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116 Cards in this Set
- Front
- Back
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Fact that a large portion of proteins consist of multiple subunits is probably due to
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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 |
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Quaternary Structure
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-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 |
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Domains
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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 |
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Fold
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is a combination of secondary structure that form the core of a domain
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Alpha/Beta
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regions of alpha helix and Beta strand alternate
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Alpha+Beta
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2nry structures arise form separate contiguous regions of a polypeptide chain
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loops
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hydrophilic residues and usually found on surface of proteins, exposed to solvent water to H-Bond
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Turns
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Loops with 5 residues most common types are tight turns. Reverse turns are Beta turns b/c they usually connect antiparallel strands
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Myoglobin
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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) |
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Hemoglobing
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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 |
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What stablizies secondary structure
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Hydrogen bonding
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What stablilizes tertiary structure
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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) |
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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 |
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B-Barrel
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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 |
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B-Pleated Group
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planar peptide groups meet each other at angles like folds in an accordian
Side chains point alternatively above and below the plane of sheet |
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Primary Structure
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Linear sequence of AA residues in a protein
N to C terminus |
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Secondary Structure
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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 |
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Fibrous Proteins
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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. |
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Globular Proteins
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Have hydrophobin interior and a hydrophilic surface, possess indentations or clefts that specifically recognize and transiently bind other compounds
Many are enzymes/biochem catalysts |
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Determining the sequence of amino acid residues. Edman Generation procedure
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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.
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Limitations of Acid Analysis
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Asparagine, Aspartic Acid
Glutamine, glutamic Acid Small losses of Serine, threonine, and tyroseine Side chain of Tryptophan is mostly destroyed |
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Guanadine
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Causes structure to unravel, stay in solution and reverse
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Denaturation
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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 |
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Chaotropic agents:
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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
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Detergents
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Hydophobic tails (sodium dodecyl Sulfate) also denature proteins by penetrating the protein interior and disrupting, hydrophobic interactions.
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Sperm Whales, Dolphins, and Seals
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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. |
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Myoglobin
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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 |
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Hydrogen Bonding
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Native structure
-H-bonds b/t ppt backbone and water,ppt backbone and polar side chains, 2 polar side chains. |
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How it H-Bonds
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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 |
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Co-Operativity of folding
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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.
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Denaturation of protein with sulfide bridges
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cleave disulfide bonds
ex: 2-mercaptol ethanol or thiol reagents disrupts hydrophobic interactions |
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Alpha Helix
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-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 |
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Alpha Helix con't
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-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. |
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Glycine
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Amino Acetic Acid
White Solid |
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Alanine
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High MP, white solid, chiral compound
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Aliphatic side chains
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Glycine (Gly)
Alanine (Ala) Valine (Val) Leucine (Leu) Isoleucine* (Iso) *two chiral centers, 4 stereoisomers |
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Sulfur side chains
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Methionine (Met*
Cysteine (Cys) *Always first acid in polypeptide chain |
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Cystine is made of
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2 Cysteine molecules with a disulfide bridge
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Hydroxylic AA
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Serine (Ser)
Threanine (Thr) |
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Basic AA
All hydrophilic |
Lysine (Lys)
Arginine (Arg)* Histidine (His) *Most hydrophilic, Most basic, + charge delocalized |
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Acidic AA
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Very hydrophilic, protein surfaces
1. Aspartic Acid (Asp) 2. Glutamic Acid (Glu) Highly Polar, hydrophilic, but not as acidic Asparigine (Asn) Glutamine (Gln) |
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Purification- Analytical Tech.
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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 |
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Ammonium Sulfate Precipitation
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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 |
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Misfolding of proteins
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mad cow, parkinsons, oldtimers
break down of the structure that takes out misfolded proteins is not working properly. |
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Inside of Hemoglobin
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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 |
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Facts on hemoglobin
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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 |
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Allosteric
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change caused by binding @one site but affecting another area of the protein
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Homotropic (same molecule)
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Binding of one oxygen affects other O2's
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Heterotropic (differ molecules)
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binding of one, affects binding of something else
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Bpg
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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. |
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Embronic Hemoglobin
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has to bind even stronger b/c you take it from mothers blood (O2)
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Allosteric effects of hemoglobin
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ppg, CO2, O2
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Ligands to Fe2+
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6 Nitro on hemes (4)
Histadine Oxygen |
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Active Site
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usually contains AA side chains so substrate fits well. Some require metal ions in the active site such as: copper, silver, gold, not cobalt.
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Michallis-Mention complexes
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Lock and Key model, must be specific
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Induced Fit Model
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Induces change in structure of protein when enzymes dont fit. Energy costs.
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Oxidoreductases
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oxidize or redox
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Transferase
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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.
