Review for Midterm

B) the folding of the polypeptide chain.

Hydrophobic amino acid sequences in myoglobin are responsible for A) covalent bonding to the heme prosthetic group. B) the folding of the polypeptide chain. C) the irreversible binding of oxygen. D) A and B above.

C. Secondary and Tertiary

In the image of the beta-barrel cytosolic protein what level(s) of protein structure are clearly indicated/given in the pictures: A) Primary, Secondary, Tertiary, and Quaternary B) Primary, Secondary, and Tertiary C) Secondary and Tertiary D) Tertiary and Quaternary E) Secondary, Tertiary, and Quaternary

FALSE only hemoglobin does

Both myoglobin and hemoglobin exhibit cooperative binding to oxygen. (T or F)

C is the correct answer because if you're looking for something to form in the interior you want a lot of hydrophobic residue, A is very hydrophobic but has a Pro in it which disrupts the formation of ALPHA helicies so, C is the best option.

1. Based on our discussions and the problems we did in class, which peptide sequence below is most likely to form an alpha-helix at pH 7 in the interior of a globular, folded protein? A) Valine-Isoleucine-Methionine-Proline-Alanine-Glycine-Tryptophan-Phenylalanine B) Aspartate-Alanine-Valine-Isoleucine-Glutamate-Phenylalanine-Methionine-Aspartate-Alanine C) Alanine-Methionine-Phenylalanine-Valine-Isoleucine-Leucine-Tryptophan-Alanine D) Proline-Glycine-Serine-Alanine-Glutamine-Valine-Asparagine-Isoleucine-Histidine-Leucine E) Histidine-Alanine-Valine-Isoleucine-Lysine-Phenylalanine-Methionine-Arginine-Alanine

E. A loop

1. The overall structure shown here is known as a beta-barrel, and is a cytosolic protein. The interior of the barrel is packed solid. Thus, the interior of the barrel is completely filled up with side chains. This barrel does not form a pore. Study the structure and its scale. The region circled at the bottom of the image can best be described as: A) A motif B) A domain C) A subunit D) A turn E) A loop

Moving the reaction from room temperature to a water bath at 37ºC to simulate body temperature will convert the reaction from exergonic to endergonic At its room temperature, the reaction is spontaneous as written under given conditions.

22ºC is the temperature of the room in which the following reaction is run: nACS <----> 2CTB The stoichiometry is 1:2 for this reaction. ΔH = -0.9 kJ/mole ΔS = -3 J/mole K Which statement(s) below are correct? Select all that are correct, deductions for incorrect selections. Pay attention to units

A. is induced by oxygenation.

7) Cooperative binding of oxygen by hemoglobin A. is induced by oxygenation. B. is induced by hemoglobin. C. is a result of different affinities for oxygen by each subunit protein. D. is a result of interaction with myoglobin.

B. different binding affinities for oxygen.

7) The main property of myoglobin and hemoglobin that makes them an efficient system for oxygen delivery from lungs to muscles is A. cooperativity. B. different binding affinities for oxygen. C. movement of the protein shapes. D. hydrophobicity. E. All of the above.

C.) RNA DNA and Ribosomes

9. Which three cellular components are present in both prokaryotes and eukaryotes? A) ribosomes, chloroplasts, mitochondria B) nucleus, ribosomes, RNA C) RNA, DNA, ribosomes D) endoplasmic reticulum, DNA, RNA E) mitochondria, DNA, RNA

A) has a single equilibrium constant for oxygen binding.

A hyperbolic binding curve, such as what myoglobin exhibits for oxygen, differs from a sigmoidal binding curve, which hemoglobin has for oxygen, in that the hyperbolic curve A) has a single equilibrium constant for oxygen binding. B) binds more oxygen after the initial proteins first bind oxygen. C) shows cooperativity. D) binds up to four molecules of oxygen. E) All of the above.

The cells has two main options: 1. Raise [reactant] concentration and/or lower [product] concentration. 2. Couple the reaction, usually via high energy intermediate, to a favorable chemical reaction. The correct answer is: The concentration of reactants could increase and the concentration of products could decrease

A reaction in the human cell has a positive actual Gibbs Free Energy change value under current conditions. ΔG = + kJ/mole What could happen to this reaction such that it converts from non-spontaneous to spontaneous in the cell? Select one: a. The cell will change the equilibrium constant for the reaction by decreasing the amount of product or reactants b. The concentration of reactants could decrease and the concentration of products could increase c. The human cell can raise the temperature to 100 degrees Celsius d. The concentration of reactants could increase and the concentration of products could decrease

at equilibrium, dG = 0 kJ/mole 0 = -10 + RTlnKeq 0 = -10 + (0.00831)(295)lnKeq 0 = -10 + 2.45lnKeq Keq = ~59 The correct answer is: 59

A reaction is currently at equilibrium at room temperature (295ºK). The standard Gibbs Free Energy change (ΔG°') for this reaction is -10 kJ/mole. R = 8.314 J/mole K R = 0.00831 kJ/mole K What is the equilibrium constant (Keq) for this reaction under the present conditions of current temperature and pressure? Report numerical answer to 1 decimal point. Do not include units.

