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BSCI222 Week 6 Notes

by: Colin Fields

BSCI222 Week 6 Notes BSCI222

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Colin Fields

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Structure and organization of DNA and transposable elements
Dr. Kocher
Class Notes
Genetics, transposons, chromosome, Chromatin
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This 12 page Class Notes was uploaded by Colin Fields on Sunday October 9, 2016. The Class Notes belongs to BSCI222 at University of Maryland taught by Dr. Kocher in Fall 2015. Since its upload, it has received 3 views. For similar materials see Genetics in Biology at University of Maryland.


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Date Created: 10/09/16
BSCI222 Genetics Chapter 10 DNA: The Chemical Nature of the Gene 1. 10.1 Genetic Material Possesses Several Key Characteristics a. Genetic material must contain complex information b. Genetic material must replicate faithfully c. Genetic material must encode the phenotype d. Genetic material must have the capacity to vary 2. 10.2 All Genetic Information is Encoded in the Structure of DNA or RNA a. Early Studies of DNA i. Kossel determined there were four nitrogenous bases ii. Leven determined that nucleotides were a phosphate-sugar-base combination iii. Chargaff determined that the ration of A=T and G=C b. DNA As the Source of Genetic Information i. Transformation was observed when heat killed bacteria were mixed with non virulent bacteria and virulence was observed ii. Griffith identified the causative agent of transformation as the transformation principle iii. Isolates of the transformation principle were treated with chemicals that breakdown specific molecules and its identity of DNA was determined c. Watson and Crick’s Discovery of the Three-Dimensional Structure of DNA i. X-ray diffraction experiments on crystallized DNA were used to determine the molecule’s structure ii. 2-antiparallel strands in a double helix with a purine base aligned with a pyrimidine base d. RNA as Genetic Material i. Viruses can contain RNA in place of DNA ii. RNA replaces thymine with uracil 3. 10.3 DNA Consists of TWO Complementary and Antiparallel Nucleotide Strands That Form a Double Helix a. The Primary Structure of DNA i. Nucleotides 1. Phosphate + Sugar + Base 2. Pentose sugars, RNA = ribose, DNA = Dexoyribose (missing 2’ hydroxyl) 3. Purine = double ring (A and G), pyrimidine = single ring (C and T/U) 4. –Phosphate become nucleosides ii. Polynucleotide Strands 1. Nucleotides are connected through phosphodiester linkages which connect the 5’ and 3’ carbons of the nucleotides’ sugars 2. Nucleotides face inwards while phosphate faces outwards a. Frequently, positive charged molecules neutralize the negative charge of the phosphate 3. 5’ end is where there is a free phosphate, 3’ end is where there is there is a free hydroxyl 4. DNA is read 5’ to 3’ b. Secondary Structure of DNA i. The Double Helix 1. The two polynucleotide strands are antiparallel 2. H-bonds between bases keep the strands together 3. Two strands are complementary and nonidentical 4. Stacking of bases further stabilizes the molecule through London forces ii. Different Secondary Structures 1. B-conformation a. Most stable b. Lots of water c. Found most frequently at cellular conditions d. Right-handed e. 10.8 bp/turn f. h/turn 3.4 nm g. Major and minor grooves 2. A-conformation a. Less water b. Right handed c. More condensed 3. Z-conformation a. Left handed b. Sugar and phosphate alternate cis/trans positions c. Regions rich in CG alternating repeats 4. C and D-conformations a. Form only under laboratory conditions and with specific base sequences 4. 10.4 Special Structures Can Form in DNA and RNA a. Sequences within a single strand of nucleotides can be complementary to itself b. Strand folds back onto itself creating a stem where the sequence pairs and a loop contain the nucleotides that are not complementary c. Hairpin is a special case where there is no loop d. H-DNA i. Palindromic regions of only purine bases or only pyrimidine bases can unwind and refold onto a spate nucleotide strand containing a complementary sequence ii. This produces a region of triple stranded DNA with the unique sequence being between the stretches of the palindrome iii. Similar things can happen with four strands e. Methylation of bases can be used to reduce transcriptional activity f. Prokaryotes can have methylation of A or C while eukaryotes only have methylation of C BSCI222 Genetics Chapter 11 Chromosome Structure and Organelle DNA 1. 