Biochem Test 1

Histidine

His

Polar, Positively Charged R Groups

Histidine (His), Lysine (Lys), and Arginine (Arg)

Be able to use the nomenclature of homo- and hetero- in multi-subunits proteins.

Homodimer - 2 identical subunits Heterodimer- 2 different subunits *Dimer is 2, Trimer is 3, Tetramer is 4*

Isoleucine

Ile

Which of the following are negatively charged amino acids at pH = 7? Select one: a. Cys, Asn. b. Glu, Asp. c. Gln, Asn. d. Thr, Tyr.

b. Glu, Asp.

What is Amphipathic?

molecule that contains a hydrophobic region (hydrocarbon) & hydrophilic region (functional group)

Alanine

Ala

Common polar covalent bonds:

C-O, O-H, and N-H.

Phenylalanine key features

bulky side chain, very hydrophobic

pKa =

pKa= -logKa

Name and briefly describe the four basic types of weak interactions encountered in biochemistry.

(1) Hydrogen bonds form between a donor group: a hydrogen atom attached to an electronegative atom, and an acceptor group (an electronegative atom). Common acceptors are oxygen, nitrogen, and sulfur. (2) Electrostatic ionic interactions occur between two atoms with opposite charges; the strength of interaction depends upon the distance between ions and the environment around them. (3) van der Waals interactions occur between nonpolar molecules and arise from temporary dipoles caused by fluctuation in electron clouds. If dipoles of opposite signs align at the appropriate distance, an interaction can occur. These interactions are quite weak, but collectively among several atoms, they have a strong cumulative effect. (4)The hydrophobic effect is driven by the tendency for hydrophobic molecules to pack together in solution. By packing closely, hydrophobic molecules decrease overall surface area, decreasing the number of water molecules forming ordered (entropically unfavorable) structures around the hydrophobic molecules.

Name the four noncovalent interactions that occur within and between biomolecules that facilitate life processes at the molecule level. Which of these noncovalent interactions directly or indirectly involve H2O.

(1) Hydrogen bonds, (2) ionic interactions, (3) van der Waals interactions, and (4) hydrophobic effects. Hydrogen bonds form directly between H2O and biomolecules and between H2O molecules themselves, whereas hydrophobic effects are indirectly caused by H2O due to "water-avoiding" interactions between nonpolar molecules.

Name and briefly describe the three proposed mechanisms of how globular proteins fold in aqueous environments.

(1) Hydrophobic collapse model: Hydrophobic residues form the interior of the protein due to the hydrophobic effect, causing a loosely defined tertiary structure called a molten globule. Then, proximal residues in the molten globule interact to form well-ordered secondary and tertiary structures through van der Waals interactions and hydrogen bonding. (2) Framework model: Initially, local secondary structures form independently. Then, local secondary structures interact to form tertiary structures. (3) Nucleation model: Random interactions lead to a localized region of correct three-dimensional structure, which facilitates the formation of the surrounding tertiary and secondary structures.

What are the two phenotypical consequences produced by protein-folding diseases?

(1) The degradation of a misfolded protein, known as a loss-of- function effect because the activity of the particular protein is missing. (2) Protein aggregation, known as a gain-of-function effect because these proteins add a process to the cell. Gain-of- function protein-folding phenotypes can result from missense mutations or from accumulation of misfolded wild type proteins.

Explain why secondary structures are so prevalent in proteins.

(1) They are formed from combinations of phi and psi angles that minimize steric hindrance (2) they allow maximum hydrogen bonding interactions in the polypeptide backbone.

Be able to compare the strength among the noncovalent interactions.

(Strong) Ionic interaction > Hydrogen bond > Hydrophobic effect > van der Waals interaction (Weak)

The polarity of the solvent and other environmental factors can affect the pKa of a weak acid. Suppose the alpha amino group of a protein has a pKa of about 8.0 when it is exposed to H20 on the outside of a protein. 1.) Would you expect the pKa to be higher or lower than 8 if the group were buried in the hydrophobic interior of the protein? Explain. 2.) This same alpha amino group in the hydrophobic interior of the protein has the opportunity to form an ionic bond in that hydrophobic environment with a carboxylate group in the side chain of a charged Asp residue. Under these conditions, how would the pKa of this alpha amino group compare with the pKa of the alpha amino group in the hydrophobic interior of the protein without a nearby Asp residue to form this ionic bond?

1.) It is energetically unfavorable for the alpha amino group to be charged in the hydrophobic interior, thus the pKa would be lower. The proton can be released, as H30+, before the amino group enters the interior during the folding process because the strong electrostatic attraction between the lone pair electrons in the N atom and the proton is outweighed by the unfavorable condition of a charge in a hydrophobic environment. 2.) The pKa for this alpha amino group would increase relative to the example in (a), and would be close to the pKa of around 8. This ionic bond neutralizes both the NH3+ charge and the COO- charge, reducing the effect of having a charged group in the hydrophobic environment. Ionic bonds are stronger in a hydrophobic environment because it is unfavorable to have unbalanced charges.

The total carbonate pool in blood plasma (blood without red blood cells) is 0.025 M and consists of both HCO3^- and CO2(aq). The pKa for the dissociation of H2CO3 to produce HCO3^- + H^- at 37 degrees C is 6.1. Because H2CO3 is readily produced in blood from dissolved CO2(aq) + H2O, in a reaction catalyzed by the enzyme carbonic anhydrase, CO2(aq) can be considered the conjugate acid and HCO3^- the conjugate base in the bicarbonate buffering system. 1.) What is the ratio of HCO3^- and CO2(aq) in blood plasma at pH 7.4? 2.) What are the individual concentrations of CO2(aq) and HCO3^- under these same conditions?

1.) Using the Henderson-Hasselbalch equation: pH = pKa + log [A-]/[HA] 7.4 = 6.1 + log [HCO3^-]/[CO2(aq)] 7.4 - 6.1 = 1.3 = log [HCO3^-]/[CO2(aq)] 10^1.3 = 10^[HCO3^-]/[CO2(aq)] [HCO3^-]/[CO2(aq)] = 20/1 2.) 0.025 M = 2.5 x 10^-2 M = [HCO3^-] + [CO2(aq)] (2.5 x 10^-2 M)/(20 + 1) = [CO2(aq)] = 1.19 x 10^-3 M [HCO3^-] = 2.5 x 10^-2 M - 1.19 x 10^-3 M = 2.38 x 10^-2 M

Be able to distinguish four general classes of tertiary protein structure.

4 classes of structure: - Alpha helix - Beta sheet - alpha/beta: intermixed alpha helix and beta strands - Aplha+beta: alpha helix adjacent to beta strands (alpha helix is in one region and beta sheets in another)

Be able to define protein domain.

A compact independent folding module within the polypeptide chain with a defined function Globular proteins fold into domains. Range from 25-30 to several hundreds of amino acids. Large proteins have 2 or more distinct domains of compacts folded region.

Be able to describe the structure the fibrous protein collagen.