D) 5, 5

A ribopyranose contains ________ carbon atoms while a ribofuranose has ________ carbon atoms. A) 6, 5 B) 6, 6 C) 5, 6 D) 5, 5

a. negative Gibb's free energy

A spontaneous chemical reaction always has a ________ change. Select one: a. negative Gibb's free energy b. positive Gibb's free energy c. negative enthalpy d. positive entropy e. positive enthalpy

negative, negative

An endergonic reaction with a ______ dH and a ______ dS can be changed into an exergonic reaction by decreasing the temperature.

a. results in the factor ΔS being positive

An increase in disorder in the system Select one: a. results in the factor ΔS being positive b. is characteristic of a system increasing in enthalpy. c. is found in every exergonic process. d. is required for a process to be spontaneous e. results in a decrease in entropy

B) via a linear intermediate, which requires the breaking of C-C bonds

Anomers can be interconverted ________. A) by rotation about carbon-carbon bonds B) via a linear intermediate, which requires the breaking of C-C bonds C) by an isotopic exchange reaction D) None of the above. Anomers cannot be interconverted.

Plot #4

Below is the rate equation for the following chemical reaction: A --> B. Rate = k[A]0 Which plot below best describes how the rate changes as the concentration of A changes? Analyze the equation exactly as written above and take the math literally.

Polymers are made up of long, repeating chains of similar molecules called monomers. Lipids are made up of fatty acids and glycerol, which do not form repetitive chains and thus cannot be considered monomers. Since lipids do not contain monomers, they are technically not polymers. monomers are held together by COVALENT bonds in polymers lipids aggregate and DO NOT form COVALENT bonds with each other

Briefly explain why nucleic acids, proteins, and carbohydrates are considered polymers, but lipids are not true polymers. Use terms and language from chemistry to bolster your argument. (Try to keep your answer to under 100 words; deductions for incorrect statements... do not stray...)

E) all of the above.

Carbohydrates are components of the following: A) the membrane of red blood cells. B) nucleic acids. C) the hormone erythropoietin. D) the bacterial cell wall. E) all of the above.

H2CO3 --> H+ + HCO3- pKa = 6.4 This is the reaction that will be relevant around physiological pH pH = 6.4 + log[bicarb/carbonic acid] solve for [bicarb/carbonic acid] BUT.... question asks for ratio of CARBONIC ACID: BICARB switch the ratio around!!!!! SNEAKY SNEAKY SNEAKY, Pay attention to language ratios are 0.13 and 0.25, respectively. 3. CO2 dissolves to form H2CO3 as CO2 increases, H2CO3 increases. H2CO3 is an acid that will lower pH cause pKa is 6.4, which is below physiological pH

Carbonic acid is H2CO3 Bicarbonate is HCO3(-) Carbonate is CO3(-2) Carbonic acid has pKa values of 6.4 and 10.4, respectively. CO2 dissolves in water under the following reaction: CO2 + H2O <----> H2CO3 1. What is the ratio of carbonic acid to bicarbonate in the blood at pH 7.3? 2. What is the ratio of carbonic acid to bicarbonate in the blood at pH 7.0, under a state of acidosis? 3. Using what you know from acid-base chemistry and Le-chatelier's principle, explain why CO2 lowers the pH of blood... especially under conditions of rapid CO2 generation.

D) quaternary

Changes in hemoglobin's oxygen affinity are primarily the result of changes in the _________ structure of the protein. A) primary B) secondary C) tertiary D) quaternary E) all of the above

1) Decrease in carbon dioxide (increase affinity, shift to the 'left') 2) Increase in 2,3-BPG (decrease affinity, shift to the 'right') 3) Increase in pH (increase affinity, shift to the 'left') 4) Loss of quaternary structure (huge decrease in affinity, shift farthest to the 'right', no cooperativity, non-sigmoidal) 5) Increase in H+, increase in 2,3-BPG, and increase in CO2 (large decrease in affinity, shift farther 'right')

Compared to purified hemoglobin, draw five ligand plots (fraction bound vs. pO2) for hemoglobin that demonstrate the following: compared to pure hemoglobin

D) All of the above.

