BIOL 3030 - Exam #1

Energy landscape of protein folding: Folded state: low energy; low entropy (Bottom of funnel)

"Global" structure reached: native state

What is the dipole moment in alpha helix?

(+) N-terminus (-) C-terminus

Protein Conformation Changes (allosteric changes): Symmetry (concerted) model/MWC model

*Equilibrium model Equilibrium exists between two distinct conformations or states. Binding of substrates or effectors shifts the equilibrium between the states Two conformational states: T and R when substrate binds, equilibrium shifts toward R state When substrate binds, creating more higher affinity binding sites for S.

Fibrous Protein: Collagen

*Triple Helix a right-handed triple helix composed of 3 left-handed helical chains Basic unit is tropocollagen: 3 intertwined polypeptides (~1000 residues each chain; 300nm long; left-handed twist) chains are more extended than a-helix (rise/residue = 2.9Å and 3.3 residues/turn) Unusual amino acid composition: - Long stretches of Gly-Pro-Pro/HyPro - Modified hydroxyproline and hydroxylysine Hydroxyproline modified by the enzyme, prolyl hydroxylase (ascorbic acid dependent) Principal component of connective tissue (tendons, cartilage, bones, teeth)

Additional Stability of Folded Proteins: Disulfide bonds

- Additional covalent bonds confer enhanced stability to folded protein - Most intracellular proteins lack disulfide bonds; extracellular environment is more oxidizing... so more S—S bonds exist.

Calculate the free energy of hydrolysis of ATP in a rat liver cell in which the ATP, ADP, and Pi concentrations are 3.4, 1.3 and 4.8 mM, respectively.

-46.7

How to reduce disulfide bond?

-can separate them via oxidations with performic acid -can also reduce with strong reducing agent and compete with disulfide bond

Details of Alpha helix: Rise/residue

0.15nm = 1.5Å

Beta-Sheets: Rise/Residue

0.347nm = 3.47Å (anti-parallel) 0.325nm = 3.25Å (parallel)

Details of Alpha helix: Rise/turn

0.54nm = 5.4Å

Beta-sheets: Rise/turn (pitch)

0.7nm = 7Å

Why do ATPs phosphoric anhydride bonds good favor hydrolysis?

1) ATP destabilized by electrostatic repulsions [electronegative P atoms are destabilizing in ATP; hydrolysis relieves tension] 2) Pi product stabilize in resonance (so product favored) 3) Entropy increases upon hydrolysis [Going from two molecules in reactants to three molecules in products] (Tautomerization converts unstable products to stable ones) [not true for ATP but for PEP]

The prevalence of the trans orientation in peptide bonds results in the R-groups of adjacent amino acids being oriented approximately _________ degrees with respect to each other

180'

Please match the correct term on the left with the appropriate structural feature of proteins listed on the right. 1) primary structure 2) secondary structure 3) tertiary structure 4) quaternary structure A) the interaction between two separate protein strands B) the sequence of AA C) small sections of organized protein structure, such as helices D) the overall fold of a single protein strand, such as the globulin fold

1:B; 2:C; 3:D; 4:A

Beta-Sheets: Residues/Turn

2

What structures do weak forces stabilize?

2', 3', 4' H-bonds form whenever possible Hydrophobic interactions drive protein folding Van der Waals interactions are ubiquitous Information for folding into "native" structure is contained in the primary structure

What is a motif?

3' Structure composed of 2' Structures smaller, repeated sub-structure

Details of Alpha helix: Residues/turn

3.6 Amino Acids

Changes in hemoglobins's oxygen affinity are primarily the result of changes in the _________ structure of the protein.

4'

The activity of an enzyme requires a glutamic acid to display its g-COOH (carboxyl) functional group in the protonated state. Suppose the pKa of the -COOH group is 4.07. b) What fraction of the enzymes will be active at pH 4.07? Explain

50% of the enzyme molecules will be active at pH 4.07. At pH = pKa, dissociated and nondissociated forms of the -COOH group exist in equal amounts.

Which of the following statements about noncovalent bonding interactions is NOT true: A) Charge-induced dipole interactions are inversely proportional to the square of the distance between the two atoms. B) Van der Waals interactions, also known as dispersion forces, are the weakest of the attractive noncovalent bonding interactions. C) All noncovalent bond interactions are inherently electrostatic in nature. D) A charge may induce formation of a dipole in a nearby polarizable molecule

A) Charge-induced dipole interactions are inversely proportional to the square of the distance between the two atoms

Much is made of water's ability to dissolve a wide variety of molecules and yet, one of its most important characteristics is its effect on nonpolar, uncharged molecules. Which of the following statements is NOT true about this effect? A) Hydrophobic molecules are driven together largely because of forces of attraction between them. B) Water molecules form clathrates or cages that surround nonpolar molecules or particles. C) The hydrophobic effect plays an important role in the folding of proteins and the assembly of lipid bilayers. D) All of the listed statements are true

A) Hydrophobic molecules are driven together largely because of forces of attraction between them.

Which of the following could contribute to protein quaternary structure? a) hydrophobic interaction between F and W b) hydrogen bond between T and H c) charge-charge interactions between R and E d) disulfide bond e) all of the above

ALL

Which of the following statements about protein quaternary structure are correct? 1) It involves a complex of two or more proteins interacting with each other. 2) The subunits of the structure can be either identical or different. 3) The interactions between subunits can give rise to indefinite growth of polymeric complexes. 4) Most assemblies of protein subunits have one or more defined axis of rotation.

ALL!

Which statements about lipid bilayers are true? 1) Their formation is driven by the hydrophobic effect. 2) The amphipathic molecules that make up the bilayers orient themselves such that their polar head groups point out toward the aqueous solvent and their hydrophobic tails are pointed toward the interior of the bilayer. 3) They serve the role of physical compartmentalization of components within a cell. 4) They can be made up of phospholipids or fatty acids.

ALL!

Chaperone Molecules: GroEL-GroES

ATP dependent "holding" occurs within a dual protein "folding chamber unfolded protein goes into chamber and ATP hydrolysis in the chamber can help with protein folding [Chamber aligned with hydrophobic residues that associated with non native protein and hold it in place] ATP binds and is hydrolyzed (lid comes on and is closed chamber; chamber becomes more hydrophilic releasing protein from sides and chamber and can fold ATP-dependent conformational changes in GroEL create hydrophobic/hydrophilic surfaces

What are the hydrophobic amino acids?

Alanine, Phenylalanine, Methionine, Proline, Valine, Isoleucine, Leucine, Glycine Tryptophan

2' Structure motifs:

Alpha-helix Beta-strand/sheet

What specifies a proteins 3D structure?

Amino acid sequence (primary structure)

What's a zwitterion?

