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AMINO ACIDS,
PEPTIDES AND
PROTEINS

BIO149

Prof. Ureah Thea A. Sevilla

Amino Acids

Amino acids are the building blocks of proteins.

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Stereoisomerism in Amino Acids

The configuration of the
common L-amino acids can
be related to the
configuration of Lglyceraldehyde (in the
Fischer projection)

Essential Amino Acids

T - Threonine

F - Phenylalanine

V - Valine

W - Tryptophan

M - Methionine

H - Histidine

I - Isoleucine

R Arginine

L - Leucine

(conditionally essential)

K - Lysine

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Non-Essential Amino Acids

G - Glycine

D - Aspartic acid

A - Alanine

E - Glutamic acid

P - Proline

C - Cysteine

S - Serine

Q - Glutamine

Y - Tyrosine

N - Asparagine

Precursors of Non-Essential Amino Acids

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Aliphatic, Non-Polar R-groups

O
GLYCINE Gly

H2N

OH
O

H3 C

OH

ALANINE Ala

NH2
CH3 O
H3C

VALINE - Val
OH

NH2

Aliphatic, Non-Polar R-groups

O
H3C

OH
CH3 NH2

H
N

LEUCINE - Leu

O
OH

CH3 O
H3C

OH

PROLINE - Pro

NH2

ISOLEUCINE - Ile

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Uncharged Polar R-groups

O
HO

OH
NH2

HS

SERINE - Ser

OH
NH2

CH3 O
HO

Cysteine - Cys
OH

NH2

THREONINE - Thr

Uncharged Polar R-groups

O
H3C

OH
NH2

METHIONINE- Met

OH
NH2

O
H2N

NH2

GLUTAMINE - Gln
OH

NH2

ASPARAGINE - Asn

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Aromatic R-groups
O
OH
O

NH2

OH

PHENYLALANINE - Phe

NH2

NH

TRYPTOPHAN - Trp

O
OH
NH2

HO

TYROSINE - Tyr

Positively Charged R-groups

O
H2N

OH

H
N

NH2

LYSINE - Lys
N
NH2
HN

OH
NH2

HISTIDINE - His

NH

OH
NH2

ARGININE - Arg

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Negatively Charged R-groups

O
HO

OH
O

NH2

ASPARTIC ACID - Asp

O

HO

OH
NH2

GLUTAMIC ACID - Glu

Common Amino Acids

Amino Acid

Symbol

Glycine
Alanine
Valine
Leucine
Isoleucine
Proline
Serine
Threonine
Cysteine
Methionine
Asparagine
Glutamine

Gly - G
-A
Val - V
Leu - L
Ile - I
Pro - P
Ser - S
Thr - T
Cys - C
Met-M
Asn - N
Gln - Q

pK1
(COOH)
2.34
2.34
2.32
2.36
2.36
1.99
2.21
2.11
1.96
2.28
2.02
2.17

pK2
(NH2)
9.60
9.69
9.62
9.60
9.68
10.96
9.15
9.62
8.18
9.21
8.80
9.13

pK R Group

13.60
13.60
10.28

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Common Amino Acids

pK2
(NH2)
9.13
9.11
9.39
8.95
9.04
9.17

pK R
Group

Phe - F
Tyr - Y
Trp-W
Lys- K
Arg - R
His - H

pK1
(COOH)
1.83
2.20
2.38
2.18
2.17
1.82

Aspartate

Asp - D

1.88

9.60

3.65

Glutamate

Glu - E

2.19

9.67

4.25

Amino Acid

Symbol

Phenylalanine
Tyrosine
Tryptophan
Lysine
Arginine
Histidine

10.07
10.53
12.48
6.00

Different Ionic Forms of an Amino Acid

Zwitterion equal number of positive and negative charges.

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Titration
curve for
Glycine
Isoelectric point
= pH at which the
zwitterion form can
be found

pKas and the Isoelectric pH

pH = pKa + log [S]/[A]
when [S] = [A]
then pH = pKa
pKa1

pKa2

PI = (pKa1 + pKa2)

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Peptide bond between amino acids

The Peptide Bond Has Partial Double

Bond Character

(a)

(b)

The actual peptide bond is best

described as a resonance hybrid
of the forms in (a) and (b).

Significantly, all of the atoms associated

with the peptide group are coplanar,
rotation about CN is restricted, and the
peptide is distinctly polar.

