Lecture 1 Flashcards
What are 6 roles of functional polypeptides?
- Switches/signal transduction
- Motors
- Structural elements
- Transport and storage machines
- Defense systems
- Catalysts
Two definitions of amino acids?
- A linear polymer of 20 diff AAs (monomers)
2. Gene product / product of ribosomal “translation”
What is the direction of synthesis of proteins on ribosomes?
- 5’ to 3’
- N to C synthesis
What are the 4 categories of proteins and give an example of each.
- Fibrous proteins – eg. Collagen
- Globular proteins – eg. Hemoglobin
- Membrane proteins – e.g. Channels
- Inherently unfolded proteins – e.g. BamC
What are the different levels of structure in proteins and describe what each consists of?
- Primary (sequence of the polymer)
- Secondary (α-helices, β-sheets, turns)
- Tertiary (domains, all-α, all-β, a/β, α+β)
- Quaternary (homo- hetero oligomers)
3 reasons to study proteins?
- Most abundant class of macromolecule in the cell.
- Most of a cell’s energy is dedicated to building
proteins and breaking them down. - They perform most of the jobs in the cell.
Draw the general L alpha-amino acid structure
N/A
Draw alpha-alanine vs. beta-alanine
N/A
Which AA(s) is/are not chiral?
Glycine
All 20 proteogenic amino acids are ____-enantiomers
except _____ which is non-chiral
All 20 proteogenic amino acids are L-enantiomers
except glycinewhich is non-chiral
The L/D nomenclature is based on a comparison to the enantiomers of
_____ as a standard of configuration.
glyceraldehyde
Draw L-Glyceraldehyde vs. D-Glyceraldehyde
In L, CH2OH group coming towards
Draw L-amino acid vs. D-amino acid
In L, R group coming towards
What are the 5 types of atoms in AA’s with their atomic #’s? The atomic # is used to determine priority.
C (6), H (1), O (8), N (7), S (16)
How to tell if you are looking at an L-amino acid or a D-amino acids
CORN
Which AA’s have more than one chiral centre?
Thr (S,R), Ile (S,S)
What does R vs. S represent?
S = counter clockwise R = clockwise
How to determine R vs. S?
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.
The Cα of the amino acids are all S except for _____ (because of the S (atomic #16) and _____ (because it
is not chiral)
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)
The 20 “standard” AA’s can be categorized into different
categories based on?
The physical and chemical properties of their
SIDECHAINS
What 2 methods that have been used to categorize AAs into polar and nonpolar categories?
- Extraction
2. Positional tendencies
What is extraction?
Extraction (partitioning) of free AAs in a water/organic
biphasic solution to develop a scale of polarity/hydrophobicity
What is positive tendencies?
Positional tendencies of AA residues in globular proteins
solvent accessibility vs. buried w/in the core of the protein
Draw the 20 proteinogenic AA’s. These are the standard amino acids that are coded for by triplet codons in the genetic code.
N/A
What are the 4 aliphatic AA’s? Their 3 letter and 1 letter name? pKa’s? Other properties?
- Alanine (Ala, A)
- Second most abundant amino acid in proteins - Valine (Val, V)
- β-branched - Leucine (Leu, L)
- Most abundant amino acid in proteins - Isoleucine (Ile, I) (2S,3S)
- β-branched
Draw the 4 aliphatics
N/A
What are the 3 aromatic AA’s? pKa’s? Their 3 letter and 1 letter name? Other properties?
- Phenylalanine (Phe, F)
- Relatively inert - Tyrosine (Tyr, Y)
- Phenol / phenolate anion pKa ~ 10.5 - Tryptophan (Trp, W)
- Least abundant amino acid in proteins (1 codon codes for W)
- AA with the most intrinsic absorbance and fluorescence
Draw the 4 aromatics
N/A
Which AA is the least abundant AA in proteins
Tryptophan (Trp, W)
Which AA is the most intrinsic absorbance and fluorescence
Tryptophan (Trp, W)
What are the 3 Basic (+) AA’s? pKa’s? Their 3 letter and 1 letter name? Other properties?
