COLLEGE OF MEDICINE AND HEALTH

SCIENCES
SCHOOL OF MEDINCE AND PHARMACY
DEPARTMENT OF MEDICAL BIOCHEMISTRY,
MOLECULAR BIOLOGY AND GENTICS

Amino Acids,
Peptides
&
Proteins
To be delivered by:
1. Prof. Mala
2. Dr. Mariama
3. Dr. Samson
4. Mr. Mugisha
Learning Objectives

• To be familiar with the buildings

blocks and molecular structure of
proteins
• To relate the ability of protein to fold
correctly to the functions of that
protein

2
 General Structure of Amino Acids

Has 4 different groups attached to

α- carbon (which is C-atom next
to COOH). CO2H
These 4 groups are :
H2N C H
•Amino group;
R
•COOH group
•Hydrogen atom and
•Side Chain (R) 3
• Amino acids found in proteins are of L-
configuration, this means that the
amino group to the left and the
hydrogen to the right of the a-carbon

• D-amino acid
L-amino acid
 Amino Acid Structure
Amino acids may be
characterized as ,  , or 
amino acids depending on the
location of the amino group in
the carbon chain.

 are on the carbon adjacent

to the carboxyl group.
 are on the 2nd carbon
 on the 3rd carbon from the
carboxyl group

5
 amino acids
Amino acids found
in proteins are
amino acids.
The amino group is
always found on
the carbon
adjacent to the
carboxyl group

6
 Classifications:

Amino acids can be classified by different

classification:

• Chemical (R-group) classification.

• Nutritional classification.
• Metabolic classification.
• Reaction classification (Charge
properties).
Classification: R-group (side chain)
• The R groups, also called side chains,
make each AA unique and distinctive.
• R groups are different in their size,
charge, hydrogen bonding capability
and chemical reactivity.
• Aas are grouped as (1) non-polar,
hydrophobic; (2) polar, neutral; (3)
basic; and (4) acidic.
Non-polar and hydrophobic AAs

• R groups are non-polar, hydrophobic

aliphatic or aromatic groups.
• R groups are uncharged.
• AAs are insoluble in H2O.
 Polar and uncharged AAs
• R groups are polar: -OH, -SH, and
-NH2.
• R groups are highly reactive.
• AAs are soluble in H2O, that is,
hydrophilic.
 Basic AAs
• R groups have one or more -NH2
(amino groups) than carboxyl groups

• R groups are positively charged at

neutral pH (=7.0).
• AAs are highly hydrophilic.
 Acidic AAs

• R groups have two –COOH (Carboxyl

groups) and only one amino group
per molecule.
• R groups are negatively charged at
physiological pH (=7.4).
• AAs are soluble in H2O.
Aspartic acid glutamic acid
(Asp or D) (Glu or E)
 Special amino acids - Gly

• optically inactive

+
H3N
-
OOC

C H

H
 Amino Acids and Optical
Isomers
• Except for glycine, all amino acids have a chiral
carbon atom. Therefore they can have optical
isomers
• The amino acids found in proteins are all
levarotatory or L forms.

18
 Special amino acids - Pro

• Having a ring structure and imino

group
 Special amino acids - Cys
• active thiol groups to form disulfide bond
 2. Nutritional classification:
They are classified into three groups:
• Essential amino acids: They are amino
acids which cannot be synthesized in the
body and must be taken in diet
• Semi essential amino acids: They are
amino acids required in the food of growing
children not in the food of adult as histidine
and arginine.
• Non essential amino acids: can be
synthesized inside the body.
Nutritional classification
 Building blocks of proteins
– Body uses 20 different amino acids to make proteins
 9 of the 20 amino acids must be consumed in the diet (essential
amino acids; EAA)
– Body cannot make them on its own
Leucine Tryptophan Methionine
Isoleucine Threonine Lysine
Valine Histidine Phenylalanine
 Other 11 amino acids are not essential (NEAA)
– Can be made from other amino acids in the diet
 Some NEAAs can become EAAs under certain conditions
– Infants have different needs for growth
– Defects in amino acid metabolism
• Tyrosine can become essential in individuals with phenylketonuria (PKU), an inborn error
of phenylalanine metabolism
22
Memory Aid for Essential Amino Acids

