Biomolecules - Nucleic Acids

Introduction to Nucleic Acids
- Essential biomolecules in living organisms
- Made up of nucleotides
- Two types: DNA and RNA
Functions of Nucleic Acids
- DNA: Genetic information storage and transmission
- RNA: Multiple roles in gene expression
Structure of Nucleic Acids
1. Nucleotides
  - Composed of a sugar, phosphate group, and nitrogenous base
  - Sugar: Deoxyribose (DNA) or Ribose (RNA)
  - Nitrogenous bases: Adenine, Guanine, Cytosine, Thymine (DNA), Uracil (RNA)
2. DNA (Deoxyribonucleic Acid)
  - Double-stranded helix structure
  - Complementary base pairing (A-T, C-G)
  - Antiparallel strands (5’ to 3’ and 3’ to 5')
3. RNA (Ribonucleic Acid)
  - Single-stranded structure
  - Different types: mRNA, tRNA, rRNA
DNA Replication
- Process of copying DNA to produce identical copies
- Semiconservative replication
- Involves enzymes like DNA helicase and DNA polymerase
Transcription
- Process of synthesizing RNA from DNA template
- Initiation, elongation, and termination stages
- RNA polymerase enzyme
Translation
- Process of protein synthesis from mRNA template
- Involves ribosomes, tRNA, and amino acids
- Codons and anticodons
Mutations
- Changes in DNA sequence
- Types: Point mutations, insertions, deletions
- Effects on protein structure and function
Genetic Code
- Universal code for protein synthesis
- Codons and their corresponding amino acids
- Start and stop codons
Examples of Nucleic Acids
- DNA extraction from fruits
- Polymerase Chain Reaction (PCR)
- DNA fingerprinting

======= 11. DNA Replication

Process of copying DNA to produce identical copies
Essential for cell division and inheritance
Semiconservative replication:
- Parent DNA molecule serves as a template for the synthesis of new DNA strands
- Each new DNA molecule consists of one parental strand and one newly synthesized strand
Steps of DNA replication:
1. Initiation:
  - DNA helicase unwinds the double helix by breaking hydrogen bonds between base pairs
  - Replication fork is formed
2. Elongation:
  - DNA polymerase adds nucleotides to the 3’ end of the growing DNA strand
  - Leading strand is synthesized continuously in the 5’ to 3’ direction
  - Lagging strand is synthesized discontinuously in short fragments called Okazaki fragments
3. Termination:
  - DNA replication ends when all the DNA has been copied
Enzymes involved in DNA replication:
- DNA helicase, DNA polymerase, DNA ligase, etc.

Transcription

Process of synthesizing RNA from a DNA template
Essential for gene expression
Steps of transcription:
1. Initiation:
  - RNA polymerase binds to the promoter region on the DNA molecule
  - DNA strands separate, forming a transcription bubble
2. Elongation:
  - RNA polymerase adds complementary RNA nucleotides to the growing mRNA strand
  - RNA synthesis occurs in the 5’ to 3’ direction
3. Termination:
  - Transcription ends when RNA polymerase reaches the termination signal
  - The mRNA molecule is released from the DNA template
Types of RNA:
- mRNA (messenger RNA): Carries the genetic code from DNA to the ribosome
- tRNA (transfer RNA): Transfers amino acids to the ribosome during protein synthesis
- rRNA (ribosomal RNA): Forms the structure of ribosomes

Translation

Process of protein synthesis from mRNA template
Takes place in the ribosomes
Steps of translation:
1. Initiation:
  - mRNA, ribosome subunits, and initiator tRNA bind together
2. Elongation:
  - Ribosome moves along the mRNA, reading the codons and bringing in the appropriate tRNA molecules
  - Amino acids are linked together to form a growing polypeptide chain
3. Termination:
  - Translation ends when a stop codon is reached
  - The polypeptide chain is released from the ribosome
Codons and Anticodons:
- Codons: Three-nucleotide sequences on mRNA that specify a particular amino acid
- Anticodons: Complementary three-nucleotide sequences on tRNA that bind to the mRNA codons
Genetic code is degenerate, meaning multiple codons can code for the same amino acid

Mutations

Changes in the DNA sequence
Can occur due to replication errors, exposure to mutagens, etc.
Types of mutations:
- Point mutations: Changes in a single nucleotide base pair
  - Silent mutation: No change in the amino acid sequence
  - Missense mutation: Change in one amino acid sequence
  - Nonsense mutation: Premature stop codon, leading to a truncated protein
- Insertions: Addition of nucleotides
- Deletions: Removal of nucleotides
Effects of mutations:
- Can lead to changes in protein structure and function
- Can result in genetic disorders or diseases
Examples of mutations:
- Sickle cell anemia, Cystic fibrosis, etc.

