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MCDB 310 1st Edition Lecture 9 Outline of Last Lecture I. Carbohydratesa. Monosaccharides and namingi. Glycosidic linkagesb. Polysaccharidesi. HomopolysaccharidesII. HeteropolysaccharidesOutline of Current Lecture I. Beta Chitin (revisted)II. Glycoconjugatesa. Proteoglycansb. Glycoproteinsc. LipoproteinsIII. Nucleotides and nucleic acidsa. Fundamentals of nucleic acidsb. Structure of Nucleic acidsc. DNAd. RNACurrent LectureI. Beta Chitin (revisited from last lecture)These notes represent a detailed interpretation of the professor’s lecture. GradeBuddy is best used as a supplement to your own notes, not as a substitute.a. How are chains of chitin bonded together to make the product strong and hydrophobic?b. Alpha chitin and beta chitin have very different bondingc. Beta chitin makes very weak hydrogen bonds, more stabilized by van der waals forces between parallel sheetsd. Alpha chitin makes very strong hydrogen bonds between antiparallel bonds because of the linearitye. Chitin is bonded so closely that it is very difficult to tell whether the structure is alpha or beta  no where to put water  water repellentII. Glycoconjugates:a. Proteoglycansb. Glycoproteinsi. 1 or more carb moieties on a protein core found of the extracellular face of cellsii. The carbohydrate is ALWAYS on the outside of the plasma membraneiii. These allow signaling and adhesion: protein part and carbohydrate part act similarly to the ECMiv. How the carbohydrates are bound to the amino acids are very important1. Serine link: O link (from the oxygen)a. Oxygen of the serine binds to where the hydroxyl was on the carb2. Asparagine: N link (from the nitrogen)a. Nitrogen binds to the hydrogen on the carbv. Can also be found inside (luminal side) of cell membrane on the golgi, ER, and lysosomes1. Spherical vessel with glycoprotein on the inside synthesized in the ER, packaged in the golgivi. Terminal sugar on most glycoproteins are sialic acidsc. Glycolipids and lipolysaccharides: membrane lipids with carbohydrates as the polar head groupi. Gangliosides: eukaryotic membrane lipids1. The polar head group is a complex carbohydrate containing SIALIC ACIDS (derivatives: neuraminic acid, N-acetyl-neuraminic acid)2. This terminal sugar is NOT present in prokaryotesa. This is how white blood cells work: they bind to molecules that do not contain this sialic acid (bacteria)3. When cells are sick/old then the sialic acid comes offa. Other cells can bind to it and destroy it ii. Lipopolysaccharides: Lipid + large carb chain 1. Long hydrophobic regions 2. Very polar head3. Major component of the outer membrane of gram negative bacteriaiii. Lectins: carbohydrate binding proteins with high specificity and affinity1. Specificity: ability to discriminate among similar structures2. Lectins discriminate using certain hydrogen-bonding domains (as specific as antibodies  can be used in the lab for labeling and carbohydrate detection)3. Used for cell recognition, cell adhesion, and signaling4. Can be used to replace Western Blot5. All organisms have lectins (plants, animals, viruses, bacteria)III. Chapter 8 & 9: Nucleotides and Nucleic acidsa. These MUST be more stable than other biomolecules because there are often far less identical copies than for other biomolecules (need DNA to synthesize proteins that sustain life)b. Fundamentals of Nucleic acids:i. The proteome (all of the proteins expressed by a genome, cell or tissue at a moment in time) of living material is stored in either DNA or RNAii. Genome: All of the genetic material of a cells including all genes, introns, exons, RNA, and DNA (CONSTANT, whereas the proteome is not constant)iii. Metabolome: All of the small molecules and chemicals found in a biological sample at any moment in time (all metabolites-the end products of cellular chemical reaction and processes)iv. Going back to the proteome: this is the fundamental, scientific definition of life (the Central Dogma)v. A gene is a segment of DNA or RNA that may NOT be a continuous sequence of bases; it contains the information required for the synthesis of functional biological molecule (RNA or protein)vi. Nucleotide vs Nucleosides: 1. Nucleotides: 3 componentsa. Nitrogenous baseb. Pentosec. Phosphatei. Note: could also be called a Nucleoside Phosphate2. Nucleoside: 2 componentsa. Nitrogenous baseb. Pentosevii. Structure of Nucleic Acids: Must be able to draw 5 Nitrogenous bases, thenucleotide and nucleoside versions, and the oxy and deoxy forms 1. Come from Purine or Pyrimidinea. Purine Nucleotides: Adenine and Guanineb. Pyrimidine Nucleotides: Cytosine, Thymidine, and Uracil2. Because they must constitute a very stable molecule, only purines can bond with pyrimidines3. The two pentoses are closed ring forms (beta furanose with two hydroxyls on the 2 and 3 carbons)a. This ring is puckered instead of planar, which is significant in complex structures (allows the sugars to “pile up” on each other to condense the DNA molecule)4. Minor Bases: most are methylated forms of the major bases (do not need to memorize these)a. Methyl group changes the ability of the bases to interact with one another; therefore, they serve very different purposesb. Some have additional rings (ie - cyclic AMP)5. Nucleotides are joined by Phosphodiester Bonds: 5’ phosphate + 3’ hydroxyl (note: always draw from 5’ to 3’ end top to bottom or left to right) a. This bonding creates a backbone with alternating pentosesand phosphatesb. Oligonucleotides: up to 50 basesc. Polynucleotides (outdated term): more than 50 basesd. Note: can create almost identical structures with DNA and RNA6. Structural Properties of Nucleotidesa. Backbones form hydrogen bonds with waterb. However, the bases are hydrophobic, so they will stack to minimize contact with waterc. The phosphates are almost completely ionized at pH 7 (when neutral, DNA is a negatively charged molecule)d. Nucleotides absorb UV light with maxima at ~260 nmi. Different from proteins that absorb light with maxima at 280 nme. The interactions (H bonds and hydrophobic bases) stabilizebinding between two or more strandsi. All hydrogen bonds between the backbone and water that can be made, will be madef. Watson and Crick model: A binds to T, G binds to Ci. Should be able to draw how these bases bind with one anotherii. A and T have 2 hydrogen bondsiii. C and G have 3 hydrogen bondsiv. The distance between C and G and A and T are almost identical  linearity  strong hydrogen


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