1 Amino acids, peptides, and proteins

Question 1

List the four groups found on an amino acid. Which carbon of the amino acid links these all together?

Answer 1

• NH₂ (amino group)
• COOH (Carboxyl group)
• R side chain
• Hydrogen atom

All four of these groups are on the alpha carbon, which can be thought of as the central carbon. This is only slightly not the case with proline (P), where the alpha carbon is a direct substituent of the cyclical side chain (R).

Because there are four different groups on the alpha carbon, the alpha carbon is a stereogenic centre. The one exception is glycine because it’s side chain (R) is just a hydrogen atom, making it achiral.

Question 2

All chiral amino acids used in eukaryotes are ____ amino acids (chirality)

Answer 2

All chiral amino acids used in eukaryotes are L-amino acids

The amino group is drawn on the left in a Fischer projection (absolute S configuration).

The ONE exception to this among the 20 proteinogenic amino acids is L-cysteine, where the Ch2SH group has priority over the COOH group and is in a absolute R configuration.

Question 3

Except for ____, all amino acids are chiral - and except for _____ all of them have an (S) absolute configuration

Answer 3

Except for glycine, all amino acids are chiral - and except for cysteine all of them have an (S) absolute configuration

Question 4

There are four amino acids with only alkyl chains as their side group. List them with their respective alkyl side chain

Answer 4

• Alanine (1 carbon methyl alkyl group)
• Valine (3 carbon isopropyl alkyl group)
• Leucine (4 carbon isobutyl group)
• Isoleucine (4 carbon sec-butyl group)

Question 5

Give the four different prefixes for denoting atom arrangements within a group.

Answer 5

• N refers to “normal” and is an unbranched chain, —in this case 4 carbons long.
• Tert-butyl is a shortening of tertiary, and indicates that the carbon to which the rest of the molecule attaches is a tertiary carbon (it has three other carbons attached to it before being attached to the parent molecule).
• Following this same logic, sec-butyl groups contain a secondary carbon, and are attached to the rest of the molecule by that specific carbon atom.
• The same naming convention (primary, secondary, tertiary) is used for carbocations, so it should be second nature to recognize these arrangements before long.

Question 6

Why does proline have such a profound effect on the secondary structure of proteins?

Answer 6

Because it is clyclical and the amino nitrogen becomes a part of the side chain, forming a five-membered ring. That ring places notable constraints on the flexibility of proline, which limits where it can appear in a protein.

Question 7

List the amino acids with aromatic side chains from largest to smallest

Answer 7

• Tryptophan (double ring system with a nitrogen atom (indole group) on the beta carbon)
• Tyrosine (phenylalanine with an OH group on the benzyl side chain)
• Phenylalanine (benzyl side chain AKA benzene ring attached to beta carbon )

Phenylalanine is non-polar, but the extra OH on tyrosine makes it polar. Tryptophan is slightly polar due to the ability of the nitrogen in the indole to make hydrogen bonds. Reminder: polar amino acids are more likely to be on the outside of proteins where they can make hydrogen bonds with the solvent.

Question 8

Not including the aromatic side chain proteinogenic amino acids, which amino acids have polar side chains? (5)

Answer 8

• Serine (OH group makes highly polar and able to hydrogen bond)
• Threonine (OH group makes highly polar and able to hydrogen bond)
• Asparagine (amide side chain)
• Glutamine (amide side chain)
• Cysteine (thiol side chain)how m

Including the aromatic polar amino acids (tryptophan and tyrosine) and histidine, there are eight polar proteinogenic amino acids.

Question 9

What are the two negatively charged (acidic) proteinogenic amino acids and what are their anions (deprotonated forms) called?

Answer 9

• Aspartic acid (carboxylic group on beta carbon)
• glutamic acid (carboxylic group on gamma carbon)
• The anion of aspartic acid is aspartate
• The anion of glutamic acid is glutamate

Question 10

What are three positively charged (basic) proteinogenic amino acids?

Answer 10

• Arginine (three nitrogen atoms in side chain with positive charge distributed among each)
• Lysine (has a terminal primary amino group - aminobutane - as side chain)
• Histidine (aromatic ring with two nitrogen atoms - imidazole)

At physiological conditions (pH ~7.4), one nitrogen in the histidine aromatic ring is protonated and the other isn’t. Under more acidic conditions both are protonated (givine the side chain a more positive/basic charge).

