Amino Acids - I

Session Objectives

  • Describe the structure of amino acids.
  • Classify amino acids based on structure, side chain chemistry, metabolic fate and nutritional requirement.
BIG PICTURE

Lysine – More than a protein monomer

L-Lysine, the biologically active form of the amino acid lysine, has several biological functions in addition to being a part of cellular proteins.

L-Lysine is used as a nutritional supplement in clinics today to treat a variety of health issues such as herpes/shingles infection, acne management, hair growth problems etc.

To get a glimpse of the functions of L-Lysine in human cells, click here .

When learning about amino acids, remember to explore a little more about their functions beyond protein building.

In the session on "Introduction to Proteins", we had a brief look at the basic building block of proteins – AMINO ACIDS. In this session and the next, we will explore the structure, classification and properties of amino acids.


WHAT ARE AMINO ACIDS?

Amino acids are small organic molecules that consist of an amino group (—NH2) and carboxylic acid group (—COOH) as the primary functional groups.

More than 500 amino acids are found in nature. Of these, only ~20 amino acids are found in the human body. These are called standard amino acids. 19 out of these 20 amino acids are also called alpha-amino acids (α-amino acids) because the amino and carboxyl groups are attached to the same carbon atom.

The visual below shows the basic structure of an α-amino acid.

Visual 7.1 General structure of an α-amino acid.
Activity 7.1

Answer the questions below based on the structure shown in visual 7.1.

Q1. Observe the groups attached to the α-carbon atom. Define “R” group so that the α-carbon becomes chiral.?



   

Classification of Amino Acids

The structures of 20 amino acids found in our body differs in the type of “R” group present. To study the physiochemical properties of amino acids as well as their biological fate/functions, amino acids are classified based on the following criteria:

  • Chemical structure (R group/side chain)
  • Nature of R group (side-chain character)
  • Metabolic fate
  • Nutritional requirement

I- Classification based on chemical structure

The visual below provides the structure and classification of the 20 standard amino acids found in the human body. Click on each of the category buttons and study the structures provided carefully.

Interactive html

Visual 7.3

II. Classification based on side group character

Activity 7.3 will present the classification of amino acids based on their side group properties using interactive questions.

Before seeing other ways of classifying amino acids, let us recall the basic chemical structure of the 20 amino acids you learnt using the above visual.

Activity 7.2

RECALL AMINO ACID STRUCTURE

II. CLASSIFY AMINO ACIDS BASED ON SIDE CHAIN PROPERTIES

Discover another way of classifying amino acids as you answer the questions in the activity below.

Activity 7.3

Explained below are two other ways of classifying amino acids. We will explore the metabolic classification of amino acids in greater details in the sessions on carbohydrate and lipid metabolism.

III. Classification based on metabolic fate

Thecarbon skeleton of amino acids that do not form proteins are recycled in the body (to form glucose or lipid) while the nitrogen is incorporated in non-protein nitrogenous compounds (like DNA) or eventually excreted as urea.

Visual 7.4 Nitrogen balance in the body.
Note the two possible fates assigned to the carbon skeleton of amino acids that get form the amino acid pool in cells.

The visual below gives the classification of amino acids based on the metabolic fate of their carbon skeleton.

Visual 7.5 Metabolic classification of amino acids.

IV. Classification based on nutritional requirements

All proteins in our body are made of amino acids and they differ significantly from one another in their amino acid composition. Hence, all the standard amino acids are essential for proper growth and development of the body.

Our body can produce few of the amino acids, but require many to be provided through diet.

The visual below explains the classification of amino acids based on our nutritional need of these amino acids.

Visual 7.6 Dietary classification of amino acids.
APPLY & INTEGRATE

IDENTIFY THE CHEMISTRY OF A STRUCTURE / PROCESS

Short Answers

The examples below showcase how you can integrate knowledge from the three subjects by applying principles of biochemistry to explain the basis of an observation in anatomy or physiology.

Activity 7.4

Q1. Glutamate and its derivative, GABA, are important neurotransmitters with opposite effects on neurons. Glutamate binds cationic ion channels in post-synaptic neurons and triggers an action potential. GABA, on the other hand, binds chloride ion channels and inhibits firing of new action potentials.

What could be one reason for difference in action of glutamate and GABA?


   

SOLVE A CLINICAL CASE

To solve clinical cases as a doctor, you need to pose the right questions to yourself about the case presentation, extend your knowledge within subjects (beyond the textbook), find the right links between subjects, and then, put all the information together to answer the questions.

We will train you to develop and sharpen case-solving skills by presenting clinical cases (and aligned questions) across topics that allow you to link anatomy, physiology and biochemistry knowledge meaningfully.

In this session, you will attempt integrating knowledge of amino acids, skeletal muscles and neurotransmission.

Clinical case presentation

A 35 year old woman sees her physician to report muscle weakness in the extraocular muscles as well as muscles of the extremities. She feels fine when she gets up in the morning, but the weakness begins when she gets active. The weakness is improved by rest. Sensation appears normal. With an acetylcholinesterase inhibitor, she notes immediate return of her muscle strength.

Activity 7.5

Q1. What is the point of contact between the nerve and the muscle called?


   

End of Session

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DEEP DIVE
Title Description Citation
Complete vs. Incomplete Proteins Explains how dietary proteins are classified based on the amino acids they contain. Marturana A. The Difference Between Complete and Incomplete Proteins. Self-Food, March 8, 2017. Accessed Source link on Aug 7, 2017.
21st and 22nd amino acids Learn about the two new additions to the standard amino acid list – selenocysteine and pyrrolysine Shweta Kumari. Expanding the genetic code: Selenocysteine and Pyrrolysine. SlideShare. Accessed Source link on Aug 7, 2017.
Amino acid absorption Get an overview of the molecular basis of amino acid absorption in the gut. Digestive enzymes: Endopeptidases and amino acid absorption. Walter John. YouTube video published on Mar 27, 2014. Accessed Source link on Aug 7, 2017.
EXAM PREP

Questions for exam preparation related to this session

1 Give the detailed classification of amino acids. Give examples for each category. [10M]

2 Classify amino acids based on their side chain properties. [4M]

3 Define alpha-amino acid and give its structure. Distinguish essential and non-essential amino acids. [4M]

4 Write a brief note on amino acid classification. [4M]

5 Give two examples of: [2M each]

  • non-polar amino acids
  • acidic amino acids
  • hydroxyl-group containing amino acids
  • amide group containing amino acids
  • derived amino acids
  • non-alpha amino acids

Resource for a quick revision

Structure of 20 amino acids, Frankly Chemistry; published on Jul 1, 2016; accessed through Source link on Dec 12, 2016.

Amino acid game  Source link