Amino acid with NET charge of zero (neutral)

Hydrophobic effect?

Association of hydrophobic molecules in aqueous solution; causes entropy to increase [as water molecules are released]

Organization of Multi-subunit proteins: Helical Symmetry

Asymmetry monomer; undergoes dynamic assembly reactions because asymmetry in monomer also assembles with axis of symmetry so its asymmetric polymer (head and tail) but has a twist

At PO2 = 40 mm Hg, what is true about the saturation of either myoglobin (Mb) or hemoglobin (Hb)?

At this partial pressure of oxygen, Mb would be almost completely saturated but Hb would not.

Protein Conformation Changes (allosteric changes): Sequential Model

Based on ligand-induced conformational changes; once ligand binds changes conformation and next subunit changes

Why does ice float on top of water?

Because h-bonds are less dense in ice than in liquid water, water floats on top of ice (solid form)

Benefit of cooperative binding in Hb?

Better ability to release O2 at lower concentrations/partial pressure Occurs because communication b/w subunits that modulate affinity of hemoglobin Cooperative binding results from communication between subunits that modulates O2 affinity of Hb

Where are H-bonds?

Between Hydrogen of Amino group and carbonyl four residues ahead

Interactions: Salt-bridges/Ionic interactions (charge-charge)

Between pair of ions; simplest interaction [Aka ionic bonds or salt bridges] Charged entities (DNA, proteins, cations and anions) exert forces on one another Force b/w pair of charges : Coulomb's Law (charges separated in a vacuum) o F = (kq1q2)/r^2 Force is positive if like charges (positive = repulsion); if negative F = attraction In cell charges surrounded/separated by water/other molecules; causes actual force b/w charges to be less than equation : screening effect expressed via dielectric constant: ε F = kq1q2 / εr^2 o ε water = 80 o ε organic liquids = 1-10 Energy bond formation/cleavage involves change in energy : drives all biochemical processes Changes in noncovalent bonding interactions = energy of interaction (E) • Energy required to separate two charged particles from a distance r to infinite distance • E = kq1q1 / εr Energy of opposite charged is negative = attraction E approaches zero as r becomes large (distance b/w particles) Energy of interaction of charge-charge is inversely proportional to first power of r (interactions are strong over great distances compared to other interactions)

How do cells carry out thermodynamically unfavorable reactions?

By coupling them with favorable ones! To find overall delta G, add two reactions together

Directionality of Beta-strand

Can be parallel (C --> N bonded with C-->N) Can be antiparallel (C-->N bonded with N-->C)

Peptide bond formation...

Carboxyl (COO-) group loses "O" Amino group (NH3+) loses two "H"s Producing peptide bond and molecule of water [Dehydration reaction] Must put energy into it Peptide bond has double bond character (in one of its resonance forms)

Waters effect on non polar molecules?

Causes them to aggregate together; thus releasing more water molecules into environment (increased entropy, lower energy) When nonpolar molecules congregate together (forming clathrate), fewer water molecules are needed (since they are all bound together); more free water molecules

What is the effect on function if altered structure?

Changes function! Mutations in hemoglobin HbS 4: b6 (A3) Glu to Val mutation Sickle cell shapes cause cells to lyse (leading to anemia) Causing clumps/clots to form because hydrophobic pocket inserted; forming long fiber structures; leads to cell lysis and anemia

Which statements regarding shape and charge complementarity are true? 1) Charge complementarity occurs when specific noncovalent binding interactions occur between two contacting surfaces. 2) The "charge" interactions can be charge-charge, H-bonding, or van der Waals interactions. 3) Shape complementarity refers to the intimate contact made between an antibody and its target antigen. 4) Shape and charge complementarity explain exclusively the interactions between an antibody and its target antigen.

Charge complementarity occurs when specific noncovalent binding interactions occur between two contacting surfaces. The "charge" interactions can be charge-charge, H-bonding, or van der Waals interactions. Shape complementarity refers to the intimate contact made between an antibody and its target antigen.

Polypeptide fragmentation: Trypsin

Cleaves at K and R [Lysine and Arginine] At Carboxy side of the amino acid (breaking peptide bond at right of amino acid) [one of polypeptide-cuts may not end with K/R if it is the end of the protein]

What is the carbonic acid/Carbonate Buffer system?

Co2 (g) <--> Co2(d) Co2(d) + H2O <--> H2Co3 H2Co3 <--> HCo3- + H+

What does proximal histidine in O2 binding pocket do?

Contact Iron

What kind of binding occurs between Hb and O2?

Cooperative binding makes O2 transport efficient and selective

Polypeptide Fragmentation Chemical Cleavage - CNBr

Cyanogen Bromide Cleavage at Met (M) On carboxy side (left of amino acids) C-terminal peptide dissociates after CNBr binds and "pushes it off" as it forms ring with Methionine

Suppose delta G° = +8,368 J/mol T = 25°C = 298°K R = 8.315 J/°K·mol [A] & [B] = 1 M and [C] & [D] = 0.1 M Delta G = Delta G° + RT ln([C][D]/[A][B] Solve for Delta G

Delta G = -3,030 J/mol = -3.03 kJ/mol Here Delta G and Delta G° are not the same sign!

Ways to separate polypeptide chains/subunits?

Disrupt weak forces: - Extremes of pH - Denaturation with 8M urea or 6M HCl - Increase salt [ ] (causes protein to aggregate because hydrophobic interactions altered)

What is the O2 binding pocket?

Distal Histidine H-bonded to O2 increases affinity of binding. Proximal Histidine contacts Iron Ligands: O2, NO, CO

Unfavorable Phi/Psi Angles: Phi = 0 Psi = 180 Phi = 180 Psi = 0 Phi = -60 Psi = 180 Phi = 0 = Psi

Due to steric crowding and non bonded radius contact

What are the N-terminal and C-terminal residues for the following peptide sequence? Peptide sequence: EASY

E is the N-terminal residue; Y is the C-terminal residue

Why is the amide-carboxyl peptide bond planar?

Electron density is dispersed over N--C--O atoms. The barrier to C—N bond rotation is high

What types of amino acids are found in Intrinsically Unstructured Proteins?

Enriched in polar amino acids; lack hydrophobic amino acids

The activity of an enzyme requires a glutamic acid to display its g-COOH (carboxyl) functional group in the protonated state. Suppose the pKa of the -COOH group is 4.07. a) Will the enzyme be more active a pH 3.5 or 4.5? Explain.

Enzyme will be more active at pH 3.5 because more of the carboxyl group will be protonated.

Function of Mb, Hb, Heme?

Evolutionary related members of globin family Function: selective and reversible binding molecular O2 for transport and storage Reversible binding as it depends on [O2]

How do intramolecular noncovalent interactions make folding favorable?

