Questions and Answers
What is the process by which a DNA double helix makes an identical copy of itself?
What is the function of histones in eukaryotic DNA?
What is the polarity of DNA?
What is the function of topoisomerase in DNA replication?
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What is the direction of DNA synthesis in eukaryotes?
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What is the function of DNA ligase in DNA replication?
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What is the mode of DNA replication in eukaryotes?
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What is the function of flap endonuclease 1 in DNA replication?
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What is the function of RNA primer in DNA synthesis?
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What is the role of the sigma factor in prokaryotic transcription?
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What type of breaks does Topoisomerase II create?
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What is the function of Telomerase?
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What is the function of the phosphonylation of the CTD tail on RNA pol II?
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What is the first step in DNA repair mechanisms?
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What is the primary function of snRNPs in RNA processing?
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What type of mutation would result in a premature stop codon?
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What type of repair is responsible for correcting base pair mismatches?
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What is the function of CRISPR?
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What is the function of the A-site on the ribosome?
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What is the energy source for the elongation step of protein synthesis?
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What is unique about the 2'-OH group on ribose in RNA?
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What type of RNA is synthesized by RNA polymerase II?
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What is the function of chaperone proteins?
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What is the function of FEN1/DNA polymerase I?
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What is the function of the TATA box?
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What is the mechanism of action of Rifampicin?
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What type of RNA is involved in the recognition and decoding of the genetic code?
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What is the function of the termination factors (RF-1, RF-2, RF-3) in protein synthesis?
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Study Notes
Central Dogma
- Describes the flow of genetic information: DNA replication, transcription into mRNA, and translation into proteins.
Replication
- DNA double helix creates an identical copy using parent strands as templates.
- Key enzymes:
- Helicase unwinds DNA helix using ATP.
- Topoisomerase relieves supercoiling.
- Single-stranded binding proteins stabilize separated strands.
- Semiconservative mechanism: each parental strand serves as a template for new strands.
Transcription
- Genetic information in DNA converted to mRNA.
- Eukaryotic transcription requires RNA polymerase II and a TATA box for initiation.
Translation
- mRNA translates to proteins via ribosomes.
- Codons (three-nucleotide sequences) specify amino acids during the process.
Exceptions to the Central Dogma
- RNA viruses use RNA as genetic material (e.g., Influenza uses viral RNA polymerase).
- HIV utilizes reverse transcriptase for DNA synthesis.
- Prions are proteins causing diseases by inducing misfolding in normal proteins.
Eukaryotic DNA Structure
- DNA localized in the nucleus, coiled around positively charged histones.
- Nucleosomes formed by histone protein octamers.
- Histone modifications (e.g., acetylation) regulate gene access.
DNA Biochemistry
- Antiparallel, linear double helix structure stabilized by hydrogen bonds.
- Negatively charged DNA denatured under alkaline conditions.
Gel Electrophoresis
- Technique for separating and visualizing DNA fragments, utilizing DNA's properties.
Topoisomerases
- Topo I causes single-strand breaks to relieve tension.
- Topo II creates double-strand breaks and requires ATP, targeted by specific antibiotics.
RNA Primer Requirement
- An RNA primer synthesized by primase is necessary for DNA synthesis, providing a free 3’-OH group.
Telomerase
- Extends telomeres (repeating sequences at chromosome ends) using its RNA template to prevent senescence.
DNA Damage and Repair Mechanisms
- DNA damage involves structural alterations, with repair processes including:
- Nucleotide Excision Repair: fixes distortions by excising damaged segments.
- Base Excision Repair: addresses mismatches or small damages; involves DNA glycosylase.
- Mismatch Repair: corrects nucleotide errors in newly synthesized DNA.
- Genetic deficiencies in repair mechanisms can lead to diseases such as Xeroderma Pigmentosum and Lynch Syndrome.
CRISPR
- A technology utilizing DNA repair mechanisms for genome editing.
RNA vs. DNA
- RNA contains 2’-OH on ribose, allowing interactions with metal ions, and is usually single-stranded.
Types of RNA
- RNA polymerase I synthesizes rRNA, II synthesizes mRNA, and III synthesizes tRNA.
Inhibition of RNA Polymerases
- Rifampicin inhibits bacterial RNA polymerase; α-amanitin blocks eukaryotic RNA polymerase II.
Transcription in Prokaryotes
- Initiated by RNA polymerase with a sigma factor for promoter specificity.
Eukaryotic Transcription
- Involves transcription factors and phosphorylation of RNA pol II’s CTD tail, necessary for initiation.
RNA Processing
- Pre-mRNA undergoes modifications like capping, polyadenylation, and splicing to produce mature mRNA.
Splicing
- Introns (non-coding regions) are removed, requiring snRNPs, which are essential for the splicing mechanism.
Genetic Mutation Types
- Various mutations include:
- Point: single nucleotide change.
- Silent: same amino acid specified.
- Missense: different amino acid specified.
- Nonsense: produces a stop codon.
- Insertion: addition of bases.
- Deletion: loss of bases.
Ribosome Structure
- Composed of 65% rRNA and 35% protein, crucial for peptide bond formation during translation.
tRNA Function
- Contains anticodons that pair with mRNA to ensure proper amino acid sequence.
Amino Acid Activation
- Requires ATP for the "charging" process by aminoacyl-tRNA synthetases.
Protein Synthesis Elongation
- Employs energy from GTP hydrolysis and involves multiple steps including peptide bond formation.
Termination of Protein Synthesis
- Triggered by stop codons, leading to the release of the peptide and ribosomal subunit dissociation.
Chaperone Proteins and Modifications
- Facilitate proper protein folding and modifications such as cleavage and functional group additions for final protein functionality.
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Description
Understand the process of replication, transcription, and translation in the central dogma, and explore exceptions to this rule, including RNA viruses.
