Biochemistry: Amino Acids, Peptides, and Proteins

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: Val-Phe; Glu-Lys-Tyr; Ile-Met-Tyr; Gly-Ala. A single amino acid on its own is not considered an oligopeptide.

What does it mean when a carbon has a chiral center?

A carbon with a chiral center has four different groups attached to it.

A peptide bond forms a specialized form of an amide bond between what groups? A. Between the -COOH group of one amino acid and the NH2 group of another amino acid. B. Between the -COOH group of one amino acid and the NH3+ group of another amino acid. C. Between the -COO^- group of one amino acid and the NH2 group of another amino acid. D. Between the -COO^- group of one amino acid and the NH3+ group of another amino acid.

A peptide bone forms a specialized form of an amide bond between: D. Between the -COO^- group of one amino acid and the NH3+ group of another amino acid. This forms the functional group -C(O)NH- and water (H20).

An improtant component of tertiary structure is the presence of disulfide bonds, the bonds form from which amino acid? A. Cysteine B. Proline C. Histidine D. Serine

A. Cysteine An improtant component of tertiary structure is the presence of disulfide bonds, the bonds form when two cysteine molecules become oxidized to form cystine. Extracellular proteins often have several disulfide bonds, whereas intracellular proteins usually lack them. Disulfide bonds create loops in the protein chain. In addition disulfide bonds determine how wavy or curly human hair is: the more disulfide bonds, the curlier it is.

Which of the following amino acids has an (R) absolute configuration? A. Cysteine B. Proline C. Methionine D. Tryptophan

A. Cysteine Cysteine has an (R) absolute configuration because the -CH2SH group has priority over the -COOH group. It is still an L-amino acid. All other chiral amino acids are L-amino acids and have an (S) absolute configuration. *Except for glycine, all amino acids are chiral --- and except for cysteine, all of them have an (S) absolute configuration.

Which amino acid is most likely to be found at the active site of an enzyme? A. His B. Pro C. Gly D. Cys

A. His Histidine, because its side chain has a pKa (6.5) roughly equal to physiological pH (7.4) thus allowing histidine to exist in both its protonated and deprotonated form. This way, His can both stabilize or destabilize a substrate during catalysis.

Which bond stabilizes the secondary structure of a protein? A. Hydrogen Bonds B. Covalent Bonds C. Van Der Waals Forces D. Dipole-dipole Interactions

A. Hydrogen Bonds The secondary structure of a protein is referred to as the way that a linear sequence of amino acids folds upon itself, such as an alpha helix or beta sheet. Secondary structure is stabilized by hydrogen bonds.

At which protein level of structure does all the information needed for folding get encoded? A. Primary Structure B. Secondary Structure C. Tertiary Structure D. Quaternary Structure

A. Primary Structure The primary structure alone encodes all the information needed for folding at all of the higher structural levels. The secondary, tertiary, and quaternary structures a protein and adopts the most energetically favorable arrangements of the primary structure.

Which level of protein structure can be determined by a laboratory technique called sequencing? A. Primary Structure B. Secondary Structure C. Tertiary Structure D. Quaternary Structure

A. Primary Structure The primary structure can be determined by a laboratory technique called sequencing.

Which level of structure of a protein is the linear arrangement of amino acids coded in an organisms DNA? A. Primary Structure B. Secondary Structure C. Tertiary Structure D. Quaternary Structure

A. Primary Structure The primary structure of a protein is the linear arrangement of amino acids coded in an organisms DNA. Here you see peptide bonds connecting the amino acids into the linear arrangement. If you have n number of amino acids, then you have n-1 number of peptide bonds. It's the sequence of amino acids listed from the N-terminus to the C-terminus.

Which of the following amino acids cause a kink when found in the middle of an alpha-helix? A. Pro B. Cys C. Arg D. Phe

A. Pro Because of its rigid and cyclic structure, proline will introduce a kink in the peptide chain when it is found in the middle of an alpha-helix. Proline residues are thus rarely found in alpha-helices, except in helices that cross the cell membrane. Similarly, it is rarely found in the middle of pleated sheets. On the other hand, proline is often found in the turns between the chains of a beta-pleated sheet, and it is often found as the residue at the start of an alpha-helix.

Which of the following amino acids forms a cyclic amino acid using the amino nitrogen group? A. Pro B. Trp C. Phe D. Tyr

A. Pro Proline is an amino acid that is nonpolar with a nonaromatic side chain. It is unique in that it forms a cyclic amino acid. In all the other amino acids, the amino group is attached only to the alpha-carbon. In proline, however, the amino nitrogen becomes a part of the side chain, forming a five-membered ring. The ring places constraints on the flexibility of proline, which limits where it can appear in a protein and can have significant effects on proline's role in secondary structure.