Any Help In Learning These Little

Molecules Proves Truly Valuable

Arginine –Histidine – Isoleucine –

Leucine – Threonine- Lysine-
Methionine –Phyenylalanine-
Tryptophan –Valine
Essential Amino Acids
 Essential Amino Acids
Essential amino acids Non-Essential amino acids
• Arginine  Alanine (from pyruvic acid)
• Histidine  Asparagine (from aspartic acid)
• Isoleucine  Aspartic Acid (from oxaloacetic
• Leucine acid)
• Lysine  Cysteine (from methionine)
• Methionine  Glutamic Acid (from oxoglutaric
• Phenylalanine acid)
• Threonine  Glutamine (from glutamic acid)
• Tryptophan  Glycine (from serine and threonine)
• Valine  Proline (from glutamic acid)
 Serine (from glucose)
 Tyrosine (from phenylalanine)
 Essential Amino Acids

Complete protein Incomplete protein

• Contains all 10  Lack one of more of the

essential amino acids essential amino acids

• Proteins derived from  Most vegetable proteins

animal sources are are incomplete proteins
complete proteins
 Beans are an exception
• Beans contain some to this generalizations
complete protein as 26
well
There are 20 different amino acids in polypeptides synthesized on ribosomes.

“Relax, no you don’t, you just

MG I HAVE TO LEARN THE need an awareness of the
NAMES OF ALL 20 !?!?” http://commons.wikimedia.org/wiki/File:Amino_Acids.svg
 Standard Amino Acids

• Building blocks of proteins

• More then 300 AA have been described
• Only 20 AA are found in mammalian tissue
• These 20 AA are called primary or standard
AA
NB:
-Amino acids found in proteins are of L-
configuration
-Amino acids found in proteins are amino acids
 Non Standard Amino Acids

• These Amino acids do not take part in

the protein synthesis but play
important role in the body.
 Non Standard Amino Acids

• Citrulline
• Ornithine
• Taurine
• DOPA
• GABA
 Amino acid not found in proteins:
• L-Ornithine is an intermediate of urea cycle . It is formed from
arginine
• L- citrulline is intermediate of urea cycle . It is formed from
ornithine
• Homoserine is an intermediate in methionine metabolism. It is
formed from serine.
• GABA: γ amino butyric acid :is an inhibitor neurotransmitter
• DOPA: Dihydroxyphenylalanine : Is formed from tyrosine and
precursor for biosynthesis of epinephrine and norepinephrine
• β alanine : occurs in coenzyme A , Pantothenic acid and it is
also formed during degeneration pyrimidine nucleotides

Selenocysteine is an amino acid containing selenium ( trace

element). It is considered as the 21st amino acid since it is
coded by the stop codon UGA. Examples of proteins containing
selenocysteine are glutathione peroxidase enzyme and
5'deiodinase .
 3. Metabolic classification:

According to the fate of carbon skeleton :

• Glucogenic amino acids: give glucose inside

the body as glycine, alanine, aspartic and
glutamic.

• Ketogenic amino acid: gives ketone bodies

as leucine.

• Glucogenic and ketogenic amino acids:

They give both glucose and ketone bodies as
lysine, tryptophan, tyrosine, phenylalanine and
isoleucine.
Peptide
Peptide and peptide bond
A peptide bond is a covalent bond
formed between the carboxyl group of
one AA and the amino group of its next
AA with the elimination of one H2O
molecule.
Peptides can be extended by adding
multiple AAs through multiple peptide
bonds in a sequential order.
dipeptide, tripeptide, oligopeptide, polypeptide

AAs in peptides are called as residues.

 Peptide
 Made up of chains of amino acids;
classified by number of amino acids in a
chain
• Peptides: fewer than 50 amino acids
- Dipeptides: 2 amino acids
- Tripeptides: 3 amino acids
- Polypeptides: more than 10 amino
acids
• Proteins: more than 50 amino acids
- Typically 100 to 10,000 amino acids
linked together
Biologically active peptides
Glutathione (GSH)

Glutamic acid cystein glycine

 H2O2 2GSH NADP+

GSH
peroxidase GSH reductase

2H2O GSSG NADPH+H+

As a reductant to protect nucleic acids and

proteins from toxin by discharging free radical
or H2O2
 Peptides
• Peptide hormones secreted from glands
– Somatostatin
– Thyrotropin-release hormone, Antidiuretic
hormone
– Insulin, Glucagon
 thyrotropin-release hormone

