Amino acids

Jana Novotná
Dept. of Biochemistry
• Amino acids are building blocks of proteins.
• 20 different amino acid are proteinogenic - encoded by
standard genetic code, construct proteins in all species .

• Their chemical structure influences three dimensional

structure of proteins.

• They are important intermediates in metabolism

(porphyrins, purines, pyrimidines, creatin, urea etc).

• They can have hormonal and catalytic function.

• Several genetic disorders are cause in amino acid

metabolism errors (aminoaciduria - presence of amino acids
in urine)
The basic structure of amino acids differ only in the
structure of the or the side chain (R-group).

L-isomer

L-isomer is normally found in proteins..

Nonionic and zwitterion forms of amino acids
The zwitterion predominates at neutral pH

Zwitterion = in German for „hybrid ion“

Week acid

Week base
A simple monoamino monocarboxyl α-amino acid
is a diprotic acid (can yield protons) when fully
protonated
 Classification of Amino Acids
Amino acids are generally divided into groups on the basis of
their side chains (R groups).
The most helpful start-point is to separate amino acids into:

Nonpolar Neutral polar Charged polar

1. Nonpolar amino acids

Only carbon and hydrogen in their side chains.

Generally unreactive but hydrophobic.
Determining the 3-D structure of proteins (they tend
to cluster on the inside of the molecule).
 Nonpolar (Hydrophobic) R Groups
Glycine (Gly) Methionine (Met)

Alanine (Ala)

Phenylalanine (Phe)

Valine (Val)

Proline (Pro)

Leucine (Leu)

Tryptophan (Trp)

Isoleucine (Ile)
http://www.indstate.edu/thcme/mwking/amino-acids.html
 The simplest amino acid is Glycine, which has a single
hydrogen atom as its side chain.

Alanine, Valine, Leucine and Isoleucine have saturated

hydrocarbon R groups (i.e. they only have hydrogen and
carbon linked by single covalent bonds). Leucine and
Isoleucine are isomers of each other.

Alanine Valine

Leucine Isoleucine
 The side chain of Methionine includes a sulfur atom
but remains hydrophobic in nature.

Phenylalanine is Alanine with an extra benzene (sometimes

called a Phenyl) group on the end. Phenylalanine is highly
hydrophobic and is found buried within globular proteins.

Methionine Phenylalanine
 Tryptophan is highly hydrophobic and tends to be found
immersed inside globular proteins.

Structurally related to Alanine, but with a two ring (bicyclic)

indole group added in place of the single aromatic ring found
in Phenylalanine.

The presence of the nitrogen group makes Tryptophan a

little less hydrophobic than Phenylalanine.
 Proline is unique amongst the amino acids – its side chain
is bonded to the backbone nitrogen as well as to the α-
carbon.

Because of this proline is technically an imino rather than

an amino acid.

The ring is not reactive, but it does restrict the geometry of

the backbone chain in any protein where it is present.
 Polar (Hydrophilic) R Groups
Serine (Ser) Cysteine
(cys)

Threonine (Thr) Asparagine (Asn)

Glutamine (Gln)
Tyrosine (Tyr)

http://www.indstate.edu/thcme/mwking/amino-acids.html
 Tyrosine is phenylalanine with an extra hydroxyl (-OH)
group attached.
It is polar and very weakly acidic. Tyrosine can play an
important catalytic role in the active site of some enzymes.
Reversible phosphorylation of –OH group in some enzymes
is important in the regulation of metabolic pathways

Serine and Threonine play important role in enzymes

which regulate phosphorylation and energy metabolism.
 Cysteine has sulfur-containing side group.The group has
the potential to be more reactive. It is not very polar.

Cysteine is most important for its ability to link to another

cysteine via the sulfur atoms to form a covalent disulfide
bridge, important in the formation and maintenance of the
tertiary (folded) structure in many proteins.

COOH-CH- CH2- HS SH- CH-2 CH- COOH

NH2 NH2

S S
Asparagine and Glutamine are the amide derivatives of
Aspartate (Aspartic acid) and Glutamate (Glutamic acid) -
see below. They cannot be ionised and are therefore
uncharged.

Asparagine Glutamine
 Negatively (Nonpolar) Charged R Groups

Aspartic acid (Asp) Glutamic acid (Glu)

Two amino acids with negatively charged (i.e. acidic) side

chains - Aspartate (Aspartic acid) and Glutamate (Glutamic
acid).

These amino acids confer a negative charge on the

proteins of which they are part.
 Positively Charged R Groups
Lysine (Lys) Arginine (Arg) Histidine (His)

Lysine and Arginine both have pKs around 10.0 and are
therefore always positively charged at neutral pH.