Favorable enthalpy contribution - van der Waals interactions are a primary contributor; there are many in the protein core - hydrogen bonding likely "cancel out" with respect to free energy change - ionic interactions may contribute due to proximity effects (variable)

Why is ATP hydrolysis so energetically favorable?

From the hydrolysis of the special phosphoric anhydride bonds (allows for ATP to be energetic)

What are the acidic amino acids?

Glutamic Acid Aspartic Acid

Weak Interactions: Hydrogen Bonds

H interacting with N, O, or F; H atom covalently bonded to another atom and a pair of nonbonded electrons on separate atom; atom hydrogen covalently bonded to = hydrogen-bond donor; atom with nonbonded electrons = hydrogen-bond acceptor more electronegative = more electron density withdraws from hydrogen its bonded to = h-bond gets partial positive charge and more strongly attracted to electron pair acceptor [only O and N are sufficiently electronegative to serve as strong donors] Dual character (can be covalent and noncovalent) due to bond length of hydrogen bond; distance b/w h-atom and acceptor atom is less than in van der waals Energy is relatively high compared to other noncovalent bonds [Highly directional] h-bonds are strongest when angle defined by donor atom and acceptor atom and H atom is 180; directionality helps organizing a regular biochemical structure (alpha helix) in proteins Commonly seen in: o 1' amines o 2' alcohol o Carboxylic acid o Ester o Aldehyde o Ether o Amide

What effectors stabilize the T-form?

H+ HCO3- 2,3-BPG

What is the Bohr Effect?

H+ ions shift hemoglobin toward the T (lower affinity) state

What does distal histidine in O2 binding pocket do?

H-bonded to O2; increases affinity of binding

Which form of phosphoric acid dominates at: At pH 4

H2PO4- will predominate (closer to pK1 than pK2)

Which form of phosphoric acid dominates at: At pH 1.5

H3PO4 will predominate in solution (below pK1)

Which form of phosphoric acid dominates at: At pH 9

HPO4-2 will predominate

What is a zwitterion?

Has net charge of zero (carrying both positive and negative charge) = zwitterion; only one point within pH range where average charge on all glycine molecules = 0; pH called isoelectric point (pI); most molecules in zwitterion

What is the polarity of Alpha-keratins?

Have 3rd/4th hydrophobic/nonpolar amino acid *Makes hydrophobic strip along helical surface will cause stabilization of two helices that come together via hydrophobic interactions

When Strong binding what is YO2?

Hb nearly saturated with O2 [high value] In lungs and gills

Organization of Multi-subunit proteins...

Helical Symmetry Point Group Symmetry

How can water protect organisms from extreme environment temperature variations?

High heat capacity Takes energy to change waters temp, so energy goes into breaking hydrogen bonds as vaporization occurs; so heat leaves body to break water bonds (ie. In sweat leading to vaporization)

How do hydrophobic molecules react in aqueous solution?

Hydrocarbons cannot form h-bonds (they're nonpolar, non-ionic); have limited solubility in water = are Hydrophobic (water fearing) Hydrophobic molecules do not dissolve they do not form hydration shells, but instead regular water lattic forms ice-like clathrate/cages about nonpolar molecules; corresponds to decrease in entropy/randomness of mixture; unfavorable thermodynamically so dissolving hydrophobic substances is entropically unfavorable (so they self associated rather than dissolve in water) Self-associate b/c surround hydrophobic molecules with two separate cages requires more water ordering...hydrophobic molecules aggregate within single cage releasing some water molecules and increasing entropy = hydrophobic effect

What Weak Force that Stabilize the 4' Structure?

Hydrogen bonding Salt bridges Hydrophobic effect Van der Waals interactions

H-bonds:

Hydrogen bonds are the interaction between a hydrogen atom bonded to an electronegative element and the lone pair of electrons on a nearby electronegative atom. The atom to which the hydrogen atom is covalently bonded is the hydrogen-bond donor Hydrogen bonds can be stronger interactions than even charge-charge interactions.

What bonding is in Collagen?

Hydrogen bonds stabilize between Gly N-H and adjacent C=O of X (Pro) [hydrogen bonding that happens between the amide glycine and the carboxy prolines (this hydrogen bonding in the core gives the protein stability] Lysine-Lysine crosslinks (intrachain) hydroxypyridinium crosslinks (interchain)

What is the surface of folded protein most likely composed of?

Hydrophilic amino acids

What is the center part of folded protein most likely composed of?

Hydrophobic amino acids

What type of binding curve is seen with Mb and O2?

Hyperbolic binding curve

How does entropy drive hydrophobic interactions?

Increased entropy of water molecules drives thermodynamically favorable process of organizing lipid molecules as micelles (cell membranes), monolayers (one direction of amphipathic molecule facing aqueous environment), or bilayers Because nonpolar molecules want to clump together; water is then left unbounded = higher entropy • Delta H = enthalpy (bond energy) • Delta S = entropy (disorganization) Favorable when water released in bulk within solution (when hydrophobic aggregation occurs) thus creating more disorder (higher entropy = thermodynamically favorable) Causing production of cell membranes [micelles], protein folding, and protein-protein and protein-ligand interactions

What is the strength of water as an acid?

Is a weak acid Easily dissociates a H+ (which associates with another H20 to make hydronium ion) Has low equilibrium constant (reflects low dissociation)

Isoelectric point of polyprotic acids?

Isoelectric point (pI) - Depends on types of functional groups on its surface; acidic groups predominate then pI will be low; if basic groups predominate then pI high pI = (pK1+pK2)/2 [If multiple ones, take two closest averaged] Where net charge = 0

What happens when strong acid dissociates?

It completely dissociates into proton and base conjugate

Dissociation constant of Mb?

Kd = [Mb][O2] / [MbO2]

An enzymatic hydrolysis of fructose-1-phosphate, fructose-1-P + H2O --> fructose + Pi (note: Pi = PO4-2 or inorganic phosphate) was allowed to proceed to equilibrium at 25°C. The original concentration of F-1-P was 0.2 M, but when the system had reached equilibrium, the concentration of F-1-P was only 6.52 x 10-5 M. Calculate the equilibrium constant for this reaction and the standard free energy change for hydrolysis of fructose-1-P.

Keq = 613 M ΔG° = -15.9 kJ/mol

Equilibrium constant of water?

Keq = [H+][OH-] / [H2O]

What is Keq = ?

Keq = [products] / [reactants]

L/D amino acids do most proteins contain?

L-amino acids Stereoselectivity of L-amino acids contributes to asymmetry in polypeptides Specific stereochemistry promotes formation of 2° structure elements in proteins Other biological molecules (carbohydrates, nucleic acids) exhibit stereoselectivity

How does entropy change of solvent arising from buying hydrophobic groups cause favorable folding?

