Biochem 1, L1: Amino Acids and Proteins

List the aa that are both glucogenic and ketogenic.

(mnemonic "PITTT"): Phenylalanine, Isoleucine, Tyrosine, Threonine, Tryptophan

Diff b/w acid hydrolysis and proteolysis?

Acid hydrolysis uses heat and is non-specific; proteolysis uses proteolytic enzymes is specific

Why do aa tend to be positively charged at very acidic pH levels (low pH)?

At very acidic levels (low pH), there are high levels of protons so aa will be fully protonated thus positively charged

Adding strong base to a sln containing an enzyme often reduces enzyme activity to 0. In addition to causing protein denaturation, which of the follow is another reason for loss of enzyme activity? A) Enzyme activity, once lost, cannot be recovered B) The base can cleave peptide residues C) Adding a base catalyzes protein polymerization D) Adding a base tends to deprotonate amino acids on the surface of proteins

B (D is true but fails to explain loss of enzyme activity)

At pH 7, the charge on a glutamic acid molecule is: a) -2 b) -1 c) 0 d) +1

B. -1

Which of the following statements is most likely true of nonpolar R groups in aqueous solution? A) They are hydrophilic and found buried within proteins B) They are hydrophilic and found on protein surfaces C) They are hydrophobic and found buried within proteins. D) They are hydrophobic and found on protein surfaces

C

Which aa have positively charged, basic side chains?

H (his), K (lys) , R (arg)

Relate pKa, pH, and protonation.

If pH>pKa, then molecule will be deprotonated. If pH<pKa, then molecule will be protonated.

Largest of the amino acids

W

Why is peptide formation and ex of condensation/dehydration?

bc it results in loss of water molecule

If a dipeptide is energetically unfavorable, then why doesn't the reverse reaction (breaking the dipeptide) occur spontaneously?

bc the activation energy of the reverse is too high to occur under normal conditions, which is why we use enzymes (proteolyses) or heat to break peptide bonds

Assuming all other conditions are equal, which of the following amino acids is expected to have the most positive charge at physiological pH? (A) ARG (B) MET (C) ASN (D) ASP

there are only 2 positively charged aa at physio pH (arginine and lysine) so ans is A

What are the four main reactants in Gabriel Synthesis of an amino acid?

1. "thad" (potassium pthalamide) 2. diethyl bromoalonate 3. Alkyl Halide 4. water

2 ways to perform hydrolysis (to break peptide bonds)?

1. acid hydrolysis 2. proteolysis (use proteolytic enzymes)

Four reactants in Strecker synthesis?

1. aldehyde/ketone 2. ammonium chloride (NH4Cl) 3. potassium cyanide (KCN) are all used to make the aminonitrile 4. Water is used to hydrolyze the aminonitrile to form amino acid

Average weight of aa

110 daltons

Pyrophosphate is unstable in aqueous sln and is hydrolyzed to form what? How is it utilized?

2 molecules of inorganic phosphate which can then be reused to form high energy bonds like in ATP

List the 5 aa that have side chains with full charges at physiological pH.

3 are positive: K, H, R and 2 are negative: D and E (lysine, histidine, arginine, aspartate, and glutamate)

If chymotrypsin cleaves at the carboxyl end of phenylalanine, tryptophan, and tyrosine, how many oligopeptides would be formed in enzymatic cleavage of the following molecule with chymotrypsin? Val-Phe-Glu-Lys-Tyr-Phe-Trp-Ile-Met-Tyr-Gly-Ala

4 (single amino acid is not considered oligopeptide)

Which of these is most likely to be preserved when a protein is denatured? A. Primary Struc B. Secondary Struc C. Tertiary Struc D. Quaternary Struc

A

Which of these amino acids has a side chain that can be ionized in cells? A) Histidine B) Leucine C) Proline D) Threonine

A (His has an imidazole side chain which can be protonated)

Describe amino acids at a low pH, neutral pH, and high pH.

Acidic: aa gets protonated thus positively-charged species neutral: aa exists in zwitterion form Basic: aa gets deprotonated thus negatively-charged species

Using knowledge of the relationship b/w temperature and kinetic energy, explain how heat denatures proteins.

