chapter 2

Question 1

how are amino acids linked together?

Answer 1

• peptide bonds (formation of an amide via the condensation of the -COOH group of one amino acid with the -NH₂ group of another)

Question 2

the average size of proteins in human cells has been estimated to be?

Answer 2

50 kDa

Question 3

what is the primary structure of a protein?

Answer 3

• the linear chain of amino acid residues that make up a protein
  
  • corresponds to what tRNA translates from a given strand of mRNA
  • held together by covalent bonds

Question 4

what is the secondary structure of the protein?

Answer 4

• refers to local structures formed by the patterns of hydrogen bonding between the amino and carboxylic acid gorups of the amino acid residues
  
  • common motifs include alpha-helices and beta-pleated sheets
  • proline can introduce kinks

Question 5

what is the tertiary structure of a protein?

Answer 5

• the 3D structures that result from interactions among the side chains of the amio acid residues of a protein
• many of these interactions are non-covalent charge-driven interactions
• charged residues interact with each other to form salt bridges
• they also have covalent bonding in disulfide bonds that form between cysteine residues

Question 6

what are the details about disulfide bonds?

Answer 6

• the formation of a disulfide bond is an oxidation reaction, because the net reaction involves the loss of 2 protons and 2 electrons
  
  • breaking up a disulfide bond is a reduction reaction “reducing environment”
    
    • one common reagent is 2-mercaptoethanol
  • relatively quite strong because they’re covalent so they play a disproportionate role in contributing to the tertiary structure

Question 7

what is the quarternary structure of a protein?

Answer 7

• larger structures generated by the assembly of protein subunits via non-covalent interactions and disulfide bonds
  
  • 2 units = dimer, 3 = trimer, 4 = tetramer

Question 8

what does protein folding refer to?

Answer 8

• how the secondary structure and tertiary structure of a protein generate a 3D structure

Question 9

breaking up the non-primary structure of a protein is known as?

Answer 9

• denaturation
  
  • common denaturing agents include temperature, high and low pH extremes, solvents such as alcohol and acetone, detergents, and other solutes such as urea
    
    • removal of these agents allows the secondary, tertiary, and quarternary structures to reassmble

Question 10

what are proteases?

Answer 10

• enzymes that can break down the primary structure of proteins
  
  • many types of proteases exist and are characterized by targeting specific amino acid residues in a protein, usually via hydrolysis
    
    • ex. a serine protease example is trypsin

Question 11

what thermodynamic concept drives protein folding?

Answer 11

• entropy

Question 12

the form of an amino acid with a deporotonated carboxylic acid groupm a protonated amine group and a net charge of zero is known as?

Answer 12

• a zwitterion

Question 13

pH = pKa + log ([A-]/[HA])

Answer 13

• pH is the measure of acidity (pH = -log[H⁺])
• pKa is the negative logarithm of the acid dissociation constant (Ka)
• and HA and A^- are shorthand representations of teh protonated and deporotonated forms of an acid, respectively
  
  • when [HA] and [A^-] are equal, the ratio is 1 so pH = pKa

Question 14

common pKa’s to know?

Answer 14

• carboxylic acid groups of amino acids tend to be quite acidic, around 2
• amine group tends to be 9-9.5, very basic
• the acidic -COOH side groups of aspartic acid and glutamic acid have pKa values around 4
• arginine and lysine are quite basic with pKa values above 10.5
• histidine has a pKa of 6 so roughly 15% of histidine is positively charged at physiological pH (can be used as a buffer at near-physiological pH values)

Question 15

what is the isoelectric point (pI)

Answer 15

• corresponds to the pH where the average charge of an amino acid is 0
  
  • Neutral AA pI is average pKa of COOH and NH3. Basic AA pI is average pKa of R and NH3. Acidic AA pI is average pKa of COOH and R.

Question 16

what are some characteristics of the peptide bond?