What does the pKa of a group refer to? A. The pKa of a group is the pH at which, on average, half of the molecules of that species are deprotonated. B. The pKa of a group is the pH at which, on average, all of the molecules of that species are deprotonated. C. The pKa of a group is the pH at which, on average, all of the molecules of that species are protonated. D. The pKa of a group is the pH at which, on average, 1/3 of the molecules of that species are deprotonated.

A. The pKa of a group is the pH at which, on average, half of the molecules of that species are deprotonated. That is, [protonated version of the ionizable group = deprotonated version of the ionizable group] or [HA] = [A-] Ionizable groups tend to gain protons under acidic conditions and lose them under basic conditions. So, at low pH, ionizable groups tend to be protonated; at high pH they tend to be deprotonated. If the pH is less than the pKa, a majority of the species will be protonated. If the pH is higher than the pKa, a majority or the species will be deprotonated. In other words: If pH < pKa = majority of the species will be protonated If pH > pKa = majority or the species will be deprotonated. If pH = pKa then exactly half of the acid have deprotonated.

In a titration curve where would the isoelectric point (pI) be? A. The vertical line between the two sigmoidal (s-shaped) curves. B. The first relatively flat region on the first sigmoidal (s-shaped) curve. C. The second relatively flat region on the first sigmoidal (s-shaped) curve. D. The starting point

A. The vertical line between the two sigmoidal (s-shaped) curves. The isoelectric point (pI) represents when there are equal parts base to a solution (added 1.0 equivalent base to a 1.0 equivalent of the amino acid). At this point the solution exists exclusively as the zwitterion form. This means that every molecule is now electrically neutral, and thus the pH equals the isoelectric point (pI) of the amino acid. For example of glycine: [+NH3CH2COO-].

Acid-Base Chemistry of Amino Acids

Acid-Base Chemistry of Amino Acids

Pair the amino acids to their correct three-letter and one-letter abbreviations. Alanine Lys Q Valine Asp N Argnine Glu C Proline Gln F Glycine His M Cysteine Ser L Methionine Leu A Asparagine Thr G Glutamine Met V Serine Asn Q Tryptophan Pro S Lysine Glu K Glutamic Acid Cys W Histidine Phe E Tyrosine Val D Aspartic Acid Trp H Isoleucine Gly I Threonine Ile Y Leucine Tyr P Phenylalanine Ala T

Alanine Ala A Argnine Arg R Asparagine Asn N Aspartic Acid Asp D Cysteine Cys C Glutamic Acid Glu E Glutamine Gln Q Glycine Gly G Histidine His H Isoleucine Ile I Leucine Leu L Lysine Lys K Methionine Met M Phenylalanine Phe F Proline Pro P Serine Ser S Threonine Thr T Tryptophan Trp W Tyrosine Tyr Y Valine Val V

The formation of quaternary structures can serve several roles such as which of the following? I. More stability II. Reduce the amount of DNA needed to encode the protein complex III. Bring catalytic sites close together IV. Induce cooperatiity or allosteric effects

All of the above! The formation of quaternary structures can serve several roles. First, they can be more stable, by further reduceing surface area of protein complex. Second, they can reduce the amount of DNA needed to encode the protein complex. Third, they can bring catalytic sites close together, allowing intermediates from one reaction to be directly shuttled to a second reaction. Lastly, they can induce cooperatiity or allosteric effects. For example, one subunit can undergo conformational or structural changes, which either enhance or reduce the activity of the other subunits.

Amino Acids

Amino Acids

At pH 7, the charge on a glutamic acid molecule is: A. -2 B. -1 C. 0 D. +1

B. -1 Glutamic acid is an acidic amino acid because it has an extra carboxyl group. At neutral pH, both carboxyl groups are deprotonated and thus negatively charged. The amino group is fully protonated (NH3+) at pH7 and has a positve charge. Overall, glutamic acid has a net charge of -1.

The alpha helix is stabilized by intramolecular hydrogen bonds between a carbonyl oxygen atom and an amide hydrogen atom how many residues away? A. 2 B. 4 C. 6 D. 8

B. 4 The alpha helix is stabilized by intramolecular hydrogen bonds between a carbonyl oxygen atom and an amide hydrogen atom 4 residues down the chain.

Which of the following amino acids can form disulfide bridges? A. S B. C C. M D. T

B. C Cysteine has a thiol (-SH) group attached to it and is prone to oxidation. Disulfide bonds form when two cysteine molecules become oxidized to form cystine. Disulfide bonds create loops in the protein chain.