A right handed triple helix fiber formed by 3 left handed helices. Helix has distinct amino acid sequence. - Gly-X-Y (X usually Proline, Y usually 4-hydroxyproline). - Glycine lies near center of the triple helix. Key amino acids: Gly, Pro Forces: - No hydrogen bonds within individual helix. - Hydrophobic effects and h bonds stabilize between the individual helices; crosslinks stabilized between the triple-helix fibers. Examples: skin, bone, teeth, tendons, cartilage Collagen add on: Within triple-helix fiber: H-bonds between amide hydrogen in Gly in one chain and carbonyl oxygen in Pro, or OH group in 4-hydroxyproline Between triple helix fiber: hydroxylated lysine cross-links stabilize between triple helix fibers

Clamp Type of chaperon protein:

ATP binding induces conformational changes that allows unfolded protein to bind. ATP hydrolysis induces another conformational change that fold and release the protein. It clamps on and induces a change that lets it bind: then it induces another change that correctly folds and releases the protein. Example: heat shock proteins

Buffer preparation is an important skill in biochemistry. Prepare the buffer as described below. Acetic acid has a pKa of 4.8. How many milliliter (mL) of 0.3M acetic acid and 0.2M sodium acetate and water are required to prepare 1 liter of 0.1M buffer solution having a pH of 5.8? (15 points)

Acetic acid = HA = 0.3M, pKa=4.8 Sodium acetate = A- = 0.2M Buffer solution = 0.1M, 1L, pH=5.8 pH = pKa + log ([A-]/[HA]) 5.8 = 4.8 + log ([A-]/[HA]) [A-]/[HA] = anti-log(5.8-4.8) [A-]/[HA] = 10 Percentage of A- = 10/11 * 100% = 90.9% Percentage of HA = 1/11 * 100% = 9.1% Use this equation: Molarity = # of moles / Volume in L In 0.1M, 1L, pH=5.8 Buffer solution: Acetic acid: Molarity = 0.1 M * 9.1% = 0.0091 M # of moles = 0.0091 M * 1 L = 0.0091 moles Volume (L) = 0.0091 moles / 0.3 M = 0.0303 L = 30.3 mL (from 0.3M acetic acid) Sodium acetate: Molarity = 0.1 M * 90.9% = 0.0909 M # of moles = 0.0909 M * 1 L = 0.0909 moles Volume (L) = 0.0909 moles / 0.2 M = 0.4545 L = 454.5 mL (from 0.2M sodium acetate) At the end, you need to bring the volume up to 1L by adding H2O = 1000 - 30.3 - 454.5 = 515.2 mL

Which macromolecule(s) is/are likely to form hydrogen bonds with water? Explain your choice(s).

All four macromolecules (lipids, proteins, nucleic acids, and carbohydrates) have the potential to form hydrogen bonds with water. This is because they all contain either hydrogen donor and/or acceptor groups.

Explain how an alpha helix can be amphipathic.

Alpha helices are amphipathic when residues that are hydrophobic (or hydrophilic) are placed three to four amino acids away from each other. Because there are 3.6 amino acids per turn, amino acids that are three to four amino acids apart will lie on the same side of the helix.

Be able to determine the L and D form of amino acids.

Always have amino group pointing away from you and on top. Carboxyl group oriented away from you and on the bottom. L form has the R-group on the left side, D form has the R-group on the right side. L and D forms are enantiomers

Be able to recognize functional groups.

Amino Hydroxyl Sulfhydryl Phosphoryl Carboxyl Methyl

Be able to explain the characteristics of protein folding.

Amino acid sequence alone determines folding Rapid (why it is so hard to study) Takes place through many intermediate states Follows the laws of thermodynamics → folded proteins will reach lower energy states → more stable Cooperative and sequential process → the formation of one part of a structure leads to the formation of the remaining parts of the structure Different domains fold independently → more efficient Some protein folding is assisted by the two types of chaperon proteins

Match the levels of protein structure with the descriptions below. Amino acid sequence from the N to C terminus. Commonly occurring folds found in proteins, such as 𝛼-helix or β-sheet. The overall three-dimensional structure of the protein chain. The arrangement of subunits in a multi-subunit protein.

Amino acid sequence from the N to C terminus = Primary Commonly occurring folds found in proteins, such as 𝛼-helix or β-sheet = Secondary The overall three-dimensional structure of the protein chain = Tertiary The arrangement of subunits in a multi-subunit protein = Quaternary

What does it mean for a molecule to be amphipathic? Why are amphipathic lipids important for life?

Amphipathic molecules contain hydrophobic and hydrophilic regions. Amphipathic lipids form biological membranes, whose hydrophobic core is relatively impermeable to polar molecules. This maintains separation of the inside of cells from the environment and allows compartmentalization within cells where specific reactions can occur.

Arginine

Arg

Asparagine

Asn

Aspartate

Asp

Polar, Negatively Charged R Groups

Aspartate (Asp) and Glutamate (Glu)

A homopolymer of histidine residues (polyhistidine) is able to form an α-helical structure or is unfolded, depending in the pH of the solution. Predict whether the structure of polyhistidine would be α-helical or unfolded at pH values of 4 and 8. Explain your reasoning.

At pH 4, the homopolymer of His residues would be unfolded. This is because at pH 4, His residues carry positive charges. These charges would repel each other preventing the formation of alpha helix. At pH 8, the homopolymer of His residues would be alpha helical. This is because at pH 8, the His residues are neutral with no repulsion among themselves. Therefore, alpha helix can be form.

Explain the function of Beta turns.

Beta Turns: function to connect Beta strands to another Beta strands in the antiparallel sheet There are type 1 and type 2 turns - differs in the orientation of the carbonyl oxygen. Both of these turns consist of four amino acids in which the carbonyl oxygen of the first amino acid residue is hydrogen bonded to the nitrogen atom of the fourth amino acid residue

Which of the macromolecules would you expect to be soluble in water? Why?

Carbohydrates (or amylose), nucleic acids (or DNA), and proteins (or peptide) would be soluble in water. These molecules have the polar groups all over their structure that allows the formation of hydrogen bonds with water, making them soluble.

· In the closely packed interior of the tertiary structure of an enzyme, an alanine residue was changed by mutation to a valine, leading to a loss of enzyme activity, although that residue was not directly involved in the catalytic function of the enzyme. However, activity was partially regained when an additional mutation at a different position in the primary structure changed an isoleucine residue to a glycine. Based on the structure of the amino acid side chains of alanine, valine, isoleucine, and glycine, explain how the first mutation Ala --> Val likely caused a loss of activity, and the second mutation in another region of the protein, Ile --> Gly resulted in a partial recovery of enzyme activity.

Changing an Ala to a Val would introduce a bulkier side chain, taking up more volume in the protein interior; the resulting structural adjustments in the tertiary structure must be serious enough to cause the enzyme to lose activity. The replacement of an Ile residue with a Gly allows a tertiary structure close enough to the original structure for partial enzyme activity.

Be able to describe the function/mechanism of two types of chaperon proteins.

Chaperon proteins: - Prevent aggregates - Protect or repair damaged protein caused by temperature increases → chaperons are also called heat shock proteins for this reason - Bind to misfolding proteins and uses ATP hydrolysis to facilitate correct folding Two Types: - Clamp Type -Chamber Type

Explain how the pKa of an amino acid can differ within a folded protein compared to that of the free amino acid in water.

Chemical properties of nearby functional groups can alter the pK. of specific amino acids if it is energetically favorable. For example, because positive or negative charges in the hydrophobic interior are energetically unfavorable, the pKa value of a side chain may be altered to favor the neutral state over the charged state at physiological pH.

Be able to describe the general structure of amino acids.

Chiral carbon, amino group, r group, and carboxylate group Used in acid-base properties Varied chemical functionality

Be able to determine the net charge of an amino acid at certain pH.

Compare ionizable groups pH values and the specific pH of the solution to determine how many groups are deprotonated and how many are still protonated to tell you overall charge

What are three ways in which quaternary structures can provide increased functionality for a protein?

Complexes can provide structural properties not present in individual subunits and can be a mechanism for regulation of protein function through conformational changes affecting subunit interfaces. Also, bringing functional components into proximity can increase efficiency of biochemical processes.

