Lecture 1

Question 1

What are 6 roles of functional polypeptides?

Answer 1

1. Switches/signal transduction
2. Motors
3. Structural elements
4. Transport and storage machines
5. Defense systems
6. Catalysts

Question 2

Two definitions of amino acids?

Answer 2

1. A linear polymer of 20 diff AAs (monomers)

2. Gene product / product of ribosomal “translation”

Question 3

What is the direction of synthesis of proteins on ribosomes?

Answer 3

• 5’ to 3’

- N to C synthesis

Question 4

What are the 4 categories of proteins and give an example of each.

Answer 4

1. Fibrous proteins – eg. Collagen
2. Globular proteins – eg. Hemoglobin
3. Membrane proteins – e.g. Channels
4. Inherently unfolded proteins – e.g. BamC

Question 5

What are the different levels of structure in proteins and describe what each consists of?

Answer 5

1. Primary (sequence of the polymer)
2. Secondary (α-helices, β-sheets, turns)
3. Tertiary (domains, all-α, all-β, a/β, α+β)
4. Quaternary (homo- hetero oligomers)

Question 6

3 reasons to study proteins?

Answer 6

1. Most abundant class of macromolecule in the cell.
2. Most of a cell’s energy is dedicated to building
   proteins and breaking them down.
3. They perform most of the jobs in the cell.

Question 7

Draw the general L alpha-amino acid structure

Answer 7

N/A

Question 8

Draw alpha-alanine vs. beta-alanine

Answer 8

N/A

Question 9

Which AA(s) is/are not chiral?

Answer 9

Glycine

Question 10

All 20 proteogenic amino acids are ____-enantiomers

except _____ which is non-chiral

Answer 10

All 20 proteogenic amino acids are L-enantiomers

except glycinewhich is non-chiral

Question 11

The L/D nomenclature is based on a comparison to the enantiomers of
_____ as a standard of configuration.

Answer 11

glyceraldehyde

Question 12

Draw L-Glyceraldehyde vs. D-Glyceraldehyde

Answer 12

In L, CH2OH group coming towards

Question 13

Draw L-amino acid vs. D-amino acid

Answer 13

In L, R group coming towards

Question 14

What are the 5 types of atoms in AA’s with their atomic #’s? The atomic # is used to determine priority.

Answer 14

C (6), H (1), O (8), N (7), S (16)

Question 15

How to tell if you are looking at an L-amino acid or a D-amino acids

Answer 15

CORN

Question 16

Which AA’s have more than one chiral centre?

Answer 16

Thr (S,R), Ile (S,S)

Question 17

What does R vs. S represent?

Answer 17

S = counter clockwise
R = clockwise

Question 18

How to determine R vs. S?

Answer 18

Rotate the amino acid such that the α-hydrogen (lowest priority) is pointing away from you.
Prioritize the other three groups (lowest to highest) around the α-carbon, based on atomic number.
Right = R, Left = S.

Question 19

The Cα of the amino acids are all S except for _____ (because of the S (atomic #16) and _____ (because it
is not chiral)

Answer 19

The Cα of the amino acids are all S except for CYSTEINE (because of the S (atomic #16) and GLYCINE (because it is not chiral)

Question 20

The 20 “standard” AA’s can be categorized into different

categories based on?

Answer 20

The physical and chemical properties of their

SIDECHAINS

Question 21

What 2 methods that have been used to categorize AAs into polar and nonpolar categories?

Answer 21

1. Extraction

2. Positional tendencies

Question 22

What is extraction?

Answer 22

Extraction (partitioning) of free AAs in a water/organic

biphasic solution to develop a scale of polarity/hydrophobicity

Question 23

What is positive tendencies?

Answer 23

Positional tendencies of AA residues in globular proteins

solvent accessibility vs. buried w/in the core of the protein

Question 24

Draw the 20 proteinogenic AA’s. These are the standard amino acids that are coded for by triplet codons in the genetic code.

Answer 24

N/A

Question 25

What are the 4 aliphatic AA's? Their 3 letter and 1 letter name? pKa's? Other properties?

Answer 25

1. Alanine (Ala, A) - Second most abundant amino acid in proteins 2. Valine (Val, V) - β-branched 3. Leucine (Leu, L) - Most abundant amino acid in proteins 4. Isoleucine (Ile, I) (2S,3S) - β-branched

Question 26

Draw the 4 aliphatics

Answer 26

N/A

Question 27

What are the 3 aromatic AA's? pKa's? Their 3 letter and 1 letter name? Other properties?

Answer 27

1. Phenylalanine (Phe, F) - Relatively inert 2. Tyrosine (Tyr, Y) - Phenol / phenolate anion pKa ~ 10.5 3. Tryptophan (Trp, W) - Least abundant amino acid in proteins (1 codon codes for W) - AA with the most intrinsic absorbance and fluorescence

Question 28

Draw the 4 aromatics

Answer 28

N/A

Question 29

Which AA is the least abundant AA in proteins

Answer 29

Tryptophan (Trp, W)

Question 30

Which AA is the most intrinsic absorbance and fluorescence

Answer 30

Tryptophan (Trp, W)

Question 31

What are the 3 Basic (+) AA's? pKa's? Their 3 letter and 1 letter name? Other properties?

