Biomolecules - Nucleic Acids

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<h3 id="primary-stylefont-size24px-structure-of-nucleic-acids-primary"><primary style="font-size:24px"> Structure of Nucleic Acids </primary></h3>
<hr>
<main>
<ul>
<li>
<p>Nucleotides</p>
<ul>
<li>Composed of a sugar, phosphate group, and nitrogenous base</li>
<li>Sugar: Deoxyribose (DNA) or Ribose (RNA)</li>
<li>Nitrogenous bases: Adenine, Guanine, Cytosine, Thymine (DNA), Uracil (RNA)</li>
</ul>
</li>
<li>
<p>DNA (Deoxyribonucleic Acid)</p>
<ul>
<li>Double-stranded helix structure</li>
<li>Complementary base pairing (A-T, C-G)</li>
<li>Antiparallel strands (5’ to 3’ and 3’ to 5')</li>
</ul>
</li>
</ul>
</main>
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<footer style = "font-size: 18px">Introduction to Nucleic Acids $\rightarrow$ Functions of Nucleic Acids $\rightarrow$ <span style = "color:blue"> Structure of Nucleic Acids </span> $\rightarrow$ Structure of Nucleic Acids $\rightarrow$ Transcription </footer>

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<h3 id="primary-stylefont-size24px-steps-of-dna-replication-primary"><primary style="font-size:24px"> Steps of DNA replication: </primary></h3>
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<main>
<ul>
<li><strong>Initiation</strong>:
<ul>
<li>DNA helicase unwinds the double helix by breaking hydrogen bonds between base pairs</li>
<li>Replication fork is formed</li>
</ul>
</li>
<li><strong>Elongation</strong>:
<ul>
<li>DNA polymerase adds nucleotides to the 3’ end of the growing DNA strand</li>
<li>Leading strand is synthesized continuously in the 5’ to 3’ direction</li>
<li>Lagging strand is synthesized discontinuously in short fragments called Okazaki fragments</li>
</ul>
</li>
<li><strong>Termination</strong>:
<ul>
<li>DNA replication ends when all the DNA has been copied</li>
</ul>
</li>
<li><strong>Enzymes involved in DNA replication</strong>:
<ul>
<li>DNA helicase, DNA polymerase, DNA ligase, etc.</li>
</ul>
</li>
</ul>
</main>
<hr>
<footer style = "font-size: 18px">Examples of Nucleic Acids $\rightarrow$ DNA Replication $\rightarrow$ <span style = "color:blue"> Steps of DNA replication: </span> $\rightarrow$ Transcription $\rightarrow$ Steps of transcription </footer>

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<h3 id="primary-stylefont-size24px-steps-of-transcription-primary"><primary style="font-size:24px"> Steps of transcription </primary></h3>
<hr>
<main>
<ul>
<li><strong>Initiation</strong>:
<ul>
<li>RNA polymerase binds to the promoter region on the DNA molecule</li>
<li>DNA strands separate, forming a transcription bubble</li>
</ul>
</li>
<li><strong>Elongation</strong>:
<ul>
<li>RNA polymerase adds complementary RNA nucleotides to the growing mRNA strand</li>
<li>RNA synthesis occurs in the 5’ to 3’ direction</li>
</ul>
</li>
<li><strong>Termination</strong>:
<ul>
<li>Transcription ends when RNA polymerase reaches the termination signal</li>
<li>The mRNA molecule is released from the DNA template</li>
</ul>
</li>
</ul>
</main>
<hr>
<footer style = "font-size: 18px">Steps of DNA replication: $\rightarrow$ Transcription $\rightarrow$ <span style = "color:blue"> Steps of transcription </span> $\rightarrow$ Types of RNA $\rightarrow$ Translation </footer>

