From amino acid to protein

 

Marie-Véronique CLEMENT Associate Professor Yong Loo Lin School of Medicine NUS Graduate School for Integrative Science and Engineering Department of Biochemistry National University of Singapore 8 Medical Drive, MD 7 #03-15 Singapore 117597 Tel: (65) 68747985 Fax: (65) 67791453 E-mail: bchmvc@nus.edu.sg  

Amino Acids
20 Amino Acids:  9 essential 11 non essential

General formula  of an Amino Acid

At physiological pH  COO­/NH3+
•Unsubstituted • Heterocyclic • Aromatic • Thioether • hydroxy • Mercapto • Carboxiamide • Monoamino, dicarboxylic • Diamino, monocarboxylic

All amino acids are in the L­configuration

All amino acids have a specific side chain Amino acid side chain can be  polar/hydrophilic Non polar/hydrophobic
   

Acid/base properties of amino acids:

Acid/base properties of side chains acid base Carboxyl group Imidazole group

webhost.bridgew.edu/fgorga/proteins/zwitterions.htm And Lippincott’s

 

 

Titration  curve of  Alanine

R­H3N+ R­COOH
   

R­NH2 + H+ + R­COO­ + H

All amino acids found in proteins are L­configuration. D­Amino acid are found in plant, antibiotics and bacterial walls D amino acid are efficiently metabolized by the liver by the D­ Amino acid oxidase. However, D­Amino acid are reaminated to  L­isomers during amino acid metabolism.

 

 

The four main families of small organic molecules  in cells

 

 

From amino acids  to protein:

Formation of a protein

Amino acid

 

 

Messenger RNA (mRNA) is translated into protein by the joint action of transfer RNA (tRNA) and the ribosome, Adapted from A. J. F. Griffiths et al., 1993, An Introduction to Genetics Analysis, 5th ed., W. H. Freeman.]

Crowded cytoplasma RNAs: blue Ribosome: green Protein: red

 

 

codon Amino acid

The genetic  code

One or more codon  correspond to 1  standard amino acid:

 

 

The dogma till 1983:  20 amino acids are enough to produce all the proteins in  our body

20  not enough!
   

When stop means go:
Stop codon

1983

Selenocysteine (21) Pyrrolysine (22)

2002
There are two ways in which the stop codon UAG could be redefined to specify the 22nd amino acid, pyrrolysine. In the first (top), special signals in mRNAs tag a subset of stop codons that are to have their meaning redefined. In the second (bottom), a codon is redefined regardless of the mRNA involved.

 

 

Selenocystein
Selenocysteine is an amino acid that is present in several enzymes
(glutathione peroxidases, tetraiodothyronine 5' deiodinases, thioredoxin reductases, formate dehydrogenases, glycine reductases and some hydrogenases). Selenocysteine has a structure similar to cysteine, but with an atom of selenium taking the place of the usual sulfur.
Selenium is a vital nutrient in animals and humans.

Proteins that contains one or more selenocysteine residues are called selenoproteins.
About 25 different selenocysteine-containing selenoproteins have so far been observed in human cells and tissues.

Since lack of selenium deprives the cell's ability to synthesize selenoproteins, many health effects of low selenium intake are believed to be caused by the lack of one or more specific selenoproteins. On the other side, too much selenium in the diet causes toxic effects and leads to selenium poisoning. The threshold between essential and toxic concentrations of this element is rather     narrow (the factor is in the range of 10-100).

Pyrrolysine
Pyrrolysine is an amino acid used by some methanogenic (organisms that produce methane) archaea in enzymes that are part of their methane-producing metabolism.

Science 24 May 2002: Vol. 296. no. 5572, pp. 1459 - 1462 DOI: 10.1126/science.1069588

Pyrrolysine Encoded by UAG in Archaea: Charging of a UAG-Decoding Specialized tRNA
Gayathri Srinivasan, Carey M. James, Joseph A. Krzycki*
Pyrrolysine is a lysine derivative encoded by the UAG codon in methylamine methyltransferase genes of Methanosarcina barkeri. Near a methyltransferase gene cluster is the pylT gene, which encodes an unusual transfer RNA (tRNA) with a CUA anticodon. The adjacent pylS gene encodes a class II aminoacyl-tRNA synthetase that charges the pylT-derived tRNA with lysine but is not closely related to known lysyl-tRNA synthetases. Homologs of pylS and pylT are found in a Gram-positive bacterium. Charging a tRNACUA with lysine is a likely first step in translating UAG amber codons as pyrrolysine in certain methanogens. Our results indicate that pyrrolysine is the 22nd genetically encoded natural amino acid. Department of Microbiology, Ohio State University, Columbus, OH 43210, USA. * To whom correspondence should be addressed. E-mail: Krzycki.1@osu.edu    

Any other amino acids?
Phospho­serine in the survival kinase Akt?