With a pK of 6.5, Histidine can be uncharged or positively

charged depending upon its local environment.
Histidine has an important role in the catalytic mechanism
of enzymes and explains why it is often found in the active
site.
 Classification Based on Chemical
Constitution

Small amino acids – Glycine, Alanine

Branched amino acids – Valine, Leucine, Isoleucine
Hydroxy amino acids (-OH group) – Serine, Threonine
Sulfur amino acids – Cysteine, Methionine
Aromatic amino acids – Phenylalanine, Tyrosine, Tryptophan
Acidic amino acids and their derivatives – Aspartate,
Asparagine, Glutamate, Glutamine
Basic amino acids – Lysine, Arginine, Histidine
Imino acid - Proline
 Essential Amino Acids in Humans

• Required in diet
• Humans incapable of forming requisite
carbon skeleton

Arginine* Lysine
Histidine* Methionine
Isoleucine Threonine
Leucine Phenylalanine
Valine Tryptophan
* Essential in children, not in adults
 Non-Essential Amino Acids in Humans

• Not required in diet

• Can be formed from α-keto acids by transamination and
subsequent reactions

Alanine Glycine
Asparagine Proline
Aspartate Serine
Glutamate Cysteine (from Met*)
Glutamine Tyrosine (from Phe*)
* Essential amino acids
The Stereochemistry of Amino Acids
Chiral molecules existing in two forms

http://www.imb-jena.de/~rake/Bioinformatics_WEB/gifs/amino_acids_chiral.gif
The two stereoisomers of alanine

α−carbon is a chiral center

Two stereoisomers are

called enantiomers.
enantiomers.

The solid wedge-shaped bonds

project out of the plane of
paper, the dashed bonds
behind it.

The horizontal bonds project out

of the plane of paper, the vertical
bonds behind.
The Stereochemistry of Amino Acids
Uncommon amino acids
found in proteins

Intermediates of biosynthesis
of arginin and in urea cycle
 Ninhydrin Reaction

This strong oxidizing agent

bring about the oxidative
decarboxylation of amino
acid.
The ammonia and
hydrindantin forme ninhydrin,
a purple pigment.
 Peptide Bond Formation

Cα COO- NH3+ Cα

amino acid 1 amino acid 2

Proteins
How a sequence of amino acids in a
polypeptide chain is translated into a
discrete, three dimensional protein
structure?

The three-dimensional structure is determined

by amino acid sequence.

The function depends on the structure.

An isolated protein exist in one or a small

number of stable structural form.

The most important forces stabilizing the

specific structure are noncovalent interactions.
The Peptide Bond Is Rigid and Planar

The carbonyl oxygen has a partial negative charge and

the amide nitrogen a partial positive charge.

The N-Cα and Cα-C can rotate on angles φ and ϕ,

resp. the peptide C-N bond is not free to rotate.

Take over from: D. L. Nelson, M. M. Cox :LEHNINGER. PRINCIPLES OF BIOCHEMISTRY Fifth edition
 Primary Structure
Knowledge of primary structure of protein is require for
understanding of :
the protein´s structure
the mechanism of protein action on molecular level
the interrelationship with other proteins in evolution
Sequencing of protein is an aids for :
the study of protein modification
the prediction of the similarity between two proteins
The determination of the primary structure of a protein requires a
purified protein.
The cloning of the genes for many proteins and the sequencing of
gene is a much faster method to obtain the amino acid sequence.
The primary structure of peptides and proteins refers to
the linear number and order of the amino acids
present.

the N-terminal end is to the left (the end bearing the residue
with the free α-amino group)
the C-terminal end is to the right (the end with the residue
containing a free α-carboxyl group) .
Knowledge of primary structure of
insulin aids in understanding its
synthesis and action.

1. Pancreas produces single chain

precursor – proinsulin
2. Proteolytic hydrolysis of 35
amino acid segment – C
peptide
3. The remainder is active insulin
(two polypeptide chains A and B)
covalently joined by disulfide bonds

Amino acid identity in different animals:

Human, hors, rat, pig, sheep, chicken

insulin have differences only in residues 8,
9, and 10 of the A chain and residue 30 of
the chain B
 HIGHER LEVELS OF PROTEIN
ORGANIZATION
Secondary structure
The second level of protein structure determined by attractive and
repulsive forces among the amino acids in the chain. It is the
specific geometric shape caused by intra-molecular and
intermolecular hydrogen bonding of amide groups.
Tertiary structure
Three dimensional structure of polypeptide units (includes
conformational relationships in space of side chains R of
polypeptide chain).
Quaternary structure
Polypeptide subunits non-covalently interact and organize into
multi-subunit protein (not all proteins have quaternary structure).

The folding of the primary structure into secondary, tertiary and

quaternary structure appears to occur in most cases
spontaneously.
Cystein disulfide bonds are made after folding
 Protein Secondary Structure
The α Helix

α-helix is a right-
right-handed coiled
conformation.

