Chapter 16 & 17 Portfolio
Explain the structure of DNA and nucleotides. Include a model of your explanation.
DNA is a structure of two strands of nucleotides whose twisting shape accounts for the name double helix. Each nucleotide has three components: a deoxyribose sugar, a phosphate group, and one of the four type of of nitrogenous bases (adenine, thymine, guanine, and cytosine). The two strands of nucleotides are held together by hydrogen bonds between nitrogenous bases, specifically a bond between a pyrimidine and a purine. There is a specific pairing between bases: adenine goes with thymine, cytosine with guanine. The curving ridge of DNA is called the sugar-phosphate backbone. The two strands of DNA also run in antiparallel fashion so that the 5’ end of one faces the 3’ end of the other, and vice versa.
Develop a model which explains the major steps to replication, specifically a replication bubble.
First and foremost, the enzyme helicase unwinds the double helix structure of DNA and creates a replication bubble, which is essentially the active site for replication. Topoisomerase enzymes ahead of the helicase's replication fork relieve the twisting stress on the unwinding DNA to prevent the molecule from breaking. Single-stranded binding proteins keep the DNA strands steady and optimize them for replication, which begins with primers. Short sequences of RNA called primers attach to the origin of replication and kickstart the actual process of recreating DNA. The leading strand (on the 3' side of the primer) is continually elongated by DNA polymerase III, which adds free nucleotides to the growing DNA strand. On the 5' side of the original primer is the lagging strand, where more primers attach to the DNA and are elongated back towards the 3' end, synthesizing the DNA in pieces rather than consistently. Once all elongation is completed, DNA polymerase I removes the RNA primers from the new DNA strands and puts the correct nucleotides in their places. Finally, ligase joins the segments created by polymerase I and all of the lagging strand pieces, called Okazaki fragments, together with the leading strand to finalize the fully formed DNA molecule.
First and foremost, the enzyme helicase unwinds the double helix structure of DNA and creates a replication bubble, which is essentially the active site for replication. Topoisomerase enzymes ahead of the helicase's replication fork relieve the twisting stress on the unwinding DNA to prevent the molecule from breaking. Single-stranded binding proteins keep the DNA strands steady and optimize them for replication, which begins with primers. Short sequences of RNA called primers attach to the origin of replication and kickstart the actual process of recreating DNA. The leading strand (on the 3' side of the primer) is continually elongated by DNA polymerase III, which adds free nucleotides to the growing DNA strand. On the 5' side of the original primer is the lagging strand, where more primers attach to the DNA and are elongated back towards the 3' end, synthesizing the DNA in pieces rather than consistently. Once all elongation is completed, DNA polymerase I removes the RNA primers from the new DNA strands and puts the correct nucleotides in their places. Finally, ligase joins the segments created by polymerase I and all of the lagging strand pieces, called Okazaki fragments, together with the leading strand to finalize the fully formed DNA molecule.
Compare and contrast the difference between replication, transcription, and translation.
Replication, transcription, and translation are similar in the sense that all 3 processes involve the "reading" of DNA or RNA to create new molecules. All 3 processes use enzymes and other proteins in order to make the desired product from the given DNA or the RNA created from it.The key differences in replication, transcription, and translation lie in their purposes. DNA replication occurs during the S phase in cell growth to double a cell's DNA content in order to prepare for mitosis or meiosis. Transcription and translation occur in conjunction with one another and are used in the process of gene expression. Transcription creates single-stranded RNA from DNA, and translation uses that RNA to build the proteins originally coded for in DNA.
Develop a model and explain how DNA is packaged into a chromosome.
It is only in eukaryotic organisms that a linear strand of nucleotides, one long DNA molecule, is formed into a chromosome through association with large amounts of proteins called histones. One of the first steps in chromatin packaging is the development of nucleosomes. These are bunches of eight histones with 10 nm unfolded chromatin wrapped twice around them with unwound “string” in-between. The next level of packing creates chromatin 30 nm in thickness; interactions between nucleosomes cause the 10 nm fiber to fold. Then, 30 nm fiber loops around a scaffold composed of proteins to make a 300 nm fiber. The looped domains then fold mysteriously into a packaged chromosome of 700 nm width. In prokaryotic organisms such as bacteria, there are dense regions of DNA called the nucleoid where chromosomes are tightly coiled. Proteins cause the packing, but the process is much less complex.
Figure 16-21a from Chapter 16: The Molecular Basis of Inheritance PowerPoint Lecture Presentation for Campbell Biology by Chris Romero and Erin Barley
Compare and contrast the key terms gene expression, transcription, and translation.