Pyroglutamic acid histidine prolinamide

 Neuropeptide
name amino acid sequence
oxytocin Cys-Tyr-Ile-Gln-Asn-Cys-Pro-Leu-Gly-NH2
└──S───S──┘
Vasopresin Cys-Tyr-Phe-Gln-Asn-Cys-Pro-Arg-Gly-NH2
└──S────S──┘
Met-enkephalin Tyr- Gly-Gly-Phe-Met

Leu-enkephalin Tyr- Gly-Gly-Phe-Leu

Atrial natriuetic Ser-Leu-Arg-Arg-Ser-Ser-Cys-Phe-Gly-Gly-Arg-

factor Met-Asp-Arg-Ile-Gly-Ala-Gln-Ser-Gly-Leu-Gly-Cys-
Asn-Ser-Phe-Arg-Tyr
Substance P Arg-Pro-Lys-Pro-Bln-Phe-Phe-Gly-Leu-Met-NH2

Bradykinin Arg-Pro-Pro-Gly-Phe-Ser-Pro-Phe-Arg
Molecular Structures of
Proteins
 Overview
• Proteins are composed of AAs.
• Distinctive properties of proteins are
determined by AA compositions, AA
sequences as well as the relative
positions of AAs in space.
• Proteins need well defined structures
to function properly. Their structures
are organized in a hierarchy format,
that is, primary, secondary, tertiary
and quaternary structure.
Primary Structure

• The primary structure of proteins is

defined as a linear sequence of AAs
along the protein chain.
• The AA sequence must be written
from the N-terminus to the C-terminus.
• Peptide bonds are responsible for
maintaining the primary structure.
 Primary structure of insulin

• Two peptides of 21 and 30 AAs

• Two inter-chain -S-S- bonds
• One intra-chain -S-S- bond
 Sickle-cell of anemia
Patient’s symptoms:
Cough, fever and headache, a
tinge of yellow in whites of eyes,
visible pale mucous membrane,
enlarged heart, well developed
physically, anemic, much less
RD cells

clinical test:
The shape of the red cells was
very irregular, large number of
thin, elongated, sickle-shaped
and crescent-shaped forms.
Difference in primary structure of Hb

• Sequence analysis showed the

difference in AA sequence.

Hb A : Val-His-Leu-Thr-Pro-Glu-Glu-Lys-
Hb S : Val-His-Leu-Thr-Pro-Val -Glu-Lys-

• This is the first case of molecular

disease identified in history. Further
studies showed that the AA variation is
due to the gene mutation.
Secondary Structure
The secondary structure of a protein is
defined as a spatial relationship of
adjacent amino acids residues (1st and
4th).
-helix
• A helical conformation is right-handed.

• 3.6 AAs per turn

• Only one chain is involved
 0.54 nm
3.6 个残基
C原子

O原子

N原子

第n＋3个肽键的H原子 H原子

第n个肽键的O原子

肽链走向

0.5 nm

（a） （b）
 -pleated sheet

• Between 2 or more separate polypeptide

chain
 -pleated sheet parallel
2 chain runs in same direction
 -pleated sheet anti-parallel.
2 chain runs in opposite direction
Protein conformational
disorders
 α-helix
β-sheet
Conformational change

the starting point is the natural protein

folded in the native and active conformation
normal protein is rich in α-helix
conformations (folded structure)
the end-point is the same protein adopting
prevalent β-sheets structure
it is disease-associated protein (misfolded
structure)

Aggregation

Gain of toxic activity Loss of biological

function
Mad cow disease and prion proteins
• A transmissible, inheritable neural
disease, destroying brain tissues by
converting them to a spongy appearance
• the conformational changes of prion
protein (PrP)
– PrPc: -helix, water soluble
– PrPsc: -sheet, water insoluble
Structural changes of prion protein

PrPc PrPsc
The conformational change
 a change in the secundary or tertiary structure of a normal protein
without alteration of the primary structure
 the biological function of a protein depends on its tridimensional
structure

Protein conformatinal disorders (PCD)

 diverse diseases arise from protein misfolding
 the conformational change may promote the disease by either gain of
a toxic activity or by the lack of biological
function of the natively folded protein
Protein misfolding causes disease!