As temp inc, kinetic energy inc which means increased molecular motion. In proteins, this increased molecular motion causes intramolecular bonds to break which causes protein to unfold

In a neutral solution, most amino acids exist as: A. Positively charged compounds B. Zwitterions C. Negatively charged compounds D. Hydrophobic molecules

B. Zwitterions

positively charged (basic) aa include:

Basically, History Loved kind Adventurers roughly Histidine (H), Lysine (K), and Arginine (R)

Collagen consists of three helices with carbon backbones that are tightly wrapped around one another in a "triple helix." Which of these amino acids is most likely to be found in the highest concentration in collagen? A) Proline B) Glycine C) Threonine D) Cysteine

Bc collagen has triple helix, C backbones are very close together thus making steric hindrance a potential problem. To reduce hindrance we'd need small side chain. Glycine has smallest side chain so ans is B

On MCAT, why will you likely see anion names (aspartate and glutamate) instead of acid names (aspartic acid, glutamic acid)?

Bc most acids in cells exist in anion/deprotonated form

Why do all aa have at least two pKa values?

Bc they have at least groups that can be deprotonated, the carboxyl group and amino group

Why doesn't the nitrogen that is part of the amide group in N and Q gain a proton and become NH3 when pH changes?

Because the amide group has resonance stabilization. Amides are very unreactive because of this resonance, hence they will not lose or gain protons easily.

Relate serine's and threonine's structure to their ability to participate in hydrogen bonding.

Both serine and threonine have -OH groups which makes them highly polar and able to participate in H bonding

An alpha-helix is most likely to be held together by: A. Disulfide bonds B. Hydrophobic effects C. Hydrogen bonds D. Ionic attractions b/w side chains

C

How many distinct tripeptides can be formed from one valine, one alanine, and one leucine molecule? A. 1 B. 3 C. 6 D. 27

C

Which of the follow is least likely to cause denaturation of proteins? A. Heating the protein to 100 C B. Adding 8M urea C. Moving it to a more hypotonic environment D. Adding a detergent such as sodium dodecyl sulfate

C

A particular alpha-helix is known to cross the cell membrane. Which of these aa is most likely to be found in the transmembrane portion of the helix? A. Glutamate B. Lysine C. Phenylalanine D. Aspartate

C (Phe is the only aa that has a hydrophobic side chain which could pass through the membrane which has hydrophobic fatty acid tails)

Why is C prone to oxidation?

C (cys) has a thiol group. Bc Sulfur atom is larger and less EN than Oxygen in the -COOH, the S-H bond is weaker than the O-H which leaves the thiol group prone to oxidation

What are the reaction types used in Strecker Synthesis (in order)?

Condensation rxn (formation of imine from a carbonyl-containg cmpd and ammonia, w loss of water) then Nucelophilic addition (addition of nitrile group) followed by Hydrolysis

What is the importance of cooperativity, or allosteric affects, resulting from the quaternary structures of proteins?

Cooperativity/allosteric affects allow a subunit to undergo conformational changes which can enhance/reduce activity of other subunits

Except for cysteine, all aa have an S configuration. Why does cysteine have an R config?

Cysteine's functional group (-CH2SH) has priority over the -COOH group

In lysine, the pKa of the side chain is ~10.5. Assuming that the pKa of the carboxyl and amino groups are 2 and 9 respectively, the pI of lysine is closest to: A) 5.5 B) 6.2 C) 7.4 D) 9.8

D

Which of the following is a reason for conjugating proteins? I. To direct their delivery to a particular organelle II. To direct their delivery to the cell membrane III. To add a cofactor needed for their activity A) I only B) II only C) II and III only D) I, II and III

D

Which of these statements concerning peptide bonds is FALSE? A. Their formation involves a reaction b/w an amino group and a carboxyl group B. They are the primary bonds that hold amino acids together C. They have partial doble bond character D. Their formation involves hydration reactions

D

Which two aa have negative charges on side chains at physiological pH (7.4)?