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Hydrolases
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catalyze hydrolysis. They are a special class of transferases
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Lyases
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catalyze lysis of a substrate, generating a double bond; these are non-hydrolytic, nonoxidative elim rxns
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Isomerases
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catalyze structural change w/in a single molecule
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Ligases
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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.
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Enzyme-substrate complexes
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Bimolecular. ES complexes are formed when ligands bind covalently in their proper places in the active site.
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High [] of substrate
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E is saturated with S, and the rxn rate is independant of the [] of substrate
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Km
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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 |
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K1
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diffusion control rate (2nd order)
10 to the 10 per second, can't go any faster Examples: Superoxide Dismutase Fumarase |
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Enyzmes don't always work at high rates why, what can u do?
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-Change V-max or Km
-Inhibitors a)Competitive b)Non-Competitive |
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Sequential reactions
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require all substrates present before any product is released
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Ping-pong reactions
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product is released before all substrates are bound
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Inhibitor (I)
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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 |
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Irreversible Inhibitors
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bound to enzymes by covalent bonds
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Reversable Inhibitors
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bound to enzymes by the same noncovalent forces that bind substrates and products
1. Competitive 2. Uncompetitive 3. Non-competitve |
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Competitve Inhibition
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The inhibitor can bind only to enzyme molecules that have not bound any substrate.
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Uncompetitive Inhibition
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binds only to ES site, the enzyme become inactive when I binds
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Noncompetitve Inhibition
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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.
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Cox I
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a constituive enzyme that regulates secretion of mucin in the stomach, thus protecting the gastric wall
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Cox II
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inductible enzyme that promotes inflammation, pain, and fever.
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Aspirin
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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
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Common Inhibitors
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Cycloxygenase, Ibuprofen, Naproxen, enzyme inhibits useful as drugs.
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Irreversible Enzyme Inhibition
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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.
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Methyl Trucate
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Inhibits enzyme in immune system
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Inhibitors are better in what state
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better in trans state so drug companies now making inhibitors for trans state and not just for substrate.
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Iodoacetate ICH2COO-
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used for proteins with cysteine residue or thiol group
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Nerve Gas
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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
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affinity labels
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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
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CN- Irreversible Inhibition
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-Binds very tightly to transition metals
-Trans metal found in active site -Shuts down electron transport sysem |
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Superoxide Dismutase
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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 |
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Zenacol
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inhibits lipids, dont get as fat, lipids come in contact with zenocol=death for lipids
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Rapid Inhibition
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uses the product to inhibit the pathway at the first step
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Feed forward
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early intermediate can speed up later steps
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Triose Phosphate Isomerase
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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 |
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Triacylglycerols
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Cooking oil, crisco, lard, all loaded with energy
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Sphinolipids
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polar end, rest hydrophobic
tissues of the nervous system |
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Eicosanoids
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-derived from long chain unsaturated fatty acids
-cause inflammation, swelling -very potent in small amts |
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Steriods
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-cholesterol, Vitamin K and A
- Structure related to 5 carbon isoprene -Terpenes -Camphor, mentol, are long units |
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Glyceral
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-Thick, vicous liquid
-advantages- pack together, very [], store energy -dont need water to store -C2 most likely to be unsaturated then end |
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Essential fatty acids
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we can't make
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Linoleic
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cis,cis 9,12 octadecadienoate
unsaturated |
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Linolenic
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all cis,cis 9,12,15 octadectrienoate
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Omega 3-fatty acids
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-count from reducing end 6 is double bond
-count from other end 3 is double bond |
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Poly Sat
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Less stable, chemically reactive, make oil go bad (nasty smell) that's why oil gets hydrogenated
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peripheral membrane
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wash with a salt soln, not tightly bound just electrostatic
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Intergral membrane
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not washed off by salt, bound tighter to membrane may even be trans in memebrane
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Recognition
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one cell can recognize that one next to it is a friend or foe
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sonicator
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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.
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Triton X-100
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can purify proteins, help stabilize
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non ionic detergent
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binds to a membrane proteins, get mixed micelles, triton x-100
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ionic detergent
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disrupts protein structure
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60-100 angstroms
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for proteins that traverse membrane, trans membrane helix
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30 angstroms, 6-7 turns in alpha helix
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hydrophobic region
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1st messenger
2nd messenger |
1. is hormonal
2. diacyl glycerol, formed in cell, small molecule or ion |
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Raft
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on surface of membrane, do not freely dissociate, super secondary structure, movement in raft but stick together
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Aquaphorin
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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 |
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Bacteria Chlorphyll
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undergoes light isomerization, structure changes
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Protein Kinase A
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Catalyzes the phorphorylation of other proteins using ATP
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Phosphdiesterylyse
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drops cycic AMP levels- hydrolyzes
Think G as a timer |
