“Molecular
Workbenches”
Protein structure
Life is a system of elements
that can replicate the entire
set of elements from
rudimentary parts to form
new copies of the whole
system.
Elements: Are large, macromolecules, such as DNA, RNA and
proteins, with 1000’s of covalently
linked atoms.
Rudimentary Parts: Are the building
blocks for the elements. DNA and
RNA are made from nucleic acids;
proteins are made from amino
acids. These are small molecules
held together by covalent bonds.
Two Types of Atomic
Interaction:
Covalent Bonds
(make molecules)
Non-covalent Bonds
(make molecules come alive)
Two Types of Covalent
Bond:
Non-polar
(electronically balanced)
Polar
(electronically unbalanced)
Molecules “see” each
other by non-covalent
interactions of their
electron shells.
4 Types of
Non-covalent Bonds:
(1) van der Waals
(2) hydrogen bonds
(3) ionic
(4) hydrophobic effect
Covalent and non-covalent
Chemical bonds:
Bond type
Covalent
Non-covalent: ionic
hydrogen
van der Waals
length (nm)
0.15
0.25
0.30
0.35
strength (kcal/mole)
in vacuum
in water
90
90
80
3
4
1
0.1
0.1
Living things have very
high information
content.
Proteins are amino acid
polymers.
Amino Acids
Building Molecules:
The Condensation
Reaction
Four levels of protein
Structure:
1°-aa sequence
2°-local folds/structure
3°-structure of polypeptide
4°-polypeptide interactions
Two common folds:
a-helix
b-sheet
cytochrome b
NAD-binding
antibody
Next ClassProtein Function:
How we study
proteins