Loss of water from protein interior and around hydrophobic groups offsets some of the entropy loss due to folding (the hydrophobic effect)

What are the basic amino acids?

Lysine Histamine Arginine

Energy landscape of protein folding: Unfolded state: high energy; high entropy (Top of Funnel)

Many local structures "local" free energy minimum

Which curve is higher? mb or Hb?

Mb has higher increase faster, then plateaus

How do Amyloid structures form?

Molecule (unfolded) self associates, and fibril forms

What is an induced dipole?

Molecules w/o permanent dipoles can become polar via electric field [produced by neighboring charge or polar particle] Molecule with induced dipole = polarizable Interactions of polarizable molecules = induced dipole interactions Anion or cation induces dipole in polarizable molecule, then is attracted to it Interactions with induced dipoles are even shorter range than permanent dipole interactions

What is a dipole?

Molecules with no net charge have internal distribution of asymmetric charge (ie. One end slightly negative, other slightly positive) Polar molecules have a dipole moment (μ); is vector among molecule (linear molecule = vector from + to -; complex molecule is vector sum) Water has greater μ b/c electrons pull toward oxygen b/c more electronegative; molecules with large dipole moments = highly polar Energy of dipole interaction depends on orientation of dipoles...ie. If dipole-dipole, charge-dipole • Pair of polar molecules must be quite close together before dipolar interaction is strong

Weak Interactions: London Dispersion/Van der Waals

Molecules without net charge or permanent dipole moment that attract one another if close enough Electronic charge distribution is NOT static; it moves/fluctuates Energy varies as 1/r^6...are only at short ranges Strong when two planar molecules stack on one another Individually weak but collectively help with stability of molecules Mutual repulsion of molecules/atoms that do not have covalent bonds as their outer electron orbitals overlap; increases rapidly as distance between centers decreases If repulsive energy combined with another attractive energies, total energy E will vary with distance of their separation : total interaction (E) = sum of energy attraction and energy repulsion; distance decreases, attractive and repulsive energy increase at different rates = longer range attraction dominates but repulsive energy increases so rapidly it acts as barrier; it then defines position of closest approach (rv) and van der waals radii (R); position of minimum energy (ro) is close to rv There is a minimum energy curve : position ro; corresponds to most stable distance between centers of two particles; if they approach this is how close they will come Repulsive potential rises so steeply at shorter distances that acts as wall barring approach closer than distance rv; distance defines Van der Waals radius, R = effective radius for closest molecular packing Ie) Two identical spherical molecules rv = 2R; molecules with van der waals radii R1 and R2, rv = R1 + R2 [But real molecules NOT spherical; have complicated shape so extend concept of van der waals radius to atoms/groups of atom]

Assembly of Intermediate Filaments: Alpha-Kertains

Monomer Coiled-coil Dimer Symmetric Tetramer Unit-length Filament [via side-side packing of Tetramer] Intermediate Filament [via end-end packing of Unit]

Is folding pathway random?

NO! Folding proceeds rapidly because the folding process retains partially correct intermediates Polypeptides composed of L-amino acids tend to undergo a right handed twist Nucleation of 2° structure (less favorable than helix extension) Hydrophobic collapse (driven by hydrophobic effect)

Are living organisms at equilibrium?

NO! but are at homeostasis Maintain energy state, so delta G is negative when in homeostasis (unlike equilibrium where delta G =0)

Does the likelihood of a reaction happening (free energy) have anything to do with speed of reaction?

NO! thermodynamics nothing to do with reaction rate

Is the energy landscape smooth?

No it is RUGGED!

The second law of thermodynamics states that any system and its surroundings must increase continually in entropy. However, living organisms constantly create highly ordered structures from less ordered raw materials. Do living organisms violate the second law?

No, living organisms DO obey the laws of thermodynamics. Organisms are open systems and continually obtain energy from the surroundings; this energy is used to generate highly ordered molecular components that constitute the organism.

What conformation is dipeptide bond normally found in?

Normally found in trans! (R-groups of each amino acid are trans; one up one down...180' of each other) [Except sometimes cis in Proline]

What is rate-limiting step in protein folding?

Nucleation

What is a homotropic effector of hemoglobin-oxygen binding? [A homotropic effector is a typical ligand and a heterotropic effector is a different molecule other than the typical ligand]

O2

Where are glycines oriented in Collagen?

Only fits in center of 3-polypeptide helix Because the three chains are so tightly packed

Polypeptide Fragmentation: Determining sequence from Fragments

Order peptide by matching overlapping segments

Which form of phosphoric acid dominates at: At pH 13

PO4-3 will predominate

What can happen to partially folded protein?

Partially folded states are prone to aggregate, driven by hydrophobic forces Kinetically trapped forms

Amphiphilic structures of protein surface...

Polar surface exposed on the surface, nonpolar face buried in the interior

What are fibrous proteins?

Polypepide chain is organized along a single axis Fibrous proteins are mechanically strong and have structural roles long fibrous proteins that are very strong (comprises hair and nails) Alpha-keratin and Collagen and Fibroin

Fibrous Proteins: Alpha-keratin

Polypeptide chains are nearly all a-helical; two polypeptides twist around each other with a left-handed helical twist every 3rd or 4th amino acid is hydrophobic/nonpolar -creates hydrophobic strip along the helical surface Disulfide bonds stabilize and "harden" the material to make hair, skin, nails, claws, beaks, etc. Also keratins are a major class of intermediate filament proteins

What does primary structure do?

Predict protein function - based on correlations of aligned sequences and known functions - if two aligned sequences share at least 25% identity, then they have similar structure and, very likely, similar functions Propose evolutionary relationships among organisms - based on sequence homology from many different organisms - Can be used to predict evolution of diversity in gene families (can determine how related they are)

Which amino acid will rarely/mostly not be found in Alpha helix conformation?

Proline - because of its side chain binding to the amid nitrogen (constrains the phi angle and will usually break the alpha helix) valine and threonine (sometimes) - have branched structures so this can sometimes break the strucutre

What is heme?

Prosthetic group

What are the advantages of Protein Instability?

Protein motion contributes to functions: - Ligand binding - Enzyme catalysis - Enzyme regulation - Metamorphic proteins Types of Motions: - Tyr ring flips, CH3-group rotation (fast) - Hinge bending between domains (slow) - Triggered conformation changes (i.e. ligand binding) - Proline cis-trans isomerization (long time scales) i.e. protein activation and membrane channel opening)

What are the challenges of a protein folding alone/in vivo?

Proteins are metastable and dynamic 20-30% are devoid of structure Protein concentrations are high (300-400 mg/ml) Small proteins fold fast (µm to ms) But large, multi-domain proteins may require min to hours to fold Increase tendency of protein aggregation

What do Chaperones do?