Conditions in the tissues which enhance the delivery of oxygen by hemoglobin are the presence of A) carbon dioxide. B) 2,3 BPG. C) protons. D) All of the above. E) A and B above. Ans: D

Protein A is more likely to have many hydrophobic residues necessary for folding when compared with Protein B BECAUSE: Protein A is entropically driven (POSITIVE dS) ; which suggests hydrophobic effect is critical and many hydrophobic residues Protein B is enthalpy driven (VERY NEGATIVE dH). Enthalpy driven suggests more non-covalent interactions

Consider the change in enthalpy and entropy of folding for two proteins, A and B, below. Both proteins are about the same size. Protein A has the following values: ΔS = + 2 kJ/molK ΔH = -1 kJ/molK Protein B has the following values: ΔS = -0.5kJ/molK ΔH = -100kJ/mole Which hypothesis below most agrees with the data observed above? Select one: a. Protein A is more likely to have many hydrophobic residues necessary for folding when compared with Protein B b. Protein A will form while it is still being translated; protein B will not fold until the entire protein has been translated c. Protein A is not likely to require chaperones to assist its folding; protein B will likely require chaperones to assist its folding d. Protein A likely has no secondary structure while Protein B is entirely alpha-helical and/or beta-sheet e. Protein A is more likely to form an extensive network of non-covalent interactions that are needed for folding when compared to protein B

+4 You know how to do this, write it out starting with NH3 and then all the amino acids with charges and then the COO- REMINDER OF PKAS TO USE: NH3: 9 Arg: 12 Lys: 11 Glu: 4 Asp: 3 His: 6 Cys: Tyr:

Consider the following peptide: Ala-Ile-Asp-Gln-Tyr-Lys-Arg-Pro-Asn-Lys-Trp-Leu What is the net charge of this peptide at pH 1?

the pI will be above 7

Consider the following peptide: Val-Ser-Thr-Leu-Gln-Arg-Asn-Lys-Ile-Pro-His-Lys-Arg-Leu Which statement below is most correct regarding this peptide's pI? Select one: a. the pI will be below 7 b. the pI will be around 7 (between 6 and 8) c. it is impossible to make an educated estimate as to a peptide's pI d. the pI will be above 7

he pI for this peptide is below 7

Consider the following peptide: Thr-Leu-Phe-Asp-Gly-Asn-Gln-Glu-Asp-Ala-Leu-Pro-Arg Which statement is most correct regarding an estimated pI for this peptide? Select one: a. the pI for this peptide is 0 b. the pI for this peptide is approximately 7 (between 6 and 8) c. the pI for this peptide is above 7 d. the pI for this peptide is below 7 e. it is impossible to reasonably estimate the pI or a peptide

How to solve: 1. Calculate Q. Q = [NH3]^3 / ( [N2][H2]^3 ) = a huge, huge number!! Way, way, way bigger than 1.2 2. Since Q >> Keq, the reaction is not at equilibrium. Reaction is at equilibrium when Q = Keq 3. Since Q>> Keq, the reaction must shift to consume more NH3 and shift back to reactants. Vice-versa if Q where smaller than Keq.

Consider the following reaction and the given parameters: N2 + 3H2 <----> 2NH3 Keq = 1.2 It is determined that there are 0.1 moles of N2, 0.02 moles of H2, and 0.3 moles of NH3 in a 2L flask 3 minutes after mixing the gases. A. Has the reaction reached equilibrium? Briefly justify your answer... a one-word answer will not suffice. B. Past this 3 minute point, do you expect more NH3 to be found in the flask in the future, or less NH3 to be found in the flask in the future? Explain.

MY ANSWER: 1.) Most Abundant: G1Br, AcO, G1Ac, Br 2.) Due to the Keq being less than 1, during equilibrium, there will be more reactants present than there are products. Since it is a reverse reaction, fewer reactants are being used, but products are still getting made. I'm not sure if the products are equalling the same amount since Br tends to break off a lot due to it being a great leaving group. CORRECT ANSWER: Tiny Keq value. Super small. Barely any products at equilibrium. Excess of G1Br over other reactant: G1Br>AcO>>G1Ac=Br 1:1 stoichiometry of reaction means equal amounts of the two products at equilibrium (albeit very small quantities

Consider the following reaction: G-1-Br + AcO --> G-1-Ac + Br Keq = 0.000001 You start the reaction with the following conditions in a beaker with suitable solvent: 100mM G1Br 10mM AcO 0mM G1Ac 0mM Br Equilibrium is reached at 1 hr. Think about what species will be present at equilibrium based on the given information. (ignore solvent molecules) Part 1: Rank the molecules abundance in the beaker at equilibrium, from greatest to least. If there is an equal amount of certain species, use the "=" to claim so. Part 2: Briefly explain your rationale for the ranking you selected.

Peptide 1 is a beta sheet because it goes in a pattern of hydrophobic hydrophilic Peptide 2 is an alpha helix because it has a hydrophobic then 3 hydrophillics then a hydrophohbic again, in a pattern.

Consider the following stretches of amphipathic peptides: WHICH ONE IS A BETA SHEET AND WHICH ONE IS AN ALPHA HELIX Peptide 1) Val-Ser-Iso-Thr-Val-Asp-Ala-Gln-Iso-Thr-Ala-Ser Peptide 2) Val-Ser-His-Thr-Iso-Asp-Gln-Ala-Asp-Thr-Ser-Ala

10

Consider the peptide below with the associated pKa values: Ala-Val-Asp-Lys-His-Arg-Ser-Thr-Asn The peptide has the following pKa values: C-terminal COOH pKa = 2 Asp pKa = 4 His pKa = 7 N-terminal pKa = 9 Lys pKa = 11 Arg pKa = 12 What is the pI of this peptide?

independently folded and stable region of a polypeptide, found at tertiary level

Define Domain

localized, common region of combined secondary structure elements (like a helix-turn-helix)

Define Motif

complete polypeptide that is one chain and part of a quaternary structure

Define Subunit

2 H-bonds per residue (106 total) because both the carbonyl oxygen of each amino acid and the amide proton of each amino acid will participate in H-bonding. #turns = 53/3.4 = about 15 turns

Hemagglutinin in the influenza virus contains a very long alpha-helix that is 53 residues long. Determine how many turns the helix will have, how many H-bonds would you expect to find in this helix?

