2. Shape = Amino Acid Sequence
Proteins are made of 20 amino acids linked by
peptide bonds
Polypeptide backbone is the repeating sequence of
the N-C-C-N-C-C… in the peptide bond
The side chain or R group is not part of the backbone
or the peptide bond
5. Protein Folding
The peptide bond allows for rotation around it and
therefore the protein can fold and orient the R groups
in favorable positions
Weak non-covalent interactions will hold the protein
in its functional shape – these are weak and will take
many to hold the shape
7. Hydrogen Bonds in Proteins
H-bonds form between 1) atoms involved in the
peptide bond; 2) peptide bond atoms and R groups;
3) R groups
8. Protein Folding
Proteins shape is determined by the sequence of
the amino acids
The final shape is called the conformation and has
the lowest free energy possible
Denaturation is the process of unfolding the
protein
Can be down with heat, pH or chemical compounds
In the chemical compound, can remove and have
the protein renature or refold
9. Protein Folding
2 regular folding patterns
have been identified –
formed between the bonds
of the peptide backbone
α-helix – protein turns like
a spiral – fibrous proteins
(hair, nails, horns)
β-sheet – protein folds
back on itself as in a ribbon
–globular protein
10. β Sheets
Core of many proteins is
the β sheet
Form rigid structures
with the H-bond
Can be of 2 types
Anti-parallel – run in an
opposite direction of its
neighbor (A)
Parallel – run in the same
direction with longer
looping sections between
them (B)
11. α Helix
Formed by a H-bond
between every 4th
peptide
bond – C=O to N-H
Usually in proteins that
span a membrane
The α helix can either coil
to the right or the left
Can also coil around each
other – coiled-coil shape –
a framework for structural
proteins such as nails and
skin
12. Levels of Organization
PrimaryPrimary structure
Amino acid sequence of the protein
SecondarySecondary structure
H bonds in the peptide chain backbone
α-helix and β-sheets
TertiaryTertiary structure
Non-covalent interactions between the R groups
within the protein
QuanternaryQuanternary structure
Interaction between 2 polypeptide chains
14. Domains
A domaindomain is a basic structural unit of a protein
structure – distinct from those that make up the
conformations
Part of protein that can fold into a stable structure
independently
Different domains can impart different functions
to proteins
Proteins can have one to many domains
depending on protein size
16. Useful Proteins
There are thousands and thousands of
different combinations of amino acids that can
make up proteins and that would increase if
each one had multiple shapes
Proteins usually have only one useful
conformation because otherwise it would not
be efficient use of the energy available to the
system
Natural selection has eliminated proteins that
do not perform a specific function in the cell
18. Proteins – Multiple Peptides
Non-covalent bonds can form interactions between
individual polypeptide chains
Binding site – where proteins interact with one another
Subunit – each polypeptide chain of large protein
Dimer – protein made of 2 subunits
Can be same subunit or different subunits