Genetic Code

Universal code for protein synthesis
Specifies the relationship between mRNA codons and amino acids
Codons are read in a non-overlapping manner
Start codon (AUG) signals the beginning of protein synthesis
Stop codons (UAA, UAG, UGA) signal the end of protein synthesis
Examples of codon-amino acid relationships:
- AUG: Methionine (start codon)
- UUU, UUC: Phenylalanine
- GCU, GCC, GCA, GCG: Alanine
- UAG, UGA, UAA: Stop codons

Examples of Nucleic Acids

DNA extraction from fruits:
- Fruits, like strawberries, contain DNA that can be extracted using common household items
- The DNA extraction process involves breaking down the fruit cells, removing proteins and other cellular components, and precipitating DNA
Polymerase Chain Reaction (PCR):
- PCR is a laboratory technique used to amplify DNA segments
- It involves a series of heating and cooling cycles to denature, anneal, and extend DNA strands
- PCR has numerous applications in research, forensic analysis, and medical diagnostics
DNA fingerprinting:
- DNA fingerprinting is a technique used to identify individuals based on their unique DNA profiles
- It utilizes highly variable regions of the DNA sequence called short tandem repeats (STRs)
- DNA fingerprinting is commonly used in forensic investigations, paternity testing, and anthropology studies

Summary

Nucleic acids are essential biomolecules in living organisms.
DNA and RNA are the two types of nucleic acids.
DNA carries and transmits genetic information, while RNA plays multiple roles in gene expression.
Nucleotides are the building blocks of nucleic acids, consisting of a sugar, phosphate group, and nitrogenous base.
DNA has a double-stranded helix structure, whereas RNA is single-stranded.
DNA replication, transcription, and translation are important processes involving nucleic acids.
Mutations can alter the DNA sequence and have various effects on protein structure and function.
The genetic code translates mRNA codons into amino acids during protein synthesis.
Examples of nucleic acids include DNA extraction from fruits, PCR, and DNA fingerprinting.

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Slide 21:

DNA Extraction from Fruits
- Materials required: Fresh fruits (strawberries, bananas, etc.), dishwashing detergent, table salt, rubbing alcohol, water, coffee filter, test tubes
- Procedure:
  1. Mash the fruit in a plastic bag to break down the cells and release the DNA.
  2. Add detergent and salt to the mashed fruit to break down the proteins and dissolve the cell membranes.
  3. Filter the mixture through a coffee filter to remove larger debris.
  4. Transfer the filtrate to a test tube and add cold rubbing alcohol to precipitate the DNA.
  5. Gently mix the test tube and observe the formation of white, stringy DNA strands.
- Explanation: 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.

Slide 22:

Polymerase Chain Reaction (PCR)
- Definition: A laboratory technique used to amplify a specific DNA segment.
- Steps:
  1. Denaturation: Heat the DNA to separate the two strands.
  2. Annealing: Cool the mixture to allow primers to bind to the target DNA.
  3. Extension: DNA polymerase adds nucleotides to extend the DNA strands.
  4. Repeat: Repeat the cycle multiple times to exponentially amplify the DNA segment.
- Applications:
  - Genetic research: DNA sequencing, gene expression analysis.
  - Medical diagnostics: Detecting infectious agents, identifying genetic disorders.
  - Forensic analysis: DNA profiling, paternity testing.
- Importance: PCR revolutionized molecular biology and has numerous applications in various fields.