Heme is hydrophobic Colored Planar Binds Fe2+ (iron) Then iron in the heme will bind to O2 Binds non-covalently to globin

Heme

tetrameric, quaternary structure 4 polypeptide chains Has 4 hemes Binds up to 4 oxygens (O2) Oxygen transporter CO2 transporter, too Lower affinity for oxygen than myoglobin at low [O2] Found in Red Blood Cells

Hemoglobin

Kd is the same math expression as Keq and the units are in molarity Lower the Kd means a TIGHTER BINDING

Kd and P50 measures affinity. Kd means the dissociation constant and mesures how tightly a ligand binds

A is the phosphoanhydride bond, B is the amide bond, and C is the phosphate ester bond

Label the amide bond, the phosphoanhydride bond, and the phosphate ester bond.

Molecule 1 is a carbohydrate; Molecule 2 is a protein

Match each description below with the correct biomolecule. Molecule 1: is used as a structural component of the cell, is a large polymer of repeating sugar units, is insoluble in water Molecule 2: is used as a structural component of the cell, is a large polymer of repeating amino acids, is insoluble in water Select one: a. Both molecules are proteins b. Both molecules are carbohydrates c. Molecule 1 is a carbohydrate, Molecule 2 is a lipid d. Molecule 1 is a lipid, Molecule 2 is a protein e. Both molecules are lipids f. Molecule 1 is a carbohydrate; Molecule 2 is a protein

1. ribosome, in cytosol 2. Nucleus - for eukaryotes; cytosol for prokaryotes 3. Mitochondria for eukaryotes and cytosol for prokaryotes 4. Plasma membrane 5. Cytosol 6. Plasma membrane 7. Cytosol 8. Mitochondria

Match the descriptions below with the biological component it describe (some terms used more than once) Components: plasma membrane, ribosome, cytosol, nucleus, mitochondria 1. Site of protein synthesis in the cell 2. Cellular compartment that contains genetic information 3. Where do you think the TCA cycle (Krebs Cycle) is catalyzed? 4. A lipid bilayer surrounding the cell 5. Defines much of the volume of the cell 6. Defines much of the surface area of the cell 7. Is an aqueous environment 8. Is the site of ATP synthesis

Monomeric, tertiary structure, 1 polypeptide chain Has heme Binds 1 oxygen (O2) Found in tissues (like muscle cells) Higher affinity for oxygen than hemoglobin at low [O2] Used for oxygen storage in cells

Myoglobin

Spectra #1 belongs to Peptide Y while Spectrra #2 belongs to peptide Z

Peptide X is placed into buffer at a 1mM concentration in a separate test tube. Peptide X is Ala-Val-Ile-Ser-Thr-Gln-Asn-His-Pro-Gly Peptide Y is placed into buffer at a 1mM concentration in a separate test tube. Peptide Y is Gly-Gly-Ala-Trp-Phe-Tyr-Gly-Val-Ala Peptide Z is placed into buffer at a 1mM concentration in a separate test tube. Peptide Z is His-Pro-Lys-Arg-Trp-Thr-Asp-Glu The absorbance spectra for each of the three test tube is separately checked and the following spectra is obtained for each test tube: Which spectra corresponds to which peptide? (spectra #1 is the solid green line; spectra #2 is the dashed blue line; spectra #3 is the dashed red line)

Lack of H-bond donor amine group when in polypeptide is a big factor, non-ideal torsion angle contributes some

There are two main reasons why Proline destabilizes a helix. What are they?

The pKa for Lys in Peptide X will likely be higher than the Lys pKa in Y

Peptides are commonly used for various biotech and pharmaceutical applications. You are working with two peptides as indicated here:Peptide X: Ala-Val-Ser-Asp-Ile-Ala-Lys-Ala-Val-Ile-Glu-Ala-ValPeptide Y: Ala-Val-Ser-Arg-Ile-Ala-Lys-Ala-Val-Ile-Arg-Ala-ValWhich statement is the best hypothesis as to the pKa values of Lysine in the two peptides? a. The pKa for Lys in Peptide X will likely be higher than the Lys pKa in Y b. The pKa values for Lysine in each peptide will be very similar and nearly identical to each other; and this value will be nearly the same as the pKa for free lysine c. The pKa value for the Lys in peptide Y will be higher than the pKa value for free lysine d. The pKa values for Lysine in each peptide will be very similar and nearly identical to each other; but this value will be different form the pKa for free lysine e. The pKa for Lys in Peptide Y will likely be higher than the Lys pKa in X