D (asp, aspartic acid) and E (glu, glutamic acid)

Which of these amino acids has a chiral carbon in its side chain? I. Serine II. Threonine III. Isoleucine A. I only B. II only C. II and III only D. I, II, and III

D (every aa except glycine is chiral)

A particular oncogene product has an unusually high number of proline residues. These residues: (A) Aid in the formation of alpha helices (B) Are more likely to be found throughout beta-pleated sheets (C) Aid only in the formation of antiparallel beta-pleated sheets (D) Are more likely to be found in turn regions of the protein

D; turn regions are loose places in protein where aa are not locked into alpha or beta structure and proline is an "alpha helix breaker" so if there's a bunch of proline then they will likely be breaking the secondary struc (alpha/beta) into a turn region

List the 7 aa that have ionizable side chains.

E, D, H, C, L, Y, and R

Where do hydrophilic aa tend to reside within a protein?

Exterior/surface bc they like water

Which aa have uncharged aromatic side chains?

F (phe), Y (tyr), and W (trp)

Which aa have alkyl groups aka nonpolar, nonaromatic side chains?

G (gly), A (Ala), V (Val), L (Leu), I (Ile), M (Met), and P (Pro)

The majority of the amino acids, with the exception of two, have the (S) absolute (counterclockwise) configuration. List the two exceptions.

Glycine and Cysteine

Use hemoglobin as support for the claim that prosthetic groups have major roles in determining the function of their respective proteins.

Hemoglobin's prosthetic group is heme, which functions in binding and carrying oxygen. One major role of hemoglobin is to carry O to the diff parts of the body

Explain why glycine is negatively charged at highly basic pH.

Highly basic solutions have low levels of H+ so this condition makes it favorable for aa to be deprotonated which would leave glycine with a negative charge

Why is Histidine useful to have at the active site of a protein.

Histidine has a pKa ~6.5 which is close to physiological pH (~7.4). So, it exists in both protonated and deprotonated form, which means that it can both stabilize or destabilize a substrate.

Cysteine's structure changes depending on whether the environment is reducing or oxidizing. What role does this play in the formation of disulfide bridges?

If cysteine is in an oxidizing environment, then it will lose H on thiol (SH) group which leads to formation of disulfide bridges

Where do hydrophobic aa tend to reside within a protein?

Interior so they don't interact with water

What's the importance of L-aa vs D-aa?

L-aa are only ones found within human body

List the aa that are only ketogenic.

Leucine and Lysine

N-terminus vs. C-terminus

N-terminus= the end of a polypeptide or protein that has a free amino group C-terminus= the end of a polypeptide or protein that has a free carboxyl group

Polar, acidic and basic amino acids are what?

Polar, acidic and basic amino acids are all hydrophilic and tend to form hydrogen bonds with water in aqueous solution.

Primary vs Secondary structure of proteins

Primary=linear chain of aa Secondary=alpha helices and B-pleated sheets as result of intermolecular H bonding

Describe the roles of Proline's secondary alpha C and Glycine's flexibility in the secondary structure of proteins.

Proline's secondary alpha C causes kinks in the alpha helix (secondary structure) of proteins and Glycine's flexibility causes the same thing thus they are known as "alpha helix breakers"

Which aa has three nitrogen atoms in its side chain?

R (arg)

Histidine has a pKa ~6.5. If it's in solution of pH 9, will it be protonated or deprotonated?

Since pH > pKa in this case, histidine will be deprotonated

Use SDS as an example of how solutes can cause denaturation.

Sodium dodecyl sulfate solubilizes proteins, disrupting non-covalent bonds and promoting denaturation.

Which aa have polar side chains?

T (thr), S (ser), N (asn, asparagine), Q (gln, glutamine), C (cys)

Discuss the imp of Anfinsen's experiment.

The hypothesis that "protein amino acid sequence determines the final shape a protein assumes in a water solution" was proven to be correct when Christian B. Anfinsen showed that if the enzyme ribonuclease was opened out into a linear chain and then allowed to reform, it reassumed the correct catalytic shape.

What happens when the pH of a solution is approximately equal to the pKa of the solute?

The solution acts as a buffer

What are the reaction types used in Gabriel Synthesis (in order)?

Two SN2 reactions; Hydrolysis; Decarboxylation

Use urea as an example of how solutes can cause denaturation.