Proteins that interact with, stabilize or help another protein acquire its functional, active conformation *Facilitate native folding pathways *Can restrict pathway that leads to ultimate death of protein (aggregated forms) help convert partially folded forms to a different form that is more en route to becoming folded Chaperones facilitate path toward properly folded state and block transition to aggregated forms (amorphous aggregates) upon hydrolysis of ATP a chaperone can form a clamp while other parts start to fold they help with the initial folding so that the protein can move on to its native form more easily

Steps to breakdown proteins:

Purify protein (develop purification strategy) Separate into individual chains (disulfide bond cleavage) Fragment polypeptides (proteases/chemical cleavage) Sequence each peptide (Mass Spec analysis) Reconstruct sequence (bioinformatics analysis)

Where are R-groups in Beta-strand/sheet?

R-groups extend above and below the plane of the b-sheet structure

Which of the following statements regarding Anfinsen's denaturing experiments with ribonuclease A are valid? 1) Exposing the denatured protein to air oxidation and then dialysis to remove urea restored the protein to its original functionality. 2) Removing urea by dialysis and then allowing air oxidation of the denatured protein restored the protein to its original functionality. 3) Denaturing the protein with both urea and β-mercaptoethanol yielded an inactive protein. 4) Protein folding is determined by its primary sequence.

Removing urea by dialysis and then allowing air oxidation of the denatured protein restored the protein to its original functionality. Denaturing the protein with both urea and β-mercaptoethanol yielded an inactive protein. Protein folding is determined by its primary sequence.

What is a beta-turn/beta-bend?

Requires 4 residues: Pro and Gly are common at positions 2 and 3 of these turns. Type I and type II differ in orientation of amide plane at end of turn. Creates anti-parallel b-pleated sheet structures.

Where do H+ ions come from?

Respiration generates CO2, which is rapidly converted to H+ and HCO3-

Consequences of Planar bond?

Restricts free rotation about the C—N bond (imparts partial rigidity to the chain) C—N Bond length is shorter than normal C—N bonds Peptide bond is relatively polar (net + on N-atom; net - on C-atom)

Process that determined 1' predicts 3': Renaturation of RNase

Ribonuclease in its active form Denatures it --> lose activity of Rnase - using urea (competes with hydrogen bonds) - Beta-Me (reduces disulfide bonds)) lost activity of the Rnase the activity of Rnase assumes a conformation that retains activity if it is allowed to renature

Three Major functional parts of Mass Spec?

Sample is ionized and fragmented Particles then accumulate varying amounts of protons and products are separated by Mass:Charge ratio Then detected

What type of binding curve is seen with Hb and O2?

Sigmoidal Binding curve

Energy landscape of protein folding: Several intermediate states, but not all possible states (Middle of funnel)

Some preferred trajectories; Stability increases with partial structure

What does 2,3-BPG do?

Stabilize the T-state 2,3-BPG binding helps organisms adapt to low [O2] by decreasing the affinity for O2. Binds in central cavity b/w subunits Highly charged, binds positive groups Decreases O2 affinity, allowing organism to adapt to low O2 High 2,3-BPG promotes O2 delivery to tissues [releasing O2 so it can go to tissues] [2,3-BPG] is elevated during adaptation to high altitude; promotes increased O2 delivery to tissues. Fetal Hb has a low affinity for 2,3-BPG

What is Delta G°'?

Standard free energy change at specific pH (reaction with protons)

What are the amino acid components of Collagen?

Stretches of Gly - Pro - Pro/HyPro

What does molecular recognition occur by?

Structural Complementarity 3D Structure (shape and charge) provide identity and potential for recognition/interaction Weak forces maintain structure and determine interactions Interactions are reversible and dynamic Interactions have different quantitative elements associated with interactions • Weakest = van der waals • Strongest = H-bonds [Although weak interactions, many occur at once making them strong]

What determines function?

Structure Ie) antibody and antigen = antibody is structurally complementally to antigen binding site

Which form, T or R, is planar?

T is not planar; R planar form (making it almost flat) [Because Fe2+ made planar in heme]

What conformational changes occur in Hb when O2 binds?

T to R transition O2 binding shifts the Fe+2 to be planar within the heme Histidine is pulled closer to heme, causing larger scale structural changes Rotation of alpha-beta dimers disrupts noncovalent interactions at a/b interfaces [Several salt bridges between subunit interfaces are dissociated]

Hydrogen bonds share both noncovalent and covalent features..T/F

TRUE

Which of the following characteristics are true about a typical peptide (amide) bond? 1) The bond is planar. 2) There is free rotation about the carbonyl carbon and nitrogen bond. 3) There is substantial double-bond character to this bond. 4) There is a net negative charge on nitrogen and net positive charge on oxygen.

The bond is planar. There is substantial double-bond character to this bond.

What drives thermodynamically favorable action of organizing lipid molecules into micelles and cell membranes?

The increased entropy of clustering the hydrocarbons together!

General Principles of Protein Folding:

The protein core is predominantly hydrophobic; surface is hydrophilic Packing is dense and restricted by van der Waals radii; small cavities exist The highly polar N-H and C=O moieties of the peptide backbone must be neutralized in the hydrophobic core, thus a-helices and b-sheets are common b-sheets are usually twisted or wrapped into barrel structures The polypeptide chain generally makes tight turns (b-turn) Unstructured regions exist as "random coil", but it is not really random

Globular Proteins: Tertiary Structures

The protein core is predominantly hydrophobic; surface is hydrophilic The highly polar N-H and C=O moieties of the peptide backbone must be neutralized in the hydrophobic core, thus a-helices and b-sheets are common B-sheets are usually twisted or wrapped into barrel structures The polypeptide chain generally makes tight turns (b-turn)

Protein surface defines function via...

The surfaces of proteins are complementary to the molecules they bind. Protein surfaces interact with solvent. Charged residues can be exposed on the surface

Human and sperm whale myoglobin have very similar primary structures. Which of the following statements are correct? 1) The two proteins are very likely related evolutionarily. 2) The differences in the sequences in many instances represent a conservative change (such L for I). 3) The differences in the sequences in many instances represent a nonconservative change (such as D for A). 4) There is no correlation between the two proteins, since they originate from very different species.

The two proteins are very likely related evolutionarily. The differences in the sequences in many instances represent a conservative change (such L for I).

