UERMMMCI College of Medicine

Subject: Biochemistry
Date: (Thursday) June19, 2014
Title: (1.1) Amino Acid & Protein Organization
Lecturer: Dr. Catherine C. Donato
Batch/section: 2018A
Sem/ A.Y.: 1st/A.Y. 2014-2015
Transcribers: Ang, Angeles, Aover, A. Aquino, and R.Aquino
Trans Subject head: Barona, F. (09164082972/fonsecabarona@gmail.com)
Evangelista, A. (09369390879 / AlanAEvangelista@gmail.com)

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I.
Outline
A. Introduction to Proteins and Amino acids
B. Amino Acids
1. Structure
2. Functional Groups
3. Properties
C. Proteins
1. Structural Organization
2. Disease applications
D. Modifications

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II.
Objectives
At the end of the lecture, the student should be able to
know the...

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1. General functions of proteins

2. Structural composition of amino acids
3. Chemical properties of amino acids
4. Hierarchy of protein organization
5. Modifications on proteins and their functions
III.

Structure: muscle protein eg. Collagen and

elastin in bone matrix and ligaments; tubulin
and actin in fibers of microtubules and
filaments
Movement and mechanical support: eg.
Myosinand actin for muscle contraction
Defense: antibodies, interferons for immune
protection; coagulation proteins to prevent
excessive blood loss on an injury to the
vascular system
Regulation: enzymes, hormones; repressor
and enhancer transcription factors control
gene transcription
Transport: hemoglobin and myoglobin for
oxygen transport; excretion of wastes and
toxic compounds
Storage: Mb, ferritin
Stress Response: hormones

B. AMINO ACIDS
1. Structure

Lecture

A. INTRODUCTION TO PROTEINS AND AMINO ACIDS

Amino acids are the building blocks of Proteins
o The alphabet of protein structure
20 common Amino acids
Essential: arginine, histidine, isoleucine,
leucine, lysine, methionine, phenylalanine,
threonine, tryptophan, and valine
o Essential Amino acids are not readily
produced by the body hence are derived from
the diet
Functions of proteins
o Catalysis:Eg. Enzymesthat catalyze chemical
reactions

Figure 1: Amino acid structure

Aptly named because of the amino group (NH3+)

and the carboxylic acid (COO-)
-carbon
o asymetric
Chiral Carbon: a Carbon atom with four different
substituents bonded to it
o Carboxylic acid group
o Amino group

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A.Y. 2014-2015

Biochemistry | Amino Acid & Protein Organization

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Hydrogen atom
The fourth valency is linked to a specific
chemical group (Functional group)

Stereocenter: amino acids exists in two

configurationsdue to difference in spatial
arrangement of the four substituents of -carbon
o L-configuration and D-configuration
o Most of amino acids in body are Lconfiguration The fourth valency is linked to a
specific chemical group (Functional group)

A. Alkyl Group
H
O

H
+

NH3
H

Alanine (Ala, A)
Methyl group
Non-polar
Aliphatic

H3C
+

NH3

H3C

H3C

NH3

O
CH3

H
O

H3C

CH3
H

Under physiologic conditions, -amino group is

protonated while the carboxylic acid group is
unprotonated
A central -carbon to which a carboxylic acid
group, an amino group, and a hydrogen atom are
covalently bonded. The fourth valency is linked to
a specific chemical group
R side-chain (functional group)
o Chemical characteristics
Polar
Polar uncharged
Non-polar
o Side-chain properties
Sulfo-amino acids
Aromatic amino acids
Basic amino acids
Acidic amino acids

NH3

**Take note: asymmetric, chiral and stereocenter

properties do not apply to glycine because it has two
hydrogen atoms bonded to the -carbon

H3C

HO

NH3

H3C

2. Functional Groups
Constitute the R-side chain in the basic
amino acid structure
Determines the properties of the amino acid

