5. Functions of Proteins
Antibody Antibodies bind to specific foreign
particles, such as viruses and bacteria, to
help protect the body.
Immunoglobulin
G (IgG)
Enzyme Enzymes carry out almost all of the
thousands of chemical reactions that take
place in cells. They also assist with the
formation of new molecules by reading the
genetic information stored in DNA.
Phenylalanine hydrox
ylase
Messenger Messenger proteins, such as some types
of hormones, transmit signals to
coordinate biological processes between
different cells, tissues, and organs.
Growth hormone
Structural
component
These proteins provide structure and
support for cells. On a larger scale, they
also allow the body to move.
Actin
Transport/storage These proteins bind and carry atoms and
small molecules within cells and
throughout the body.
Ferritin
6. 6
Amino Acids
Amino acids
Are the building blocks of proteins.
There are 20 standard amino acids
Contain a carboxylic acid group and an amino group
on the alpha () carbon.
Are ionized in solution.
Each contain a different side group (R).
R R
│ + │
H2N—C —COOH H3N—C —COO−
│ │
H H
ionized form
7. 7
Examples of Amino Acids
H
+ │
H3N—C—COO−
│
H glycine
CH3
+ │
H3N—C—COO−
│
H alanine
13. 13
Learning Check
Identify each as (P) polar or (NP) nonpolar.
+
A. H3N–CH2–COO− (Glycine)
CH3
|
CH–OH
+ │
B. H3N–CH–COO− (Threonine)
14. 14
Solution
Identify each as (P) polar or (NP) nonpolar.
+
A. H3N–CH2–COO− (Glycine) (NP) nonpolar
CH3
|
CH–OH
+ │
B. H3N–CH–COO− (Threonine) (P) polar
15. 15
Optical Activity
Amino acids
Are chiral except for glycine.
Have Fischer projections that are stereoisomers.
That are L are used in proteins.
L-alanine D-alanine L-cysteine D-cysteine
CH2SH
H2N H
COOH
CH2SH
H NH2
COOH
CH3
H NH2
COOH
CH3
H2N H
COOH
Fischer Projections of Amino Acids
16. 16
• Amino acids are amphoteric molecules have both basic
and acidic group
• Zwitterions (dipolar molecules), have charged —NH3
+
and COO- groups.
• Forms when both the —NH2 and the —COOH groups
in an amino acid ionize in water.
• Has equal + and − charges at the isoelectric point (pI).
O O
║ + ║
NH2—CH2—C—OH H3N—CH2—C—O–
Glycine Zwitterion of glycine
Amphoteric Properties
Zwitterions and Isoelectric Points
17. At physiological pH (7.4), a zwitterion forms
Both + and – charges
Overall neutral
Amphoteric
Amino group is protonated
Carboxyl group is deprotonated
Soluble in polar solvents due to ionic character
Structure of R also influence solubility
Zwitterions
18. 18
In solutions more basic than the pI,
The —NH3
+ in the amino acid donates a proton.
+ OH–
H3N—CH2—COO– H2N—CH2—COO–
Zwitterion Negative ion
at pI pH > pI
Charge: 0 Charge: 1−
Amino Acids as Acids
19. 19
In solutions more acidic than the pI,
The COO− in the amino acid accepts a proton.
+ H+
+
H3N—CH2—COO– H3N—CH2—COOH
Zwitterion Positive ion
at pI pH< pI
Charge: 0 Charge: 1+
Amino Acids as Bases
20. 20
pH and Ionization
H+ OH−
+ +
H3N–CH2–COOH H3N–CH2–COO– H2N–CH2–COO–
positive ion zwitterion negative ion
(at low pH) (at pI) (at high pH)
21. Aas have multiple pKa’s due to multiple ionizable groups
Acid-base Properties
pK1 ~ 2.2
(protonated below 2.2)
pK2 ~ 9.4
(NH3
+ below 9.4)
pKR
(when applicable)
23. Titration of Glycine
pK1
[cation] = [zwitterion]
pK2
[zwitterion] = [anion]
First equivalence point
Zwitterion
Molecule has no net charge
pH = pI (Isoelectric point)
pI = average of pKa’s = ½ (pK1 + pK2)
pIglycine = ½ (2.34 + 9.60) = 5.97
Animation
24. 24
Electrophoresis: Separation of
Amino Acids
In electrophoresis, an electric current is used to separate
a mixture of amino acids, and
The positively charged amino acids move toward the
negative electrode.
