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BIOL2161 Exam
| Question | Answer |
|---|---|
| Germline mutation | A genetic alteration occurring in reproductive cells, making it transmissible to offspring. |
| Base pairing rules | Principle that adenine pairs with thymine via two hydrogen bonds and guanine pairs with cytosine via three hydrogen bonds. |
| Phosphodiester bond | The covalent linkage joining the 3′‑hydroxyl of one sugar to the 5′‑phosphate of the next, forming the backbone of nucleic acids. |
| Antiparallel strands | Orientation where one strand runs 5′→3′ and the opposite runs 3′→5′. |
| Somatic mutation | A genetic change arising in non‑reproductive cells, affecting only the individual organism. |
| DNA polymerase I | The enzyme that removes RNA primers and fills the resulting gaps with DNA in prokaryotes. |
| Nucleotide | The basic building block of nucleic acids, consisting of a sugar, a phosphate group, and a nitrogenous base. |
| Pyrimidine | A single‑ring nitrogenous base, examples include cytosine, thymine, and uracil. |
| Human mutation rate | Approximately three changes per hundred million nucleotides per generation. |
| Nucleotide excision repair (NER) | Cellular pathway that cuts out a short single‑stranded segment containing a bulky lesion and fills the gap using a polymerase. |
| Purine | A two‑ring nitrogenous base, examples include adenine and guanine. |
| Double helix | A right‑handed, twisted ladder structure formed by two complementary strands. |
| Okazaki fragments | Short DNA segment synthesized on the discontinuously replicated strand, later joined by ligase. |
| Helicase | Motor protein that separates the two strands of the double‑stranded molecule by breaking hydrogen bonds. |
| Pyrimidine dimer | Covalent linkage formed between two adjacent pyrimidine bases after absorbing UV light, causing a distortion in the helix. |
| DNA | A macromolecular polymer that stores genetic information for all living organisms. |
| DNA polymerase III | The primary enzyme responsible for rapid, high‑fidelity synthesis of the new strand during bacterial replication. |
| Lagging strand | The newly synthesized DNA segment that is formed discontinuously in short pieces opposite the fork movement. |
| Primase | RNA‑polymerizing enzyme that creates a short primer providing a 3′‑hydroxyl for DNA synthesis initiation. |
| Leading strand | The newly synthesized DNA segment that is extended continuously in the direction of the replication fork. |
| Photolyase | Light‑activated enzyme that directly reverses UV‑induced cyclobutane pyrimidine dimers using visible light energy. |
| Translesion synthesis | DNA‑damage tolerance strategy where specialized polymerases replicate across lesions that stall the normal replicative enzyme. |
| Microsatellite instability | Condition characterized by frequent changes in length of short tandem repeats due to defective mismatch correction. |
| Base excision repair (BER) | Process that removes small, non‑bulky damaged bases, creates an abasic site, fills the gap with the correct nucleotide, and seals the strand. |
| Polymerase I | Enzyme that removes RNA primers and fills short gaps during lagging‑strand maturation. |
| Deamination | Spontaneous chemical reaction converting cytosine to uracil, adenine to hypoxanthine, or guanine to xanthine. |
| Tumor suppressor gene | Gene whose product normally restrains cell proliferation; loss‑of‑function mutations predispose to cancer. |
| Nucleotide excision repair (NER) | Mechanism that excises a short single‑strand DNA segment containing bulky lesions and restores the original sequence through resynthesis and ligation. |
| Mismatch repair | Pathway that corrects base mispairings and small insertion‑deletion loops left after replication by excising the newly synthesized strand segment. |
| Synthetic lethality | Situation where simultaneous loss of two genes leads to cell death, whereas loss of either alone is tolerated. |
| DNA glycosylase | Enzyme that cleaves the N‑glycosidic bond to release a damaged base, generating an abasic site. |
| Polymerase ζ | Polymerase that extends from nucleotides inserted by other TLS enzymes and is highly mutagenic. |
| DNA polymerase | Protein that catalyzes the addition of deoxyribonucleotides to the 3' end of a DNA strand during replication. |
| Polymerase V | Error‑prone enzyme that replaces the replicative polymerase at stalled sites to insert nucleotides opposite bulky lesions. |
| Pyrimidine dimer | UV‑induced covalent linkage between adjacent pyrimidine bases that distorts the DNA helix. |
| AP endonuclease | Enzyme that incises the DNA backbone at an abasic site, producing a 3′‑OH and a 5′‑deoxyribose phosphate. |
| PARP inhibitor | Drug that blocks poly(ADP‑ribose) polymerase activity, causing accumulation of single‑strand breaks in cells lacking homologous recombination. |
| Polymerase II | Polymerase recruited during repair that possesses a 3′→5′ proofreading activity but lacks exonuclease activity for primer removal. |
| Polymerase η | Polymerase that accurately bypasses UV‑induced cyclobutane pyrimidine dimers with relatively high fidelity. |
| Polymerase III | Primary high‑fidelity replicative enzyme responsible for bulk DNA synthesis on both leading and lagging strands. |
| DNA repair | Cellular mechanisms that locate and fix damaged nucleic acid structures to preserve genetic information. |
| 5-methylcytosine deamination to thymine | Transformation of methylated cytosine into thymine, creating a guanine–thymine mismatch that can become a C→T transition after replication. |