NH3

Threonine (Thr, T)
Hydroxyl containing side
chain
Polar uncharged

C. Sulfur Group
O
H
O
HS

A.Y. 2014-2015

Leucine (Leu, L)
Isobutyl (-carbon)
Non-polar
Aliphatic

B. Hydroxyl Group
H
Serine (Ser, S)
O
hydroxymethyl
Polar uncharged

HO

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Valine (Val, V)
Isopropyl group
Non-polar
Aliphatic

Isoleucine (Ile, I)
Isobutyl (-carbon)
Non-polar
Aliphatic

NH3

Glycine (Gly, G)
No side chain
Non-chiral
Non-polar
Aliphatic

Cysteine (Cys, C)
thiolmethyl
Polar uncharged

NH3

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Biochemistry | Amino Acids and Protein Organization

O
H
H3C

O
S

NH3

Methionine (Met, M)
Methyl ethyl thiol ether
Non-polar
Aliphatic

G. Aromatic Group
O
O

Phenylalanine (Phe, F)
Benzene ring
Non-polar
Aliphatic

NH3

D. Carboxylic Acid Group

O

Glutamic acid (Glu, E)

H
O

HO

Tyrosine (Tyr, Y)
Phenol group
Polar uncharged

H
O

NH3

NH3

O
O

Additional carboxyl side

chain
Negatively charged

Aspartic acid (Asp, D)

H
O

Additional carboxyl side

chain
Negatively charged

H
N
H

O
-

+
NH3

Tryptophan (Trp, W)
indole
Non-polar
Aliphatic

NH3

E. Amide Group
O
H
O

+
NH3

Glutamine (Gln, Q)
Amide containing side
chain
Polar uncharged

H. Looped/Cyclic Group
Proline (Pro, P)
O
H2+
Imino acid side chain
N
Non-polar
Aliphatic
O

NH2

O
O

H
O

H2N

+
NH3

Asparagine (Asn, N)
Amide containing side
chain
Polar uncharged

F. Amino Group
+

Lysine (Lys, K)

H3N

NH3

N-butyl amine on Carbon

Positively charged
Arginine (Arg, R)

O
H
H2N

NH

Guanidino group
Positively charged

NH3

+
NH2

Table 1: Common Amino acids

3. Properties
Group
Negatively
charged
(acidic)
Positively
charged
(basic)
Polar
uncharged
(hydrophilic;
easily
excitable)
Nonpolar
aliphatic
(hydrophobic;
linear)

Histidine (His, H)
H
N
O
+

N
H

H3N

Imidazole group
Positively charged

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Aromatic

Characteristic
Additional carboxyl
group

Amino Acids
Glutamic acid,
Aspartic acid

Guanidino group
Imidazole
e amino grp
OH containing

Arginine
Histidine
Lysine
Serine,
threonine
Asparagine,
glutamine
Cysteine
Glycine
Proline
Alanine, valine,
leucine,
isoleucine
Methionine

Amide group
Thiol group
No side chain
Imino group
Hydrophobic alkyl
group
Thioether sulfur
atom
Bulky aromatic side
chains

Phenylalanine,
tyrosine,
tryptophan

Table 2: Summary of Amino acids accdg. to Property

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Biochemistry | Amino Acids and Protein Organization

a. Negatively Charged / Acidic Group / Carboxylic

Acid Group
o Amino acids whose side chains

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contain a carboxylic acid group with a

low pKa values that easily lose their
protons (Devlin, 7th Ed.)
With extra carboxylic acid group

electrons with a pKa of 9.5 and exists as

NH3+ at pH values near neautrality.
(Devlin, 7th Ed.)
amino acids whose R groups contain
nitrogen atoms, therefore they are also
part of the amino group
at physiologic pH, they are usually in their
acidic form and are positively charged.
(Devlin, 7th Ed.)

