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Protein Structure
Protein Structure
Protein Structure
and Function
Proteins
Make
regulation
Special functions
Polypeptide
Backbone
Amino Acids
NOTE: You need to know this table
Hydrophilic
Hydrophobic
Protein Folding
The
Globular Proteins
The
H-bonds
Protein Folding
Proteins
Folding@home
The
Refolding
Molecular
Protein Folding
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
Levels of Organization
Primary
Amino
structure
acid sequence of the protein
Secondary
H
structure
-helix
Tertiary
and -sheets
structure
Non-covalent
Quanternary
Interaction
structure
Protein Structure
Domains
A domain
Domains
Useful Proteins
There
Protein
Families
Have
another
Subunit each polypeptide chain of large
protein
Dimer protein made of 2 subunits
Can
globin
subunits
2 globin
subunits
2
Protein Assemblies
Proteins
Types of Proteins
Globular
surfaces
Enzymes are globular
Fibrous
cytoskeleton
Structural
Keratin
filaments of the
Extracellular
matrix
Bind
Stabilizing Cross-Links
Cross
Proteins at Work
The
Ligand Binding
Antibody Family
A family
Antibodies
Y-shaped
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
Enzymes as Catalysts
Enzymes
be 1 or more molecules
Output
Enzymes at Work
Lysozyme
Lysozyme
Non-covalent
Enzyme Performance
E + S ES EP E + P
Step 1 binding of the substrate
Limiting
State
Reaction Rates
KM
Prosthetic Groups
Occasionally
When
These
a metal or vitamin
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
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
Allosteric Regulation
Enzyme
Phosphorylation
Some
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)
Molecular
Switches
Motor Proteins
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