Explain the features of functional groups:

Contains electronegative atoms, i.e. O, N, S Are usually electrically charged or polar Make organic molecules amphipathic Create multifunctional molecules that increase functional diversity Provide sites for intra- and intermolecular interaction: - Hydrogen bonding - Ionic interaction

Covalent bond definition:

Covalent bonds are formed by atoms sharing their valence shell electrons to completely fill each atom's outer most shell. · Not all covalent bonds are created equal. · The more pairs of electrons shared between the atoms, the stronger the bond strength and the shorter the distance. · Covalent bonds can be either polar or nonpolar depending on the electronegativity difference between two atoms (Polar = > 0.5, Nonpolar = < 0.5). Common polar covalent bonds: C-O, O-H, and N-H.

Cysteine

Cys

Be able to explain the differences between protein degradation and denaturation.

Degradation: Protein chain is destroyed with covalent bonds of primary sequence cleaved. Denaturation: Protein chain unfolded with covalent bonds of primary sequence unbroken. - Loss of structural integrity and activity. - Ex. Boiled egg- goes from clear to white when boiled

Be able to explain how misfolded proteins can lead to disease.

Degrades: reduces the level of functional protein (loss of function). - Ex: Cystic Fibrosis: gene is mutated, leads to misfolded protein, leads to a degraded protein with loss of function. Aggregated: Interfere with cellular processes (gain of function). - Ex: Huntington's Disease: gene is expanded, misfolded protein, aggregated protein: gain of function. Creutzfeldt-Jakob Syndrome: Gene encodes wildtype protein, protein is in the wrong conformation, aggregated protein: gain of function. Transmissible Spongiform Encephalopathies: Accumulation of misfolded proteins that form large aggregates in brain tissues - Prion proteins

What is the difference between motifs and domains?

Domains when separated from each other can still function but when the structures in motifs are separated from each other it disrupts the nature of the folding and therefore loses its function.

Be able to compare and contrast fibrous and globular proteins.

Fibrous Proteins: - Long extended chains, with high tensile strength. - Composed on 1 type of secondary structure. - 3-4 particular amino acids. - Insoluble in water because long hydrophobic chains. Globular Proteins: - spherical 3D structures, compact. - Incorporate multiple types of secondary structure. - Charged/polar amino acids on surface. - Hydrophobic amino acids on the interior. - Soluble

Be able to determine the ionic state of an amino acid at certain pH.

Found in the properties of the common amino acids found in proteins chart

Be able to identify the buffering region(s) in a titration curve.

Found within one pH unit above and below the pka

van der Waals interaction example:

Gecko feet: The tips of the furs on a Geckos feet branch out. The molecule on these branches allows for van der Waals interactions to occur with the molecule on the wall. (Same reason why Spiderman can climb a wall)

Be able to explain the thermodynamics of protein folding.

Gibbs free energy (Delta G): the difference between folded and unfolded state must be favorable (LESS THAN ZERO) in order to drive the folding process. Enthalpy (DeltaH) the heat content of the system , favorable because more interactions (covalent or disulfide) in the folded state than in the unfolded state. LESS THAN ZERO - In unfolded states there are ionic bonds that haven't formed and hydrophobic residues are exposed to polar molecules which is why this state is not favorable. Entropy (Delta S): the degree of freedom of a system. Unfavorable from protein folding (less than 0). However, it is highly favorable with surrounding water (S>>>>>)). Overall: GREATER THAN ZERO Energy landscape model of protein folding: Unfolded: high gibbs free energy= energetically unfavorable Native state is the best of them all Oligomers can often dissociate back into monomers Aggregates and amyloid fibrils are super stable, larger reduction in gibbs free energy, but often come from mutations.

Glutamine

Gln

Briefly explain in terms of the thermodynamics of protein folding why the folded structures of water-soluble globular proteins have extensive secondary structure.

Globular proteins will have some polar backbone groups (amide NH and carbonyl O groups) buried inside the protein. When these groups are in the protein's interior, they have lost their favorable hydrogen bond interactions with H20. The enthalpy change (delta H) for this process would be unfavorable (breaking bonds) if new hydrogen bonds were not made within the protein by secondary structures (hydrogen bonding within alpha helices and between Beta strands to form Beta sheets).

Glutamate

Glu

Glycine

Gly

Nonpolar, Hydrocarbon R Groups

Glycine (Gly), Alanine (Ala), Valine (Val), Leucine (Leu), Isoleucine (Ile), Proline (Pro), and Methionine (Met)

Explain why Gly and Pro are common in turns and loops.

Glycine is often the second or third residue in β turns because the Hydrogen- atom side chain allows glycine to adopt the unusual dihedral angles necessary to make tight turns. Proline is often in a β turn because the cyclic ring side chain fits perfectly to make a turn Turns will have Pro and Gly next to each other. This is because the turn caused by the proline kink needs to be followed by a small sidechain (the hydrogen is the smallest side chain) to avoid steric hindrance

Covalent bond example:

H2O: the hydrogen atom has 1 electron and the oxygen atom has 6 electrons. Two hydrogen atoms can completely fill the outermost shell of an oxygen atom by sharing the electrons. When one pair of electrons is shared, it forms a single, covalent bond.

Be able to describe the structure of a protein.

How many amino acids? How many domains? (count colors) What is the major secondary structure (of each domain)? (From 4 general classes) What type of motif (does each domain have)?

How do you describe the quaternary structure?

How many subunits? Are these subunits the same? How do you call them? How many amino acids? How many domains? What are the secondary structures of each domain? What are the motifs in each domain?

Hydrogen bond example:

Hydrogen bond between two water molecules. The O attached to the other H is the Hydrogen-bond acceptor. The Other O is the Hydrogen bond-donor.

Hydrogen bond definition:

Hydrogen bonds can form when a hydrogen that is covalently bonded to an electronegative atom (e.g. oxygen), is in proximity to another electronegative atom. · Second strongest Noncovalent interaction (partial charges). · All hydrogen bonds have a hydrogen-bond acceptor and a hydrogen-bond donor. · The strength of the hydrogen bond depends on the donor and the acceptor. · Linear bonds are stronger than angled bonds. · NH and OH form hydrogen bonds. Hydrogen bond depends on formation of partial charges between the H and O molecules - H partially positive, O partly negative Main attractive force holding protein Secondary Structures in place

Be able to describe the differences among the three proposed protein folding pathways.

Hydrophobic collapse: Hydrophobic residues first form the interior and then form the secondary and tertiary structures Framework model: Local secondary structures form independently and then leads to the tertiary structures Nucleation model: Localized tertiary structures lead to other secondary and tertiary structures

Hydrophobic effect definition:

Hydrophobic effects are due to the tendency of nonpolar molecules to pack close together away from water. · Second weakest Noncovalent interaction (nonpolar, more permanent). · Hydrophobic effect is one of the main factors behind: protein folding, protein-protein association, formation of lipid micelles, and enzyme-substrate complex formation. · When nonpolar molecules are in polar solvent, they are surrounded by water. This is energetically unfavorable because there is a reduce in water movement. These nonpolar molecules group together, which reduces the surface area surrounded by water. This allows for fewer water molecules needed to be ordered (can move around freely), which makes it more energetically favorable. Main attractive force holding protein Tertiary and Quaternary Structures in place

Be able explain stabilizing forces in protein tertiary structure.

Hydrophobic interactions (major stabilizing force) and van der waals: hydrophobic portions stay away from H2O by compacting which can cause van der waals forces between neutral side chains . Hydrophobic residues are buried inside of protein - Disrupted by detergents Hydrogen bonds: between the r groups. - Disrupted by heat Ionic interactions: charged polar side chains will attract or repel each other based on charge. Metal ions like zinc and iron can form electrostatic interactions with charged side chains. - Disrupted by ph changes Disulfide bridges between cysteine amino acids:cysteines close to each other causes a bond through the oxidation of the SH bond. - Disrupted by a reductive environment

Be able to distinguish right-handed from left-handed.

