BIO201/ SPRING2020

Introduction to
Biochemistry & Biotechnology

Lecture #3
Lehninger
Principles of Biochemistry
Amino Acids
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3
 Amino Acids
What are the building blocks of proteins?
Proteins play crucial roles in almost all
biological processes and amino acids are
the building blocks of it. A large
proportion of our cells, muscles and Proteins are made up of amino acids.
tissue is made up of amino acids.

http://www.building-muscle101.com/food-high-in-protein.html

Q1. What makes proteins?

Q2. Draw the general structure of amino acids.
 Amino Acids
Some Functions of Proteins

Q1. Give an example of protein function in biological systems.

 Amino Acids
What are amino acids?

An amino acid is a type of organic acid that contains a carboxyl

functional group (-COOH) and an amine functional group (-NH2)
as well as a side chain (designated as R) that is specific to the
individual amino acid. 

Q1. Define amino acids.

 Amino Acids
How amino acids are linked together in proteins?

Proteins are made up of hundreds of smaller units called amino

acids that are attached to one another by peptide bonds, forming a long
chain.

http://www.interactive-biology.com/6711/the-basics-of-protein-structure-and-function/

Q1. What is the monomeric unit of proteins?

 Amino Acids
Chiral Center
Chiral center: Chiral molecules contain at least one carbon atom with four non-
identical substituents. Such a carbon atom is called a chiral center.

Except glycine, all other amino acids are

chiral. Glycine is achiral.

http://slideplayer.com/slide/6990130/

Q1. What is chiral center?

Q2. Show the chiral center in an amino acid.
Q3. Draw the structure of amino acid that is not chiral.
 Amino Acids
Chiral & Achiral Molecules

http://icanhasscience.com/chemistry/through-the-looking-glass/

http://jinavie.tumblr.com/post/42210918094/mirror#.WI76QdJ97cs

A chiral molecule can’t be superimposed on its mirror image, no

matter how you rotate it. One could say that his or her body is
chiral.
An achiral molecule cannot be distinguished from its mirror
image. The chair in the picture above is achiral.
Q1. Define chiral and achiral molecules.
 Amino Acids
Enantiomers
Stereoisomers: Stereoisomers are compounds with the same structural formula but with a
different arrangement in space.
Enantiomers: Enantiomers are chiral molecules that are mirror images of each other.
An enantiomer is one of two stereoisomers that are mirror images of each other which means they
are non-superimposable. For all chiral compounds, stereoisomers having a configuration related to
that of L-glyceraldehyde are designated L, and stereoisomers related to D-glyceraldehyde are
designated D.
Racemic mixture: In chemistry, a racemic mixture, or racemate is one that has equal amounts of left-
and right-handed enantiomers of a chiral molecule. 

Q1. Define enantiomers.

Q2. What is racemic mixture?
Q3. Draw structures of the enantiomers of alanine.
 Amino Acids
Amino acids in proteins are L stereoisomers
The amino acids in protein molecules are exclusively L stereoisomers.
D-Amino acids have been found only in a few, relatively small peptides of
bacterial cell walls and certain peptide antibiotics.
Cells are able to specifically synthesize the L isomers of amino acids because the
active sites of enzymes are asymmetric, causing the reactions they catalyze to be
stereospecific.
Not in proteins;
In proteins only in some bacterial peptides

There are no scientific explanation why proteins are primarily made up of only
L-amino acids.
Q1. Which stereoisomer of amino acids exist in proteins?
 Classification of Amino Acids
Amino acids can be classified by R group
Amino acids are grouped into five classes based on their tendency to interact with water at
biological pH (7.0).

Q1. What is the

basis of amino acid
classification?
Q2. Name the five
different classes of
common amino
acids.
Classification of Amino Acids
Amino acids can be classified by R group

Q1. Draw the structure of an amino acid with non-polar, aliphatic R groups.
Classification of Amino Acids
Amino acids can be classified by R group

Q1. Draw the structure of an amino acid with polar, uncharged R group.
Classification of Amino Acids
Amino acids can be classified by R group

Q1. Draw the structure of an amino acid with aromatic R group.

Classification of Amino Acids
Amino acids can be classified by R group

Q1. Draw the structure of an amino acid with positively charged R group.
Classification of Amino Acids
Amino acids can be classified by R group

Q1. Draw the structure of an amino acid with negatively charged R group.
 Classification of Amino Acids
Disulfide bonds
Cysteine is readily oxidized to form a covalently linked dimeric amino acid called cystine,
in which two cysteine molecules are joined together by disulfide bonds.

http://www.interactive-biology.com/6711/the-basics-
of-protein-structure-and-function/

Q1. Show how disulfide bonds are formed.

http://positivemed.com/2012/12/09/why-is-some-hair-curly-and-some-hair-straight/ Q2. Why some hair are curly whereas some are straight?
 Classification of Amino Acids
Amino acids can act as Acids and Bases
Zwitterion: A molecule or ion having separate positively and negatively charged groups.

