Amino Acids, Peptides & Proteins: Theory + Calcs

Question 1

At what point is the pH of an amino acid solution equal to the pK of one of its functional groups?

Answer 1

when half of that functional group has been deprotonated

ex: glycine’s carboxyl pK = 2.3 so…

With 20 ml of 0.1 N glycine solution, addition of 10 ml 0.1 NaOH will cause deprotonation of half the carboxyls and thus give the solution a pH of 2.3

Question 2

How does an ⍺-ketoacid’s structure differ from the amino acid it is derived from?

Answer 2

The H and amino groups of the alpha carbon are replaced by a double-bonded oxygen.

Thus they have a ketone on the alpha carbon…

Question 3

What are the non-polar amino acids?

Answer 3

aliphatic - Met, Gly, Ala, Val, Leu, Ile, Pro,

aromatic - Phe, Trp

Many Gleeful Alligators Try Phor Vaping Leisurely In Ponds

Question 4

Which amino acids are polar?

Answer 4

aliphatic - Ser, Thr, Cys, Gln, Asn

aromatic - Tyr

Several Throbbing Cysts Glow As Turqouise

Question 5

What amino acids have aliphatic side chains?

Answer 5

this is most easily remembered by just knowing the aromatic side chain amino acids and knowing that ALL others are aliphatic

Question 6

What amino acids have aromatic side chains?

Answer 6

Phe, Trp, Tyr, His

Tyrannosauruses Trying to Hi-five are Phunny

Question 7

How does one indicate the number of carbons in an amino acid?

Answer 7

The number of carbons plus the letter C in parentheses

EX: Ala (3C), Gly (2C)

Question 8

What is transamination?

Answer 8

Transamination (AKA aminotransfer)

• an exchange between two molecules (an amino acid and a keto acid) of the amino group -NH₂ and the keto group =O

Question 9

What are the branched chain amino acids?

How can their structures be remembered?

Answer 9

Valine, Leucine and Isoleucine

• Valine is the simplest and contains a “V” of methyls branching off a carbon
• Leucine is just valine with an extra carbon
• Isoleucine is just leucine with its branching from the first carbon instead

Question 10

How can buffers be formed from fully protonated amino acid solutions?

Answer 10

By **partially neutralizing **the solution with NaOH so that the acidic and conjugate base forms of the amino acid exist in equal amounts.

EX: 10 ml of a 1 M fully protonated AA solution can be made into a buffer with the addition of 5 ml 1M NaOH

Question 11

What is a peptide bond?

What groups make it up?

Via what kind of reaction?

What conformation does it have?

How does it move and why?

Answer 11

a bond formed between two amino acids

• between the alpha amino and alpha carboxyl groups
• occurs via condensation reactions (AKA dehydration)
• has a trans configuration
• has limited rotation because it is a partial double bond between the C and N

Question 12

Which amino acids have a net positive charge at neutral pH?

Answer 12

Arg, Lys, His

Question 13

Which amino acids have a net negative charge at neutral pH?

Answer 13

Asp, Glu

Question 14

Which amino acids have basic side chains?

Answer 14

same as those with positive charge

His, Lys, Arg

• all also have N in their side chains

Question 15

Which amino acids have acidic side chains?

Answer 15

Glu, Asp

• same as those with ‘negative’ side chains
• both have COOH groups

Question 16

What are the free amino and carboxyl ends of the amino acids called?

Answer 16

N terminus and C terminus, respectively

Question 17

Describe the electromagnetic forces that influence peptide bonding.

Answer 17

• highly electronegative =O draws e^-s from lone pair on N
• this creates a semi-double bond between carboxyl C and amino N (allows no rotation)

(amino H becomes H bridge donor and =O becomes H bridge acceptor)

Question 18

In what direction are polypeptides formed?

Answer 18

N terminus to C terminus

Question 19

What determines the net charge of a polypeptide chain?

Why only this?

