Introduction to Proteins:

The Primary Level of Protein

Structure

Chapter 5
 Overview of
protein
biosynthesis
 DNA is transcribed to
form mRNA in the
nucleus
 mRNA is exported to the
cytoplasm
 mRNA is translated into
a linear sequence of
amino acids that folds
into a three-dimensional
structure
 Proteins
• Make up about 15% of the cell
• Have many functions in the cell
– Enzymes
– Structural
– Transport
– Motor
– Storage
– Signaling
– Receptors
– Gene regulation
– Special functions
• Amino acids are the building blocks of proteins,
which have structural and functional properties in
our bodies.

• Proteins function as follows:

– They transport oxygen in the blood.
– They are the primary components of skin and
muscle.
– They work as defense mechanisms against
infection.
– They serve as biological catalysts called
enzymes.
– They also control the metabolism of hormones.
• Proteins are polymers of amino acids
covalently bonded in specific sequences.

• There are 20 commonly occurring amino acids

that make up proteins, and the order of amino
acids in proteins determines its structure and
biological function.

• When amino acids are covalently linked to one

another, this chain can twist and fold to form
a unique three-dimensional structure that has
a specific function.
Amino Acid Structure

• Amino acids contain two functional groups, a

protonated amine and carboxylic acid in the
form of a carboxylate group.

• These functional groups are bonded to a

central carbon atom known as the alpha ()
carbon, and are referred to as alpha amino
acids.
• The  carbon is also bonded to a hydrogen
atom and a larger side chain. The side chain is
unique for each amino acid.

• The  carbon on all amino acids, except

glycine, is a chiral carbon because it has four
different groups bonded to it.
• An amino acid, with a chiral center, has two
forms called enantiomers, which are
nonsuperimposable mirror images.

• When drawing the Fischer projection, the

carboxylate group is at the top of the
structure and the side chain (R group) is at
the bottom.

• The protonated amine group can be on the

left-hand side (L form) or right-hand side (D
form) of the structure.
The L-amino acids are the building blocks for
proteins. Some D-amino acids occur in nature, but
not in proteins.
• The R group gives each amino acid its unique
identity and characteristics.
• Twenty amino acids are found in most proteins.
• There are nine different families of organic
compounds represented in the structures of
different amino acids. They are as follows:
1. Alkanes
2. Aromatics
3. Thioethers
4. Alcohols
5. Phenols
6. Thiols
7. Amides
8. Carboxylic acids
9. Amines
• The functional groups divide the amino
acids into the following four
categories:
1. Nonpolar, consisting of ten amino
acids
2. Polar, consisting of five amino
acids
3. Acidic, consisting of two amino
acids
4. Basic, consisting of three amino
acids
Amino Acids Classified as Nonpolar

• Side chains consists entirely of carbon and

hydrogen.

• Carbon–hydrogen bond is nonpolar.

• Compounds composed of only carbon and

hydrogen are nonpolar and hydrophobic.
The structure of the amino acids, including side
chains, names, functional groups, and
abbreviations are shown in the next few slides.
Amino Acids Classified as Polar
• Contain functional groups, such as hydroxyl
(–OH) and amide (–CONH2).
• Side chains can form hydrogen bonds with
water.
• Side chains are hydrophilic.
• An exception is cysteine, which does not
form hydrogen bonds.
• Polar acidic and basic amino acids have
charged side chains that can form ion–
dipole interactions with water. These amino
acids are more polar than those classified
as polar neutral.
• There are 10 amino acids that are essential
amino acids because they cannot be
synthesized in the human body and must be
obtained in the diet.
• The 10 essential amino acids are: valine,
leucine, isoleucine, phenylalanine, methionine,
tryptophan, threonine, histidine, lysine, and
arginine.

• Two of these amino acids, arginine and

histidine, are essential in children, but not
adults.

• Nonessential amino acids can be synthesized

in the body from essential amino acids.
• Proteins that contain all the essential amino
acids are called complete proteins.

• Soybeans and most proteins found in animal

products are complete proteins.

• Some plant proteins are incomplete proteins

because they lack one or more essential amino
acid.

• Complete proteins can be obtained by

combining foods like rice and beans.
 Protein Formation
• When two amino acids condense, a dipeptide
is formed.

• The carboxylate ion (–COO-) of one amino acid

reacts with the protonated amine (–NH3+) of a
second amino acid.

• A water molecule is lost and an amide

functional group is formed. An amide bond is
formed between the two amino acids.
When amino acids combine in a condensation
reaction, the amide bond that is formed between
them is called a peptide bond.
 Peptide bond cleavage

• Peptides are stable unless strong acid or a catalyst is present

• 6N HCl at high temperature will degrade proteins to free amino
acids
• Proteases: enzymes that cleave specific peptide bonds
• Cyanogen bromide (CNBr) Cleaves proteins specifically at
methionyl residues
• Formerly, protein amino acid sequences were determined by
selective cleavage followed by separation and sequence analysis
of individual proteins. Each peptide could have its amino acid
sequence determined by stepwise release of amino acids in the
Edman degradation
• The product formed during the condensation
of alanine and valine is known as a dipeptide,
which is represented as Ala—Val or AV.

