Download BioN03 Amino acids, peptides, proteins Summer 2015

Amino acids, peptides, and
proteins
Dr. Mamoun Ahram
Nursing
Summer semester, 2015
General structure
Proteins are polymers of α-amino
acids (or amino acids).
An amino acid consists of
a central carbon atom, called the 
carbon, linked to four groups
an amino group (-NH2),
a carboxylic acid group (-COOH),
a hydrogen atom, and
a specific R group (the side chain)
L and D isomers
With four different groups connected to the tetrahedral αcarbon atom, amino acids can be present in two forms that are
mirror-images of each other (they are enantiomers).
They are called L isomer and D isomer.
Amino acids with their two isomers are said to be chiral (when a
central carbon is bonded to four different groups).
The presence of one chiral carbon atom always produces a chiral
molecule that exists in mirror-image forms.
Only L amino acids naturally
make up proteins.
Types of amino acids
There are twenty kinds of amino acids depending on
the side chains varying in:
size
Shape
Charge
hydrogen-bonding capacity
hydrophobic character
chemical reactivity
Non-polar, aliphatic
Polar
Positivelycharged
Negativelycharged
Glycine
Phenylalanine
Serine
Lysine
Glutamate
Alanine
Tryptophan
Threoeine
Arginine
Aspartate
Valine
Glutamine
Histidine
Leucine
Asparagine
Isoleucine
Cysteine
Methionine
Tyrosine
Proline
Non-polar, aliphatic amino
acids
Glycine
The simplest one is
glycine, which has just a
hydrogen atom as its
side chain.
With two hydrogen
atoms bonded to the carbon atom, glycine is
unique in being achiral
(not chiral).
Alanine
Alanine, the next simplest amino acid, has a methyl
group (-CH3) as its side chain.
Valine, leucine, and isoleucine
Larger hydrocarbon side chains are found in valine,
leucine, and isoleucine.
Methionine
Methionine contains an aliphatic side chain that
includes a thioether (-S-) group.
Thioether
Ether
Proline
Proline also has an aliphatic
side chain, but is bonded to
both the nitrogen and the carbon atoms.
The ring structure of proline
makes it more rigid than the
other amino acids.
-nitrogen
Phenylalanine and Tryptophan
Phenylalanine contains a phenyl ring.
Tryptophan has an indole ring; the indole group
consists of two fused rings and an NH group.
Positively-charged amino
acids
Lysine and arginine
Lysine and arginine have
relatively long side chains
that terminate with
groups that are positively
charged at neutral pH.
Lysine ends with a
primary amino group and
arginine by a guanidinium
group.
Histidine
Histidine contains an imidazole group, an aromatic ring
that also can be positively charged.
Negatively-charged amino
acids
Aspartic acid and glutamic acid
Two amino acids contain
acidic side chains:
aspartic acid and
glutamic acid.
These amino acids are
often called aspartate
and glutamate when
they are charged.
Polar amino acids
serine and threonine
Serine and threonine, contain aliphatic hydroxyl
groups.
The hydroxyl groups on serine and threonine make
them hydrophilic and reactive.
Cysteine
Cysteine contains a sulfhydryl or thiol (-SH), group. The
sulfhydryl group is reactive.
Asparagine and glutamine
Asparagine and glutamine
are uncharged derivatives
of aspartate and glutamate.
Each contains a terminal
carboxamide in place of a
carboxylic acid.
carboxamide
Tyrosine
The aromatic ring of
tyrosine contains a
hydroxyl group. This
hydroxyl group is reactive.
Amino acids are
often designated
by either a threeletter abbreviation.
Amino acid
Three-letter abbreviation
Alanine
Ala
Arginine
Arg
Asparagine
Asn
Aspartic Acid
Asp
Cysteine
Cys
Glutamine
Gln
Glutamic Acid
Glu
Glycine
Gly
Histidine
His
Isoleucine
Ile
Leucine
Leu
Lysine
Lys
Methionine
Met
Phenylalanine
Phe
Proline
Pro
Serine
Ser
Threonine
Thr
Tryptophan
Trp
Tyrosine
Tyr
Valine
Val
Ionization of amino acids
Why do amino acids get ionized?
Amino acids can become ionized since the carboxyl group and
amino group can become protonated (gain a proton) and
unprotonated (lose a proton).
Therefore, they can act as acids or bases. Such molecules are
said to be amphoteric.
Effect of pH
The ionization state of an amino acid varies with pH since each group
has its own pKa.
Amino acids at physiological pH (pH 7.4) exist as dipolar ions where
the carboxyl group is unprotonated (-COO-) and the amino group is
protonated (-NH3+).