Amino acids as Zwitterions: When an amino acid is dissolved in water (pH 7.0), it exists in
solution as dipolar ion, or zwitterion.
A zwitterion can act as either an acid (proton donor) or a base (proton acceptor).
Amino acid as an acid (proton donor) Amino acid as a base (proton acceptor)

Q1. What is a zwitterion? Draw diagrams to show how amino acids can act as zwitterions.
Q2. Show how amino acids can act as both proton-donor and proton-acceptor.
 Amino acids have characteristic titration curves
Isoelectric point (pI) of amino acids
Isoelectric pH or point: The isoelectric pH or point (pI), is the pH at which a particular
molecule carries no net electrical charge. 

Q1. What is isoelectric point?

No questions about values of isoelectric points of glycine in exam.
 Amino Acids
How a peptide bond is formed?
A peptide bond is a chemical bond formed between two molecules when the carboxyl
group of one molecule reacts with the amino group of the other molecule, releasing a
molecule of water (H2O).
This is a dehydration synthesis reaction (also known as a condensation reaction), and
usually occurs between amino acids.

https://drgpinstitute.wordpress.com/2014/12/27/protein/

Q1. How a peptide bond is formed?

Q2. Show the chemical reaction of peptide bond formation.
 Amino Acids
What is a peptide bond?

Amino acids are joined to its neighbor by covalent bonds in proteins.

A peptide bond (amide bond) is a covalent chemical bond linking two consecutive amino
acid monomers along a polypeptide or protein chain.

http://www.interactive-biology.com/6711/the-basics-of-protein-structure-and-function/

Q1. What is a peptide bond?

Q2. Draw a diagram to show peptide bonds in a polypeptide.
 Amino Acids
What is a peptide bond?

Oligopeptides: 10 or less; Polypeptides: 50 or less; Proteins: More than 50 amino acids.

Q1. What are oligopeptides, polypeptides, and proteins?
 How many levels of protein structure exist?
There are several levels of protein structure
There are four levels of protein structure: Primary, secondary, tertiary, quaternary. 

Secondary structure: Within the long protein chains there are regions in which the chains
are organized into regular structures known as alpha-helices (alpha-helixes) and beta-
pleated sheets. These are the secondary structures in proteins. These secondary structures
are held together by hydrogen bonds.
Tertiary structure: The overall three dimensional arrangement of all atoms in a protein is
referred to as the protein’s tertiary structure.
Quaternary structure: Protein quaternary structure is the number and arrangement of
multiple folded protein subunits in a multi-subunit complex.
Q1. Explain the four levels of protein structure.
Primary structure of protein: It is simply the
sequence of amino acids in a polypeptide chain
 Protein secondary structure
α helix & β sheets are examples of secondary structures

Q1. What kind of bonding stabilizes both α helix and β sheet in proteins?
 α helix & β sheets are examples of secondary structures

• In an α helix, the carbonyl (C=O) of • In a β pleated sheet, two or

one amino acid is hydrogen bonded more segments of a
to the amino H (N-H) of an amino
acid that is four down the chain. polypeptide chain line up next
• This pattern of bonding pulls the to each other.
polypeptide chain into a helical • This pattern forms a sheet-like
structure that resembles a curled structure held together by
ribbon, with each turn of the helix
containing 3.6 amino acids.
hydrogen bonds.
• The R groups of the amino acids • The hydrogen bonds form
stick outward from the α helix, between carbonyl and amino
where they are free to interact. groups of backbone, while the
R groups extend above and
below the plane of the sheet.
Tertiary structure Quaternary structure

• Many proteins are made up of a

• The overall three-
single polypeptide chain and
dimensional structure of a have only three levels of
polypeptide is called structure.
its tertiary structure. • However, some proteins are
• The tertiary structure is made up of multiple polypeptide
primarily due to chains, also known as subunits.
• When these subunits come
interactions between the R
together, they give the protein
groups of the amino acids its quaternary structure.
that make up the protein.
 The different
types of
structures of
proteins

Image modified from OpenStax Biology's modification of

work by the National Human Genome Research Institute.
 Proteins
Domains
Domain: A part of a polypeptide chain with a folded structure that does not depend for its
stability on any of the remaining parts of the protein.

http://slideplayer.com/slide/8430672/

Q1. What is domain of a protein?

No question in exam on the images of this slide.
 Proteins
Examples of principal classes of fold
Protein with α helix: Myoglobin.
Protein with β strand: The variable region of an immunoglobulin (antibody).
Protein with mixed α helix and β strand domains: Small GTPase, Ras.

Some proteins contain small domains with very little secondary structure.
Q1. Give an example of protein with (i) α helix, (ii) β strand, (iii)
both α helix and β strand.
No question in the exam about the images on this slide.
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