Urea directly affects the bonds that hold proteins together.

aromatic amino acids

WYF (tryptophan, tyrosine, and phenylalanine)

Tyrosine (Y) has an -OH in its side chain and tryptophan (W) has a nitrogen in its side chain. Why are Y and W nonpolar despite having EN atoms in their side chains?

Y has a benzene ring which makes the molecule nonpolar; W has two rings which also makes it nonpolar

Explain why aa become dipolar ions aka Zwitterions.

Zwitterions are neutral molecules with both negative and positive charges. They reach this state when they are in a pH that is basic enough to deprotonate the -COOH to -COO- but not basic enough to deprotonate the amino group so the amino group remains fully protonated and in its conjugate acid form NH3+

Why is peptide formation considered an acyl substitution reaction?

acyl substitution rxns occur when Nu- attacks E- (electrophile) & the -OH group is kicked off which results in formation of bond; this happens in peptide formation: Nu- is NH3+, which attacks E- (carbonyl C) then -OH on -COOH is kicked off resulting in peptide (amide) bond formation

Define peptide bond

amide bond b/w 2 aa

negatively charged (acidic) aa include:

aspartic acid and glutamic acid

Explain why a perfect Strecker synthesis could at best give you a 50% yield.

bc Strecker produces racemic mixture (L- and D-) thus only up to 50% will be biologically relevant (L-)

Why is phosphoric acid an excellent buffer?

bc it has 3 hydrogens, each one having very diff pKa values; this allows phosphoric acid to gain/lose a proton depending on pH, making it a good buffer of most of the pH scale

Why is proline considered a secondary alpha aa?

bc its side chain forms a second bond with the amino group, forming a ring

Using knowledge of G's structure, explain why it can fit into other hydrophobic or hydrophilic environments.

bc its the smallest amino acid due to the fact that its side chain is simply an H

Explain how the C-N bond in the amide has partial double bond character.

bc of resonance, which is a result of ability of e- to be delocalized in the lone pair on the amino N and pi e- in the carbonyl

Why is valine (V) more hydrophobic than Alanine (A)?

because it has more hydrocarbons (methyl groups) and more hydrocarbons means more hydrophobicity (nonpolar)

Both the Strecker Synthesis and Gabriel Synthesis can produce racemic mixtures (both L- and D- amino acids). Explain how this is possible.

both processes start with a planar carbonyl-containing compound which means Nu- can equally attack from either side of the carbonyl thus producing enantiomers

What is the significance of an molecule being chiral?

chirality means that the molecule exists as enantiomers (diff conformations, same formula; non superimposable mirror images) which is important biologically bc diff structure means diff function.

Trypsin and Chymotrypsin, Carboxypolypeptidase, & Aminopeptidases are all proteolytic enzymes, which cleave at specific points in peptide chains. What is the general mechanism these enzymes use to perform cleavage?

cleavage of polypeptides is done by hydrolysis (reverse reaction of condensation) which entails using water to add a H+ to amide N and an -OH to the carbonyl C

What causes loops in protein chains?

disulfide bridges

Tyrosine is a precursor to:

epinephrine/norepinephrine biosynthesis

Explain why Glycine is not chiral.

glycine's side chain (R) is a duplicate group coming off the alpha carbon, which makes it achiral

Nonpolar amino acids are

hydrophobic

What 2 characteristics make inorganic phosphate useful for transfer of energy biologically?

inorganic phosphate is very negative. So, when it's bonded to other phosphate groups like in a nucleotide triphosphate, it has strong repulsion with the other phosphates which inc the bond energy; also, inorganic phosphate can be resonance-stabilized

What is the key to stability in both primary and secondary protein structures?

intermolecular H bonds b/w diff residues

Proteins with lipid, carbohydrate, and nucleic acid prosthetic groups are referred to as

lipoproteins, glycoproteins, nucleoproteins

Which of the following segments of amino acids would be most likely to be found in the membrane-spanning domain of the sodium channel in a nerve axon? (A) DDR (B) EVE (C) LAD (D) LIV

middle of membrane is hydrophobic so we'd find aa that are hydrophobic, D and E are negatively charged species so that eliminates A-C; so its D

polar amino acids tend to have terminal groups containing

oxygen, nitrogen, or sulfur

pH range for Zwitterion form of aa

pH 4-7

For a generic amino acid NH2CRHCOOH, with an uncharged side chain, what would be the predominant form at each of the following pH values? > pH = 1 > pH = 7 > pH = 11

pH=1: high levels of H+ so aa will be fully protonated and thus positively-charged species pH=7: aa will in Zwitterion form pH=11: low levels of H+/high levels of -OH so aa will be fully deprotonated and thus negatively-charged species