• In this dipeptide, alanine is called the

N-terminus because it has an unreacted
-amino group.

• Valine is called the C-terminus because it has

an unreacted -carboxylate group.
• Structures are always written from N-
terminus to C-terminus.

• Two amino acids can combine in two ways

forming two different dipeptides.

• The two dipeptides formed from condensation

of Ala and Val are Ala—Val and Val—Ala. They
are structural isomers, different compounds,
and have different properties.
Peptides formed in the condensation of three
amino acids are known as tripeptides; ones
with four amino acids are tetrapeptides; ones
with five amino acids are pentapeptides; etc.
• A polypeptide is a compound that is formed when
the number of amino acids increases.

• A biologically active polypeptide consisting of 50

or more amino acids is referred to as a protein.
Proteins are made by controlled polymerization
of amino acids
water is eliminated

O O

two amino acids H2N CH C OH H2N CH C OH

condense to form...
R1 R2

N or amino C or carboxy
terminus O O terminus

...a dipeptide. If H2N CH C NH CH C OH + HOH

there are more it
becomes a polypeptide. R1 R2
Short polypeptide chains
are usually called peptides
while longer ones are called peptide bond is formed
proteins.
residue 1 residue 2
 “Peptides”
• Short polymers of amino acids
• Each unit is called a residue
• 2 residues - dipeptide
• 3 residues - tripeptide
• 12-20 residues - oligopeptide
• many - polypeptide
 “Protein”
One or more polypeptide chains
• One polypeptide chain - a monomeric protein
• More than one - multimeric protein
• Homomultimer - one kind of chain
• Heteromultimer - two or more different chains
• Hemoglobin, for example, is a heterotetramer
• It has two alpha chains and two beta chains
Polypeptides as polyampholytes
(substance whose groups have both acidic
and basic groups) they have many weakly
acidic and basic groups even a small shift
in pH can significantly affect the
structure and interactions of a protein
molecule
 The pKa of a side chain is influenced by
its environment
 Unperturbed, the pKa
of glutamic acid is 4.2
 In proximity to a
negative charge, the
pKa of the glutamic acid
is raised
 In proximity to a
positive charge, the pKa
of glutamic acid is
lowered
 Peptides and proteins as polyampholytes

As pH increases the overall charge on a peptide will become more negative.

As pH decreases the overall charge on a peptide will become more positive.

 The amino acid
sequences of human
and whale
myoglobin
 Conservative mutations
conserve the chemical property
(e.g. charge) and/or the size of
the amino acid, while
nonconservative mutations
involve larger differences in
polarity/size
 Evolutionary relationships are
inferred from protein amino
acid sequences
 Protein sequence analysis can be
complicated by multiple chains
 Insulin has two chains linked by disulfide bonds

 Protein amino acid sequence analysis by DNA sequencing of the

gene is rapid and inexpensive, but does not identify post-
translational modifications, so a combination of approaches must
be used
 Biosynthesis of insulin involves a variety of post-translational
modifications
 Flow of genetic information

• Central Dogma: DNA  RNA  protein

– Transcription: DNA  RNA
– Translation: RNA  protein
• Ribosome = site of translation
The Genetic Code

For each gene, one

DNA strand is the
template strand

mRNA (5’  3’)

complementary to
template

mRNA triplets
(codons) code for
amino acids in
polypeptide chain
The Genetic Code

64 different codon
combinations
Redundancy: 1+ codons
code for each of 20
AAs
Reading frame: groups
of 3 must be read in
correct groupings
This code is universal:
all life forms use the
same code.
The Genetic Code
DNA RNA Protein
 BLAST alignment of human myoglobin and
hemoglobin α chain

Amino acid sequence comparisons help establish evolutionary relationships, but can also
predict the biological function of an unknown protein when compared against the sequence
of a known protein.
One protocol for comparison is the Basic Local Alignment Search Tool (BLAST), used
here to compare human myoglobin with human hemoglobin α chain. BLAST searches for
maximum sequence identity. 25% identity means proteins probably possess similar
functions.
 Multiple sequence alignments can be used to
probe evolutionary relationships

 Alignment of cytochrome c sequences, a mitochondrial respiratory protein,

from 27 organisms

 Hydrophobic a.a., gray; basic, blue; acidic, red; polar uncharged, green (except
Asn and Gln, magenta)

 The more similar two homologous protein sequences are, the more closely
they are related evolutionarily