 the hallmark event in PCD is a formation of β-sheet

conformations
 the production of β-sheets is usually stabilized by protein
oligomerization and aggregation
 the misfolded protein self-associates and becomes deposited in
amyloid-like aggregates in diverse organs, inducing tissue damage
and organ dysfunction
Diseases Protein involved
Alzheimer‘s disease Amyloid-β
Parkinson disease α-Synuclein
Diabetes type 2 Amylin
Amyotrophic lateral sclerosis Superoxide dismutase
Haemodialysis-related amyloidosis β2-microglobulin

Cystic fibrosis Cystic fibrosis transmembrane

regulator
Sickle cell anemia Hemoglobin
Hungtington disease Huntingtin
Creutzfeldt-Jakob disease Prion protein
Amyloidosis Ten other proteins
Tertiary Structure

The final arrangement of a single

polypeptide chain ( resulting from
spatial relationship of more distant
amino acid residues)

Overall 3-dimensional shape of protein

Four types of interactions stabilize the
protein tertiary structure.
• hydrophobic interaction
• ionic interaction
• hydrogen bond and van der Waals
interaction
• Disulfide bonds
Interactions stabilizing proteins
• 2 forms of tertiary structure

• Globular protein:
Compact form ， soluble in water;
including enzymes, transporters,
receptors, regulators, …
• Fibrous protein:
highly elongated/extended; insoluble
in water; including collage, elastin, α-
keratin, …
 The amino acid sequence determines the three-dimensional conformation of a protein.

Proteins are commonly described as

either being fibrous or globular in nature.
Fibrous proteins have structural roles whereas globular
proteins are functional (active in a cell’s metabolism).

In globular proteins the hydrophobic R groups are folded into the core of the molecule, away from the
surrounding water molecules, this makes them soluble. In fibrous proteins the hydrophobic R groups
are exposed and therefore the molecule is insoluble.
Myoglobin (Mb)

• Located in muscle
to supply O2
• 153 AAs
• 75% of structure
is -helix in 8
regions.
• the interior almost
entirely nonpolar
residues
Chaperon

Chaperones are large, multisubunit

proteins that promote protein foldings
by providing a protective environment
where polypeptides fold correctly into
native conformations or quaternary
structures.
 How does chaperon work?

• Reversibly bind to the hydrophobic

portions to advance the formation of
correct peptide conformations
• Bind to misfolded peptides to induce
them to the proper conformations
• Assist the formation of correct
disulfide bonds
Quaternary Structure

The quaternary structure is defined

as the spatial arrangement of
multiple subunits of a protein.
• Proteins need to have two or more
polypeptide chains to function properly.
• Each individual peptide is called
subunit.
• These subunits are associated through
H-bonds, ionic interactions, and
hydrophobic interactions.
• Polypeptide chains can be in dimer,
trimer .., as well as homo- or hetero-
form.
 Hemoglobin(Hb)
• O2 transporter in erythrocyte
• 2  subunits, 141 AAs
2  subunits, 146 AAs
• 4 subunits are maintained together
by 8 pairs of ionic interactions.
• Each subunit contains one heme
group.
Structure of hemoglobin
From primary to quaternary structure
 Hemoglobin

• Hb can bind O2 reversibly, just like Mb.

• Both  and  chains are strikingly
similar to that of Mb.
Structural similarity of Mb and Hb
Oxygen-disassociation curve
• The saturation Y
is defined as the
fractional
occupancy of all
O2-binding sites.
• Y varies with the
concentration of
O2 . The
equilibrium
constants for Hb
subunits are
different.
 Binding behavior of Hb
• Hb has a lower affinity for O2 than Mb
(lower P50).
• The O2–binding to the 1st subunit
enhances the O2–binding to the 2nd and
3rd subunits. Such process further
enhances the O2–binding to the 4th
subunit significantly.
• Hb binds O2 in a positive cooperative
manner, which enhances the O2
transport.
Global structural change

The quaternary
structure of Hb
changes markedly
for the tense (T)
form to the relaxed
(R) form upon
oxygenation.
 Allosteric effect
• The behavior that the ligand-binding
to one subunit causes structural
changes and stimulate the further
binding to other subunits is termed
as allosteric effect.
• The protein is allosteric protein, and
the substrate is allosteric effector.
• Allosteric effect can be influenced by
activators as well as inhibitors.
 Concerted versus sequential

 

   

1  

non-oxygenized Hb  
（T conformation） oxygenized Hb
（R conformation）
 

     

  
Protein classification
• Constituents
simple protein =amino acid residues only.
E.g Albumin, globulins, globins
conjugated protein = amino acids +
prosthetic groups

Prosthetic group is non-protein part,

binding to protein by covalent bond. This
group can be carbohydrates, lipids, nucleic
acids, phosphates, pigments, or metal ions.
Biological Functions of
Proteins
 off

on

Regulation Movement

proteins B

Signaling Catalysis

Immune Transport
Usage of proteins Nothing can compare with the versatility of proteins.
Their functionality and usage in organisms is
unrivalled.