A) chair;

Pyranose rings are usually most stable when the ring adopts a ________ conformation with the bulkiest ring substituents in ________ positions.

dG = dH - TdS dG = 4J/mole -(297)(3000)J/mol dG = -891000 J/mole Anything within 10,000J of this is close enough The correct answer is: -894000

REPORT ANSWER TO 1 DECIMAL PLACE WITH ROUNDING. A reaction at 25 degrees Celsius has a change in entropy of +3kJ/mole•K and a change in enthalpy of +4J/mole. What is the change in Gibbs Free Energy for this reaction in J/mole? Do not write units in your answers. Numbers only.

tail Wax < TAG < 20C fatty acid < 10C fatty acid

Rank the following lipids from least to most soluble in water: 20 carbon saturated fatty acid, 10 carbon saturated fatty acid, 20 carbon wax, TAG with each chain made of 20 carbon saturated fatty acyl tail

A) myoglobin binds oxygen more strongly than hemoglobin

Recent studies have shown that the H-bond between the distal histidine and oxygen molecule in myoglobin has a strength of ~ 15 kJ/mol, but in hemoglobin, the strength of the bond is only ~8 kJ/mol. What does this suggest about the differences between myoglobin and hemoglobin? A) myoglobin binds oxygen more strongly than hemoglobin B) hemoglobin binds oxygen more strongly than myoglobin C) the iron in myoglobin is more easily oxidized than in hemoglobin D) the iron in hemoglobin is more easily oxidized than in myoglobin E) none of the above

Mg2+ is small, but it is certainly not hydrophobic at all! Benzene is fairly small (smaller than glucose) and certainly hydrophobic. The answer is Benzene

Small, hydrophobic molecules are, generally, able to enter the cell on their own with the most ease. This process is called simple diffusion. The can have no more than 8 carbon atoms. Of the answer option below, select the molecule that can most easily enter the cell on its own, through simple diffusion: Select one: a. Glucose b. A polypeptide of 100 amino acids in length c. Benzene d. Mg2+ ion

True

TRUE OR FALSE D-ribose can form a ring structure with either four or five carbons in the ring

Cooperative

The ________ binding of oxygen to hemoglobin is facilitated by changes in protein conformation upon oxygen binding to one subunit that affect the binding of oxygen to another subunit.

Histidine

The conserved residues in the hemoglobins and myoglobins include the ________ proximal and distal to the heme iron.

D) All of the above

The intramolecular cyclization reaction of glucose in solution ________. A) generates a chiral center B) proceeds by nucleophilic attack on the carbonyl carbon C) usually forms a pyranose D) All of the above

pH = 4.76 + log[10/50] pH = 5.5 Whenever you do a H-H problem, STOP, and THINK about your answer. First make sure there are enough molecules to actually be measurable. There are mM concentrations here, so we have enough. There is MORE conjugate base than weak acid. Therefore, the pH MUST be above the pKa. The correct answer is: 5.5

The pKa value for acetic acid is 4.76 A beaker contains 50mM sodium acetate and 10mM acetic acid. What is the pH of this solution? Report answer to one decimal point.

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

The plot of oxygen saturation versus partial pressure of oxygen for myoglobin (orange) and hemoglobin (green) is shown below; based on this plot, which of the following statements is true? A) at oxygen pressure >100 mm Hg, hemoglobin dissociates into individual subunits so that it is able to bind oxygen similar to myoglobin B) at typical resting capillary oxygen pressure of ~30 mm Hg, hemoglobin has only 1 of its 4 oxygen binding sites filled while myoglobin is nearly saturated with oxygen C) if under periods of extreme muscle exertion, capillary oxygen pressure can drop to 10 mm Hg, thus allowing release of ~90% of oxygen carried by hemoglobin D) the structure of hemoglobin allows for complete release of oxygen in capillary beds at all times E) none of the above

True

True or False: Pentoses and hexoses can form stable ring structures by internal hemiacetal formation.

False! Oxygen binds more tightly at low pH and less tightly at a lower pH

True or False: The Bohr effect describes the effect of pH on hemoglobin's ability to bind oxygen. Oxygen binds more tightly at low pH and less tightly at higher pH values.

