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 Proteins

A macromolecule that consists of one or more

polypeptide chains folded and coiled into specific
conformations
Made up of various 20 amino acids
Vary widely in structure and function
Abundant about 50% of cellular dry weight

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What do proteins do?
off

on

Regulation Movement

proteins B

Signaling Catalysis

Immune Transport
Enzymatic proteins Defensive proteins
Function: Selective acceleration of chemical reactions Function: Protection against disease
Example: Digestive enzymes catalyze the hydrolysis Example: Antibodies inactivate and help destroy
of bonds in food molecules. viruses and bacteria.

Antibodies

Enzyme Virus Bacterium

Storage proteins Transport proteins

Function: Storage of amino acids
Examples: Casein, the protein of milk, is the major
source of amino acids for baby mammals. Plants have
storage proteins in their seeds. Ovalbumin is the
protein of egg white, used as an amino acid source
for the developing embryo.
Function: Transport of substances
Examples: Hemoglobin, the iron-containing protein of
vertebrate blood, transports oxygen from the lungs to
other parts of the body. Other proteins transport
molecules across cell membranes.
Transport
protein

Ovalbumin Amino acids

for embryo Cell membrane
Hormonal proteins
Function: Coordination of an organisms activities
Example: Insulin, a hormone secreted by the
pancreas, causes other tissues to take up glucose,
thus regulating blood sugar concentration
Receptor proteins
Function: Response of cell to chemical stimuli
Example: Receptors built into the membrane of a
nerve cell detect signaling molecules released by
other nerve cells.

Receptor
Signaling protein
Insulin
High secreted Normal molecules
blood sugar blood sugar

Contractile and motor proteins Structural proteins

Function: Movement
Examples: Motor proteins are responsible for the
undulations of cilia and flagella. Actin and myosin
proteins are responsible for the contraction of
muscles.
Function: Support
Examples: Keratin is the protein of hair, horns,
feathers, and other skin appendages. Insects and
spiders use silk fibers to make their cocoons and webs,
respectively. Collagen and elastin proteins provide a
fibrous framework in animal connective tissues.

Actin Myosin
Collagen

Muscle tissue Connective

100 m tissue 60 m
Key Points
General structure of -amino acids
Chiral, D- and L-forms of AAs
The Classification of Amino Acids
Nonpolar, uncharged polar, aromatic, acidic and basic amino
acids
Essential amino acids
Zwitterion, pI
Characteristics of the peptide bond
Glutathione (GSH): structure and function
 1. General structure of -amino acids
Basic unit of protein
carboxyl group

amino group
Different side chains, R,
determin the properties
of 20 amino acids.

side chain
(or R group, R=Remainder of the molecule)
 Types of Amino Acids

Amino acids are classified as

Nonpolar (hydrophobic) with hydrocarbon side chains.
Polar (hydrophilic) with polar or ionic side chains.
Acidic (hydrophilic) with acidic side chains.
Basic (hydrophilic) with NH2 side chains.
 1.Nonpolar (hydrophobic) with hydrocarbon side chains.
(nineinall)

Each of these amino acids has a side chain that does not
Imino acid- Proline bind or give off protons or participates in hydrogen or ionic
bonds
2.Polar (hydrophilic) with polar or ionic side chains.
(sixinall)

These amino acids are

uncharged at neutral pH,
although the side chains of
cysteine and Tyrosine can lose
a proton at an alkaline pH
.
Serine , Threonine and Tyrosine
each contains a polar hydroxyl
group that can participate in
hydrogen bond formation.

Aromatic amino acids-

Phenyl alanine and tyrosine
3.Acidic (hydrophilic) with acidic side chains
Amino acids with a negatively charged
side-chain:
The acidic amino acids- Glutamic
acid and Aspartic acid
They are hydrophilic in nature.
4.Basic (hydrophilic) with NH2 side chains
Amino acids
with a
positively
charged side-
chain:

Heterocyclic Amino Acids: Tryptophan and Histidine

Classification based on Physical
Properties
Amino acid abbreviations

Biochemistry For Medics 14

 Non standard amino acids
Of the over 300 naturally occurring amino acids, 20
constitute the monomer units of proteins
These 20 amino acids are called the Primary or Standard
amino acids.
Aside from the 20 standard amino acids, there
are many other amino acids that are called non-
proteinogenic or non-standard.
Seleno cysteine is the 21st Amino Acid
The other are Pyroglutamate and Pyrolysine.
Modified Amino Acids in Proteins
Many amino acids are modified
after the chain is synthesized.
Hydroxyproline is made from
proline, and the responsible
enzyme is dependent upon
vitamin C.
Hydroxyproline and hydroxy
lysine They are found in few
connective tissue proteins such as
collagen
-carboxyglutamate is
synthesized from glutamate,
and requires vitamin K.
Additionally amino acids may have
sugars, or phosphates attached.
 Biologically Active Amino Acid
Derivatives

Thyroxine is different from

tyrosine in having an extra
iodine containing aromatic
group on the side chain
It is found only in the thyroid
gland
 Proteins are linear polymers of
amino acids
R1 R2
NH3 C COO NH3 C COO

H H A carboxylic acid
H2 O condenses with an
H2 O
amino group with the
R1 R2 R3 release of a water

NH3 C CO NH C CO NH C CO
Peptide Peptide
H H H
bond bond
The amino acid
F T D sequence is called
A G N S K A
G S as primary structure
Structure of Proteins

=>
19
 Special groups in amino acids
Arginine- Guanidinium group
Phenyl Alanine- Benzene group
Tyrosine- Phenol group
Tryptophan- Indole group
Histidine- Imidazole group
Proline- Pyrrolidine
Proline has a secondary amino group, hence it is
an imino acid.

