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Things to Remember - Biochemistry.docx

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Department
Biochemistry
Course
BIOC 2580
Professor
Peter Dawson
Semester
Winter

Description
Things to Remember - Biochemistry Lipids  Defined by their hydrophobicity  Use organic solvents to dissolve lipids  TAGs are used for energy storage (fats and oils)  Phospholipids are the structural components of biological membranes  Glycolipids and lipoproteins are used for cell to cell communication  Fatty acids are the building blocks of fats o Label the carboxylic acid as carbon 1 and number from there, C2 is awhere the double bonds o We write fatty acids by: number of carbons: number of double bonds (Δ are - separated )y commas  Nutritionists also use omega-3 or omega-6 for naming fatty acids - this means that there is a double bond on either the 3 or the 6 carbon starting from the methyl end of the fatty acid chain o Saturated (“extended”) - no double bonds, high melting point, low solubility in water o Unsaturated - at least one double bond, low melting point and high solubility in water, not packed close together  Double bonds are in „cis‟ conformation which means they are methylene-bridged and there are not two in a row o Trans fats are when the double bond is in the „trans‟ formation therefore there can be two in a row, happens through partial dehydrogenation  High melting points, low solubility, dangerous health effects o Overall, as the number of carbons in the chain increases and the degree of saturation increases (less double bonds), the higher the melting point and the lower the water solubility o Fatty acids are often 4-36 carbons in length with an even number of carbons, un-branched o The most common saturated fatty acids are: laurate, myristrate, palmitate, stearate, and arachidate  Esters are formed between an acid and an alcohol, anhydrides are formed between two acids, both are condensation reactions  TAGs consist of three fatty acid chains and 1 glycerol molecule o Highly hydrophobic (more so than the individual fatty acids) and melting points depend on the individual fatty acids o Can be simple (3 of the same fatty acids) or mixed  Animal fat is normally found in solid form - high melting point and low unsaturation, while plant oil is normally found as liquid - low melting point and high unsaturation  Phosphoric acids is a triprotic acid that can form 3 bonds (either phosphate esters for phosphoanhydride bonds), the negative charge of the phosphoric acid group can make molecules more water soluble (polar)  Glycerophospholipids are the main component of the cell membrane and they consist of 2 fatty acid chains, 1 glycerol, 1 phosphoric acid group and either choline, ethanolamine, serine or glycerol esterfied with the phosphoric acid group o The phosphate is the polar, hydrophilic head, the 2 fatty acids are the non polar, hydrophobic tails (the molecule it self is ampliphilic)  Phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine or phosphatidylglycerol are the classes of phospholipids, they can differ through the fatty acid chains o Phospholipids can aggregate into micelles, bilayers or vesicles because of their properties  Analysis of lipids o Lipids move into chloroform area because hydrophobic while other biomolecules move into hydrophilic water layer  lipids are extracted and either go through TLC or adsorption chromatography (most non polar comes out first)  can then break ester bonds and identify the fatty acid chains by creating a new ester bond with methanol (making the molecule more volatile) and putting it through gas-liquid chromatography, high performance liquid chromatography, or mass spec Carbohydrates  Most abundant biomolecule on earth  Monosaccharides - 1 sugar molecule o Has a carbonyl group (ketone or aldehyde) and several hydroxyl groups o Water soluble but not soluble in organic solvents, sweet, colour-less, general formula is (CH 2) n o The simplest sugars are the trioses (dihydroxyacetone and glyceraldehyde) o All monosaccharides except for dihydroxyacetone have at least 1 chiral carbon - this gives rise to optically isomeric forms o D sugars are ones that the chiral carbon furthest from the carbonyl group has a hydroxyl group on the right side, L sugars are when this hydroxyl group is on the left side  Most naturally occurring sugars are D sugars o A sugar with „n‟ chiral carbon atoms has 2 stereoisomers (same molecular formula)  Enantiomers are molecules that are mirror images of each other (e.g. L-glyceraldehyde and D- glyceraldehyde), they have the same chemical properties but they rotate polarized light in the opposite directions  Diastereomers are molecules with the same molecular formula but differ in the arrangement at one or more carbon atoms (e.g. glucose and fructose), do not have identical chemical properties o Epimers are a special type of diastereomers that the molecule is the same except for at one carbon atom (e.g. L- glucose and D-glucose)  Fischer projection formula - vertical lines are behind the plane, horizontal lines are coming out from the plane  Perspective formula - solid wedge lines are coming towards you, dashed lines are going away from you  Hemiketals - reaction between ketone and alcohol  Hemiacetals - reaction between aldehyde and alcohol o These are the basis behind cyclization of sugars o In aldohexose, the -OH from carbon 5 attacks the aldehyde group to form a pyranose molecule o In ketohexose, the -OH from carbon 5 