index
Announcements
Quiz
Questions
Homework Problems for Chapter 3
Chapter 3: Amino Acids
Section 3.1: General Structure of Amino Acids
Amino Acids are Chiral
L-Amino Acids are Used in Biomolecules
A Left-Handed Mnemonic
The RS System
Section 3.2: The 20 Standard Amino Acids
The Amino Acids Organized into 6 Groups
The 5 Aliphatics
The 3 Aromatics
The 4 Sulfur/Alcohols
The 3 Basics
The 4 Acid/Amides
The 1 Oddball
AA-Tetris: A Game for Learning the Side Chains
Questions
References
Next Lecture: Sections 3.3 - 3.7

Fundamentals of Biochemistry

Biochem 380 - Fall 2006

Lecture 007

Outline

Announcements
Quiz
Questions about previous lecture
Section 3.1: General Structure of Amino Acids
Section 3.2: The 20 Standard Amino Acids

Announcements

Lecture 6 notes are online

Quiz

Quiz on Chapter 2

Questions

Any questions on the material from the previous lecture?

Homework Problems for Chapter 3

Assigned homework problems for Chapter 3:
- 1, 3, 5, 10, 12, 13, 15

Chapter 3: Amino Acids

Chapter 3 covers the amino acids, the building blocks of proteins. The amino acids could be considered the primary 'alphabet' or 'ABCs' that should be learned as a solid foundation for subsequent material in biochemistry
Their importance is a reflection of the widespread and versatile roles of proteins in the cell. Proteins help to fulfill many functions and purposes, including catalytic activity as enzymes, storage and transport molecules such as hemoglobin and myoglobin, structural elements such as actin and collagen, as components of motors like those in flagella, information decoding molecules such as transcription factors and the ribosome, and immune system elements such as antibodies

Section 3.1: General Structure of Amino Acids

Amino acids are amino derivatives of carboxylic acids. In the 20 common amino acids, the amino group and the carboxyl group are both bonded to the same central atom, which is referred to as the α-carbon atom
The other two bonds go to a hydrogen atom and a side chain, which is a variable group of atoms (also called the 'R' group) that define the particular type of the amino acid
For example, in serine, the amino acid shown above, the side chain is a methanol group

Amino Acids are Chiral

The central α-carbon atom in most amino acids has the property of being chiral. A chiral atom is one that is asymetrical, giving the molecule a 'handedness', similar to the handedness of right- and left-handed gloves
Two molecules with the same set of atoms that are bonded in different spatial configurations are called stereoisomers. Amino acids that are mirror images of each other are particular kinds of stereoisomers called enantiomers

L-Amino Acids are Used in Biomolecules

One convention for describing the mirror-image configurations of amino acids is the L-D system. L stands for 'left' (laevus in Latin) and D stands for 'right' (dextro in Latin).
Above are the L and D isomers of the amino acid serine. In nature, only the L-isomers of amino acids are used as components of proteins. Why is this?
Like the standardization of left-handed threads in industrial technology, the asymmetrical prevalence of amino acid configurations in nature results from an ancient commitment to a particular geometrical orientation of the molecular machines that create them (enzymes)

A Left-Handed Mnemonic

One way to remember the arrangement of atoms in the L-configuration might be to think of a left-handed discus thrower
With the convention of the carboxyl group drawn at the top and the side chain drawn at the bottom, we can imagine the amino acid as a person bent forward with arms outstretched towards the back. Then, the amino group would be the discus in the left hand, and the small hydrogen would be the right hand

The RS System

The RS System is another method for distinguishing between different stereoisomers. This system has an advantage over the L-D system in being more general and less ambiguous. It works by assigning priorities to atoms based upon their atomic mass
The rules for determine the S or R configuration of a molecule are as follows:
- Point the atom with lowest priority away from you
- Determine the direction from highest priority to lowest
- CCW = S Configuration, CW = R Configuration

Section 3.2: The 20 Standard Amino Acids

Although there are hundreds of different kinds of amino acids, as distinguished by variations in the side chain, there are only 20 common or standard amino acids that are used in building proteins
You will be expected to know the names, abbreviations and 1-letter symbols for all 20 of the standard amino acids
You will also be expected to be able to draw the structures of all 20 AA's
We'll go over the structures of the side chains today. Drawing the structures by hand is a good way to remember them
At the end of the lecture, I'll also mention a game that you can play that may help to learn them

The Amino Acids Organized into 6 Groups

A good way to learn the structures of the 20 common amino acids is to organize them into 6 distinct groups:
- The 5 Aliphatics
- The 3 Aromatics
- The 4 Sulfur/Alcohols
- The 3 Basics
- The 4 Acid/Amides
- The 1 Oddball

The 5 Aliphatics

The 3 Aromatics

The 4 Sulfur/Alcohols

The 3 Basics

The 4 Acid/Amides

The 1 Oddball

AA-Tetris: A Game for Learning the Side Chains

AA-Tetris is a small game that I created for learning the structures of the 20 different side chains
In addition to structure, it also teaches a little about the chemical properties of the side chains: which ones are nonpolar, polar and charged
The game runs on Windows and Gnu/Linux platforms and is available in the software section of the course web pages

Questions

Questions about the material covered today?

References

Nomenclature and Symbolism for Amino Acids and Peptides
International Union of Biochemistry and Molecular Biology web page,
http://www.chem.qmul.ac.uk/iupac/AminoAcid/AA1n2.html

Next Lecture: Sections 3.3 - 3.7

Read Sections 3.3 - 3.7

Table of Contents

Fundamentals of Biochemistry

Biochem 380 - Fall 2006

Lecture 007

Outline

Announcements

Quiz

Questions

Homework Problems for Chapter 3

Chapter 3: Amino Acids

Section 3.1: General Structure of Amino Acids

Amino Acids are Chiral

L-Amino Acids are Used in Biomolecules

A Left-Handed Mnemonic

The RS System

Section 3.2: The 20 Standard Amino Acids

The Amino Acids Organized into 6 Groups

The 5 Aliphatics

The 3 Aromatics

The 4 Sulfur/Alcohols

The 3 Basics

The 4 Acid/Amides

The 1 Oddball

AA-Tetris: A Game for Learning the Side Chains

Questions

References

Next Lecture: Sections 3.3 - 3.7