DNA Replication

CMB 704 = Fundamental Biochemistry DENT 604 = Fundamental Biochemistry MacOS 14 = Operating System Examplify = Testing Software

Dr. Maryam Syed = Course Instructor Dr. Raucher = Exam Challenge Recipient Exam Challenge Representative = Collects and justifies exam challenges Apple = Creator of MacOS 14

Examplify = Not compatible with MacOS 14 MacOS 14 = Not compatible with Examplify Exam Soft = Compatible with MacOS 14 Apple = Compatible with Examplify

Updating operating system = Should be avoided until compatibility is confirmed Sending exam challenge document = Within 24hrs after the release of the exam and key Collecting exam challenges = Ongoing Justifying exam challenges = As needed

14 = Version number of MacOS 704 = Course code for CMB 604 = Course code for DENT 24 = Hours to send exam challenge document after release of exam and key

Examplify = Testing software MacOS 14 = Operating system Exam Challenge Representative = Person who collects and justifies exam challenges Exam Soft = Testing software

Sonoma = Codename for MacOS 14 Dr. Maryam Syed = Instructor for CMB 704/DENT 604 Dr. Raucher = Recipient of exam challenge document Examplify = Testing software incompatible with MacOS 14

Leading strand = Continuous growth in 5’ to 3’ direction, same direction as replication fork movement Lagging strand = Discontinuous growth in 5’ to 3’ direction, copied in direction away from replication fork Trombone Model = Model for lagging strand synthesis where the strand is looped to pass through polymerase active site in the 3′ → 5′ direction Termination Utilization Substance (Tus) = Protein sequence-specific binding protein that binds replication termination sites on DNA to stop movement of replication fork

ORC = Origin recognition complex MCM = Minichromosome maintenance RPA = Replication protein A PCNA = Proliferating cell nuclear antigen

Reactive Oxygen Species (ROS) = Can cause DNA strand breaks, generated by errors during cellular processes Nucleotide excision repair = Repair pathway for larger mutations that distort DNA structure Mismatch excision repair = Repair pathway for incorrect pairing of bases during synthesis Nonhomologous end joining = One of the DNA strand break repair pathways

Telomeres = Found at linear ends of chromosomes, protect from damage by nucleases Telomerase = Maintains telomeric length in cells, high activity is a characteristic of cancer cells FEN = Flap endonuclease Somatic cells = Divide about 52 times before losing the ability to divide again

DNA glycosylases = Involved in the removal of damaged DNA in repair mechanisms DNA polymerase = Involved in filling the gap after damaged DNA is removed DNA ligase = Involved in sealing the strand after the gap is filled Protein kinases = Regulate cell cycle indirectly in repair mechanisms

Xeroderma pigmentosum (XP) = Rare genetic disease caused by recessively inherited defects in different NER genes, patients have increased sensitivity to sunlight Mismatch Excision Repair = Repair pathway that corrects errors made during replication, if errors slip through proofreading, they are found on newly synthesized strands and corrected Proofreading enzymes = Correct errors made during replication, have 3’ – 5’ exonuclease activity which recognizes mismatched bases and excises them Methyl-directed mismatch repair = In bacteria, finds these errors on newly synthesized strands and corrects them

Reactive Oxygen Species (ROS) = Generated by errors during cellular processes, can cause DNA strand breaks V(D)J recombination, class switch recombination = Can cause DNA strand breaks Radiation = Can cause DNA strand breaks Chemotherapy = Many chemotherapeutics inhibit topoisomerase, can cause DNA strand breaks

Nucleotide = A unit consisting of a base, a sugar and a phosphate group, connected via a phosphodiester bond Antiparallel = Refers to the opposite orientations of the two strands of a DNA molecule Complimentary bases = Bases that pair together via hydrogen bonds in a DNA molecule Phosphodiester bond = A bond that connects one nucleotide to another, linking the 3'-carbon of one sugar to the 5'-carbon of the next sugar via the phosphate group

DNA helicase = Unwinds the DNA double helix Topoisomerase = Removes supercoils in DNA double helix by cleaving one or both DNA strands Primase = Synthesizes short RNA strand (~10 bp) complementary to DNA DNA polymerase = Synthesizes DNA only in the 5' to 3' direction

S phase = Phase of interphase during which DNA synthesis occurs Semiconservative = Refers to the method of DNA replication where each new DNA molecule is a hybrid of one 'old' strand and one 'new' strand Replication fork = The site of DNA replication where both strands are copied simultaneously Okazaki fragments = Short fragments of DNA synthesized on the lagging strand during DNA replication