If you go up the stairs, which hand would you put on the handrail? If the handrail is on your right, that's a right-hand helix, otherwise it's a left-handed helix.

Be able to explain the function and importance of biological buffer systems.

Important in maintaining blood pH level. When blood pH falls below 7.4, acidosis. When blood pH level rises above 7.4, alkalosis. To counter acidosis: Removal of excessive protons as H2O. To counter alkalosis: Addition of protons through an increase of H2CO3.

Absorption of food in the stomach and intestine depends on the ability of molecules to penetrate the cell membranes and pass into the bloodstream. Because hydrophobic molecules are more likely to be absorbed than hydrophilic or charged molecules, the absorption of orally administered drugs may depend on their pKa values and the pH in the digestive organs. Aspirin (acetylsalicylic acid) has an ionizable carboxyl group (circled below; pKa = 3.5). Calculate the percentage of the protonated form of aspirin available for absorption in the stomach (pH = 2.5) and in the intestine (pH = 5.0). (5 points)

In the stomach, pH = 2.5: pH = pKa + log [deprotonated] / [protonated] 2.5 = 3.5 + log [deprotonated] / [protonated] [deprotonated] / [protonated] = anti-log (2.5-3.5) [deprotonated] / [protonated] = 0.1 / 1 percentage of protonated form = 1 / (0.1 + 1) * 100% = 90.91% ---------------------- In the intestine, pH = 5.0: pH = pKa + log [deprotonated] / [protonated] 5 = 3.5 + log [deprotonated] / [protonated] [deprotonated] / [protonated] = anti-log (5-3.5) [deprotonated] / [protonated] = 31.62/ 1 percentage of protonated form = 1 / (31.62 + 1) * 100% = 3.07%

Ionic interaction example:

Ionic interaction between a Sodium atom (a cation, Na+) and a Chloride ion (an anion, Cl-) to form Sodium chloride (NaCl): The sodium atom has one outermost electron, which can be transferred to the chlorine atom, which has 7 valence electrons. This transfer allows both atoms to become more stable and creates a positive sodium ion and a negative chloride ion. These opposite charged ions attract each other, creating an ionic interaction.

Ionic interaction definition:

Ionic interactions occur between opposite charged atoms or groups. · Strongest Noncovalent interaction (full positive/negative charges). · AKA also called charge-charge interactions or salt bridges. · The electronegativity difference between two atoms must be >2 (often formed between the most and the least electronegative atoms).

Name the four types of noncovalent interactions that stabilize tertiary and quaternary structures of proteins.

Ionic interactions, hydrogen bonds, van der Waals interactions, an hydrophobic interactions.

Ka =

Ka= (H+ *A-)/HA pKa= -logKa

Leucine

Leu

Which macromolecule(s) is/are likely to form hydrophobic effects? Explain your choice(s).

Lipids would be likely to experience hydrophobic effects because it has long nonpolar hydrocarbon chains.

Which macromolecule(s) is/are likely to form ionic interactions with another molecule? Explain your choice(s) by identifying the functional groups that allow such interaction.

Lipids, proteins (or peptide), and nucleic acids (or DNA) could form ionic interactions with another molecule. The negatively charged phosphate groups on the lipids and nucleic acids and the negatively charged COO- (carboxylate) groups and positively charged NH3+ (amino) groups on the proteins allow them to form ionic interactions with an opposite charge on another molecule.

Explain the function of loops.

Loops: functions to connect a Beta sheet to and Alpha helix. Usually range from 6- 20 residues long. They are rigid due to the multiple weak interactions between the tightly packed atoms. They are usually on the surface of proteins and contribute to the specificity of protein-protein interactions.

Lysine

Lys

Be able to explain why weak acids are important in biochemistry.

Many biological molecules or their components are weak acids (e.g. amino acids, DNA & RNA). The ionization state of weak acids regulates not only their function but also their interaction with other biological molecules. The structure and function of these molecules is often regulated by the pH of the solution.

Methionine

Met

Alpha-alpha corner and Beta alpha beta loops motifs:

Most common motifs that provides 2 layers of secondary structure

Be able to define quaternary protein structure.

Multiple polypeptide chain interactions to form a functional protein (multisubunit complex).

Be able to explain how amino acids are arrange to form amphipathic α helix.

Must not have like charges in close proximity that will repel each other and prevent helix formation Every 3-4 amino acids (takes 3.6 amino acids to make an alpha helical turn) must be a hydrophobic or hydrophilic amino acid, creating a hydrophilic and a hydrophobic surface This can be visualized with a helical wheel diagram

Be able to identify the N- and C-terminus.

N terminus of an alpha helix has a partial positive charge and the C terminus has a partial negative charge caused by the dipoles in each peptide bonds.

Be able to differentiate nucleophiles and electrophiles.

Nucleophiles: electron-rich (either negative charge or unshared pair of electrons) - Ex: O, N, S, C Electrophiles: Positively charged Nucleophiles attack electrophiles - Ex: water can act as both nucleophilic and electrophilic; lone pair on oxygen (nucleophile) attacks the H of another water (electrophile)

Distinguish parallel and antiparallel β-sheets.

Parallel: the strands in the N to C terminus direction forms a hydrogen bond with an adjacent strand that is also in the direction of N to C Antiparallel: the strands in the N to C terminus direction forms a hydrogen bond with an adjacent strand that is in the direction of C to N - Antiparallel is stronger due to the perpendicular angle of the hydrogen bonds

What is a peptide bond and how is it formed?

Peptide bond: joins the carboxylic acid group of one ammoacid and the amine group of another amino acid; formed by condensation reactions catalyzed by the ribosome. The reaction is unfavorable and requires ATP hydrolysis.

Be able to explain the resonance structure and the properties of the peptide bond.

Peptide bonds are rigid and has partial double bond characteristics due to resonance structures. The resonance is in the C-N and C=O bonds. - This restricts and confines the bond to either cis or trans. Almost always trans, glycine is the only amino acid that readily accepts cis formation which helps in Beta turns. Proline also helps in beta turns due to its intrinsic curve. Peptide grows towards C-terminus.

Be able to draw the peptide bond formation between amino acids.

Peptide bonds form between the carbon from the carboxylic group of one amino acid and the nitrogen from the amino group of another. An oxygen from the carboxylic group and 2 hydrogens from the amino group form H2O as peptide bonds between amino groups form. This is a condensation reaction.

Phenylalanine

Phe

Nonpolar, Aromatic R Groups

Phenylalanine (Phe), Tyrosine (Tyr), and Tryptophan (Trp)

Be able to explain the phi and psi angles and how these angles between amino acids are used to generate a Ramachandran plot.

Phi ϕ angles: The torsional angle between the amide nitrogen and the Cα Psi ψ angles: the torsional angle between the Cα and the carbonyl carbon energetically favored combinations of ϕ and ψ angles can be plotted as ϕ versus ψ angles in a Ramachandran plot. Ideal combinations that do not result in steric hindrance are darkly colored areas.

Explain the physical relevance of phi and psi angles.

Phi: The torsional angle between the alpha carbon and the amide nitrogen of an amino acid psi: The angle between the alpha carbon and the carbonyl carbon. The values of phi and psi affect the conformation of the peptide backbone.

Prion Protein Transmissible Spongiform Encephalopathy:

PrPC= normal prion protein - Alpha helix PrPSC: Scrapies protein, accumulate in brain cells and form plaques -- infectious - Beta strands so they aggregate into trimers and then stack

Be able to explain the forces between the protein subunits.

Primarily hydrophobic effects. Ionic interactions help the alignment of the subunits and provide specificity. Hydrogen bonds and van der Waals can also be used to maintain quaternary structure because they easily associate and dissociate which allows for regulation of protein function.

Be able to describe the structure the fibrous protein silk fibroin.