What type of bond is a peptide bond? A. Ionic Bond B. Covalent Bond C. Hydrogen Bond D. None of the above

B. Covalent Bond A peptide bond is an amide type of covalent chemical bond linking two consecutive alpha-amino acids from C1 (carbon number one) of one alpha-amino acid and N2 (nitrogen number two) of another along a peptide or protein chain

Which bond stabilizes the primary structure of a protein? A. Hydrogen Bonds B. Covalent Bonds C. Van Der Waals Forces D. Dipole-dipole Interactions

B. Covalent Bonds The primary structure describes the linear sequence of amino acids stabilized by peptide bonds.

Looking under a microscope, you see that there is a disruption in the pattern of a protein's secondary structure. Which amino acid(s) is/are likely responsible for this pattern of disruption? I. R II. G III. P A. I Only B. II and III Only C. I and III Only D. I, II, and III

B. II and III Only Proline and glycine are likely to cause a disruption in an alpha helix protein structure because proline has an inflexible secondary alpha amino group tied up with its side chain. This inflexible ring ends up adding a kink to the alpha helix. Glycine has a hydrogen atom as its side chain, making it very small and flexible. Remember this: glycine & proline = "alpha helix breakers."

Which of the following is true? Most chiral amino acids used in eukaryotes are: A. D-amino acids with an (S) absolute configuration B. L-amino acids with an (S) absolute configuration C. D-amino acids with an (R) absolute configuration D. L-amino acids with an (R) absolute configuration

B. L-amino acids with an (S) absolute configuration All chiral amino acids used in eukaryotes are L-amino acids, so the amino group is drawn on the left in a Fischer projection. In the Cahn-Ingold-Prelog system, this translates to an (S) absolute configuration for almost all chiral amino acids. The only exception is cysteine, which, while still being an L-amino acid, has an (R) absolute configuration because the -CH2SH group has priority over the -COOH group. *Except for glycine, all amino acids are chiral --- and except for cysteine, all of them have an (S) absolute configuration.

Which amino acid does every protein begin with? A. Arginine B. Methionine C. Proline D. Cysteine

B. Methionine (Met, M) Every protein begins with methionine, the codon for methionine (AUG) is considered the start codon for translation of the mRNA into protein.

Which amino acid will introduce a kink in the peptide chain when found in the middle of an alpha-helix? A. Cysteine B. Proline C. Histidine D. Serine

B. Proline Because of its rigid cyclic structure, proline will introduce a kink in the peptide chain when found in the middle of an alpha-helix. Proline residues are rarely found in alpha-helices, except in helices that cross the cell membrane. Similarly, it is rarely found in the middle of pleated sheets. On the other hand, proline is often found in the turns between the chains of a beta-pleated sheet, and it is often found as the residue at the start of an alpha-helix.

Which level of protein structure are primarily the result of hydrogen bonding between nearby amino acids? A. Primary Structure B. Secondary Structure C. Tertiary Structure D. Quaternary Structure

B. Secondary Structure A proteins secondary structure is the local structure of neighboring amino acids. Secondary structures are primarily the result of hydrogen bonding between nearby amino acids. The two most common secondary structures are α helices and the β pleated sheets, which both result from intramolecular hydrogen bonds.

Which level of protein structure do the α helix and the β pleated sheet represent? A. Primary Structure B. Secondary Structure C. Tertiary Structure D. Quaternary Structure

B. Secondary Structure The two most common secondary structures are α helices and the β pleated sheets, which both result from intramolecular hydrogen bonds.

In a titration curve where would pKa1 be? A. The vertical line between the two sigmoidal (s-shaped) curves. B. The first relatively flat region on the first sigmoidal (s-shaped) curve. C. The second relatively flat region on the first sigmoidal (s-shaped) curve. D. The starting point

B. The first relatively flat region on the first sigmoidal (s-shaped) curve. pKa1 represents when 0.5 equivalents of base have been added to a 1.0 equivalent solution, the concentration of fully protonated and zwitterion is equal, for example of glycine: [+NH3CH2COOH] = [+NH3CH2COO-] and the pH = pKa1. The carboxyl group will deprotonate first because it is more acidic than the amino group.

Which of the following is not a polar amino acid? A. Ser B. Tyr C. Asn D. Cys

B. Tyr Tyrosine is an amino acid with an aromatic side chain

A peptide bond formation is what type of reaction? A. Reaction Formation B. Combustion C. Dehydration/Condensation D. Oxidation/Reduction

C. Dehydration/Condensation A peptide bond formation is a condensation or dehydration reaction because it results in the removal of a water molecule. It can also be viewed as an acyl substitution reaction, which can occur with all carboxylic acid derivatives.

Which of the following amino acids are not optically active? A. Alanine B. Phenylalanine C. Glycine D. Arginine

C. Glycine Glycine is not optically active because it is achiral. All the other amino acids contain a chiral carbon making them optically active. Glycine is the smallest amino acid.

What type of reaction does Strecker synthesis use to create amino acids? I. Condensation II. Nucleophilic Addition III. SN2 Reaction IV. Hydrolysis V. Decarboxylation A. I only B. I and II C. I, II, and IV D. I, II, III, IV, and V

C. I, II, IV Strecker synthesis is a condensation reaction (formation of an imine from carbonyl-containing compound and ammonia, with loss of water), followed by a nucleophilic addition (addition of nitrile group, followed by hydrolysis.