*Note:
Histidine contains a side chain that has a
five-member heterocyclic structure called the
imidazole group (pKa = 6.0 in solution)
at physiologic pH, the side chains of lysine
and arginine are fully ionized and positively
charged while histidine is weakly basic and
the free amino acid is largely uncharged
when histidine is incorporated into a protein,
the imidazole side chain can either be
positively charged or neutral depending on
the ionic environment provided (this is an
important property of histidine that contributes
to the role it plays in the functioning of
proteins such as myoglobin)

c. Hydrophilic / Polar Uncharged

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At physiologic pH, these amino acids are

uprotonated and negatively charged

b. Positively Charged / Basic Group / Amino Acid

Group
o the amino group has an unshared pair of

Asparagine replace amino group with

carboxyl group = aspartate
Glutamine replace amino group with
carboxyl group = glutamate

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Tyrosine is also included in the hydroxyl

group because of the presence of OH in
its benzene ring
Cysteine contains a thiol group
Methionine also has thiol group but
is nonpolar
Although undissociated cysteine is
nonpolar, cysteine in dissociated
form is polar. (Devlin, 7th Ed.)

d. Hydrophobic / Nonpolar

Nonpolar amino acids includes those with

large, aliphatic, aromatic, or undissociated
sulfur groups. (Devlin, 7th Ed.)
Aliphatic: alanine, isoleucine,
leucine, valine
Aromatic: phenylalanine, tryptophan
Sulfur groups: cysteine
(undissociated), methionine
Hydrophobic/nonpolar amino acids have
the same number of methyl groups, the
difference lies in their branching
Aliphatic group membrane proteins tend
to cluster together within the membrane
because of hydrophobicity (hydrophobic
interactions)
Proline its a-amine is a secondary
amine with its nitrogen having 2 covalent
bonds to carbon
Constrains the rotational freedom
around the -carbon and polypeptide chain conformations
With unique characteristic that alters
flexibility of proteins
Can be inserted at certain folding
because of the presence of imino
group

e. Aromatic Group

Most hydrophobic most hydrophilic

(phenylalaninetryptophantyrosine)

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Biochemistry | Amino Acids and Protein Organization

Ionic State
o All amino acids are at least dibasic acids
(presence of -amino acid and -carboxyl
groups), the ioncionic state being a function of
pH
o Net charge of the amino acid depends on the
environment pH

Zwitterions
o Amino acids are dipolar at neutral pH with a
net charge of 0

Quantitative measure of pKa amino

acids are weak acids and therefore do
not completely dissociate; instead of pH,
we get its isoelectric pH/point (pI),
unique to each AA because of functional
groups; denotes electric charge of
amino acids; manner in which we
measure how proteins dissociate

Isoelectric point (pI)

o pH at which a particular molecule or surface
carries no net electric charge

*Basic Amino acid pI = (pK2+pK3 or highest pK)/2

*All the rest = (pK1+pK3 or highest pK)/2
Figure 2: Zwitterionic form of Amino acids

Acid-Base Properties
o Titration
Quantitative method of knowing the
concentration of a chemical solution
(analyte)
Via a reagent of known concentration
(strong alkali solutions ie. NaOH)known
as the titrant
to obtain titrable properties and to
separate amino acid

Acid dissociation constant Ka

o Quantitative measure of the strength of an
acid
o pKa = -log10Ka
o Importance
1) activity of enzymes and the stability of
proteins
2) essential for working with buffers

pK values
o Each amino acid has its own unique pK values
due to the R side chains
o Can be used to identify amino acids and how
they dissociate

Figure 3: Ionization state as a function of pH

Figure 4: Titration Curve of Alanine

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A.Y. 2014-2015

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Biochemistry | Amino Acids and Protein Organization

Table 5: pKa values for polyfunctional amino acids

Figure 5: Titration curve of Lysine

Buffering capacity
o Buffers ability to resist change in pH when

C. PROTEINS
1. Structural Organization
The four levels of protein structure are
distinguished from one another by the degree of
complexity in the polypeptide chain
a) Primary
DNA-dependent: sequence of amino acids
determined by genes
o sequence determines protein folding,
folding determines protein function
involves release of water (dehydration
reaction)
limits rotation against each other because
they are coplanar
semi-rigid character is very important in the
higher order of protein structure
less steric hindrance if the trans form is
favored

small amounts of acids and bases are added

Figure3:6:pK
Table
pKvalues
valuesfor
forionizable
ionizablegroups
groups
Dissociating groups
carboxyl

pKa range
3.5 43.5 - 43.5 -4

Non -carboxyl
4 4.8
Imidazole
6.5 7.4
SH
8.5 - 9
OH
9.5 10.5
-amino
8-9
-amino
9.8 10.4
guanidinium
12
Table 4: pKa range of dissociating groups