Primarily made of beta sheets Amino acids: Gly, Ala, Ser Forces: Within sheet, H bonds within antiparallel beta strands (between backbone NH and CO groups on separate strands) and, van der Waals interaction between separate beta sheets Example: Silk protein of insects and spiders

Be able to define primary protein structure.

Primary protein structure is the amino acid sequence, which determines how the polypeptide backbone folds into an energetically stable 3-d structure.

Be able to compare and contrast the stabilizing forces in 1°, 2°, 3° & 4° protein structure.

Primary structure stabilizing forces: Peptide bonds (covalent bonds) Secondary structure stabilizing forces: Hydrogen bonds between atoms of the backbone Tertiary structure stabilizing forces: Hydrophobic effects is main Quaternary structure stabilizing forces: Hydrophobic effects and ionic interactions

Proline

Pro

What are the enthalpic and entropic factors that lead to the stabilization of a protein upon protein folding?

Protein folding introduces favorable enthalpic changes because there are more interactions in the folded state than in the unfolded state. These changes result from noncovalent interactions (or disulfide bond formation) because covalent bonds other than disulfide bonds do not change during folding. It is entropically unfavorable because it restricts the number of conformations a polypeptide can take, but the folded protein causes an increase in the disorder of water molecules, which is entropically favorable.

Hydrophobic effect example:

Protein folding: Hydrophobic effects are the driven force for protein folding. The nonpolar amino acids tend to group together and stay inside of the folded protein, so that they can stay away from aqueous solution.

Be able to explain the reason why many proteins form multisubunit complexes.

Provide active sites (where proteins can carry out their functions) that are not present in individual subunits. More stable (lower delta G). Increase functionality and efficiency by linking functional component in close proximity. Provide a mechanism for regulation of protein function through conformational changes that alter the protein subunit interfaces.

Phosphoryl Functional Group

Replace the O- on the left side with an R

Be able to explain the ribonuclease A folding experiment and its contribution to the understanding of protein folding.

Ribonuclease A was used to study protein folding. It has Disulfide bridges that help prevent unfolding. First, you have this protein with the correct disulfide bridges, is active and fully folded. Urea ( a denaturing agent) and Beta-mercaptoethanol (BME, and reducing agent) are added to the RibonucleaseA. - Urea: disrupt noncovalent bonds - BME: break disulfide bridges through reduction This will result in an inactive protein that is unfolded with broken disulfide bonds. IF you remove urea and BME, the protein will refold properly with correct disulfide bonds. IF you remove BME and then Urea, there will be randomly formed disulfide bonds in the protein so it will be incorrectly folded. - This can be undone by adding trace BME and no Urea. This will allow the incorrect bonds to be broken and the correct bonds to be formed. Overall the contribution of this experiment was that the amino acid sequence alone determine the native conformation.

Serine

Ser

Polar, Uncharged R Groups

Serine (Ser), Threonine (Thr), Cysteine (Cys), Asparagine (Asn), and Glutamine (Gln)

Be able to explain the difference between strong and weak acids.

Strong acid: acids that completely dissociate in water - Ex: HCl → H+ + Cl- - Single forward arrow: symbolized complete dissociation Weak acid: acid that partially dissociate in water - Ex: CH3COOH ⇋ H+ + CH3COO- - Partial half arrows show it can go back and forth

Be able to distinguish and explain the features of different protein motifs.

Super secondary structures consisting of a combination of alpha helices, sheets, and loops in close proximity. Associated with particular functions. Motifs: - Alpha-alpha corner - Beta alpha beta loops - Helix bundle - Beta barrel - Greek key fold - Rossman fold - Tim barrel

Be able to describe how each different factors below disrupt a native protein: Temperature pH Detergents Chaotropic agents

Temperature: - Disrupts H-bonds and van der Waal's interaction. (In high temp., the energy increases the movement of the molecules so that the interactions become unstable.) - Looking at the graph, T(m)= transition curve midpoint where 50% of the proteins are fully folded and 50% are fully denatured. pH: - Can disrupt ionic interaction. - pH affects the ionization state of charged amino acids that are important for protein folding. Detergents: - Disrupt hydrophobic effect because the hydrophobic tail can penetrate into the protein interior and disrupt the hydrophobic effects among the nonpolar amino acids. Chaotropic agents: - Urea and guanidinium chloride are excellent H-bond formers. - Disrupt H-bonds because they compete H bonding in protein structure. - Disrupt hydrophobic effect by disrupting regular water structures.

Be able to calculate the pI for an amino acid.

The average of the two pKas between the zwitterion

Be able to describe the basic structure of α helix.

The hydrogen bonds between the carbonyl oxygen and the hydrogen atom attached to the nitrogen is optimal with an N-O distance of 2.8A. There are 3.6 residues per 360 turn. The distance along each axis between turns is 5.4A All hydrogen bonding backbone atoms (except terminus) form hydrogen bonds within the helix. An average alpha helix in proteins are around 10-14 residues Sidechains are sticking outwards

Explain how H-bonds are formed in β-sheets.

The hydrogen bonds in pleated sheets form between the amino hydrogen and carbonyl oxygen of adjacent beta strands. (antiparallel is stronger due to its perpendicular angle)

Be able to explain why knowing the ionic state of amino acid side chain is important.

The ionic state of an amino acid influences protein folding which affects the 3-d structure of the protein. The ionic state influences the activity of the proteins.

What kind of scale is the pH scale? What values are considered acidic, neutral, and basic?

The pH scale is a logarithmic scale. A value of 0--6.5 is considered acidic; 7.5-14 is considered basic. Anything in between those two ranges (6.5-7.5) is considered pH neutral.

Explain the position and the role of R group in β-sheets.

The r-groups are positioned up and down in an alternating pattern. Depending on the polarity and arrangements of the r-groups the beta sheets can have a hydrophilic and hydrophobic surface. - Hydrophilic r groups face the aqueous solvents. - Hydrophobic r groups face the inside of protein.

Be able to explain the position and the role of R group in alpha helix.

The r-groups in secondary structures face outwards in helices R-groups play a key role in determining the structure and function of the protein. Folding of polypeptides depend on the r-groups involved. - I.e. electrostatic repulsions between amino side chains in an alpha helix can cause the helix to unfold. Steric hindrance caused by bulky side chains close to each other can cause disruption in the formation of Hbonds.

Why is delta S negative when a nonpolar molecule such as limonene is dissolved in water?

The water molecules hydrogen bond into a cage-like structure around the hydrophobic limonene, increasing the order of the water molecules. This is entropically unfavorable, and therefore delta S is negative.

Be able to explain the structure of a water molecule.

There is an unequal electron distribution. - Oxygen is more electronegative than hydrogen. The angle of H-O-H bonds is 104.5 H2O exhibits permanent dipole moments.

Threonine

Thr

Tryptophan

Trp

Be able to describe the structure the fibrous protein keratin.

Two right-handed helices combine to form overall left-handed helix Homodimer of 2 helical peptides that wrap around each other to form a coiled coil structure Key amino acid: Cys Forces: Hydrogen bonding within the individual helix, hydrophobic effects between 2 helices, disulfide bonds between the Cysteine residues Examples: hair, nails, wool, claws the disulfide bonds are formed between Cys residues between the Coiled-coil dimer

Tyrosine

Tyr

A homopolymer of lysine residues (polylysine) can adopt an alpha-helical conformation or is unfolded, depending on the pH of the solution. Predict whether the conformation of polylysine would be alpha-helical or unfolded at pH values of 1, 7, and 11. Explain your reasoning.

