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-
COO
l
+
H 3N – C a – H
l
R
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Amino acids
 There are 20 standard amino acids.
 All proteins are built from the same amino acids.
 The most important criteria for classification is affinity to water:
hydrophilic and hydrophobic.
 Hydrophilic are aliphatic and aromatic.
 Hydrophobic are divided into aliphatic and aromatic.
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AMINO ACIDS
Natural (D,L)
Protein (L)
primary
exogenous
Synthetic (D, L or DL)
Non-protein (D or L)
secondary
tertiary
endogenous
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glycine
alanine
valine
leucine
isoleucine
Thiol group
proline
methionine
cysteine
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phenylalanine
tyrosine
tryptophan
phenol group can participate in creating hydrogen bond
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Amino acids with hydrophilic charged polar side chains
In neutral pH :
Cations
histidine
arginine
lysine
Anions
Aspartic acid
Glutamic acid
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Amino acids with hydrophilic no-charged polar side chains
Amid group can participate in creating hydrogen bond
asparagine
Polar character
serine
glutamine
threonine
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Cannot be synthesized in human body (exogenic):
 leucine
 isoleucine
 lysine
 phenyloalanine
 methionine
 threonine
 tryptophan
 histidine
 Valine
 arginine - semiessential, needed for children’s growth
The highest daily requirement for adults is for leucine,
the least for tryptophan.
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Non-essential (nutritionally) amino acids
Can be synthesized in human body ( endogenic):








glycine
alanine
proline
serine
aspartic acid
glutamic acid
glutamine
arginine
Amino acids partially nonessential:
 Tyrosine is synthesized from essential phenylalanine
 cysteine is synthesized from:
 Essential methionine
 Essential serine
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Non-protein amino acids
Non-protein amino acids: other important biological role, ex.:
 b-alanine
CH2 – CH2 – COOl
NH3+
Is formed during metabolism
of pirimidic bases.
It is a component of:
•pantothenic acid
•coenzyme A
•carnosine
 g-aminobutyric acid (GABA)
CH2 – CH2 – CH2 – COOl
NH3+
It is synthesized from glutamine in
brain (neurotransmitter)
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Intermediates in metabolism:
 ornitine and cytruline – are involved in biosynthesis of urea
NH3+
l
+H N–CH –CH –CH–COO3
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2
CH2–CH2–CH2–CH–COOl
l
NH
NH3+
l
H2N–C=O
 homocysteine ( 2-amino-4 mercaptobutyric acid)
NH3+
l
HS–CH2–CH2–CH–COOIt is a product of the demethylation of methionine and intermediate metabolite
in methionine synthesis
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 Independent risk factor for development of:
- hart failure
- atherosclerosis
- stroke
 Factors leading to increased level of homocysteine :
 genetic factors
 smoking
 alcohol abuse
 excessive coffee drinking
 some drugs
 defficiency:
 vitamin B6
 vitamin B12
 folic acid
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Amino acids in water solution are in 99.5% in ionic form.
Different pH of solution allows for amino acid’s separation.
+H+
COOH
l
+H N – C – H
3
l
R
cation
COOl
+H N – C – H
3
l
R
zwitterion
-H+
COOl
H2N – C – H
l
R
anion
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
Isoelectric point (pI) of amino acids it’s such a value
of pH at which amino acids exist as a zwitterion.
 at pH equal to pI amino acids do not have a net
charge and do not migrate in electric field
 at pH < pI - amino acids are cations
 at pH > pI – amino acids are anions
 pH value which is equal to pI is an average of pK1
and pK2
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anion
zwitterion
cation
Equivalents of OH-
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Stereoisomers of amino acids
Except glycine, all amino acids are optically active, they can rotate the plane of
polarization of linearly polarized light
 amino acids can exist as a pair of enantiomers.
 they have a chiral center
 water solutions of amino acids:
 rotate polarised light to the left or to the right
 exist in two stereoisomeric forms L and D
 in proteins almost only L- forms can exist
 D – form can exist in bacteria cell wall and some antibiotics.
L- alanine
D- alanine
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Amino acids form peptides:
• oligopeptides – up to 25 amino acids
• polypeptides – above 25 amino acids, proteins
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