Question 11

How can you determine if an amino acid is hydrophillic or hydrophobic?

Answer 11

Sometimes you just have to memorize, but ten of them are easily distinguishable.

• Hydrophillic: charged, reactive, polar
  
  • Histidine, arginine, lysine, glutamic acid, aspartic acid, asparagine, glutamine
  • Note: the reactivity of the two nitrogens in histidine make up for the aromatic ring and the amino acid is net hydrophillic due to it’s positive charge (though it becomes hydrophobic under basic conditions where the nitrogens would be deprotonated and therefore charge-neutral)
• Hydrophobic: long alkyl side chains, non-polar
  
  • Alanine, isoleucine, leucine, valine, phenylalanine
  • Even though tryptophan and tyrosine are polar, their aromatic rings make them hydrophobic like phenylalaine

Question 12

What is the pK_a of a group and what does this mean for amino acids?

Answer 12

The pH at which, on average, half of the molecules of that species are deprotonated; that is,

[HA] = [A-]

If the pH is less than the pK_a, a majority of the species will be protonated. If the pH is higher than the pK_a, a majority of the species will be deprotonated.

Amino acids are amphoteric species, meaning they can accept a protoon or donate a proton, and how they react depends on the pH of their environment.

Question 13

What are the two pK_a values of amino acids that are almost always constant?

Answer 13

The pK_a of the carboxyl group is around 2 and the pK_a of the amino group is between 9 and 10.

For amino acids with an ionizable side chain, there will be three pK_a values (including the carboxyl and amino group pK_a values)

Question 14

When is glycine a zwitterion?

Answer 14

At physiological pH or any pH above 2 (meaning the carboxyl will be deprotonated) and below 9-10 (meaning the amino group will be protonated).

• The carboxyl will have a negative charge
• The amino group will have a positive charge
• The side chain is not ionizable
• The net charge of glycine at physiological pH will be neutral despite the molecule having both a positive and negative charge (zwitterion)

Question 15

Recall what the titration curve for glycine looks like. How does this differ from other amino acids with charged side chains?

Answer 15

Other amino acids with a charged, ionizable side chain will have three curves. Glycine only has two, one for the amino group and one for the carboxyl group.

Question 16

what is the isoelectric point of amino acid/base titration and how do you calculate it?

What are the two exceptions to this calculation?

Answer 16

When the pH of an amino acid solution equals the isoelectric point (pl) of the amino acid, it exists as electrically neutral molecules (exclusively zwitterions). The pl is calculated as the average of the two nearest pK_a values. For amino acids with non-ionizable side chains, the pl is usually around 6.

This is different for acidic (aspartic acid, glutamic acid) and basic amino acids (arginine, histidine, lysine).

Acidic AA pI: (The pKa of the R group + pKa of carboxyl group)/2

Basic AA pI: (The pKa of the R group + pKa of amino group)/2

Question 17

When is the titration curve of an amino acid nearly flat and when is it nearly vertical. What are the real world consequences of this?

Answer 17

The titration curve for an amino acid is nearly flat (horizontal) when the pH is at one of the pK_as for the molecule. It is vertical at the isoelectric point.

This means that amino acids are very sensitive to the change in pH at the isoelectric point, but the amino acid solution acts as a buffer when the pH is approximately equal to the pK_a

Question 18

What is the functional group of a peptide bond?

Answer 18

-C(O)NH-

It is an amide bond between the carboxyl and amino group of two amino acids

Peptide bond formation is an example of a condensation or dehydration reaction because it results in the removal of a water molecule. It is also an example of a acyl substitution reaction, which can occur with all carboxylic acid derivatives.

Question 19

Draw/recount a peptide bond formation and cleavage

Answer 19

Bond formation (condensation/dehydration)

1. The electrophilic carbonyl carbon on the first amino acid is attacked by the nucleophilic carbonyl carbon on the second amino acid
2. The hydroxyl group of the carboxylic acid is kicked off

Bond cleavage (hydrolysis - physiologically assisted by enzymes)

1. Hydrogen atom is added to amide nitrogen and hydroxide group added to carbonyl carbon

Question 20

Describe resonance in the peptide bond

What is the consequence of this in terms of protein structure?

Answer 20

Because amide groups have delocalized pi electrons in the carbonyl and in the lone pair on the amino nitrogen, they can exhibit resonance.

