...g A New Molecule of Life Life as we know it is far more complex than one can imagine. The smallest molecule in human body can play a large role in determining the genetic outcome or the overall well being of a person. In Peter Nielsen’s “Designing a New Molecule of Life”, he speaks of a molecule that hopefully one day will create a scientific and medical breakthrough. In this essay you will read a summary of Peter Nielsen’s article and the research he has done with this molecule. Peter Nielson, along with many other scientists, have spent years creating and experimenting with a synthetic molecule called peptide nucleic acid (PNA). PNA is an artificial polymer that has many similarities to deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). It has the same storing features as DNA and RNA while being built on a protein based backbone therefore making it sturdier and simpler than the sugar phosphate-backbone. The molecule was created in hopes of having an immediate affect by pursuing a drug that would target DNA’s composing specific genes, to either enhance or block the gene’s expression. This new drug would be in efforts to interfere with the production of disease producing proteins. Although this molecule has produced highly anticipated medical research, it has also lead to speculations of being the origins of life. In his years of research, Peter Nielsen and his colleagues wanted to achieve the ability of PNA recognizing double-stranded or duplex DNA having specific...
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...other people has been attributed, and has been cited and referenced. 3. This report is my own. 4. I have not allowed, and will not allow anyone to copy my work with the intention of passing it off as his/her own work. Signature date Question: Discuss what are the nucleotides and nucleic acids in human health and disease Almost all living cells contain two very important substances, deoxyribonucleic acid or DNA and ribonucleic acid or RNA. These molecules carry instructions for making proteins. The help specify the amino acid sequence and thus which proteins will be made. When nucleotides join together they form the functional units of the structure of DNA and RNA where DNA contains one less hydroxyl group than RNA. Nucleotides serve as a source of energy therefore playing an important role in metabolism, for example mitochondria produce ATP or Adenosine triphosphate. They also serve as co-factors in enzymatic reactions and participate in cell signalling for example as Camp messengers. A single nucleotide is made up of three smaller molecules, a phosphate group which helps to form the sugar phosphate backbone via phosphodiester bonds which is between the three carbon sugar of one atom and the four carbon sugar of another, a pentose sugar, deoxyribose or ribose, and a nitrogenous base thymine, adenine, guanine and cytosine or uracil in RNA. These bases can be purines...
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...8.1.1 Study: DNA Replication Study Sheet Biology Core (S3342899) Main idea 1: DNA is a long chain of nucleotides. Represents a ring of five carbon atoms. Four carbons and an oxygen make up the five-membered ring; the other carbon branches off the ring. Represents a ring of five carbon atoms. Four carbons and an oxygen make up the five-membered ring; the other carbon branches off the ring. A salt or ester of phosphoric acid, containing PO43− or a related anion or a group such as —OPO(OH)2 A salt or ester of phosphoric acid, containing PO43− or a related anion or a group such as —OPO(OH)2 * Adenine – A * Guanine – G * Cytosine – C * Thymine - T * Adenine – A * Guanine – G * Cytosine – C * Thymine - T Deoxyribose Deoxyribose Main idea 2: The structure of DNA is a double helix. It was discovered through the work of several scientists. Hydrogen bonds play important roles in the secondary, tertiary, and quaternary structures of proteins. (In alpha helices and beta sheets, the three dimensional, folded structure of the protein, and the joining together of subunits of the protein). In DNA, H bonds hold together the two strands. This attraction is weak enough so that the strands can be pulled apart in replication and transcription. Hydrogen bonds play important roles in the secondary, tertiary, and quaternary structures of proteins. (In alpha helices and beta sheets, the three dimensional, folded structure of the protein, and...
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...REVIEW: Studies on ligand binding to histidine triad nucleotide binding protein 1 Guoyun Bai, Bo Feng, Jia Bei Wang, Edwin Pozharski, Michael Shapiro * Introduction This review provides a summary of the NMR studies conducted by G Bai et al on the ligand binding interactions of the histidine triad nucleotide binding protein 1 (HINT1). As its name suggest the HINT1 has a conserved sequence of three polar histidine amino acids which create a binding site for an α-phosphate. Although the exact function of HINT1 remains elusive the α-phosphate binding site suggests it can bind to purine nucleotides. In vitro studies showed that HINT1 also bind to purine nucleosides which are absent of the phosphate group. Bai et al aimed to use NMR to identify chemicals compounds that bind to HINT1 and therefore allow for HINT1 structure based drug design. Method Previous NMR and protein crystallography studies recognised two ligands that bound to HINT1 to be GMP and 5-aminoimidazole-4-carboxyamide-ribonucleoside (AICAR). Bai et al 2009 have previously reported the backbone assignments of HINT1 using isotopically labelled (C13 N15) and expressed and purified the labelled HINT1 protein. Saturation transfer difference (STD)-NMR spectroscopy was used to check for the binding of the different ligands to isotopically unlabelled HINT1. GMP is known as a HINT1 nucleotide ligand was used to validate the binding of AICAR and AICAR phosphate. AICAR is a known nucleoside mimetic and X-ray crystallography...