DnaA = Binds DnaA Box within Ori to initiate replication DNA helicase = Binds to ssDNA at Ori and unwinds the double helix Single-stranded DNA-binding protein = Binds to ssDNA created by helicase and protects it from nucleases Topoisomerases = Remove supercoils in DNA double helix by cleaving one or both DNA strands

Chromatin = Histone-wrapped DNA stored in a highly condensed structure Heterochromatin = Tightly packed and inactive chromatin Euchromatin = Unwound and active chromatin Histone proteins = Positively charged proteins around which DNA wraps

Leading strand = Strand of DNA synthesized continuously in the 5' to 3' direction Lagging strand = Strand of DNA synthesized discontinuously in the 5' to 3' direction DNA pol III = Enzyme that synthesizes DNA only in the 5' to 3' direction Primer = Short strand complementary to the template that contains a 3'-OH to begin the first DNA polymerase-catalyzed reaction

DnaA = Binds DnaA Box within Ori to initiate replication DNA helicase (DnaB) = Unwinds the double helix at the Ori Single-stranded DNA-binding protein = Keeps the strands separated in the replication bubble and protects DNA from nucleases Topoisomerases I and II = Remove supercoils in DNA double helix by cleaving one or both DNA strands

Mismatch Repair (MMR) = Mediated by Mut proteins, recognizes mismatch and repairs the daughter strand based on methylation. Base Excision Repair = Repairs DNA bases damaged by alkylation, deamination, oxidation, and lost bases (abasic sites). DNA Double Strand Break Repair = Repairs double-strand breaks which can cause deletions, translocations and fusions. Non-homologous End-Joining (NHEJ) = A type of DNA double strand break repair where broken ends are directly ligated without using a repair template.

Remove altered base = Performed by glycosylase Remove the phosphoribose backbone = Performed by AP endonuclease and deoxyribose phosphate lyase Fill in the gap = Performed by DNA polymerase Seal the strand = Performed by DNA ligase

Origin of replication = The site at which replication begins Replication fork = The site at which replication is occurring Okazaki fragments = Small fragments created during discontinuous synthesis of one parental strand Primer = An RNA sequence synthesized by the enzyme primase, providing a free 3'-hydroxyl group required by DNA polymerase for replication

Helicases and Topoisomerases = Required to unwind the DNA helix of the parental strands DNA Polymerase = Reads the parental template strand in the 3'-to-5' direction, producing new strands in a 5'-to-3' direction Primase = Synthesizes the primer, providing a free 3'-hydroxyl group required by DNA polymerase for replication Telomerase = Synthesizes the ends of linear chromosomes (telomeres)

Mismatch Repair (MMR) = Enzymes recognize mis-incorporated bases, remove them from DNA, and replace them with the correct bases Nucleotide Excision Repair = Enzymes remove incorrect bases with a few surrounding bases, which are replaced with the help of a DNA polymerase and the template DNA DNA Non-Homologous End-Joining (NHEJ) = A major DSB repair pathway where broken ends are directly ligated Homologous Recombination (HR) = A major DSB repair pathway where a sister chromatid is required for repair

Homologous Recombination (HR) = Requires sister chromatid S and G2 phase Non-homologous end-joining (NHEJ) = Occurs in post mitotic cells and cycling cells in G1

Ku = Binds to the double stranded break and recruits necessary polymerase and ligase to repair the break Polymerase = Involved in the repair process after Ku binds to the double stranded break Ligase = Involved in sealing the repaired break

Mismatched bases = Mismatch Repair (MMR) Damaged bases (alkylation, deamination, oxidation, lost bases) = Base Excision Repair Incorrect bases = Nucleotide Excision Repair Double strand breaks = DNA Double Strand Break Repair (DSBR)

Parental strands = The original strands of DNA that serve as a template for the synthesis of a complementary strand Deoxyribonucleotide triphosphates = The precursors for replication 5'-to-3' direction = The direction in which DNA polymerase produces new strands 3'-to-5' direction = The direction in which DNA polymerase reads the parental template strand

Antiparallel = DNA strands run in opposite directions Negatively charged = The charge of DNA due to the phosphate group Complimentary bases = Bases held together via hydrogen bond Phosphodiester bond = The connection between each nucleotide in the chain

DnaA = Binds DnaA Box within Ori to initiate replication DNA helicase = Forces the strands apart and unwinds double helix Single-stranded DNA-binding protein = Keeps the strands separated in replication bubble Topoisomerase = Removes supercoils in DNA double helix by cleaving one or both DNA strands