Covalent bond formed
between a-amine group of
one amino acid and acarboxylic group of another
amino acid.
free pair of electrons from
nitrogen atom in peptide bond
is delocalized as a result of
orbitals’ overlapping from
carbonyl group
peptide bond is stiff and flat
atoms forming peptide bond
are positioned in one plane
hydrogen from amine group
almost always is in trans
position in respect to oxygen
atom from carbonyl group. 18
 There is no possibility of free
rotation around C – N bond.
 There is possibility of rotation
around Ca-N and Ca-C
 Rotation angles influences
polypeptide chain conformation.
 The angles allow for predicting
shape of polypeptide.
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• 1st: amino acid with a
free amine group + -yl
ending
• 2nd: amino acid with a
free carboxylic group
(C-end)
• peptide name always
starts with name of
amino acid with free
amino group
alanine (Ala)
glycine (Gly)
glycylalanine
alanine (Ala)
glycine (Gly)
alanylglycine
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 –COOH dicarboxylic amino acids
 –NH2 diamine amino acids
 –OH tyrosine and threonine
 –SH cysteine
 imidazol residue of histidine
 imine residue of arginine
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glutation – g-glutamylcysteinylglycine
 Angiotensin II :
 contracts blood vessels (vasoconstrictor)
 the strongest factor increasing blood pressure
 stimulates the release of aldosterone (from adrenal
cortex) which increases sodium (Na+) resorption in
kidney and counteracts loosing of this ions with urea.
 Bradykinin, nanopeptide :
 dilates blood vessels and
 lowers blood pressure.
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Oligopeptides
glutation – g-glutamylcysteinylglycine
• Vasopressin and oxytocin:
nanopeptides with hormone activities produced in hypothalamus and
stored in posterior pituitary.
Both have very similar structure (only 2 amino acids different).
• Vasopressin (antidiuretic hormon, ADH) increases water reabsorption in distal kidney tubules.
ADH deficiency leads to diabetes insipidus .
• Oxytocin stimulates contraction of uterus smooth muscles and mammary
gland.
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 Penicillin is created from:
Tiazolidine ring
D – valine and L – cysteine
 It contains a β- lactam ring and
thiazolidine ring.
 Carboxylic group is connected to β-
b-lactam ring
lactam ring by peptide bond.
 Penicillin, thanks to the reactive β-
lactam ring, inhibits bacterial
glycopeptide transpeptidase
L-cysteine
D-valine
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 Actinomycin D
- polypeptide antibiotic; inhibits RNA
synthesis
 Valinomycine
- most potent agent against severe acute
respiratory syndrome (SARS), cause by
coronavirus
 Gramicidin S
- an antibiotic effective against some
Gram-positive and Gram-negative
bacteria as well as some fungi
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
Primary structure – composition
and sequence of amino acids in
polypeptide chain. It is stabilized by
peptide bonds.

Secondary structure – space
conformation of polypeptide chain.
is hold by noncovalent bonds such
as:

hydrogen bonds

hydrophobic interaction

electrostatic interaction

van der Waals forces
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
Tertiary structure – spatial connection
between structural elements of secondary
structure. It shows mutual interaction
between domains (cluster units connected
by polypeptide skeleton).

stabilized by disulfide bonds and
electrostatic forces.

Quaternary structure – proteins
consisting of two or more peptide chains
connected by noncovalent bonds:
electrostatic interaction
hydrogen bonds
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cysteine
cystine
cysteine
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 Two molecules of cysteine reacting
with each other form disulfide
bridge
 (oxidizing of thiol group (-SH)).
oxidation
disulfide bond
 they can be formed:
 between amino acids from the
same chain
 between amino acids from
different chains
 disulfide bonds are present often in
extracellular peptides and very
rarely in intracellular peptides.
reduction
disulfide bond
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Nonparallel arrangement of peptide chains
Parallel arrangement of peptide chains
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 Tertiary structure refers to spatial
configuration of amino acids being in
linear sequence and those which are
next to each other (neighborhood)
 Polypeptide chain folds in the following
way:
 most of the hydrophobic side chains
become directed into inner part of
the structure
 most of their polar side chains, with
charge, are on the surface.
 Biologically active spatial conformation
of peptide is also hold by electrostatic
forces, hydrogen bonds and covalent
disulfide bonds.
Ionic bonds
Hydrogen
bonds
van der Waals
interaction
 Electrostatic forces include ionic forces
between groups with opposite charge,
and van der Waals forces between
tightly packed aliphatic side chains
inside peptide.
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THE END
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