PCB 3063 Exam 3 Study Guide Solutions

PCB 3063 Exam 3 Study Guide Solutions The 1˚and 2˚molecular structure of DNA - ANSWER-Its function: to store, replicate, and transmit genetic information The 3˚structure of DNA - ANSWER-Determines its ability to express the encoded information as a phenotype DNA's 3˚structure must be flexible and dynamic - ANSWER-A vast amount of genetic information must be packed into a cell of limited size This material must be tightly condensed for chromosomes to move as individual units during cell division But DNA must be de-condensed at other times to be accessible for replication and transcription. Genome size - ANSWER-The genomes of different species contain different amounts of DNA. The complexity of an organism doesn't necessarily match the amount of DNA in its genome Humans have a 6 billion base pair genome a single-celled protist, Polychaos dubium, has the largest genome of all organisms with 670 billion base pairs ©EMILLECT 2024/2025 ACADEMIC YEAR. ALL RIGHTS RESERVED FIRST PUBLISH OCTOBER 2024 Page 2/76 Regardless of genome size, all organisms must contain their genetic information inside the cell Levels of DNA structure: Primary - ANSWER-Nucleotide sequence Levels of DNA structure: Secondary - ANSWER-Double helix of antiparallel strands Levels of DNA structure: Tertiary - ANSWER-Folding and packing to fit in confined space of cell Relaxed helical DNA - ANSWER-Not supercoiled. 10 turns = 100 bp of DNA The lowest energy state is B-DNA with 10 bases per turn Supercoiling - ANSWER-Stress on the helix that over-winds or under-winds it will cause the helix to twist back on itself Positive supercoiling - ANSWER-Over-rotated Negative supercoiling - ANSWER-Under-rotated Topoisomerases - ANSWER-Enzymes that can add or remove a turn in DNA by breaking sugar- phosphate backbone, rotating, and then rejoining ends Most DNA is negatively supercoiled - ANSWER-Helps pack DNA into small space Strand separation during replication and transcription is more rapid and requires less energy ©EMILLECT 2024/2025 ACADEMIC YEAR. ALL RIGHTS RESERVED FIRST PUBLISH OCTOBER 2024 Page 3/76 Most Bacterial genomes are contained in a single circular chromosome - ANSWER-Bound proteins help compact the DNA circle into supercoiled loops in the nucleoid region of the cell Many bacteria also have additional DNA in small circular, plasmids that replicate independent of the chromosome Eukaryotic Chromosomes - ANSWER-The multiple linear chromosomes in a eukaryotic nucleus are highly condensed Degree of coiling and packing changes throughout cell cycle Interphase: relatively more relaxed = less condensed Mitotic phase: relatively more compact = fully condensed for movement of individual chromosomes during cell division Chromatin - ANSWER-DNA complexed with proteins; 2 types Euchromatin - ANSWER-Will become more condensed and less condensed during different stages of the cell cycle, making DNA more and less accessible for transcription Heterochromatin - ANSWER-Remains highly condensed throughout cell cycle, preventing most transcription ©EMILLECT 2024/2025 ACADEMIC YEAR. ALL RIGHTS RESERVED FIRST PUBLISH OCTOBER 2024 Page 4/76 Constitutive: Permanent; telomere and centromere regions Facultative: Changeable condensation; X-inactivation Most chromatin is composed of histone proteins - ANSWER-5 types: H1, H2A, H2B, H3 & H4 Histones contain a large proportion of positively-charged arginine and lysine amino acids DNA is composed of negatively-charged phosphates, so histones are attracted to and bind tightly to DNA Nucleosomes - ANSWER-"Beads" made of DNA wrapped 2x around 8 histone proteins (2 each of H2A, H2B, H3 & H4) Each histone has a positively charged "tail" Chromatosomes - ANSWER-Histone H1 (not in the octet), binds to wrapped DNA to clamp nucleosome in place: nucleosome + H1 Linker DNA - ANSWER-Stretches of DNA between nucleosomes Change in