Vladimíra Kvasnicová

The figure was adopted from: J.Koolman, K.H.R
öhm / Color Atlas of Biochemistry, 2 nd edition, Thieme 2005

• amino acids found in proteins
• peptides
• description of stucture of proteins
• classification of proteins
• physicochemical properties of proteins

• biopolymers of amino acids
• macromolecules (M r
> 10 000)
The figure was adopted from: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed.
Wiley-Liss, Inc., New York, 1997. ISBN 0-471-15451-2

L -aminocarboxylic acids
• 21 proteinogenic AAs
• other AAs are formed by a posttranslational modification
The figures were adopted from: Devlin, T. M. (editor): Textbook of
Biochemistry with Clinical Correlations, 4th ed. Wiley-Liss, Inc., New York,
1997. ISBN 0-471-15451-2

Amino acids belong among optical active compounds
2 enantiomers:
L- a D-
The figure was found at http://www.imb-jena.de/~rake/Bioinformatics_WEB/gifs/amino_acids_chiral.gif
(October 2007)

The figure was adopted from http://webschoolsolutions.com/biotech/macro.htm (2006)

The figure was adopted from http://webschoolsolutions.com/biotech/macro.htm (2006)

Modified amino acids
The figure was adopted from: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley-Liss, Inc.,
New York, 1997. ISBN 0-471-15451-2

• essential in a diet, they are not synthetized in a human body
1) branched chain AAs (Val, Leu, Ile)
2) aromatic AAs (Phe, Trp)
3) basic AAs (Lys, Arg, His)
4) Thr, Met

Isoelectric point (pI)
= pH value at which the net charge of a compound is zero pI = (pK
COOH
+ pK
NH3+
) / 2
Solutions of AAs belong among ampholytes
(= amphoteric electrolytes)
„AMPHION“
The figure was adopted from: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley-Liss, Inc.,
New York, 1997. ISBN 0-471-15451-2

The figure was adopted from: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley-Liss, Inc.,
New York, 1997. ISBN 0-471-15451-2

Absorption of UV radiation
• Tyr and Trp strongly absorb in 250 – 300 nm
spectrophotometric determination
Ability to bind other compounds
• Ser, Thr, (Tyr)
phosphate or saccharide
• Asn
saccharide
Formation of disulfide bonds (oxidation/reduction):
• 2 Cys-SH
Cys-S-SCys („cystine“)

1) dissociation (formation of salts)
2) decarboxylation → biogenic amines
3) transamination → 2-oxoacids
4) oxidative deamination → 2-oxoacids
5) formation of peptide bonds
→ peptides or proteins

• contain 2 or more AAs bound by peptide bond(s)
• common names are used
• systematic names: AA
1
-yl -AA
2
-yl -AA
3 oligopeptides: polypeptides: proteins:
2 – 10 AMK

10 AMK polypeptides of M r

10 000

• border: polypeptide /protein is not sharp (~ 50 AAs)
• AAs are bound by peptide bonds
• the order of AAs in a chain
(= primary structure) is given by a genetic information
• the order of AAs is reported from Nto Cterminal
The figure was adopted from: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley-Liss, Inc.,
New York, 1997. ISBN 0-471-15451-2

• the macromolecule contains various AAs , in an exactly defined order and quantity
• spacial arrangement and biological function are DEPENDENT on the amino acid composition
• native protein
 biological active conformation

side chains of AAs influence a final structure of proteins
The figure was adopted from http://fig.cox.miami.edu/~cmallery/255/255prot/fig5x5.jpg (2007)

• the peptide chain has a special
space arrangement:
• only some proteins are composed of
subunits (= quaternary structure)
The figure was adopted from Albert L. Lehninger et al.: Principles of Biochemistry, ISBN 0-87901-500-4

1) covalent
 peptide bond
 disulfide bond
-CO-NH-
-S-S-
2) noncovalent interactions
 hydrogen bonds -H .....
O-H .....
N-
 hydrophobic interactions nonpolar side chains
 ionic interactions -COO / + H
3
N-

= order of amino acids
• read: from N- to C- end
• it is coded on a genetic level
• stabilization: peptide bonds
The figure was adopted from: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley-Liss, Inc.,
New York, 1997. ISBN 0-471-15451-2

= spatial arrangement of the polypeptide chain given by rotation of the planar peptide bonds around

-carbons stabilization: hydrogen bonds between –CO- and -NHof the peptide bonds real proteins: different parts of the polypeptide chain exist in various secondary structures
The figure was adopted from http://fig.cox.miami.edu/~cmallery/150/protein/sf3x10b.jpg (October 2007)