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<h3 id="primary-stylefont-size24px-steps-of-translation-primary"><primary style="font-size:24px"> Steps of translation: </primary></h3>
<hr>
<main>
<ul>
<li><strong>Initiation</strong>:
<ul>
<li>mRNA, ribosome subunits, and initiator tRNA bind together</li>
</ul>
</li>
<li><strong>Elongation</strong>:
<ul>
<li>Ribosome moves along the mRNA, reading the codons and bringing in the appropriate tRNA molecules</li>
<li>Amino acids are linked together to form a growing polypeptide chain</li>
</ul>
</li>
<li><strong>Termination</strong>:
<ul>
<li>Translation ends when a stop codon is reached</li>
<li>The polypeptide chain is released from the ribosome</li>
</ul>
</li>
<li><strong>Codons and Anticodons</strong>:
<ul>
<li>Codons: Three-nucleotide sequences on mRNA that specify a particular amino acid</li>
<li>Anticodons: Complementary three-nucleotide sequences on tRNA that bind to the mRNA codons</li>
</ul>
</li>
<li>Genetic code is degenerate, meaning multiple codons can code for the same amino acid</li>
</ul>
</main>
<hr>
<footer style = "font-size: 18px">Types of RNA $\rightarrow$ Translation $\rightarrow$ <span style = "color:blue"> Steps of translation: </span> $\rightarrow$ Mutations $\rightarrow$ Effects AND EXAMPLES of mutations: </footer>

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<h3 id="primary-stylefont-size24px-mutations-primary-1"><primary style="font-size:24px"> Mutations </primary></h3>
<hr>
<main>
<ul>
<li>Changes in the DNA sequence</li>
<li>Can occur due to replication errors, exposure to mutagens, etc.</li>
<li><strong>Types of mutations</strong>:
<ul>
<li>Point mutations: Changes in a single nucleotide base pair
<ul>
<li>Silent mutation: No change in the amino acid sequence</li>
<li>Missense mutation: Change in one amino acid sequence</li>
<li>Nonsense mutation: Premature stop codon, leading to a truncated protein</li>
</ul>
</li>
<li>Insertions: Addition of nucleotides</li>
<li>Deletions: Removal of nucleotides</li>
</ul>
</li>
</ul>
</main>
<hr>
<footer style = "font-size: 18px">Translation $\rightarrow$ Steps of translation: $\rightarrow$ <span style = "color:blue"> Mutations </span> $\rightarrow$ Effects AND EXAMPLES of mutations: $\rightarrow$ Genetic Code </footer>

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<h3 id="primary-stylefont-size24px-genetic-code-primary-1"><primary style="font-size:24px"> Genetic Code </primary></h3>
<hr>
<main>
<ul>
<li>Universal code for protein synthesis</li>
<li>Specifies the relationship between mRNA codons and amino acids</li>
<li>Codons are read in a non-overlapping manner</li>
<li>Start codon (AUG) signals the beginning of protein synthesis</li>
<li>Stop codons (UAA, UAG, UGA) signal the end of protein synthesis</li>
<li><strong>Examples of codon-amino acid relationships</strong>:
<ul>
<li>AUG: Methionine (start codon)</li>
<li>UUU, UUC: Phenylalanine</li>
<li>GCU, GCC, GCA, GCG: Alanine</li>
<li>UAG, UGA, UAA: Stop codons</li>
</ul>
</li>
</ul>
</main>
<hr>
<footer style = "font-size: 18px">Mutations $\rightarrow$ Effects AND EXAMPLES of mutations: $\rightarrow$ <span style = "color:blue"> Genetic Code </span> $\rightarrow$ Examples of Nucleic Acids $\rightarrow$ Summary </footer>