CO2: covalently binds N-terminus of subunits, promotes T-state through conformational changes, oxygen affinity goes down H+ : interfers with charge-charge interactions between subunits, promotes conformational changes to T-state, oxygen affinity goes down 2,3-BPG: one molecule binds in the center of tetramer through charge-charge interactions. 2,3-BPG binds deoxyhemoglobin and 'locks' deoxyhemoglobin into the T-state, thus decreasing oxygen affinity

We looked at 3 major allosteric effectors for hemoglobin: CO2, H+, and 2,3-BPG. Make a table stating where each effector binds to hemoglobin, what impact it has on hemoglobin's oxygen affinity and briefly describing what it's molecular mechanism

f. Q and Keq have the same mathematical expression a. Q is valid at all times, Keq is only valid when a reaction is at equilibrium e. Q will vary with changing concentrations, Keq is a constant

What is the relationship between the reaction quotient, Q, and the equilibrium constant, Keq? Select all that are correct: Select one or more: a. Q is valid at all times, Keq is only valid when a reaction is at equilibrium b. Q can have a negative value, Keq can never be negative c. Q and Keq are both constants d. Q will vary with changing concentrations, Keq is a constant e. Q is the inverse of Keq f. Q and Keq have the same mathematical expression

D) histidine; histidine

When oxygen is bound to myoglobin, the amino acid _____ is complexed to the iron ion of the heme group while _______ forms a hydrogen bound to the oxygen. A) cysteine; serine B) cysteine; histidine C) serine; cysteine D) histidine; histidine E) histidine; cysteine

dG, actual Gibbs free energy, due to the reason that standard Gibbs free energy is based around that all concentration is 1M, and cells have various concentrations at pH 7

Which change in Gibbs Free Energy is more applicable to biochemical settings: ΔG or ΔGº'? BRIEFLY justify your answer in 20 words or less

e. All proteins have primary structure g. Some proteins are biologically active when they have multiple polypeptide chains that associate non-covalently h. The Phi and Psi angles of (also called torsion angles) are generally constrained and cannot adopt any 360 degree conformation i. Hydrogen bonds in alpha helices are formed between atoms in the polypeptide backbone

Which of the following are correct regarding protein structure? (select all that apply) a. Beta-sheets can never be amphipathic b. Motifs are larger than domains c. Beta-sheets are formed due to hydrogen bonds that arise between side chains in opposing strands d. All proteins have alpha-helices e. All proteins have primary structure f. The subunits in proteins with quaternary structure always associate through covalent interactions g. Some proteins are biologically active when they have multiple polypeptide chains that associate non-covalently h. The Phi and Psi angles of (also called torsion angles) are generally constrained and cannot adopt any 360 degree conformation i. Hydrogen bonds in alpha helices are formed between atoms in the polypeptide backbone

B) the globin proteins provide a hydrophobic environment that prevents oxidation

Which of the following explains why the ferrous ion is not oxidized to the ferric state in the globin proteins even though free heme in solution is readily oxidized? A) when bound to globins, the heme is always planar; when free in solution, heme adopts a non-planar configuration which allows the oxidation of the iron B) the globin proteins provide a hydrophobic environment that prevents oxidation C) coordination with the proximal histidine allows any oxidized iron to be rapidly reduced back to the ferrous state D) since the oxygen is hydrogen bound to the distal histidine, if oxidation of iron does occur, the distal histidine allows for rapid reduction E) none of the above

C) salt bridge formed by a1-Arg141 to the carboxylate of a2Asp126

Which of the following interactions causes a change from the R state (oxy form) to the T state (deoxy form) of hemoglobin? A) interactions between heme groups B) protonation of the R-group of His146 on the b subunit to allow formation of a salt bridge with Lys40 on the a subunit C) salt bridge formed by a1-Arg141 to the carboxylate of a2Asp126 D) protonation of the a1 subunit terminal carboxyl group disrupts a salt bridge with a2Lys 127 E) none of the above

Actual dG is negative for a protein that folds, For a globular protein in the cytosol, the interior core of the protein is more likely to be contain hydrophobic amino acids, When proteins fold, they do not test every possible conformation

Which of the following is correct regarding protein folding? (select all that apply, deductions for incorrect selections) Select one or more: a. Folding can only begin once the entire poplypeptide has been made by the ribosome b. Assisted folding by chaperones does not require ATP and thus is not energetically costly to the cell c. When proteins fold, they do not test every possible conformation d. For a globular protein in the cytosol, the interior core of the protein is more likely to be contain hydrophobic amino acids e. Actual dG is negative for a protein that folds f. Both beta-sheets and alpha helices always form immediately upon exiting the ribosomes g. Folding for most proteins is entropically driven

A) an increase in blood pH will cause hemoglobin to bind more tightly to oxygen

Which of the following is true regarding the effectors of hemoglobin-oxygen binding? A) an increase in blood pH will cause hemoglobin to bind more tightly to oxygen B) increased CO2 from increased muscle activity will result in an increase in the R state of hemoglobin C) increased Cl- will cause the formation of a salt bridge between two Lys residues, one on an a subunit, the other on a b subunit D) the binding site of 2,3-BPG contains several Asp and Glu residues which are repelled by the similar charge, pushing the two b subunits away from each other E) all of the above

E) B and C

Which of the following observations helps to explain the conformational changes that occur in hemoglobin upon binding to oxygen? A) The four heme groups are positioned close to the surface of the molecule. B) An αβ dimer rotates and slides with respect to the other dimer upon binding oxygen. C) Neither the heme nor the iron ion in the deoxy conformation is in a planar conformation. D) All of the above E) B and C

a. The reacting molecules must contact each other with the proper (ie, productive) alignment c. The reacting molecules must collide with the necessary velocity (or momentum) d. Electrons are transferred or re-arranged g. Bonds are broken and bonds are formed

