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1. The polymerase chain reaction (PCR) is used by scientists to amplify DNA, particularly when the quantity of DNA is very small, mixed, or contaminated with other organisms. Explain (with words) the how PCR works using a diagram to help illustrate this (show a minimum of three cycles to illustrate your point).

1. The polymerase chain reaction (PCR) is used by scientists to amplify DNA, particularly when the quantity of DNA is very small, mixed, or contaminated with other organisms. Explain (with words) the how PCR works using a diagram to help illustrate this (show a minimum of three cycles to illustrate your point).

Human Anatomy & Physiology (11th Edition)
Human Anatomy & Physiology (11th Edition)
11th Edition
ISBN:9780134580999
Author:Elaine N. Marieb, Katja N. Hoehn
Publisher:Elaine N. Marieb, Katja N. Hoehn
Chapter1: The Human Body: An Orientation
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### Understanding PCR and Its Components **1. Explanation of Polymerase Chain Reaction (PCR)** The polymerase chain reaction (PCR) is used by scientists to amplify DNA, particularly when the quantity of DNA is very small, mixed, or contaminated with other organisms. To illustrate how PCR works, the process can be broken down into three main steps that repeat for each cycle: - **Denaturation:** The double-stranded DNA is heated to around 94-98°C, causing the hydrogen bonds between nucleotide bases to break and the DNA strands to separate into two single strands. - **Annealing:** The temperature is lowered to 50-65°C to allow primers (short sequences of nucleotides) to bind to the complementary sequences of the single-stranded DNA. - **Extension:** The temperature is raised to about 72°C, which is the optimal temperature for Taq polymerase to synthesize a new strand of DNA by adding nucleotides to the primer. Each cycle doubles the number of DNA molecules, leading to exponential amplification. A visual diagram illustrating at least three cycles of these steps would include: 1. Initial DNA double helix denaturing into two single strands. 2. Primers annealing to these single strands. 3. Taq polymerase extending the DNA from the primers, forming new double-stranded DNA. **2. Designing Primers for Specific Sequence Amplification** To design primers for amplifying a specific sequence of the "16S rDNA," that would be found in the Clostridium family, you must focus on both the "highly conserved" and "highly variable" regions: - **Highly Conserved Regions:** These regions show minimal variation across different species, ensuring that primers bind effectively to a broad range of DNA sequences from different Clostridium species. - **Highly Variable Regions:** These regions show significant variation among different species, allowing differentiation and identification of specific Clostridium species. Excellent primer design involves: - Ensuring primers have 18-22 base pairs for adequate specificity. - Avoiding sequences that can form secondary structures, like hairpins. - Checking the melting temperatures of the primers to ensure that they anneal at the same temperature. - Positioning the primers around the conserved flanking regions of the target variable region to ensure amplification. **3. Target Sequence Copies by 30 PCR Cycles** Starting with a single copy of the target sequence, after 30 PCR cycles, the number of molecules can be
Transcribed Image Text:### Understanding PCR and Its Components **1. Explanation of Polymerase Chain Reaction (PCR)** The polymerase chain reaction (PCR) is used by scientists to amplify DNA, particularly when the quantity of DNA is very small, mixed, or contaminated with other organisms. To illustrate how PCR works, the process can be broken down into three main steps that repeat for each cycle: - **Denaturation:** The double-stranded DNA is heated to around 94-98°C, causing the hydrogen bonds between nucleotide bases to break and the DNA strands to separate into two single strands. - **Annealing:** The temperature is lowered to 50-65°C to allow primers (short sequences of nucleotides) to bind to the complementary sequences of the single-stranded DNA. - **Extension:** The temperature is raised to about 72°C, which is the optimal temperature for Taq polymerase to synthesize a new strand of DNA by adding nucleotides to the primer. Each cycle doubles the number of DNA molecules, leading to exponential amplification. A visual diagram illustrating at least three cycles of these steps would include: 1. Initial DNA double helix denaturing into two single strands. 2. Primers annealing to these single strands. 3. Taq polymerase extending the DNA from the primers, forming new double-stranded DNA. **2. Designing Primers for Specific Sequence Amplification** To design primers for amplifying a specific sequence of the "16S rDNA," that would be found in the Clostridium family, you must focus on both the "highly conserved" and "highly variable" regions: - **Highly Conserved Regions:** These regions show minimal variation across different species, ensuring that primers bind effectively to a broad range of DNA sequences from different Clostridium species. - **Highly Variable Regions:** These regions show significant variation among different species, allowing differentiation and identification of specific Clostridium species. Excellent primer design involves: - Ensuring primers have 18-22 base pairs for adequate specificity. - Avoiding sequences that can form secondary structures, like hairpins. - Checking the melting temperatures of the primers to ensure that they anneal at the same temperature. - Positioning the primers around the conserved flanking regions of the target variable region to ensure amplification. **3. Target Sequence Copies by 30 PCR Cycles** Starting with a single copy of the target sequence, after 30 PCR cycles, the number of molecules can be
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