The figure was adopted from http://fig.cox.miami.edu/~cmallery/150/protein/5x20.jpg (October 2007)

Helical structure (helix)
• various types of the spiral: different steepness, direction of rotation, number of AAs per turn
• peptide bond planes are parallel to the axis of the helix with Rperpendicular to it
• H-bonds are formed between AAs found above and below themselves
the most common:
 
-helix (right-handed)
 collagen helix (left-handed, steeper)
The figure was adopted from: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley-Liss, Inc.,
New York, 1997. ISBN 0-471-15451-2


-pleated sheet (

-structure)
• direction of parts of the polypeptide chain is either parallel or antiparallel
N → C
N → C
N → C
C → N
• R- are placed above or below the plane of the sheet
• H-bonds are formed between peptide bonds of the neighboring parts of the polypeptide chain
• it brings strength to proteins The figure was adopted from: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley-Liss,
Inc., New York, 1997. ISBN 0-471-15451-2


-bend (reverse or

-turn)
• reverse the direction of a polypeptide chain, helping it form a compact, globular shape
• often connect successive strands of antiparallel sheets
Nonrepetitive secondary structure
• loop or coil conformation
• not random but less regular structure than

- or

-
• one half of a protein molecule exist in it

= spatial arrangement of the secondary structures (folding of domains) stabilization: between side chains of AAs
1) hydrogen bonds
2) ionic (electrostatic) interactions
3) hydrophobic interactions
4) disulfide bonds

tertiary structure secondary structures
The figure was adopted from http://fig.cox.miami.edu/~cmallery/150/protein/5x20.jpg (October 2007)


-helix

-sheet motif: barrel
The figure was adopted from: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley-Liss, Inc.,
New York, 1997. ISBN 0-471-15451-2

1) globular proteins (spheroproteins)
 spheroidal shape
 both secondary structures are abundant
2) fibrous proteins (scleroproteins)
 rod-like shape
 one secondary structure predominates
 e.g.

-keratin, collagen

= oligomeric structure of a protein (2 or more subunits ~ monomers)
• i.e. the structure is found only in proteins composed from 2 or more chains (subunits)
• stabilization: noncovalent interactions
• the proteins have an „allosteric effect“

The figure was adopted from http://fig.cox.miami.edu/~cmallery/150/protein/5x23.jpg (October 2007)

of protein structure description
The figure was adopted from http://fig.cox.miami.edu/~cmallery/150/protein/5x24.jpg (October 2007)

a function is related to the spatial structure
IT DEPENDS ON AMINO ACIDS COMPOSITION
The figure was adopted from http://fig.cox.miami.edu/~cmallery/255/255prot/ecb4x19.jpg (October 2007)

1) by localization in an organism
 intra- / extracellular
2) by function
 structural / biological active
3) by shape
 globular / fibrous
4) by chemical composition
 simple / complex (conjugated) proteins

→ conjugated proteins contein polypeptide chain
(= apoprotein) + prosthetic group
 glycoproteins
 metalloproteins
 hemoproteins
 phosphoproteins
 nucleoproteins
 (lipoproteins)
The figure was adopted from http://connection.lww.com/Products
/porth7e/documents/Ch24/jpg/24_0
02.jpg (October 2007)

protein mus be properly folded
NATIVE PROTEIN
The figure was adopted from Alberts, B. a kol.: Základy buněčné biologie. Úvod do molekulární biologie buňky. Espero Publishing, s.r.o., Ústí nad Labem, 1998. ISBN 80-902906-0-4

• water solubility depends on the structure
• proteins form colloidal solutions
(viscosity, sedimentation, light dispersion) colloidal-osmotic pressure = onkotic pressure
• proteins can be salting-out of the solution
(~ water sheet removing)

• proteins can be denaturated
 heat, whipping, shaking, radiation
 strong pH changes, salt of heavy metals, organic solvents, detergents
The figure was adopted from http://stallion.abac.peachnet.edu/sm/kmccrae/BIOL2050/Ch1-13/JpegArt1-
13/05jpeg/05-06_denaturation_1.jpg (October 2007)

• proteins act as antigens antibodies formation of
• proteins give positive reaction with biuret reagent

• proteins strongly absorb UV radiation

• proteins are ampholytes
-COOH -COO + H +
-NH
2
+ H + -NH
3
+ under physiological pH proteins are negatively charged
ANIONS

• chemical reacion of peptide bonds with biuret reagent spectrophotometry
• complementary reaction with an antibody
immunochemistry
• separation in an electric field
electrophoresis
• denaturation