structure of proteins vladimíra kvasnicová. chemical nature of proteins biopolymers of amino acids...
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Structure of proteins
Vladimíra Kvasnicová
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Chemical nature of proteins
• biopolymers of amino acids
• macromolecules (Mr > 10 000)
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Amino acids in proteins
L--aminocarboxylicacids
• 21 proteinogenic AAs
• other AAs are formed by a posttranslational modification
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Side chains of AAs determine final properties of proteins
Isoelectric point (pI)
= pH value at which the net charge of a compound is zero
pI = (pKCOOH + pKNH3+) / 2
Solutions of AAs belong among ampholytes
(= amphoteric electrolytes)
„AMPHION“
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Important reactions of AAs
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
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Peptides and proteins
• contain 2 or more AAs bound bypeptide
bond(s)
• common names are used
• systematic names: AA1-yl-AA2-yl-AA3
oligopeptides: 2 – 10 AA
polypeptides: 10 AA
proteins: polypeptides of Mr 10 000
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• border: polypeptide /protein isnot sharp (~ 50 AAs)
• AAs are bound by peptide bonds
• the order of AAs in a chain(= primary structure) is givenby a genetic information
• the order of AAs is reportedfrom N- to C- terminal
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Description of structure of proteins
• the macromolecule contains various AAs,in an exactly defined order and quantity
• spacial arrangement and biological functionare DEPENDENT
on the amino acid composition
• native protein biological active conformation
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Side chains of AAs influence a finalstructure of proteins:
polar side chain
nonpolar side chain
unfolded protein
final conformation of the protein in water
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• the peptide chain has a specialspatial arrangement:
• only some proteins are composed of subunits(= quaternary structure)
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Bonds found in proteins
1) covalent peptide bond -CO-NH-
disulfide bond -S-S-
2) noncovalent interactions hydrogen bonds -H...O- -H...N-
hydrophobic interactions nonpolar side
chains
ionic interactions -COO- / +H3N-
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Primary structure of proteins
= order of amino acids
• read: from N-to C- end
• it is coded on a genetic level
• stabilization:peptide bonds
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Secondary structure of proteins
= spatial arrangement of the polypeptide chain given by rotation of the planar peptide bonds around -carbons
stabilization:hydrogen bondsbetween –CO- and -NH- of the peptide bonds
real proteins: different parts of the polypeptide chain exist in various secondary structures
-helix -pleated sheet -turn
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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 R-
perpendicular to it
• H-bonds are formed between AAs
found above and below themselves
the most common: -helix (right-handed)
collagen helix (left-handed,
steeper)
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-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
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-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
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Tertiary structure of proteins
= 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
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tertiary structure
secondary structures
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-helix
-sheet
motif: barrel
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Classification of proteins according to their tertiary structure
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
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Quaternary structure of proteins
= 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“
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SUMMARYof
protein structure description
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funkční domény
properties and functions of proteinsare related to their spatial arrangement
IT DEPENDS ON AMINO ACIDS COMPOSITION
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Physicochemical properties
• 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)
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• proteins can be denaturated heat, whipping, shaking, radiation
strong pH changes, salt of heavy metals, organic solvents, detergents
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• proteins strongly absorb UV radiation
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• proteins are ampholytes
-COOH -COO- + H+
-NH2 + H+ -NH3+
under physiological pHproteins are negatively charged
ANIONS
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Classification of proteins
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
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→ conjugated proteins contein polypeptide chain + prosthetic group:
glycoproteins (saccharide)
metalloproteins (metal ion)
hemoproteins (heme)
phosphoproteins (phosphoric acid)
nucleoproteins (nucleic acid)
(lipoproteins)