Basic Biochemistry. Classes of Biomolecules
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1 Basic Biochemistry ABE 580 Classes of Biomolecules Carbohydrates Lipids Amino Acids Nucleic Acids Other 1
2 Carbohydrates Sugars Composed of C, H, O (C n H 2n O n ) Biological Uses Energy source/storage Structural Strength or Support Tag for IDing proteins, etc. Monosaccharides Oligo- and Polysaccharides Monosaccharides Aldose Sugars having an aldehyde moiety Ketose Sugars having a ketone moiety Hexoses Sugars having 6 carbons: C 6 H 12 O 6 Pentoses Sugars having 5 carbons: C 5 H 10 O 5 Ribose, Xylose 2
3 Hexose Isomers Fischer Projections Glucose Aldose Fructose Ketose Chain vs Ring Structure Aldehyde (aldoses) and ketone (ketose) can form hemiacetal with hydroxyl of carbon on opposite end of chain 3
4 Ring Structures Aldohexoses form 6 member rings pyranose Ketohexoses form 5 member rings - pyranose Aldopentoses form 5 member rings - furanose Haworth Projection Glucose (pyranose ring) Frutose (furanose ring) Ribose (furanose ring) Mutarotation Equilibrium in Water 4
5 Carbohydrate Bonds Glycosidic Bonds: C O C Between hydroxyls Ring structures form these bonds! Glucose α 1-2 fructose Sucrose Two Important Polysaccharides Polysaccharide many saccharides Starch = Glucose α1-4 Glucose Two forms Amylose (straight chain) Amylopectin (branched chain) Important energy storage (plants) and food Cellulose = Glucose β1-4 Glucose Important structural sugar (wood) Straight chain 5
6 Difference in Glycoside Bonds Makes All the Difference Starch Amylose chains form helix by hydrogen bonds between the hydroxyl groups of glucose Allows it to be compacted for storage Easy to break hydrogen bonds with water to uncoil and hydrolyze into glucose Cellulose Straight, ribbon-like chains that stack into crystals through hydrogen bonds Very strongly bound (high number of H-bonds) Gives cellulose strength and resistance to hydrolysis 3-D Models Lipids Hydrocarbons (largely C & H) Important Functions Membranes! Cells, organelles Energy storage (higher energy density than carbohydrates) Fatty acids carbon chains with acetyl on one end Saturated: no C=C (double bonds) Unsaturated: Some C=C (double bonds) Phospholipids hydrophobic carbon chains with hydrophillic head 6
7 Lipids are Amphiphilic Hydrophilic Head Hydrophobic Tail Lipid-Lipid Bilayer Lipid Micelle Amino Acids 20+ Amino acids Amino acid polymers = proteins Amino acids = amine + carboxylic acid R = side chain Chiral Center R = acidic, basic, hydrophilic, hydrophobic, charged, uncharged 7
8 Proteins Proteins are linear polymers of amino acids Peptide bonds = amine to carboxylic acid Structure and function of protein determined by 3-D structure that polymer assumes in water 3-D structure a function of lowest energy confirmation Hydrophobic groups associate away from water Hydrophilic groups associate toward water Protein Function Enzymes catalyze biochemical reactions Structure and support Communication between cells (hormones) Protein Folding Folding@Home Distributed computing project studying protein folding using novel computational methods and large scale distributed computing, to simulate the thermodynamics of protein folding. 3-D Models 8
9 Nucleic Acids Composed of 3 parts Pentose (sugar) Heterocyclic Base Phosphate A unit of all 3 (sugar+base+phosphate) called a nucleotide Nucleic Acids Pentose Ribose (RNA) Deoxyribose (DNA) = lacking 1 hydroxyl group on sugar C2 Ribose Deoxyribose 9
10 Nucleic Acids Bases 5 bases 4 used in RNA (U, A, C, G) 4 used in DNA (T, A, C, G) 2 Types Purine (A, G) Pyrimidine (T, U, C) Adenine Thymine Polynucleotides DNA and RNA polymers store and convey genetic information Polymer consists of sugar backbone linked by -C-PO 4 -C- Bases (esp. DNA) can associate through complementary pairing (A-T, C-G) 3-D structure is double helix 3-D Model 10
11 Genetic Code Sets of 3 bases (codon) 4 3 = 64 codons Each codon specifies a unique amino acid Each amino acid specified by at least 1 codon Start codon (methionine) Stop codons (UAG, UAA and UGA) Central Dogma of Biology DNA is transcribed to mrna mrna is translated into protein DNA makes RNA RNA makes Proteins 11
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