Chapter 16 PDF

12/15/24, 6:29 PM Chapter 16 Chapter 16 R and S cells refer to two different strains of pneumonia bacteria wh...

12/15/24, 6:29 PM Chapter 16 Chapter 16 R and S cells refer to two different strains of pneumonia bacteria where S is the smooth variant (virulent, causing disease) and R stands for the rough strain (non-virulent). They key difference is that the S strain has a protective Frederick Griffith’s experiment. What principle polysaccharide capsule while R strain lacks it, was shown? making the S strain more deadly when injected into mice. Transformation principle/genetic transformation: heat-killed S strain could transform the R strain into virulent S strain Expanded on Griffith’s experiment. They took heat-killed S bacteria and destroyed certain parts. Oswald Avery and Maclyn McCarty’s experiment Mice only lived when DNAase was added and the DNA of the S bacteria was destroyed. → supports DNA as source that direct genetic transformation attachment of phage (head filled with DNA) and injection of DNA → replication of phage DNA Viral DNA programming cells and synthesis of phage proteins → assembly of phage components → release of new phage particles with cell lyse (burst) separated and quantified the four nitrogenous bases found in DNA samples from diff organisms - ratio of A to T was close to 1:1 - ratio of G to C was close to 1:1 What did Chargaff do? Species that are closely related will have comparable ratios Different species had different overall base compositions, indicating that DNA variation exists between organisms Semi conservative replication 1. The double helix of DNA unwinds. https://knowt.com/flashcards/31bd0679-b48b-480e-aa39-31a7fa860c62 1/8 12/15/24, 6:29 PM Chapter 16 2. Each strand of the double helix separates and remains intact. 3. New complementary strands are synthesized using the old strands as templates. 4. Each new double helix is made up of one old strand and one new strand. after one round of replication, half of the new DNA double helices would be composed of completely old, or original, DNA, and the Conservative replication other half would be completely new. Then, during the second round of replication, each double helix would be copied in its entirety each strand of the resulting DNA double helix is a mixture of both new and original DNA. This means that each Dispersive replication round of replication produces DNA double helices that are part new DNA and part original DNA. Meselson-Stahl experiment demonstrates that DNA replicates in a semi- conservative manner used bacteria grown in a medium containing a heavy isotope of nitrogen https://knowt.com/flashcards/31bd0679-b48b-480e-aa39-31a7fa860c62 2/8 12/15/24, 6:29 PM Chapter 16 (N15) to label the parent DNA, then transferred the bacteria to a medium w/ normal nitrogen (N14) and observed the density of the DNA after subsequent rounds of replication using a technique called density gradient centrifugation. After one round of replication, the DNA showed an intermediate density, indicating that each new DNA molecule contained one strand from the original “heavy” parent DNA and one new “light” strand, support semi-conservative model. Replication in E. Coli unlike prokaryotes, eukaryotic chromosomes have multiple origins of replication scattered along their length, allowing for simultaneous replication at many points to efficiently replicate large genomes; these Origin of replication in eukaryotes origins are recognized by a protein complex called the Origin Recognition Complex (ORC) which initiates the replication process by recruiting other necessary proteins like helicases and polymerases. Why do eukaryotes have multiple replication eukaryote chromosomes have more DNA and sites? one origin of replication would not be sufficient https://knowt.com/flashcards/31bd0679-b48b-480e-aa39-31a7fa860c62 3/8 12/15/24, 6:29 PM Chapter 16 What does DNA require to initiate replication Primers → primase polymerizing enzyme that generates short RNA primase primer molecules. Attaches new nucleotides to existing strand of DNA. DNA can’t start from scratch; needs something Why is primase used? to attach to. RNA primer is then removed and replaced with DNA a short, single-stranded RNA molecule that serves as a starting point for DNA replication RNA primer since DNA polymerase can only add nucleotides to an existing chain. Helicase separates two strands from each other the two strands are being separated downstream has more and more strain being Topoisomerase held and applied to the downstream of DNA, leading to breakages. This enzyme relieves this strain. allows the two strands of DNA to be separates by each other after the helicase breaks them apart and now allow them to reform through single-stranded binding proteins hydrogen bonds while the cell is trying to copy them helicase breaks apart, single-stranded binding proteins hold them apart What is the main protein/copy machine of DNA DNA polymerase catalyzes the elongation of DNA chain that are DNA polymerase required for copying DNA initially present to act as a template using What does DNA polymerase require? dATP dATP a nucleotide used in DNA synthesis and replication. As they bring a nucleotide to the template strand (covalently bind to the 3’ hydroxyl end of the growing chain), two phosphate groups are released (endergonic). Energy is used to form the new nucleotide attaching to the strand. Each nucleotide is joined through a phosphodiester bond between 5’ https://knowt.com/flashcards/31bd0679-b48b-480e-aa39-31a7fa860c62 4/8 12/15/24, 6:29 PM Chapter 16 carbon and hydroxyl group on the 3’ end of the previously added nucleotide What direction does elongation occur in? 5’ → 3’ a DNA sequence that contains a higher-than- A-T rich region average number of adenine and thymine bases compared to guanine and cytosine bases. A-T base pairs only have two hydrogen bonds, Why are A-T rich regions the origin of making it easier to separate the DNA strands at replication? that region. G-C base pairs have three hydrogen bonds, requiring