Gene expression is the broadest of the three terms. It is defined as the process by which DNA directs the synthesis of proteins and of RNA molecules involved in protein synthesis. In a larger context, the DNA inherited by an organism dictates which physical traits are going to be passed on to the generation under observation. Transcription and translation are the two steps of gene expression. Transcription is the process of synthesizing RNA from DNA, usually the mRNA that is so important to making proteins. The nucleotide “language” of DNA is simply translated into a slightly different one that makes up instructions understandable to protein-makers outside the nucleus. Translation is the synthesis of a protein using the instructions of mRNA. There is another change in language in this process as the nucleotide sequence of RNA is coded into a series of amino acids by ribosomes.
Photo credit to Bio-Social Methods Collaborative at University of Michigan, http://biosocialmethods.isr.umich.edu/epigenetics-tutorial/
Develop a model and explain the process of transcription and translation.
Explain how eukaryotic cells modify RNA after transcription and why it is necessary.
One type of modification to RNA following transcription is the alteration of mRNA ends. A 5’ cap is a modified form of guanine added to the 5’ end of the strand. A poly-A tail is a series of 50-250 adenine nucleotides at the 3’ end. This type of modification serves three purposes: to help export mRNA from the nucleus, to help protect it from hydrolytic enzymes, and to help ribosomes attach to the 5’ end later on.
Another type of modification to RNA is RNA splicing. Because there DNA sequences are so long but much shorter sequences are needed to code for the proteins, there are long stretches of RNA that serve little purpose in protein synthesis. Removing these sequences makes protein synthesis more efficient. The noncoding segments of nucleic acid are introns while the other regions are caused exons. Spliceosomes are large complexes of proteins and small RNAs that bind to sequences, release introns, and join the exons on either side of the introns. Below is a visual of how RNA splicing removes portions of sequences.
Photo credit to www.bio.utexas.edu and Pearson Education, Inc.
Develop a model which explains how point and frameshift mutations can impact a protein.
Point mutations are the smallest-scale mutation that DNA can experience, as only a single nucleotide pair is affected; in some cases, the mutation has no effect on the completed protein, as each amino acid has multiple similar combinations of 3-base codons to keep order in spite of mutations. The non-effective mutations are considered silent and usually occur as 2 paired nucleotides (usually in the 3rd position of the codon) switching sides of the DNA double helix, but producing a new codon for the originally coded amino acid. For example, if the original codon in a gene was GGC for glycine, and the third G-C pair flipped, the new codon would be GGG, which also codes for glycine. Other point mutations, however, are not silent; these are called missense and nonsense mutations. Missense mutations alter a codon so that it calls for a different amino acid, which frequently results in a dysfunctional protein. Nonsense mutations produce a stop codon instead of an amino acid codon, which would end the production of the protein prior to its completion, rendering it useless. Another type of mutation, called a frameshift mutation, is even more frequently devastating than point mutations. In an insertion, new base pairs are added to a DNA strand; a deletion is just the opposite. These are considered frameshift mutations because they move the 3-base "frame" that makes up amino acid codons - even if only one base pair is added or removed, the entire nucleotide sequence following it is affected. Proteins produced from frameshift mutations are even further from the originally coded protein as every amino acid in the sequence could be changed.
Figure 17.26 from Chapter 17: Gene Expression: From Gene to Protein PowerPoint Lecture Presentation for Campbell Biology by Nicole Tunbridge and Kathleen Fitzpatrick
Point mutations are the smallest-scale mutation that DNA can experience, as only a single nucleotide pair is affected; in some cases, the mutation has no effect on the completed protein, as each amino acid has multiple similar combinations of 3-base codons to keep order in spite of mutations. The non-effective mutations are considered silent and usually occur as 2 paired nucleotides (usually in the 3rd position of the codon) switching sides of the DNA double helix, but producing a new codon for the originally coded amino acid. For example, if the original codon in a gene was GGC for glycine, and the third G-C pair flipped, the new codon would be GGG, which also codes for glycine. Other point mutations, however, are not silent; these are called missense and nonsense mutations. Missense mutations alter a codon so that it calls for a different amino acid, which frequently results in a dysfunctional protein. Nonsense mutations produce a stop codon instead of an amino acid codon, which would end the production of the protein prior to its completion, rendering it useless. Another type of mutation, called a frameshift mutation, is even more frequently devastating than point mutations. In an insertion, new base pairs are added to a DNA strand; a deletion is just the opposite. These are considered frameshift mutations because they move the 3-base "frame" that makes up amino acid codons - even if only one base pair is added or removed, the entire nucleotide sequence following it is affected. Proteins produced from frameshift mutations are even further from the originally coded protein as every amino acid in the sequence could be changed.
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