In acid solution (e.g., pH 1), the amino group is protonated (-NH3+)
and the carboxyl group is not (-COOH).
As the pH is raised, the carboxylic acid gives up a proton.
The dipolar form persists until the pH approaches 9, when the
protonated amino group loses a proton.
Zwitterion and isoelectric point
Even though this amino acid is charged, it is electrically
neutral.
Such a molecule with two opposite charges and a net
charge of zero is termed a zwitterion.
The pH where the net charge of a molecules such as an
amino acid or protein is zero is known as isoelectric
point or pI.
Ionization of side chains
Nine of the 20 amino acids have ionizable side chains.
These amino acids are tyrosine, cysteine, arginine,
lysine, histidine, serine, threonine, aspartic and
glutamic acids.
Each side chain has its own pKa values for ionization of
the side chains.
At neutral pH
aspartic acid and glutamic acid are negatively charged.
Arginine and lysine are positively charged.
Histidine
An important amino acid in the function of many
proteins and enzymes in terms of its pKa is histidine.
With a pKa value near 6, the imidazole group can be
uncharged or positively charged near neutral pH.
Glutamate (same for Asp)
Total
charges: +1
pH < 2
0
pH = 3
-1
pH > 4
-2
pH > 10
Lysine (similar to arginine)
Total +2
charges:
pH < 2
+1
pH > 3
0
-1
pH > 10
pH > 11
Note
You need to know the names of amino acids, the
special structural features of amino acids, their
abbreviations or designations, the pKa of groups (not
exact numbers, but which ones are acidic, basic, or
near neutral).
Essential amino acids
There are nine amino acids that are essential.
Essential nutrients are those not made by the human
body in significant amounts and must be derived from
diet
These are: Histidine, Isoleucine, Leucine, Lysine,
Methionine, Phenylalanine, Threonine, Tryptophan,
and Valine.
The other 11 amino acids are non-essential amino
acids.
Four Levels of Protein structure
The primary structure of a protein is the sequence of amino
acid residues that constitute the polypeptide chain.
Secondary structure refers to the localized organization of
parts of a polypeptide chain.
Tertiary structure refers to the three-dimensional structure
of a polypeptide chain, that is, the three-dimensional
arrangement of all the amino acids residues.
Some proteins are made of multiple polypeptides
crosslinked (connected) with each other. These are known
as multimeric proteins.
Quaternary structure describes the number and relative
positions of the subunits in a multimeric protein.
Peptide bond
Proteins are linear polymers formed by covalently
linking the α-carboxyl group of one amino acid to the
α-amino group of another amino acid with a peptide
bond (also called an amide bond).
A condensation reaction
The formation of a dipeptide from two amino acids is
accompanied by the loss of a water molecule in a
condensation reaction that is energetically
unfavorable.
Definitions
The short chain of amino acids is known as an
oligopeptides or just peptide.
Each amino acid unit in a polypeptide is called a
residue Longer peptides are referred to as
polypeptides.
Peptides generally contain fewer than 20-30 amino
acid residues, whereas polypeptides contain as many
as 4000 residues.
Polypeptide chains that have organized threedimensional structures are referred to as proteins .
Directionality of reading
A polypeptide chain has polarity because its ends are different,
with an α-amino group at one end and an α-carboxyl group at
the other.
The amino end is the beginning of a polypeptide chain.
Backbone and side chains
A polypeptide chain consists of a regularly repeating
part, called the main chain or backbone, and a variable
part, comprising the distinctive side chains.
Features of the backbone
The backbone is made of the α-amide N, the α C, and the α
carbonyl C atoms.
The polypeptide backbone is rich in hydrogen-bonding (an
exception is proline, which has an NH group, but not C=O).
It has a zig-zag structure and is planar.
It has a double bond character rigid, and charged.
Importance of peptide bond
The primary structure of a protein determines the
other levels of structure.
A single amino acid substitution can give rise to a
malfunctioning protein, as is the case with sickle-cell
anemia.
Sickle cell hemoglobin (HbS)
It is caused by a change of amino
acids in the 6th position of 
globin (Glu to Val).
The mutation results in: 1) arrays
of aggregates of hemoglobin
molecules, 2) deformation of the
red blood cell, and 3) clotting in
blood vessels and tissues.
How is protein structure determined?
The folding of a protein chain is determined by many different sets of
weak noncovalent bonds that form between one part of the chain and
another.
These involve atoms in the polypeptide backbone, but mainly by atoms in
the amino acid side chains.
Hydrogen bonds
Polypeptides contain numerous proton donors and
acceptors both in their backbone and in the R-groups
of the amino acids.