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<h3 id="primary-stylefont-size24px-examples-of-nucleic-acids-primary-1"><primary style="font-size:24px"> Examples of Nucleic Acids </primary></h3>
<hr>
<main>
<ul>
<li><strong>DNA extraction from fruits</strong>:
<ul>
<li>Fruits, like strawberries, contain DNA that can be extracted using common household items</li>
<li>The DNA extraction process involves breaking down the fruit cells, removing proteins and other cellular components, and precipitating DNA</li>
</ul>
</li>
<li><strong>Polymerase Chain Reaction (PCR)</strong>:
<ul>
<li>PCR is a laboratory technique used to amplify DNA segments</li>
<li>It involves a series of heating and cooling cycles to denature, anneal, and extend DNA strands</li>
<li>PCR has numerous applications in research, forensic analysis, and medical diagnostics</li>
</ul>
</li>
<li><strong>DNA fingerprinting</strong>:
<ul>
<li>DNA fingerprinting is a technique used to identify individuals based on their unique DNA profiles</li>
<li>It utilizes highly variable regions of the DNA sequence called short tandem repeats (STRs)</li>
<li>DNA fingerprinting is commonly used in forensic investigations, paternity testing, and anthropology studies</li>
</ul>
</li>
</ul>
</main>
<hr>
<footer style = "font-size: 18px">Effects AND EXAMPLES of mutations: $\rightarrow$ Genetic Code $\rightarrow$ <span style = "color:blue"> Examples of Nucleic Acids </span> $\rightarrow$ Summary $\rightarrow$ DNA Extraction from Fruits </footer>

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<h3 id="primary-stylefont-size24px-summary-primary"><primary style="font-size:24px"> Summary </primary></h3>
<hr>
<main>
<ul>
<li>Nucleic acids are essential biomolecules in living organisms.</li>
<li>DNA and RNA are the two types of nucleic acids.</li>
<li>DNA carries and transmits genetic information, while RNA plays multiple roles in gene expression.</li>
<li>Nucleotides are the building blocks of nucleic acids, consisting of a sugar, phosphate group, and nitrogenous base.</li>
<li>DNA has a double-stranded helix structure, whereas RNA is single-stranded.</li>
<li>DNA replication, transcription, and translation are important processes involving nucleic acids.</li>
<li>Mutations can alter the DNA sequence and have various effects on protein structure and function.</li>
<li>The genetic code translates mRNA codons into amino acids during protein synthesis.</li>
<li>Examples of nucleic acids include DNA extraction from fruits, PCR, and DNA fingerprinting.</li>
</ul>
</main>
<hr>
<footer style = "font-size: 18px">Genetic Code $\rightarrow$ Examples of Nucleic Acids $\rightarrow$ <span style = "color:blue"> Summary </span> $\rightarrow$ DNA Extraction from Fruits $\rightarrow$ Polymerase Chain Reaction (PCR) </footer>

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<h3 id="primary-stylefont-size24px-dna-extraction-from-fruits-primary"><primary style="font-size:24px"> DNA Extraction from Fruits </primary></h3>
<hr>
<main>
<ul>
<li><strong>Materials required</strong>: Fresh fruits (strawberries, bananas, etc.), dishwashing detergent, table salt, rubbing alcohol, water, coffee filter, test tubes</li>
<li><strong>Procedure</strong>:
<ol>
<li>Mash the fruit in a plastic bag to break down the cells and release the DNA.</li>
<li>Add detergent and salt to the mashed fruit to break down the proteins and dissolve the cell membranes.</li>
<li>Filter the mixture through a coffee filter to remove larger debris.</li>
<li>Transfer the filtrate to a test tube and add cold rubbing alcohol to precipitate the DNA.</li>
<li>Gently mix the test tube and observe the formation of white, stringy DNA strands.</li>
</ol>
</li>
<li><strong>Explanation</strong>: By using common household items, it is possible to extract DNA from fruits, providing a visual demonstration of the presence of genetic material in living organisms.</li>
</ul>
</main>
<hr>
<footer style = "font-size: 18px">Examples of Nucleic Acids $\rightarrow$ Summary $\rightarrow$ <span style = "color:blue"> DNA Extraction from Fruits </span> $\rightarrow$ Polymerase Chain Reaction (PCR) $\rightarrow$ DNA Fingerprinting (DNA Profiling) </footer>

