Chapter 4
Protein Structure
and Function
Proteins
● Make up about 15% of the cell
● Have many functions in the cell
● Enzymes
● Structural
● Transport
● Motor
● Storage
● Signaling
● Receptors
● Gene regulation
● Special functions
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
Polypeptide
Backbone
Amino Acids
NOTE: You need to know this table
Hydrophili Hydrophobic
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
Non-covalent Bonds in Proteins
Globular Proteins
● The side chains will help determine the
conformation in an aqueous solution
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
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
Refolding
● Molecular chaperones are small proteins that
help guide the folding and can help keep the
new protein from associating with the wrong
partner
Protein Folding
● 2 regular folding patterns
have been identified –
formed between the
bonds of the peptide
backbone
● -helix – protein turns like
a spiral – fibrous proteins
(hair, nails, horns)
● -sheet – protein folds
back on itself as in a
ribbon –globular protein
● Core of many proteins is
Sheets the 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)
● Formed by a H-bond
Helix between every 4th
peptide bond – C=O to N-
H
● Usually in proteins that
span a membrane
● The 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
Levels of Organization
● Primary structure
● Amino acid sequence of the protein
● Secondary structure
● H bonds in the peptide chain backbone
● -helix and -sheets
● Tertiary structure
● Non-covalent interactions between the R
groups within the protein
● Quanternary structure
● Interaction between 2 polypeptide chains
Protein Structure
Domains
● A domain 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
Domains
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
Protein
Families
● Have similarities in amino acid sequence and
3-D structure
● Have similar functions such as breakdown
proteins but do it differently
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
Single Subunit Proteins
Different Subunit Proteins
● Hemoglobin
● 2 globin
subunits
● 2 globin
subunits
Protein Assemblies
● Proteins can form very
large assemblies
● Can form long chains if
the protein has 2
binding sites – link
together as a helix or a
ring
● Actin fibers in muscles
and cytoskeleton – is
made from thousands
of actin molecules as a
helical fiber
Types of Proteins
● Globular Proteins – most of what we
have dealt with so far
● Compact shape like a ball with irregular
surfaces
● Enzymes are globular
● Fibrous Proteins – usually span a long
distance in the cell
● 3-D structure is usually long and rod
shaped
Important Fibrous Proteins
● Intermediate filaments of the
cytoskeleton
● Structural scaffold inside the cell
● Keratin in hair, horns and nails
● Extracellular matrix
● Bind cells together to make tissues
● Secreted from cells and assemble in long
fibers
● Collagen – fiber with a glycine every third amino
acid in the protein
● Elastin – unstructured fibers that gives tissue an
elastic characteristic
Collagen and Elastin
Stabilizing Cross-Links
● Cross linkages can be between 2 parts of a
protein or between 2 subunits
● Disulfide bonds (S-S) form between adjacent -SH
groups on the amino acid cysteine
Proteins at Work
● The conformation of a protein gives it a
unique function
● To work proteins must interact with other
molecules, usually 1 or a few molecules from
the thousands to 1 protein
● Ligand – the molecule that a protein can bind
● Binding site – part of the protein that interacts
with the ligand
● Consists of a cavity formed by a specific
arrangement of amino acids
Ligand Binding
Formation of Binding Site
● The binding site forms when amino acids from
within the protein come together in the folding
● The remaining sequences may play a role in
regulating the protein’s activity
Antibody Family
● A family of proteins that can be created
to bind to almost any molecule
● Antibodies (immunoglobulins) are made
in response to a foreign molecule ie.
bacteria, virus, pollen… called the
antigen
● Bind together tightly and therefore
inactivates the antigen or marks it for
destruction
Antibodies
● Y-shaped molecules with 2 binding sites at
the upper ends of the Y
● The loops of polypeptides on the end of
the binding site are what imparts the
recognition of the antigen
● Changes in the sequence of the loops
make the antibody recognize different
antigens - specificity
Antibodies
Protein Machines
● Complexes of 10 or
more proteins that work
together such as DNA
replication, RNA or
protein synthesis, trans-
membrane signaling
etc.
● Usually driven by ATP
or GTP hydrolysis
