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PHYS 4xx Intro 2 1 PHYS 4xx Intro 2 - Molecular building blocks We now describe in more detail the nomenclature and composition of several classes of compounds of relevance to the cell, including: membrane components: fatty acids and phospholipids biopolymers: sugars, amino acids and proteins the genetic blueprint: DNA and RNA. Fatty acids and phospholipids Phospholipids contain two fatty acids linked to a glycerol backbone. The remaining OH group in the glycerol is replaced by a phosphate group PO4 that is linked a the polar head group: O O O PO 4 O Head group The polar head groups of phospholipids may be chosen from a variety of organic compounds, including NH3 + CH3 CH3 CH3 choline CH2 OH OH COO- NH3 + N+ CH2 CH CH CH2 CH2 CH2 CH2 CH2 ethanolamine glycerol serine Because PO4 has a negative charge, serine and glycerol phospholipids are negative while choline and ethanolamine phospholipids are neutral. The naming convention for a phospholipid mirrors, in part, its fatty acid composition. Common abbreviations (italics provided for ease of pronounciation) include: phosphatidylcholine phosphatidylglycerol PC PG phosphatidylethanolamine phosphatidylserine PE PS. 2010 by David Boal, Simon Fraser University. All rights reserved; further copying or resale is strictly prohibited. PHYS 4xx Intro 2 2 Some fatty acids commonly found in membrane lipids __________________________________________________________________ Acid name Total number of Number of Position of carbon atoms double bonds double bond __________________________________________________________________ lauric 12 0 myristic 14 0 palmitic 16 0 palmitoleic 16 1 9-cis stearic 18 0 oleic 18 1 9-cis linoleic 18 2 9-cis, 12-cis arachidonic 20 4 9-cis, 8-cis, 11-cis, 14-cis __________________________________________________________________ Column 4 displays the C-C bond numbers on which any double bonds occur. Not all phospholipids are based solely on fatty acids. For example, sphingomyelin OH CH CH NH CH2 PO 4 CH2 CH2 N+ (CH3 )3 O Some lipids present in cellular membranes are not phospholipids: sugar cholesterol OH O glycolipid HO NH O Sugars Sugar molecules are one component of DNA and of the peptidoglycan network of the bacterial cell wall. A single sugar molecule has the chemical formula (CH2O)n, the most biologically important sugars having n = 5 or 6. Examples of the conformations available for the glucose molecule (n = 6) are: 2010 by David Boal, Simon Fraser University. All rights reserved; further copying or resale is strictly prohibited. PHYS 4xx Intro 2 3 CH2OH OH HO CH2OH H OH O O CH2OH OH OH HO OH OH OH HO OH (a) O HO (b) (c) Panel (a) shows the molecule as a linear chain. Five of the oxygens are part of -OH groups while the sixth is double-bonded as an aldehyde. The double-bonded oxygen can be placed at one of several different positions on the chain, each corresponding to an inequivalent, yet related, molecule. The chain can be closed into a ring using one of the oxygens in a hydroxyl group (not the oxygen in the aldehyde group (RCOH)) as illustrated in Panel (b). As drawn, the ring in part (b) appears planar, in spite of the lack of in-plane double bonds such as are present in planar compounds like benzene. In fact, the actual configuration of a glucose ring is the bent form in part (c), just as it is in the single-bonded ring of cyclohexane. A single sugar molecule in isolation is referred to as a monosaccharide. But sugar molecules can polymerize through reactions in which two alcohol groups (one on each ring) combine to give a single bond between rings, liberating H2O as a product. Two glucose molecules may combine to form the disaccharide maltose (as shown) or longer polysaccharides. CH2OH CH2OH O O OH HO O OH OH OH OH Amino acids and proteins Proteins are linear chains of amino acids, a family of organic compounds containing an amino group (-NH3+) and a carboxyl group (-COO-). Amino acids can join together to form chains through an amide linkage (-OC-N-) referred to as a peptide bond. The reaction liberates H2O, and has the general form: H H N C H R1 O H + C OH R2 N C H H O H2 O H C H N C OH H R1 O R2 C N C C H H O OH peptide bond The side groups R1 and R2 are chosen from only 20 different residues in protein construction, none of which