Initiation = Starts at specific nucleotide sequences – origins of replication (Ori) Elongation = The site of replication called the replication fork and both strands are copied simultaneously Termination = The end of the replication process

Leading strand = Synthesized continuously in the 5′ → 3′ direction Lagging strand = Synthesized discontinuously (Okazaki fragments) in the 5′ → 3′ direction

Heterochromatin = Tightly packed and inactive Euchromatin = Unwound and active

DNA pol III = Synthesizes DNA only in the 5′ → 3′ direction Primer = Short strand complementary to the template contains a 3’-OH to begin the first DNA polymerase-catalyzed reaction Primase = Synthesizes short RNA strand (~10 bp) complementary to DNA DNA pol I = Removes primers and replaces RNA with DNA

Topoisomerase I = Cuts one strand, rotates it around intact strand, and reseals the nick Topoisomerase II = Makes a transient break in both strands, passes a different section of double helix through the break and reseals it

Mismatch repair (MMR) = Mediated by Mut proteins, the mismatched strand is identified based on methylation. The endonuclease nicks DNA, DNA is removed by exonuclease, the gap is filled by DNA pol, and sealed by DNA ligase. Base Excision Repair = Repairs DNA bases damaged by alkylation, deamination, oxidation, and lost bases. The process involves removal of altered base and phosphoribose backbone, filling in the gap, and sealing the strand. DNA Double Strand Break Repair = DSBs can cause deletions, translocations and fusions leading to genomic rearrangements. Two pathways for repairing DSBs are Homologous Recombination (HR) and Non-homologous end-joining (NHEJ). Non-homologous End-Joining (NHEJ) = Repair template is not used. Broken ends are directly ligated. Ku binds to the double stranded break and recruits necessary polymerase and ligase to repair the break.

Origin of replication = The site at which replication begins. Replication fork = The site at which replication is occurring. Okazaki fragments = Small fragments created due to discontinuous synthesis of one of the parental strands. Telomerase = The enzyme that synthesizes the ends of linear chromosomes (telomeres).

Unwinding of DNA helix = This process requires helicases and topoisomerases. Synthesis of new strands = DNA polymerase reads the parental template strand in the 3'-to-5' direction, producing new strands in a 5'-to-3' direction. Primer synthesis = DNA polymerase requires a free 3'-hydroxyl group of a nucleotide primer in order to replicate DNA. The primer is synthesized by the enzyme primase, which provides an RNA primer. Joining of Okazaki fragments = This is necessary because DNA polymerase can only synthesize DNA in the 5'-to-3' direction.

Mismatched bases = Mismatch repair enzymes recognize these, remove them from DNA, and replace them with the correct bases. Incorrect bases with a few surrounding bases = In nucleotide excision repair, enzymes remove these and replace them with the correct bases with the help of a DNA polymerase and the template DNA. Double Strand Breaks (DSBs) = The two major DSB repair pathways are DNA non-homologous end-joining (NHEJ) and homologous recombination (HR). Damaged DNA bases = Base Excision Repair fixes these.

Helicases and topoisomerases = Required to unwind the DNA helix of the parental strands. DNA polymerase = Reads the parental template strand in the 3'-to-5' direction, producing new strands in a 5'-to-3' direction. Deoxyribonucleotide triphosphates = The precursors for replication. Primase = Synthesizes the primer which is required by DNA polymerase to replicate DNA.

Mut S = Recognizes mismatch and recruits Mut L in Mismatch repair (MMR). Mut H = Activated by Mut S and Mut L, cleaves daughter strand in Mismatch repair (MMR). Glycosylase = Removes altered base in Base Excision Repair. AP endonuclease, deoxyribose phosphate lyase = Remove the phosphoribose backbone in Base Excision Repair.

Mismatch repair (MMR) = Mismatch identified, endonuclease nicks DNA, DNA removed by exonuclease, gap filled by DNA pol, sealed by DNA ligase. Base Excision Repair = Remove altered base, Remove the phosphoribose backbone, Fill in the gap, Seal the strand. DNA Double Strand Break Repair = Two pathways for repairing DSBs are Homologous Recombination (HR) and Non-homologous end-joining (NHEJ). Non-homologous End-Joining (NHEJ) = Repair template is not used, Broken ends are directly ligated, Ku binds to the double stranded break and recruits necessary polymerase and ligase to repair the break.

Okazaki fragments = Small fragments created due to discontinuous synthesis of one of the parental strands. Origin of replication = The site at which replication begins. Replication fork = The site at which replication is occurring. Telomerase = The enzyme that synthesizes the ends of linear chromosomes (telomeres).

