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
    bchmvc@nus.edu.sg
E-mail:
 Amino Acids
9 essential
20 Amino Acids:  11 non essential

General formula At physiological pH 
 of an Amino Acid
COO­/NH3+

All amino acids are in the L­configuration
•Unsubstituted
• Heterocyclic
• Aromatic
• Thioether
• hydroxy
All amino acids have a specific side chain • Mercapto
• Carboxiamide
• Monoamino, dicarboxylic
• Diamino, monocarboxylic
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+ R­NH2 + H+
R­COO­ + H
+
R­COOH
   
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  Formation of a protein Amino acid

to protein:

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 The genetic 
code
Amino acid

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.

  correspondence should be addressed. E-mail: Krzycki.1@osu.edu
* To whom  
 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  Do not incorporate into a protein
into the protein. Biologically active amino acids:

• Hydroxylation • GABA (2 amino isobutiric acid)
• Acetylation • Dopamine (neurotransmitter)
• Phosphorylation • Taurine (essential for development)
• Cross­linking of cystein • 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)
   
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:
Dopamine:
GABA: Synthesized from tyrosine
gamma Amino butyric acid
In the brain, dopamine functions as a
Synthesised from glutamate neurotransmitter, activating dopamine
receptors. Dopamine is also a
GABA acts at inhibitory synapses in neurohormone released by the
the brain. GABA acts by binding to hypothalamus. Its main function as a
specific receptors in the plasma hormone is to inhibit the release of
membrane of both pre- and prolactin from the anterior lobe of the
postsynaptic neurons. pituitary.
Neurotransmetter

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:

   
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  Hepatic 
plasma protein  cirrhosis
and diseases

Inflamation
 cause by 
infection

Nephrotic
 syndrome

Hypoγ globulinemia
 immunosupressive disease