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116 Cards in this Set

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Fact that a large portion of proteins consist of multiple subunits is probably due to
1. Oligomers more stable than their dissociated subunits, suggest quaternary structure prolongs the life of a protein
2. Active sites of some olig enzymes are formed by residues from adjacent polypeptide chains
3. 3D structures of many oligomeric proteins change when proteins bind ligands
4. Differ proteins can share same subunits. Differ combinations of subunits carry out related func't
Quaternary Structure
-Refers to organization and arrangement of subunits in a protein with multiple subunits, each subunit is a separate polypeptide chain, a multi-subunit protein is referred to as an oligomer
-Proteins in over whelming cases are diamers and tetramers
-In Vivo however the subunits usually remain tightly associated
Domains
several discrete independantly folded, compact units, domains consist of combinations of motifs 25-300 amino acid residues

-Usually connected by loops, but bound by weak interactions from aa's side chains
Fold
is a combination of secondary structure that form the core of a domain
Alpha/Beta
regions of alpha helix and Beta strand alternate
Alpha+Beta
2nry structures arise form separate contiguous regions of a polypeptide chain
loops
hydrophilic residues and usually found on surface of proteins, exposed to solvent water to H-Bond
Turns
Loops with 5 residues most common types are tight turns. Reverse turns are Beta turns b/c they usually connect antiparallel strands
Myoglobin
small monomeric protein that facilitates the diffusion of oxygen in vertebrates. It is responsible for supplying oxygen tot muscle tissue in reptiles, birds, and mammals

Myoglobin bonds strong to oxygen

Myoglobin is a single peptide with 4 chains (heme)
Hemoglobing
larger tetrameric protein that carries oxygen in blood

In vertebrates oxygen is bound to molecules of hemoglobin for transport in red blood cells

Has alpha2,beta2 structure
What stablizies secondary structure
Hydrogen bonding
What stablilizes tertiary structure
Non-covalent bonds interactions (most likely hydrophobic effect) b/t the side chains of amino acid residues

Disulfide bridges, through covalent, are also elements of 3rd structure (not primary because they only form after the protein folds)
B-sheets
1. Parallel
2. Anti-Parallel
1. Same N to C terminus, not perpendicular, h-bonds distorted so less stable

2. Opposite N to C terminus, H-bonds nearly perpendicular to extend polypeptide chain
B-Barrel
1.Bends in structure to keep structure compact
2. 4 residues to make loop/tight turns common
3. Tends to be hydrophobic on outside of protein
4. Everything else is random coil
5. Stabilized by H-bonds b/t carbonyl oxygens and amide hyrogens on adjacent structure
6. Twists slightly in Rt-hand direction/CW
B-Pleated Group
planar peptide groups meet each other at angles like folds in an accordian

Side chains point alternatively above and below the plane of sheet
Primary Structure
Linear sequence of AA residues in a protein

N to C terminus
Secondary Structure
Refers to regularities in local conformations, maintained by H-bonds b/t amide hydrogens and carbonyl oxygens of peptide backbone.

Major secondary are A-Helices, and B-sheets
Fibrous Proteins
are particular class of structural proteins that provide mechanical support to cells or organisms
ex: Alpha Keratin
-Major components of
hair and nails
-Collegen tendons,
skin, bones, teeth

Other structural proteins include components that makeup viruses, bacteriophages,spores, and pollen.
Globular Proteins
Have hydrophobin interior and a hydrophilic surface, possess indentations or clefts that specifically recognize and transiently bind other compounds

Many are enzymes/biochem catalysts
Determining the sequence of amino acid residues. Edman Generation procedure
Removal and identification of one residue at a time from the N-terminus protein (must treat with pH 9 and PITC) PITC reacts with free N-terminus of chain to form a PTC-peptide, treat with anhydrous acid (trifluoroacetic acid), the peptide bond of N-terminus residue is selectively cleaved, releasing an anilinothearyloinone, this is extracted with organic solvent (CH3)3CL, then treated with aq acid=amino acid. Now one residue shorter, back to pH 9 and start over.
Limitations of Acid Analysis
Asparagine, Aspartic Acid
Glutamine, glutamic Acid

Small losses of Serine, threonine, and tyroseine

Side chain of Tryptophan is mostly destroyed
Guanadine
Causes structure to unravel, stay in solution and reverse
Denaturation
Envir or chem change may disrupt the native confirmation of a protein.

