Amino Acids and Proteins

1
Instructor Frederic Pio Email
fpio_at_sfu.ca Office Hours Monday,
Wednesday Friday, 2 to 3 pm Office Number
SSB 6112
2
Lecture Notes and Problem sets
To get a copy of the presented material
http//www.sfu.ca/mbb/mbb/undergraduate/lectures/
fall_lectures.htm
3
Protein Structure-function Lecture contents
IV. Amino Acids and their Chemical
Properties V Peptides Levels of Protein
Structure -Secondary Structure ?-helices,
?-sheets and ?-turns -Tertiary and Quaternary
Structure Coiled-Coils etc VI. Protein
folding Examples of protein Structure and
function VII. Enzymes VIII. Transport
proteins (hemoglobin)
4
Problem sets -Problem sets have been posted
on the web. -You will have to hand in the
answers by Friday September 20th. -Answers
to the question will be also posted on the web
the same day Quiz will be Monday September
23th. It will cover lecture I to VIII.
5
Lecture IV Mathews ( p126-147, p161-193)
IV. Amino Acids and their Chemical
Properties Classification Special
amino-acids G,P,C. Structures Important you
will have to know them for the QUIZ Properties
Weak acids bases, Zwitterion Peptide bond
Define backbone of polypeptides Primary
Structure of polypeptide. An example insulin
6
Figure 5.1 3D Structure of Myoglobin
a-helix
- first to be determined by x-ray crystallography
Heme ligand
a-amino-acids Side chain
- revealed how the protein bound heme (loaded
with oxygen) and gave the first detailed look at
a protein structure
- now over 2000 protein structures are known
7
Amino Acid structure
Side chain
? - carbon
Carboxyl group
Amino group
While most free amino acids have a net zero
charge at neutral pH, they have both and
charges. Zwitterion
NH3
COO-
8
Acidic and Basic Amino Acids- Hydrophilicmost
often found at the outer surface of proteins,
exposed to solvent
- these are charged at neutral pH (physiological
conditions)- contribute to charge of protein
9
These have uncharged amide and hydroxyl groups
that participate in H bonding
Polar amino acids with uncharged R group

• branched
• amino-acid

10
Hydrophobic amino acids
Insoluble in water, cluster on the inside of
proteins
b- branched
Nonpolar, hydrocarbons
Aromatic side chains
Two W ring can stack with each other inside
proteins forming van der waals interaction
11
Special amino-acids
Cysteine Glycine Proline (cys, C) (Gly,
G) (Pro, P)
12
Proline (Pro, P)

• Proline is a special amino acid in fact, it is
  more appropriately named an imino acid
• it is the only group that is cyclic, where the
  side chain forms a covalent bond with the
  nitrogen atom
• It cyclic properties made Proline difficult to
  fold into proteins because it break the
  polypeptidic chain.

13
Glycine (Gly) G
H H2NCCOO- H
- smallest and most versatile of amino
acids can readily fit into any protein
structural element The only amino-acid which does
not have a-carbon
14
Cysteine
Cysteine side chains can form a disulfide bond to
form cystine often plays important role in
protein structure
15
Amino acid structures
aspartic acid (D)
glutamic acid (E)
valine (V)
leucine (L)
methionine (M)
isoleucine (I)
phenylalanine (F)
tyrosine (Y)
tryptophan (W)
aspargine (N)
glutamine (Q)
serine (S)
threonine (T)
glycine (G)
lysine (K)
histidine (H)
arginine (R)
cysteine
proline
alanine (A)

2

3
know all of them for this course!
16
Amino acid single letter code and Alphabet
Leucine Methionine N-gt Asparagine O Proline Q-gt
Glutamine R-gt ArginineSerine ThreonineU
Alanine B Cysteine D-gt Aspartate E-gt
GlutamateF-gtPhenylalanine GlycineHistidine K-gt
Lysine
Valine W-gt tryptophan X Y-gt tyrosine Z
know all of them for this course!
17
Amino acids in proteins

• Average molecular weight is 113- allows you to
  calculate how many amino acid residues are in a
  protein of a given size
• Leucine, serine, lysine and glutamic acid are the
  most abundant- constitute 32 of amino acids in
  proteins
• Cysteine, tryptophan, methionine are rare-
  together total 5

18
Stereoisomers of Amino Acids
All of the Amino Acids incorporated by organisms
into proteins are in the L form
Note glycine is not chiral because of H- being
its side chain.
19
Amino acids are weak acids bases
-all free amino acids are acids and bases because
of free carboxyl and amino ends - in peptides
and proteins these are involved in peptide bonds
so in proteins only some of the amino acids
posses acid/base properties - in the
three-dimensional environment of proteins the
pKas of the amino acids can differ significantly
from the values in table 5.1 (for the free amino
acids)
Table 5.3
20
Peptide bond formation
Glycine(G)
Alanine(A)
The peptide bond has partial double bond character
-
O
C ter

N ter
C
N
H
Resonant Structures
Glycylalanine (GA)
21
Polypeptides of defined sequence Fig 5.15
The primary structure of bovine insulin two
polypeptidic chains A and B joined by disulfide
bonds.
Intra chain disulfide bond
A chain S---------S
Nter GIVEQCCASVCSLYQLENYCN Cter
/
S
S
B chain S
S
Nter FVNQHLCGSHLVEALYLVCGERGFFYT
PKA Cter
Inter chain disulfide bond