biochem exam 2 Flashcards

Question

Quarternary (4°) Structure what causes the 4* structure what do these strategies use to associate to from larger functional clusters? What drives the Quarternary Association?

Answer 1

Results from the association of two or more polypeptide subunits into a larger functional cluster These polypeptide subunits associate into a larger functional cluster via side chain – side chain and side chain – polypeptide backbone interactions What drives the Quarternary Association?: Stability: reduction of surface-to-volume ratio Genetic economy and efficiency (using quarternary structure makes our genome more efficient) Bringing catalytic sites together Cooperativity (biological function may be regulated by complex interactions of multiple subunits)

Answer 2

Contain protein segments that lack a definable structure. Or, the entire protein The protein can remain in a primary structure indefinitely, or it may have a domain that can interact with other molecules, but the rest of the protein will remain disordered. Possibly 1/3 of all human proteins fit this designation. They are composed of amino acids whose higher concentration forces a less-defined structure: Lys, Arg, Glu, and Pro. They usually lack a hydrophobic core Disordered regions can conform to interact with many different proteins, facilitating possible interactions with numerous partner proteins

Answer 3

Proteins can exist in native conformation, or other conformations; flexibility is important Proteostasis is the constant level of the active set of proteins in a cell. Maintaining proteostasis is a complex process, involving: synthesis, folding, unfolding, degradation, modification, etc

Answer 4

Most protein’s function depends on its 3D-structure. To be active a protein must be correctly folded (native conformation) The order of amino acids can help determine what this 3D conformation will be Loss of structural integrity and function/activity is called denaturation Proteins can be denatured by: 1. Strong acid or base 2. Organic solvents 3. Detergents 4. Reducing agents 5. Salt concentration 6. Heavy metal ions 7. Temperature 8. Mechanical stress Think about cooking for a lot of these…. A detergent (soap) can get into the hydrophobic core and disrupt those interactions Reducing agents will break disulfide bonds Salt can break salt-bridges (ionic interactions) Heavy metal ions tend to be reducing agents Temperature can increase the instability (break) bonds We can also physically break/reform proteins (kneading dough, tenderizing meat) MAYBE REVERSIBLE – RENATURATION These protein interactions are why life tends to occupy a narrow range of conditions. Denaturation– lose structure and thus function. Ex: breaking put disulfide bonds. Order to amino acids can determine protein Reducing agents oIL, RIG, changing elctrons changing charges, changing amount of H+ on molecule which is disput lots of this Salt concentration: change ionic character and change side chain interactions an disrupt proteins Heavy metal: reducing agents Temp: melt it, ex: egg Mechanical stress: knead dough, changing structure and breaking proteins All of this requires knowledge of previous. Chapters Renaturation: maybe you do not get rid of all of the hydrogen bonds

Answer 5

Proteins fold to the lowest-energy (most stable) conformation in the microsecond to second-time scales. It is not a “search” The direction is biased towards thermodynamically and sterically possible conformations Nonpolar inside, polar outside! (we’ve gone over this) Folding of secondary structures can occur at multiple sites at the same time. Then, secondary structures interact to find the lowest energy minima (conformation) Folding often begins before protein synthesis is complete

Answer 6

Not all proteins can fold by themselves < 100 AA  fold autonomously > 100 AA need assistants from other proteins (ha!) to fold correctly Some proteins require other molecules – chaperones to promote correct folding. For example: Hsp70 (Heat Shock Protein 70) family protects unfolded proteins from denaturation and aggregation Chaperonins promote correct folding Isomerases make sure we have the correct stereochemistry PDI – Protein disulfide isomerase PPI – Peptide prolyl cis-trans isomerase

Answer 7

normally, misfolded proteins are fixed (remodeled) or degraded (many cellular pathway for this, such as the unfolded protein response (UPR) defects in any of the cellular systems (ex: genetic defects) may affect the degreeof protein misfolding

