Lesson 13_GRQs_Flow of Genetic information Part 1

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BIOL 101: Guided Reading Questions (GRQs) Complete and submit this GRQ as a PDF before lecture and before your online Mastering Assignment L13 GRQs: Flow of Genetic information I Reading Objectives: • Draw how the monomers of DNA are put together to form polynucleotides. • Explain how four nucleotides create so much variation. • Describe how specific DNA nucleotides encode specific protein sequences and how mutations in DNA affect proteins. • Name all the components of transcription, and how they function. • Name all the components of translation and how they function. • Compare and contrast the processes and outcomes of DNA replication, transcription, and translation. Module 10.2: DNA and RNA are polymers of nucleotides 1. What makes up a nucleotide? How do the four nucleotides differ from each other? A nucleotide, the fundamental building block of nucleic acids such as DNA and RNA, consists of three essential components. Firstly, a phosphate group, composed of one phosphorus atom and four oxygen atoms, links to the 5' carbon of the sugar molecule, forming the structural backbone. Secondly, a pentose sugar, either deoxyribose in DNA or ribose in RNA, provides the framework for the nucleotide. Lastly, the nitrogenous base, which can be adenine (A), thymine (T), cytosine (C), or guanine (G), distinguishes one nucleotide from another. In DNA, adenine pairs with thymine, and cytosine pairs with guanine, while in RNA, uracil replaces thymine. The specific arrangement of these nucleotides along the DNA or RNA strands encodes genetic information, with complementary base pairing ensuring the stability of the double helix structure in DNA. The sequence of nucleotides forms the genetic code, crucial for the transmission of genetic information and the synthesis of proteins. 2. What kind of bonds hold a nucleotides together in a polynucleotide? Are they strong? The bonds that hold nucleotides together in a polynucleotide chain are phosphodiester bonds, which form between the phosphate group of one nucleotide and the 3' carbon of the sugar molecule of the adjacent nucleotide. These bonds are covalent and strong, creating a sturdy backbone for DNA and RNA. The covalent nature of phosphodiester bonds ensures the stability of the polynucleotide chain under normal physiological conditions. Along with other interactions, such as hydrogen bonds between complementary bases, these bonds contribute to the overall strength and integrity of nucleic acids in storing and transmitting genetic information. 3. What kind of bonds hold two polynucleotides together (what holds the double helix together)? Are they strong? The DNA double helix is held together by hydrogen bonds between complementary nitrogenous bases in two polynucleotide strands. Adenine pairs with Thymine through two hydrogen bonds, while Cytosine forms three hydrogen bonds with Guanine. Although individual hydrogen bonds are relatively weak compared to covalent bonds, the cumulative effect of numerous hydrogen bonds along the length of the DNA molecule results in a strong and stable double-stranded structure. The specificity of base pairing, guided by hydrogen bonds, ensures the accurate transmission of genetic