Amt of energy needed is only 3-4 H-Bonds

Some may unfold completely to a random coil

Can denature by heat
Ex: Egg
Chaotropic agents:
urea and guanidium salts/high []'s of these denature proteins by allowing water to solvate non polar molecules in the interior of proteins. The water molecules disrupt the hydrophobic interactions that stablize the native confirmation
Detergents
Hydophobic tails (sodium dodecyl Sulfate) also denature proteins by penetrating the protein interior and disrupting, hydrophobic interactions.
Sperm Whales, Dolphins, and Seals
Have alot more myoglobin because they hold their breaths for long pds of time, unlike us. We have less myoglobin and less oxygen

tertiary structure of a sperm whale myoglobin shows that the protein consists of a bundle of eight alpha helices. It is a member of all alpha structural category.
Myoglobin
1.Facilitates the diffusion of oxygen in molecules

2. Responsible for supplying
oxygen to muscle tissue in reptiles, birds, and mammals.

Myo=Muscle
Globin=Soluable protein

Spherical, oxygen carrier, single polypep chain, bonds stronger to oxygen
Hydrogen Bonding
Native structure
-H-bonds b/t ppt backbone and water,ppt backbone and polar side chains, 2 polar side chains.
How it H-Bonds
H-bonds in hydrophobic core are much more stable than those near the surface b/c internal H-bonds don't compete with water molecules

Van der Waals: Cumulative effect may contribute to stability b/c nonpolar sidechains in interior are densely packed

Charge-Charge: contribute minimally on surface but much stronger when not in water
Co-Operativity of folding
one part of a structure leads to the formation of the remaining parts of the structure. As the protein begins to fold it adopts lower and lower energies.
Denaturation of protein with sulfide bridges
cleave disulfide bonds

ex: 2-mercaptol ethanol or thiol reagents

disrupts hydrophobic interactions
Alpha Helix
-Most right handed, C/W
-Each residue is H-bonded to 2 other residues 1 turn away
-Max # of H-bonds make it so stable
-3.6 residues per turn, 100 degrees away
-ampathy-one face polar, one not
-each loop has 13 atoms: carb oxygen, 11 back bone atoms, the amide H
Alpha Helix con't
-all carbonyl groups pt toward C-terminus
-entire helix is dipole
(+)N-terminus, (-) C-terminus

-Alanine prevalent in alpha helics, tryoseine and asparagine with bulky sides not so much. Glycine (start to finish, carbon is too unconstrained). Proline-no! cyclic side chain disrupts helix occupies neighbors space.
Glycine
Amino Acetic Acid
White Solid
Alanine
High MP, white solid, chiral compound
Aliphatic side chains
Glycine (Gly)
Alanine (Ala)
Valine (Val)
Leucine (Leu)
Isoleucine* (Iso)

*two chiral centers, 4 stereoisomers
Sulfur side chains
Methionine (Met*
Cysteine (Cys)

*Always first acid in polypeptide chain
Cystine is made of
2 Cysteine molecules with a disulfide bridge
Hydroxylic AA
Serine (Ser)
Threanine (Thr)
Basic AA

All hydrophilic
Lysine (Lys)
Arginine (Arg)*
Histidine (His)

*Most hydrophilic, Most basic, + charge delocalized
Acidic AA
Very hydrophilic, protein surfaces
1. Aspartic Acid (Asp)
2. Glutamic Acid (Glu)

Highly Polar, hydrophilic, but not as acidic
Asparigine (Asn)
Glutamine (Gln)
Purification- Analytical Tech.
1. Prep soln of proteins, whole cells in buffer and homogenized, differ for cell membrane proteins

2. Fractional- Crude separation by salt solubilities. (NH4)2SO4 used for this, percipitates less soluable impurities

3. Dialysis with buffer, draws solutes out, keeps big proteins in

4. Column Chromotography, come out depending on how attracted protein is to eluate head
Ammonium Sulfate Precipitation
1. Take cell lysed material, add ammonium sulfate, proteins will ppt, centrifuge, will be globular in shape, hydrophobic on inside, hydrophilic on outside.

2. Add (NH4)2SO4 to stabilize proteins (dissociates in water), as you pull water from protein, reaction leans to the right and proteins ppt.

