Basic Aspects of Amino acids Flashcards
What is the importance of amino acids?
In the formation of proteins - Amino acids represent building blocks for proteins
In the formation of compounds of biochemical importance
In contributing energy to the body
Some amino acids act as neurotransmitters
•In general, 20 different types of amino acids are present in proteins.
(However, Selenocysteine, an amino acid present in certain proteins, is named as the 21st amino acid
What does the general structure of an amino acid look like?
- In general amino acids are the compounds having at least one acidic group and a basic amino group
- Structure of a typical amino acid (present in proteins) is represented as—
•R group (also called as side chain) is different for different amino acids
Draw out each amino acid ( 20 in total)
What is the classification of amino acids based on?
•Based on acid base behavior;
– Acidic, basic & neutral
•Based on polarity;
– Polar & non polar
•Based on the presence of certain groups;
– Sulfur containing, branched chain, hydroxyl group containing etc.
•Based on metabolic fate;
– Glucogenic, ketogenic & mixed
•Based on Nutritional significance;
– Indispensable (essential) &
dispensable (non essential)
What are some Modified amino acids present in proteins
- Examples:
- Hydroxyproline — in collagen
- Hydroxylysine — in collagen
- Gamma (γ) carboxyglutamate — in prothrombin
What are some non-protein amino acids?
- β alanine
- Ornithine
- Citrulline
- Homocysteine
- Homoserine
- Gamma (γ) amino butyric acid
- Taurine
What is isomerism and what are isomers?
- These are the compounds that exhibit same molecular formula but differ in structural pattern
- It is the phenomenon by which two or more compounds exhibit same molecular formula but differ in structural pattern
What is D & L isomerism?
- Optical isomerism / Enantiomerism / Mirror image isomerism) – A type of isomerism seen among the certain organic compounds (including amino acids)
- To exhibit such type of isomerism the compound must possess at least one asymmetric carbon atom
- The compound that contains asymmetric carbon atom is said to be optically active
- With the exception of glycine, all the amino acids present in proteins have asymmetric carbon atoms, hence they exhibit optical isomerism
Based on optical activity what can D and L isomers be ?
- Based on optical activity, the D and L isomers can be either dextrorotatory (+) or levorotatory
- Example:
L - Alanine is dextrorotatory (+) D - Alanine is levorotatory (-)
- All naturally occurring amino acids present in proteins belong to the L category. (However, glycine is without either L or D configuration)
- D amino acids are present in certain bacterial cell wall and in some peptide antibiotics
What are the ionizable groups present on amino acids?
Apart from this, what are other additional ionizable groups?
- All the amino acids exhibit acid base behavior
- This feature is by virtue of different ionizable acid/base groups present in amino acids.
- The two common ionizable groups present in all the amino acids are;— α- Carboxyl & α- Amino
- Apart from this, certain amino acids contain additional ionizable groups;
- — Extra Carboxyl groups (β & γ carboxyl groups)in
Aspartate & Glutamate, respectively
- — Extra amino group (Epsilon(ε) amino group) in lysine
- — Guanido (guanidino) group in Arginine
- — Imidazole group in Histidine
Ionizable groups of amino acids can exist in two group. What are they?
What can the dissociation behaviour of different ionizible groups, present in amino acids be assessed in terms of?
What is the definition of this value?
•The dissociation behavior of different ionizable groups, present in amino acids,can be assessed in terms of pK values.
•The dissociation behavior of different ionizable groups, present in amino acids,can be assessed in terms of pK values.
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•pK is negative log. of dissociation constant, K.
•
•pK is defined as the pH at which an acid group is half dissociated or in other words, pK is the pH at which both protonated (undissociated) & deprotonated (dissociated) forms of acid group are present at equal concentration.
What are the pk values of different ionizable groups of amino acids ?
α – Carboxyl , β - Carboxyl (Aspartate) ,γ - Carboxyl (Glutamate) ,Imidazole (Histidine), α - Amino,ε - Amino (Lysine),Guanidino (Arginine)
Ionizable groups pK (Approx.)
α – Carboxyl 2.0 α - Amino 9.5 β - Carboxyl (Aspartate) 3.9
γ - Carboxyl (Glutamate) 4.3
ε - Amino (Lysine) 10.5
Guanidino (Arginine) 12.5
Imidazole (Histidine) 6.1
Guanidino group only donates much later then for example a-carboxyl so it is a very poor acid
What can you tell by looking at the pH values of different dissociable groups of amino acids?
- Based on the pK values it is obvious that among different dissociable groups of amino acids, carboxyl group dissociates at lower pH and guanidino (guanido) group of arginine dissociates at higher pH
- Since the pK of all the carboxyl groups are much below pH 7.0, and since these carboxyl groups are in dissociated states at neutral pH, they are considered as acidic groups.
- On the other hand, pK values of α - amino groups, ε-amino group of lysine and guanido group of arginine are much higher than 7.0. Moreover, these groups exist in fully protonated (undissociated) form at neutral pH. Hence these groups are called as basic groups.
- The acid base/ionic properties of a protein is determined by the side chains of the amino acids such as aspartate, glutamate, histidine, lysine & arginine
What is the definition of the Henderson-Hasselbalch equation? What does it help do?
This is the equation that depicts relationship among, pK, pH and concentration of acid and its conjugate base
pH = pKa + log
pH = pK + log ([A-]/[HA])
- Henderson Hasselbalch (H.H.)equation helps to assess the dissociation pattern of the compounds having proton donor groups
- The extent dissociation of certain drugs (having proton donor groups) in G.I.tract may be measured by H.H. equation – helps to assess the absorption of these drugs
What does the dissocition behaviour of a neutral amino acid look like?
What does the dissociation behaviour of an acidic amino acid look like?
What does the dissociation behaviour of an basic amino acid look like?
The first amino group has a pK of 9.5 so it donates first then then second amino group goes and donates because it has a slight higher pK of 10.5. The zwitter ion is the 3rd one.