Which of the following occur in the course of a productive chemical reaction in which reactants are converted to products? Select all that apply. Incorrect selections result in deductions. Select one or more: a. The reacting molecules must contact each other with the proper (ie, productive) alignment b. In all reactions, covalent bonds must first spontaneously break before molecules collide in a productive reaction c. The reacting molecules must collide with the necessary velocity (or momentum) d. Electrons are transferred or re-arranged e. The protons of the two colliding atoms exchange f. A negative charge is transferred from a proton on one atom onto the electron of another atom; thus, converting a negative charge into a positive charge. g. Bonds are broken and bonds are formed

E) all of the above

Which of the following occurs when hemoglobin switches from the T (deoxy) state to the R (oxy) state? A) the heme group goes from a slightly puckered conformation to a flat conformation B) the ferrous ion is pulled into the plane of the heme group C) the F8 (proximal) histidine rotates about 8° to better align with the ferrous ion D) movement of the F8 histidine causes a shift in the F helix, thus weakening interactions with other subunits E) all of the above

C) reaction with the N-terminal amino groups to form a carbamate

Which of the following reversible reactions of carbon dioxide explains how hemoglobin serves as a transporter of carbon dioxide? A) reaction with the imidazole group of the distal histidine where oxygen would normally be bound B) reaction with the carboxyl group of glutamic acid to form a carbonic acid anhydride C) reaction with the N-terminal amino groups to form a carbamate D) reaction with the hydroxyl group of serine to form a carbonate E) none of the above

D) The iron in both hemoglobin and myoglobin has two coordination sites that bind to oxygen.

Which of the following statements is FALSE? A) Myoglobin is a single polypeptide chain folded about a heme prosthetic group. B) Hemoglobin is a tetramer, each of which binds a heme group. C) In both hemoglobin and myoglobin, iron is chelated by a tetrapyrole ring system. D) The iron in both hemoglobin and myoglobin has two coordination sites that bind to oxygen. E) Hydrogen bonding to a histidine residue assists stabilization of the Fe2+ -O2 complex in both hemoglobin and myoglobin. Answer: D

Ala-Gln-Val-Lys-Ile-Arg-Leu-Ser-Gly-Pro-Ala-His-Val-Thr-Leu-Asn-Ile-Asp-Ala TO SOLVE THIS: it can go in a pattern of hydrophilic hydrophobic hydrophilic hydrophobic OR the reverse OR it can also be hydrophilic hydrophobic amphipathic OR it can be hydrophobic hydrophobic hydrophilic hydrophilic these patterns can all be in one string, as long as it follows a pattern or has a good balance.

Which sequence below is most likely for short amphipathic, anti-parallel beta strands that make up part of a beta sheet? The beta-strands are adjacent to each other in the primary structure. Consider what is needed for an anti-parallel sheet when the two strands follow each other in the primary structure.... Select one: a. Pro-Gly-Ala-Val-Ile-Leu-Ala-Val-Ile-Leu-Ser-Thr-Asn-Gln-Ser-Thr-Asn-Gln-Pro-Gly b. Ala-Val-Ile-Leu-Ala-Val-Ile-Leu-Trp-Phe-Tyr-Asp-Glu-Asp-Glu-Asp-Glu c. Ala-Gln-Val-Lys-Ile-Arg-Leu-Ser-Gly-Pro-Ala-His-Val-Thr-Leu-Asn-Ile-Asp-Ala d. Ala-Gln-Ile-Arg-Leu-Asn-Val-Ser-Ala-Thr-Met-Val-Asn-Ile-Ser-Pro e. Lys-Arg-His-Lys-Arg-His-Lys-Arg-His-Ala-Val-Ile-Asp-Glu-Asp-Glu-Asp-Glu-Asp-Glu

D. Because A beta-strand is exposed to solvent on one side and the interior of the folded protein on the other side. Look for an amphipathic strand that alternates. Further, the beginning of the strand is probably signaled by a turn, so, look for something that starts (or ends) with x-Pro-Gly-x

Which sequence below is most likely to be found at the region labelled as the beta-strand in the image of the beta-barrel? A) Valine-Isoleucine-Methionine-Proline-Alanine-Glycine-Tryptophan-Phenylalanine B) Aspartate-Alanine-Valine-Isoleucine-Glutamate-Phenylalanine-Methionine-Aspartate-Alanine C) Alanine-Methionine-Phenylalanine-Valine-Isoleucine-Leucine-Tryptophan-Alanine D) Proline-Glycine-Serine-Alanine-Glutamine-Valine-Asparagine-Isoleucine-Histidine-Leucine Histidine-Alanine-Valine-Isoleucine-Lysine-Phenylalanine-Methionine-Arginine-Alanine

d. The ribosome is a ribozyme that is the site of protein synthesis and the mitochondria is the site of ATP synthesis in eukaryotes

Which statement below best describes the ribosome and mitochondria: Select one: a. The mitochondria serves as a lipid bilayer in prokaryotes while the ribosome serves as a lipid bilayer in eukaryotes. b. The ribosome and mitochondria are both ribozymes, but the mitochondria contains its own genome c. The ribosome contains DNA and RNA while the mitochondria is the site of ATP synthesis as well as protein synthesis d. The ribosome is a ribozyme that is the site of protein synthesis and the mitochondria is the site of ATP synthesis in eukaryotes

A) When oxygen binds to heme, the iron ion is oxidized from Fe2+ to Fe3+.