3. Separate w/ column chromotography, Ion exchange units are used, works best w/o salt b/c small charges will act w/ resion and interfere w/ protein interactions, make proteins come off resin with salt

4. Gel Filtration-exclusion chromotography-separates by size, big come off first little come off later
Misfolding of proteins
mad cow, parkinsons, oldtimers

break down of the structure that takes out misfolded proteins is not working properly.
Inside of Hemoglobin
Fe2+ more commone than Fe3+ if Fe3+ forms a complex of O2-(superoxide very reactive)

Goes on in body, body protects against it

1/2 of hemoglobin undergoes oxidation everyday

CO is very similar to O2, stronger then FeO why we get poisioned, Oxygen can't bind, converts to CO structures
Facts on hemoglobin
1.Hb Binds O2 cooperatively unlike myoglobin

2. O2 binding is pH dependant

3. Hb binds CO2, Myoglobin doesn't

4. Hb binds bisphosphoglygerate and Mb doesn't

5. Hb binds Nitric oxygen
Allosteric
change caused by binding @one site but affecting another area of the protein
Homotropic (same molecule)
Binding of one oxygen affects other O2's
Heterotropic (differ molecules)
binding of one, affects binding of something else
Bpg
in red blood cells, same [] as red blood cells, weakens it's bending

can interact with all 4 subunits in center cavity (in deoxy form) destablizes one, stabilizes the other.
Embronic Hemoglobin
has to bind even stronger b/c you take it from mothers blood (O2)
Allosteric effects of hemoglobin
ppg, CO2, O2
Ligands to Fe2+
6 Nitro on hemes (4)
Histadine
Oxygen
Active Site
usually contains AA side chains so substrate fits well. Some require metal ions in the active site such as: copper, silver, gold, not cobalt.
Michallis-Mention complexes
Lock and Key model, must be specific
Induced Fit Model
Induces change in structure of protein when enzymes dont fit. Energy costs.
Oxidoreductases
oxidize or redox
Transferase
catalyze group transfer rxns, may require the prescence of a coenzyme. A portion of the substrate molecule usually binds covalently to the enzyme or its coenzyme. This group includes kinases that transfer a P from ATP to else where.
Hydrolases
catalyze hydrolysis. They are a special class of transferases
Lyases
catalyze lysis of a substrate, generating a double bond; these are non-hydrolytic, nonoxidative elim rxns
Isomerases
catalyze structural change w/in a single molecule
Ligases
Ligases catalyze ligation, or joining of two substrates. These reactions require the input of the chemical potential energy of a nucleoside triphospate such as ATP.
Enzyme-substrate complexes
Bimolecular. ES complexes are formed when ligands bind covalently in their proper places in the active site.
High [] of substrate
E is saturated with S, and the rxn rate is independant of the [] of substrate
Km
is the initial concentration of substrate at half-maximum velocity or at half saturation of E with S.

Lower the value the more tightly the substrate is bound
K1
diffusion control rate (2nd order)

10 to the 10 per second, can't go any faster

Examples:
Superoxide Dismutase
Fumarase
Enyzmes don't always work at high rates why, what can u do?
-Change V-max or Km
-Inhibitors
a)Competitive
b)Non-Competitive
Sequential reactions
require all substrates present before any product is released
Ping-pong reactions
product is released before all substrates are bound
Inhibitor (I)
is a compound that binds to an enzyme and interferes with its activity by preventing either the formation of ES complex or its breakdown to E+P

Natural inhibitors regulate metabolism, and many drugs are enzyme inhibitors. Inhibitors also are used experimently to investigate enzyme mechanisms and to decipher metabolic pathways
Irreversible Inhibitors
bound to enzymes by covalent bonds
Reversable Inhibitors
bound to enzymes by the same noncovalent forces that bind substrates and products