Unfolded at pH 1 (the charge repulsion from the numerous positively charged alpha amino groups); mostly unfolded at pH7 (even though the pKa of the alpha amino groups in the alpha-helix would be lower than the normal about 10.8, it would not be as low as pH7, and therefore still mostly protonated); alpha helical at pH 11 (above the pKa of 10.8, so slightly more than half of the alpha amino groups would be deprotonated and uncharged).

Chamber Type of chaperon protein:

Upper and Lower chambers, each one made of 7 subunits for 14 total subunits. GroES and ATP bind to the GroEL rings, trapping the unfolded protein within the folding chamber. Conformational changes releases GroES and folded protein exits the lower chamber. ATP hydrolysis causes a conformational change in the upper chamber that facilitates protein folding and resets the lower chamber for another round. A new unfolded protein inters the lower camber and this moves on in the same cycle.

Explain the roles of urea and Beta-mercaptoethanol in Arifinsen's experiments on protein folding using the protein ribonuclease. What was the most important conclusion resulting from this experiment that earned Arifinsen the Nobel Prize?

Urea is a denaturing agent: It unfolds proteins by disrupting noncovalent interactions; Beta-mercaptoethanol is a reducing agent: It breaks disulfide bonds. With sufficient amounts of both urea and Beta- mercaptoethanol, ribonuclease protein was completely unfolded. The important conclusion was that the primary structure has all the information necessary to specify the tertiary structure.

Be able to calculate the volume needed to prepare buffer solutions using weak acids and conjugate bases.

Use henderson-hasselbalch equation to find the ratio of deprotonated to protonated ions or the concentration of conjugate base to acid - pH=pKa + log([A-]/[HA]) - Solving for [A-]/[HA] Find the percent [A-] and percent [HA] - % [HA]= [HA] /{[HA] + [A-]} x 100 - % [A-]= [A-]/ {[A-]+[HA]} x 100 *Follow the next steps if you are given the molarity of the buffer solution* If given a molarity of the buffer solution the % [A-] and % [HA] will tell you the molarity of the acid and conjugate base within the buffer solution. - Multiply the molarity of the buffer by the decimal form of the percent of each to give you the molarity of acid and base. Convert from molarity to mol by multiplying your molarity of each by the volume of buffer. Divide the moles of acid by the molarity of the stock solution of acid to give you volume of acid in the buffer. Divide the moles of base by the molarity of the stock solution of base to give you the volume of base in the buffer ***Subtract your acid and base volumes from the total volume of buffer to give you the volume of water needed***

Be able to calculate the percentage of a weak acid and its conjugate base at certain pH.

Use henderson-hasselbalch equation to find the ratio of protonated and deprotonated ions or the ratio of conjugate base and weak acid. - pH = pKa + log ([A-]/[HA]) Next find the percent protonated form which gives you % of weak acid. - % [HA]= [HA] /{[HA] + [A-]} x 100 Find the percent deprotonated from which gives you % of conjugate base. - % [A-]= [A-]/ {[A-]+[HA]} x 100

Valine

Val

Which macromolecules would you expect to have the greatest contribution from van der Waals interactions? Explain your choice(s).

Van der Waals interactions would be most prevalent in the lipids because of the nonpolar hydrocarbon chains. Nonpolar atoms are required to form van der Waals interactions.

Be able to explain why water is a good solvent for hydrophilic substances but not a good solvent for hydrophobic substances.

Water can act as a hydrogen-bond donor AND a hydrogen-bond acceptor Due to this hydrogen-bond forming character, water is a good solvent for ionic and polar substances (hydrophilic) - Amino acids and peptides, Small alcohols, Carbohydrates. (These substances contain functional groups (all but methyl groups) that allow them to form hydrogen bonds with water.) Water forms hydration layer around hydrophobic substances that it cannot form hydrogen bonds to - Water is not a good solvent for hydrophobic substances because interaction between nonpolar atoms and water causes an unfavorable change in free energy (ΔG>0) - Cannot bond with hydrocarbons, aromatic rings, and amphipathic molecules

Be able to explain the ionization of water.

Water ionization constant @ 25 C: Kw= [H+][OH-]=1.0x10-14 M2 [H+] and [OH-] are reciprocally related Only small % of water ionizes most stay at H2O

Be able to explain how weak acids and bases behave in water.

Weak acids and bases partially dissociate in water - Partial dissociation forms either a conjugate base/acid Use pKa to determine the strength of weak acid; how much it will dissociate → become deprotonated Ka= (H+ *A-)/HA pKa= -logKa

Briefly explain how proteins manage to "neutralize" the polarity of main-chain carbonyl O and amide NH groups that have to be buried in the hydrophobic interior of the protein when the protein folds.

When the amide and carbonyl groups are involved in hydrogen bonding, such as in alpha-helix and Beta-sheet structures, this serves to minimize the effects of these polar groups.

Be able to construct titration curves for weak acids.

Y-axis should be labeled: pH range and spacing between numbers should be consistent X-axis should be labeled OH- equivalents and spacing between numbers should be consistent Label the title of the chart Titration Curve for X molecule Label the pKa value at the ionizable group points, values from the chart provided by Kenny - This value tells you where 50% of that ionizable group is protonated and 50% is deprotonated Graph starts at 0,0 Graph flattens out at the pKa values for the ionizable groups then jumps up sharply to the next one

Be able to define zwitterion and isoelectric point.

Zwitterion- A molecule carrying both positive and negative charges with a zero net charge Isoelectric point (PI): A point on the pH range where the average charge on the molecule sums to exactly zero.

The basic structure of collagen consists of ___ _____ -handed helices, which form a _____ -handed _____- helix fiber. Select one: a. 3; left; right; triple b. 3; right; left; triple c. 2; left; right; double d. 2; right; left; double

a. 3; left; right; triple

Which one of the following statements comparing alpha keratin and silk fibroin is true? Select one: a. Both fibers are heavily stabilized by hydrogen bonds. b. Both are primarily 𝛼-helical in character. c. Both fibers are intracellularly located. d. Both have covalently cross-linked strands.

a. Both fibers are heavily stabilized by hydrogen bonds.

Which statement regarding protein secondary structures is correct? Select one: a. Protein 𝛼-helices and β-strands differ in that 𝛼-helices are stabilized by intrahelical hydrogen bonds, whereas β-strands are stabilized by hydrogen bonds across adjacent strands. b. Protein 𝛼-helices alternate with β-strands in stabilizing protein structure. c. β-strands allow 𝛼-helices to interact with one another. d. Protein 𝛼-helices are left-handed, whereas β-sheets are right-handed in arrangement.

a. Protein 𝛼-helices and β-strands differ in that 𝛼-helices are stabilized by intrahelical hydrogen bonds, whereas β-strands are stabilized by hydrogen bonds across adjacent strands.

Which statement about the 𝛼-helix is true? Select one: a. The amide backbone dipoles line up in one direction. b. The helical backbone structure is stabilized by ionic interactions. c. There are about five amino acids per helical turn. d. The center of the helix is an open channel.

a. The amide backbone dipoles line up in one direction.

At what point does the isoelectric point or pI occur? Select one: a. at the pH when all negative charges on a zwitterion counter the positive charges. b. when the molecule has a single electric charge. c. at pH = 7.0. d. when all of the acidic protons are neutralized with base.

a. at the pH when all negative charges on a zwitterion counter the positive charges.

Which gives rise to a favorable entropic (∆S) driving force for protein folding? Select one: a. the decrease in ordered water molecules as hydrophobic amino acids pack together b. the limiting of possible conformations as the protein folds c. the lining up of hydrogen bonds as the protein folds d. the stabilization caused by favorable electrostatic interactions of amino acid side chains

a. the decrease in ordered water molecules as hydrophobic amino acids pack together

The interaction between nonpolar molecules is best characterized as Select one: a. van der Waals interactions. b. a hydrogen bond. c. ionic interactions. d. a covalent bond.

a. van der Waals interactions.

