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

Hydrophilic 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
Folding@home

• The Stanford Folding@home research goal is to

understand protein folding, misfolding, and
related diseases.
• Calculations to create models requires a
supercomputer OR many smaller computers
(distributed computing).
• You can participate by visiting:
• Fold@home web site: http://folding.stanford.edu/
• Article on Folding@home:
http://www.sciencedaily.com/releases/2002/10/0210220
70813.htm
 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
 Sheets • Core of many proteins is
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)
 Helix • Formed by a H-bond
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
CD from Text

• The CD that is included on your textbook back cover has some

video clips that will show the  helix and  sheets as well as
other things in this chapter. You will want to look at them.
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
Binding Strength
• Can be measured directly
• Antibodies and antigens are mixing around in
a solution, eventually they will bump into each
other in a way that the antigen sticks to the
antibody, eventually they will separate due to
the motion in the molecules
• This process continues until the equilibrium is
reached – number sticking is constant and
number leaving is constant
• This can be determined for any protein and its
ligand
Equilibrium
Constant

• Concentration of antigen, antibody and

antigen/antibody complex at equilibrium can be
measured – equilibrium constant (K)
• Larger the K the tighter the binding or the more non-
covalent bonds that hold the 2 together
Enzymes as Catalysts

• Enzymes are proteins that bind to their ligand as

the 1st step in a process
• An enzyme’s ligand is called a substrate
• May be 1 or more molecules
• Output of the reaction is called the product
• Enzymes can repeat these steps many times
and rapidly, called catalysts
• Many different kinds – see table 5-2, p 168
Enzymes at Work
• Lysozyme is an important enzyme that
protects us from bacteria by making holes in
the bacterial cell wall and causing it to break
• Lysozyme adds H2O to the glycosidic bond in
the cell wall
• Lysozyme holds the polysaccharide in a
position that allows the H2O to break the bond
– this is the transition state – state between
substrate and product
• Active site is a special binding site in enzymes
where the chemical reaction takes place
 Lysozyme

• Non-covalent bonds hold the polysaccharide in

the active site until the reaction occurs
Features of Enzyme Catalysis
Enzyme Performance

E + S  ES  EP  E + P
• Step 1 – binding of the substrate
• Limiting step depending on [S] and/or [E]
• Vmax – maximum rate of the reaction
• Turnover number determines how fast the substrate
can be processed = rate of rxn  [E]
• Step 2 – stabilize the transition state
• State of substrate prior to becoming product
• Enzymes lowers the energy of transition state and
therefore accelerates the reaction
Reaction Rates

• KM – [S] that allows rxn to proceed at ½ it

maximum rate
Prosthetic Groups

• Occasionally the sequence of the protein is not

enough for the function of the protein
• Some proteins require a non-protein molecule
to enhance the performance of the protein
• Hemoglobin requires heme (iron containing
compound) to carry the O2
• When a prosthetic group is required by an
enzyme it is called a co-enzyme
• Usually a metal or vitamin
• These groups may be covalently or non-
covalently linked to the protein
Regulation of Enzymes

• Regulation of enzymatic
pathways prevent the
deletion of substrate
• Regulation happens at
the level of the enzyme in
a pathway
• Feedback inhibition is
when the end product
regulates the enzyme
early in the pathway
Feedback Regulation

• Negative feedback –
pathway is inhibited by
accumulation of final
product
• Positive feedback – a
regulatory molecule
stimulates the activity of
the enzyme, usually
between 2 pathways
•  ADP levels cause the
activation of the glycolysis
pathway to make more
ATP
Allostery
• Conformational coupling of 2 widely
separated binding sites must be responsible
for regulation – active site recognizes
substrate and 2nd site recognizes the
regulatory molecule
• Protein regulated this way undergoes
allosteric transition or a conformational
change
• Protein regulated in this manner is an
allosteric protein
Allosteric Regulation

• Method of regulation is also used in other

proteins besides enzymes
• Receptors, structural and motor proteins
 Allosteric Regulation

• Enzyme is only partially active with sugar only but

much more active with sugar and ADP present
Phosphorylation

• Some proteins are regulated by the addition of

a PO4 group that allows for the attraction of +
charged side chains causing a conformation
change
• Reversible protein phosphorylations regulate
many eukaryotic cell functions turning things
on and off
• Protein kinases add the PO4 and protein
phosphatase remove them
Phosphorylation/Dephosphorylatio
n
• Kinases capable of
putting the PO4 on 3
different amino acid
residues
• Have a –OH group on R
group
• Serine
• Threonine
• Tyrosine
• Phosphatases that
remove the PO4 may
be specific for 1 or 2
reactions or many be
non-specific
 GTP-Binding Proteins (GTPases)

• GTP does not release its PO4

group but rather the guanine
part binds tightly to the protein
and the protein is active
• Hydrolysis of the GTP to GDP
(by the protein itself) and now
the protein is inactive
• Also a family of proteins
usually involved in cell
signaling switching proteins on
and off
Molecular Switches
 • Proteins can move in the cell,
Motor Proteins say up and down a DNA
strand but with very little
uniformity
• Adding ligands to change the
conformation is not enough to
regulate this process
• The hydrolysis of ATP can
direct the the movement as
well as make it unidirectional
• The motor proteins that move
things along the actin
filaments or myosin
 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
• See video clip on CD in book