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Figure 7: Primary structure of proteins

Bond(s):
o Peptide chain
Linkage of amino acids by covalent bonds
-carboxyl group bonds with -amino
group of another amino acid via
dehydration process
These peptide bonds have a partial
double-bond character

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Biochemistry | Amino Acids and Protein Organization

 Bond(s):
o Hydrogen bonds
Maintains structural integrity
Forms between 2 non-adjacent AAs
During coiling, they are at close proximity
Structure(s):
o -helix
most common type of secondary structure
right-handed
o -pleats
anti-parallel orientation
Figure 8: Peptide bond formation

Disulfide bonds
formed between the thiol (SH) groups of
two cysteines (oxidation reaction)

Structure(s):
o Linear
NH3+ to COO- (left to right)
Partial double bond
Coplanar, limits rotation
Cis/Trans configuration
Cis: R chains from 2 aa on the same
plane; less stable due to steric
hindrance
Trans: R chains from 2 AAs on
opposite planes; more stable, hence
more favored
b) Secondary
Spatial arrangement of polypeptide chain
(regular, repeating structural elements) that
functions to stabilize the protein
Van der Waals forces is seen in the
secondary structure; hydrogen bonds
maintain structural integrity of the proteins
together with the Van der Waals forces

Figure 10: Peptides structural organization (-helix; -pleats)

c) Tertiary
Highest order for a monomeric protein and
biologically active

Figure 11: Types of interactions in a tertiary structure

Figure 9: Secondary structure of proteins

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Bond(s):
o Between distant or non-adjacent amino acids
o Salt Bridges
Also known as ionic bridges

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Biochemistry | Amino Acids and Protein Organization

Formed between two charged/ionic

(positive - NH3+ and negative - COO- ) side
chains
Opposites attract

Intra-disulfide bonds
Formed between 2 cysteine residues

Hydrogen bonds
Formed between polar (hydrophilic)
residue chains

Hydrophobic interactions
Formed when 2 nonpolar groups are
attracted by a mutual repulsion of water
Includes van der Waals interaction
between 2 nonpolar aas

Structure(s):
o 3D arrangement of a single polypeptide chain
Interactions between R side chains are
important in tertiary folding of proteins
d) Quaternary
Interactions between 2 or more subunits
(tertiary structures) of multimeric proteins

Figure 12: Quaternary structure of hemoglobin consisting of 4

polypeptides

Bond(s):
o Non-covalent bonds
Maintained by the same forces active in
tertiary structures; hydrophobic interaction
is the main stabilizing force
Structure(s):
o Homomeric
subunits are the same; multiple copies of
the same protein
o Heteromeric
made up of different subunits

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Unstructured Proteins
o Proteins that do not follow the classical
structure; lack a stable folded structure
Chemical structure can be recognized
from the amino acid sequences of their
polypeptide
Biologic relevance the binding strength
of unstructured proteins to their binding
partners is generally weaker than for a
binding of a molecule to a preformed state
This property is often advantageous
as weak and transient interactions are
required for many biological
processes
2. Disease Applications (abnormalities in protein
structure)
Sickle Cell Anemia
o Caused by a single amino acid substitution
The underlying problem in sickle cell
anemia is that the valine for glutamic acid
substitution results in hemoglobin
tetramers that aggregate into arrays upon
deoxygenation in the tissues
This aggregation leads to deformation of
the red blood cell into a sickle-like shape
making it relatively inflexible and unable
to traverse the capillary beds
Alzheimers Disease
o Caused by protein misfolding
Due to the accumulation of abnormally
folded amyloid beta protein in the brain
*Proteins usually fold and unfold many
times as they carry out their tasks, and
each cycle is an opportunity for it to
misfold. When that happens, the body
generally destroys and discards the
useless protein. But when that process
fails, misfolded proteins can form the
gummy amyloid plaques
Creutzfeldt-Jakob disease
o Caused by abnormal protein
foldingsynthesis of prions death of brain
cells release of more prions to infect other
brain cells
o Prions can survive in nerve tissue, such as
the brain or spinal cord, for a very long time,
even after death

