acetylation marks in the DNA. Select one: a. Methylation of the DNA repels the nucleosomes from each other, and relaxes the conformation of the DNA. b. When DNA is methylated and histones are deacetylated, nucleosomes are relatively close together and transcription is suppressed. c. When DNA is phosphorylated or methylated and histones are acetylated, transcriptional activity is stimulated at specific DNA regions. d. Nucleosome spacing depends on parental imprinting of acetylation marks in the DNA..

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Describe how specific nucleosome positioning can promote transcriptional activation, or, alternatively, prevent it. If you wanted to precisely position a nucleosome on a given stretch of DNA, how could you do it? Describe how specific nucleosome positioning can promote transcriptional activation, or, alternatively, prevent it. If you wanted to precisely position a nucleosome on a given stretch of DNA, how could you do it? Solution Answer: Eukaryotes often possess complex euchromatin & heterochromatic organization with histone protein coiled around DNA so that a variety of enzymes may modify structure finally causes either gene expression by deacetylation or demethylation. Sometimes, high-uninterrupted gene expression may lead to due to methylation or epigenetic changes so that there are multiple level are there to exhibit gene regulation. DNA unwinding and template formation for coding mRNA from histone proteins; Eukaryotic cells possess increased levels of DNA binding proteins as transcriptional activators and gene repressors as well. Specific nucleosome positioning can promote transcriptional activation, or, alternatively, prevent it becuase the close proximity of DNA to either exit or entry points may have high likelihood to uncoil finally to undergo transcription from the DNA stretch using protein-nucleosomal remodeling complexes. The energy is used in the form of ATP to promote \"disruption of histone-DNA association\" finally promote gene expression. If you wanted to precisely position a nucleosome on a given stretch of DNA, it is crucial to ensue the accessibility of a binding site on \"histone-DNA binding point\" where it is the most critical point for \"activator or repressor\" to bind. We can change these positions on nucleosomes, using “DNA-binding proteins” to promote either transcription or repress transcription. Histone Acetylation only promotes gene expression but histone methylation inhibits gene expression During transcription regulation synergy can also achieved by binding one factor that change the structure of the chromatin thereby another binding site is going to be available more easily and readily or less readily. Initially, “transcription activating factor” is going to recruit a coactivator, which is followed by a histone acetyltransferase by acetylation associate with pulling chromatin apart. Regulatory domains of most activators interact with TFIID (transcription factor complexes) TFIIC, and TFIID to initiate transcription. Later repressor is going to recruit a corepressor, which is followed by a histone deacetylase that enable to squish the chromatin together. Synergy enable switching the genes on and off based on the DNA binding specificity finally promote integration of different transcription possible signals..

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Prokaryotic cells do not contain nuclei or other membrane-bound organelles. The nucleoid is the area of a prokaryotic cell in which the chromosomal DNA is located. Chromosome is several orders of magnitude larger than the cell itself. So, if bacterial chromosomes are so huge, how can they fit comfortably inside a cell—much less in one small corner of the cell? Most prokaryotes do not have histones (except some species of Archaea). Thus, one way prokaryotes compress their DNA into smaller spaces is through supercoiling. Most bacterial genomes are negatively supercoiled during normal growth. Multiple proteins act together to fold and condense prokaryotic DNA. One most abundant protein HU, found in the nucleoid, works with topoisomerase I to bind DNA and introduce sharp bends in the chromosome, Generating the tension necessary for negative supercoiling. Recent studies… other proteins like integration host factor (IHF), can bind to specific sequences within the genome and introduce additional bends. The folded DNA is then organized into a variety of conformations that are supercoiled and wound around tetramers of the HU protein, much like eukaryotic chromosomes are wrapped around histones.