BIOL 101: Guided Reading Questions (GRQs) Complete and submit this GRQ as a PDF before lecture and before your online Mastering Assignment information during essential processes such as DNA replication and transcription. The strength of hydrogen bonds is pivotal in maintaining the integrity of the DNA double helix under normal physiological conditions, highlighting their crucial role in the structural stability of genetic material. 4. Draw a simple picture of a DNA polynucleotide (one half of the double helix), showing sugars, phosphates, bases. Module 10.3: DNA is a double-stranded helix 1. Who was Rosalind Franklin? What did she contribute to the discovery of DNA’s structure? Rosalind Franklin, a British biophysicist and X-ray crystallographer, made significant contributions to understanding molecular structures, including DNA. In 1951, she produced a crucial X-ray diffraction image called Photo 51, revealing a cross-shaped pattern indicative of a helical structure. Although her work played a key role in deciphering DNA's structure, she did not receive full credit during her lifetime. James Watson and Francis Crick used Franklin's data without her knowledge to propose the double helix structure of DNA in 1953. While Watson, Crick, and Maurice Wilkins were awarded the Nobel Prize, Franklin's posthumous recognition has grown, highlighting her vital role in advancing our understanding of DNA's structure and function. 2. Women in science have faced many hurdles. Much has been written about the gender harassment Franklin put up with. Read more about it here if you are interested: https://www.sciencemag.org/careers/2018/08/rosalind-franklin-and-damage-gender-harassment 3. What did Watson and Crick do to solve the structure? James Watson and Francis Crick, with crucial insights from Rosalind Franklin's X-ray diffraction data and Maurice Wilkins, solved the structure of DNA in 1953. They utilized Franklin's Photo 51, which revealed a helical pattern, and Chargaff's rules, indicating specific base pairings (A-T, G-C). Combining these data, Watson and Crick proposed a groundbreaking double helix model for DNA, where two antiparallel strands are held together by hydrogen bonds between complementary bases. Their model elegantly explained the stability and replication of DNA, offering a foundational understanding of genetic information storage. The duo published their findings in Nature, earning them the Nobel Prize in Physiology or Medicine in 1962, although the role of Rosalind Franklin was not fully acknowledged at the time. Their work laid the cornerstone for molecular biology. 4. What is the Watson-Crick pairing rule? The Watson-Crick pairing rule, also known as Chargaff's rules, dictates the specific base-pairing interactions in DNA. Adenine (A) always pairs with Thymine (T), and vice versa, while Guanine (G) always pairs with Cytosine (C), and vice versa. These pairings are governed by hydrogen bonds: Adenine forms two hydrogen bonds with Thymine, and Guanine forms three hydrogen bonds with Cytosine. This complementary and specific base pairing is fundamental to the stability and structure of the DNA double helix. The Watson-Crick pairing rules play a crucial role in processes

BIOL 101: Guided Reading Questions (GRQs) Complete and submit this GRQ as a PDF before lecture and before your online Mastering Assignment such as DNA replication, transcription, and translation, ensuring the faithful transmission of genetic information. 5. If a DNA molecule was made of 20% A, what percent of the DNA would be T? And what % would consist of G? C? If a DNA molecule is made up of 20% adenine (A), according to Chargaff's rules, it would also have 20% thymine (T), as A pairs with T. The complementary base pairing in DNA ensures that the amount of adenine always equals the amount of thymine. Similarly, if 20% of the DNA consists of guanine (G), then cytosine (C) would also be 20%, as G pairs with C. Therefore, the percentages would be A=20%, T=20%, G=20%, and C=20%. The sum of A, T, G, and C percentages always equals 100% in a DNA molecule. 6. Which 3 scientists won the Nobel Prize for the discovery of the structure of DNA? The Nobel Prize for the discovery of the structure of DNA was awarded to James Watson, Francis Crick, and Maurice Wilkins in 1962. They received the prize in Physiology or Medicine for their groundbreaking work, which elucidated the double helix structure of DNA and provided a foundational understanding of the molecular basis of genetic information. 7. Why didn’t Rosalind Franklin win the prize? Rosalind Franklin did not win the Nobel Prize for the discovery of the structure of DNA, primarily due to her unfortunate passing in 1958, four years before James Watson, Francis Crick, and Maurice Wilkins were awarded the prize in 1962. The Nobel Committee does not posthumously award Nobel Prizes, and this policy prevented Franklin from being recognized alongside her colleagues for her crucial contributions to understanding the structure of DNA through X-ray diffraction studies. Franklin's work, particularly the famous Photo 51, provided critical insights into the helical structure of DNA, laying the foundation for the groundbreaking model proposed by Watson and Crick. While she was not acknowledged at the time of the award, Franklin's contributions to science are now widely recognized and appreciated. 8. Where does the variation of DNA sequences come from? That is, you and an emu and an elephant and a bacterium all possess DNA, but how is your DNA different? The variation in DNA sequences across different species and individuals arises from genetic mutations, recombination during sexual reproduction, natural selection, environmental influences, and population dynamics. Genetic mutations, caused by factors like radiation or errors during replication, introduce changes in DNA sequences. Recombination shuffles genetic material between parents, contributing to unique combinations of genes in offspring. Natural selection favors traits that confer a survival advantage, leading to the accumulation of beneficial variations. Environmental factors and population dynamics further influence genetic diversity. While the overall structure of DNA remains consistent, these processes result in the distinctive DNA sequences observed in

