Download Protein Function - Gleason Chemistry

Protein Function
Zinc-finger
nuclease cleaves
nucleotides in DNA
ATP Synthase adds
phosphate to ADP
Carbonic Anhydrase
• CO2 is a byproduct of cell metabolism and is carried back to
the lungs through the bloodstream for disposal.
• The majority is converted to soluble carbonic acid (bicarbonate)
and carried out by the lungs.
K = 1.7×10-3
(Not product favored)
• The unassisted reaction is too slow to sufficiently remove CO2.
• The protein Carbonic anhydrase speeds up reaction rate by 106 x
• The same protein re-establishes equilibrium in
lungs to convert back to CO2, which we breathe out.
• It’s why carbonated beverages taste fizzy once
they hit our tongue and CA converts it to CO2(g).
Enzyme: catalyst that facilitates a biochemical reaction
• Active site: region of the protein where the reaction occurs
• Binding site: region that binds the substrate
• High specificity for a single type of substrate
Cleaves (breaks) peptide bonds at:
Aromatics
Basic (+) Small, neutral
(Tyr, Phe, Trp) (Arg, Lys) (Ala, Gly, Val)
Catalytic triad of a protease:
Frequently observed active site in
hydrolases (with Asp, His, Ser)
Enzymes may need cofactors (coenzymes e.g. vitamins/
peptides or metal ions) to assist in catalysis.
ATP is found in
kinases: enzymes
that add phosphate
groups to other
proteins.
Vitamin A: Undergoes
cis/trans isomerization
when hit with light.
(Opsin proteins found
in eye tissue).
Carbonic anhydrase active site:
3 Histidines coordinated to a Zn+2
+2
TedEd: How do Vitamins work; www.youtube.com/watch?v=ISZLTJH5lYg
SciShow: How the Vitamins Got Their Names; www.youtube.com/watch?v=NnmgM_Lz3o0
Carbonic Anhydrase Mechanism
• Every enzyme has a unique mechanism (pathway) in its function.
• Upon finishing, enzymes regenerate their original state to repeat.
1. Zn+2 bound H2O is polarized
enough to dissociate as an ionic
compound (OH-/H+). Loses H+
2. CO2 substrate binds in active site
3. OH- attacks CO2 and converts it
into bicarbonate ion.
4. Release of HCO3- and addition of
another H2O regenerate native site.
Some Mechanisms are very complex with many steps
Catalytic mechanism of chymotrypsin
(cleaving amide bonds at aromatic residues)
Trypsin & chymotrypsin
structure similarity
Despite binding different substrates,
their pathways are nearly identical
The enzyme-substrate binding complex
Lock-and-key model devised by Emil
Fischer in 1894. Substrate fits into
corresponding rigid binding site on
enzyme.
Induced fit model: substrate fits into
flexible pocket and imparts a
conformational change in the enzyme.
It is now observed that the
conformational change is necessary in
many proteins for their function.
Conformational changes can occur upon binding the
substrate.
Myoglobin upon binding O2
ATP Synthase
www.youtube.com/watch?v=PjdPTY1wHdQ
Inhibitors slow or prevent enzyme catalysis
A large fraction of medicines act as enzyme inhibitors.
• NSAIDs (aspirin & ibuprofen) inhibit cyclooxgenase which
make prostaglandin, causing inflammation.
• Opioids inhibit the neural cell receptors that communicate pain.
Natural metabolites are involved in regulatory processes
as inhibitors (feedback inhibition)
High norepinephrine conc. inhibits Tyrosine hydroxylase to prevent further production.
DNews: What Happens When You’re Hooked?; https://www.youtube.com/watch?v=GKpAZgrMTC8
SciShow: Why We Have Pain, & How We Kill It; www.youtube.com/watch?v=GmHGUTNoL-I
Inhibitors function in different ways
Competitive Inhibitors seek the same binding site
as the substrate and compete for binding.
Noncompetitive (allosteric) Inhibitors bind
elsewhere on the enzyme and alter the protein
conformation making it less efficient.
Suicide Inhibitors irreversibly bind to active site.