What type of reaction does Gabriel synthesis use to create amino acids? I. Condensation II. Nucleophilic Addition III. SN2 Reaction IV. Hydrolysis V. Decarboxylation A. I only B. I and II C. III, IV, and V D. I, II, III, IV, and V

C. III, IV, and V Gabriel synthesis proceeds through two SN2 reactions, hydrolysis, and decarboxylation.

The presence of disulfide bonds are an important component of which protein structure level? A. Primary Structure B. Secondary Structure C. Tertiary Structure D. Quaternary Structure

C. Tertiary Structure A particularly important component of tertiary structure is the presence of disulfide bonds, the bonds that form when two cysteine molecules become oxidized to form cystine.

At which level of protein structure is its three-dimensional shape? A. Primary Structure B. Secondary Structure C. Tertiary Structure D. Quaternary Structure

C. Tertiary Structure A protein's tertiary structure is its three-dimensional shape

The loss of which protein structure level is known as denaturation? A. Primary Structure B. Secondary Structure C. Tertiary Structure D. Quaternary Structure

C. Tertiary Structure If a protein loses its tertiary structure (three-dimensional structure), a process called denaturation, it loses its function. The two main causes of denaturation are heat and solutes. When the temperature of a protein increases, its average kinetic energy increases. When it gets high enough the extra energy can overcome the hydrophobic interactions that hold a protein together, causing the protein to unfold. Solutes such as urea denature proteins by directly interfering with the forces that hold the protein together. They can disrupt tertiary and quaternary structures by breaking disulfide bridges, reducing cystine back to two cysteine residues. They can even overcome hydrogen bonds that hold alpha-helices and beta-pleated sheets intact.

At which level of protein structure can hydrophilic residues be found on the surface of proteins and hydrophobic residues in the interior of proteins? A. Primary Structure B. Secondary Structure C. Tertiary Structure D. Quaternary Structure

C. Tertiary Structure Putting hydrophilc residues on the exterior of the protein allows nearby water molecules more latitude in their positioning, thus increasing their entropy (delta S > 0 ---> increasing disorder), and making the overall solvation process spontaneous. Thus, by moving hydrophobic residues away from water molecules and hydrophilic residues toward water molecules, a protein achieves maximum stability.

At which level of protein structure are interactions between the side chains (R groups) most important? A. Primary Structure B. Secondary Structure C. Tertiary Structure D. Quaternary Structure

C. Tertiary Structure Tertiary Structures are mostly determined by hydrophilic and hydrophobic interactions between R groups of amino acids.

In a titration curve where would pKa2 be? A. The vertical line between the two sigmoidal (s-shaped) curves. B. The first relatively flat region on the first sigmoidal (s-shaped) curve. C. The second relatively flat region on the first sigmoidal (s-shaped) curve. D. The starting point

C. The second relatively flat region on the first sigmoidal (s-shaped) curve. pKa2 represents when 1.5 equivalents of base have been added to a 1.0 equivalent solution, the concentration of the zwitterion form equals the concentration of fully deprotonated form, for example of glycine: [+NH3CH2COO-] = [NH2CH2COO-] and the pH = pKa2 When we've added 2.0 equivalents of base, the amino acid becomes fully deprotonated, and all that remains is NH2CH2COO- (of our glycine example). Additional base will only increase the pH further.

What happens to the structure of cysteine when it goes from the intracellular to the extracellular space?

Cysteine changes from its reduced form (-SH) in the intracellular environment to its oxidized form (disulfide bond S-S) in the extracellular space.

What is the difference between Cysteine and Cystine?

Cysteine refers to the reduced form. Cystine refers to the oxidized form. Think about the e being electrons, which are found in the reduced form (OIL RIG). Oxidation is loss of electrons, thus loss of e.

What are molecules that have both a positive and negative charge called? A. Polar ions B. Dipolar ions C. Zwitterions D. B and C

D. Dipolar ions or zwitterions. *Zwitterions exist in water as internal salts. For example: At physiological pH (7.4), you will not find amino acids with the carboxylate group protonated (-COOH) and the amino group unprotonated (-NH2). Instead, the carboxyl group will be in its conjugate base form and be deportonated, becoming -COO^-. Conversely, we're still below the pKa of the basic amino group, so it will remain fully protonated and in its conjugate acid form (-NH3+). Therefore, we have a positively and negatively charged molecule, but overall the molecule is electrically neutral.

The resonance structure of the peptide bond has a double bond character. Which of the following correctly describe the peptide bond? I. Rigid II. Planar III. Does not rotate A. I Only B. I and II Only C. II and III Only D. I, II, and III

D. I, II and III Only Since there is double bond character in a peptide bond, the peptide bond is very rigid, planar, and does not rotate.

