PROTEINS
Proteins
• Protein functions:
– enzyme (catalyst)
– defense
– transport
– support
– motion
– regulation
– storage
7 Classes of Proteins
• Structural
– Spider silk
– Mammal hair
– Fibers of tendons
and lipids
• Contractile
– Muscular movement
• Storage
– Egg white
• Defense
– Antibodies
• Transport
– Hemoglobin
• Signal
– Some hormones
• Chemical catalyst
– Enzymes
Structure is related to function!
• Structurally
sophisticated.
• Shape determines
function and is crucial
to the job of a protein.
• Composed of amino
acids joined together
by peptide bonds.
– 20 types of amino
acids
– Made at the
ribosomes in a cell.
Monomer: Amino Acids (AA)
• contain an amino group (-NH2), a carboxyl
group (-COOH) and a hydrogen atom, all
bonded to a central carbon atom
– twenty common AA
grouped into five classes
based on side groups
•
•
•
•
•
nonpolar AA
polar uncharged AA
charged AA
aromatic AA
special-function AA
Structural Formulas for the 20 Amino Acids
Amino Acids
• Peptide bond links two amino acids.
– A protein is composed of one or more long
chains of amino acids linked by peptide bonds
(dipetide and polypeptides).
The Polypeptide Backbone
• Amino acids joined together end-to-end
– COOH of one AA covalently bonds to the NH2 of the
next AA
– Special name for this bond - Peptide Bond
• Two AAs bonded together – Dipeptide
• Three AAs bonded together – Tripeptide
• Many AAs bonded together – Polypeptide
– Characteristics of a protein determined by composition
and sequence of AA’s
– Virtually unlimited number of proteins
Protein Structure
• Protein function is determined
by its shape.
• The shape is driven by a number
of noncovalent interactions
such as hydrogen bonding, ionic
interactions, Van der Waals’
forces and hydrophobic packing.
• Protein structure
• primary - specific amino
acid sequence
• secondary - folding of
amino acid chains
Protein Structure
• tertiary - final
folded shape of
globular protein
• quaternary - forms
when two or more
polypeptide chains
associate to form a
functional protein
Summary: Levels of Structure
• Primary:
– Literally, the sequence of amino acids
– A string of beads (up to 20 different colors)
• Secondary:
– The way the amino acid chain coils or folds
– Describing the way a knot is tied
• Tertiary:
– Overall three-dimensional shape of a polypeptide
– Describing what a knot looks like from the outside
• Quaternary:
– Consists of more than one polypeptide
– Like several completed knots glued together
Levels of Protein Organization
Examples of Fibrous
Proteins
Protein-folding Diseases
• Assembly of AA’s into protein extremely complex
• Process overseen by “chaperone” molecules
– Inhibit incorrect interactions between R groups as
polypeptide grows
– Defects in these chaperones can corrupt the tertiary
structure of proteins
– Mad cow disease could be
due to mis-folded proteins
– Other protein folding
errors: Alzheimer's
and Cystic Fibrosis
Enzymes
• Enzymes are proteins that function as a
catalyst - they control the rate of a reaction
without being consumed by the reaction.
• They usually speed up the rate of a reaction
by lowering the
amount of activation
energy needed to
start the reaction.
• End with -ase.
• Ex. lactase
•
Reaction with enzyme
How enzymes work…Induced Fit Model
• The substrate (what the enzyme is going to
work upon) comes into contact with the active
site of the enzyme.
• The enzyme “wraps” around the substrate
breaking or forming bonds.
• The product is released.
Enzyme at work
Double Check
• Which one is the
enzyme?
• How do you know?
Unfolding Proteins
• Denaturation refers to
the process of changing
a protein’s shape.
– usually rendered
biologically inactive
• salt-curing and pickling used to preserve food
• temperature - high temperatures break bonds.
• pH - designed to work at a specific pH!
Examples
• You can not use fresh pineapple in jello but you
can used canned! Why?
• Pepsin is an enzyme that helps break down
proteins in the stomach during digestion. It
works at a pH of 2!
• Trypsin is an enzyme that helps break down
proteins as well. It works in the intestines with
a pH of 8.
• Many snake venoms are enzymes that work when
directly injected into blood or tissue (pH = 7.4).
If swallowed, they are denatured by the acidity
of the stomach! (Don’t try it, just take my word
for it!)
• Why do people without refrigeration salt their
food for long term storage?
Regulating Enzymes
• Non-competitive inhibitors
– Compound which binds to some other area,
called the allosteric site, not the active site.
This causes a change in the shape of the active
site. The substrate no longer fits!
– Usually temporary, allows the body to control
the production of many chemicals.
– Example: Nerve gas!
– http://www.bbc.co.uk/education/asguru/biolog
y/02biologicalmolecules/01proteins/11enzymes
/05enzymes_d/index.shtml
Competitive Inhibitors
• Blocks the active site so the substrate can not
get to it!
• This is usually permanent inhibition
• Ex. DDT blocks the site of enzymes of the
nervous system.
• Penicillin blocks enzymes used by bacteria to
produce the cell wall, stopping bacterial
reproduction!
• http://www.bbc.co.uk/education/asguru/biology/02biolo
gicalmolecules/01proteins/11enzymes/04enzymes_c/ind
ex.shtml
Competitive Inhibitor Example
• Ethanol is metabolized in the body by
oxidation to acetaldehyde, which is in turn
further oxidized to acetic acid by aldehyde
oxidase enzymes. Normally, the second
reaction is rapid so that acetaldehyde does
not accumulate in the body.
• A drug, disulfiram (Antabuse) inhibits the
aldehyde oxidase which causes the
accumulation of acetaldehyde with subsequent
unpleasant side-effects of nausea and
vomiting. This drug is sometimes used to help
people overcome the drinking habit.