Answer 19

the ratio of the acidic and basic amino acid residues

the charges of the amines and carboxyls involved in peptide bonding are lost in the bonding process

Question 20

What is the primary structure of a protein and what bonds are responsible for it?

Answer 20

the amino acid sequence

covalent bonds between amino and carboxyl groups forming peptide bonds

Question 21

What is the secondary structure of a protein and what kind of bonds are responsible for it?

Answer 21

• general three-dimensional form of local segments of a protein (⍺ helix, β sheet etc.)
• formed by H bonds between carboxyl and amino groups of the peptide bonds

Question 22

How are ⍺ helices formed?

How many AAs in one turn of the helix?

Where are the side chains in relation the helix?

Answer 22

• every backbone N-H group donates a hydrogen bond to the C=O group 4 amino acids earlier in the sequence
  ex: 4 to 1… 5 to 2… 6 to 3… etc.
• 3.6 AAs per turn
• side chains stick out from the sides of the helix like bristles from a pipe cleaner

Question 23

What is a disulfide bridge?

What AA forms them?

Where do proteins with them often go and why?

Answer 23

• side chain bonds between the thiols of two cysteine residues
• usually in proteins meant for extracellular purposes because disulfide bonds are unstable in the reducing environment of the cytosole

Question 24

What decreases the stability of an alpha helix?

Answer 24

1. electrostatic **repulsion **of charged side chains
2. bulkiness of side chains
3. **ionic interaction **of side chains spaced 4 residues apar
4. terminus charges (+ amino at C terminus, - at N terminus)
5. proline

R B I T P

Question 25

Describe the general structure of a beta sheet.

Answer 25

• At least two beta strands (usually 3-10 AAs long with extended conformation backbone)
• at least 2-3 hydrogen bonds between the backbones
• pleatedness of the sheet forms ‘peaks’ and ‘troughs’ and side chains stick ‘up’ from the peaks and ‘down’ from the troughs

Question 26

What is the name for the curved area between two anti-parallel strands of a beta sheet?

How many amino acids make it up and which are common in it?

What bond holds it together?

Where is it found in the protein?

Answer 26

Beta turn

• made up of 4 AAs … often with **Gly **and Pro
• **H bonds **between AA 1 and 4 peptide groups
• found near surface of protein

Question 27

What is the tertiary structure of a protein?

Examples of common tertiary structures?

What affects tertiary structure?

Answer 27

• its 3 dimensional structure
• **globular **and **fibular **structures are common
• affected by side chain interactions and long-range** aspects** of the AA sequence

Question 28

What types of interactions are important in tertiary structure formation?

Answer 28

• **noncovalent **interactions
• **hydrophobic **interactions
• polar interactions
• H bonds
• **salt bridges **(ionic interactions)

N H P H S

No Phuss

Question 29

What is a protein’s quaternary structure?

What bonds hold it together?

Answer 29

• a structure made up of multiple protein sub-units
  i. e. hemoglobin
• bonds between side chains of different polypeptides

Question 30

What is a protein’s domain?

In an enzyme, what might two examples of domains be?

Answer 30

a section of the protein structure meant for a certain task

• enyzmes can have substrate-binding domains and coenzyme-binding domains

Question 31

How can quaternary structures be categorized based on…

… their number of sub units?

… the similarness/differentness of the sub units?

Answer 31

1 subunit = monomer, 2 = dimer… 4 = tetramer etc.

two of the same subunit = homodimer

two different subunits = heterodimer

Question 32

What are chaperones?

Answer 32

• proteins which assist in protein folding during synthesis
• help move hydrophobic regions of proteins to their interior

Question 33

What molecule helps in disulfide bridge formation?

Answer 33

Protein Disulfide Isomerase

Question 34

What molecule can aid in creating beta turns by altering conformation of a peptide bond?

Answer 34

Proline-cis, trans-isomerase

• can alter a proline’s peptide bond to give optimize it for a turn

Question 35

What 3 auxiliary molecules aid in protein folding?

Answer 35

1. chaperones
2. protein disulfide isomerase
3. proline cis trans isomerase