Which of the following is considered a protein? I. Enzymes II. Hormones III. Membrane pores and receptors IV. Elements of cell structure A. I only B. I and II C. I, III, and IV D. I, II, III, and IV

D. I, II, III, and IV Proteins serve many functions in biological systems, such as enzymes, hormones, membrane pores and receptors, and elements of cell structure.

Hemoglobin and Immunoglobulin are classic examplies of which protien structure? A. Primary Structure B. Secondary Structure C. Tertiary Structure D. Quaternary Structure

D. Quaternary Structure The quaternary structure is an aggregate of smaller globular peptides, or subunits, and represents the functional form of the protein. Classic examples of quaternary structure are hemoglobin and immunoglobulin. Hemoglobin consists of four distinct subunits, each of which can bind one molecule of oxygen. Similarly, immunoglobulin G (IgG) antibodies also contain a total of four subunits each.

True or False: A single amino acid on its own can be considered an oligopeptide.

False: A single amino acid on its own is not considered an oligopeptide.

True or False: Amino acids have both a basic carboxylic acid group and an acidic amino group.

False: Amino acids have both an acidic carboxylic acid group and a basic amino group.

True or False: Amino acids with acidic side chains have isoelectric points (pI value) well above 6.

False: Amino acids with acidic side chains have isoelectric points (pI value) well below 6. Because all amino acids have at least two groups that can be deprotonated, they all have at least two pKa values. The first pKa (pKa1) is for the carboxyl group and is usually around 2. The second pKa (pKa2) is for the amino group, which is usually between 9 and 10. For amino acids with acidic side chains (negatively charged) there are two carboxyl groups and one amino group. The first deprotonation occurs like normal from the main carboxyl like it would with a neutral a.a. At this point, it is electrically neutral. As more base is added and a second proton is lost its overall charge will be -1 like a neutral a.a.. However, the second proton removed in this case comes from the side chain carboxyl group, NOT the amino group! This is a relatively acidic group with a pKa of around 4.2. The result is a lower pI around 3.2. When calculating pI values for acidic side chained a.a. average the pKa values for the main carboxyl group (pKa1) and the side carboxyl group (pKaR). Disregard the amino pKa (pKa2). pI acidic a.a. = (pKa of R group + pKa of COOH group) / 2

True or False: Fibroin, the primary protein component of silk fibers, is composed of alpha-helices.

False: Fibroin, the primary protein component of silk fibers, is composed of beta-pleated sheets.

True or False: All amino acids contain an alpha chiral carbon.

False: For most amino acids, the alpha carbon is a chiral (or stereogenic) center, as it has four different groups attached to it. The one exception is glycine, which has a hydrogen atom as its R group, making it achiral. The alpha-carbon is the carbon that the amino group and the carboxylic acid group are bonded to. NH2-C-COOH In addition to the amino and carboxyl group the alpha-carbon has a hydrogen atom and a side chain (also called an R group) attached to it.

True or False: Peptides are drawn with the C-terminus on the left and the N-terminus on the right; similarlirly, they are read from C-terminus to N-terminus.

False: Peptides are drawn with the N-terminus on the left and the C-terminus on the right; similarlirly, they are read from N-terminus to C-terminus. * The peptide is drawn in the same order that it is synthesized by ribosomes: from the N-terminus to the C-terminus.

True or False: Protein folding is a slow process.

False: Protein folding is an extremely rapid process, it typically takes seconds.

True or False: The beta-pleated sheet is an important component in the structure of keratin.

False: The alpha-helix is an important component in the structure of keratin, a fibrous structural protein found in human skin, hair, and fingernails.

True or False: There are only two amino acids that contain a sulfur atom in its side chain and both are polar.

False: There are only two amino acids that contain a sulfur atom in its side chain and one is polar while the other is nonpolar. Cystein has a thiol (-SH) group attached to it and it is a polar amino acid. Methionine has a sulfur atom in its side chain which is attached to a methyl group, so it is considered nonpolar.

True or False: There is only one way of synthesizing amino acids, called the Strecker Synthesis.

