DNA Damage and Repair Quiz

DNA Damage and Repair

• Uracil is not typically found in DNA, making its presence easy to recognize.
• Deamination of 5-methylcytosine transforms it to thymine, creating a repair challenge since thymine is naturally a component of DNA.
• Pyrimidine dimers, caused by UV light, link two thymine or cytosine bases, disrupting helical structure and preventing DNA replication.
• DNA affected by pyrimidine dimers may become trapped in the nucleus, leading to cell death.

Nucleotide Functions

• ATP hydrolysis (ATP → ADP + phosphate) is the primary method for energy release in cellular processes.
• Coenzyme A transports two-carbon units in the citric acid cycle, contributing to ATP synthesis.
• Cyclic AMP has phosphate groups at both 3' and 5' positions.
• Notable nucleotide coenzymes:
  • ATP provides energy for biochemical reactions.
  • NAD+ is crucial for energy transfer within cells.

DNA Technologies

• DNA and RNA polymerases synthesize DNA and RNA, respectively.
• Cloning produced by transformed cells yields abundant recombinant DNA without needing restriction enzymes.
• Artificial BAC (Bacterial Artificial Chromosomes) enable cloning large DNA sequences and rely on lac Z for selection through color changes.
• Eukaryotic chromosomes are linear, larger than prokaryotic circular chromosomes, with multiple origins of replication.

PCR (Polymerase Chain Reaction)

• Denaturation, annealing with primers, and extension using Taq polymerase are the key steps in PCR.
• Variants include:
  • Reverse Transcriptase PCR converts mRNA to cDNA.
  • Quantitative PCR measures DNA concentrations in real time, using fluorescent dyes.
  • Directed mutagenesis introduces specific changes via non-complementary primers.
  • DNA fingerprinting amplifies Short Tandem Repeats (STR) for identification.

Laboratory Analysis of DNA

• Gel electrophoresis separates DNA fragments by size and charge, exploiting DNA's negative charge.
• Recombinant proteins can be produced using proteins instead of animal sources, which is important for therapeutic applications like insulin production.

Protein Purification

• Proteins are purified based on properties such as charge and size, often through chromatography techniques.
• Fusion proteins, with reporter genes (like GFP for visibility under UV light), facilitate purification processes.

Transgenic Organisms and Gene Therapy

• Gene modification technologies include electroporation, microinjection, liposomes, and viral vectors for effective gene transfer.

Human Genome Insights

• Sequencing human genomes is now affordable, identifying potential disease risks associated with individual lifestyles.
• A small portion of the human genome codes for proteins, with many regions consisting of introns.

SNPs and Haplotype Analysis

• Single nucleotide polymorphisms (SNPs) are common variations among humans.
• Haplotypes indicate specific combinations of SNPs that can distinguish individuals and disease susceptibility.

Nucleic Acid Sequencing Techniques

• Sanger sequencing uses terminator nucleotides for controlled sequencing but is limited in scale.
• Nanopore sequencing employs electrical current to directly read DNA as it passes through a nanopore, allowing simultaneous sequencing of millions of strands.

DNA Structure in Organisms

• E. coli, as a prokaryote, lacks a nucleus and organizes its genetic material into a compact nucleoid structure.
• Supercoiling is a mechanism for compacting DNA, akin to a twisted phone cord secured at both ends.

Test your knowledge on DNA damage, focusing on issues like uracil in DNA and thymine formation from deaminated methylcytosine. Additionally, explore the effects of UV light on DNA, particularly the formation of pyrimidine dimers. This quiz will cover various aspects of DNA stability and repair mechanisms.