BSCI222 Exam 2 Study Guide Chapter 10 DNA The Chemical Nature of the Gene DNA consists of two complementary and antiparallel nucleotide strands that form a double helix DNA is a polymer a chain made up of many repeating nucleotides linked together deoxyribonucleotides Nucleotides joined together by phosphodiester strong covalent linkages comprised of Sugar pentose sugars have five carbons o DNA deoxyribose H RNA ribose OH at 2 carbon o The additional oxygen atom in RNA makes it more reactive and less chemically stable than DNA Phosphate phosphorus atom bonded to four oxygen atoms always bonded to the 5 carbon atom of the sugar in a nucleotide Nitrogen containing base purines and pyrimidines o Purines six sided ring attached to five sided ring Adenine Guanine o Pyrimidines six sided ring only Cytosine Thymine Uracil Polynucleotide Strands DNA is made up of nucleotides connected by phosphodiester strong covalent bonds which joining the 5 phosphate group of one nucleotide to the 3 carbon atom of the next nucleotide 5 end a free phosphate group is attached to the 5 carbon atom of the sugar in the nucleotide 3 end has a free OH group attached to the 3 carbon atom of the sugar Secondary structures of DNA the double helix Consists of two polynucleotide strands wound around each other the sugar phosphate linkages on outside of helix and the bases are stacked in the inside of the molecule The two strands run antiparallel to each other complementary to each other not identical Strands are held together by hydrogen bonds weak between opposite bases o A and T bound together by 2 H bonds o C and G bound together by 3 H bonds stronger B DNA structure Watson and Crick model o This structure exists when plenty of water surrounds the molecule and there is no unusual base sequence in the DNA o Most stable configuration for a random sequence of nucleotides under physiological conditions o It is an alpha helix clockwise spiral 10 bp per 360 degree rotation bp s are 0 34 nm apart each complete rotation encompasses 3 4 nm diameter of helix is 2 nm bases are perpendicular to long axis of DNA molecule o Spiraling of the nucleotide strands creates major and minor groove features important for the binding of some proteins that regulate expression of genetic information permits proteins to read the sequence w o unwinding DNA o Exists if less water is present o Alpha helix but is shorter and wider than B DNA and its bases tilt away from the main axis of the o Can result if molecule contains particular base sequences such as a stretch of C and G nucleotides o Forms a left handed helix the sugar phosphate backbone zigzags back and forth o May play a role in gene expression Easier for transcription and replication of DNA in major grooves because the bases are not blocked by the backbone Major information pathway Central Dogma DNA RNA Protein A DNA structure molecule Z DNA structure 1 DNA replication 2 Transcription DNA RNA 3 Translation RNA Protein C value Paradox genome size does not correlate with organismal complexity Chapter 11 Chromosome Structure and Transposable Elements Supercoiling one type of DNA tertiary structure which occurs when the DNA helix is subjected to strain by being overrotated positive supercoiling or underrotated negative supercoiling Partial solution to DNA packaging problem because it occupies less space than relaxed DNA Relies on topoisomerases enzymes that add or remove rotations from the DNA helix by temporarily breaking the nucleotide strands rotating the ends around each other and then rejoining the broken ends induces and relieves supercoiling Bacterial Chromosome consist of a single circular DNA molecule not attached to histone proteins but is complexed to a number of proteins that help compact it Nucleoid contains DNA in definite region of cytoplasm Eukaryotic Chromosomes consists of a single extremely long molecule of DNA requires tremendous packing and folding In the course of the cell cycle the level of DNA packing changes from a highly packed to extreme condensation state Chromatin combination of DNA and proteins o 1 Euchromatin undergoes normal process of condensation and decondensation in cell cycle o 2 Heterochromatin remains in highly condensed state throughout cell cycle lack of transcription crossing over and replication o Histone proteins most abundant protein in chromatin small positively charged proteins 5 o Positive charge of histones attracts negative charge of DNA Nucleosome particle consisting of DNA wrapped about two times around an octamer of histone proteins simplest level of chromatin structure H2A H2B H3 H4 2 COPIES EACH o Each of the histone proteins that make up the nucleosome core particles has a flexible tail containing 11 37 a a that extend out from nucleosome o Positively charged a a in the tails of histones interact with the negative charges of the phosphates on DNA keeping the DNA and histones tightly associated about 150 bp o Tails of one nucleosome interact with tails of another to facilitate nucleosome compaction o Chemical modifications to tails bring changes to chromatin structure necessary for gene expression o DNAse 1 cuts open regions of chromatin and correlate with genes being expressed DNA sequences unique sequence DNA consists of sequences that are present only once or at most a few times in genome moderately repetitive DNA consists of sequences from 150 300 bp long that are repeated thousands of times tandem and interspersed highly repetitive DNA short sequences less than 10 bp long are present in thousands and millions of copies that are repeated in tandem and clustered in mainly centromeres and telomeres Transposable Elements 10 100 bp DNA sequence capable of moving from one place to another within the genome type of moderately repeated DNA often cause mutations either by insertion or promoting DNA rearrangements such as chromosome deletions duplications and inversions make up at least 45 of human DNA act as protein binding sites codes for transposase element specific enzyme cuts and pastes 1 Retro transposons Class I Copy and Paste transpose through an RNA intermediate 2 Transposons Class II Cut and Paste transpose as DNA transposase made transposase binds to ITRs inverted terminal repeats transposase excises element synaptanemal complex target site selection cut target and integrate element Consequences of Transposable Elements increase genome size mutagenesis rearrangements gene formation and modulate gene expression Chapter 12