| Homologous recombination (HR) | Accurate repair pathway that uses an undamaged homologous template to guide restoration of a broken DNA duplex. |
| DNA glycosylase | Enzyme that recognizes a specific abnormal base and cleaves the N‑glycosidic bond, leaving an apurinic/apyrimidinic site. |
| DNA polymerase β | Enzyme that inserts the appropriate deoxynucleotide into a single‑base gap using the opposite strand as a template. |
| Non-homologous end joining (NHEJ) | Rapid ligation of broken DNA ends without a template, often resulting in small insertions or deletions. |
| Double-strand break (DSB repair) | Processes that rejoin both DNA strands after a break, restoring chromosome continuity. |
| Base mismatch | Incorrect pairing of complementary nucleotides during replication or after chemical alteration. |
| A-rule | Tendency of translesion polymerases to insert adenine opposite an abasic site during DNA synthesis. |
| DNA ligase (in BER) | Catalyst that joins adjacent 3′‑hydroxyl and 5′‑phosphate ends, sealing the nick after nucleotide insertion. |
| AP endonuclease | Protein that incises the DNA strand at an apurinic/apyrimidinic location, generating a single‑strand break for further processing. |
| Deamination | Removal of an amino group from a nucleobase, altering its base‑pairing properties. |
| Holliday junction | Four‑strand DNA crossover structure formed during strand invasion in homologous recombination. |
| Cytosine deamination to uracil | Conversion of cytosine into uracil, changing a three‑hydrogen‑bond pair with guanine into a two‑bond pair with adenine. |
| Ap (apurinic/ apyramidinic site) | Location in DNA where the base has been removed, leaving only the sugar‑phosphate backbone. |
| Loss of heterozygosity (LOH) | Event where one allele of a gene is lost, leaving a cell homozygous for the remaining allele, frequently observed in tumor suppressor regions. |
| Bloom's helicase | Helicase that promotes dissolution of Holliday junctions by directing symmetric cleavage, thereby suppressing crossover formation. |
| Telomerase | Reverse transcriptase that adds repetitive DNA sequences to chromosome ends, solving the end‑replication problem. |
| Proofreading | Exonuclease activity that removes incorrectly incorporated nucleotides immediately after addition, enhancing fidelity. |
| Single-strand binding protein | Factor that coats separated DNA strands, preventing them from re‑annealing during unwinding. |
| Positive supercoil | Over‑twisted state of DNA with more helical turns than the relaxed form, hindering strand separation. |
| Origin of replication | AT‑rich DNA region where initiator proteins bind to start the assembly of the replisome. |
| Negative supercoil | Under‑twisted DNA conformation with fewer turns than relaxed, facilitating helix opening. |
| Topoisomerase (gyrase) | Enzyme that creates transient breaks in DNA to relieve positive supercoils ahead of the replication fork. |
| Nucleoid | Region of bacterial cytoplasm where the circular chromosome is densely associated with DNA‑binding proteins, lacking a surrounding membrane. |
| Nucleosome | Segment of about 147 base pairs wrapped around an octamer of core histone proteins, forming the basic repeating unit of chromatin. |
| Werner syndrome | Inherited disorder caused by mutations in a DNA helicase gene, leading to accelerated telomere loss and premature age‑related symptoms. |
| Chromatin | Complex of DNA with histone and non‑histone proteins that constitutes the functional genome in eukaryotic nuclei. |
| Hayflick limit | Maximum number of divisions (~40–60) that a normal somatic cell can undergo before entering a non‑dividing state. |
| HeLa cells | Human cervical‑cancer derived cell line that proliferates indefinitely due to elevated telomerase and genomic instability. |
| Supercoiling | Over‑winding or under‑winding of the double helix that creates torsional strain and compacts the molecule. |
| End-replication problem | Inability of DNA polymerases to fully synthesize the extreme 3′ end of the lagging strand, leading to progressive shortening of chromosome ends. |
| Histone octamer | Complex of eight core histone proteins (two each of H2A, H2B, H3, and H4) that provides the scaffold around which DNA is wound. |
| Looped domain | Chromatin segment anchored to a scaffold by cohesin, creating loops of roughly 300 nm that regulate gene accessibility. |
| 30nm fiber | More compacted helix formed by folding of the 10 nm fiber into stacked nucleosome arrays. |
| Linker histone H1 | Protein that binds to DNA where it enters and exits the nucleosome core, stabilizing higher‑order chromatin structures. |
| Telomere | Repetitive guanine‑rich DNA sequence at chromosome termini that shields ends from degradation and fusion. |
| 10nm fiber | Relaxed chain of nucleosomes linked by H1, appearing as beads‑on‑a‑string under electron microscopy and accessible for transcription. |
| Stem cell telomerase activity | High level of telomere‑maintaining enzyme present in embryonic and adult progenitor cells, allowing extensive proliferative capacity. |
| Cellular senescence | Stable growth arrest accompanied by metabolic activity, triggered by critically short telomeres or DNA damage. |
| Telomerase reverse transcriptase (TERT) | Catalytic protein subunit of the telomere‑extending enzyme that synthesizes DNA from its RNA template. |
| Gyrase | Bacterial enzyme that introduces negative supercoils into DNA using ATP, relieving torsional stress during replication. |
Created by:
Samara Hayes