Amino Acids and proteins

M1 lecture
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:

Did you know?

Amino acids are among the most common nutritional supplements taken by athletes
Effect of protein and amino-acid supplementation on athletic performance, Richard B kreider, phD


Amino acids are major constituent for brain, nerve, muscle, blood, skin and internal organs. your body, minus water, is: • 75 percent amino acids • 95 percent of hormones are amino acids • 100 percent of all protein is amino acids



3 different ways to identify amino acids

20 amino acids:

9 Essential amino acids
cannot be manufactured by the body

11 Non-essential amino acids (+ selenocystein)
can be manufactured by the body with proper nutrition.

Alanine Arginine Aspartic Acid Asparagine Cysteine-Cystine

Glutamic Acid Lysine Glutamine Glycine Histidine Isoleucine Leucine

Threonine Tryptophan


Phenylalanine Tyrosine Proline Serine Valine

How to remember the essential amino acid?
cannot be manufactured by the body

A helpful mnemonic for remembering essential amino acids is

"Private Tim Hall” (PVT TIM HALL)
P V T  T I M H A L L

Alanine Not required in adult But required in infant diet



Where are amino acids coming from?

From the variety of foods in our diet
Meat, milk, cheese, and egg are complete proteins that have all the essential amino acids. Other sources of protein include whole grains, rice, corn, beans, legumes, oatmeal, peas, and peanut butter. For vegetarians, vegans and/or those who do not eat meat, fish, eggs, or dairy products, it is important to eat a variety of these other foods in order to get enough protein.

Essential amino acids 
come from breakdown  of proteins from our food 

Non essential amino acid

are metabolized in our body from glucose

Glycolysis and the citric acid cycle provide the precursors needed to synthesize many important biological molecules including amino acids



/Chapter 2  

The general formula of an amino acid:
α-carbon atom

Amino group

Carboxyl group Side chain



Few examples of specific side chains



The simplest  amino acid

The most occurent in protein (9.2%)

The least  occurent in protein (1.4%) Side  chains



Read chapter 3/ Devlin p 95­98 for  more details



2 Enantiomers

By convention , if NH3+ is projected to the left,  the amino acid has an L configuration.



Not an amino acid
It is the simplest of all common aldoses. It is a sweet colorless crystalline solid that is an intermediate compound in carbohydrate metabolism



In mammalian proteins only  amino acid  of  L­configuration are found.

L-Alanine (Ala / A)

L-Asparagine (Asn / N) L-Arginine (Arg / R)

L-Aspartic acid (Asp / D)

L-Threonine (Thr / T)



• Unsubstituted • Heterocyclic • Aromatic • Thioether • hydroxy • Mercapto • Carboxiamide • Monoamino, dicarboxylic • Diamino, monocarboxylic Non Polar Polar charged Polar uncharged





Polar /non Polar: the definition
Polar molecules
Polar molecules are generally able to dissolve in water (hydrophilic) due to the polar nature of water. Polar molecules have slightly positive and slightly negatively charged ends. Examples of household polar molecules include table salt, ammonia and sugar (glucose).

Non-polar molecules
Most non-polar molecules are water insoluble (hydrophobic) at room temperature. Examples of household non-polar compounds include fats, oil and petrol.



Polar:  Non polar:

hydrophilic hydrophobic









Amino acid are in an ionized form at pH 7



At pH 7:
Amino  Group

Carboxylic acid  Group
(unprotonated in its  carboxylate ion form

(protonated in its  amoniun anion form)

Hydrogen  atom



Ionization State as a Function of pH. The ionization state of amino acids is altered by a change in pH. The zwitterionic form predominates near physiological pH.





Ionizable  side chain



3 acid/base groups

Leucine 2 acid /base sites



Glutamic  acid  3 acid /base  sites



Amino Acids Building block of proteins 20 Amino Acids:  9 essential 11 non essential

General formula  of an Amino Acid

All amino acids have a specific side chain

•Unsubstituted • Heterocyclic • Aromatic • Thioether • hydroxy • Mercapto • Carboxiamide • Monoamino, dicarboxylic • Diamino, monocarboxylic

All amino acids are in the L­configuration Amino acid side chain can be  polar/hydrophilic Non polar/hydrophobic  


Amino acids view trough photomicrographs (photographs taken through a microscope)











The titration curve of acetic acid (CH3COOH). The pKa for the dissociation of acetic acid to hydrogen and acetate ions is 4.75. At this pH, half the acid molecules are dissociated. Because pH is measured on a logarithmic scale, the solution changes from 91 percent CH3COOH at pH 3.75 to 9 percent CH3COOH at pH 5.75. The acid has maximum buffering capacity in this pH range.

pH = pKa when [A-] = [HA]

The four main families of small organic molecules  in cells



Amino acids are weak acids because of their ionizable groups