False: There are two ways of synthesizing amino acids:Strecker Synthesis and Gabriel Synthesis (malonic-ester). Strecker Synthesis Step 1: -Start with aldehyde, ammonium chloride (NH4Cl), and potassium cyanide (KCN). -Formation of imine occurs when ammonia (NH3+) attacks carbonyl carbon -Formation of nitrile (C triple bonded to N) occurs when CN- attacks - Final molecule at the end of step 1 is an aminonitrile - a compound containing an amino group (-NH2) and a nitrile bonded to one carbon Step 2: -Nitrile nitrogen is protonated -Water molecule attacks, leading to formation of a molecule with both imine and hydroxyl moieties on the same carbon -Imine is attacked by another water molecule forming a carbonyl carbon, kicking off ammonia and creating the carobxylic acid functionality. Gabriel (malonic-ester) Synthesis -Potassium phthalimide and diethyl bromomalonate react via SN2 reaction forming a phthalimidomalonic ester -Base is added which causes deprotonation. Then a SN2 reaction occurs with bromoalkane. -The molecule is hydrolyzed with a strong base and heat. The phthalimide moiety is removed as phthalic acid (with two carboxylic acids). The malonic ester is hydrolyzed to dicarboxylic acid with an amine on the alpha carbon. -Lastly, acid and heat is added which causes decarboxylation of the dicarboxylic acid. The loss in the formation of carbon dioxide results in the formation of the complete amino acid.

True or False: Under highly basic (alkaline) conditions most amino acids are positively charged.

False: Under highly basic (alkaline) conditions most amino acids are negatively charged. For example, at pH 10.5 the carboxylate group is already deprotonated and the amino group is also deprotonated because we are above both pKa values (2 and 9-10 respectively). This yields -COO^- and -NH2 -- a molecule with a net negative charge.

Which amino acids are hydrophilic (water loving)?

Hydrophilic Amino Acids: - All the polar amino acids cysteine, serine, threonine, asparagine, glutamine, tyrosine - All the charged amino acids (both negatively and positively charged) aspartate (aspartic acid), glutamate (glutamic acid), arginine, lysine, and histidine These amino acids are more likely to be found on the exterior surface of proteins, in contact with water.

Which amino acids are hydrophobic (water hating)?

Hydrophobic Amino Acids: -All the non-polar amino acids: glycine, alanine, valine, leucine, isoleucine, methionine, proline, phenylalanine, tryptophan These amino acids are more likely to be found in the interior of proteins, away from water on the surface of the protein.

Which amino acids are ketogenic?

Lysine (Lys, K) and Leucine (Leu, L) are the only two amino acids that are solely ketogenic. Ketogenic amino acids are unable to be converted to glucose as both carbon atoms in the ketone body are ultimately degraded to carbon dioxide in the citric acid cycle The rest of the amino acids are either glucogenic or both glucogenic and ketogenic. Both glucogenic and ketogenic amino acids include: - The aromatic amino acids: Tryptophan (Trp, W), Phenylalanine (Phe, F), and Tyrosine (Tyr, Y) - Threonine (Thr, T) - Isoleucine (Ile, I)

Which of the following amino acids are Negatively Charged (Acidic)? - Arginine - Aspartate - Asparagine - Histidine - Lysine - Glutamate - Glutamine

Only two of the 20 amino acids have negative charges on their side chains at physiological pH (7.4): - Aspartic Acid (Aspartate) (Asp, D) - Glutamic Acid (Glutamate) (Glu, E) - These two amino acids are related to asparagine and glutamine respectively but have terminal carboxylate (-COO^-) anion groups in their side chains rather than amides. - Aspartate and Glutamate are simply the deprotonated form of aspartic acid and glutamic acid. * Think Delaware --->DE

Peptides

Peptides

Organize the five polar amino acids based on their side chains: Side chains: A. -OH groups B. Amide groups (nitrogen atom bonded to one side of a carbonyl group) C. Thiol groups (-SH) Amino Acids: Cycteine (Cys, C) Asparagine (Asn, N) Serine (Ser, S) Glutamine (Gln, Q) Threonine (Thr, T)

Polar amino acids tend to have terminal groups containing oxygen, nitrogen, and sulfur. The 5 Polar Amino Acids based on side chains: A. -OH groups -Serine (Ser, S) -Threonine (Thr, T) The -OH group makes these amino acids highly polar and able to participate in hydrogen bonding. -Think ShoT B. Amide groups (nitrogen atom bonded to one side of a carbonyl group) -Asparagine (Asn, N) -Glutamine (Gln, Q) The amide nitrogens do NOT gain or lose protons with changes in pH; they do not become charged. C. Thiol groups (-SH) -Cycteine (Cys, C) Because sulfur is larger and less electronegative than oxygen, the S-H bond is weaker than the O-H bond. This leaves the thiol group in cysteine prone to oxidation. *Think Polar Brain ---> CNS QTY *Y is for Tyrosine (Tyr, Y) which has an -OH group making it relatively polar

Protein and Protein Structure

Protein and Protein Structure

How do you calculate the isoelectric point of an amino acid?