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1.) What does “exonuclease” activity mean? Which enzyme important for DNA polymerization has both 5’ – 3’ AND 3’ – 5’ exonuclease activity? Which is important for proofreading function? 2.) How are the site(s) where replication begin(s) is/are characterized as in both prokaryotes and eukaryotes? What is beneficial about this? Are the sites the same in prokaryotes and eukaryotes? 3.) Arrange the following proteins in the proper order in which they participate in DNA replication. 1 = Primase 2 = Helicase 3 = Single-strand binding proteins 4 = DNA polymerase I 5 =DNA polymerase III 4.) When does DNA replicate in the cell cycle of eukaryotes and prokaryotes? 5.) Why are Okazaki fragments only found on the lagging strand, but not on the leading strand of DNA? 6.) What protein transports the histones of Nucleosomes into the nucleus? 7.) Describe the differences between Topoisomerase I and Topoisomerase II. 8.) During DNA replication, ___________ adds an RNA primer to naked template strands of DNA. Why is this necessary during replication? What fills the gap after removal of this RNA primer? 9.) What is the problem with the ends of linear eukaryotic chromosomes? How does telomerase help the issue? Solution 1. Exonuclease activity means that enzymes work by cleaving nucleotides one at a time from the end (exo) of a polynucleotide chain. A hydrolyzing reaction breaks phosphodiester bonds at either the 3’ or the 5’ ends. DNA polymerase I is the enzyme important for DNA polymerization and has both 5’ – 3’ and 3’ – 5’ exonuclease activity, which is used in editing and proofreading DNA for errors. The 3\' to 5\' can remove only one mononucleotide at a time, whereas the 5\' to 3\' activity can remove up to 10 nucleotides at a time. 2. Sites from which the process of replication starts are different in prokaryotes and Eukaryotes. Prokaryotes have only one origin of replication per DNA molecule, whereas in ekaryotes, there are multiple sites for origin of replication. To initiate DNA replication in Eukaryotes, multiple replicative proteins assemble on and dissociate from these replicative origins. DNA double helix is unwound and an initial priming event by DNA polymerase occurs on the leading strand.To initiate the process of DNA replication, multiple replicative proteins assemble on and dissociate from these replicative origins. The individual factors work together to direct the formation of the pre-replication complex (pre-RC), a key intermediate in the replication initiation process. In case of prokaryotes, Helicase separates the DNA to form a replication fork at the origin of replication where DNA replication begins. Replication forks extend bi-directionally as replication continues. The initiation of DNA replication is mediated by DnaA, a protein that binds to a region of the origin known as the DnaA box. E. coli, has 4 DnaA boxes, each of which contains a highly conserved 9 bp consensus sequence 5\' - TTATCCACA - 3\'. 3. Enzymes that participate in DNa.

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Genes code for gene products. What does this statement mean? Briefly describe the structure of DNA by using the following terms: nucleotide, strand, complementary, deoxyribose, phosphate, anti-parallel, base pairing, adenine, cytosine. How many DNA molecules are in a chromosome? How many genes are in an average bacterial chromosome? What is the purpose of DNA replication? (\"To make more DNA\" would not be a complete answer.) Summarize the process of DNA replication by using the following terms: replication fork, template, nucleotide, primer, DNA polymerase, DNA ligase. (Know what each term means.) Summarize the process of RNA synthesis (transcription) by using the following terms: template, promo RNA polymerase, rRNA, mRNA, tRNA, terminator. (Know what each term means.) Where are operons found and what is the advantage of organization of genes within operons? What are some fundamental differences in organization of genes between prokaryotes and eukaryotes? How do eukaryotes produce mRNA that they can use for translation? Summarize the process of protein synthesis (translation) by using the following terms: genetic code, ribosome, mRNA, protein, amino acid, tRNA, codon, anticodon, start codon, stop codons, polypeptide. (Know what each term means.) Be able to predict the sequence of a complementary strand in both DNA and RNA synthesis, w hen the template sequence is given. Be able to use genetic code table to predict amino-acid sequence of a encoded by a nucleic acid, when the nucleic acid sequence is given. Classify mutations by type and briefly describe how mutations arise, are prevented or repaired. Explain why mutations are important by giving at least three different examples. Why do bacteria and viruses mutate so much faster than eukaryotes? What are some consequences of Briefly explain (and be able to compare and contrast) three different mechanisms of horizontal gene in bacteria: transformation, conjugation and transduction. What are some practical implications of these phenomena? Solution 3. Genes code for gene products Gene is a portion of DNA. It is made up of nucleotide sequences. It expresses itself and transfer from one generation to next generation. Gene expression means the nucleotide sequence is used for synthesizing a biomolecules- generally it is protein but it may be RNA molecules. Here gene products are those proteins and RNAs. 4. Structure of DNA DNA or deoxyribonucleic acid is the molecule that contains all genetic information of an organism. DNA has a double helix shape, which is like a ladder twisted into a spiral. Each spiral is composed of polynucleotides. Each nucleotide is made up of - deoxyribose, a kind of sugar with 5 carbon atoms; a phosphate group made of phosphorus and oxygen, and nitrogenous base. There are four types of nucleotide: Adenine (A), Thymine (T), Cytosine (C), Guanine (G). Nucleotides are joined to one another by covalent bonds between the sugar of one nucleotide and the phosphate of the next, kn.

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