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MOLECULES
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Monomer vs polymer
amino acid monomer
R is a side group
O
H2N-CH-C-OH
R
E.g. protein
Monomer
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O
H2N-CH-C-OH
R
R R R R
The 20 amino acids found
in proteins each have
different side chains, R
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Each amino acid has at least one carboxyl group
O
X
C
OH
At cell pH, the carboxyls dissociate to
form carboxylate ions
O
O
OH
4
+H
X C
X C
+
O
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Proteins are the working language of biology
The 20 amino acids found in proteins
are the alphabet
A
A
5
Let's start with the letter
Alanine, Ala, A
All the common amino acids have 3-letter
and 1-letter abbreviations
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Note asymmetry around the carbon
(all 4 side groups are different)
Most amino acids have D- and L- isomers*
COO
H3 N C H
R
*But only L-amino acids
are present in typical proteins
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Glycine, Gly, G is unusual
COO
H3 N C H
H
R group is a second H-atom
Hence, no asymmetry round carbon
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No L- and D- isomers
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Classes of amino acid R-groups
COO
H3 N C H
CH2OH
e.g. Serine, Ser, S
R group Polar, uncharged
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Classes of amino acid R-groups
COO
H3 N C H
CH2
COO
e.g. Aspartic acid, Asp, D
R group* is negatively charged
*An additional -COO- group
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Classes of amino acid R-groups
COO
H3 N C H
(CH2) 4
NH3
e.g. Lysine, Lys, K
R group positively charged
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R group hydrophobic
COO
H3 N C H
CH3
e.g. Alanine, Ala, A
COO
H3 N C H
CH2
OH
Tyrosine, Tyr, Y
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"Special" amino acids
COO
H3 N C H
H
Glycine, Gly, G (mentioned before)
The "baby" (smallest) of the amino acids
No special hydrophilic or hydrophobic
character
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"Special" amino acids
COO
H3 N C H
CH2
SH
Cysteine, Cys, C
Important in forming disulfide (S-S)
crosslinks within a protein
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A protein with two disulfide bonds
-S-S14
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C of Cys
CH2
S
H
H
S
DISULFIDE BOND
C of cysteine
CH2
S
S
2H
CH2
C of cysteine
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CH2
C of cysteine
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Special amino acids Proline. This amino acid
produces a “kink” in a polypeptide
COO
H
C
HN
H2C
Proline, Pro, P
CH2
CH2
+H
3N-
Pro is an imino acid (not, strictly speaking,
an amino acid
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Forming a peptide bond
between 2 amino acids

+H 3N C 
O
C-O -
R1
+ H 3N
H20

O
C
C
R1
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+

+H N C 
3

N C
H R2
O
C-O -
R2
O
C-O -
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A dipeptide. All peptides and proteins have:
and a
an amino end
carboxyl end

+H 3 N
C
R1
N-terminal end
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O
C
N
H

C
O
C-O
-
R2
C-terminal
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Polypeptide structure
Primary
 Secondary
 Tertiary
 Quaternary

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1. Primary structure
 Amino
acid sequence
 Disulfide crosslinking within
the polypeptide
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1. Primary structure: portion of
-chain of human hemoglobin
N-terminus
Val His Leu Thr Pro Glu Glu Lys
1 2 3 4 5 6 7 8
bla bla bla bla bla bla bla bla
bla bla Tyr Arg
140 141
C-terminus
aa substitution; Val instead of Glu at position 6
is found in the disease sickle cell anemia
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2. Secondary stucture of a
protein
 The
folding of portions
(domains) of the protein to
form:
-helices
-pleated sheets
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Secondary structure: -helix
Hydrogen
bonding
3.6 aa's per turn
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Secondary structure: -pleated sheet
R
R
R
Edge view
R
Polypeptide
chains

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H-bond


R
R
R

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3. Tertiary structure of protein
 Overall
folding of:
 helices
-pleated sheets and
– the regions between them
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4. Quaternary structure of
protein
Ordering of several different polypeptide
strands to form a functional protein complex




e.g. Hemoglobin
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