Which is a plausible explanation for the fact that folding of myoglobin occurs with no net change in enthalpy while the enthalpic change during folding of cytochrome c is -52kj/mol? [Change in enthalpy for myoglobin= 0; change in enthalpy for cytochrome c = -52] A) myoglobin contains abudnance of hydorphobic residues B) cytochrome contains abudnance of hydrohobic residues C) unfolded cytochomr participates in weak interactions with solvent equivalent to those in the folded polypeptide D) The unfolded form of the myoglobin participates in weak interactions with solvent equivalent to those in the folded polypeptide E) Myoglobin has high content of alpha helices and cytochrome c is primarily unstructured F) energetic of myoglibn folding are noncanoonical G) heme group of myoglbin imparts additonally stability compared to cytochome c

The unfolded form of the myoglobin participates in weak interactions with solvent equivalent to those in the folded polypeptide

Which statements about turns are correct? 1) Their purpose is to reverse the direction of the polypeptide chain. 2) There are two types, I and II, which differ mainly in the conformation about the i+1 and i+2 residue amide bond. 3) They typically contain large, hydrophobic residues. 4) Their conformation is held in place through H bonds.

Their purpose is to reverse the direction of the polypeptide chain. There are two types, I and II, which differ mainly in the conformation about the i+1 and i+2 residue amide bond. Their conformation is held in place through H bonds.

What happens if disulfide bonds are present in Alpha-Keratins?

They stabilize the material; hardening it

Dissociation of Amino acids: Lysine

Three protons COOH, NH3+, NH3+ --> +2 COO- , NH3+, NH3+ --> +1 COO-, NH2, NH3+ --> 0 COO-, NH2, NH2 --> -1

Dissociation of Amino acids: Glu

Three protons can dissociate: COOH, COOH, NH3+ --> +1 COO-, COOH, NH3+ --> 0 COO-, COO-, NH3+ --> -1 COO-, COO-, NH2 --> -2

What are the polar amino acids?

Threonine Serine Asparagine Cysteine Tyrosine Glutamine

Where is the DNA binding domain of Alpha helix?

Towards N terminus because has (+) charge

How does proteostasis fail?

Toxic oligomers form [Oligomers are most toxic species that can cause neurodegenerative diseases] Stable fibrillar amyloid structures form, typically rich in b-sheet Disease ensues

Formation of Collagen Fibers?

Tropocollagen aligns as staggered array to form a collagen fiber Hydroxylysine crosslinks stabilize and stiffen the fibers and increase with age (covalent linkage) [causing brittle bonds to form] not a lot of cystein groups in collagen fibrils.

What is basic unit of Collagen?

Tropocollagen; Three intertwined poly peptides (alpha helices) that are more extended than alpha helices

What makes folding favorable?

Unfavorable conformational change in polypeptide, favors unfolded state [unfolded polypeptide is higher entropy than folded conformation] Favorable entropy change of the solvent arising from burying hydrophobic groups [Loss of water from protein interior and around hydrophobic groups offsets some of the entropy loss due to folding (the hydrophobic effect)] Favorable enthalpy contribution arising from intramolecular noncovalent interactions - van der Waals interactions are a primary contributor; there are many in the protein core - hydrogen bonding likely "cancel out" with respect to free energy change -ionic interactions may contribute due to proximity effects (variable)

Calculate the concentration of formate in a 10mM solution of formic acid at pH 4.15. pKa for formate = 3.75

Use Henderson-Hasselbalch equation: 4.15 = 3.75 + log ([A-]/[HA]) Start with 10 mM formic acid, so at equilibrium, will have [HA] + [A-] = 10 and [A-] = 10 - [HA] 0.4 = log [A-]/[HA] 2.51 = [A-]/[HA] = (10 - [HA]) / [HA] 2.51[HA] = 10 - [HA] 3.51[HA] = 10 [HA] = 2.85 mM [A-] = 10 - [HA] = 10 mM - 2.85 mM = 7.15 mM

The activity of an enzyme requires a glutamic acid to display its g-COOH (carboxyl) functional group in the protonated state. Suppose the pKa of the -COOH group is 4.07. c) At what pH will the enzyme show 78% of maximal activity?

Use the Henderson-Hasselbalch equation. At 78% of max activity, -COOH (a.k.a. HA) is 78% and -COO- (a.k.a. A-) is 22% pH = pK + log (22/78) = 3.52

A 2-year old child presents in the emergency room with metabolic acidosis after ingesting an unknown number of flavored aspirin tablets. At presentation, her blood pH was 7.0. Given that the pKa of aspirin (salicylic acid) is 3, calculate the ratio of its ionized to un-ionized forms at pH 7.0.

Use the Henderson-Hasselbalch relationship: 7 = 3 + log ([A-]/[HA]) Solve for [A-]/[HA] = 104

What type of interactions are prominent in Fibroin?

Van der Waals between methyl groups (giving silk flexibility) H-bonds between strands

what defines how tight 2' structures can pack together?

Van der Waals radii define many boundaries Creates many small cavities that allow for flexibility

Weak acids/bases or strong acids/bases are good buffers?

WEAK

How do hydrophilic molecules react in aqueous solution?

Water dissolves molecules (proteins and nucleic acids) that display on their solvent-accessible surfaces groups that can h-bond [hydroxyl, carbonyl, ester groups; they're polar uncharged...also charged groups = protonated amines, carboxylates and phosphate ethers Molecules with internal h-bonds dissolve in water, some/all internal h-bonds may be in dynamic exchange with h-bonds in water Polar nature of water contributes to ability to dissolve non-ionic polar organic molecules = phenols, esters, amides; have large dipole moments and interaction with water dipole promotes solubility in water

What properties of water make life possible?

Water's high dielectric constant allows it to dissolve polar and charged molecules alike Water is less dense as a solid than as a liquid. Water has strong hydrogen bonding interactions between molecules, which allow it to exist at ambient temperature as a liquid.

What are hydration shells?

When binding with ionic compounds (like NaCl) water forms hydration shells (water molecules completely surround Na+ or Cl-) via charge-dipole interactions Solid state stable latices of ions dissolve easily in water b.c polar nature of water molecule; interactions of negative ends of water dipoles with cations and positive ends with anions; ions become hydrated (surrounded by shells of oriented water molecules = hydrated shells) (energy released compensates for loss of charge-charge interactions stabilizing crystal), and high dielectric constant of water screens and decreases electrostatic force b/w opp charged ions that would pull back together

Water and non polar molecules: Low energy, high entropy

When nonpolar molecules congregate together (forming clathrate), fewer water molecules are needed (since they are all bound together); more free water molecules

Symmetry (concerted) model/MWC model - Protein Changes: When is R favored over T?

When substrate binds [R = oxygenated; T = nonoxygenated]

Water and non polar molecules: High energy, low entropy

When water surrounds singular groups of nonpolar molecules (like hydrocarbons); not energetically favorable

The acyl-CoA synthetase reaction activates fatty acids (R-COO-) for oxidation in cells. The fatty acid is converted to an activated form, fatty acyl-CoA. R-COO- + CoASH + ATP g <--> + AMP + pyrophosphate The reaction is driven forward, in part, by cleavage of ATP to AMP and pyrophosphate. However, pyrophosphate also undergoes further cleavage to yield two phosphate anions. pyrophosphate + H2O g <--> 2 PO4-2 Discuss the energetics of this reaction both in the presence and absence of pyrophosphate cleavage.