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...THE TAS2R38 GENE AND ITS SPECIFIC NUCLEOTIDE DIFFERENTIATIONS TO DETERMINE ABILITY TO TASTE PHENYLTHIOCARBAMIDE INTRODUCTION Although humans are essentially genetically identical as a whole, there are some minute variances in our gene coding that allow for differences in our interactions with the world. These genetic modifications may have extensive detrimental effects, small effects, or no apparent effect at all. A few of these alterations can even affect our senses. In this lab, we examine how a discovery by a scientist gives us insight into how a relative dissimilarity between humans can affect the ability or inability to taste certain chemicals. Scientist Arthur Fox learned that the chemical phenylthiocarbamide, or PTC, could be tasted by certain people while others could not (Dolan DNA Learning Center 2006). When this was revealed, it was inferred that the ability or inability to taste this substance may be genetically related. It was also possible that there was a specific gene that coded for this capability. The gene that was found to encode for the capacity to taste PTC is named the TASR38 gene (Dolan DNA Learning Center 2006). However, it is not just the gene itself that causes differences in the ability to taste this substance, but the differences of coding within certain locations of this gene. These distinctions in gene coding across human populations at nucleotide positions 145, 785, and 886 are called single nucleotide polymorphisms (SNPs), which alter the...
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...Analysis of Single Nucleotide Polymorphism (SNPs) of Liver cancer, Breast cancer, and Lung cancer B.Sc Hons. Biotechnology Institute of Industrial Biotechnology GOVT.COLLEGE UNIVERSITY LHR. INTRODUCTION Single nucleotide polymorphisms (SNPs), present in the protein encoding regions of the genome can have a profound influence on the structure and function of a protein. Simply these are the changes that could be silent or can be expressive, but mostly are silent. SNPs sometimes have very deleterious effects, such as change in only one nucleotide can cause missarrangement of whole of the sequence and thus codon is misread, accordingly wrong protein will form. In this study effect of SNPs on cancerous diseases will be studied. Many genes have been reported whicg have many silent and some expressive but deleterious mutations or SNPs. We will use different databases to collect the relevant data of SNPs and genes such as FASTA sequence, position, number of chromosome etc. then by usin different softwares for computational analysis of SNPs, this data will be explained on genomic level. To analyse the effect on protein level computational analysis of codones will be done. This give a brief role of SNPs(change) and its effect(disease). OBJECTIVE and SCOPE Main purpose of this work is to find out the mechanism through which SNPs cause changes at protein level. As the data will provide briefly the changes in the gene (at nucleotide level) and also...
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...called mitochondrial DNA. The main components of DNA are: a phosphate group, 5 carbon sugar and a nitrogenous base. The four nitrogenous bases are adenine, guanine, thymine, as well as cytosine. The order and sequences of these bases determine information to help build as well as maintain an organism or to allow for different information to be transmitted from one and another. Each of the bases is attached to sugar and phosphate molecules which are held together by phosphodiesterase bonds. Together they form what is called a nucleotide. Nucleotides are arranged in two long strands, these strands form something known as a double helix. By doing so it allows for more DNA to be in a smaller place and more organised, than what it would be if it were all straight. DNA can be looked at through smaller components that codes for single amino acids. These components, called codons are made up of a sequence of three nucleotides. These are typically called nucleotide triplets and together they form a unit. Within this unit contains information for the genetic code. Each...
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...consists of several polymerase accessory factors. DNA polymerase synthesizes DNA only in the 5 ' to 3 ' direction and only one of the several different types of polymerases is involved at the replication fork. As the DNA strands are anti parallel, the DNA polymerase functions asymmetrically. On the leading (forward) strand, the DNA is synthesized continuously. On the lagging strand (retro strand) the DNA is synthesized in short (1-5 kb) fragments. These DNA fragments are called as okazaki fragments. The proof function identifies copying errors and corrects them. Polymerase III is an enzyme with high processivity and catalysing capacity than others. The initiation of DNA synthesis requires priming by a short length of RNA about 10-200 nucleotides long. This priming process involves the nucleophilic attack by the 3' -OH...