Every backbone N-H group of peptide bond

donates a hydrogen bond to the backbone C=O
group of the amino acid four residues earlier.

3.6 amino acid residues are per 360o turn.

The formation of the α-helix is spontaneous.

The β–Structure
Structure

2 strands (segments) of polypeptide chains are stabilized by H-bonding

between amide nitrogens and carbonyl carbons.
Polypeptide segments are aligned in parallel or anti-parallel direction to
its neighboring chains.

β-structure gives plated sheet appearance – side chain groups are

projected above and below the plane generated by the hydrogen-bonded
polypeptide chains.
 The β–Structure
Structure
In parallel sheets adjacent peptide
chains proceed in the same direction
(i.e. the direction of N-terminal to C-
terminal ends is the same).

In anti-parallel sheets adjacent

chains are aligned in opposite
directions.

The large number of hydrogen bonds

maintain the structure in a stretched
shape.
shape.
 Protein Tertiary Structure
Total three-dimensional structure of the polypeptide units of
given protein

The tertiary structure of a protein Forces that give rise to tertiary structure

Hydrophobic
β plated sheets interaction

α helical regions
 Examples of the Tertiary Structure

Examples of α,β-folded domains Examples of β-

in which β-structural strands form folded domains
a β barrel in the centre of the
domain
 Protein Quaternary Structure
The arrangement of the protein subunit in the three-
dimensional complex constitutes quaternary structure.

Hemoglobin

Four subunits (two α and two β subunits) are associated in the quaternary structure
Forces Controlling Protein Structure
Hydrophobic interaction forces:
Interaction inside polypeptide chains (amino acids contain either
hydrophilic or hydrophobic R-groups).
Interaction between the different R-groups of amino acids in polypeptide
chains with the aqueous environment.

A non-polar residues dissolved in water induces in the water solvent a solvation shell in
which water molecules are highly ordered.
Two non-polar groups in the solvation shell reduce surface area exposed to solvent and
come very close come together.

Hydrogen bonds
onds:
Proton donors and acceptors within and between polypeptide chains
(backbone and the R-groups of the amino acids).
H-bonding between polypeptide chains and surrounding aqueous
medium.
Forces Controlling Protein Structure
Electrostatic forces:
Charge-charge interactions between oppositely charged R-groups such
as Lys or Arg (positively charged) and Asp or Glu (negatively charged).

Ionized R-groups of amino acids with the dipole of the water molecule.

van der Waals forces:

Weak non-colvalent forces of great importance in protein structure, the
sum of the attractive or repulsive forces between molecules
Force is caused by the attraction between electron-rich regions of one
molecule and electron-poor regions of another
Protein Denaturation and Folding
Denaturation is a loss of the three-
dimensional. The protein loss of it
function.

Denaturation by heat has complex effect

on the weak interactions (primarily by
disrupting hydrogen bonds).

Extremes of pH alter the net charges on

the protein, causing electrostatic
repulsion and the disruption of some
hydrogen bonding.

Organic solvents and detergents act

primarily by disrupting hydrophobic
interactions

Renaturation is process in which protein

regains its native structure

Take over from: D. L. Nelson, M. M. Cox :LEHNINGER. PRINCIPLES OF BIOCHEMISTRY Fifth edition
 Some Proteins Undergo Assisted Folding
Not all proteins fold spontaneously and require molecular chaperons.
chaperons. Chaperons
interact with partially or improperly folded polypeptides

Take over from: D. L. Nelson, M. M. Cox :LEHNINGER. PRINCIPLES OF BIOCHEMISTRY Fifth edition
 Defects in Protein Folding
Amyloid fibre is an insoluble extracellular formation (amyloidoses).
They arise from at least 18 inappropriately folded versions of proteins
and polypeptides present naturally in the body.

β-sheet undergoes partial folding, associates

partially with the same region in another
polypeptide chain (the nucleus of amyloid).

Alzheimer´
Alzheimer´s disease

Take over from: D. L. Nelson, M. M. Cox :LEHNINGER. PRINCIPLES OF BIOCHEMISTRY Fifth edition
 Protein Structure

1. Globular proteins are compactly folded and coiled.

2. Fibrous proteins are more filamentous or elongated.

1. Peptides
Small peptides (containing less than a couple of
dozen amino acids) are called oligopeptides.
Long peptides are called polypeptides.
Peptides have a "polarity"; each peptide has only one
free α-amino group (on the amino-terminal residue)
and one free (non-side chain) carboxyl group (on the
carboxy-terminal residue)
Functional Roles of Proteins