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Biochemistry | Amino Acids and Protein Organization

 Phenylketonuria (PKU)
o An autosomal recessive disorder that results
from an accumulation of phenylalanine
o

Treatment approach: intake of

phenylalanine to prevent mental retardation
and other metabolic complications; tyrosine is
also essential in the diet of PKU patients

D. MODIFICATIONS
Protein synthesis occurs by a process known as
translation. After translation, proteins are further
modified, a process called posttranslational
modification.
These modifications change the structure of
amino acids in a way that may serve a regulatory
function, target or anchor the protein in
membranes, enhance a proteins association with
other proteins, or target it for degradation.
1. Hydroxylation/Oxidation
o Addition of a hydroxyl group to the protein
o Often facilitated by enzymes called
hydroxylases
o Principal residue to be hydroxylated is proline
o Important in making collagen flexible and rigid
(addition of OH to Proline)
2. Carboxylation
o Addition of a carboxyl group to the protein
o Important in blood clotting, bone growth, and
extraosseus calcification
o Mediated by calcium ions by binding to the two
negatively charged carboxyl groups of
gamma-glutamate and 2 additional negatively
charged groups provided by phospholipids in
the cell membrane
3. Denaturation
o Process of unfolding secondary, tertiary, and
quaternary protein structures (protein loses its
structure and function)
o Accomplished by change in environmental
conditions:
a change in pH
an increase in temperature
an increase in ionic strength from
concentrated inorganic salts
the addition of an organic solvent

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4. Regulation
a) Phosphorylation
o is the addition of a phosphate (PO43)
group to a protein or other organic
molecule
o turns many protein enzymes on and off,
thereby altering their function and activity
(eg. Phosphorylation of an OH group on
serine, threonine, or tyrosine by a protein
kinase introduces a large, bulky,
negatively charged group that can alter
the activity of a protein
o Stimulates an enzyme
b) Acetylation
o the addition of an acetyl group, either at
the N-terminus of the protein or at lysine
residues
o Inhibits an enzyme
c) ADP-ribosylation
o is the transfer of an ADP-ribose from NAD
to an arginine, glutamine, or a cysteine
residue on a target protein in the
membrane (primarily in leukocytes,
skeletal muscles, brain, and testes). This
modification may regulate the activity of
these proteins
o These reactions are involved in cell
signaling and the control of many cell
processes, including DNA repair and
apoptosis

IV.
Guide questions
1. What are the polar amino acids? What are the nonpolar amino acids?
- Polar amino acids are: Cysteine, Serine,
Threonine, Tyrosine, Asparagine and Glutamine.
(Cysters Serine Threonine play TAG)
- *The non-polar amino acids are: Tryptophan,
Proline, Isoleucine, Glycine, Leucine,
Phenylalanine, Alanine, Valine, Methionine. (Three
pretty Indian girls like patient and valiant men.)
2. What are the types of interactions occur in tertiary
protein structures?
- Salt bridges, intra-disulfide bridges, hydrogen
bonding, hydrophobic interactions
3. What is a Zwitterion?
- The form of amino acids where the positive charge
on the amino group balances the negative charge
on the carboxyl group, which results in a net
charge of zero.

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Biochemistry | Amino Acids and Protein Organization

V.
Sources
Devlin, T. (2011). Textbook of Biochemistry with Clinical
Correlations, Wiley-Liss 7th Edition. New York: A
John Wiley & Sons, Inc., Publication.
Lehninger, A., et al. (2008). Principles of Biochemistry,
Worth Publishers 5th Edition. New York: W H.
Freeman and Company, Publication.

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Biochemistry | Amino Acids and Protein Organization