18. Organic III (AMINO ACIDS + CHROMATOGRAPHY))

NH2CHRCOOH –> contains an amine group and carboxyl groups

Alpha amino acid/ 2-amino acid

Neutral - one basic NH2 group and COOH group Acidic - one basic NH2 group and two acidic COOH group Basic - two basic NH2 groups and one acidic COOH group (the extra NH2 group or COOH group comes from the R group)

chrial (apart from glycine as its R group is hydrogen)

+H3NCRHCOO- The zwitterion is overall neutral but the positive charge on one zwitterion is strongly attracted to the negative charge on a neighbouring zwitterion.

The oppositely charged groups of the zwitterions attract each other strongly forming a strong giant ionic lattice. These ionic forces require a lot of energy to overcome so therefore a high melting point.

COO- is protonated to COOH due to H+ from acid Eg: H+ +NH3CH2COO- —> NH3+CH2COOH Amino acid bcommes postivley charged overall

NH3+ looses an H+, reforming the NH2 group Eg: H+ NH3+CH2COO- —> NH2CH2COO- + H2O Amino acid becommes negatively charged overall

The pH at which the zwitterion exists in aqueous solution Different amino acids have different isoelectronic points. An acidic amino acid would have a low isoelectronic point. A basic amino acid would have a high isoelectronic point

Only one carboxylic acid group has lost a proton (COO-) and the amino group is protonated (NH3+) at the isoelectric point. This is because the zwitterion must be neutral However, all COOH and NH2 groups are affected in acidic/ alkaline conditions

Secondary amide functional group (only called a dipeptide bond if between just 2 amino acids) Condensation reactions

The amine group NH2 is protonated to NH3, so the amino acid carries an overall positive charge Carboxylic acid group is still COOH Eg: NH2CHRCOOH + H+ —> NH3+CHRCOOH

The COOH is deprotonated ie, looses a H+, to COO-. The amino acid carries an overall negative charge Eg: NH2CHRCOOH + OH —> NH2CHRCOO-

Hydrolysis reaction (reflux with concentrated HCl)

Thin layer chromatography - different amino acids have different affinity for either the mobile phase or stationary phase

Stationary phase - solid. Silica gel coated onto a plastic back plate Mobile phase - liquid. A solvent that is adsorbed up the stationary phase eg: mixture of organic solvents –> Process of separation is known as relative adsorption –> Amino acids are separated based on their solubility in the solvent. If a substance is more soluble in a solvent, substance rises further of the plate to give a greater Rf value. –> Can use a locating agent to visualize spots - eg: ninhydrin used for amino acids Method: -Sealed system is used ie, a lid which reduces loss of solvent -Base line must be drawn in pencil, drops on amino acids are added to the line. -Plate is placed in solvent but base line must be above solvent level. -Leave solvent to travel up. - Mark solvent front. Develop chromatogram + using either UV light or ninhydrin, which colors the amino acids

Rf value: Distance travelled by substance (compnonent)/ distance travelled by solvent To identify the amino acid, compare calculated value to a database of Rf values If Rf value is greater, substance has a greater affininty to the mobile phrase

GC Stationary phase: solid silica beads packed into a column GLC stationary phase: silica beads coated in high boiling point liquid packed into a column GC and GLC Mobile phase: inert carrier gas, often nitrogen. This gas is pushed through the column carrying the sample –> process of separation relative solubility –> Temperature and flow of gas in the column also need to be controlled so typically preformed in an oven compare retention times

Retention times can be compared to external data values Retention times are the time take for a component to travel through the column from injection If the intensity of the peak is doubled, it means there twice the amount a substance

A has a longer retention time than B because A adsorbs stronger/ is more soluble in the stationary phase than B A has a larger retention factor than B because A adsorbs stronger/ is more soluble in the mobile phase than B.

Stationary phase: liquid (coated onto a solid) packed into a column Mobile phase: high pressure liquid carries sample through column –> process of separation is relative solubility –> compare retention times Both GC/ GLC and HPLC work in conjunction with mass spec. In the chromatography, the mixture is separated. Then in mass spec, each component is analyzed

The mobile phase as it contains polar solvents, so high Rf value But if solvent isn’t polar, then it takes more time to travel up the plate