Nerve gases are acetylcholinesterase
inhibitors which prevent the muscles
from retracting.
Cyanide inhibition of ATP synthesis
www.youtube.com/watch?v=fBXSJGxfnbU
Article link: http://www.compoundchem.com/2014/10/07/nerveagentspart1/
Enzyme Classification
Reaction Catalyzing
Redox reaction: electron transfer
Functional group transfer
Hydrolysis (breaking) of various
covalent bonds using water
Cleavage or formation of double
bonds without water
Rearrange groups within a molecule
to form a similar isomer
Joining of two molecules, forming
single bonds
E.C. 1: Oxidoreductase: change the oxidation state of the
substrate. Some reduce O2 to H2O in the process.
coenzyme
Tyrosinase is a Cu-enzyme that catalyzes the production of melanin and other pigments from
tyrosine by oxidation, as in the blackening of a peeled or sliced potato exposed to air.
E.C. 2: Transferase: transfer functional groups to a protein.
(e.g. Kinases add phosphate, very important in cell signaling)
Choline acetyl-transferase produces acetylcholine, the neurotransmitter responsible
for triggering muscle contraction, by transferring an acetyl group to a choline.
+
acetyl group from
Acetyl-CoA coenzyme
choline
acetylcholine
E.C. 3: Hydrolase: Cleave molecules by adding H2O across
the bond. (e.g. proteases cleave peptides, lipases break fats)
Elastase
cleaves proteins at small
non-polar residues
Maltose
Starch: glucose polymer
(polysaccaharide)
Most common carbohydrate
Amylase
E.C. 4: Lyase: breaks bonds without water; often forming or
breaking double bonds.
Both
neurotransmitters
AsapScience: Your Brain on Drugs: Alcohol
https://www.youtube.com/watch?v=vkpz7xFTWJo
End product of Glycolysis
Ethanol production via yeast by fermentation.
E.C. 5: Isomerase: interconverts isomers by
rearranging molecule (no net addition or subtraction).
Found in pathway to use glycerol as energy source once removed from Fatty compounds
Phosphoglucose Isomerase
Glucose-6-phosphate
Fructose-6-phosphate
Glycolysis step # 2 to utilize glucose to produce ATP in this anaerobic process
E.C. 6: Ligase: connect two molecules together; commonly
use ATP energy to drive reaction.
DNA Ligases connect
complementary DNA
strands in repair of breaks
by forming phosphodiester
bonds.
Mechanism of Recombination: https://www.youtube.com/watch?v=8rXizmLjegI
Motor Proteins: promote
cellular motion by ATP
hydrolysis.
Myosin enables muscle contraction in
muscle fibers enabling all (in)voluntary
motions from lifting to blinking.
Trillions of Myosin proteins use ATP
energy to contract to generate muscle
movement.
SciShow: What is Sarin Gas?
www.youtube.com/watch?v=w3sJEbcT7IE
Motor Proteins: Kinesin and Dynein
• Move along microtubules that act like cell scaffolding
• Intracellular transport (when diffusion isn’t good enough)
• Separation of the chromosomes during mitosis & meiosis.
• Used in cilia and flagella (cell motility)
SciShow: Motor Proteins; www.youtube.com/watch?v=SgR4ojtPw5Q
Lipid Vesicle with “cargo”:
• New proteins
• Enzymes
• Antibodies
• Molecules
• Cell Waste
The Kinesin Linear Motor
www.youtube.com/watch?v
=kOeJwQ0OXc4
Fibrous Microtubules (tubulin: structural protein polymer)
Structural proteins are fibrous, insoluble, and
give cells and organelles stability and rigidness.
• Collagen is the most abundant protein in mammals, making up more
than a third of the body’s protein.
• Composed of 3 chains in a helix. The sequence normally follows the
pattern “Gly-Pro-X” and can span over 1,400 residues per chain.
• It is the major structural protein of connective tissues (e.g. cartilage)
• It forms a network of fibers and provides tensile strength to the tissue.
• Gram for gram, collagen is stronger than steel.
TedEd: How do scars form?; https://www.youtube.com/watch?v=ucRMDdw82yw
Antibodies: the Immune response
• In response to foreign molecules, white blood cells produce
Y-shaped proteins called antibodies (or immunoglobins).
