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

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/2002/10/0210
22070813.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
Amino

structure
acid sequence of the protein

Secondary
H

structure

bonds in the peptide chain backbone

-helix

Tertiary

and -sheets

structure

Non-covalent

interactions between the R

groups within the protein

Quanternary
Interaction

structure

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

globin
subunits
2 globin
subunits
2

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

cytoskeleton
Structural
Keratin

filaments of the

scaffold inside the cell

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 proteins 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 noncovalent 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 enzymes 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 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

These

a metal or vitamin

groups may be covalently or noncovalently 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/Dephosphorylation
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

Motor Proteins

Proteins can move in the

cell, 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, transmembrane signaling
etc.
Usually driven by ATP
or GTP hydrolysis
See video clip on CD in
book