Without phosphate hydrolysis, the acyl-CoA synthase reaction is only slightly favorable. With pyrophosphate hydrolysis, the net ΔG°' for the reaction is -33.6 kJ/mol, a far more favorable value.

Fractional saturation expression of Mb?

YO2 = sites occupied / total available sites YO2 = [O2] / (Kd + [O2])

Is it thermodynamically favorable for hydrocarbons to associate with themselves in aqueous solution?

Yes because increases entropy (favorable) and produces reduced free energy (favorable)

Do water's h-bonds constantly change/are dynamic in liquid form?

Yes! Water h-bonds are dynamic (constantly re-bond and form new h-bonds) when in liquid form

Is folding favorable?

Yes! Folding is favorable and spontaneous - Although unfavorable for protein to fold (because decrease in entropy; favors unfolded state) - Favorable Entropy change when solvent folds because hydrophobic effect (bury hydrophobic groups when folded) - Favorable enthalpy change due to intramolecular noncovalent interactions [van der waals forces make hydrophic effects possible (what holds the hydrophobic chains together)]

Ka = ?

[H+][A-] / [HA]

What is a domain?

a compact, locally folded region (i.e., a kinase domain). Small compact subset of polypeptide chain; may carry out specific function Domains put together with flexible regions of protein usually so have hinge/mobile area between proteins

The presence of a hydrophobic amino acid at every third or fourth residue in α-keratin results in what?

a strip of hydrophobic surface area that, when combined with another monomer, results in the formation of a dimer through hydrophobic interactions

For the process: AD< --> B, the Keq (AB) is 0.02 at 37°C. For the process: BD< -->C, the Keq (BC) is 1000 at 37°C. a) Determine Keq (AC), the equilibrium constant for the overall process A D<--> C. b) Determine standard-state free energy changes for all three processes and use ΔG° (AC) to determine Keq (AC). Does the value agree with that determined in part (a) of this problem?

a) Keq(AC) = 20 ΔG°AC = -7.7kJ/mol b) Yes.

Assume you have a solution of 0.1 M glucose-6-phosphate (G-6-P). To this solution you add the enzyme phosphoglucomutase, which catalyzes the reaction: glucose-6-phosphate D <--> glucose-1-phosphate The ΔG°' of this reaction is 7.5 kJ/mol a) Does this reaction proceed at al as written, and if so, what are the final concentrations glucose-6-phosphate (G-6-P) and glucose-1-phosphate (G-1-P). b) Under what cellular conditions, if any, would this reaction continuously produce glucose-1-phosphate at a high rate.

a) Yes. Final concentrations are: [G-6-P] = 0.0954 M and [G-1-P] = 0.0046 M b) If G-6-P is constantly supplied and G-1-P constantly consumed by other reactions to maintain a high ratio of [G-6-P]/[G-1-P], then G-1-P production continues at an appreciable rate.

Hydrolysis of a peptide bond produces:

an amine and a carboxylic acid

Free-Rotation around peptide bond: Phi and Psi Angles

angle about Alpha Carbon—C bond is ψ (psi) angle about Alpha Carbon—N bond is φ (phi) allow for the certain degree of freedom that these bonds have

Myoglobin without a heme group would be considered a(n) ___________ .

apoprotein

Which of the following statements is true about a protein that is in an aqueous solution that has a pH equal to the pI of the protein? a) At pH = pI, there is a net positive charge on the protein. b) At pH = pI, there is a net negative charge on the protein. c) At pH = pI, there is no net charge on the protein. d) There is not enough information to answer this question.

c) At pH = pI, there is no net charge on the protein

Which of the following statements regarding the folding of proteins is NOT true? a) Internal H bonds stabilize the fold. b) Salt bridges stabilize the fold. c) Hydrophobic residues pack together because the side chains are attracted to each other through weak Van der Waals interactions. d) Van der Waals interactions have a stabilizing, cumulative effect.

c) Hydrophobic residues pack together because the side chains are attracted to each other through weak Van der Waals interactions. The driving force for this packing is the increase in entropy experienced by solvent when hydrophobic groups pack together. Although packing of hydrophobic molecules increases the order (a decrease in entropy), there is a greater increase in disorder in the solvent, which compensates for this. This is the essence of the hydrophobic effect.

Which of the following atoms could interact through a hydrogen bond? a) none of the above b) the hydrogen on an aromatic ring and the oxygen of carbon dioxide c) the hydrogen of an amine and the oxygen of an alcohol d) the oxygen of a ketone and the hydrogen of an aldehyde e) the oxygen of methanol and a hydrogen on the methyl carbon of methanol

c) the hydrogen of an amine and the oxygen of an alcohol

Why are weak acids and bases good buffers?

can withstand changes in pH over broad ranges so are important and can act as buffers

Intrinsically Unstructured Protein:

contact their target proteins over a large surface area and adopt a well-defined structure when bound. are unstructured in solution Enriched in polar amino acids; lack hydrophobic amino acids adopts different conformations depending on its target

The binding of oxygen to hemoglobin is said to be ___________ .

cooperative

Which of the following is FALSE when considering van der Waals interactions? a) The total interaction energy is the sum of the attractive and repulsive forces. b) Molecules that interact by van der Waals forces do not interpenetrate. c) Van der Waals radii can determine molecular surfaces. d) They are not important in determining the stability of three-dimensional structures of proteins. e) The van der Waals radius represents the most stable distance between two interacting centers

d) They are not important in determining the stability of three-dimensional structures of proteins.