Electrostatic interactions
These include charge-charge interactions between
oppositely charged R-groups of amino acids such as
lysine or arginine and aspartic acid or glutamic acid.
These are also known as salt bridges.
van der Waals attractions
Although van der Waals forces are extremely weak, it is
the huge number of such interactions that occur in
large protein molecules that make them significant to
the folding of proteins.
hydrophobic interactions
A system is more stable when hydrophobic groups are
clustered together rather than extended into the
aqueous surroundings.
Very important
The nonpolar (hydrophobic) side chains in a protein belonging to such
amino acids as phenylalanine, leucine, valine, and tryptophan, tend to
cluster in the interior of the molecule. This enables them to avoid
contact with the water that surrounds them inside a cell.
Charged and polar side chains tend to arrange themselves near the
outside of the molecule, where they can form hydrogen bonds and
electrostatic interactions with water and with other molecules.
Disulfide bonds
Tertiary structure is stabilized by the formation of
disulfide bonds between cysteine residues.
The side chain of cysteine contains a reactive sulfhydryl
group (—SH), which can oxidize to form a disulfide
bond (—S—S—) to a second cysteine.
The crosslinking of two cysteines to form a new amino
acid, called cystine.
Insulin (an example)
Importance of amino acid sequence?
Certain sequence or order of amino acids within a
small region of protein are organized in specific shapes
These conformations are determined by the primary
sequence of the amino acids.
Polypeptide chains can fold into regular structures such
as:
the alpha helix
the beta sheet
Loops
Turns
The  helix
It looks like a helical rod.
The  helix is stabilized by hydrogen
bonds between the NH and CO
groups spaced four residues apart of
the backbone.
The hydrogen bonds lie vertically
along the helix, and the R groups
extend to the outside of the coil.
β pleated sheet (β sheet)
These is composed of two or more straight chains (β strands).
The sheet is stabilized by hydrogen bonds between the strands.
the R groups extending above and below the sheet.
What is tertiary structure?
Proteins with their secondary structures can folds into threedimensional structures.
Tertiary structure, therefore, refers to the overall conformation
of a polypeptide chain, that is, the three-dimensional
arrangement of all the amino acids residues.
What is it?
Some proteins exhibit a fourth level of structural
organization where proteins are composed of more
than one polypeptide chain.
This is the quaternary structure of proteins. Each
polypeptide chain in such a protein is called a subunit.
Quaternary structure, thus, refers to the spatial
arrangement of multiple subunits of a protein and the
nature of their interactions.
Sometimes subunits are disulfide-bonded together,
other times, noncovalent bonds stabilize interactions
between subunit.
More on naming
The simplest sort of quaternary structure is a dimer,
consisting of two subunits:
If these two subunits are the same, the protein is said
to be made of a homodimer
If the subunits are different, then it is a heterodimer
Proteins made of three subunits are trimers, and of
four subunits are tetramers, and soon on.
Simple proteins
These are proteins that are made of only amino acids.
Other proteins are complex made of amino acids plus nonamino acid groups such as sugars, lipids, metals, phosphate
group, nucleic acids, and organic groups.
Glycoproteins
Proteins that are covalently conjugated with
carbohydrates
Lipoproteins
Proteins can also be associated with lipid and are termed
lipoproteins
Phosphoproteins
Other proteins are phsophorylated and these are known
as phosphoproteins
Metalloproteins
These have a metal group associated to it
Hemoproteins
Proteins with a heme group (organic group)
Nucleoproteins
Proteins with RNA associated to them
Native protein
Each protein molecule folds in a distinctive manner
that is determined by its primary structure and results
in its maximum stability.
A protein with the shape in which it functions in living
systems is known as a native protein.
Ribonuclease is classified as a simple protein because
it is of one polypeptide.
Myoglobin is a conjugated monomeric protein that is
composed of one polypeptide and a nonprotein group.
Hemoglobin is a conjugated protein with a quaternary
structure.
Classes of proteins
Fibrous proteins
Made predominantly of a secondary structure
Structural proteins
Tough, insoluble proteins
Hair, fingernails, wool, silk
Examples: Collagen, keratins, elastins
Globular proteins
Made of multiple secondary structures
Compact, globe-like, water-soluble proteins
Hydrophilic exterior, hydrophobic interior
Multiple functions
Common Fibrous and Globular Proteins
Biological Functions of Proteins
Enzymes--catalysts for reactions
Transport molecules--hemoglobin; lipoproteins,
channel proteins
Contractile/motion--myosin; actin
Structural--collagen; keratin, actin
Defense--antibodies
Signaling—hormones, receptors
Toxins--diphtheria; enterotoxins
Collagen
The collagens are a family of fibrous proteins found in all
multicellular animals.
