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MBB 324 > Lecture 1 > Flashcards

Lecture 1 Flashcards

1
Q

What are 6 roles of functional polypeptides?

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

Two definitions of amino acids?

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

2. Gene product / product of ribosomal “translation”

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3
Q

What is the direction of synthesis of proteins on ribosomes?

A
  • 5’ to 3’

- N to C synthesis

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4
Q

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

A
  1. Fibrous proteins – eg. Collagen
  2. Globular proteins – eg. Hemoglobin
  3. Membrane proteins – e.g. Channels
  4. Inherently unfolded proteins – e.g. BamC
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5
Q

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

A
  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)
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6
Q

3 reasons to study proteins?

A
  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.
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7
Q

Draw the general L alpha-amino acid structure

A

N/A

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8
Q

Draw alpha-alanine vs. beta-alanine

A

N/A

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9
Q

Which AA(s) is/are not chiral?

A

Glycine

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10
Q

All 20 proteogenic amino acids are ____-enantiomers

except _____ which is non-chiral

A

All 20 proteogenic amino acids are L-enantiomers

except glycinewhich is non-chiral

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11
Q

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

A

glyceraldehyde

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12
Q

Draw L-Glyceraldehyde vs. D-Glyceraldehyde

A

In L, CH2OH group coming towards

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13
Q

Draw L-amino acid vs. D-amino acid

A

In L, R group coming towards

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14
Q

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

A

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

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15
Q

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

A

CORN

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16
Q

Which AA’s have more than one chiral centre?

A

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

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17
Q

What does R vs. S represent?

A 
S = counter clockwise
R = clockwise
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18
Q

How to determine R vs. S?

A

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.

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19
Q

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

A

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)

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20
Q

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

categories based on?

A

The physical and chemical properties of their

SIDECHAINS

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21
Q

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

A
  1. Extraction

2. Positional tendencies

22
Q

What is extraction?

A

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

biphasic solution to develop a scale of polarity/hydrophobicity

23
Q

What is positive tendencies?

A

Positional tendencies of AA residues in globular proteins

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

24
Q

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

A

N/A

25
Q

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

A
  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
26
Q

Draw the 4 aliphatics

A

N/A

27
Q

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

A
  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
28
Q

Draw the 4 aromatics

A

N/A

29
Q

Which AA is the least abundant AA in proteins

A

Tryptophan (Trp, W)

30
Q

Which AA is the most intrinsic absorbance and fluorescence

A

Tryptophan (Trp, W)

31
Q

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

A
  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
32
Q

Draw the 4 basic AAs

A

N/A

33
Q

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

A
  1. Aspartic acid / Aspartate (Asp, D)
    - pKa ~ 4.0
  2. Glutamic acid / Glutamate (Glu, E)
    - pKa ~ 4.0
34
Q

Draw the 4 acidic AAs

A

N/A

35
Q

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

A
  1. Asparagine (Asn, N)

2. Glutamine (Gln, Q)

36
Q

Draw the 2 Amides AAs

A

N/A

37
Q

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

A
  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.
38
Q

Draw the 2 Hydroxyl AAs

A

N/A

39
Q

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

A
  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
40
Q

Draw the 2 sulfur AAs

A

N/A

41
Q

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

A
  1. Glycine (Gly, G)

- Important for flexibility of the mainchain and turns

42
Q

Draw the smallest AA

A

N/A

43
Q

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

A
  1. Proline (Pro, P)
44
Q

Draw the cyclical AA

A

N/A

45
Q

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

A
  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)
46
Q

Describe the bonding in tetrahedral geometry:

  1. Solid wedge
  2. Dashed wedge
  3. Normal line
A
  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.
47
Q

Describe the bond angles:

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

2. trigonal planar (sp2 hybridized atoms) = 120 degrees

48
Q

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

A
  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
49
Q

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

A
  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
50
Q

What is the pka for the a-amino group?

A

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

51
Q

What is the pka for the a-carboxylate group?

A

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

52
Q

Steps to drawing chiral carbons

A
  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)

MBB 324 (17 decks)

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