ch 10 - Nitrogen- and Phosphorous-Containing Compound Flashcards Preview

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Flashcards in ch 10 - Nitrogen- and Phosphorous-Containing Compound Deck (21)
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1

amino acids

contain an amino group and a carboxyl group attached to a single carbon atom (and the alpha-carbon). The other substituents attached to alpha-carbon are hydrogen and an R group

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Glycine

only achiral amino acid with R group of just H

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cysteine

only R configured amino acid because the sulfur in its R group takes priority

4

amphoteric

molecular property in which molecules can act as both acids and bases. This applies to amino acids because of their acidic carboxyl group and basic amino group

5

carboxyl

-C(double bond O)OH

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zwitterion

molecule that has both positive and negative charges

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nonpolar nonaromatic amino acid R groups

tend to have side chains that are saturated hydrocarbons: alanine, valine, leucine, isoleucine but also include glycine, proline (cyclic with a secondary amine), and methionine (which contains sulfur)

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aromatic amino acid side chains

tryptophan, phenylalanine, tyrosine

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polar amino acid side chains

tend to have terminal groups containing oxygen, nitrogen, or sulfur: serine, threonine, asparagine, glutamine, cysteine

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negatively charged (acidic) amino acid side chains

aspartic acid, glutamic acid (have terminal carboxylate anions in their R groups)

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positively charged (basic) amino acid side chains

arginine, lysine, histidine (have protonated amino group in R groups)

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peptide bonds

bonds formed by amino acids through condensation reactions

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polypeptides

molecules formed by peptide bonds; comprise proteins

14

Strecker synthesis

step 1: aldehyde, ammonium chloride (NH4Cl), and potassium cyanide (KCN): carbonyl oxygen is protonated, increasing electrophilicity of carbonyl carbon; then ammonia can attacked carbonyl carbon, forming imine; then CN- from KCN attacks, forming a nitrile group (--C(triple bond)N); final molecule at end of step is aminonitrile (containing an amino group (--NH2) and nitrile group. Step 2: nitrile nitrogen is protonated increasing electrophilicity of nitrile carbon; water attacks, creating molecule with imine and hydroxyl moieties at same C; this imine is attacked by another equivalent of water forming carbonyl and kicking off ammonia; creates carboxylic acid functionality which is performed in aqueous acid and sped up with heat; racemic mixture pathway and can produce L- or D-amino acids; pg 231, 232

15

Gabriel Synthesis

also called malonic-ester synthesis, another way of synthesizing amino acids; potassium phthalimide reacted with diethyl bromomalonate via SN2 (leaving group is bromo); then add base, leaving group H, C is negative; then add Br-R through SN2, R group attaches to C; then add NaOH with water and heat (delta) to get a dicarboxylic acid and an NH2 connected to the C where that used to be. Finally add H3O+ and heat (and a CO2 is released) forming the amino acid. pg 233

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Phosphoric acid

sometimes referred to as phosphate group or inorganic phosphate, denoted P sub I. extremely important molecule biochemically; forms high-energy bonds that carry energy in adenosine triphosphate

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inorganic phosphate at physiological pH

contains molecules of hydrogen phosphate (HPO4)2-, and phosphate (H2PO4)-.

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phosphorous in DNA

found in backbone of DNA forming phosphodiester bonds linking sugar moieties of nucleotides

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pyrophsophate

denoted as PP sub i. (P2O7)4- when a new nucleotide is joined to a growing strand of DNA by a DNA polymerase, it releases this ester dimer of phosphate; its hydrolytic release provides energy for formation of new phosphodiester bond

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organic phosphates

nucleotides (like ATP, GTP, and those in DNA) with presence of phosphate group bonded to a carbon-containing molecule

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properties of phosphoric acid

three acidic hydrogens each with their own pKa which makes it a good buffer because these hydrogens span so widely; the term refers to the form that predominates in strongly acidic conditions: H3PO4 which can lose proton (pKa is then 2.15) in mildly acidic conditions to become dihydrogen phosphate (H2PO4)- and will lose a second proton (pKa then of 7.20) to become hydrogen phosphate (HPO4)2- in weakly basic solutions; strongly basic solution it turns to phosphate (PO4)3- (pKa then of 12.32)