The negatively charged amino acids move toward the
positive electrode.
An amino acid at its pI does not migrate.
The amino acids are identified as separate bands on
the filter paper or thinlayer plate.
26. 26
CH3 CH3
+ | |
H3N—CH—COOH H2N—CH—COO–
(1) (2)
Which structure represents:
A. Alanine at a pH above its pI?
B. Alanine at a pH below its pI?
Learning Check
27. 27
CH3 CH3
+ | |
H3N—CH—COOH H2N—CH—COO–
(1) (2)
Which structure represents:
A. Alanine at a pH above its pI? (2)
B. Alanine at a pH below its pI? (1)
Solution
30. 30
The Peptide Bond
A peptide bond
Is an amide bond.
Forms between the carboxyl group of one amino acid
and the amino group of the next amino acid.
O CH3 O
+ || + | ||
H3N—CH2—C—O– + H3N—CH—C—O–
O H CH3 O
+ || | | ||
H3N—CH2—C—N—CH—C—O– + H2O
peptide bond
35. 35
Write the three-letter abbreviations and names of the
tripeptides that could form from two glycine and one
alanine.
Learning Check
36. 36
Write the names and three-letter abbreviations of the
tripeptides that could form from two glycine and one
alanine.
Glycylglycylalanine Gly-Gly-Ala
Glycylalanylglycine Gly-Ala-Gly
Alanylglycylglycine Ala-Gly-Gly
Solution
37. 37
Learning Check
What are the possible tripeptides formed from one
each of leucine, glycine, and alanine?
38. 38
Solution
Tripeptides possible from one each of leucine,
glycine, and alanine
Leu-Gly-Ala
Leu-Ala-Gly
Ala-Leu-Gly
Ala-Gly-Leu
Gly-Ala-Leu
Gly-Leu-Ala
39. 39
Learning Check
Write the three-letter abbreviation and name for the
following tetrapeptide:
CH3
│
CH3 S
│ │
CH–CH3 SH CH2
│ │ │
CH3 O H CH2 O H CH2O H CH2 O
+ │ ║ │ │ ║ │ │ ║ │ │ ║
H3N–CH–C–N–CH–C–N–CH–C–N–CH–CO–
46. 46
Secondary Structure – Alpha Helix
The secondary structures of proteins indicate the
three-dimensional spatial arrangements of the
polypeptide chains.
An alpha helix has
A coiled shape held in place by hydrogen bonds
between the amide groups and the carbonyl
groups of the amino acids along the chain.
Hydrogen bonds between the H of a –N-H group
and the O of C=O of the fourth amino acid down
the chain.
48. 48
Secondary Structure – Beta
Pleated Sheet
A beta-pleated sheet is a secondary structure that
Consists of polypeptide chains arranged side by
side.
Has hydrogen bonds between chains.
Has R groups above and below the sheet.
Is typical of fibrous proteins such as silk.
51. 51
Indicate the type of protein structure as
1) primary 2) alpha helix
3) beta-pleated sheet 4) triple helix
A. Polypeptide chains held side by side by H bonds.
B. Sequence of amino acids in a polypeptide chain.
C. Corkscrew shape with H bonds between amino
acids.
