Proteins Biochemistry (Biokimia Protein) 2020 version

1
Amino Acids and Proteins
Proteins and Amino Acids
(Amino Acids as Acids and Bases)
Copyright © 2007 by Pearson Education, Inc.
Publishing as Benjamin Cummings

Proteins are molecular tools
They are a diverse and complex group of
macromolecules
Protein Diversity
From McKee and McKee, Biochemistry, 5th Edition, © 2011 by Oxford University Press
Proteins

4
Functions of Proteins
 Proteins perform many different functions in the body.
TABLE 19.1

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
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
Examples of Amino Acids
H
+ │
H3N—C—COO−
│
H glycine
CH3
+ │
H3N—C—COO−
│
H alanine

8
Types of Amino Acids
Amino acids are classified as
 Nonpolar (hydrophobic)
with hydrocarbon side
chains.
 Polar (hydrophilic) with
polar or ionic side chains.
 Acidic (hydrophilic) with
acidic side chains.
 Basic (hydrophilic) with
–NH2 side chains.
Nonpolar Polar
Acidic Basic

9
Amino Acids Classification Table

10
Nonpolar Amino Acids
A nonpolar amino acid has
 An R group that is H, an alkyl group, or aromatic.

11
Polar Amino Acids
A polar amino acid has
 An R group that is an alcohol, thiol, or amide.

12
Acidic and Basic Amino Acids
An amino acid is
 Acidic with a carboxyl R group (COO−).
 Basic with an amino R group (NH3
+).
Basic Amino Acids
D E

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
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
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
• 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

 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

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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
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
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)

 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)

Table 3-1
Note 3-letter and
1-letter
abbreviations
Amino acid
organization chart

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

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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.

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Electrophoresis
With an electric current, a mixture of lysine, aspartate,
and valine are separated.

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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
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

28
Essential amino acids
 Must be obtained
from the diet.
 Are the ten amino
acids not
synthesized by the
body.
 Are in meat and
diary products.
 Are missing (one or
more) in grains and
vegetables.
Essential Amino Acids
TABLE 19.3
Copyright © 2007 by Pearson Education, Inc Publishing as Benjamin Cummings

29
Formation of Peptides
Copyright © 2007 by Pearson Education, Inc

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

31
Formation of A Dipeptide

32
Learning Check
Write the dipeptide Ser-Thr.
OH CH3
| |
CH2 O HCOH O
+ | ║ + | ║
H3N─CH─C─O – + H3N─CH─C─O–
Ser Thr

34
Naming Dipeptides
A dipeptide is named with
 A -yl ending for the N-terminal amino acid.
 The full amino acid name of the free carboxyl group
(COO-) at the C-terminal end.

35
Write the three-letter abbreviations and names of the
tripeptides that could form from two glycine and one
alanine.
Learning Check

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
Learning Check
What are the possible tripeptides formed from one
each of leucine, glycine, and alanine?

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
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–

40
Solution
Ala-Leu-Cys-Met Alanylleucylcysteylmethionine
CH3
│
CH3 S
│ │
CH–CH3 SH CH2
│ │ │
CH3 O H CH O H CH2O H CH2 O
+ │ ║ │ │ ║ │ │ ║ │ │ ║
H3N–CH–C–N–CH–C–N–CH–C–N–CH–CO–
Ala Leu Cys Met

41
Protein Structure: Primary and
Secondary Levels

Protein Diversity
From McKee and McKee, Biochemistry, 5th Edition, © 2011 by Oxford University Press
Proteins

43
Primary Structure of Proteins
The primary structure of a protein is
 The particular sequence of amino acids.
 The backbone of a peptide chain or protein.
Ala─Leu─Cys─Met
CH3
SH
CH2
CH3
S
CH2
CH2CH O
O-
CCH
H
N
O
CCH
H
N
O
CCH
H
N
O
CCHH3N
CH3
CH3CH

44
Primary Structures
The nanopeptides oxytocin and vasopressin
 Have similar primary structures.
 Differ only in the amino acids at positions 3 and 8.

45
Primary Structure
of Insulin
Insulin
 Was the first protein to
have its primary structure
determined.
 Has a primary structure of
two polypeptide chains
linked by disulfide bonds.
 Has a chain A with 21
amino acids and a chain B
with 30 amino acids.

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.

47
Secondary Structure – Alpha Helix

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.

49
Secondary Structure: β-Pleated
Sheet

50
Secondary Structure: Triple Helix
A triple helix
 Consists of three alpha
helix chains woven
together.
 Contains large amounts
glycine, proline, hydroxy
proline, and
hydroxylysine that contain
–OH groups for hydrogen
bonding.
 Is found in collagen,
connective tissue, skin,
tendons, and cartilage.

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
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

53
Protein Structure: Tertiary and
Quaternary Levels

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

55
Tertiary Structure
 The interactions
of the R groups
give a protein
its specific
three-
dimensional
tertiary
structure.

56
Tertiary Structure
TABLE 19.5

57
Globular Proteins
Globular proteins
 Have compact,
spherical shapes.
 Carry out synthesis,
transport, and
metabolism in the
cells.
 Such as myoglobin
store and transport
oxygen in muscle.
Myoglobin

58
Fibrous Proteins
Fibrous proteins
 Consist of long, fiber-like shapes.
 Such as alpha keratins make up hair, wool, skin,
and nails.
 Such as feathers contain beta keratins with large
amounts of beta-pleated sheet structures.

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
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

61
Quaternary Structure
The quaternary structure
 Is the combination of two or
more tertiary units.
 Is stabilized by the same
interactions found in tertiary
structures.
 Of hemoglobin consists of two
alpha chains and two beta
chains. The heme group in
each subunit picks up oxygen
for transport in the blood to the
tissues.
hemoglobin

62
Summary of Protein Structure

63
Summary of Protein Structures

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
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

66
Protein Hydrolysis and Denaturation

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
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
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

70
Denaturation of protein occurs
when
 An egg is cooked.
 The skin is wiped with
alcohol.
 Heat is used to cauterize
blood vessels.
 Instruments are sterilized in
autoclaves.
Applications of Denaturation

• 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
What are the products of the complete hydrolysis of
the peptide Ala-Ser-Val?
Learning Check

73
The products of the complete hydrolysis of the
peptide Ala-Ser-Val are
alanine
serine
valine
Solution

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
Acid and heat cause the denaturation of protein.
They both break bonds in the secondary and tertiary
structures of proteins.
Solution

Proteins Biochemistry (Biokimia Protein) 2020 version

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