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<h3 id="primary-stylefont-size24px-polymerase-chain-reaction-pcr-primary"><primary style="font-size:24px"> Polymerase Chain Reaction (PCR) </primary></h3>
<hr>
<main>
<ul>
<li><strong>Definition</strong>: A laboratory technique used to amplify a specific DNA segment.</li>
<li><strong>Steps</strong>:
<ol>
<li>Denaturation: Heat the DNA to separate the two strands.</li>
<li>Annealing: Cool the mixture to allow primers to bind to the target DNA.</li>
<li>Extension: DNA polymerase adds nucleotides to extend the DNA strands.</li>
<li>Repeat: Repeat the cycle multiple times to exponentially amplify the DNA segment.</li>
</ol>
</li>
<li><strong>Applications</strong>:
<ul>
<li>Genetic research: DNA sequencing, gene expression analysis.</li>
<li>Medical diagnostics: Detecting infectious agents, identifying genetic disorders.</li>
<li>Forensic analysis: DNA profiling, paternity testing.</li>
</ul>
</li>
<li><strong>Importance</strong>: PCR revolutionized molecular biology and has numerous applications in various fields.</li>
</ul>
</main>
<hr>
<footer style = "font-size: 18px">Summary $\rightarrow$ DNA Extraction from Fruits $\rightarrow$ <span style = "color:blue"> Polymerase Chain Reaction (PCR) </span> $\rightarrow$ DNA Fingerprinting (DNA Profiling) $\rightarrow$ DNA Fingerprinting Process (Continued) </footer>

<h3 id="success-stylefont-size25px-biomolecules-nucleic-acids-success-23"><Success style="font-size:25px"> Biomolecules Nucleic Acids </Success></h3>
<h3 id="primary-stylefont-size24px-dna-fingerprinting-dna-profiling-primary"><primary style="font-size:24px"> DNA Fingerprinting (DNA Profiling) </primary></h3>
<hr>
<main>
<ul>
<li><strong>Definition</strong>: A technique used to identify individuals based on their unique DNA profiles.</li>
<li><strong>Short Tandem Repeats (STRs)</strong>:
<ul>
<li>Short sequences of DNA that repeat multiple times in tandem.</li>
<li>Highly variable between individuals due to different numbers of repeats.</li>
<li>Used as genetic markers in DNA fingerprinting.</li>
</ul>
</li>
<li><strong>Procedure</strong>:
<ol>
<li>Isolate DNA from the sample.</li>
<li>Amplify STR regions using PCR.</li>
<li>Analyze the amplified DNA fragments using gel electrophoresis.</li>
<li>Compare the banding patterns to create a unique DNA profile.</li>
</ol>
</li>
<li><strong>Applications</strong>: Forensic investigations, paternity/maternity testing, genealogical research.</li>
</ul>
</main>
<hr>
<footer style = "font-size: 18px">DNA Extraction from Fruits $\rightarrow$ Polymerase Chain Reaction (PCR) $\rightarrow$ <span style = "color:blue"> DNA Fingerprinting (DNA Profiling) </span> $\rightarrow$ DNA Fingerprinting Process (Continued) $\rightarrow$ Case Study: Use of DNA Fingerprinting in Solving Crimes </footer>

