Chap10-Learn Obj - Learning objectives for Farmer PDF

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Chapter 10- Learning Objectives (Chromosome Organization) Outline the general organization of bacterial chromosome sequences (see Figure 10.1).  Circular chromosomal DNA  Single type of chromosome that may be present in multiple copies  Chromosome is a few million bp in length  Several thousand different genes are interspersed throughout the chromosome (short regions between adjacent genes are intergenic regions)  One origin of replication is required for initiation  Repetitive sequences are interspersed throughout the chromosome Define nucleoid (see Figure 10.2).  A darkly staining region that contains the genetic material of mitochondria, chloroplasts, or bacteria Explain the two mechanisms for the compaction of bacterial chromosomes (see Figures 10.3, 10.4).  LOOP DOMAINS: (macro and microdomains) o Nucleoid-associated proteins (NAPs- DNA binding proteins) facilitate chromosome compaction & organization o NAPs bend the DNA or act as bridges that cause different regions of DNA to bind o NAPs facilitate chromosome segregation and gene regulation  SUPERCOILING: o Left-handed turn (underwinding) leads to:  Unstable- fewer turns  Negative supercoil o Right-handed turn (overwinding) leads to:  Unstable- more turns  Positive supercoil Describe how negative supercoiling enhances DNA function (see Figure 10.5).  Greatly decreases the size of the bacterial chromosome  Creates tension on DNA strands that may be released by their separation  Force of negative supercoiling promotes DNA strand separation in small regions o Enhances genetic activities such as replication and transcription that requires DNA strands to be separated Outline the general organization of eukaryotic chromosome sequences and their functions (see Figure 10.7)  Linear chromosomes  Chromosomes in sets o Diploid  10mil-100mil bp in length  Genes are interspersed within chromosome o Few 100- several thousand  Origins of replication (interspersed every 100,000 bp)  Centromere o Recognition site for kinetochore proteins  Telomeres that contain specialized sequences at both ends of chromo  Repetitive sequences near centromeric and telomeric regions o May be interspersed throughout chromo Explain the two reasons why eukaryotic species have more DNA than bacteria (see Figures 10.8, 10.9).

GENOME SIZE: Additional DNA is due to the accumulation of short repetitive DNA sequences that do not encode for genes and are present in many copies o Gene number varies among different eukaryotes o Amount of repetitive sequences varies  REPETITIVE SEQUENCES: multiple copies of the same gene o Important for proper segregation of chromosomes during meiosis o Alu sequences are interspersed throughout genome o Tandem Arrays: a short nucleotide sequence is repeated many times in a row Describe the structure of a nucleosome and explain the results of Noll’s experiments regarding the “beads-on-a-string” hypothesis (see Figures 10.10, 10.11).  146-147 bp of DNA wrapped around an octamer of core histone proteins  Nucleosomes compact into chromatin (euchromatin and heterochromatin  Result: o The entire sample of chromo DNA was digested into fragments of approx. 200 bp (beads on a string) o Low-medium concentration lead to longer pieces in multiples of 200 bp  Reasoning: o Occasional linker regions remained uncut at low-medium concentration  If one region is uncut, DNA piece would contain two nucleosomes (400 bp)  If two consecutive regions are uncut, DNA piece would contain three nucleosomes (600 bp) Describe the structure of the 30-nm fiber and how it is anchored to form radial loop domains (see Figures 10.13, 10.14). 

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30-nm Fiber: shortens the total length of DNA another sevenfold SOLENOID MODEL: o Helical w/ nucleosome contact produces symmetrically compact structure ZIGZAG MODEL: o Linker regions are bent and twisted o Little face to face contact

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Interphase: chromatin is organized into loops which anchor to nuclear matrix MARs/SARs bind to specific proteins in nuclear matrix and form chromosomal loops

Define chromosome territory (see Figure 10.15).  A region in the cell nucleus occupied by a chromosome (nonoverlapping) Describe the levels of compaction leading to a metaphase chromosome (see Figure 10.17 1. Wrapping of DNA around histone octamers to form nucleosomes

2. Formation of 30nm fibero nucleosomes form a zigzag or solenoid via binding of H1 and nonhistone proteins to DNA 3. 30nm fiber forms radial loop domains o by anchoring to protein filaments of nuclear matrix

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 Explain the functions of condensin and cohesin (see Figures 10.20, 10.21).  CONDENSIN: (multiprotein complex) o Plays a role in the condensation of interphase chromosomes to become metaphase chromosomes 1. Coats individual chromatids as the chromosomes become highly compacted 2. Condensing proteins form a ring around DNA then compaction occurs due to condensing proteins bringing loops closer  COHESIN: (multiprotein complex) o Facilitates the alignment of sister chromatids o Promotes binding between sis chromatids o Cohesins along chromosome arms are released during prophase  Allows arms to separate o Some cohesins remain attached to centromeric regions  Leaves centromeric region as main linkage before anaphase o At anaphase, cohesins are degraded and sis chromatids are separated...