The pI for a simple compound can be calculated by averaging the 2 pKa's that are relevant to the concentration of the molecule in its neutral charge state. Neutral R group: the pI is the average of the carboxylic acid group and amino group pKa values. pI(neutral a.a) = (pKa of NH+ group + pKa of COOH group) / 2 Acidic R group: the pI is the average of the carboxylic acid group and side chain pKa values. pI acidic a.a. = (pKa of R group + pKa of COOH group) / 2 Basic R group: the pI is the average of the amino group and side chain pKa values. pI basic a.a. = (pKa of NH2 group + pKa of R group) / 2

What are the seven amino acids with nonpolar, nonaromatic side chains?

The seven amino acids with nonpolar, nonaromatic side chains: Glycine (Gly, G) Alanine (Ala, A) Valine (Val, V) Leucine (Leu, L) Isoleucine (Ile, I) Methionine (Met, M) Proline (Pro, P) Nonpolar nonaromatic amino acids tend to have side chains that are saturated hydrocarbons. These amino acids are hydrophobic and tend to be sequestered in the interior of proteins. Isoleucine has a second chiral carbon in addition to the alpha carbon (its the carbon attached to the alpha carbon). Methionine contains a sulfur atom. *Think VAG LIMP FW - F is for phenylalanine which has a benzyl side chain (a benzene ring plus a -CH2 group) making it relatively nonpolar. -W is for Tryptophan which is also a nonpolar aromatic amino acid in addition to phenylalanine.

True or False: When the pH is close to the pKa value of a solute, a solution is acting as a buffer.

True: When the pH is close to the pKa value of a solute, a solution is acting as a buffer. Also, at this point the titration curve is relatively flat.

Which of the following amino acids are Positively Charged (Basic)? - Arginine - Aspartate - Asparagine - Histidine - Lysine - Glutamate - Glutamine

Three of the 20 amino acids are positively charged (Basic): Lysine, Arginine, and Histidine. They all have a protonated amino group (NH3+) in their R group/side chain. - Lysine (Lys, K) Lysine has a terminal primary amino group. - Arginine (Arg, R) Arginine has three nitrogen atoms in its side chain. The positive charge is delocalized over all three nitrogen atoms. - Histidine (His, H) Histidine has an aromatic (5-membered ring) with two nitrogen atoms. This ring is called an imidazole. Chymotrypsin makes use of the histidine side chains ability to gain a proton. The histidine residue in its active site removes a proton from the -COOH group in an aspartic acid residue, which can then deprotonate a serine residue. *Think Kay RH Positive ---> KRH

True or False: Amino acids are molecules that contain two functional groups: an amino group (-NH2) and a carboxyl group (-COOH).

True. Amino acids are molecules that contain two functional groups: an amino group (-NH2) and a carboxyl group (-COOH).

True or False: Another term for the alpha amino acids encoded by the human genetic code is proteinogenic amino acids.

True. Another term for the alpha amino acids encoded by the human genetic code is proteinogenic amino acids.

True or False: All proteins have elements of primary, secondary, and tertiary structure; not all protiens have quaternary structure.

True: All proteins have elements of primary, secondary, and tertiary structure; not all protiens have quaternary structure. Quaternary structures only exist for proteins that contain more than one polypeptide chain. The quaternary structure is an aggregate of smaller globular peptides, or subunits, and represents the functional form of the protein. Classic examples of quaternary structure are hemoglobin and immunoglobulin.

True or False: Amino acids are amphoteric species, as they can either accept a proton or donate a proton; how they react depends on the pH of their environment.

True: Amino acids are amphoteric species, as they can either accept a proton or donate a proton; how they react depends on the pH of their environment. Amphoteric - able to react both as a base and as an acid

True or False: Amino acids don't need to have both the amino and carboxyl groups bonded to the same carbon.

True: Amino acids don't need to have both the amino and carboxyl groups bonded to the same carbon. For example, the neurotransmitter GABA (gamma-aminobutyric acid) has the amino group on the gamma (Y) carbon.

True or False: Amino acids with basic side chains have isoelectric points (pI value) well above 6.

True: Amino acids with basic side chains have isoelectric points (pI value) well above 6. Because all amino acids have at least two groups that can be deprotonated, they all have at least two pKa values. The first pKa (pKa1) is for the carboxyl group and is usually around 2. The second pKa (pKa2) is for the amino group, which is usually between 9 and 10. For amino acids with basic side chains (positvely charged) there are two amino groups and one carboxyl group. Thus the charge in its fully protonated state is +2 not +1 (there are two NH3+ groups). The first deprotonation occurs like normal from the main carboxyl like it would with a neutral a.a. and it brings the charge down to +1. The a.a. does not become electrically neutral until it loses a proton from its main amino group at around pH 9. As more base is added a second proton is lost from the amino side chain at around pH 10.5 and its overall charge will be -1 like a neutral a.a.. Thus, the pI of basic side chains is the average of the pKa values for the amino group and side chain. The result is a higher pI around 9.75. When calculating pI values for basic side chained a.a. average the pKa values for the main amino side chain (pKa2) and the side amino group. Disregard the carboxyl pKa (pKa1). pI basic a.a. = (pKa of NH2 group + pKa of R group) / 2

True or False: Amino acids with neutral chains have isoelectric points (pI value) around 6.

