Bioqumica 2016

Laboratorio de Bioqumica y Biologa Molecular

Departamento de Biologa
Facultad de Ciencias-Universidad de Chile

Estructura y caracterizacin de protenas Jorge Babul

jbabul@uchile.cl
 Proteins structure leads to protein
function
Precise placement of chemical groups allows proteins
to have :
Catalysis function
Structural role
Transport function
Regulatory function

Then the determination of 3-dimentional structure of

proteins is important.
 How Protein Folds

Figure 3-6. How a protein folds into a compact conformation. The polar amino acid side chains tend to gather on the outside of the protein, where they
can interact with water; the nonpolar amino acid side chains are buried on the inside to form a tightly packed hydrophobic core of atoms that are hidden
from water. In this schematic drawing, the protein contains only about 30 amino acids
 Amino Acid Properties
Polarity: the degree to which AA electrons are
distributed asymmetrically
Charge: the ability to gain or lose an electron
pK value: tendency of AA to ionize (related to pH
where half AA are ionized)
Aliphatic vs. aromatic sidechains
Hydrophobicity: tendency to hide from water
molecules
Interesting AA: histidine (often active site of
enzyme)
Resonance in the Peptide Bond
 The Rigid Peptide Plane and
the Partially Free Rotations
Rotation around the peptide bond is not permitted
Rotation around bonds connected to the alpha carbon
is permitted
f (phi): angle around the -carbonamide nitrogen
bond
y (psi): angle around the -carboncarbonyl carbon
bond
In a fully extended polypeptide, both y and f are
180
Ramachandran Plot
4 Levels of Protein Structure
 Estructura secundaria
Arreglo espacial local de los tomos del esqueleto polipeptdico sin importar la
conformacin de sus cadenas laterales. Existen 2 tipos de estructuras regulares
en protenas:

hlice hoja
 The Helix Dipole
Recall that the peptide bond has a strong dipole
moment
Carbonyl O negative
Amide H positive
All peptide bonds in the helix have a similar
orientation
The helix has a large macroscopic dipole moment
Negatively charged residues often occur near the
positive end of the helix dipole
 Sheets
The planarity of the peptide bond and tetrahedral
geometry of the -carbon create a pleated sheet-like
structure
Sheet-like arrangement of backbone is held together by
hydrogen bonds between the backbone amides in
different strands
Side chains protrude from the sheet alternating in up
and down direction
Topologa
Biochemistry 2/e - Garrett & Grisham

Protein Modules
An important insight into protein structure
Many proteins are constructed as a composite of
two or more "modules" or domains
Each of these is a recognizable domain that can
also be found in other proteins
Sometimes modules are used repeatedly in the
same protein
There is a genetic basis for the use of modules in
nature

Copyright 1999 by Harcourt Brace & Company

 Estructura terciaria

Se refiere a la estructura
tridimensional de todo el
polipptido.

Ribonucleasa
 Estructura cuaternaria
Muchas protenas estn compuestas de 2 o ms cadenas polipeptdicas,
llamadas subunidades. La estructura cuaternaria se refiere al arreglo espacial
de las subunidades.

Subunidades = gris y celeste Subunidades = rojo y azul

 Binding Strength

Figure 3-43. How noncovalent bonds mediate interactions between macromolecules