1. Competitive
2. Uncompetitive
3. Non-competitve
Competitve Inhibition
The inhibitor can bind only to enzyme molecules that have not bound any substrate.
Uncompetitive Inhibition
binds only to ES site, the enzyme become inactive when I binds
Noncompetitve Inhibition
Can bind to E or ES site. Then enzyme become inactive when I binds. Although the EI complex can still bind S, no product is formed.
Cox I
a constituive enzyme that regulates secretion of mucin in the stomach, thus protecting the gastric wall
Cox II
inductible enzyme that promotes inflammation, pain, and fever.
Aspirin
Has both Cox I and Cox II, physicans would like to have Cox II isolated so the medicine will not cause stomach irritation any longer
Common Inhibitors
Cycloxygenase, Ibuprofen, Naproxen, enzyme inhibits useful as drugs.
Irreversible Enzyme Inhibition
forms a stable covalent bond with an exzyme molecule, thus removing active molecules from the enzyme population. Typically occurs by alkylation or acylation of the side chain of an active-site AA residue.
Methyl Trucate
Inhibits enzyme in immune system
Inhibitors are better in what state
better in trans state so drug companies now making inhibitors for trans state and not just for substrate.
Iodoacetate ICH2COO-
used for proteins with cysteine residue or thiol group
Nerve Gas
DFP interacts with Serine residues becomes some type of organophorphorus compound. And these compounds are used at insecticides and nerve gas. Catalyzes hydrolysis of the neurotransmitter acetylcholine. Need regular Acetylcholine or become paralyzed
affinity labels
more useful than general substituating reagents are irreversible inhibitors with structures that allow them to bind specifically to an active site. Known as active site-directed reagents or affinity labels
CN- Irreversible Inhibition
-Binds very tightly to transition metals
-Trans metal found in active site
-Shuts down electron transport sysem
Superoxide Dismutase
Reacts with first thing it comes into contact with, does alot of damage, and why antioxidants are so important

Lou Gehrings-lower than normal levels superoxide dismutase
Zenacol
inhibits lipids, dont get as fat, lipids come in contact with zenocol=death for lipids
Rapid Inhibition
uses the product to inhibit the pathway at the first step
Feed forward
early intermediate can speed up later steps
Triose Phosphate Isomerase
catalyzes the rapid interconversion of the dihydroxyacetone phosphate DHAP, and G3P in the glycolysis and gluconeogeneis pathway

Most inmportant regulatory enzyme in pathway

Allosteric

Acts like Hemoglobin
Triacylglycerols
Cooking oil, crisco, lard, all loaded with energy
Sphinolipids
polar end, rest hydrophobic

tissues of the nervous system
Eicosanoids
-derived from long chain unsaturated fatty acids

-cause inflammation, swelling

-very potent in small amts
Steriods
-cholesterol, Vitamin K and A

- Structure related to 5 carbon isoprene

-Terpenes

-Camphor, mentol, are long units
Glyceral
-Thick, vicous liquid

-advantages- pack together, very [], store energy

-dont need water to store

-C2 most likely to be unsaturated then end
Essential fatty acids
we can't make
Linoleic
cis,cis 9,12 octadecadienoate

unsaturated
Linolenic
all cis,cis 9,12,15 octadectrienoate
Omega 3-fatty acids
-count from reducing end 6 is double bond

-count from other end 3 is double bond
Poly Sat
Less stable, chemically reactive, make oil go bad (nasty smell) that's why oil gets hydrogenated
peripheral membrane
wash with a salt soln, not tightly bound just electrostatic
Intergral membrane
not washed off by salt, bound tighter to membrane may even be trans in memebrane
Recognition
one cell can recognize that one next to it is a friend or foe
sonicator
violent shaking lipids will organize selfs into liposomes, several layers can study permeability, pure no proteins just bilayer, could add drugs, ions, cholesterol ect to liposomes.
Triton X-100
can purify proteins, help stabilize
non ionic detergent
binds to a membrane proteins, get mixed micelles, triton x-100
ionic detergent
disrupts protein structure
60-100 angstroms
for proteins that traverse membrane, trans membrane helix
30 angstroms, 6-7 turns in alpha helix
hydrophobic region
1st messenger
2nd messenger
1. is hormonal
2. diacyl glycerol, formed in cell, small molecule or ion
Raft
on surface of membrane, do not freely dissociate, super secondary structure, movement in raft but stick together
Aquaphorin
transports water, gets in passively, protein with some type of channel (polar channel)( wont let much of ne thing threw)

Others allow glucose to pass threw them
Bacteria Chlorphyll
undergoes light isomerization, structure changes
Protein Kinase A
Catalyzes the phorphorylation of other proteins using ATP
Phosphdiesterylyse
drops cycic AMP levels- hydrolyzes

Think G as a timer