True: Amino acids with neutral chains have isoelectric points (pI value) around 6. Because all amino acids have at least two groups that can be deprotonated, they all have at least two pKa values. The first pKa (pKa1) is for the carboxyl group and is usually around 2. The second pKa (pKa2) is for the amino group, which is usually between 9 and 10. Negatively and Positively charged amino acids are slightly different. For neutral amino acids, the pI can be calculated by averaging the two pKa values for the amino and carboxyl groups: pI(neutral a.a) = (pKa of NH+ group + pKa of COOH group) / 2 *For amino acids with non-ionizable (neutral, no charge) side chains, the pI is usually around 6.

True or False: Conjugated (complex) proteins derive part of their function from covalently attached molecules called prosthetic groups.

True: Conjugated (complex) proteins derive part of their function from covalently attached molecules called prosthetic groups. These prosthetic groups can be organic molecules, such as vitamins, or even metal ions, such as iron. Proteins with lipid, cabohydrate, and nucleic acid prosthetic groups are referred to as lipoproteins, glycoproteins, and nucleoproteins, respectively. These prosthetic groups have major roles in determining the function of their respective protein. For example, each of hemoglobin's subunits (as well as myoglobin) contains a prosthetic group called heme, which contains an iron atom in its core, binds to and carries oxygen; such as hemoglobin is inactive without the heme group. These groups can also direct a protein to be delivered to a certain location (such as cell membrane, nucleus, lysosome, or endoplasmic reticulum).

True or False: In beta-pleated sheets, which can be parallel or antiparallel, the peptide chains lie along side one another, forming rows or strands held together by intramolecular hydrogen bonds between carbonyl oxygen atoms on one chain and amide hydrogen atoms in an adjacent chain.

True: In beta-pleated sheets, which can be parallel or antiparallel, the peptide chains lie along side one another, forming rows or strands held together by intramolecular hydrogen bonds between carbonyl oxygen atoms on one chain and amide hydrogen atoms in an adjacent chain.

True or False: It is true for all amino acids that the isoelectric point (pI) is the pH at which the molecule is electrically neutral, i.e. the zwitterion form is dominant.

True: It is true for all amino acids that the isoelectric point (pI) is the pH at which the molecule is electrically neutral, i.e. the zwitterion form is dominant. For neutral amino acids, it can be calculated by averaging the two pKa values for the amino and carboxyl groups: pI(neutral a.a) = (pKa of NH+ group + pKa of COOH group) / 2 *For amino acids with non-ionizable (neutral, no charge) side chains, the pI is usually around 6.

True or False: Proteins are polypeptides.

True: Proteins are polypeptides that range from just a few amino acids in length up to thousands.

True or False: Proteins can be divided into fibrous proteins and globular proteins which are caused by tertiary and quaternary protein structures, both of which are the result of protein folding.

True: Proteins can be divided into fibrous proteins and globular proteins which are caused by tertiary and quaternary protein structures, both of which are the result of protein folding. Fibrous proteins, such as collagen, have structures that resemble sheets or long strands. Globular proteins, such as myoglobin, tend to be spherical (like a globe).

True or False: Rotation of the protein backbone around the C-N peptide bonds is restricted due to resonance, which makes the protein more rigid.

True: Rotation of the protein backbone around the C-N peptide bonds is restricted due to resonance, which makes the protein more rigid. Rotation around the remaining backbone is not restricted because those remain as single sigma bonds.

True or False: The alpha-helix can be described as a rodlike structure in which the peptide chain coils clockwise around the central axis.

True: The alpha-helix can be described as a rodlike structure in which the peptide chain coils clockwise around the central axis. The side chains of the amino acids in the alpha-helical conformation point away from the helix core.

True or False: The term oligopeptide is used for relatively small peptides; while longer chains are called polypeptides.

True: The term oligopeptide is used for relatively small peptides (up to 20); while longer chains are called polypeptides. Peptides are composed of amino acid subunits sometimes called residues. The residues in peptides are joined together through peptide bonds.

True or False: Under highly acidic conditions most amino acids are positively charged.

True: Under highly acidic conditions most amino acids are positively charged. For example, at pH 1 there are plenty of protons in solution and we are far below the pKa of the amino group and also below the pKa of the carboxyl group, therefore both groups will be fully protonated, yeilding -NH3+ and COOH -- a molecule with a net positive charge.

True or False: When a peptide bond forms the free amino end is know as the amino terminus or N-terminus, while the free carboxyl end is the carboxy terminus or C-terminus.

True: When a peptide bond forms the free amino end is know as the amino terminus or N-terminus, while the free carboxyl end is the carboxy terminus or C-terminus.