Slide 23:

DNA Fingerprinting (DNA Profiling)
- Definition: A technique used to identify individuals based on their unique DNA profiles.
- Short Tandem Repeats (STRs):
  - Short sequences of DNA that repeat multiple times in tandem.
  - Highly variable between individuals due to different numbers of repeats.
  - Used as genetic markers in DNA fingerprinting.
- Procedure:
  1. Isolate DNA from the sample.
  2. Amplify STR regions using PCR.
  3. Analyze the amplified DNA fragments using gel electrophoresis.
  4. Compare the banding patterns to create a unique DNA profile.
- Applications: Forensic investigations, paternity/maternity testing, genealogical research.

Slide 24:

DNA Fingerprinting Process (Continued)
- Gel Electrophoresis:
  - Technique that separates DNA fragments based on their size and charge.
  - DNA samples are loaded onto a gel matrix and subjected to an electric field.
  - Smaller DNA fragments migrate faster and move farther on the gel.
  - Stained DNA bands are visualized under UV light.
- Interpretation of Results:
  - Each individual has a unique DNA profile based on the number and sizes of the amplified STR fragments.
  - Matches between profiles indicate a high probability of relatedness or identification.
  - Further statistical analysis is performed to determine the significance of the match.

Slide 25:

Case Study: Use of DNA Fingerprinting in Solving Crimes
- Example 1: O.J. Simpson trial (1995)
  - DNA evidence from blood samples found at the crime scene and Simpson’s residence implicated him in the murder trial.
  - The DNA fingerprinting analysis played a crucial role in the conviction.
- Example 2: Golden State Killer (2018)
  - Cold case homicide and rape crimes were solved using DNA evidence.
  - The offender’s DNA profile was matched to a close family member on a genealogy website.
  - Law enforcement used the family tree information to identify the suspect.
- These cases highlight the power of DNA fingerprinting in establishing guilt or innocence and solving long-standing criminal cases.

Slide 26:

Summary: Nucleic Acids
- Nucleic acids are essential biomolecules in living organisms, including DNA and RNA.
- DNA carries and transmits genetic information, while RNA plays multiple roles in gene expression.
- Nucleotides are the building blocks of nucleic acids, consisting of a sugar, phosphate group, and nitrogenous base.
- DNA has a double-stranded helix structure, whereas RNA is single-stranded.
- DNA replication, transcription, and translation are important processes involving nucleic acids.
- Mutations can alter the DNA sequence and have various effects on protein structure and function.
- The genetic code translates mRNA codons into amino acids during protein synthesis.
- Examples of nucleic acids include DNA extraction from fruits, PCR, and DNA fingerprinting.

Slide 27:

Exam Practice Questions
1. What are the functions of nucleic acids in living organisms?
2. Explain the structure of nucleotides and their role in DNA and RNA.
3. Describe the process of DNA replication and the enzymes involved.
4. Discuss the steps of transcription and the significance of RNA polymerase.
5. Explain how genetic mutations can impact protein structure and function.
6. Describe the process of translation and the role of tRNA in protein synthesis.
7. What is the genetic code, and how does it translate mRNA codons into amino acids?
8. Give examples of nucleic acid applications in DNA extraction, PCR, and DNA fingerprinting.

Slide 28:

Exam Practice Questions (Continued) 9. Demonstrate the steps involved in DNA extraction from fruits. 10. Outline the PCR technique and its significance in research and diagnostics. 11. Explain the concept of DNA fingerprinting and the use of STRs as genetic markers. 12. Describe the gel electrophoresis technique and its role in analyzing DNA fragments. 13. Discuss real-life examples where DNA fingerprinting has been used in criminal investigations. 14. Summarize the key concepts and applications of nucleic acids in biology and forensics. 15. Can you think of any ethical, legal, or societal issues associated with DNA fingerprinting? Explain.

Slide 29:

Further Reading and Resources
- Books:
  1. “Molecular Biology of the Cell” by Bruce Alberts et al.
  2. “Genes IX” by Benjamin Lewin.
- Websites:
  1. National Center for Biotechnology Information (NCBI): www.ncbi.nlm.nih.gov
  2. Khan Academy: www.khanacademy.org
  3. DNA Interactive: www.dnai.org
  4. Virtual Museum of Genomics: www.museumgenome.rockefeller.edu

Slide 30:

Questions and Discussion
- Encourage students to ask questions related to nucleic acids and the covered topics.
- Facilitate a class discussion on the applications, future prospects, and ethical considerations of nucleic acids in various fields.
- Provide additional clarification or examples as needed.

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