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Amino acids
number of coded AA:
(proteinogenic AA)
polar (hydrophilic) AA
 on the outside of proteins that function in an
aqueous environment
 in the interior of membrane-associated proteins
20 + 1
structural characteristics:
- COOH group
- NH2 group (-NH- in proline)
- characteristic side chain (- R)
Side chains determine properties of proteins, e.g.:

 attached to „ - carbon“ (= 2nd carbon)
COOH

H2N  *C  H

R
side chains as sites of attachment for other
compounds:
Ser, Thr, (Tyr)  e.g. phosphate
or saccharide
 saccharide
Asn

proline residues (ring) cause bends that interrupt
secondary structures (-helices) of proteins

absorption of UV radiation
Tyr and Trp strongly absorb between 250 and
300 nm
AA in human proteins:
L - configuration (exception: Gly)
optical activity
L- and D- enantiomers rotate the plane of
polarized light to the same extent, but in oposite
directions
 photometric determination of protein concentration
racemic mixture
both enantiomers in equal amounts
essential AA:
* branched chain AA (Val, Leu, Ile)
* aromatic AA (Phe, Trp, His)
* basic AA (Arg, Lys)
* „special“ side chain (Thr, Met)
ionizable functional groups:
 charged at physiologic pH:
- COO- NH3+
isoelectric point (pI):
pH value at which the net charge of a compound
is zero
(the sum of the positive charges equals the sum of the
negative charges)
reactions of AA:
1) formation of salts
2) decarboxylation
3) transamination
4) oxidative deamination
5) formation of peptides
At its pI AA is said to be „zwitterionic“:
it has both anionic and cationic properties  AA
belong among ampholytes
bonds between AA in proteins:
ampholytes (amphoteric electrolytes)
= substances that can act either as
an acid or a base
covalent
 peptide bond
 disulfide bond (cystine bridge)
The net charge of peptides and proteins is almost
exclusively determined by the ionizable groups
in the side chains of their AA.
additional bonds
 hydrogen bonds
 hydrophobic interactions
 ionic bonds
types of side chains:
* nonpolar
* polar uncharged
* acidic (can be charged)
* basic (can be charged)
Peptides and proteins
= compouds comprising two or more AA linked by
peptide bonds
location of AA in proteins:
* oligopeptides:
* polypeptides:
* proteins:
nonpolar (hydrophobic) AA
 in the interior of proteins that function in an
aqueous environment
 on the surface of proteins that interact with lipids
1
2 to 10 AA
 10 AA
polypeptides of MW  10 000
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sequence of AA in a (poly)peptide:
2 common types of the secondary structure:
it is read from the amino-terminal end
(free -NH3+ group)
1) helix
2) beta-sheet (-pleated sheet)
to the carboxy-terminal end of a chain
(free -COO- group)
helix:
different types of the spiral (-helix is right-handed,
collagen helix is left-handed)
naming of peptides:
suffix -yl (all AA in the chain except of AA having
free -COO- group)
beta-sheet:
parallel or antiparallel sheets
e.g.
+ beta-bends (reverse turns)
glutamyl-cysteinyl-glycine
peptide bond:
 rigid and planar configuration
 C - N bond has a partial double-bond character
(no free rotation)
 formed by a reaction between -COOH group of
one AA and a -NH2 group of the other AA; H2O
is eliminated
supersecondary structures (motifs):
produced by packing side chains from adjacent
secondary structural elements close to each
other
(e.g. -- unit, -meander,...)
H2N-CH(R1)-COOH + H2N-CH(R2)-COOH
↓
H2N-CH(R1)-CO-NH-CH(R2)-COOH
tertiary structure:
= spatial arrangement of the secondary
structures (folding of domains)
+ H2O
-CO-NHR1, R2
=
=
domains = fundamental functional and three-dimensional
structural units of the tertiary structure
peptide bond
side chains of AA
 formed from combinations of motifs
stabilization:
 disulfide bonds (Cys - Cys)
 hydrophobic interactions
 hydrogen bonds
 ionic bonds (electrostatic interactions)
important peptides:
 glutathione (GSH) = tripeptide
 enkefalins,endorfins
 some hormons (insuline), antibiotics, toxins
 artificial sweetener Aspartam
(between side chains of AA)
Proteins
chaperons:
a specialized group of proteins required for the
proper folding of many species of proteins
contain various AA in a different order
structure:
 primary
 secondary
 tertiary
 quaternary (not all proteins)
There are two types of proteins according to the tertiary
structure:
1) globular proteins (spheroproteins)
2) fibrous proteins (scleroproteins)
 stabilized by various types of bonds
primary structure
= linear sequence of amino acids
(it is determined by a genetic code)
Random folding of a protein
 formation of a „random coil“
stabilization: peptide bonds (= covalent)
quaternary structure:
= oligomeric structure of a protein
secondary structure
= regular arrangements of AA that are located
near to each other in the linear sequence
 proteins consisting of more than one polypeptide
chain (subunit) have the quaternary structure
stabilization: noncovalent bonds
stabilization: hydrogen bonds
(between CO and NH of peptide bonds)
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Properties of proteins
„allosteric effect“
change in conformation of one subunit caused by
binding of some effector to it is transfered to other
subunits present in the same molecule

charged molecules (dependent on pH)
 proteins are ampholytes
 electrophoretic separation

water solubility (albumins / globulins)
 the least at pI of a protein

their solutions have properties of colloidal
solutions

colourless (exception: hemoproteins and
flavoproteins  prosthetic group)

absorption of UV radiation (280 nm)
 Tyr, Trp, Phe

reacts with „biuret reagent“
 laboratory determination of proteins

proteins are „antigens“

proteins can be denaturated:
Classification of proteins
a) by composition:
1) simple proteins - contain only AA
2) conjugated proteins - contain AA + „prosthetic group"

nucleoproteins (+ nucleic acid)

lipoproteins (+ lipids)

glycoproteins (+ saccharides)

phosphoproteins (+ phosphate)

hemoproteins (+ iron protoporphyrin)

flavoproteins (+ FAD)

metalloproteins (+ metal ion)
denaturation of proteins:
= loss of native structure (i.e. secondary, tertiary,
and quaternary)
b) by shape of molecule
1) fibrous proteins (collagens, keratins)
2) globular proteins (albumins, globulins)
 reversible or irreversible
c) by function
native protein = biological active

enzymes

contractile proteins

signal proteins (e.g. hormones)

storage proteins

transport proteins

violent whipping, shaking, ultrasound

structural proteins

strong acids and bases

protective proteins


toxins
hydrogen bonding solvents (ethanol,
aceton, 2-propanol)

soaps

heavy metals salts (Ag+, Hg2+, Pb2+)

oxidizing agents (2 -SH  -S-S- )
denaturated protein = biological inactive
caused by:
 heat, microwave and UV radiation
d) by localization
 intracellular
 extracellular
Common functions of body proteins:
 buffering of body fluids
 maintenance of oncotic pressure
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