At equilibrium what is delta G?

delta G = 0; no net change in the system

What happens when weak acid/base dissociates?

dissociate only partly; weak acid in aq there is equilibrium between acid and conjugate base (which can accept H+ to become acid again)

What additionally stabilizes a folded protein?

disulfide bonds - additional covalent bonds confer enhanced stability to folded protein - Most intracellular proteins lack disulfide bonds; extracellular environment is more oxidizing, so more S—S bonds exist. prosthetic groups and ion binding - further enhance stability of folded forms

The peptide hormone insulin is composed of two peptides held together primarily by what mechanism?

disulfide bonds between cysteine residues

Why is water universal solvent?

due to its polar nature - Forms charge-dipole interactions with Salt compounds (making hydration shells) - Forms h-bonds

Which of the following statements regarding structural proteins is true? a) silk fibroin is made from a repeat of three amino acids where each third amino acid is Gly b) none of the above c) generally speaking, structural proteins are soluble in water d) α-keratin is composed of peptides that contain mostly α-helical structure with the exception of short sequences where the peptide folds back on itself e) collagen has its own helical structure where the three individual peptides are wound around each other in a left-handed helix

e) collagen has its own helical structure where the three individual peptides are wound around each other in a left-handed helix

What is standard state?

every reactant starts out at 1 molar and gas is at 1 atmosphere is the free energy change when all products and reactants are present at unit activity or standard state (solid, a 1 molal solution or 1 atmosphere (gas); solvent = unit activity by convention)

Where are R-groups in alpha helix?

extend out from axis of the helix Outward because no space inward

Additional Stability of Folded Proteins: Prosthetic Groups and ion Bonding

further enhance stability of folded forms

Fibrous Protein: Fibroin

has beta-sheet structure; makes silk like structure Van-der waals interaction between methyl groups; [so many that is allows flexibility of silk strand and the strength of it] Alternating ß-strands of sequence: Gly-Ala-Gly-Ala-Gly-Ser-Gly-Ala-Ala-Gly-(Ser-Gly-Ala-Gly-Ala-Gly)8 Individual r-groups orient in one direction (glycine on top, alanine on bottom) Strands are organized/stabilized via h-bond interactions Have unstructured regions and can extend

Which of the following is true of hemoglobin? a) hemoglobin undergoes a transition from a high affinity state under low oxygen pressures to a low affinity state under high oxygen pressures b) at low oxygen pressures, hemoglobin is in a high oxygen affinity state c) hemoglobin undergoes a transition from low affinity state under low oxygen pressure to a high affinity state under high oxygen pressure d) at high oxygen pressures hemoglobin is in a low oxygen affinity state e) none of the above

hemoglobin undergoes a transition from low affinity state under low oxygen pressure to a high affinity state under high oxygen pressure

What contributes to 3' Structure?

hydrophobic interaction between leucine and valine disulfide bond hydrogen bond between serine hydroxyl group and the amide of glutamine charge-charge interaction between lysine and aspartic acid

Amphipathic molecules and membrane formation: Micelles

if mixture stirred, spherical structures form via single layer of molecules; aka bilayer vesicles; hydrocarbon tail lies in roughly parallel arrays allowing them to interact via van der waals interactions; polar ionic head groups are strongly hydrated via water around them

If [O2] in tissues is 30 mmHg, how much Mb is bound?

myoglobin is ~95% saturated

What are amphipathic/amphiphilic molecules?

non polar and polar characteristics hydrophilic and hydrophobic properties; ie) fatty acids, detergents, lipids à have head hydrophilic and tail hydrophobic; when dissolved in water they form one or more structures...

Amphipathic molecules and membrane formation: Monolayers

on water surface; only head group is immersed

pKw = ?

pH + pOH = 14 ie) pH = -log(10^-7) = 7

How to get pH from [H+]?

pH = -log10[H+]

How to find pH from pKa?

pH = pKa + log10 [A-]/[HA]

pKw of water?

pKw = 14 = pH + pOH

What is the titration midpoint?

pka = pH pH minimal change [HA] = [A-]

What causes denaturation of a protein when disulfide bonds are present?

reducing agent detergent heat pH changes

What do allosteric effector molecules do?

regulate protein function (positively and negatively).

When does myoglobin dissociate O2?

releases O2 at lower [O2] when needed for respiration [as actively respiring, Myoglobin releases O2]

Why is the surface of proteins important?

relevant structural parts of the protein (they define how substrate and binding pockets are made and where mutations might occur and this can affect the structure)

Polypeptide Fragmentation: Chymotrypsin

specific for cleavage at the carboxy side of large aromatic amino acids (Y, F, W...sometimes L) [Cleaves at right side of amino acids YFW, and L)

When will 2' structure motifs form?

stabilized by hydrogen bonding with sterically permissible values of φ & ψ

Amphipathic molecules and membrane formation: Biological bilayer membrane

surrounding cells/between cell compartments; made via phospholipids

If have multiple protons that can dissociate, which are used to find pI?

take the two closest ones to add together; then divide by 2

What does reflection point on image represent?

the pH where the solution would function most effectively as a buffer the weak acid is 50% protonated, 50% deprotonated concentration of weak acid and conjugate base are equal pH of solution equals pKa of weak acid

What are Metamorphic proteins?

they can take on different conformations both parts of the equilibrium have to there for protein to carry out role

Based on the plot of oxygen saturation versus partial pressure of O2, which of the following statements is true?

under periods of extreme muscle exertion, capillary oxygen pressure can drop to 10 mm Hg, allowing release of ~90% of oxygen carried by hemoglobin

Why is it an unfavorable conformation change in polypeptide chain folding?

unfolded polypeptide is higher entropy than folded conformation

What types of acids/bases are amino acids?

weak acids and bases

Stronger the acid = _____ the base

weaker greater tendency of acid to donate proton, less conjugate base accepts proton and re-forms acid

At physiological pH, most amino acids are ______________, meaning that they contain both a positive and negative charge

zwitterions

When weak binding what is YO2?

~70% of O2 released [low value] in tissues

The standard-state free energy of hydrolysis for acetyl phosphate is ΔG° = -42.6 kJ/mol. Acetyl-P + H2O g --> acetate + Pi Calculate the free energy change for acetyl phosphate hydrolysis in a solution of 2 mM acetate, 2 mM phosphate, and 3 nM acetyl phosphate

ΔG = -24.5 kJ/mol @ 25°C or ΔG = -23.7 kJ/mol @ 37°C

Beta-sheets: Parallel Phi and Psi Angles

Φ = -120° & ψ = 105° (parallel)

Beta-sheets: Antiparallel Phi and Psi Angles

Φ = -135° & ψ = -140° (anti parallel)

Details of Alpha Helix: Phi and Psi values...

Φ = -60° & ψ = -45°

Interactions: Charge-induced dipole

• Anion or cation induces dipole in polarizable molecule, then is attracted to it • Energy proportional to 1 / r^4

Interactions: Dipole-Dipole

• In aqueous environment, polar molecule attracted to another polar molecule [dipolar interactions] • Energy is proportional to 1 / r^3

Interactions: Charge-Dipole

• In aqueous environment, polar molecule attracted to nearby ion [dipolar interactions] • Energy is proportional to 1 / r^2

Interactions: Dipole-induced dipole

• Permanent dipole induces dipole in polarizable molecule then it is attracted to it • Energy proportional to 1 / r^5

What are buffers?

• Solutions that resist changes in pH • Consist of weak acid and conjugate base • Produce almost flat slope when pH = pKa (minimal change in pH) • Only work when in about a pH unit of their pKa

Organization of Multi-subunit proteins Point-Group Symmetry

• Symmetry down center of molecule