has a high molecular mass: 2010 by David Boal, Simon Fraser University. All rights reserved; further copying or resale is strictly prohibited. PHYS 4xx Intro 2 CH3 alanine 4 CH2 CH2 CH2 C NH arginine C + NH2 CH CH3 CH2 C HN CH3 NH+ isoleucine HC histidine COO HN - CH2 CH2 CH2 SH O cysteine O C aspartic O Oacid glutamic acid C - CH2 C NH2 O glutamine NH2 CH2 H glycine NH2 O asparagine CH2 CH2 CH2 CH CH2 CH CH3 CH3 leucine CH2 CH2 CH2 CH2 CH2 CH3 S methionine phenylalanine CH2 lysine CH2 NH2 H C CH2 CH2 CH2 proline CH2 OH serine CH OH CH3 threonine CH2 N tryptophan H CH2 CH CH3 CH3 valine tyrosine OH A protein chain of high molecular mass will be built up as this reaction occurs repeatedly; for example, the two inequivalent spectrin proteins in the human erythrocyte have molecular masses of ~220 000 and ~230 000 Da. Amino acids appear in a protein with varying relative abundance, and some, such as tryptophan, are uncommon. In a large protein, the average molecular mass of the amino acids is 115 Da. Nucleotides and DNA Ribonucleic acid, or RNA, directs protein synthesis in the cell, whereas deoxyribonuclei acid, or DNA, is the carrier of genetic information. The elementary chemical units of DNA and RNA are nucleotides, which are composed of subunits, namely a sugar, an organic base and a phosphate group. phosphate base nucleotide: sugar 2010 by David Boal, Simon Fraser University. All rights reserved; further copying or resale is strictly prohibited. PHYS 4xx Intro 2 5 The two different sugars found in nucleotides, ribose in RNA and deoxyribose in DNA, are five-membered rings differing from each other by only one oxygen atom. HOCH2 OH O H H H H OH OH HOCH2 O OH H H H H OH H deoxyribose ribose In either molecule, the OH groups are potential reaction sites for addition of a base. Five organic bases are found in nucleotides, and they fall into two chemically similar groups - purines and pyrimidines. Only four of the five bases are present in a given DNA or RNA molecule, and the one "missing" base is different for each: RNA: adenine, guanine, cytosine, uracil DNA: adenine, guanine, cytosine, thymine. O NH2 C N HN C CH CH Purines C C N HC C N N N H2N H H Adenine (DNA + RNA) Guanine (DNA + RNA) O O NH N C C N 2 Pyrimidines O C CH HN C N CH C N H Cytosine (DNA + RNA) O C C CH3 N CH H Thymine (DNA) HN O C C N CH CH H Uracil (RNA) The reaction of a sugar with a base releases water (an -OH from the sugar plus an H from the base) and produces a sugar-base combination called a nucleoside. Addition of a phosphate to a nucleoside releases water and produces a nucleotide, two of which are shown in the chain of Panel (a). The nucleotides themselves can polymerize to form DNA and RNA, through a linkage between a sugar from one nucleotide and a phosphate from another, as schematically illustrated in Panel (a). 2010 by David Boal, Simon Fraser University. All rights reserved; further copying or resale is strictly prohibited. PHYS 4xx Intro 2 6 O-O P O sugar base O H2C O H H H PO4 sugar H O OH -O P O sugar PO4 base O O H2C H PO4 H PO4 sugar H H OH OH (a) (b) In the double-stranded helix of DNA, the bases lie in the interior of the helix, and hold the helix together through hydrogen bonding between base-pairs. Each matching base pair on the opposing strands consists of one purine and one pyrimidine: adanine/thymine and guanine/cytosine. ADP and ATP The energy currency of the cell is based upon a sugar-base-phosphate nucleotide whose elementary components are the same as RNA. The sugar of the currency is ribose of RNA, and the most common base is adenine (or, much less frequently, guanine). The currency differs from RNA by the presence of more than one phosphate group: the lower energy state of the pair has two phosphate groups (adenosine diphosphate, or ADP), while the higher energy state has three (adenosine triphosphate, or ATP). adenine PO4 PO4 ribose phosphorylation adenine PO4 PO4 PO4 hydrolysis ribose The energy-consuming process of adding a phosphate is called phosphorylation, while the release of a phosphate is hydrolysis. Depending on conditions, the energy change for a single phosphate group is 11-13 kcal/mol, corresponding to 8 x 10-20 J = 20kBT per reaction. 2010 by David Boal, Simon Fraser University. All rights reserved; further copying or resale is strictly prohibited.