- Lysine (Lys, K)
- The ε-amino group has a pKa ~ 10.5. - Arginine (Arg, R)
- Guanidinium group is planar and has a delocalize positive charge, pKa ~ 12.5 - Histidine (His, H)
- Catalytically versatile: general acid/base, nucleophile, metal ligand, pKa ~ 6.5
Draw the 4 basic AAs
N/A
What are the 2 Acidic (-) AA’s? pKa’s? Their 3 letter and 1 letter name? Other properties?
- Aspartic acid / Aspartate (Asp, D)
- pKa ~ 4.0 - Glutamic acid / Glutamate (Glu, E)
- pKa ~ 4.0
Draw the 4 acidic AAs
N/A
What are the 2 Amides AA’s? pKa’s? Their 3 letter and 1 letter name? Other properties?
- Asparagine (Asn, N)
2. Glutamine (Gln, Q)
Draw the 2 Amides AAs
N/A
What are the 2 Hydroxyl AA’s? pKa’s? Their 3 letter and 1 letter name? Other properties?
- Serine (Ser, S)
- Has an alkoxide anion
group when deprotonated, pKa ~ 14 - Threonine (Thr, T)
- Contains a side chain chiral center (2S, 3R), pKa ~ 14
- Like Ile, and Val has a β-branched sidechain.
Draw the 2 Hydroxyl AAs
N/A
What are the 2 sulfur AA’s? pKa’s? Their 3 letter and 1 letter name? Other properties?
- Cysteine (Cys, C)
- Thiol (mercapto, sulfhydral) group,
- Most reactive side chain, pKa ~ 8.5
- When deprotonated (pH above 8.5): thiolate anion group - Methionine (Met, M)
- Thioether side chain
Draw the 2 sulfur AAs
N/A
What is the smallest AA? 3 letter and 1 letter name? pKa and other properties?
- Glycine (Gly, G)
- Important for flexibility of the mainchain and turns
Draw the smallest AA
N/A
What is the cyclical AA? 3 letter and 1 letter name? pKa and other properties?
- Proline (Pro, P)
Draw the cyclical AA
N/A
What are the 12 functional groups within AAs? Which AAs contain which?
- Amino (Lys, N-terminus)
- Carboxyl, Carboxylate (Asp, Glu, C-terminus)
- Amide (Asn, Gln, peptide bond)
- Guanidinium (Arg)
- Imidizole (His)
- Pyrrole (Pro)
- Thiol, Thiolate (Cys)
- Hydroxyl, Alkoxide (Ser, Thr)
- Phenyl (Phe)
- Phenol, Phenolate (Tyr)
- Indole (Trp = benzene ring + pyrrole ring, bicyclic/heterocyclic)
- Thioether (Met)
Describe the bonding in tetrahedral geometry:
- Solid wedge
- Dashed wedge
- Normal line
- The solid wedge (bond) signifies above the plain (board).
- Dashed wedge (bond) signifies behind the plain (board).
- Normal line signified bonds laying in plain of the board.
Describe the bond angles:
- tetrahedral (sp3 hybridized atoms)
- trigonal planar (sp2 hybridized atoms)
- tetrahedral (sp3 hybridized atoms) = 109 degrees
2. trigonal planar (sp2 hybridized atoms) = 120 degrees
List is bond distances of the following (Å = 10^-10 M):
- C-C 1.54
- C=O 1.21
- C-O 1.43
- N-C 1.47
- C-H 1.10
- N-H 1.00
- O-H 0.96
- C=C 1.34
What are the 7 greek letters in order and their symbol?
- Alpha A α
- Beta B β
- Gamma G γ
- Delta D δ
- Epsilon E ε
- Zeta Z ζ
- Eta H η
What is the pka for the a-amino group?
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
What is the pka for the a-carboxylate group?
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
Steps to drawing chiral carbons
- The α-H is shown behind the plane of the paper (dashed wedge).
- The R-group (sidechain) is shown in front of the plane of the paper (dark wedge).
- The bond between the Cα and α-ammonium group is in the plane of the paper (straight line).
- The bond between the Cα and α-carboxylate group is in the plane of the paper (straight line)