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<h3 id="primary-stylefont-size24px-dna-fingerprinting-process-continued-primary"><primary style="font-size:24px"> DNA Fingerprinting Process (Continued) </primary></h3>
<hr>
<main>
<ul>
<li><strong>Gel Electrophoresis</strong>:
<ul>
<li>Technique that separates DNA fragments based on their size and charge.</li>
<li>DNA samples are loaded onto a gel matrix and subjected to an electric field.</li>
<li>Smaller DNA fragments migrate faster and move farther on the gel.</li>
<li>Stained DNA bands are visualized under UV light.</li>
</ul>
</li>
<li><strong>Interpretation of Results</strong>:
<ul>
<li>Each individual has a unique DNA profile based on the number and sizes of the amplified STR fragments.</li>
<li>Matches between profiles indicate a high probability of relatedness or identification.</li>
<li>Further statistical analysis is performed to determine the significance of the match.</li>
</ul>
</li>
</ul>
</main>
<hr>
<footer style = "font-size: 18px">Polymerase Chain Reaction (PCR) $\rightarrow$ DNA Fingerprinting (DNA Profiling) $\rightarrow$ <span style = "color:blue"> DNA Fingerprinting Process (Continued) </span> $\rightarrow$ Case Study: Use of DNA Fingerprinting in Solving Crimes $\rightarrow$ Summary: Nucleic Acids </footer>

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<h3 id="primary-stylefont-size24px-case-study-use-of-dna-fingerprinting-in-solving-crimes-primary"><primary style="font-size:24px"> Case Study: Use of DNA Fingerprinting in Solving Crimes </primary></h3>
<hr>
<main>
<ul>
<li><strong>Example 1</strong>: O.J. Simpson trial (1995)
<ul>
<li>DNA evidence from blood samples found at the crime scene and Simpson’s residence implicated him in the murder trial.</li>
<li>The DNA fingerprinting analysis played a crucial role in the conviction.</li>
</ul>
</li>
<li><strong>Example 2</strong>: Golden State Killer (2018)
<ul>
<li>Cold case homicide and rape crimes were solved using DNA evidence.</li>
<li>The offender’s DNA profile was matched to a close family member on a genealogy website.</li>
<li>Law enforcement used the family tree information to identify the suspect.</li>
</ul>
</li>
<li>These cases highlight the power of DNA fingerprinting in establishing guilt or innocence and solving long-standing criminal cases.</li>
</ul>
</main>
<hr>
<footer style = "font-size: 18px">DNA Fingerprinting (DNA Profiling) $\rightarrow$ DNA Fingerprinting Process (Continued) $\rightarrow$ <span style = "color:blue"> Case Study: Use of DNA Fingerprinting in Solving Crimes </span> $\rightarrow$ Summary: Nucleic Acids $\rightarrow$ Exam Practice Questions </footer>

<h3 id="success-stylefont-size25px-biomolecules-nucleic-acids-success-26"><Success style="font-size:25px"> Biomolecules Nucleic Acids </Success></h3>
<h3 id="primary-stylefont-size24px-summary-nucleic-acids-primary"><primary style="font-size:24px"> Summary: Nucleic Acids </primary></h3>
<hr>
<main>
<ul>
<li>Nucleic acids are essential biomolecules in living organisms, including DNA and RNA.</li>
<li>DNA carries and transmits genetic information, while RNA plays multiple roles in gene expression.</li>
<li>Nucleotides are the building blocks of nucleic acids, consisting of a sugar, phosphate group, and nitrogenous base.</li>
<li>DNA has a double-stranded helix structure, whereas RNA is single-stranded.</li>
<li>DNA replication, transcription, and translation are important processes involving nucleic acids.</li>
<li>Mutations can alter the DNA sequence and have various effects on protein structure and function.</li>
<li>The genetic code translates mRNA codons into amino acids during protein synthesis.</li>
<li>Examples of nucleic acids include DNA extraction from fruits, PCR, and DNA fingerprinting.</li>
</ul>
</main>
<hr>
<footer style = "font-size: 18px">DNA Fingerprinting Process (Continued) $\rightarrow$ Case Study: Use of DNA Fingerprinting in Solving Crimes $\rightarrow$ <span style = "color:blue"> Summary: Nucleic Acids </span> $\rightarrow$ Exam Practice Questions $\rightarrow$ Exam Practice Questions (Continued) </footer>