Which statement is false about the heme group? A) When oxygen binds to heme, the iron ion is oxidized from Fe2+ to Fe3+. B) If exposed to air, a free heme group (not associated with hemoglobin) is readily oxidized converting Fe2+ to Fe3+ and can no longer bind oxygen. C) The heme group is tightly, but non-covalently, held in myoglobin molecule. D) The chemical structure of the heme groups in myoglobin and hemoglobin are identical.

The lower the pKa value, the more that given acid will dissociate in water. In a titration curvethe pH = pKa at the midpoint Polyprotic acids will have multiple pKa values

Which statement(s) below are correct regarding pKa values? Select all that apply Select one or more: a. The pKa value will occur as the pH at which a given endpoint is reached on a titration curve The endpoint does not indicate the pKa b. Polyprotic acids will have multiple pKa values c. In a titration curve, the pH = pKa at the midpoint d. pKa values are only applicable to acidic functional groups (such as R-COOH), therefore, amino groups do not have pKa values e. The lower the pKa value, the more that given acid will dissociate in water. f. A stronger acid will have a higher pKa value because the Ka value is larger

One water molecule abstracts a proton from another water molecule, The lone pair on the oxygen of one water molecule removes a proton from another water molecule, Water molecule X loses a proton to water molecule Y. The electrons in the sigma bond of water molecule X that held the abstracted proton will be transferred to the oxygen atom in X.

Which statement(s) below best describe(s) the bi-molecule reaction of water to ionize into hydronium ion and hydroxyl ion? Select all that apply Select one or more: a. Water molecule X loses a proton to water molecule Y. The electrons in the sigma bond of water molecule X that held the abstracted proton will be transferred to the oxygen atom in X. b. One water molecule abstracts a proton from another water molecule c. The lone pair on the oxygen of one water molecule removes a proton from another water molecule d. The reaction proceeds with a large Keq value to indicate that equilibrium lies far to the right and favors product formation. e. Water serves as a nucleophile to donate a proton to an acceptor water molecule. The resulting product is two charged species.

ΔG depends on the concentration of reactants and products while ΔGº" applies to a precise concentration of reactants and products

Which statement(s) below best describe(s) the difference between the actual change in Gibbs Free Energy (ΔG) and the standard change in Gibbs Free Energy (ΔGº')? Select all that apply. Deductions for incorrect selections. Select one or more: a. ΔG applies only to physiological temperature while ΔGº" varies with temperature b. ΔG depends on the concentration of reactants and products while ΔGº" applies to a precise concentration of reactants and products c. ΔG equals 0.0kJ/mole at equilibrium while ΔGº" can never equal 0.0kJ/mole and standard conditions can never be equal to equilibrium conditions By pure chance it is theoretically possible that some random chemical reaction is perfectly at equilibrium under standard conditions. There is nothing about that which would violate any known properties of this universe. d. ΔG is applicable to conditions in the cell due to the aqueous environment of the cell while ΔGº" is applicable to conditions in a lab setting when all species must be in the gas phase e. ΔG is path independent for the concentrations of reactants and products while ΔGº" is path dependent on the concentration of reactants and products

Ala-Ile-Val-Asp-Gly-Pro-Glu-Lys-Pro-Ser-Thr BECAUSE: Lots of Pro disrupts ALPHA HELIX FORMATION because Lack of H-bond donor amine group when in polypeptide is a big factor, non-ideal torsion angle contributes some

Which stretch of amino acids below is LEAST likely to form an alpha-helix? Select one: a. Val-His-Phe-Cys-Asn-Ser-Thr-Gln-Ala-Leu b. Ala-Ile-Val-Asp-Gly-Pro-Glu-Lys-Pro-Ser-Thr c. Glu-Asp-Asn-Thr-Met-His-Gln-Ala-Val-Ile d. Leu-Arg-Val-Ile-Glu-Asp-Thr-Tyr-His-Ala

Ala-Val-Ser-Ile-Leu-Ala-Gln-Leu-Val-Thr-Val-Ile-Leu-Asp Goes in a pattern of hydrophobic, hydrophilic, hydrophobic, etc or reverse. A REGULAR Alpha helix would have a hydrophobic molecule then 3-4 hydrophilic molecules pattern.

Which stretch of amino acids below is most likely to be an amphipathic alpha helix that can rest at the solvent interface of a folded protein?

It contains fewer than 3 carbons, "n" must be greater than or equal to 3 for the definition of a carbohydrate.

Why is formadehyde not considered a carbohydrate?