Mismatched bases = Mismatch repair enzymes recognize these, remove them from DNA, and replace them with the correct bases. Incorrect bases with a few surrounding bases = In nucleotide excision repair, enzymes remove these and replace them with the correct bases with the help of a DNA polymerase and the template DNA. Double Strand Breaks (DSBs) = The two major DSB repair pathways are DNA non-homologous end-joining (NHEJ) and homologous recombination (HR). Damaged DNA bases = Base Excision Repair fixes these.

Mismatch Repair (MMR) = This method recognizes mismatched bases, removes them from DNA, and replaces them with the correct bases. Base Excision Repair = This method repairs DNA bases damaged by alkylation, deamination, oxidation, and lost bases (abasic sites). DNA Double Strand Break Repair = This method repairs double strand breaks which can cause deletions, translocations and fusions leading to genomic rearrangements. Non-homologous End-Joining (NHEJ) = In this method, the broken ends are directly ligated. Ku binds to the double stranded break and recruits necessary polymerase and ligase to repair the break.

Replication Fork = The site at which replication is occurring. Helicases and Topoisomerases = These are required to unwind the DNA helix of the parental strands. Okazaki Fragments = These are small fragments created due to discontinuous synthesis in one parental strand. Primase = This enzyme synthesizes an RNA primer, providing a free 3'-hydroxyl group for DNA polymerase to replicate DNA.

Mut S, Mut L, Mut H = These proteins are involved in Mismatch Repair (MMR), recognizing and repairing mismatches in DNA. Glycosylase = This enzyme is involved in Base Excision Repair, removing altered bases from the DNA. AP Endonuclease = This enzyme removes the phosphoribose backbone in Base Excision Repair. Ku = This protein binds to the double-stranded break in Non-homologous End-Joining (NHEJ) and recruits necessary polymerase and ligase to repair the break.

Origin of Replication = The site at which replication begins. Deoxyribonucleotide Triphosphates = These are the precursors for replication. Telomerase = This enzyme synthesizes the ends of linear chromosomes (telomeres). DNA Polymerase = This enzyme reads the parental template strand in the 3'-to-5' direction, producing new strands in a 5'-to-3' direction.

Mismatch Repair = This method identifies mismatched bases, removes them from DNA, and replaces them with the correct bases. Nucleotide Excision Repair = In this method, incorrect bases with a few surrounding bases are removed and replaced with the correct bases with the help of a DNA polymerase and the template DNA. Base Excision Repair = This method repairs DNA bases damaged by alkylation, deamination, oxidation, and lost bases (abasic sites). Non-homologous End-Joining (NHEJ) = In this method, the broken ends are directly ligated. Ku binds to the double stranded break and recruits necessary polymerase and ligase to repair the break.

Helicases and Topoisomerases = These enzymes unwind the DNA helix of the parental strands. DNA Polymerase = This enzyme reads the parental template strand in the 3'-to-5' direction, producing new strands in a 5'-to-3' direction. Okazaki Fragments = These small fragments are created due to discontinuous synthesis in one parental strand. Primase = This enzyme synthesizes an RNA primer, providing a free 3'-hydroxyl group for DNA polymerase to replicate DNA.

Mismatch Repair (MMR) = This pathway recognizes mismatched bases, removes them from DNA, and replaces them with the correct bases. Base Excision Repair = This pathway repairs DNA bases damaged by alkylation, deamination, oxidation, and lost bases (abasic sites). DNA Double Strand Break Repair = This pathway repairs double strand breaks which can cause deletions, translocations and fusions leading to genomic rearrangements. Non-homologous End-Joining (NHEJ) = In this pathway, the broken ends are directly ligated. Ku binds to the double stranded break and recruits necessary polymerase and ligase to repair the break.

Mismatched Bases = Mismatch Repair (MMR) Alkylation, Deamination, Oxidation, Lost Bases = Base Excision Repair Double Strand Breaks = DNA Double Strand Break Repair Broken Ends = Non-homologous End-Joining (NHEJ)

Mut S, Mut L, Mut H = These enzymes are involved in Mismatch Repair (MMR), recognizing and repairing mismatches in DNA. Glycosylase, AP Endonuclease = These enzymes are involved in Base Excision Repair, removing altered bases and the phosphoribose backbone from the DNA. DNA Polymerase = This enzyme is involved in Nucleotide Excision Repair, replacing incorrect bases with correct ones using the template DNA. Ku = This protein is involved in Non-homologous End-Joining (NHEJ), binding to the double-stranded break and recruiting necessary polymerase and ligase to repair the break.