7/5/2012 Biochemistry For Medics 20

 Ionization ofAminoAcids

In most body fluids the carboxylic group (COOH) and the

amino group (NH2) are ionized.
R R
amino acid that has a positive
An ionized + and negative charge
is aHdipolar
2NC ionCOOH H3NC COO
called a zwitterion.

H H
Zwitterion (ionized form)

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 Isoelectric point
Amino acids can exist as ampholytes or zwitterions in solution,
depending upon pH of the medium.
The pH at which the amino acids exist as zwitterions, with no net
charge on them is called Isoelectric pH or Isoelectric point.
In acidic medium, the amino acids exist as cations
In alkaline medium , they exist as anions.

Due to no net charge, there is no

electrophoretic mobility at
Isoelectric pH.
Solubility and buffering capacity are
also minimum at Isoelectric pH
22
Structure of glycine at differing pH values
Amphoteric

Isoelectric point
AAs in solution at certain pH are
predominantly in dipolar form, fully
ionized but without net charge due to
-COO- and -NH3+ groups.
This characteristic pH is called isoelectric
point, designated as pI.
pI is determined by pK, the ionization
constant of the ionizable groups.
Table 3.2 (Part 1)

The side groups of

amino acids
determine folding of
polypeptide
 Side chains of amino
acids:
show a wide variety of chemical
properties

are important to determine the:

of the protein
3D structure
function
 hydrophi hydropho
lic amino bic amino
acids acids

Where do you expect these types of

amino acids to be placed in the ion
channel spanning the plasma
membrane?
WHY hydroph
ilic
?
amino
acidshydropho
bic amino
acids

Ions (black) can only pass through the pore

of the ion channel because this is the only
part with hydrophilic amino acids lining the
pore (green = area of ion channel with
hydrophilic water-loving amino acids).
The rest of the ion channel mostly
consists of hydrophobic amino acids
ORDER of the side chains of
amino acids in a protein :

determines how it folds into a

three dimensional configuration
 From amino acids to
proteins
two amino acids dipeptide
three amino acids tripeptide
more than 50 amino polypeptide
acids
6 000-1000 000 protein
Physical and Chemical
Properties of Proteins
Amphoteric property
Side-chains of a protein have many ionizable groups,
making the protein either positively or negatively
charged in response to the pH of the solution.
The pH at which the protein has zero net-charge is
referred to as isoelectric point (pI).
Isoelectric point (pI):
Isoelectric point is the pH of a solution at which the net charge
of protein is zero. In electrophoresis there is no motion of the
particles in an electric field at the isoelectric point.
NH3+ NH2
NH3+
COOH
COO-
COO-
NH3+ NH2
NH3+
COOH
COO-
COO-
pH < pI pH > pI
Positive charge pH = pI
Negative charge

2
Isoelectric point
Net charge

0
2 3 4 5 6 7 8 9 10 11
-1

-2
pH
-3
Physical and Chemical
Properties of Proteins
 Amphoteric
Isoelectric point
AAs in solution at certain pH are predominantly in
dipolar form, fully ionized but without net
charge due to -COO- and -NH3+ groups.
This characteristic pH is called isoelectric point,
designated as pI.
pI is determined by pK, the ionization constant of
the ionizable groups.
 Amphoteric property
Side-chains of a protein have many ionizable groups,
making the protein either positively or negatively
charged in response to the pH of the solution.
The pH at which the protein has zero net-charge is
referred to as isoelectric point (pI).
Isoelectric point (pI):
Isoelectric point is the pH of a solution at which the net charge
of protein is zero. In electrophoresis there is no motion of the
particles in an electric field at the isoelectric point.
NH3+ NH2
NH3+
COOH
COO-
COO-
NH3+ NH2
NH3+
COOH
COO-
COO-
pH < pI pH > pI
Positive charge pH = pI
Negative charge

2
Isoelectric point
Net charge

0
2 3 4 5 6 7 8 9 10 11
-1

-2
pH
-3
 COOH COO- COO-
+ OH- + OH-
P P P
+ H+ +
+ H+
NH3+ NH3 NH2

cation amphoteric anion

pH < pI pH = pI pH > pI

pI of most protein is ~ 5.0, and negatively charges in

body fluid (pH7.4)
pI > 7.4: basic proteins: protamine, histone
pI < 7.4: acidic proteins: pepsin
pH > pI
pH = pI

pH < pI