They are the most abundant proteins in mammals, constituting
25% of the total protein mass in these animals.
It is present in tissues such as skin, bones, blood vessels,
tendons, and other connective tissues.
Overall function
The main function of collagen molecules is to provide
structural support to tissues.
Therefore, the primary feature of a typical collagen
molecule is its stiffness.
Structure
It is a left-handed triple-stranded helical protein, in which three
collagen polypeptide chains, called  chains, are wound around one
another in a ropelike superhelix.
This basic unit of collagen is called tropocollagen, which consists of
three interwined chains.
Tropocollagen assembles into larger fibers quaternary structure).
Composition of collagens
Collagens are extremely
rich in glycine (33% of all
amino acids in collagen)
and proline (13%).
It also contains 4hydroxyproline (9%).
Functional purpose of amino acids
Glycine allows the three helical a chains to pack tightly
together to form the final collagen superhelix because
it is small.
Proline makes the structure rigid and creates the
helical conformation in each  chain.
Hydroxyproline stabilizes the structure via formation of
hydrogen bonds among them.
Every third residue is glycine, which, with the
preceding residue being proline or hydroxyproline in a
repetitive fashion as follows:
Gly-pro-Y
Gly-X-hydroxyproline
Scurvy
Scurvy is a disease is caused by a
dietary deficiency of ascorbic
acid (vitamin C).
Deficiency of vitamin C prevents
proline hydroxylation.
The defective pro-α chains fail to
form a stable triple helix and are
immediately degraded within the
cell.
Blood vessels become extremely
fragile and teeth become loose
in their sockets.
Myoglobin and hemoglobin
The main function of myoglobin is storage of O2 in
muscles for use in case of oxygen deprivation.
The main function of hemoglobin is transport of O2
and CO2 and blood buffering.
Both proteins contain a
heme group (conjugated or
complex proteins).
The molecule has iron in its
center.
Iron binds to oxygen.
Myoglobin
Myoglobin is a monomeric heme
protein found mainly in muscle
tissue where it serves as an
intracellular storage site for oxygen.
It can be present in two forms:
oxymyoglobin when it carries
oxygen and deoxymyoglobin when
it is free of oxygen.
During periods of oxygen
deprivation, oxymyoglobin releases
its bound oxygen.
Tertiary structure of myoglobin
The tertiary structure of
myoglobin is unusual in that it
contains a high proportion of
α-helical secondary structure.
A myoglobin polypeptide is
comprised of 8 α-helices that
are connected by short nonhelical regions.
Hemoglobin structure
Hemoglobin is tetrameric hemeprotein (conjugated
protein).
It is made of four protein chains known as globins.
In adults, the four globin proteins are of two different
types known as α and β.
So a hemoglobin protein is an α2β2 globin protein.
The α and β chains contain multiple α-helices where α
contains 7 α-helices and β contains 8 α-helices (similar
to myoglobin).
Each chain has a heme group, so it can carry four
oxygen molecules.
Function of hemoglobin
Hemoglobin is found in red blood cells where it is
responsible for binding oxygen in the lung and
transporting the bound oxygen throughout the body.
It can then carry CO2 from tissues to lungs for its
release.
Denaturation
Denaturation is the disruption of the native
conformation of a protein, the characteristic threedimensional structure that it attains after synthesis,
with no effect on the primary structure of the protein.
Denaturation involves the breaking of the noncovalent
bonds, which determine the structure of a protein.
Denaturing agents
Heat disrupts low energy van der Waals forces in proteins.
Extremes of pH change the charge of the protein’s amino acid
side chains and result in the disruption of electrostatic and
hydrogen bonds.
Detergents disrupt the hydrophobic forces which fold proteins
Inorganic salts disrupt salt bridges.
Organic compounds such as ethanol and acetone disrupt
hydrogen bondings (disinfectants).
Mechanical agitation such as beating an egg.
Renaturation
Renaturation is the process in
which the native conformation
of a protein is re-acquired.
For many proteins, especially
small ones, renaturation can
occur quickly and
spontaneously and disulfide
bonds are formed correctly.
Electrophoresis
A molecule with a net charge will move in an electric
field according to its charge.
Proteins with positive charges more than negative
charges will move towards the cathode
Proteins with negative charges more than positive
charges will move towards the anode
This phenomenon is termed electrophoresis.
Once proteins move, they can stained (colored) with a
dye to visualize them.
The roles of pI and pH
In gel electrophoresis, proteins are separated as they
move through a gel in a medium with a specific pH.
When the protein reaches a position where its
isoelectric point (pI) equals the pH of the medium, the
protein stops moving.
pH 3
+
10
-