Amino Acids Flashcards
What are amino acids?
Building blocks of proteins
How do amino acids differ?
-Differ in the nature of R groups
What do all amino acids contain?
- Alpha amino group
- alpha carboxylic group
- H atom
- R group
Why is glycine unique?
The simplest amino acid with an achiral carbon atom
Describe the structural components of amino acids
- All amino acids have a chiral carbon except glycine
- it is determined by the placement of the amino group
- If the amino group is on the left it is an L-amino acid. If the amino group is in the right, D-amino acid
What are D-L based on?
Based on the structure of glyceraldehyde
What is the isoelectric point/pH?
The characteristic pH at which the net electric charge of an amino acid is zero (still charged but net charge is 0)
What is glycine’s pI?
5.97
How is charge affected by pH and pI?
The further the pH of an amino acid solution is from its pI, the greater the electric charge on that population of molecules
What is pka?
A measure of the tendency of a group to give up a proton
What happens at pH=pka?
A weak acid is half dissociated
Give the formula for pH
pH= pka + log ( [proton acceptor]\ [proton donor] )
What are essential amino acids?
Based on human nutrition, cannot be synthesized y humans and gained via diet
What are the essential amino acids that must be known?
A little humility in learning 10 tiny molecules pleases Vanessa
Arginine, leucine, histidine, isoleucine, lysine, tryptophan, threonine, methionine, phenylalanine and valine
List 3 non polar R groups amino acids
Alanine, valine and leucine
What are polar, uncharged R group amino acids?
Cysteine, serine
List aromatic R group amino acids
Phenylalanine and tyrosine
List the negatively charged(acidic ) R group amino acids
Aspartic acid, glutamic acid
List the positively charged (basic) R group amino acids
Histidine, lysine, arginine
What are characteristics of amino acids with non-polar side chains?
- they do not bind nor give protons
- they do not form hydrogen bonds
- they take part in hydrophobic interactions
What are characteristics of amino acids that have acidic side chains?
- They are proton donors
- At neutral pH(physiological), side chains fully ionized or dissociated (COO-) and carry a net negative charge
- they contribute a negative charge to proteins
- typically have a pk lower than 7
What are the characteristics of amino acids with basic side chains?
- side chains accept protons
- They contribute a positive charge to proteins that contain them
- have a pk above 7
Describe Lys and Arg side chains at physiological pH
Side chains are fully ionized, positively charged (NH3+) they are basic side chains
Describe the side chain of Histidine at physiological pH
Weakly basic and partially positively charged at physiological pH good buffering capacity
Compare and contrast UV absorbance between Try, Trp and phenylalanine
Try and Trp stringly absorb UV light at 280nm.
Absorbance at 280nm is approx, 4x higher for TRP than for Try
Phenylalanine does not show much absorbance
How are derive amino acids formed?
Amino acids formed by enzymatic modification of an amino acid after translation
Give examples of derived amino acids
- hydroxylysine and hydroxyproline(collagen)
- y(gamma)-Carboxyglutamic acid (blood clotting)
- 3-methylhistidine, E-N- methyl lysine(muscle)
Describe the most important biological reaction of amino acids
Amino acids are combined in peptide linkages
Formed by linking alpha-COOH(C-terminal) of one amino acid to the alpha a-NH3 (N-terminal) group of another amino acid
Water is eliminated
What is the charge of amino acids with uncharged polar side chains at neutral pH?
0 charge
What amino acids can lose a proton at an alkaline pH but have uncharged polar side chains?
Cys and Tyr
What amino acids with uncharged polar side chains can form hydrogen bonds via -OH group?
Ser, Thr and Tyr
What amino acids with uncharged polar side chains, can form hydrogen bonds due to COOH and CONH groups?
Asn and Gln(glutamine) contain COOH/carboxy and CONH(Carboxyamine)
What is a polypeptide?
Series of amino acids joined by pride bonds
What is eliminated in the formation of peptide bonds?
Water
What reaction forms a peptide bond?
Condensation redaction (dehydration) involving 2 reactions
What is residue ?