11.1 Large Amounts of DNA Are Packed into a Cell a. Supercoiling i. Helix is being overwound or underwound ii. Overrotation leads to positive supercoiling and underrotation leads to negative supercoiling iii. Occurs when the strain cannot be compensated for by turning of the ends of the helix iv. Topoisomerases are enzymes that add or remove rotations by breaking the strands, rotating the ends, and reattaching them v. Most cellular DNA is negatively supercoiled b. The Bacterial Chromosome i. Usually a single circular chromosome ii. Clumps together forming a nucleoid c. Eukaryotic Chromosomes i. Chromatin 1. Combination of DNA and proteins 2. Euchromatin a. Undergoes normal condensation and decondensation during cell cycle b. Region of active transcription c. Most cellular DNA 3. Heterochromatin a. Remains highly condensed throughout the cell cycle b. Not transcriptionally active c. Least cellular DNA 4. All chromosomes have permanent, constitutive heterochromatin at the centromeres and telomeres 5. Facultative heterochromatin occurs during certain developmental stages such as with Barr bodies 6. Histones are the most abundant protein associated with DNA in chromatin a. H1, H2A, H2B, H3, H4 b. High percentage of arginine and lysine to give a net positive charge ii. The Nucleosome 1. The repeating structure of a core particle consisting of protein and DNA 2. DNA is wrapped twice around an octamer of histones (2 copies of non H1 histones) and is around 145-147 bp in length 3. The octameric histones each have a flexible, positively charged, tail that extrudes from the nucleosome and tightly associate with the negative phosphates of the DNA 4. H1 binds to ~20 to 22 bp of DNA where it joins and leaves the octamer and helps lock it inplace 5. Linker DNA which is ~30 to 40 bp long separates histones iii. Higher-Order Chromatin Structure 1. Nucleosomes fold onto each other forming a fiber with a 30 nm diameter 2. Fibers then form loops that are average 300 nm in length and held together by proteins 3. The loops are then packaged to form a 250 nm wide fiber 4. Tight helical coiling of these fibers produces 700 nm wide chromatids d. Changes in Chromatin Structure i. Polytene Chromosomes 1. Produced when there is DNA replication without cell division 2. Relax to create chromosomal puffs where DNA is being actively transcribed indicating chromatin’s dynamic nature ii. DNase I Sensitivity 1. DNase I degrades DNA and is less active when DNA is tightly bound to histones 2. This enzyme’s activity has been strongly correlated with gene activity 3. This indicates that less tightly bound regions of DNA are where transcription occurs 2. 11.2 Eukaryotic Chromosomes Possess Centromeres and Telomeres a. Centromere Structure i. Span hundreds of thousands of base pairs, mostly heterochromatin ii. No specific sequences found in all centromeres iii. Nucleosomes in the centromere usually has CenH3 histones b. Telomere Structure i. Consist of repeated units of a series of A and T followed by several Gs ii. G rich strand protrudes past the complementary strand producing the 3’ overhang iii. Proteins bind to this overhang to prevent association between the ends of different chromosomes iv. Shelterins bind to telomeres and protect them from being repaired as a double-stranded DNA break v. Sometimes the overhand associates with a small region of DNA forming a t-loop that also protects the DNA 3. 11.3 Eukaryotic DNA Contains Several Classes of Sequence Variation a. C value is the amount of DNA per cell b. The Denaturation and Renaturation of DNA i. Heating DNA can reduce strength of H-bonds and cause the strands to separate called denature or melting ii. Slowly cooling the single strands of DNA allows then to collide and reform H-bonds called renaturing or reannealing iii. DNA strands from separate organisms can be reannealed based on partial sequence complementation which is called hybridization 1. This can be used to measure the similarity between organisms c. Types of DNA Sequences in Eukaryotes i. Unique-sequence DNA consists of sequences that are repeated at most a few times in the genome 1. Makes up 25-50% of the genes that encode