<h3 id="success-stylefont-size25px-biomolecules-nucleic-acids-success-27"><Success style="font-size:25px"> Biomolecules Nucleic Acids </Success></h3>
<h3 id="primary-stylefont-size24px-exam-practice-questions-primary"><primary style="font-size:24px"> Exam Practice Questions </primary></h3>
<hr>
<main>
<ul>
<li>What are the functions of nucleic acids in living organisms?</li>
<li>Explain the structure of nucleotides and their role in DNA and RNA.</li>
<li>Describe the process of DNA replication and the enzymes involved.</li>
<li>Discuss the steps of transcription and the significance of RNA polymerase.</li>
<li>Explain how genetic mutations can impact protein structure and function.</li>
<li>Describe the process of translation and the role of tRNA in protein synthesis.</li>
<li>What is the genetic code, and how does it translate mRNA codons into amino acids?</li>
<li>Give examples of nucleic acid applications in DNA extraction, PCR, and DNA fingerprinting.</li>
</ul>
</main>
<hr>
<footer style = "font-size: 18px">Case Study: Use of DNA Fingerprinting in Solving Crimes $\rightarrow$ Summary: Nucleic Acids $\rightarrow$ <span style = "color:blue"> Exam Practice Questions </span> $\rightarrow$ Exam Practice Questions (Continued) $\rightarrow$ Further Reading and Resources </footer>

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<h3 id="primary-stylefont-size24px-exam-practice-questions-continued-primary"><primary style="font-size:24px"> Exam Practice Questions (Continued) </primary></h3>
<hr>
<main>
<ul>
<li>Demonstrate the steps involved in DNA extraction from fruits.</li>
<li>Outline the PCR technique and its significance in research and diagnostics.</li>
<li>Explain the concept of DNA fingerprinting and the use of STRs as genetic markers.</li>
<li>Describe the gel electrophoresis technique and its role in analyzing DNA fragments.</li>
<li>Discuss real-life examples where DNA fingerprinting has been used in criminal investigations.</li>
<li>Summarize the key concepts and applications of nucleic acids in biology and forensics.</li>
<li>Can you think of any ethical, legal, or societal issues associated with DNA fingerprinting? Explain.</li>
</ul>
</main>
<hr>
<footer style = "font-size: 18px">Summary: Nucleic Acids $\rightarrow$ Exam Practice Questions $\rightarrow$ <span style = "color:blue"> Exam Practice Questions (Continued) </span> $\rightarrow$ Further Reading and Resources $\rightarrow$ Questions and Discussion </footer>

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<h3 id="primary-stylefont-size24px-further-reading-and-resources-primary"><primary style="font-size:24px"> Further Reading and Resources </primary></h3>
<hr>
<main>
<ul>
<li><strong>Books</strong>:
<ol>
<li>“Molecular Biology of the Cell” by Bruce Alberts et al.</li>
<li>“Genes IX” by Benjamin Lewin.</li>
</ol>
</li>
<li><strong>Websites</strong>:
<ol>
<li>National Center for Biotechnology Information (NCBI): <a href="https://www.ncbi.nlm.nih.gov" target="_blank" rel="noopener">www.ncbi.nlm.nih.gov</a></li>
<li>Khan Academy: <a href="https://www.khanacademy.org" target="_blank" rel="noopener">www.khanacademy.org</a></li>
<li>DNA Interactive: <a href="https://www.dnai.org" target="_blank" rel="noopener">www.dnai.org</a></li>
<li>Virtual Museum of Genomics: <a href="https://www.museumgenome.rockefeller.edu" target="_blank" rel="noopener">www.museumgenome.rockefeller.edu</a></li>
</ol>
</li>
</ul>
</main>
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<footer style = "font-size: 18px">Exam Practice Questions $\rightarrow$ Exam Practice Questions (Continued) $\rightarrow$ <span style = "color:blue"> Further Reading and Resources </span> $\rightarrow$ Questions and Discussion $\rightarrow$  </footer>