Marie-Véronique CLEMENTAssociate ProfessorYong Loo Lin School of MedicineNUS Graduate School for Integrative Science and EngineeringDepartment of BiochemistryNational University of Singapore8 Medical Drive, MD 7 #03-15Singapore 117597Tel: (65) 68747985Fax: (65) 67791453E-mail: bchmvc@nus.edu.sg

From amino acid to protein

Amino Acids

20 Amino Acids: 9 essential11 non essential

All amino acids are in the L-configuration

General formula of an Amino Acid

All amino acids have a specific side chain

•Unsubstituted• Heterocyclic• Aromatic• Thioether• hydroxy• Mercapto• Carboxiamide• Monoamino, dicarboxylic• Diamino, monocarboxylicAmino acid side chain can be

polar/hydrophilicNon polar/hydrophobic

At physiological pH

COO-/NH3+

webhost.bridgew.edu/fgorga/proteins/zwitterions.htm

And

Lippincott’s

Acid/base properties of amino acids:

Carboxyl group

Imidazole group

Acid/base properties of side chains

acid base

Titration curve of Alanine

R-H3N+ R-NH2 + H+

R-COOH R-COO- + H+

All amino acids found in proteins are L-configuration.

D-Amino 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, D-Amino acid are reaminated to L-isomers during amino acid metabolism.

The four main families of small organic molecules in cells

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.]

From amino acids to protein:

Amino acidFormation of a protein

Crowded cytoplasma

RNAs: blueRibosome: green

Protein: red

The genetic code

One or more codon correspond to 1 standard amino acid:

codon

Amino acid

20 not enough!

The dogma till 1983:

20 amino acids are enough to produce all the proteins in our body

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.

When stop means go:

Selenocysteine (21)

Pyrrolysine (22)

1983

2002

Stop codon

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.

Proteins that contains one or more selenocysteine residues are called selenoproteins.Selenium is a vital nutrient in animals and humans.

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).

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

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.

Any other amino acids?

Phospho-serine in the survival kinase Akt?

Neurotransmitter, Dopamine?

The non standard amino acids

Non Standard amino acids

Modified after it is incorporated into the protein.

• Hydroxylation• Acetylation• Phosphorylation• Cross-linking of cystein

Do not incorporate into a proteinBiologically 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).

• Epinephrine (or adrenaline, is a neurotransmitter

and an hormone)

Produce from modifications of standard 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.

Post-translational modifications of amino acids:

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

most often occurs in extracellular proteins, and

can contribute to their three-dimensional

structure

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

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.

Biologically active amino acids: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.

GABA: gamma Amino butyric acidSynthesised 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

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 proteinBiologically active amino acids:

Amino acids protein?

How to make a protein?

?

Amino acids join together to form proteins:

R

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

Variable side chains

Formation of a peptide bond:

Trans is theFavorite conformation

Except!

Cis

Peptide bond

Amino acid

C-terminus terminates by a carboxyl group

N-terminus terminates

by an amino group

A peptide: Phe-Ser-Glu-Lys (F-S-E-K)

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.

Amino Acid Sequences Have Direction:.

Components of a Polypeptide Chain.

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

BackboneVariable side chains

Trans

What is the difference between a peptide and a protein?

Peptide < 50 amino acids

Protein > 50 amino acids

Most natural polypeptide chains contain between 50 and 2000 amino acid residues and

are commonly referred to as proteins.

A protein (from the Greek protas meaning "of primary importance")

Some biochemical properties of proteins

Molecular weight Isoelectric point

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).

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.

Proteins from the plasma can be separated by

charge

Electrophoresis of plasma protein

and diseases

Inflamation cause by infection

Hypo globulinemia immunosupressive disease

Hepatic cirrhosis

Nephrotic syndrome