attacks the ketone group to form a furanose o This makes C1 chiral and can make two anomeric forms, α and β  This is called the anomeric carbon and it is the only carbon atom that is attached to two oxygen groups o Cyclization keeps all other configurations (Left, Above, Beta - Haworth projections)  Anomers are when the molecule is the same except for the conformation at the anomeric carbon  Mutarotation is the fact that when a monosaccharide is found in water it is in equal parts α, β, and linear forms and it slowly reaches this equilibrium  Reducing sugars are sugars that the anomeric carbon can be oxidized by Cu while Cu is formed making red cuprious oxide - must be able to open up to the linear form in order to do this  Disaccharides - 2 sugar molecules o The anomeric carbon of a monosaccharide is reactive and can form glycosidic bonds (C- O) or glycosylic bonds (C-N) with other molecules including other sugars  If the anomeric carbon is involved in a glycosidic bond it is no longer a reducing sugar because it cannot open up to its linear form o Disaccharides are when there is a glycosidic bond formed between two monosaccharides, at least one of the monosaccharides must give up their anomeric carbon (many different structural isomers) o If both anomeric carbons are in the bond we use a double headed arrow and it becomes a non reducing sugar  Polysaccharides - 3+ sugar molecules o Highly branched because of many -OH groups o Homopolysaccharides - single type of sugar monomer  E.g. glucans - glucose homopolymers o Heteropolysaccharides - more than one type of sugar monomer Nucleic Acids  DNA first described as nuclein by Miescher  Nucleosides are a base + sugar (ribose or deoxyribose - no OH group on C2)  Nucleotides are base + sugar + phosphate group  DNA has sugar phosphate backbone connected by phosphodiester bonds (carbons 3 and 5 of sugar)  RNA contains D-ribose and DNA contains D-deoxyribose and both are in beta furanose form  Pyrimidines consist of cytosine, thymine (DNA) and uracil (RNA)  Purines consist of adenine and guanine  When in glycosylic bond with sugar, names become: o Adenosine, guanosine, thymidine, uridine, cytidine o Pyrimidines attach to position 1 and anomeric carbon hydroxyl group o Purines attach to position 9 and anomeric carbon hydroxyl group  RNA rapidly hydrolyzes under alkaline conditions because -OH group is close to the phosphate group - why DNA is more stable  Chargaff‟s rules state that the proportion of T is equal to the proportion of A and the proportion of C is equal to the proportion of G in the complementary strand of DNA - remember % of CG and TA are different  Rosalind Franklin and Maurice Wilkins used x-ray diffraction to see the secondary structure of DNA o Produced photo 51 which showed that DNA was in a helical pattern and that there were 2 repeating periodicities - one every 34 Å and one every 3.4 Å o It was Crick and Watson that got the credit for the DNA secondary structure  Said that it was right handed, the phosphate sugar backbone faced the hydrophilic surroundings while the base pairs were perpendicular to the back bone and facing the hydrophobic environment  The two strands are antiparallel and complementary (each can be used to synthesize the other)  Every 34Å vertically is one turn of the helix and 3.4Å is the vertical height between base pairs  It takes approx. 10.5 base pairs per turn  There are 3 hydrogen bonds between C and G and two between T and A therefore the higher % there is of C and G the harder it is to separate the strands  The two strands are then supercoiled - you cannot unwind them by pulling on the end of the molecule  The double helix also has 2 grooves, one major and one minor  This is because the glycosidic bonds are not parallel  The major and minor grooves alternate as you go up the molecule - the larger the size of the major groove, the more accessible it is for interactions with proteins that recognize specific DNA sequences  The bonds holding together the DNA double helix are hydrogen bonds, hydrophobicity and van der Waals interactions ATP  Discovered by Lippmann and has adenosine + 3 phosphate groups connected by phosphoanhydride bonds  ATP is the link between catabolism and anabolism  The free energy of ATP hydrolysis is negative and large therefore breaking one of the phosphoanhydride bonds can push a reaction towards completion o Hydrolysis releases the electrostatic repulsion among the negative phosphate groups o The inorganic phosphate has greater resonance stabilization than ATP does o The ADP rapidly ionizes to release a proton into a medium of very low H driving the hydrolysis to completion  We can either hydrolyze the β - γ bond or we can hydrolyze the α - β bond and release twice the amount of energy because the phosphoanhydride bond of pyrophosphate is hydrolyzed as well  ATP provides energy through group transfer o ATP reacts with glutamate to transfer phosphate group onto it o NH a3tacks the C=O bond and inorganic phosphate is released as the leaving group - glutamine is produced Enzyme Cofactors 2+ 2+ 2+ 2+ 2+  Inorganic ions: Cu , Mg , Mn , Zn , Fe  Coenzymes: act as carriers of specific functional groups o ATP - carries phosphate o NAD /NADP - carry electron pairs  Come from niacin (vitamin B3)  Pyridines: dinucleotide with adenine and nicotinamide  Water soluble  Redox chemistry is similar (both accept a hydride ion - proton and 2 electrons) but NAD is a better oxidizing agent and NADPH is a
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