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Peptides

Commercially important Oligopeptides

Aspartame
Glutathione

Polypeptides

Quick Review
They are amino acids that are not synthesized
by the body and must be obtained from
dietary sources.
a) Polar amino acids
b) Essential amino acids
c) Aromatic amino acids
d) Non-essential amino acids

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Quick Review
The following are amino acids except
a)

b)
c)
d)

Asparagine
Cysteine
Tyrosine
Guanine

Quick Review
True or False. All amino acids exhibit
stereoisomerism.
Which enantiomer form is used to construct
proteins L- or D-?

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Quick Review
Which of the following is not an essential amino
acid?
a)
b)
c)
d)

Tryptophan
Tyrosine
Arginine
Lysine

Quick Review
How many water molecules are formed from the
linkage of 70 amino acids?
a)
b)

c)
d)

69
70
35
71

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Quick Review
The type of bond that connects amino acids
together
a)
b)
c)

d)

peptide bond
hydrogen bond
glycosidic bond
phosphodiester bond

Quick Review
The type of chemical reaction involved in linking
sugar units together
a)
b)

c)
d)

Combustion reaction
Hydrolysis reaction
Condensation reaction
Decomposition reaction

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Quick Review
Which of the following statement is true?
a)

b)

c)

d)

Aspartame is a protein.
Aspartame is a food sweetener that consists
of carbohydrates.
Aspartame cannot be taken by diabetic
persons.
Aspartame is a dipeptide.

Proteins

Proteins are the most diverse biological molecule

(structural, nutritious, enzyme, transport,
communication, and defense proteins)
Proteins are organic compounds composed of one
or more chains of amino acids

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Types of Protein

Transport ex. hemoglobin

Storage ex. myoglobin
Contractile ex. actin and myosin
Structure or support ex. keratin and collagen
Defense ex. immunoglobulins
Regulatory insulin
Biological catalyst enzymes

Levels of Protein Structure

Primary structure
The

unique amino acid sequence of a protein

Secondary structure
The

polypeptide chain folds and forms hydrogen bonds

between amino acids

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Levels of Protein Structure

Tertiary structure
A

secondary structure is compacted into structurally

stable units called domains
Forms a functional protein

Quaternary structure
Some

proteins consist of two or more folded

polypeptide chains in close association
Example: hemoglobin

Hemoglobin structure

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Myoglobin structure

Myosin and Actin Structures

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Immunoglobulin Structure

a Protein primary structure: Amino acids bonded as a polypeptide

chain.

Fig. 3-17a, p. 45

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Regular Secondary Structure:

The -helix and -sheets

Alpha helix

Beta Sheets

Keratins A coiled coil (2structure)

Two important classes of proteins that have similar
amino acid sequences and biological function are
called - and -keratins.
-keratins - major proteins of hair and fingernails
and compose a major fraction of animal skin.
-keratins - contains much more -sheet structure
-keratins are found mostly in birds and reptiles, in
structures like feathers and scales.

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Such twisted cables are stretchy and

flexible, but in different tissues -keratin is
hardened, to differing degrees, by the
introduction of disulfide cross-links within
the several levels of fiber structure.

Collagen A Triple Helix (2structure)

Collagen is the most abundant single protein in most

vertebrates. In large animals, it may make up a third of
the total protein mass.
Collagen fibers form the matrix, or cement, material in
bone, on which the mineral constituents precipitate. These
fibers constitute the major portion of tendons. A network
of collagen fibers is an important constituent of skin.
Basically, collagen holds most animals together.
The basic unit of the collagen fiber is the tropocollagen
molecule, a triple helix of three polypeptide chains, each
about 1000 residues in length.

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Plantar Fascia - highly organized, dense

networks of collagen fibers.

Plantar fascia is a connective tissue

band which extends from the heel
bone to the ball of the foot. It
supports a tremendous amount of
weight. As the heel lifts off the
ground when walking, the plantar
fascia tightens, like a dynamic
rope under tension.
This increases the rigidity of the foot and improves
efficiency as the calf muscles contract and propel the
body forward.

Plantar Fascia - highly organized, dense

networks of collagen fibers.

The plantar fascia is composed of highly

organized, dense networks of collagen fibers.
Collagen is essentially woven together (or coiled) in
strands, and then organized into bundles. This
arrangement is what increases the strength of the
plantar fascia.

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Silk Fibroin sheets (2structure)

Silkworm fibroin contains long regions of

antiparallel sheet, with the polypeptide chains
running parallel to the fiber axis. The sheet
regions comprise almost exclusively multiple
repetitions of the sequence
[Gly - Ala - Gly - Ala - Gly - Ser - Gly
- Ala - Ala - Gly - (Ser - Gly - Ala - Gly
- Ala - Gly)]

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Silk Fibers

Protein Tertiary Structure

Protein tertiary
structure: A chains
coils, sheets, or both
fold and twist into
stable, functional
domains such as
barrels or pockets.