Answer 8

The native (correctly folded) β-amyloid is a soluble globular protein that is critical for neuronal growth, survival, and post-injury repair In Alzheimer’s disease, it is clipped from the cell membrane, fragmented, and then, misfolds This misfolding promotes aggregation Correctly folded helices are lost, and peptides form β strands, β helices, and β sheets  now insoluble These insoluble plaques collect around the neurons and disrupt their environment and connectivity

Answer 9

Parkinson’s Disease, Lewy-Body Dementia: misfolded α-synuclein forms aggregates  Lewy Bodies Huntington’s Disease: genetic mutation that increases CAG repeats (increases #of amino acids) causes misfolding and aggregation  neuronal death

Answer 10

- storage of ions & molecules myoglobin, ferritin transport of ions and molecules: hemoglobin, serotonin transport defense against pathogen: antibodies, cytokines muscle contraction: actin and myosin biological catalysts: chymotrypsin & lysozyme myoglobin, ferritin and hemoglobin: store oxygen and iron Hgb carries things Defend: antibodies are globular proteins Being a catalyst for a rxn ex: phosphofructokinase *be able to know one kind from each topic

Answer 11

a molecules reversibly bound specific location on protein very important (breathing)-- indices fit regulation binding. important Binding is via noncovalent forcesthat dictate protein structure! Remember this! This allows the interactions to betransient!

Answer 12

O2 is critically important (obvs), but poorly soluble Transition metals (esp. Fe) can transport O2 but can damage cells So there is a need to sequester Fe How? Heme! Heme is a prosthetic group – a porphyrinring complex with an iron ion (Fe2+) Binds oxygen reversibly Oxygen binds via heme as amino acidscannot bind oxygen 6 coordination sites: 1-4 (nitrogen),5 (amino acid), 6 (oxygen) Lets talk about myoglobin and binding Find myoglobin in muscle Hgb in red blood cells Porphyrin ring with an iron ion that binds O2 reversibily which means that oxygen is a ligand – binds Hgb and drops it off in tissues because that is where we need it Exercise: use O2 to make ATP so no O2 in muscle because form CO2 in the muscle and so we exhale a lot Heme is stabilized in the Hgb in 6 places. AA that helps it is histidine

Answer 13

High specificity can be explained by the complementary nature of the binding site and the ligand Molecular complementarity: size, shape, charge, hydrophobicity Lock and key model: proteins and ligands have a rigid interaction with each other Proteins are FLEXIBLE! Induced Fit Model: both the ligand and theprotein can change conformations uponbinding; makes binding site more complementary to the ligand Binding: non covalent forces: van der waals, hydrophobic interactions– allows to be transient. Want molecules to release from the site. Want transient interactions so we can regulate ---why it cannot be permanent Complementary forces: allows and generates high specificity Complementary fit Ligand can fit into the protein drug design: binding pocket

Answer 14

Myoglobin is a compact globular protein composed of a single polypeptide chain (153 amino acids in length) Mainly α helices; there are 8. Also some intrinsically disordered regions (flexibility) Carries and stores oxygen (poorly soluble)for muscles Contains a heme prosthetic group Histidines interact with heme and O2 Sterically inhibits oxygen from bindingperpendicularly to the heme plane (specific!) Shaped/folded to form a “cradle” thatnestles the heme prosthetic group Protects iron from oxidation (free radicals  bad!) Shape means function so for Myo. Where shape determines function, histidenn inhibits O2 from binding perpendically Myo is shaped to nestle heme prosthetic group because heme is nestled it protects heme from getting oxidized. Cradle prevents iron from being oxidized to prevent free radical from forming Free radicals Histidine ensures specificity for O2