Function Description Key examples

There are thousands of different enzymes to catalyse specific
Catalysis Rubisco
chemical reactions within the cell or outside it.
Actin and myosin together cause the muscle contractions used
Muscle contraction
in locomotion and transport around the body.
Tubulin is the subunit of microtubules that give animals cells
Cytoskeletons
their shape and pull on chromosomes during mitosis.
Tensile Fibrous proteins give tensile strength needed in skin, tendons,
collagen
strengthening ligaments and blood vessel walls.
Plasma proteins act as clotting factors that cause blood to turn
Blood clotting
from a liquid to a gel in wounds.
Transport of Proteins in blood help transport oxygen, carbon dioxide, iron
nutrients and gases and lipids.
Usage of proteins Nothing can compare with the versatility of proteins.
Their functionality and usage in organisms is
Function unrivalled. Description Key examples
Membrane proteins cause adjacent animal cells to stick to each
Cell adhesion
other within tissues.
Membrane proteins are used for facilitated diffusion and active
Membrane
transport, and also for electron transport during cell respiration
transport
and photosynthesis.
Some such as insulin, FSH and LH are proteins, but hormones are
Hormones Insulin
chemically very diverse.
Binding sites in membranes and cytoplasm for hormones,
Receptors neurotransmitters, tastes and smells, and also receptors for light rhodopsin
in the eye and in plants.
Histones are associated with DNA in eukaryotes and help
Packing of DNA
chromosomes to condense during mitosis.
This is the most diverse group of proteins, as cells can make
Immunity immunoglobulins
huge numbers of different antibodies.
Biotechnologically has allowed us to use proteins in industry examples are:
•enzymes for removing stains in clothing detergent
•monoclonal antibodies for pregnancy tests
•insulin for treating diabetics
•Disease treatments
Physical and Chemical
Properties of Proteins
§5.1 Amphoteric
Isoelectric point
• AAs in solution at certain pH are
predominantly in dipolar form, fully ionized
but without net charge due to -COO- and -
NH3+ groups.
• This characteristic pH is called isoelectric
point, designated as pI.
• pI is determined by pK, the ionization
constant of the ionizable groups.
 R CH COOH
NH2

R CH COOH +OH -
R CH COO - +OH -
R CH COO-
NH3+ +H+ NH3+ +H+ NH2

pH<pI pH=pI pH>pI

cation amphoteric anion

• Side-chains of a protein have many
ionizable groups, making the protein
either positively or negatively
charged in response to the pH of the
solution.
• The pH at which the protein has zero
net-charge is referred to as
isoelectric point (pI).
 COOH COO- COO-
+ OH- + OH-
P P P
+ H+ +
+ H+
NH3+ NH3 NH2

cation amphoteric anion

pH < pI pH = pI pH > pI

• pI of most protein is ~ 5.0, and negatively charges in

body fluid (pH7.4)
• pI > 7.4: basic proteins: protamine, histone
• pI < 7.4: acidic proteins: pepsin
§5.3 Protein denaturation

The process in which a protein loses

its native conformation under the
treatment of denaturants is referred to
as protein denaturation.

• The denatured proteins tend to

- decrease in solubility;
- increase the viscosity;
- lose the biological activity;
- lose crystalizability;
- be susceptible to enzymatic digestion.
• Cause of denaturation
the disruption of hydration shell and
electric repulsion
• Denaturants
physical: heat, ultraviolet light, violent
shaking, …
chemical: strong acids, bases, organic
solvents, detergents, …
• Applications
sterilization, lyophilization
 Renaturation

• Once the denaturants are removed, the

denatured proteins tend to fold back to
their native conformations partially or
fully.

• The renatured proteins can restore their

biological functions.
Renaturation