What is the dominant secondary structure found in hair keratin? Select one: a. 𝛼-helices b. disulfide bonds c. β-sheets d. loop structures

a. 𝛼-helices

An 𝛼-helix has the sequence: NH3+-Ser-Glu-Gly-Asp-Trp-Gln-Leu-His-Val-Phe-Ala-Lys-Val-Glu-COO-. The carbonyl oxygen (in the peptide bond) of the histidine residue is hydrogen bonded to the amide nitrogen of Select one: a. Asp. b. Lys. c. Trp. d. Ala.

b. Lys.

Which of the following statements about β-sheet structures is true? Select one: a. All amino acid side chains in antiparallel and parallel β-sheet structures point to one side of the sheet. b. The individual strands of all β-sheet structures are connected by turns, helices, or loops. c. All β-sheet structures form a spiraling backbone chain. d. Antiparallel β-sheets have a larger number of stabilizing H-bonds between backbone amides than parallel β-sheets.

b. The individual strands of all β-sheet structures are connected by turns, helices, or loops.

Using the figure below, which of the following best describes the titration curve? Select one: a. The equivalence point for the titration is pH = 7. b. The pKa for this weak acid is 4.76. c. This is a titration of a weak base by NaOH. d. The midpoint of the titration is pH = 7.

b. The pKa for this weak acid is 4.76.

What is a current hypothesis that explains the infectious nature of prion diseases? Select one: a. The small molecule denaturants found in infected cells are passed on to healthy cells. b. The presence of an improperly folded prion protein promotes the misfolding of normal prion proteins. c. Unfavorable environmental factors negatively influence healthy cells. d. The virus responsible for prion diseases is transmissible.

b. The presence of an improperly folded prion protein promotes the misfolding of normal prion proteins.

What is the difference between clamp-type and chamber-type chaperone proteins? Select one: a. One type is found extracellularly and one intracellularly. b. They are shaped differently. c. One folds proteins, whereas the other just protects them from unfolding. d. One uses ATP and the other does not.

b. They are shaped differently.

If an unknown solution has low pKa value, it can be said with certainty that it is Select one: a. a weak acid. b. a strong acid. c. pure water. d. a nonpolar solution.

b. a strong acid.

It is important for cells to degrade misfolded proteins. If misfolded proteins are not degraded, the misfolded proteins may Select one: a. waste excessive ATP in attempts to refold them. b. aggregate and interfere with normal cellular function. c. be excreted from the cell rather than recycled for building blocks. d. eventually refold, but not until excessive and sometimes fatal levels of cellular energy are spent.

b. aggregate and interfere with normal cellular function.

Which stabilizing force in protein tertiary structures is a covalent bonding force? Select one: a. van der Waals bonding b. disulfide bonding c. ionic bonding d. hydrophobic interactions

b. disulfide bonding

Limonene is a nonpolar molecule. The water molecules around it form Select one: a. hydrogen bonds with limonene and entropy increases. b. hydrogen bonds with themselves and entropy decreases. c. covalent bonds with limonene and entropy increases. d. ionic bonds with themselves and entropy decreases.

b. hydrogen bonds with themselves and entropy decreases.

Which of the following is true? Select one: a. A basic solution does not contain H+. b. A neutral solution contains [H2O] = [H+]. c. An acidic solution has [H+] > [OH-]. d. A neutral solution does not contain any H+ or OH-.

c. An acidic solution has [H+] > [OH-].

Which statement about amino acids is true? Select one: a. All naturally occurring amino acids in proteins are chiral. b. Most naturally occurring amino acids in proteins are D-amino acids. c. Most common natural amino acids in proteins are L-amino acids. d. Naturally occurring amino acids in proteins occur as a mixture of enantiomers.

c. Most common natural amino acids in proteins are L-amino acids.

Given a solution with pH > pKa, what are the relative concentrations of A- and HA? Select one: a. [HA] = [A-] = 1 b. [HA] = [A-] c. [HA] < [A-] d. [HA] > [A-]

c. [HA] < [A-]

In multi-subunit proteins, such as hemoglobin, the different subunits are usually bound to one another by all of the following EXCEPT Select one: a. hydrophobic effects. b. hydrogen bonds. c. covalent bonds. d. ionic bonds.

c. covalent bonds.

At the interface between subunits of a protein with quaternary structure, which of the following interactions between amino acid side chains would contribute to the stability of the dimer? Select one: a. leucine-aspartate b. phenylalanine-lysine c. glutamate-lysine d. Glutamate-aspartate

c. glutamate-lysine

Below is an image of the top view of the triple-helix fiber of collagen. What is the identity of the amino acid labeled X (X is the 3 in the middle)? Select one: a. hydroxylated lysine b. 4-hydroxyproline c. glycine d. Proline

c. glycine

Hydrophobic interactions between nonpolar molecules result from the Select one: a. tendency to maximize water's interaction with nonpolar molecules. b. strong attractions between nonpolar molecules. c. water becoming more ordered around the nonpolar molecule. d. water ionically bonding to the nonpolar molecule.

c. water becoming more ordered around the nonpolar molecule.

Classify all of the amino acids into the categories charged, hydrophobic, hydrophilic, and aromatic.

charged: aspartate, glutamate, lysine, arginine, histidine hydrophobic: glycine, alanine, proline, valine, leucine, isoleucine, methionine hydrophilic: serine, threonine, cysteine, asparagine, glutamine aromatic: phenylalanine, tyrosine, tryptophan

Rossman fold motif

complex protein fold in which there are alternating alpha helices and beta strands. Found in proteins that bind nucleotides such as dehydrogenases.

Greek key fold motif

consists of 4 or more beta strands linked together to form a beta sheet structure; many channel proteins contain this motif to allow it to pass through hydrophobic cell membrane

Tim barrel motif

consists of alternating alpha helix and beta strand in the structure. Is found in large metabolic enzymes

Helix bundle motif

contains 4 or more alpha helices that provides hydrophobic pockets or hydrophilic channels in membrane protein to allow movement of hydrophilic molecules across membranes

Beta barrel motif

contains multiple twisted beta strand forming a beta sheet barrel structure. It forms an antiparallel beta sheet and forms a channel to allow polar molecules to pass through cellular membranes

Proline key features

cyclic structure with restricted confirmation, cannot form H-bonds in polypeptide, and found at protein turns because of shape

What is the maximum number of covalent bonds a carbon atom can make? a. 2 b. 8 c. 6 d. 4

d. 4

Which of the following statements regarding protein domains is true? Select one: a. A domain is a region absent of 𝛼-helices and β-sheets. b. Multiple domains require multiple subunits and a quaternary structure. c. Each protein has one unique domain. d. A domain can be composed of smaller structural units called motifs.

d. A domain can be composed of smaller structural units called motifs.

The proteins collagen, silk fibroin, and hair keratin have all of the following in common, EXCEPT that they Select one: a. are fibrous proteins. b. are composed of repeating amino acid sequences. c. play important structural roles in biology. d. are composed of 𝛼-helical structures.

d. are composed of 𝛼-helical structures.

The amino acid with a neutral side chain at neutral pH is Select one: a. aspartate. b. arginine. c. glutamate. d. asparagine.

d. asparagine.

Of the three proposed models of globular protein folding, which one describes the initial formation of all secondary structures, followed by the arrangement of those secondary structures into a final tertiary structure? Select one: a. nucleation model b. hydrophobic collapse model c. mutant globule d. framework model

d. framework model

Which interaction largely stabilizes protein secondary (2°) structures? Select one: a. hydrophobic effect. b. van der Waals interactions. c. disulfide bonds. d. hydrogen bonds.

d. hydrogen bonds.