Fig. 3-17c, p. 45

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Globular
Proteins

Protein Quaternary Structure

Protein quaternary structure:

two or more polypeptide
chains associated as one
molecule.

Fig. 3-17d, p. 45

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Enzymes

Most enzymes are proteins.

They function as catalyst in biological reactions.
Enzymes are globular proteins - their molecules are
round in shape.
Each enzyme has a specific catalytic action.
Their normal activity depends on their environment.
- Abnormal conditions cause reduced activity

Classification of Enzymes
Class

Type of reaction catalyzed

Oxidation- reduction reactions; transfer of
Oxidoreductases
electrons
Transferases
Transfer of functional groups
Hyrolysis reactions; transfer of functional
Hydrolases
groups to water
Addition to double bonds or reverse to that
Lyases
reaction
Transfer of groups within molecules to yield
Isomerases
isomeric forms
Formation of C-C, C-S, C-O and C-N bonds by
Ligases
condensation reaction coupled to ATP
cleavage

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Oxidoreductase
COO-

NAD+

COO-

NADH + H+

HO C H

O C

CH2

CH2

malate dehydrogenase

COO

COO-

Transferase
OH
H

H
OH H

OH

HO

OH

HO

OH

C O-

ADP

H
--

Rn-1

H
OH H

OH
H

OH

Hydrolase
H

--

OH
H

OPO 3-2
ATP

OH

C O-

Rn-1

Lyase
H2C

H OH

COOaconitase

HO

C
H2C

COOCOO-

H2C
C
HC

COOCOOCOO-

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Isomerase

COO-

-OOC
C
H

-OOC
C

C
COO-

Ligase

O
O

ATP
C
H3C

O
C

CO2

C
-O

O-

C
CH2

O
C

ADP
O-

Enzymes catalysis

Enzymes have an area - usually thought of as a

pocket-shaped gap in the molecule - which is called
the active site.
Some enzymes are found inside cells (intracellular
enzymes), and some - especially digestive enzymes
- are released so they have their effects outside the
cell (extracellular enzymes).

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(Only) the substrate (or substrates) fits/fit into

the active site.

How Enzymes Work

A catalyst works simply by lowering the energy

barrier of a reaction.

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The Lock and Key Model

(Emil Fischer, 1894)
The lock-and-key model
proposes that an enzymesubstrate pair is like a lock
and key. It explains the
specificity of enzymesubstrate pairs.
-substrate binds to that
portion of the enzyme with a
complementary shape

The Induced Fit Model

(Daniel Koshland, 1958)
The model proposes that
distortion of the enzyme
and the substrate is an
important event in catalysis.
-binding of the substrate
induces a change in the
conformation of the enzyme
that results in a
complementary fit

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Effect of Temperature on Enzyme Activity

Catalyst: -amylase structure

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Quick Review
Actin and myosin
a)

b)
c)
d)

regulate functioning of tissues.

provide structure and support in tissues.
are involve in the cells response to stimuli.
are responsible for muscle movement.

Quick Review
Keratin and collagen
a)
b)
c)

d)

regulate functioning of tissues.

provide structure and support in tissues.
are involve in the cells response to stimuli.
are responsible for muscle movement.

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Quick Review
Protein structure which occur commonly helical and
pleated forms
a)
b)
c)
d)

primary structure
secondary structure
tertiary structure
quaternary structure

Quick Review
When proteins such as enzymes are denatured, it
means that it
a)
b)

c)
d)

has lost its native form.

was cut into component amino acids.
is in the inactive form.
is converted into the active form.

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Quick Review
An example of quaternary structure of protein
a)

b)
c)
d)

Keratin
Collagen
Myoglobin
Hemoglobin

Quick Review
Proteins have tertiary structures because of
a)
high number of hydrogen bonding and covalent
bonding in the polypeptide
b)
high number of hydrophobic R-groups in the
polypeptide
c)
high number of hydrophilic R-groups in the
polypeptide
d)
low number of hydrogen bonding and covalent
bonding in the polypeptide

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References:
Voet, Voet and Pratt. Principles of Biochemistry,
3rd edition, 2008, John Wiley & Sons, Inc.
Garret, R. and Grisham, C., Biochemistry 4 th
edition, 2010, Brooks/Cole, Cengage Learning.

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