Answer 16

• quite stable under intercellular conditions, and are characterized by resonance
  
  • this resonance allows the peptide bonds to be planar and do not rotate freely which helps contribute to the structural stability of 3D polypeptide structures

Question 17

how are peptide bonds broken?

Answer 17

• through hydrolysis, which is simply the reverse of the condensation reaction
  
  • the hydrolysis of peptide bond is energetically favourable, but is extremely slow under physiological conditions so the breaking of peptide bonds is generally accomplished by specific enzymes in living cells

Question 18

2 chemical reactions used to synthesize amino acids in laboratory conditions?

Answer 18

• Strecker synthesis and the Gabriel synthesis

Question 19

Strecker synthesis overview:

Answer 19

• overview: starts with an aldehyde where the carbon chain corresponds to the side chain (or R) of the amino acid that we’re trying to synthesize, and that aldehyde is then reacted with KCN and NH₄Cl to form an aminonitrile. in an acidic aqueous environment, hydroxyl groups are added across that triple bond until, with appropriate proton juggling, we form an amino acid.

Question 20

what are the details of the Strecker synthesis?

Answer 20

• the first step involves reacting the aldehyde with a combination of KCN and NH₄Cl, the latter of which is essentially just a delivery mechanism for the ammonium ion, or NH₄⁺, which plays a double role here- first NH₄⁺ protonates the aldehyde oxygen, and then in its deprotonated form, as NH₃, it adds to the carbonyl carbon
• Next, the resulting hydroxyl group becomes protonated and leaves as water, which allows the cyanide ion to add to what used to be the carbonyl carbon. this step generates the aminonitrile intermediate
• the second stage is united by the common theme of re-adding oxygen. H⁺ from solution protonates the nitrogen in the nitrile group, and then a water molecule adds to the carbon in that group. now we have a C=N double bond and a positively charged -OH₂⁺ group. through some proton transfer, of the type that readily takes place in acidic conditions, we can rearrange this structure so that we have an uncharged -OH group and a positively charged NH₂+ group. this primes the pump to repeat the process.
• Water adds again, creating a tetrahedral intermediate. Through proton transfer, we put a positive charge on the amine group, converting it into NH₃⁺, and then the lone pairs of one of the oxygen atoms attacks the carbon atom to kick out the amine group and form a carbon-oxygen double bond, thereby generating a carbonyl group where we need it

Question 21

basic steps of Strecker synthesis?

Answer 21

1. take an aldehyde and convert the carbonyl group to an amine
2. add a nitrile group, which provides an extra carbon and a scaffold in the form of a triple bond for subsequent addition of water
3. keep adding water to that triple bond and shuffling of protons around until the amine can be kicked out to generate a carboxylic acid.

Question 22

“gabriel synthesis” can refer more broadly to?

Answer 22

• the amine synthesis step

Question 23

what are the steps of Gabriel synthesis?

Answer 23

• the amine synthesis step starts with a very carefully protected nitrogen arom, at which point it can be reacted with an alkyl halide.in that reaction, the halide is kicked off of the alkyl chain, and the alkyl chain is essentially added to the nitrogen atom, which is still also part of the phthalimide molecule. the next task is to remove that nitrogen atom from the phthalimide ring structure to form a primary amine. this is actually quite complicated, and there are multiple ways of doinf it
• traditionally, an important reagent for this process was hydrazine which will yield phthalhydrazie plus our product of interest, a free primary amine.
• acid hydrolysis can also do the job and yields our primary amine plus phthalic acid
• base-catalyzed hydrolysis would also logically enough yield the primary amine plus phthalate
• The Gabriel syntehsis of primary amines can be “hacked” to produce an alpha-amino acid by carefully choosing the alkyl halide. in particular, a symmetrical molecule known as malonic ester is used, where -X donates a halide.
• after an intermediate structure is formed by adding the malonic ester to phthalimide, another halide is added
• then a decarboxylation step removes the extra carboxyl group
  
  • phthalimide is the source of the -NH₂ group, the malonic ester is the source of the alpha-carbon and the COOH group, and the R-X is the source of the side chain