DNA Replication Overview

DNA Replication

• Theta replication: Circular DNA (like in bacteria) copies itself. It opens at an origin, forms a bubble, and two enzymes replicate DNA in opposite directions. Two new DNA circles result.
• Rolling circle replication: A nick is created in one DNA strand. The intact strand acts as a template, while the nicked strand is unwound and copied. This creates a long continuous strand that can be cut into pieces later. This method is common in viruses and plasmids.
• dNTPs: Building blocks of DNA, consisting of a deoxyribose sugar, a nitrogenous base, and three phosphate groups.
• RNA primer: Short RNA strand that initiates DNA replication.
• Initiator protein: Recognizes and binds to the origin of replication, starting the process.
• Helicase: Unwinds the DNA double helix.
• Gyrase: Introduces negative supercoils to prevent DNA from tangling or breaking during unwinding.
• SSBP: Protein that binds to single-stranded DNA to stabilize it and prevent it from forming unwanted structures. This is important during replication or repair when DNA is single-stranded.
• Primase: Creates short RNA primers.
• DNA polymerase I: Removes RNA primers and replaces them with DNA nucleotides.
• DNA polymerase II: Involved in DNA repair, helping fix errors during replication.
• DNA polymerase III: Main enzyme for DNA replication; adds nucleotides to the growing DNA strand.
• Ligase: Glues together DNA strands.
• DNA Pol alpha: Starts DNA replication by adding initial RNA-DNA primer to DNA strand.
• DNA Pol epsilon: Synthesizing leading strand during replication.
• DNA Pol delta: Synthesizes lagging strand during DNA replication and helps with repair.
• Nucleosome: Basic unit of DNA packaging in cells. Consists of DNA wrapped around histone proteins.
• Histone: Proteins that help organize DNA into nucleosomes.
• Chromatin: Material that makes up chromosomes. Consists of DNA wrapped around histone proteins, forming nucleosomes.
• Telomere: Protective cap at the end of each chromosome. Prevents degradation and attachment to other chromosomes.
• Telomerase: Enzyme that maintains telomere length by adding repetitive DNA sequences to their ends.
• MCM Complex: Unwinds DNA for copying. A motor that helps open up DNA for other enzymes to work.
• ORC: Protein group that binds to the origin of replication on DNA, marking the starting point for replication. Helps recruit other proteins that begin unwinding the DNA.

RNA Processing

• rNTPs: Building blocks of RNA, consisting of a nitrogenous base, a ribose sugar, and three phosphate groups.

• RNA polymerase holoenzyme: multi-part enzyme complex consisting of alpha (2 copies) beta, beta prime, and omega subunits. Sigma factor guides the RNA polymerase to promoter regions on DNA for initiation of transcription.

• Rho dependent vs Rho independent transcription termination: Rho protein recognizes a specific RNA sequence, moves along the RNA, and disrupts the DNA-RNA hybrid to terminate transcription. Rho-independent termination relies on a hairpin loop followed by uracils to destabilize the DNA-RNA hybrid.

• Kozak Sequence: Sequence that initiates translation (5'GCCa or gCCAUGG3').

• EF-G, EF-Tu, Ef-Ts: Facilitate translocation, delivery of aminoacyl-tRNA, and guanine nucleotide exchange.

• RF-1, RF-2, RF-3: Recognize stop codons and facilitate polypeptide release from the ribosome.

• RNA polymerase I, II, III: Pol I transcribes rRNA genes, while Pol II transcribes mRNA, snRNA, and miRNA. Pol III transcribes tRNA, 5S rRNA etc.

• TFIIA: Stabilizes binding of TFIID to promoter.

• TFIIB: Helps RNA polymerase II recognize start site & bind to TFIID.

• TFIID: Contains TBP (TATA-binding protein) that helps RNA polymerase to bind to the promoter.

• TFIIE: Recruits/ Regulates TFIIH

• TFIIF: Escorts RNA Pol II to promoter & stabilizes complex

• TFIIH: Unwinds DNA, phosphorylates RNA Pol II to start transcription.

• RAT1: 5' to 3' exonuclease in eukaryotes. Helps in transcription termination by degrading RNA from the 5' end.

• PIC: Set of transcription factors assemble at promoter. They prepare DNA and RNA Pol for beginning transcription.

• Mediator: Protein complex that links transcription factors to RNA polymerase II. It helps control gene expression by communicating between enhancers, promoters, and the transcription machinery.

Co-linearity, Codons, UTRs; mRNA processing

• Co-linearity: Direct correspondence between DNA and amino acid sequence.
• 5' UTR and 3' UTR: Regions at the ends of mRNA that are not translated into protein but play roles in translation regulation and mRNA stability.
• snRNAs: Type of RNA that assists in splicing.
• Spliceosome: Complex of snRNAs and proteins that removes introns from pre-mRNA and joins exons.
• 3' Poly A Tail: String of adenines added to the 3' end of mRNA, protecting it from degradation.
• 5' cap: Modified guanine added to the 5' end of mRNA, aiding in translation.
• Branch point: Special adenine in the middle of introns, crucial for splicing process.
• Alternative splicing: Different combinations of exons are joined together, resulting in multiple RNA/mRNA versions from a single gene, creating more protein isoforms.

Gene Mutations and DNA Repair

• Somatic mutations: Occur in body cells and affect only the individual.
• Germinal mutations: Occur in gametes and can be inherited.
• Base substitutions (transition/transversion): Changes in a single nucleotide base.
• Insertions: Addition of nucleotides.
• Deletions: Removal of nucleotides.
• Frameshift mutations: Shifts the reading frame of the gene.
• In-frame mutations/ deletions: Do not shift the reading frame but still change the protein.
• Tautomeric shifts: Changes in chemical structure of bases leading to mispairing.
• Dynamic mutations: Changes in severity over generations, often involves repeated expansions.
• Forward mutation: Changes function in a typical direction.
• Reverse mutation: Restores original function.
• Missense mutation: Changes one amino acid.
• Nonsense mutation: Changes a codon to a stop codon, shortening the protein.
• Silent mutation: Changes codon, but not the amino acid.
• Neutral mutation: Does not affect protein function.
• Loss-of-function mutation: Reduces or eliminates protein function.
• Gain-of-function mutation: Creates a new or enhanced function.
• Conditional mutation: Phenotype change only under certain conditions.
• Lethal mutation: Causes death, often during development.
• Suppressor mutation: Compensates for another mutation.
• Spontaneous replication errors: Mistakes in DNA copying that occur naturally.

Other Key Concepts

• EPA sites: Ribosome binding sites during protein synthesis.

• MET tRNA: Carries methionine in eukaryotes, initiating protein synthesis.

• Endonuclease: Enzyme that cuts DNA within a strand.

• Jumping Genes (Transposable Genetic Elements): DNA segments that can move within the genome, including: Class I and Class II retrotransposons

• snoRNAs: modify rRNA by adding methyl groups, impacting ribosome function.

• siRNAs and miRNAs: Involved in gene silencing (regulating gene expression) through mRNA degradation or blocking translation.

• Crispr RNA: used for gene editing.

• LncRNA: Non-coding RNA type, involved in gene expression, chromatin structure, and cellular processes.