proteins 2. Gene families are several similar but nonidentical copies of a gene located near each other ii. Repetitive DNA are sequences with many copies throughout the genome 1. Moderately repetitive DNA are sequences from 150-300 bp in length that are repeated thousands of times a. Tandem Repeats appear one after another and are usually clustered at specific locations on the chromosomes b. Interspersed Repeats are scattered throughout the genome i. Short interspersed elements (SINEs) are usually around 300 bp in length ii. Long interspersed elements (LINEs are several thousands of base pairs long 2. Highly Repetitive DNA are short sequences less than 10 bp a. Clustered in tandem with hundreds of thousands to millions of copies b. Also called satellite DNA 4. 11.4 Organelle DNA Has Unique Characteristics a. Mitochondrion and Chloroplast Structure i. Mitochondria 1. Tubular 2. 0.5 to 1 micrometer in diameter ii. Chloroplast 1. Tubular 2. 4 to 6 micrometers in diameter iii. Surrounded by two membranes that enclose the matrix or stroma, respectively iv. Replicate independently of the cell cycle v. Contain their own set of DNA and protein generating proteins that are used by the plastid b. Endosymbiotic Theory i. Eubacteria were engulfed by eukaryotic cells and allowed to persist as an endosymbiont ii. Over time many of the original genes of he eubacteria were lost because the host cell already had then or were transferred to the host nucleus iii. Drugs that are active against eubacteria but not eukaryotes are active against the plastids iv. DNA of the plastids is more closely related to eubacteria than eukaryotes c. The Mitochondrial Genome i. A single, highly coiled, circular DNA molecule ii. Can be many copies in each cell iii. Contain genes for respiration and oxidative phosphorylation, translation, transcription, RNA processing, and the import of proteins into the cell BSCI222 Genetics Chapter 18.4 Moveable Genes-Transposable Elements 1. General Characteristics of Transposable Elements a. Flanking direct repeats are 3-12 bp long and are present on both sides of a transposable element i. Are not part of the transposable element ii. Are made when TEs are inserted into staggered DNA breaks when the single-strand break is repaired b. Terminal inverted repeats are 9-40 bp long and are inverted complements of one another i. Are recognized by enzymes that catalyze transposition and required for transposition to take place 2. Transposition a. Movement of a transposable element from one location to another b. Staggered breaks in DNA are made followed by single strand joining of the TE and the DNA strands followed by repair of the single strand breaks c. Transposase is an enzyme often encoded by the TE that is used to make the break and insert the TE into the DNA d. Replicative transposition is when a new copy of a TE is inserted somewhere else in the DNA and the old copy remains in place e. Nonreplicative transposition is when the TE moves itself to a new place 3. The Mutagenic Effects of Transposition a. Movement of TEs into or near other genes can affect their functionally and transcriptional activity 4. Transposable Elements in Bacteria a. Simple transposable elements i. Insertion sequences ii. Carry only the information required for movement b. Composite transposons i. Contain DNA sequences not directly related to movement c. Insertion Sequences i. Can infect plasmids, viruses, and other bacteria ii. Can be passed from one cell to another d. Composite Transposons i. Can be created anywhere when two copies of an insertion sequence flank a segment of DNA ii. Generate flanking direct repeats when inserted iii. Defects in the insertion sequence can cause the segment in the transposon to increase to the nearest similar insertion sequence e. Noncomposite Transposons i. Lack insertion sequence ii. Have a gene for transposase and inverted repeats 5. Transposable Elements in Eukaryotes a. Class I (retrotransposons) i. Long terminal direct repeats and short flanking direct repeats at target site ii. Reverse transcriptase gene and occasionally others iii. RNA intermediate used for transposition b. Class II (DNA transposons) i. Short terminal inverted repeats and short flanking direct repeats at target site ii. Transposase gene and occasionally others iii. Transposition of DNA segment


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