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BIOL 101: Guided Reading Questions (GRQs) Complete and submit this GRQ as a PDF before lecture and before your online Mastering Assignment individuals within a species and contribute to the genetic differences between species, such as humans, emus, elephants, and bacteria. Module 10.4: DNA replication depends on specific base pairing 1. Where does DNA replication occur in the cell? __nucleus________ 2. Describe the semiconservative models of DNA replication. Why is it important? The semiconservative model of DNA replication, proposed by Watson and Crick, posits that during replication, each newly formed DNA molecule contains one original (parental) strand and one newly synthesized (daughter) strand. This process begins at origins of replication, where the DNA strands unwind and separate, forming replication bubbles. DNA polymerase then synthesizes new strands in the 5' to 3' direction, leading to the continuous synthesis of one strand (leading strand) and the discontinuous synthesis of the other (lagging strand) in the form of Okazaki fragments. The accuracy of DNA replication is maintained through proofreading mechanisms. This model is crucial for genetic stability, accuracy, cell division, and inheritance, providing a foundational understanding of how genetic information is faithfully transmitted and preserved across generations in living organisms. Module 10.6: Genes control phenotypic traits through the expression of proteins 1. Think about the overview of what you are about to learn related to “information” and put these words in order in a simple diagram: Translation, RNA, DNA, transcription, protein. 2.What is The Central Dogma (you might have to Google it!)? The Central Dogma of molecular biology, proposed by Francis Crick, delineates the flow of genetic information in biological systems. It comprises three main processes: replication, transcription, and translation. Replication involves the faithful duplication of DNA to ensure the transmission of genetic information during cell division. Transcription is the synthesis of RNA, particularly messenger RNA (mRNA), from a DNA template, capturing the genetic code. The final step, translation, occurs at ribosomes, where the information carried by mRNA guides the assembly of proteins from amino acids. Although the Central Dogma serves as a foundational principle, exceptions like reverse transcription in certain viruses highlight the complexity of genetic processes in nature. Nonetheless, this model remains integral to our understanding of how genetic information is transmitted and expressed in living organisms. FOUNDATIONAL KNOWLEDGE FUN! Check out this short (3 min) video to get an overview of the rest of the modules of this assignment. It will help you keep the overview in mind. Take notes if it helps you! https://www.youtube.com/watch?v=gG7uCskUOrA Module 10.7: Genetic information in codons is translated into amino acid sequences 1. Genes provide the information for making ______proteins________ 2. How is the language of RNA different from DNA?

BIOL 101: Guided Reading Questions (GRQs) Complete and submit this GRQ as a PDF before lecture and before your online Mastering Assignment The language of RNA is different from DNA in terms of the sugar present in the backbone and one of the nucleotides. RNA contains ribose sugar instead of deoxyribose and uracil instead of thymine. 3. What is a codon? A codon is a three-nucleotide sequence in mRNA that codes for a specific amino acid or serves as a start or stop signal for protein synthesis. 4. What is the relationship between codons and amino acids? The relationship between codons and amino acids is defined by the genetic code. Each codon corresponds to a specific amino acid or a signal for the start or termination of protein synthesis. The sequence of codons in mRNA during translation determines the sequence of amino acids in the synthesized protein. Module 10.8: The genetic code dictates how codons are translated into amino acids 1. What is the goal of translation? The goal of translation is to synthesize a polypeptide chain, or a protein, using the information encoded in mRNA. It involves the conversion of the mRNA nucleotide sequence into a corresponding sequence of amino acids in a protein. 2. Using figure 10.8A, practice translating the code: • What amino acid is coded by the mRNA sequence CAU? • What is the codon(s) for the amino acid valine (Val)? The mRNA sequence CAU codes for the amino acid histidine (His) . The codon(s) for the amino acid valine (Val) are GUC, GUU, GUA, and GUG. 3. How many codons are there?___64____ 4. What three letters are the “start” codon? ___ AUG ____ What amino acid does this code for? methionine (Met) . 5. What are the three stop codons? ___ UAA ___, __ UAG _____, and ___UGA____. 6. Do they stop codons code for amino acids? No, stop codons do not code for amino acids. Instead, they signal the termination of the protein synthesis process during translation. Module 10.9: Transcription produces genetic messages in the form of RNA 1. Draw a gene that includes a promoter and terminator DNA. 2. In a few sentences that are your own, describe the process of transcription . Be sure to explain where it occurs in the eukaryotic cell, how it starts, what the enzyme does, and how it ends. Be sure to include these terms in your description: RNA polymerase, template strand, promoter, RNA nucleotides, terminator, and RNA transcript. Transcription is the process of synthesizing an RNA transcript from a DNA template. In eukaryotic cells, transcription occurs in the nucleus. The process begins when RNA polymerase, guided by a