1. Dynamic function
transport
metabolic control
contraction
catalysis of chemical transformation

2. Structural function
bone, connective tissue
 Classification of Proteins by Bioloical
Function

1. Enzymes (lactate dehydrogenase, DNA polymerase)

2. Storage proteins (ferritin, cassein, ovalbumin)
3. Transport proteins (hemoglobin, myoglobin, serum
albumin)
4. Contractile proteins (myosin, actin)
5. Hormones (insulin, growth hormone)
6. Protective proteins in blood (antibodies, complement,
fibrinogen)
7. Structural proteins (collagen, elastin, glycoproteins)
Types of Proteins
Globular proteins
Spheroid shape
Variable molecular weight
Relatively high water solubility
Variety function roles – catalysts, transporters, control proteins (for the
regulation of metabolic pathways and gene expression)

Fibrous proteins
Rodlike shape
Low solubility in the water
Structural role in the organism

Lipoproteins
Complex of lipids with protein

Glycoproteins
Contain covalently bound carbohydrate
 Globular Proteins
• Globular proteins, such
as most enzymes,
usually consist of a
combination of the two
secondary structures.
• For example,
hemoglobin is almost
entirely alpha-helical,
and antibodies are
composed almost
entirely of beta
structures.
 Fibrilar Proteins
Collagen Keratin
 Lipoproteins
Lipoproteins are multicomponent complexes of protein
and lipids.
The lipids or their derivatives may be covalently or
non-covalently bound to the proteins.
Many enzymes, transporters, structural proteins,
antigens, adhesins and toxins are lipoproteins.
Lipoproteins have wide variety function in blood
(transport of lipids from tissue to tissue) and lipid
metabolism.
The function of lipoprotein particles is to transport
lipids (fats) and cholesterol around the body in the
aqueous blood, in which they would normally dissolve
 Glycoproteins
Glycoproteins have covalently attached sugar
molecules at one or multiple points along the
polypeptide chain

Glycoproteins are:
• hormones
• extracellular matrix proteins
• proteins involved in blood coagulation
• antibodies
• mucus secretion from epithelial cells
• protein localized on surface of cells
• receptors (transmit signals of hormones or growth
factors from outside environment into the cell)
Sugar molecules are:
glucose, galactose, mannose, fucose, xylose, N-
acetylglucosamine, N-acetylgalactosamine
 Structure-Function Relationship of
Protein Families

Antibodies
Immunoglobulin molecules have a
tetrammeric structure
Two H - heavy chains
Two L – light chains

Immunoglobulin classes:

heavy chain
IgG γ
IgM µ
IgA α
IgD δ
IgE ε
Hemoglobin and Myoglobin

Human hemoglobin occurs in

several forms.
Consist of four polypeptide
chains of two different primary
structure.
Bind oxygen in the lung and
transport the oxygen in blood to
the tissues and cells.
 Myoglobin is a single polypeptide
chain with one oxygen binding site.
Binds and release oxygen in
cytoplasm of muscle cells.

Hemoglobin and myoglobin

molecules each contain a heme
prosthetic group.
Protein without prosthetic group is
designated as apoprotein.
apoprotein.
Complete protein is a holoprotein
 Contractile Elements of Muscles

Myosin – thick filament of the muscle

Actin – thin filament of the muscle G-actin (globular actin) F-actin
(fibrilar actin)
Tropomyosin
Troponin
One of the biologically important properties of myosin is its ability to combine with
actin to generate muscle contraction.
 Biological Membrane Proteins

Integral membrane proteins

Peripheral membrane
proteins
Channels and pores
Erythrocyte membrane

Diagram of a voltage-sensitive sodium channel α-subunit. G - glycosylation, P- phosphorylation, S - ion

selectivity, I - inactivation, positive (+) charges in S4 are important for transmembrane voltage sensing.
 Membrane Receptors

1. β-polypeptide stretch
extendings from α-helix.
2. Seven membrane-spanning
domains.
3. Recognize catecholamines,
principally norepinephrine.

Hormone activates receptor.

Hormone-receptor mediated
stimulation of intracellular
signalling cascade.

Proposed model for insertion of the β2 adrenergic

receptor in the cell membrane
Proteolytic Enzymes
Proteolytic enzymes are classified based on their
catalytic mechanism
Substrate binding site catalytically hydrolyze peptide
bonds

Serine-proteases (utilize an activated serine

residuein substrate binding site)
Cysteine-proteases (utilize an activated cysteine
residue)
Aspartate-proteases (utilize an activated aspartate
residue)
Metallo-proteases (utilize an activated metal ion)
 DNA Binding Proteins
Regulatory proteins binding to DNA sequence can promote
either an activation or repression of the rate of gene
transcription into mRNA

Helix-
Helix-turn-
turn-helix binding proteins
The zinc finger motif
The leucine zipper motif

The zinc finger motif

Helix-turn-helix motif