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...swiveling, and rejoining DNA strands. 5. RNA Primase (enzyme) binds in the initiation point of the 3’ – 5’ parent chain. It can attract RNA nucleotides which bind to the DNA nucleotides of the 3’ – 5’ strand due to the hydrogen bonds between the bases. RNA nucleotides are the primers (starters) for the binding of DNA nucleotides. 6. DNA Polymerase III (enzyme) link up the free, matched nucleotide triphosphates by removing the terminal di-phosphate and using energy so released to carry out the very non-spontaneous chemical reaction of joining the phosphate to the deoxyribose sugar. 7. The strand that is synthesized continuously is called the leading strand and the strand that is synthesized in short pieces is called the lagging strand. The short pieces of synthesized DNA, which make up the lagging strand are called the Okazaki fragments. 8. Only one primer is required for DNA Polymerase III to synthesize the leading strand. 9. The lagging strand is the DNA strand of the replication fork, which is opposite to the leading strand. It is synthesized in the opposite direction, that is, 5' to 3' instead of the 3' end as in the leading strand. 10. Each Okazaki fragment on the lagging strand must be primed separately. After DNA polymerase III forms an Okazaki fragment, DNA polymerase I replaces the RNA nucleotides of the...
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...Background Genes and DNA Genes code for proteins. It is the specific action or function of these proteins that determines cellular shape and cellular function. The processes that take us from the sequence of nucleotides to protein are collectively called the Central Dogma of Molecular Biology. The process begins with a sequence of nucleotides. There are four nucleotides in DNA- adenine, guanine, cytosine, and thymine abbreviated A, G, C, and T, respectively. The structure of DNA is a double helix- a winding staircase structure where the rungs of the staircase are made up of the nucleotides; the railing, or backbone, is made up of sugar- in the case of DNA, the backbone is made up of the sugar, deoxyribose. The nucleotides pair up as complementary pairs to make up the “rungs”- A always pairs with T, C always pairs with G; this is called the Law of Complementary Base Pairs. The complementary pairs are held together by hydrogen bonds- weak bonds that can be broken and reformed to allow the double-strand to be separated and read (transcribed). This means that if you have a strand of DNA and you want to separate the double helix to make more DNA, the two strands will have complementary sequences. RNA and Amino Acids The specific sequence of DNA nucleic acids (nucleotides) is transcribed into the sequence of nucleic acids of messenger RNA (mRNA); this...
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...Associate Program Material DNA Worksheet Answer the following in at least 100 words: Describe the structure of DNA. 1. A DNA molecule consist of very long chains of monomers and polymers that are known as nucleotides. The grouping of the nucleotides into the polynucleotides then forms these two chains in particular which composes of DNA strain. The nucleotide is made up of a nitrogenous base, of sugar and of a phosphate group. In the DNA case, there are four nucleotides that are found along the DNA chain, the four nucleotides ate (T) thyme, (A) adenine, (C) cytosine, and (G) guanine. These four nucleotides are joined together by their covalent bonds, or more specific, the phosphates and the sugar, which composes the sugar/phosphate, back bone of the polynucleotide. 2. How does an organism’s genotype determine its phenotype? The genotype of the organism is the genetic make up of that organism, it’s the nucleotide base in the organisms DNA. The phenotype is considered the physical traits of the organism, which comes from the actions of various proteins. Structural proteins make up the structure of an organism and the enzymes catalyze the metabolic activities. Protein is not built by a gene, but it gives the instructions to do so in the form of RNA, which programs the synthesis of the protein. 3. Describe each stage of the flow of information starting with DNA and ending with a trait. Genes are what carry our traits thought...