• Each antibody binds tightly to a specific antigen.
• Binding inactivates the antigen or marks it for degradation
via other enzymes.
The Immune System Explained
www.youtube.com/watch?v=zQGOcOUBi6s
SciShow: All About Allergies
www.youtube.com/watch?v=hmb066Vzdek
Antibodies: Vaccination
•
Vaccines are dead/weakened organisms (or their product)
that can be introduced to yield antibodies for the pathogen.
• The immune system generates and
keeps available antibodies for
future protection.
• The body can more effectively
destroy disease causing pathogens
when it has already made
antibodies to target them.
Measles Explained — Vaccinate or Not?
www.youtube.com/watch?v=y0opgc1WoS4
SciShow: Anti-vaccination
www.youtube.com/watch?v=Rzxr9FeZf1g
http://www.compoundchem.com/2015/02/10/vaccines/
Transport proteins facilitate the movement of
molecules/particles across the body, cell, or membrane.
Storage proteins keep a reserve of metal ions, amino acids,
nucleic acids or other chemical species needed quickly.
Hemoglobin:
O2 transport
from lungs
Dopamine Transporter:
removes dopamine from
between synaptic clefts
of nerve cells to end the
signal.
~4,500
Fe atoms
• Stores and releases Iron in a controlled fashion
• Free Iron can be toxic to the cell
Asap Science: What is Gluten?; www.youtube.com/watch?v=DXjpb7SFi3s
Membrane Channels: Carrier proteins
• Many lipophilic molecules can pass through a
membrane by simple diffusion.
• Polar molecules can not passively transport
themselves through a membrane and require a channel
Membrane Transport Channels
• Highly selective for a particular ion.
• Can exist in open and closed states and are heavily regulated
• Needed to create cell electric potentials for nervous system
Benzocaine (commonly found in cough drops and topical
creams) is used as a local anesthetic and functions by
inhibiting sodium ion membrane channel.
Crash Course: Membranes & Transport; www.youtube.com/watch?v=dPKvHrD1eS4
Cell Receptors bind ligands to
pass along a signal into a cell.
• Embedded in cell’s plasma membrane
• Each protein is very specific to ligand
• Ligands: peptide, toxin, hormone, neurotransmitter, etc
• Over 50% of pharmaceuticals bind to cell receptors
TedEd: The Science of Spiciness
www.youtube.com/watch?v=qD0_yWgifDM
Capsaicin
coord.info/GC446DJ
http://www.compoundchem.com/2014/02/27/chemical-structures-of-neurotransmitters/
Regulatory Proteins
The addition of ubiquitin can affect proteins in many ways: It can signal for
their degradation via the proteasome, alter their cellular location, affect
their activity, and promote or prevent protein interactions
Lysosome Organelle
Contain more than 50 different
enzymes, which are all optimally
active at an acidic environment of
about pH 4.5 (about the pH of black
coffee). Thus lysosomes act as the
waste disposal system of the cell by
digesting unwanted materials in the
cytoplasm, both from outside of the
cell and obsolete components inside
the cell.
Proteasome
Denaturation: the loss of protein folded conformation
• Loss of structure results in a
loss of protein function.
• Not normally reversible (need
chaperones)
• Can lead to protein
aggregation: non-specific
folding (gathering) of proteins.
• Coagulation: precipitation of
unfolded protein
SciShow- Prions: The Real Zombie Maker
www.youtube.com/watch?v=Cubu-k7kSvw
Ways to Denature a Protein
Temperature: increases molecular movement and
breaking of stabilizing bonding forces.
pH: Alter protonation state of ionizable residues, disrupt
electrostatic interactions. (Buffers are often used to regulate pH)
Organic solvents: disrupt exterior H-bonds between residues & H2O
Detergents: disrupt
hydrophobic interactions
Chaotropic reagents: small chemicals that can be
added to disrupt H-bonds (e.g. urea, Arg-side chain)
TedEd: How to unboil an egg; www.youtube.com/watch?v=CHMY4G9gTPA