more energy to separate a theoretical or actual sequence that represents the most common consensus sequence nucleotides or amino acids at a specific position in a group of related sequences one strand is continuously replicated while the leading and lagging strand other strand is replicated in parts what does the direction of replication depend DNA polymerase direction on? hydrolyzes ATP to perform the mechanical work necessary to unwind the double stranded DNA. how does helicase perform mechanical work? ATP moves along helicase in 5’ → 3’ direction, breaking the hydrogen bonds between the complementary bases. what do single-stranded binding proteins the formation of hairpin structures → can hinder prevent? DNA synthesis. tangling of DNA during replication. Rotate to relieve the DNA. Once relaxed, topoisomerase What does topoisomerase prevent? dissociates → energy drives the spontaneous formation of phosphodiester bonds within the backbone. degrades DNA by cleaving the phosphodiester bond between two adjacent nucleotides → nuclease reversible: bonds will form when the protein leaves https://knowt.com/flashcards/31bd0679-b48b-480e-aa39-31a7fa860c62 5/8 12/15/24, 6:29 PM Chapter 16 acts as a sliding clamp (on leading strand) that holds the DNA polymerase onto the DNA PCNA strand, allowing for efficient and processive DNA synthesis a ring-shaped protein that encircles the DNA strand, acting as a platform to hold DNA polymerase in place, allowing for efficient and continuous DNA synthesis by preventing the sliding clamp polymerase from detaching from the DNA template powered by ATP hydrolysis, specifically by the enzyme helicase. Uses ATP to open and close clamp around DNA lagging strand; DNA polymerase can’t synthesize in the 5’ → 3’ direction. As the fork Where are Okazaki fragments created and why moves foward, DNA polymerase jumps from one are they short? section to the next and copies them in fragments okazaki fragments are synthesized in small DNA ligase fragments and later joined together by this enzyme both go in the same direction (5’ → 3’), but synthesized in the opposite direction leading strand moves in the same direction as directionality of leading and lagging strand the replication fork lagging strand moves in th4e opposite directi0on of the fork Large complex formed by the proteins that participate in DNA replication. Proteins don’t work independently but rather work as a multi- enzyme complex. Remains in one piece as DNA is threaded through Referred as a replisome: coordinates the DNA replication machine leading and lagging strand, which ensures that both strands are synthesizes simultaneously by utilizing a looping mechanism on the lagging strand while the leading strand is straight, allowing the DNA polymerases on each strand to move in the same direction despite the antiparallel nature of DNA what direction does the replisome move in? direction of the fork https://knowt.com/flashcards/31bd0679-b48b-480e-aa39-31a7fa860c62 6/8 12/15/24, 6:29 PM Chapter 16 a process that corre4cts errors in DNA DNA polymerase proofreading replication by removing and replacing incorrectly added nucleotides DNA repair mechanism that removes bulky DNA damage caused by radiation and other mutagens. Sequence changes may become Nucleotides excision repair permanent and passed to next generation → mutations (source of genetic variation and appearance of new species) We know that RNA primer is used for polymerase to build a strand off of because the DNA polymerase can’t synthesize one through scratch. However, at the end of the strand, RNA End Replication Problem primer is removed, but the polymerase isn’t able to synthesize DNA without the primer. There is no primer since it’s at the end of the chromosome → causes overhanging DNA. another round of replication occurs. Because overhanging happens, DNA gets shorter with How is overhanging DNA rid of? each replication, causing cells to die (except stem cells) specialized nucleotides sequences in eukaryotes. They don’t prevent the shortening of DNA but Telomeres they do postpone the erosion of genes near the end of the DNA molecules if chromosomes of germ cells become shorter in every cell cycle, essential genes would eventually be missing from the gametes they produce. This enzyme catalyzes the lengthening of telomeres in germ cells. Keeps cell alive by telomerase adding DNA to telomeres. Adds telomere repeated sequences to the ends of chromosomes. Binds to 3’ end.Overhang remains, but ensures DNA won’t get shorter What does a chromosome consist of? a DNA molecue packed together with proteins two types of chromatins. A complex of DNA and protein that makes up chromosomes. The main ecuchromatin and heterochromatin difference is how tightly packed the chromatin fibers are. https://knowt.com/flashcards/31bd0679-b48b-480e-aa39-31a7fa860c62 7/8 12/15/24, 6:29 PM Chapter 16 less condenses, more accessible to RNA polymerase (allowing it to be actively Euchromatin transcribed). Made up of repeating subunits called nucleosomes, which are similar to an unfolded string of beads. Highly condensed, gene-poor, and transcriptionally silent. Typically found ay centromeres and telomeres and is made up of repetitive DNA sequences. Inaccessible to RNA polymerase, so it cannot be transcribed. Plays a Heterochromatin role in important biological functions, such as chromosome segregation during cell division. It also has the ability to silence euchromatic gene expression (a chromatin in which genes are actively expressed) Histone acetylation looser packaging histone methylation tighter packaging add methyl groups to DNA (assuming it codes Epigenetics for something) → you silence that gene 3’ end has OH hanging 3’ end and 5’ end 5’ end is the end where phosphate binds Why can’t polymerase add directly to 5’ end? has phosphate which is too electronically dense Charge of histone positively charged → can add groups to it polys read 3’ → 5’ read and make in what direction make 5’ → 3’ https://knowt.com/flashcards/31bd0679-b48b-480e-aa39-31a7fa860c62 8/8