amino acids 1

Glycine is the only non-chiral amino acid

Alpha carbon must’ve COOH and NH2 bonded to it

Proteins contain only L-isoforms. They’re amphoteric

Major 4 elemtents in amino acids, C H O N (S)

Structures of proteins

1. primary; the straight linear chain

2. seoncdary: i. alpha helix; bacbone lies inside the helix and side chains project outwards. The Oxygen from Amino Acid #1 reaches out and "grabs" the Hydrogen from Amino Acid #4 (specifically, the 4th one ahead of it).
   ii. beta pleated sheets;chains lying side by side, their hydrogen bonds are oriented towards the long axis of the chain

3. tertiary: van der waals, hydrogen bond and ionic bond, contain secondary structures

4. quartenary: subunits can be made of disulfide covalent bonds.

Hemoglobin molecule，consists of four globin chains joined by noncovalent bonds

Functions

1. precursors for other metabolites; egs purines and pyrimiedine bases

2. Some non-proteinogenic amino acids function as intermediates in the synthesis and breakdown of proteinogenic amino acids and the urea cycle

3. Components of lipids; serine in phopholipids,glycine in bile salts

4. As neurotransmitters, hormones and chemical mediators

Properties

colorless, non-volatile, crystalline solids and melt at temp above 200 degrees celsius, varied structure,chirality

Ionizable properties

COOH =>COO- + H+ （proton donor)

-NH2 + H+ =>NH3+ (proton acceptor)

Ubiquitin-Proteasome System (UPS) destroys damged proteins

Digestion of proteins

trypsinogen=>trypsin via enzyme enteropeptidase

Trypsin cleaves:

Chymotrypsinogen to chymotrypsin

Proelastase to elastase

Procarboxypeptidase to carboxypeptidase

CLASSIFICATION OF AMINO ACIDS

They may be classified

1into five groups based on the reactivities of their R groups

2metabolically on their catabolic products

3On weather they are essential or non essential

4On the extra-functional groups available

4 major rxns of aa

transamination,transdeamination, oxidative deamination, decarboxylation

Table of the 20 Standard Amino Acids

mnemonic for non polar GAVI Liked My Fat Pro Twin

• G - Glycine

• A - Alanine

• V - Valine

• I - Isoleucine

• L - Leucine

• M - Methionine

• F - Phenylalanine (the "Ph" sounds like F)

• P - Proline

• T-Tryptophan

the first five thats G,A,V,I and L are aliphatic

mnemonic for polar Santa's Team Crafts Yearly New Quilts

• S – Serine

• T – Threonine

• C – Cysteine

• Y – Tyrosine (The letter Y)

• N – Asparagine (The letter N)

• Q – Glutamine (The letter Q — "Q-tamine")

mnemonic for acidic and neg charged is Dont Eat

• D-Aspartate

• E-Glutamate

mnemonic for basic and pos charged is King Roy’s Home

K-Lysine R-Arginine H-Histidine

They’ve an extra NH in their structure

NB:1.Phenylalanine and tryptophan are aromatic and non polar

       2.Tyrosine is aromatic

Aromatic

All very hydrophobic

All contain aromatic group

Absorb UV at 280 nm

Phenylalanine (Phe, F)

Tyrosine (Tyr, Y) – -OH ionizable (pKa = 10.5), H-Bonding

Conditionally essential

(i) ARG: can be made, but not enough

(ii) HIS: controversial (essential for growth in children)

(iii) PHE essential, TYR can be made from PHE but when enzyme is missing, PKU. then PHE not equal to TYR; Therefore TYR is essential

(iv) MET& CYS; Similarly, if MET not essential CYS then CYS essential

1amino acids with aliphatic side chains : These are monoamino monocarboxylic acids. This group consists of the most simple amino acids—glycine, alanine, valine, leucine and isoleucine. The last three amino acids (Leu, Ile, Val) contain branched aliphatic side chains, hence they are referred to as branched chain amino acids.

2Hydroxyl group containing amino acids :Serine, threonine and tyrosine are hydroxyl group containing amino acids. Tyrosine—being aromatic in nature—is usually considered under aromatic amino acids.

3Sulfur containing amino acids : Cysteine with sulfhydryl group and methionine with thioether group are the two amino acids incorporated during the course of protein synthesis. Cystine, another important nt sulfur containing amino acid, is formed by condensation of two molecules of cysteine.

4Acidic amino acids and their amides : Aspartic acid and glutamic acids are dicarboxylic monoamino acids while asparagine and glutamine are their respective amide derivatives. All these four amino acids possess distinct codons for their incorporation into proteins.

5Basic amino acids : The three amino acids lysine, arginine (with guanidino group)and histidine (with imidazole ring) are dibasic monocarboxylic acids. They arehighly basic in character.

6Aromatic amino acids :

GROUPING BASED ON CATABOLIC INTERMEDIATES

1.Amino acids may also be classified into glucogenic and ketogenic types depending on the metabolic intermediates they generate on catabolism

Glucogenic amino acids are catabolised to pyruvate, succinyl CoA, α-ketoglutarate, fumarate or oxaloacetate

Examples are Alanine, Asparagine, Aspartate, Arginine, Cysteine, Glutamine, Histidine, Methionine, Proline, Threonine and Valine

2.Ketogenic amino acids are catabolised to acetyl CoA or acetoacetyl CoA

Examples of purely ketogenic amino acids are Leucine and Lysine

Glucogenic and ketogenic : Isoleucine, Phenylalanine, Tryptophan and Tyrosine

Unusual amino acids

Result from modifications of the common amino acids (hydroxyproline, ornithine, norleucine)

Peptides

Oligopeptides − condensation of 2 – 10 AA units

Polypeptides − condensation of 11 – 100 AA units

Proteins − more than 100 AA units

GENERAL REACTIONS OF AMINO ACIDS

1. Decarboxylation

Amino acids are decarboxylated to amines. Eg. Histidine to Histamine

Histamine stimulates gastric secretion and involved in immune response (itching)

5 hydroxy tryptophan → hydroxy tryptamine + CO2

Serotonin - neurotransmitter mediating mood, memory..

2. DOPA → Dopamine + CO2

Dopamine is an intermediate in the formation of adrenaline, a vasoconstrictor

3. TRANSAMINATION

Transamination involves the transfer of an amino group from an amino acid to a keto-acid to form the corresponding amino acid

The reaction is catalyzed by amino transferases which require pyridoxal phosphate (PLP), a derivative of vitamin B6 as a prosthetic group. Its the carrier at the active site

PLP undergoes reversible transformation between the aldehyde form and the aminated form, pyridoxamine phosphate

Examples of aminotransferases are AST and ALT

What is their importance/role as biomarkers?

In mammals, all alpha amino acids except lysine and threonine can be transaminated

Proline, which has a secondary amino group, cannot participate in PLP dependent reactions including transamination and decarboxylation

4. OXIDATIVE DEAMINATION

The oxidative deamination of glutamate occurs in the mitochondria of the liver yielding ammonia ions

L-Glutamate + H2O ↔ α-ketoglutarate + NH4+

This reaction is catalyzed by glutamate dehydrogenase which is a complex allosteric enzyme

glutamate dehydrogenase allosteric activators are GDP and ADP. its a link between catabolic and anabolic pathways, and is, therefore, ubiquitous in eukaryotes

GLDH role

Its activity increases when fuel is needed(low energy, high GDP and ADP)

The combined action of the aminotransferases and glutamate dehydrogenase is referred to as transdeamination

The coupling of oxidative deamination with transamination of L-glutamate creates an avenue for deaminating all amino acids