BIOL 101: Guided Reading Questions (GRQs) Complete and submit this GRQ as a PDF before lecture and before your online Mastering Assignment promoter region on the DNA, binds to the template strand. The RNA polymerase unwinds the DNA double helix, and RNA nucleotides complementary to the template strand are added, forming an RNA transcript. This process continues until the RNA polymerase reaches the terminator region, signaling the end of transcription. The newly synthesized RNA transcript is then released, and it may undergo further processing, such as splicing and capping, before being transported out of the nucleus for translation in the cytoplasm. Module 10.10: Eukaryotic RNA is processed before leaving the nucleus as mRNA 1. What happens to the mRNA after it is synthesized but before it leaves the nucleus? After mRNA is synthesized but before it leaves the nucleus, it undergoes processing. This includes modifications such as capping at the 5' end, addition of a poly-A tail at the 3' end, and, in some cases, splicing to remove introns. These modifications enhance stability, facilitate nuclear export, and ensure proper translation in the cytoplasm. Module 10.11: Transfer RNA molecules serve as interpreters during translation 1. What are the two important sites that every tRNA has? (Draw a cartoon tRNA). Every tRNA has two important sites: the amino acid attachment site (3' end) , where the appropriate amino acid binds, and the anticodon region , a three-nucleotide sequence that recognizes and base-pairs with the complementary mRNA codon during translation. Module 10.12: Ribosomes build polypeptides 1. Ribosomes bring together what players in the process of translation? Ribosomes bring together several players in the process of translation. These include mRNA, tRNA molecules carrying amino acids, and various protein factors. 2. Why is it significant that there are structural differences between prokaryotic and eukaryotic ribosomes? The structural differences between prokaryotic and eukaryotic ribosomes are significant because they allow for the development of selective antibiotics. Many antibiotics target bacterial (prokaryotic) ribosomes without affecting eukaryotic ribosomes, providing a basis for antibiotic specificity and minimizing harmful effects on eukaryotic cells. Module 10.13-14: An initiation codon marks the start of an mRNA message / Elongation adds amino acids to the polypeptide chain until a stop codon terminates translation 1. Translation begins at the first AUG on the mRNA. What amino acid would the first tRNA that recognizes AUG be holding? _ methionine (Met) . ___________ 2. Elongation of the polypeptide continues until the ribosome comes to what codon(s) in the mRNA?

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BIOL 101: Guided Reading Questions (GRQs) Complete and submit this GRQ as a PDF before lecture and before your online Mastering Assignment Elongation of the polypeptide continues until the ribosome comes to the codons UAA , UAG , or UGA in the mRNA, which are the stop codons. 3. The bonds between amino acids are called __peptides____ bonds. They form during translation but are not catalyzed by an enzyme. The ____ribsome_______ catalyzes the bond formation. STUDY FUN: Review the video you watched earlier. Try turning off the sound and narrating it yourself: https://www.youtube.com/watch?v=gG7uCskUOrA

Lesson 13_GRQs_Flow of Genetic information Part 1

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