Each amino acid unit in protein
What must be done with amino acid samples before composition test?
Pure sample must be used, contamination results used in errors
List the 3 methods of amino acid identification of a polypeptide
- Acid hydrolysis
- Chromatography
- Quantitative analysis
Describe acid hydrolysis
- Hydrolyzed by strong acid at 110 degrees Celsius for 24 Hours
- Peptide bonds cleaved
- Tryp mostly destroyed
- Procedure gives composition but not sequence
Describe chromatography of amino acid identification
- Individual amino acids are separated by cation-exchange chromatography
- Anion-exchanges resin used for positively charged amino acids
- Eluted from column by buffers of increasing ionic strength and pH
- amino acids separated at different ionic strength and pH
How are individual amino acids separated by chromatography?
- individual aa’s separated by cation-exchange chromatography
- Anion-exchange resin for positively charged amino acids
- Amino acids separated at different ionic strength and pH
Describe the quantitative analysis in amino acid identification
- Quantified with ninhydrin -> purple compound with amino acids, NH3 and amines(yellow color with imine group of Pro)
- intensity of color is measured in spectrophotometer
- if MW of protein known, number of residues can be known, otherwise, only ratio of number of molecules of each amino acid determined
What is quantitative analysis done using?
Amino acid analyzer
Ninhydrin is added to a chemical and a purple solution is present, what chemical group is indicated?
Imine group of Pro
What is the abbreviation of arginine?
Arg
What is the abbreviation of leucine?
Leu
What is the abbreviation of histidine?
His
What is the abbreviation of isoleucine
ILe
What is the lysine abbreviation?
Lys
What is the abbreviation of tryptophan?
Trp
What is the abbreviation of threonine?
Thr
What is the abbreviation of methionine?
Met
What is the abbreviation of phenylalanine?
Phe
What is the abbreviation of valine?
Val
Describe a method of sequencing the peptide
Terminal residue analysis
Peptides can be sequenced either from the N terminal usually referred to as Edman degradation or from the C-terminal
What is Edman reagent and what us it used to do?
Phenylisothiocyanate- used to label N-terminal residue under mildly alkaline conditions
How does Edman reagent chemically do its job?
It makes N-terminal residue peptide bonds weak: break it without breaking others
What chemical change does Edman reagent undergo when used for sequencing
Phenylisothiocyanate -> phenylthiohydanton
What are requirements./ limitation of the Edman reagent?
- Works under mildly alkaline conditions
- can be used for polypeptides of 100 amino acids or less
Explain the actions of phenylisothiocyanate in N terminal labeling
- labeling, Edman reagent binds to end terminal amino acid
- release of amino acid derivative by acid hydrolysis.
Binding Edman reagent with the formin N terminal amino acid
What methods can be used to sequence amino acids from the C-terminus?
No efficient method for sequencing peptones from the C-terminus
What enzyme can be used to identify the C-terminal amino acid?
Carboxypeptidase
Explain how carboxypeptidase is used to analyze C-terminal amino acids
- Carboxypeptidase cleaves the C-terminal peptide bond, producing C-terminal a. acid and shortened peptide
- further reaction cleaves the second amino acid that has now become the new C-terminal of the shortened peptide
- eventually the entire peptide is hydrolyzed into its individual amino acid
What kind f reactions are undergone by amino acids?
- Many standard reactions of amines and carboxylic acids
- Conditions must be right, so that the amino group does not interfere with a carboxylic group reaction and vice versa
List some typical reactions of amino acids
- Esterification of amino group
- Acylation of the amino group (formation of amides)
- reaction with ninhydrin
What is ninhydrin?
Common reagent for visualizing spots or bands of amino acids that have been separated by chromatography or electrophoresis
What happens when ninhydrin reacts with amino acids?
One of the product is a deep violet, resonance stabilized anion called Ruhemann’s purple
How does structure of amino acids affect reaction with ninhydrin?
Side Chain of amino acid is lost as an aldehyde.
Ninhydrin produces the same purple dye regardless of structure
What is Ninhydrin used for?
To detect amino acids in a wide variety of substrates