Neurotransmitter, Dopamine? The non standard amino acids
   

Non Standard amino acids
Produce from modifications of standard amino acids
Modified after it is incorporated  into the protein. • Hydroxylation • Acetylation • Phosphorylation • Cross­linking of cystein Do not incorporate into a protein Biologically active amino acids: • GABA (2 amino isobutiric acid) • Dopamine (neurotransmitter) • Taurine (essential for development) • Histamine (neuritransmitter) • Thyroxine (thyroid hormone, increase the basal
metabolic rate, affect protein synthesis and increase the body's sensitivity to catecholamines (such as adrenaline). and an hormone)

• Epinephrine (or adrenaline, is a neurotransmitter 
   

Post-translational modifications of amino acids:

Acetylation greatly decreases protein degradation, since many proteases require an amino terminus to act

In structural protein such as collagen, hydroxylation of proline occurs to afford hydroxyproline. Since hydroxyproline has a hydrogen-bonding side chain, it is used to lend additional strength to the collagen structure, and hence to tendons and other like tissues.

Phosphorylation of serine /threonine or tyrosine is used in cell signaling

 

 

Crosslinking of two cysteines to form a new amino acid, called cystine

most often occurs in extracellular proteins, and can contribute to their three-dimensional structure

 

 

Biologically active amino acids:
GABA: gamma Amino butyric acid Synthesised from glutamate
GABA acts at inhibitory synapses in the brain. GABA acts by binding to specific receptors in the plasma membrane of both pre- and postsynaptic neurons. Neurotransmetter

Dopamine: Synthesized from tyrosine
In the brain, dopamine functions as a neurotransmitter, activating dopamine receptors. Dopamine is also a neurohormone released by the hypothalamus. Its main function as a hormone is to inhibit the release of prolactin from the anterior lobe of the pituitary.

Taurine : 2-aminoethanesulfonic acid, formed by the decarboxylation of cysteine In vivo studies in various species have shown taurine to be essential in certain aspects of mammalian development, and have demonstrated that low levels of taurine are associated with various pathological lesions, including cardiomyopathy, retinal degeneration, and growth retardation,   especially if deficiency occurs during development.  

Standard amino acids • 9 essential + selenium • 11 non essential Non standard amino acids

• Modified after it is incorporated into the  protein. • Do not incorporate into a protein Biologically active amino acids:

Amino acids
 

?
 

protein

How to make a protein?

?

 

 

Amino acids join together to form proteins:

R

 

 

Variable  side chains
Components of a Polypeptide Chain. A polypeptide chain consists of a constant backbone and variable side chains.    

Formation of a peptide bond:

 

 

Trans is the Favorite conformation
   

Except!

Cis
   

A peptide: Phe­Ser­Glu­Lys (F­S­E­K)
N­terminus  terminates  by an amino group Peptide bond

Amino acid

 

 

C­terminus  terminates by a  carboxyl group

Amino Acid Sequences Have Direction:.

This pentapeptide, Leu-enkephalin, is an opioid peptide that modulates the perception of pain. The reverse pentapeptide, Leu-Phe-Gly-Gly-Tyr (LFGGY), is a different   molecule and shows no such effects.  

Components of a Polypeptide Chain.
A polypeptide chain consists of a constant backbone and variable side chains.

Trans

Backbone

Variable side chains

 

 

What is the difference between a  peptide and a protein?
Peptide < 50 amino acids Protein > 50 amino acids
A protein (from the Greek protas meaning "of primary importance")

Most natural polypeptide chains contain between 50 and 2000 amino acid residues and are commonly referred to as proteins.
   

Some biochemical properties of proteins

Molecular weight

Isoelectric point

 

 

The molecular weight of a protein:
Molecular weight of protein is expressed in Dalton
Dalton: A unit of mass very nearly equal to that of a hydrogen atom. Named after John Dalton (1766-1844), who developed the atomic theory of matter. The mean molecular weight of an amino acid residue is about 110, and so the molecular weights of most proteins are between 5500 and 220,000. We can also refer to the mass of a protein, which is expressed in units of daltons; one dalton is equal to one atomic mass unit. A protein with a molecular weight of 50,000 has a mass of 50,000 daltons, or 50 kd (kilodaltons).
   

 

 

 

 

Proteins from  the plasma can  be separated by  charge

 

 

Electrophoresis of  plasma protein  and diseases

Hepatic  cirrhosis

Inflamation  cause by  infection

Nephrotic  syndrome

Hypoγ globulinemia  immunosupressive disease