Answer 15

In free heme, carbon monoxide (CO) binds 20,000x better than O2 Why? “smagic” (science magic – stuff about HOMOs and LUMOs) In Mb, heme binds CO only 40X better than O2 The protein structure acts as a gate. The effect of histidine (His E7), forces ligands to bind at an angle. Significantly improves O2 vs CO binding Why not evolve Mb to bind O2 more preferentially and tightly relative to CO? Highest occupied molecular orbital/lowest unoccupied molecular orbital and sigma/pi bonds Why do we transport oxygen? To let it go. If it bound even better, then O2 might not be able to dissociate as easily when it reaches the target tissues. Heme in Myo. CO binds only 40X Decreases specificity for heme is from 20,000X to 40X Why CO doesn’t bind as well when….yay histidine

Answer 16

typical receptor-ligand interactions sequence-specific protein- DNA biotin-avidin Remember your equilibrium constants: Keq = [products]/[reactants] So, if P = protein, L = ligand, then the protein-ligand reaction is… A lower Kd corresponds to a higher affinity (stay tuned) Binding affinity Kd: concentration of molecule where you get 50% binding Low Kd: higher the affinity, how well and specific the binding is High Kd: lower the affinity Keq is adapted to Kd Protein + ligand = proteinligand so protein ligand rxn is … Kd = 1/Ka because they are opposite Ka: forward direction, proteinligand is product, protein + ligand is reactant Kd is protein + ligand / proteinligand

Answer 17

Proteins fold to the lowest-energy (most stable) conformation in the microsecond to second-time scales. It is not a “search” The direction is biased towards thermodynamically and sterically possible conformations Nonpolar inside, polar outside! (we’ve gone over this) Folding of secondary structures can occur at multiple sites at the same time. Then, secondary structures interact to find the lowest energy minima (conformation) Folding often begins before protein synthesis is complete! Local structures probably form first, followed by longer-range interactions. It is a sequence of fold, unfold, fold, unfold, etc until we reach the lowest energy minima

Answer 18

Not all proteins can fold by themselves < 100 AA can fold autonomously > 100 AA need assistants from other proteins (ha!) to fold correctly Some proteins require other molecules – chaperones to promote correct folding. For example: Hsp70 (Heat Shock Protein 70) family protects unfolded proteins from denaturation and aggregation Chaperonins promote correct folding Isomerases make sure we have the correct stereochemistry PDI – Protein disulfide isomerase PPI – Peptide prolyl cis-trans isomerase

Answer 19

Alzheimer's: Beta-amyloid peptide familial amyloidotic polyneuropathy: transthyretin cancer: p53 creutzfeldt-jacob disease: prion hereditary emphysema: alpha 3 antitrypsin cystic fibrosis: CFTR

Answer 20

Remember this when you’re thinking about medicinal chemistry. If the binding were covalent, the connection/binding would be too strong for the ligand to release on its own/very easily (also would take the enzyme/receptor out of commission) Pharmacy is molecule binding to receptor Ligand can bind and unbind Binding site: can be active site, allosteric site (somewhere else) Flexbibility: proteins are dynamic due to van der waalls ect, they are not fixed so we can have iiinduced fit: enzyme changes change and chages shaepe of ligand – not really lock and key but really induced fit Regulate: prevent, encourage, one thing bndiing one helps another bind a second time: coopoerativlity Active site: where rxn happens in Substrate: what is part of the rxn

Answer 21

6 bonds or coordination sites

Answer 22

– it is 20,000x stronger BUT in Mb, heme binds CO only 40X better than O2 WHICH IS DUE TO THE Histidine in Mb

Answer 23

Ka = ([PL]/[P][L]) Kd = ([P][L]/[PL])

Answer 24

the amount of oxygen bound to Mb would increase with oxygen concentration reach a maximum value, this is referred to as saturation theta = ([PL]/[P]total = [L]/[L] + Kd or rearranged [L] = (theta/(1-theta)) x Kd slope of the curve (how quickly we reach saturation) depends upon the affinity of the interactions Total protein is protein + protein + ligand Eqns will be given Fraction saturation or fractional binding is theta 10 protein total but only 5 is PL, we have 5/10 = 0.50, we have half binding

biochem exam 2 Flashcards

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