Answer 31

1. Lysine (Lys, K) - The ε-amino group has a pKa ~ 10.5. 2. Arginine (Arg, R) - Guanidinium group is planar and has a delocalize positive charge, pKa ~ 12.5 3. Histidine (His, H) - Catalytically versatile: general acid/base, nucleophile, metal ligand, pKa ~ 6.5

Question 32

Draw the 4 basic AAs

Answer 32

N/A

Question 33

What are the 2 Acidic (-) AA's? pKa's? Their 3 letter and 1 letter name? Other properties?

Answer 33

1. Aspartic acid / Aspartate (Asp, D) - pKa ~ 4.0 2. Glutamic acid / Glutamate (Glu, E) - pKa ~ 4.0

Question 34

Draw the 4 acidic AAs

Answer 34

N/A

Question 35

What are the 2 Amides AA's? pKa's? Their 3 letter and 1 letter name? Other properties?

Answer 35

1. Asparagine (Asn, N) | 2. Glutamine (Gln, Q)

Question 36

Draw the 2 Amides AAs

Answer 36

N/A

Question 37

What are the 2 Hydroxyl AA's? pKa's? Their 3 letter and 1 letter name? Other properties?

Answer 37

1. Serine (Ser, S) - Has an alkoxide anion group when deprotonated, pKa ~ 14 2. Threonine (Thr, T) - Contains a side chain chiral center (2S, 3R), pKa ~ 14 - Like Ile, and Val has a β-branched sidechain.

Question 38

Draw the 2 Hydroxyl AAs

Answer 38

N/A

Question 39

What are the 2 sulfur AA's? pKa's? Their 3 letter and 1 letter name? Other properties?

Answer 39

1. Cysteine (Cys, C) - Thiol (mercapto, sulfhydral) group, - Most reactive side chain, pKa ~ 8.5 - When deprotonated (pH above 8.5): thiolate anion group 2. Methionine (Met, M) - Thioether side chain

Question 40

Draw the 2 sulfur AAs

Answer 40

N/A

Question 41

What is the smallest AA? 3 letter and 1 letter name? pKa and other properties?

Answer 41

1. Glycine (Gly, G) | - Important for flexibility of the mainchain and turns

Question 42

Draw the smallest AA

Answer 42

N/A

Question 43

What is the cyclical AA? 3 letter and 1 letter name? pKa and other properties?

Answer 43

1. Proline (Pro, P)

Question 44

Draw the cyclical AA

Answer 44

N/A

Question 45

What are the 12 functional groups within AAs? Which AAs contain which?

Answer 45

1. Amino (Lys, N-terminus) 2. Carboxyl, Carboxylate (Asp, Glu, C-terminus) 3. Amide (Asn, Gln, peptide bond) 4. Guanidinium (Arg) 5. Imidizole (His) 6. Pyrrole (Pro) 7. Thiol, Thiolate (Cys) 8. Hydroxyl, Alkoxide (Ser, Thr) 9. Phenyl (Phe) 10. Phenol, Phenolate (Tyr) 11. Indole (Trp = benzene ring + pyrrole ring, bicyclic/heterocyclic) 12. Thioether (Met)

Question 46

Describe the bonding in tetrahedral geometry: 1. Solid wedge 2. Dashed wedge 3. Normal line

Answer 46

1. The solid wedge (bond) signifies above the plain (board). 2. Dashed wedge (bond) signifies behind the plain (board). 3. Normal line signified bonds laying in plain of the board.

Question 47

Describe the bond angles: 1. tetrahedral (sp3 hybridized atoms) 2. trigonal planar (sp2 hybridized atoms)

Answer 47

1. tetrahedral (sp3 hybridized atoms) = 109 degrees | 2. trigonal planar (sp2 hybridized atoms) = 120 degrees

Question 48

List is bond distances of the following (Å = 10^-10 M):

Answer 48

1. C-C 1.54 2. C=O 1.21 3. C-O 1.43 4. N-C 1.47 5. C-H 1.10 6. N-H 1.00 7. O-H 0.96 8. C=C 1.34

Question 49

What are the 7 greek letters in order and their symbol?

Answer 49

1. Alpha A α 2. Beta B β 3. Gamma G γ 4. Delta D δ 5. Epsilon E ε 6. Zeta Z ζ 7. Eta H η

Question 50

What is the pka for the a-amino group?

Answer 50

The pKa for the α-amino group varies slightly for the different amino acids (10.8-8.8) average = 9.8 , we will remember 10

Question 51

What is the pka for the a-carboxylate group?

Answer 51

The pKa for the α-carboxylate group varies slightly for the different amino acids (2.6-1.8) average = 2.2 , we will remember 2

Question 52

Steps to drawing chiral carbons

Answer 52

1. The α-H is shown behind the plane of the paper (dashed wedge). 2. The R-group (sidechain) is shown in front of the plane of the paper (dark wedge). 3. The bond between the Cα and α-ammonium group is in the plane of the paper (straight line). 4. The bond between the Cα and α-carboxylate group is in the plane of the paper (straight line)