D. Three peptide chains woven like a rope.
Learning Check
52. 52
Indicate the type of protein structure as:
1) primary 2) alpha helix
3) beta-pleated sheet 4) triple helix
A. 3 Polypeptide chains held side by side by H bonds.
B. 1 Sequence of amino acids in a polypeptide chain.
C. 2 Corkscrew shape with H bonds between amino
acids.
D. 4 Three peptide chains woven like a rope.
Solution
54. 54
The tertiary structure of a protein
Gives a specific three dimensional shape to the
polypeptide chain.
Involves interactions and cross links between
different parts of the peptide chain.
Is stabilized by
Hydrophobic and hydrophilic interactions.
Salt bridges.
Hydrogen bonds.
Disulfide bonds.
Tertiary Structure
59. 59
Select the type of tertiary interaction
1) disulfide 2) ionic
3) H bonds 4) hydrophobic
A. Leucine and valine
B. Two cysteines
C. Aspartic acid and lysine
D. Serine and threonine
Learning Check
60. 60
Select the type of tertiary interaction as:
1) disulfide 2) ionic
3) H bonds 4) hydrophobic
A. 4 Leucine and valine
B. 1 Two cysteines
C. 2 Aspartic acid and lysine
D. 3 Serine and threonine
Solution
64. 64
Identify the level of protein structure as:
1) Primary 2) Secondary
3) Tertiary 4) Quaternary
A. Beta-pleated sheet
B. Order of amino acids in a protein
C. A protein with two or more peptide chains
D. The shape of a globular protein
E. Disulfide bonds between R groups
Learning Check
65. 65
Identify the level of protein structure
1. Primary 2. Secondary
3. Tertiary 4. Quaternary
A. 2 Beta-pleated sheet.
B. 1 Order of amino acids in a protein.
C. 4 A protein with two or more peptide chains.
D. 3 The shape of a globular protein.
E. 3 Disulfide bonds between R groups.
Solution
67. 67
Protein hydrolysis
Splits the peptide bonds to give smaller peptides
and amino acids.
Occurs in the digestion of proteins.
Occurs in cells when amino acids are needed to
synthesize new proteins and repair tissues.
Protein Hydrolysis
68. 68
Hydrolysis of a Dipeptide
In the lab, the hydrolysis of a peptide requires acid or
base, water and heat.
In the body, enzymes catalyze the hydrolysis of
proteins.
+
H3N CH COH
OCH3
+
H2O, H
+
++
heat,
CH2
OH
H3N CH C
O
N
H
CH C
O
OH
CH3
CH2
OH
CH C
O
OHH3N
69. 69
Denaturation involves
The disruption of bonds in the secondary, tertiary
and quaternary protein structures.
Heat and organic compounds that break apart H
bonds and disrupt hydrophobic interactions.
Acids and bases that break H bonds between polar
R groups and disrupt ionic bonds.
Heavy metal ions that react with S-S bonds to form
solids.
Agitation such as whipping that stretches peptide
chains until bonds break.
Denaturation
71. • Ribonuclease is a small protein that
contains 8 cysteins linked via four
disulfide bonds
• Urea in the presence of 2-
mercaptoethanol fully denatures
ribonuclease
• When urea and 2-mercaptoethanol
are removed, the protein
spontaneously refolds, and the
correct disulfide bonds are reformed
• The sequence alone determines the
native conformation
• Quite “simple” experiment, but so
important it earned Chris Anfinsen
the 1972 Chemistry Nobel Prize
Ribonuclease
Refolding
Experiment
72. 72
What are the products of the complete hydrolysis of
the peptide Ala-Ser-Val?
Learning Check
73. 73
The products of the complete hydrolysis of the
peptide Ala-Ser-Val are
alanine
serine
valine
Solution
74. 74
Tannic acid is used to form a scab on a burn. An egg
is hard boiled by placing it in boiling water. What is
similar about these two events?
Learning Check
75. 75
Acid and heat cause the denaturation of protein.
They both break bonds in the secondary and tertiary
structures of proteins.
Solution