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...while permitting the changes in rRNA conformation that are necessary for this RNA to catalyze efficient protein synthesis. The large and small ribosome subunits are assembled at the nucleolus, where newly transcribed and modified rRNAs associate with the ribosomal proteins that have been transported into the nucleus after their synthesis in the cytoplasm. These two ribosomal subunits are then exported to the cytoplasm, where they join together on an mRNA molecule, usually near its 5? end, to initiate the synthesis of proteins. The mRNA is then pulled through the ribosome, three nucleotides at a time. The small subunit provides the framework on which the tRNAs are accurately matched to the codons of the mRNA, while the large subunit catalyzes the formation of the peptide bonds that link the amino acids together into a polypeptide chain. As its codons enter the core of the ribosome, the mRNA nucleotide sequence is translated into an amino acid sequence using the tRNAs to add each amino acid in the correct sequence to the growing end of the polypeptide chain. When a stop codon is encountered, the ribosome releases the finished protein, and its two subunits separate again. These subunits can then be used to start the synthesis of another protein on another mRNA molecule. Ribosomes contains four binding sites for RNA molecules during protein synthesis. As Figure 5 shows, the process begins with a tRNA molecule is held tightly at the A and P sites of the...
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...Associate Program Material DNA Worksheet Answer the following in at least 100 words: 1. Describe the structure of DNA. A DNA molecule which is abbreviation for deoxyribonucleic acid is made up of very long chains of monomers and polymers that are called nucleotides. These two chains in particular which composes of DNA strain are then formed by the grouping of the nucleotides into the polynucleotides. The nucleotide is made up of a nitrogenous base, of sugar and of a phosphate group. In the DNA case, there are four nucleotides that are found along the DNA chain, the four nucleotides ate (T) thyme, (A) adenine, (C) cytosine, and (G) guanine. These four nucleotides are joined together by their covalent bonds, or more specific, the phosphates and the sugar which composes the sugar/phosphate back bone of the polynucleotide. 2. How does an organism’s genotype determine its phenotype? The genotype of an organism is the genetic makeup of that organism, it is the nucleotide bases in the organism’s DNA. The phenotype is considered the physical traits of the organism which comes from the actions of the broad variety of proteins. The body of an organism is made up by the structural proteins and the metabolic activities are catalyzed by the enzymes. The synthesis of the proteins is specified by the DNA. However, a protein is not directly built by a gene, but dispatches the instructions to do so in the form of the RNA, which in turn programs the synthesis of...
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...Associate Program Material DNA Worksheet Answer the following in at least 100 words: 1. Describe the structure of DNA. A DNA molecule which is abbreviation for deoxyribonucleic acid is made up of very long chains of monomers and polymers that are called nucleotides. These two chains in particular which composes of DNA strain are then formed by the grouping of the nucleotides into the polynucleotides. The nucleotide is made up of a nitrogenous base, of sugar and of a phosphate group. In the DNA case, there are four nucleotides that are found along the DNA chain, the four nucleotides ate (T) thyme, (A) adenine, (C) cytosine, and (G) guanine. These four nucleotides are joined together by their covalent bonds, or more specific, the phosphates and the sugar which composes the sugar/phosphate back bone of the polynucleotide. 2. How does an organism’s genotype determine its phenotype? The genotype of an organism is the genetic makeup of that organism, it is the nucleotide bases in the organism’s DNA. The phenotype is considered the physical traits of the organism which comes from the actions of the broad variety of proteins. The body of an organism is made up by the structural proteins and the metabolic activities are catalyzed by the enzymes. The synthesis of the proteins is specified by the DNA. However, a protein is not directly built by a gene, but dispatches the instructions to do so in the form of the RNA, which in turn programs the synthesis of the...
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...Introduction: Translation Lab will allow you to study the importance of the nucleotide sequence of mRNA as the fundamental basis for the genetic code universally deciphered by living cells. You will produce sequences of ribonucleotides that will be translated into protein to simulate the landmark experiments involving cell-free extracts that were essential for interpreting and understanding the genetic code. A major step forward in figuring out the code was the discovery by Nirenberg in 1961 that a cell-free extract made from E. coli cells could translate RNA added to the extract into proteins. The composition of the newly synthesized proteins could be determined by measuring the incorporation of radioactive amino acids into these proteins as they were translated. In his first experiment he made poly U RNA, using the enzyme polynucleotide phosphorylase, and translated it into a peptide of polyphenylalanine using the cell-free extract. This was definitive proof that RNA could code for the synthesis of proteins and gave the first possible assignment of a nucleotide code to the amino acid it specified. Methods and Materials: For each of the four bottles of ribonucleotides that appear, click on the arrow to select a nucleotide. Do this for two nucleotides initially. Click the Make RNA button to display the sequence of mRNA that you created. Click Add to Notes to create a record of your experiment. To translate this sequence into amino acids, click on the To Translation Mix...
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