Chromatin Structure & Transcription - ANSWER-For DNA to be transcribed, chromatin structure must relax to allow access for the transcriptional enzymes Chromosome puff - ANSWER-Drosophila giant polytene chromosomes A localized swelling of relaxed chromatin ©EMILLECT 2024/2025 ACADEMIC YEAR. ALL RIGHTS RESERVED FIRST PUBLISH OCTOBER 2024 Page 5/76 Active transcription correlates with chromosomal regions of relaxed chromatin How does chromatin structure change? - ANSWER-1) If attraction between histones and DNA decreases, then chromatin packing decreases = more relaxed, permitting transcription factors to bind to DNA. How to decrease attraction? = Make histones LESS positive Acetyltransferases: Enzymes that attach acetyl groups to lysines of histone tails, make histones less positive Increase transcription 2) DNA methylation can also alter chromatin structure to inhibit binding of transcription factors Decrease transcription 3) Add variant histones to nucleosome Epigenetics - ANSWER-Some changes in chromatin structure may be passed on through cell division or to future generations ex: Different cell types differentiate during embryonic development ©EMILLECT 2024/2025 ACADEMIC YEAR. ALL RIGHTS RESERVED FIRST PUBLISH OCTOBER 2024 Page 6/76 Some genes expressed only in particular cell types Chromatin remodeling can help determine which genes are expressed where and when, and which genes are not. Epigenetic - "on top of the DNA sequence" Epigenetic change - ANSWER-Stable alteration of chromatin DNA sequence is not changed, but its expression can change, leading to changes in phenotype Environment can affect epigenome - the overall pattern of chromatin modification possessed by an individual Centromeres - ANSWER-Constricted region of chromosome where spindle microtubules attach to kinetochore. Mostly heterochromatin = no genes Defined NOT by the DNA sequence Defined by nucleosomes containing a variant histone called CenH3 that alters chromatin structure to promote formation of kinetochore Telomeres - ANSWER-Natural ends of linear chromosomes; heterochromatin ©EMILLECT 2024/2025 ACADEMIC YEAR. ALL RIGHTS RESERVED FIRST PUBLISH OCTOBER 2024 Page 7/76 Serve as a cap that stabilizes chromosome end so it is not degraded (as a broken chromosome would be) Provide a means for replicating the end of a chromosome Telomeric sequences - ANSWER-Repeats of A or T followed by Gs In humans, 5'-TTAGGG-3' repeated 100's-1000's X G-rich strand extends beyond C-rich strand as a 3' overhang Proteins bind to the overhang to help prevent degradation and prevent ends from sticking together In some cells, the G-rich 3' overhang can loop back to pair with a short stretch of DNA (in a triplex) to form a T-loop to protect DNA end from degradation Shelterin - ANSWER-Prevents ends from being repaired as a double stranded DNA break Models Proposed for DNA Replication: Conservative - ANSWER-Original DNA strands reform original double helix Two new DNA strands form a new double helix Models Proposed for DNA Replication: Dispersive - ANSWER-Original DNA strands break down into pieces New DNA reassembled as a mixture of old and new pieces of DNA ©EMILLECT 2024/2025 ACADEMIC YEAR. ALL RIGHTS RESERVED FIRST PUBLISH OCTOBER 2024 Page 8/76 Models Proposed for DNA Replication: Semi-conservative - ANSWER-Original DNA strand remains intact and combines with a new DNA strand Meselson and Stahl - ANSWER-Cells can incorporate either a light nitrogen isotope 14N, or a heavy 15N isotope into their nitrogenous bases. Separate molecules based on density. Modes of Replication: Bacteria - ANSWER-Circular chromosome Single origin of replication (ori) - the DNA sequence where replication starts Modes of Replication: Eukaryote - ANSWER-Linear chromosomes Multiple origins of replication Ends of linear molecules require special replication Bacteria: Theta Replication - ANSWER-Initiator proteins bind an