Proteins fold into their functional three-dimensional shapes due to interactions between the amino acid side chains. The primary structure of a protein is its amino acid sequence, while secondary structures like alpha helices and beta sheets form due to hydrogen bonds within the peptide backbone. Tertiary structure is determined by non-covalent interactions between the side chains that stabilize the overall three-dimensional structure of the protein. Quaternary structure refers to the interaction between multiple polypeptide subunits in a single protein.

1. Protein Structure
and Function

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

3. Polypeptide
Backbone

4. Amino Acids
NOTE: You need to know this table
Hydrophilic Hydrophobic

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

6. Globular Proteins
The side chains will help determine the
conformation in an aqueous solution

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

13. Protein Structure

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

15. Domains

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

17. Protein
Families
Have similarities in amino acid sequence and
3-D structure
Have similar functions such as breakdown
proteins but do it differently

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

19. Single Subunit Proteins

20. Different Subunit Proteins
Hemoglobin
2 α globin
subunits
2 β globin
subunits