BIOL 4003 Week 6 Notes
BIOL 4003 Week 6 Notes 4003
U of M
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This 7 page Class Notes was uploaded by Rachel Heuer on Sunday February 28, 2016. The Class Notes belongs to 4003 at University of Minnesota taught by Robert Brooker in Spring 2016. Since its upload, it has received 26 views. For similar materials see Principles of Genetics in Biology at University of Minnesota.
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Date Created: 02/28/16
Chapter 9 (Structure of DNA and RNA): Lecture 1: - Genetic material must: o Information: must contain the information necessary to make an entire organism o Transmission: it must be passed from parent to offspring o Replication: it must be copied o Variation: must be capable of changes - Frederick Griffith (Streptococcus pneumoniae): comes in two strains o Smooth strain, S (has a capsule) § Capsule protects bacterium from the immune system of animals and does not get killed o Rough strain (R) does not have capsule § Easy to be killed by immune system o Injected living Type-S into mice (Dead mouse) § All blood samples end up with smooth bacterium o Inject living Type-R into mice (living mouse) § No bacteria found in blood o Inject heat killed Type-S (living mouse) § No bacteria in sample o Inject heat killed Type-S and live Type-R (dead mouse) § Living Type-S bacteria on plate - Griffith concluded that some material was being transferred from the heat killed bacteria into the live Type-R bacteria, transforming them into Type S - Avery, MacLeod/McCarty o Review figure in textbook (Fig 9.2) o Knew that DNA, RNA, protein and carbohydrates were the major components of the cell o When o Showed that DNA was the genetic material (transforming principle) § Not protein or RNA - Hershey and Chase studied Bacteriophage T2 o Figure 9.5 o Made up of only a capsid (protein) and genetic material (DNA) o Started with phages that were radioactively labeled with either a label that attaches to either protein or DNA, but not both o They found that the phage only injected DNA into the cells o The protein was not found inside of the cell o In the supernatant was mostly protein and the pellet was mostly DNA - DNA and RNA are large macromolecules with several levels of complexity o Nucleotides form repeating units of nucleic acid o Covalent bonding between nucleotides to form a linear double helix o 3D structure results from folding and bending of double helix § Interaction between DNA and proteins produce chromosomes (Fig 9.6) - Nucleotide Structure o Nucleotide is the repeating structural unit of RNA and DNA o 3 components: (Fig 9.7) § Phosphate group (negatively charged) § Pentose sugar • Ribose (RNA) or deoxyribose (DNA) (deoxy = missing oxygen at 3’ carbon) § Nitrogenous Base o Purines (Double Ring) § Adenine and guanine o Pyrimidine (Single Ring) § Thymine and Cytosine and Uracil o Phosphate attaches to 5’ carbon on ring o Base attaches to 1’ carbon o Nucleotides are covalently linked by “phosphodiester linkages” § Two phosphoester bonds make up a phosphodiester linkage § Phosphate connects 5’ C of one nucleotide to 3’ C of another § This gives the strand directionality (5’ à 3’) • Run antiparallel o Sugars and phosphate creates the backbone § Bases project off of backbone o Watson and Crick discovered DNA double helix § Via the help of other scientists findings • Linus Pauling, Rosalind Franklin, Maurice Wilkins, Erwin Chargaff (A=T, G=C) § Used ball and stick models with sugar-phosphate backbone on the outside with the bases projecting towards eachother § Found out hydrogen bonding of AT was structurally similar to bonding of GC § Fig 9.15 o DNA double helix is right-handed and antiparallel § Clockwise rotation when laid horizontally § B-DNA is the predominant type in living cells § 360 degree turn = 10 bp = 3.4 nm of length o Bases are planar à stack on top of each other § Stabilizing the structure by protecting the hydrophobic backbone from water § Hydrogen bonding stabilizes the structure as well o Has two grooves § Minor and major • Major is wider § Proteins bind to specific sequence of bases • usually binds to major groove o DNA can have alternative double helices § Can be Z-DNA (left handed helix à moves counterclockwise when looking at it horizontally • Backbone is more zigzagged (not helix) • Grooves are more flat and shallow • Not sure what the role of Z-DNA in cells is • Tilted bases o RNA Structure (Fig 9.19 and 9.20) § Much like a DNA strand § Shorter than DNA strand (only hundred to thousands long) § Single stranded à only one strand is made (not a complementary strand) § Have uracil instead of thymine § Have ribose instead of deoxyribose § Double stranded regions are antiparallel and complementary • loops and hairpins can be formed § Complementary regions are held together by hydrogen bonds § Noncomplementary regions have bases projected away from double stranded regions § Don’t want the anticodon to complementary bind with itself Chapter 10: Lecture 1: - Chromosomes are the structures that contain the genetic material o Complexes of DNA and proteins - Genome comprises all the genetic material that an organism possesses o Bacteria: single circular chromosome o Eukaryotes: one complete set of nuclear chromosomes § Also have a mitochondrial genome § Plants: Have a chloroplast genome - Main function of genetic material is to store the information required to produce an organism o DNA molecule does this through its base sequence, which are necessary for § Synthesis of RNA and cellular proteins § Replication of chromosomes § Proper segregation of chromosomes § Compaction of chromosomes - Bacterial Chromosomes o Circular and only have one or a few copies of the same chromosome o Only a few million nucleotides long o Contains a few thousand genes § Protein encoding genes account for majority of bacterial DNA § Nontranscribed DNA between adjacent genes are termed intergenic regions o Have an origin of replication (few hundred nucleotides in length) o Found in the nucleoid § Nucleoid not bound by membrane § DNA is in direct contact with the cytoplasm o To fit within the bacterial cell, the chromosomal DNA must be compacted about a 1000 fold § This involves the formation of loop domains, which compact the chromosome 10-fold o Number of loops depends on size of chromosomes and species § DNA is then supercoiled à second important way to compact the bacterial chromosome • Supercoiling is typically negative supercoiling • Negative supercoiling often causes strand segregation which is useful for replication and RNA transcription - Eukaryotic Chromosome o Contain one or more sets of chromosomes § Each chromosome is a single, linear molecule of DNA • Tens to hundreds of millions of base pairs • A few hundred to several thousand genes • Each chromosome has multiple origins of replications • Telomeres located on each end o protect chromosomes from chromosomal rearrangements/translocations o have a specialized replication of DNA to prevent chromosome shortening • Purpose of centromere is aiding chromosome sorting o Formed by kinetochore proteins o Kinetochore microtubules attach to them and link them to the spindle apparatus o Necessary during meiosis and mitosis o Has much more DNA than bacterial cells § Contain many more genes § Also have many more repetitive sequences (at telomere and the centromere) o Repetitive Sequences § Sequence complexity: refers to the number of times a particular base sequence appears in the genome § Three types of repetitive sequences: • Unique or non-repetitive • Moderately Repetitive • Highly repetitive • Highly and moderately repetitive sequences come from two sources: o Tandem repeats à short sequences that are repeated many times in a row o Transposable elements § Only about 2% of DNA is actually coding for proteins § 24% is introns and other parts of genes § 15% unique sequences not in genes § 59% is repetitive DNA - Eukaryotic chromosomes in nondividing cells o End to end, a single set of human chromosomes is over 1 m long (cell nucleus is only 2-4 micrometers in diameter) § DNA must be extremely compact o Compaction of linear DNA requires interactions between DNA and several proteins § DNA protein complex is called chromatin § Proteins bound to DNA are subject to change during the life of a cell • This change affects compaction greatly § Nucleosome: repeating structural unit within eukaryotic chromatin • Composed of double-stranded DNA wrapped around an octamer of histone proteins o Histone octamer is composed of two copies each of four different histone proteins o Each nucleosome consists of 146 bp of DNA that makes 1.65 negative superhelical turns around the octamer • Figure 10.11 • Much like “beads on a string” • Connected via linker region (50 nm) • Each nucleosome is 11 nm in diameter • Shortens DNA length 7 fold o Marcus Noll determined the structure of the nucleosome § Exposed DNA to low, medium, and high levels of DNAse § He extracted the DNA and loaded it onto a gel § The DNA was found in 200 bp increment sizes, suggesting that 200 bp of DNA are wrapped around the histones o Nucleosomes form to create the 30nm fiber • 2 models o Solenoid model § Very organized into a spiral o Zigzag model § More movement and freedom § Nucleosomes have little face to face contact o Along with the nucleosomes, the 30 nm fiber compacts DNA 50 fold § Third level of compaction involves the interaction between the nuclear matric and the 30 nm fiber • Nuclear matrix o 2 parts § Nuclear lamina: fibers that line the inner nuclear membrane § Internal Matrix Proteins: connected to nuclear lamina and fills interior of nucleus o Hypothesized to be an intricate fine network of fibers with proteins bound to them o Proteins link the DNA to the matrix (Matrix attach regions MARs or scaffold attach regions SARs) § MARs are attached to the nuclear matrix § Creates a radial loop domain • Attachment of radial loops to nuclear matrix is important in two ways: o Plays a role in compaction o Serves to organize the chromosomes within the nucleus § Each chromosome has a discrete and nonoverlapping chromosome “territory” in the nucleus o Heterochromatin vs Euchromatin: interphase chromosomes § Heterochromatin • Tightly compacted • Transcriptionally inactive • Radial loop domains compacted even further • Two kinds o Constitutive heterochromatin § Regions that are always heterochromatic § Permanently inactive transcription-wise § Centromere and telomere § Contain highly repetitive sequences o Facultative heterochromatin § Can interconvert between euchromatin and heterochromatin § Such as a barr body § Euchromatin • Less condensed regions of chromosomes • Transcriptionally active • 30 nm fiber forms radial loop domains - Chromosomes during Cell Division o During M phase, level of compaction changes greatly § By end of prophase, sister chromatids are entirely heterochromatic § Much shorter than in interphase (long, stretched out, relaxed, euchromatin) § These compact genes undergo little gene transcription - Hierarchy of compaction o 1.) nucleosomes – 11 nm diameter o 2.) 30 nm fiber o 3.) radial loop domains (euchromatin) o 4.) metaphase chromosomes (heterochromatin)
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