Given the following pKa values, what's the value of the pI for the aa listed below? Arginine (pKa1=2.17, pKa2=9.04, pKa3=12.48)

pI is the average of the two nearest pKa values ~11

Given the following pKa values, what's the value of the pI for the aa listed below? Aspartic acid (pKa1=1.88, pKa2=3.65, pKa3=9.60)

pI is the average of the two nearest pKa values ~3

Why do aa with nonionizable side chains have pI values of around 6?

pI values are the average of the two nearest pKa values of aa side chains. So if the aa has side chains that are neither acidic nor basic, then only need to account for the carboxyl group (pKa ~2) and amino group (pKa ~11) when calculating pI which would be ~5.5 (around 6)

Why do aa with basic side chains have pI values well above 6?

pI values are the average of the two nearest pKa values of the side chains of the aa. So if the pKa values are higher (by they're basic) then the pI (the average of the pKa values) will also be higher and in the basic range which is 7-14.

Why do aa with acidic side chains have pI values well below 6?

pI values are the average of the two nearest pKa values of the side chains on the aa. So, if an aa has acidic side chains, then they have lower pKa values thus the average (essentially the pI) will be low or in the acidic range which is 1-6

Explain why an acid with high pKa in a solution with low pH will be protonated.

pKa measures affinity for protons; pH measures the concentration of protons in a solution. High pKa means molecule really wants protons; low pH means high proton concentration. So, if an acid with high pKa is in solution with low pH, then the acid will be protonated because it has a high affinity for protons and there is a high concentration of protons in the solution.

How does the formation of quaternary structures reduce the amount of DNA needed to encode the protein complex?

quaternary structures involves linking many polypeptides, each polypeptide being built accord to DNA. It's poss for like 4 separate chains to be built accord to same codons and be put together to form a diff struc, which would mean a diff function or poss for 3 diff chains to be made accord to same code but just experiencing modifications (maybe allosteric affect) after the fact resulting in distinct polypeptide chains that eventually come together to form a functional protein (with a specific function of course)

Nonpolar nonromantic amino acids tend to have side chains that are

saturated hydrocarbons

Why is methionine nonpolar despite having S in its side chain?

the EN of S (2.58) and of C (2.55) are very close which makes methionine relatively nonreactive or nonpolar; also the S is kind of hidden from environment in b/w the carbons on the side chain

What mostly determines the tertiary structure of proteins?

the hydrophobic and hydrophilic interactions of the aa side chains, more specifically the aa hydrophobic side chains moving toward interior of protein to avoid water

How does the burial of hydrophobic aa in protein and exposure of hydrophilic side chain to the surrounding polar environment cause an increase in entropy?

the inc in entropy is referring to the solvent (water molecules); if you didn't hide the hydrophobic side chains, then the H2O molecules would be forced to form in an orderly fashion around the aa, which is nonspontaneous (decrease in entropy)

Which H in histidine is the acidic one? Why?

the one connected to the pi bond because that one has already donated two electrons basically to resonance

pKa

the pH at which half the molecules of the species is deprotonated [HA]=[A-]

Why do you use phthalimide rather than ammonia in the Gabriel synthesis?

using pthalimide leads to a pthalamidomalonic ester, which is a huge Nu-; a large Nu- is beneficial bc it prevents the carbonyl C from undergoing several substitutions; under these rxn conditions ammonia would not be good Nu- bc it would be a cation but if we change the rxn conditions then it runs the risk of unwanted substitution rxns

Big picture, why does variation in aa side chains matter?

variation allows for different chemical properties aka diff aa will engage in diff reactions

Given the following pKa values, what's the value of the pI for the aa listed below? Valine (pKa1=2.32, pKa2=9.62)

~6