Thus, the C-N bond in the amide has partial double bond character.

As a result, rotation of the protein backbone around its C-N amide bond is restricted, which makes the protein more rigid. Rotation around the remaining bonds in the backbone, however, is not restricted, as those remain single sigma (σ) bonds.

Question 21

How do sigma and pi bonds effect proteins?

Answer 21

Sigma bonds are the FIRST bonds to be made between two atoms. They are made from hybridized orbitals. Pi bonds are the SECOND and THIRD bonds to be made. They are made from leftover “p” orbitals

There are pi electrons in the carbonyl and in the lone pair on the amino nitrogen of amino acids in peptide bonds. The consequence of this is resonance in the peptide bond, which limits rotation.

Question 22

What are the four levels of structure in proteins?

Answer 22

1. Primary
   
   1. linear arrangement of amino acids listed from N terminus to C terminus (left to right) with covalent peptide bonds between adjacent amino acids.
2. Secondary
   
   1. Hydrogen bonding between nearby amino acids
      
      1. alpha-helices: clockwise chain around a central axis. Side chains point away from helix core
      2. beta-pleated sheets: paralell or antiparallel. Peptide chains lie alongside 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.
3. Tertiary
   
   1. Influenced by hydrophilic/hydrophobic residues and hydrogen bonds
   2. Oxidation of cysteine to form cystine disulfide bonds
4. Quaternary
   
   1. Only exist for ptoeins that contain more than one polypeptide chain.
   2. Aggregate of smaller globular proteins (subunits)

Question 23

What must be remembered about proline and protein secondary structure?

Answer 23

Due to its cyclic structure proline will introduce a kink in the peptide chain when it is found in alpha helices and middle of beta pleated sheets. For this reason it is rarely found in the middle of alpha helices and the middle of pleated sheets but is often found at the turn between the chains of a beta pleated sheet and often found as the residue at the start of an alpha helix.

Question 24

What are the main influences of tertiary structure in a protein?

Answer 24

Fibrous/globular tertiary structure influenced by: ​

• Hydrophobic/hydrophillic interactions between R groups
  
  • Hydrophillic usually on outside of protein
  • Hydrophobic usually on inside
• hydrogen bonding
• acid-base interactions
• disulfide bonds (cysteine oxidized to form cystine), which create loops in a protein chain

Losing tertiary structure is denaturing.

Question 25

Why do hydrophobic residues tend to ocupy the interior of a protein, while hydrophilic residues tend to accumulate on the exterior portions?

Answer 25

Entropy

• Negative changes in entropy represent increasing order (decreasing disorder), and thus are unfavourable.
  
  • Water must rearrange itself in a specific way to accomodate hydrophobic residues that cannot hydrogen bond. This is unfavourable.
  • Water molecules have more latitude in their positioning with hydrophilic residues, and therefore entropy is higher (ΔS > 0 and ΔG > 0), making the solvation process and subsequent protein folding spontaneous.
• By moving hydrophobic residues away from water molecules and hydrophilic residues twoard water molecules, a protein achieves maximum stability.

Question 26

What are the four major functions of quaternary structures? Which is the most important?

Answer 26

1. Reduce amount of DNA needed for protein complex (in the case of repeating subunits). Especially in the cases of organisms like viruses with extremely minimal amounts of genetic material.
2. Reducing the surface area of the protein complex
3. Bringing catalytic sites close together allowing intermediates from one reaction to be directly shuttled to a second
4. Inducing cooperativity or allosteric effects, where subunits can undergo a conformational or structural change to enhance or reduce the activity of the other subunits.

Allosteric effects are most important function of quaternary structures.

Question 27

What are conjugated proteins?

Answer 27

Proteins that derive part of their function from covalently attached molecules called prosthetic groups (e.g. vitamins, metal ions, lipids/lipoproteins, carbs/glycoproteins, and nucleic acids/nucleoproteins).

Prosthetic groups have major roles in determining the function of proteins (e.g. the heme group, which contains an iron atom in its core)

Question 28

Why are proteins denatured by heat and solutes?

Answer 28

Heat: raising kinetic energy increases movement and the extra energy can be enough to overcome hydrophobic interactions that hold a protein together, causing it to unfold.

Solutes: Interfering with forces that hold the protein together (e.g. breaking hydrogen bonds, breaking disulfide bonds etc. etc. ).