In a hydrogen bond between a water molecule and another water molecule, Select one: a. the hydrogen atom forms an ionic bond with a carbon on the other water. b. a hydrogen ion on the water molecule forms an ionic bond with the oxygen ion on the other water. c. a hydrogen on the water molecule forms a covalent bond to a hydrogen atom on the other water. d. the hydrogen bond typically forms between the oxygen atom of the water and the hydrogen on the other water.

d. the hydrogen bond typically forms between the oxygen atom of the water and the hydrogen on the other water.

The amino acid with the most hydrophobic side chain is Select one: a. asparagine. b. threonine. c. aspartate. d. valine.

d. valine.

Valine/Leucine key features

highly hydrophobic

Isoleucine key features

highly hydrophobic and additional stereocenter at second carbon

What is the isoelectric point of a protein? What is the specific term that describes amino acids at this point?

lsoelectric point of a protein: The pH at which it carries no net charge term: zwitterions

Be able to define pH and pKa.

pH is the negative logarithm of the concentration of H+ → which is the acidity or basicity of an aqueous solution (pH = -log[H+]) - pH tells the extent of dissociation of a solution pKa is the negative logarithm of Ka → which is the constant for acid dissociation - The lower the pKa, the stronger the weak acid

Be able to solve weak acid problems with the Henderson-Hasslebalch equation.

pH= pKa + log([A-]/[HA]) Tells how much of the weak acid will become deprotonated Shows direct relationship between the pH of a solution and the ratio of the deprotonated form [A-] to the protonated form [HA] of some ionizable group.

Describe the basic structure β-strand.

polypeptide chains adjacent to each other held together by hydrogen bonds between the backbone The distance between 2 amino acids is 3.2-3.4 -> they are almost fully extended

Be able to identify the cis and trans configuration of a polypeptide.

polypeptides are usually in trans 6 configuration.

Glycine key features

small and flexible, used in turns in proteins and non-chiral alpha carbon

Alanine key features

small, chemically inactive, large portion of proteins

Be able to explain how H-bonds are formed in alpha helix.

the hydrogen bonds that form in an α helix between the carbonyl oxygen (residue n) and the hydrogen atom attached to the nitrogen in the peptide bond located four amino acids away (n + 4).

𝛂 helix:

the most common elements of secondary structure in proteins is the right-handed 𝛂 helix. Stabilized by numerous intrastrand hydrogen bonds and it rotates around an imaginary central rod in a right-hand direction. Right hand helix: favorable and abundant Left hand helix: unfavorable, less stable, short, and infrequent *proline can disrupt the alpha helix because its rotation is restricted due to its r-group and its amino group does not have an H available for hydrogen bonding.*

Be able to define secondary protein structure.

the regular repetitive arrangement of local regions of the polypeptide backbone. There are three major structures: β strands, α helices, and β turns. (backbone interactions)

Be able to define tertiary protein structure.

the spatial location of all the atoms in the polypeptide chain. The overall 3-D arrangement of polypeptides. (interactions between secondary structure and conformations of side chains). - A protein becomes functional when it is folded into its tertiary structure.

Methionine key features

unreactive sulfur makes up thioester side chain, 1st amino acid in polypeptides

van der Waals interaction definition:

van der Waals interactions occur between neutral molecules/atoms by temporary dipole moments because of fluctuation in electron clouds. · Weakest Noncovalent interaction (nonpolar, transient). · Interactions between nonpolar molecules. · Strong repulsion is when atoms are too close. Weak attraction is when atoms are farther apart. · Maximum van der Waals attraction occurs at a distance slightly greater than the sum of the van der Waals radii of the two atoms.

Tyrosine/Tryptophan key features

very hydrophobic, amphipathic and found at transition from exterior to interior of a protein

Covalent bond features

· Not all covalent bonds are created equal. · The more pairs of electrons shared between the atoms, the stronger the bond strength and the shorter the distance. · Covalent bonds can be either polar or nonpolar depending on the electronegativity difference between two atoms (Polar = > 0.5, Nonpolar = < 0.5). · Common polar covalent bonds: C-O, O-H, and N-H.

Hydrogen bond features:

· Second strongest Noncovalent interaction (partial charges). · All hydrogen bonds have a hydrogen-bond acceptor and a hydrogen-bond donor. · The strength of the hydrogen bond depends on the donor and the acceptor. · Linear bonds are stronger than angled bonds. · NH and OH form hydrogen bonds. Hydrogen bond depends on formation of partial charges between the H and O molecules - H partially positive, O partly negative Main attractive force holding protein Secondary Structures in place

Hydrophobic effect features:

· Second weakest Noncovalent interaction (nonpolar, more permanent). · Hydrophobic effect is one of the main factors behind: protein folding, protein-protein association, formation of lipid micelles, and enzyme-substrate complex formation. · When nonpolar molecules are in polar solvent, they are surrounded by water. This is energetically unfavorable because there is a reduce in water movement. These nonpolar molecules group together, which reduces the surface area surrounded by water. This allows for fewer water molecules needed to be ordered (can move around freely), which makes it more energetically favorable. Main attractive force holding protein Tertiary and Quaternary Structures in place

Ionic interaction features:

· Strongest Noncovalent interaction (full positive/negative charges). · AKA also called charge-charge interactions or salt bridges. · The electronegativity difference between two atoms must be >2 (often formed between the most and the least electronegative atoms).

van der Waals interaction features:

· Weakest Noncovalent interaction (nonpolar, transient). · Interactions between nonpolar molecules. · Strong repulsion is when atoms are too close. Weak attraction is when atoms are farther apart. · Maximum van der Waals attraction occurs at a distance slightly greater than the sum of the van der Waals radii of the two atoms.

Valine (Val), Leucine (Leu), and Isoleucine (Ile) details

• Branched hydrocarbon side chain. • Highly hydrophobic. • Ile has an additional stereocenter (at *).

Phenylalanine (Phe), Tyrosine (Tyr), and Tryptophan (Trp) details

• Bulky aromatic side chain. • Very hydrophobic, but Phe is more hydrophobic. • Tyr and Trp are amphipathic and are often found at the transition of exterior and interior of a protein. • Tyr and Trp absorb UV light at 280 nm, can be used to measure protein concentration.

Proline (Pro) details

• Forms cyclic structure with restricted conformation. • Cannot form H-bonds in a polypeptide. • Usually found at the turns of polypeptide chain.

Asparagine (Asn) and Glutamine (Gln) details

• Highly hydrophilic because the side chains can form hydrogen bonds. • Their side chains can act as both H-bond donor or acceptor.

Alanine (Ala) details

• Methyl group side chain. • Relatively small. • Chemically inactive. • Flexible. • Gly + Ala = 15% in proteins.

Serine (Ser), Threonine (Thr), and Cysteine (Cys) details

• Ser & Thr have a hydroxyl group, can be phosphorylated to regulate enzyme function. • Thr has a second stereocenter (at *). • Cys has a sulfhydryl group, can form disulfide bridge in folded protein. • They are hydrophilic and good nucleophiles playing key roles in enzyme activity.

Aspartate (Asp) and Glutamate (Glu) details

• Side chains are negatively charged --> highly hydrophilic. • Asp and Glu are dicarboxylic amino acid. • These charges are important for protein separation.

Histidine (His), Lysine (Lys), and Arginine (Arg) details

• Side chains are positively charged --> highly hydrophilic. • His carries a positive charge at pH 6, function as both a hydrogen donor and acceptor at neutral pH. • These charges are important for protein separation.

Methionine (Met) details

• Thioester sidechain makes it hydrophobic. • Sulfur is unreactive. • 1st amino acid in a polypeptide.

Glycine (Gly) details

• α-carbon is not chiral. • Smallest. • Chemically inactive. • Flexible and able to form sharp turns in proteins.