OUR LADY OF FATIMA UNIVERSITY

COLLEGE OF PHARMACY Learning Outcomes

• Demonstrate knowledge on structures, functions,
synthesis and levels of organization of proteins.
Proteins • To understand the processes associated with
proteins and enzymes.
PHARMACEUTICAL BIOCHEMISTRY • To understand the clinical aspects related to proteins
and enzymes.
PBIO211

Proteins Amino Acids

• Naturally-occurring , unbranching polymer of amino • An organic compound with amino and carboxyl
acids units groups attached to the same carbon
• Most abundant molecule (15%) in cells after water • Side chains vary in size, shape, charge, acidity,
• From the Greek word “Proteios” meaning primary functional groups, hydrogen bonding ability and
importance
chemical reactivity
• These molecules were first described and named by
the Swedish chemist Jӧns Jakob Berzelius in 1838. – 20 standard amino acids
• However, proteins’ central role in living organisms was – >700 amino acids
not fully appreciated until 1926, when James B. are known
Sumner showed that the enzyme urease was a protein

Amino Acids Amino Acids: Nomenclature

• Non-Polar • Common names are currently used
• R-groups are non-polar, hydrophobic, insoluble in H2O • Three letter abbreviations – widely used for
• When present in proteins, they are located in the
naming
interior where there is no polarity – First letter is compulsory and capitalized followed by
next to letters not capitalized except for Asparagine
• Polar (Asn), Glutamine (Gln) and Tryptophan (Trp).
• R-groups are polar • One letter symbols – commonly used for
• Neutral – contains polar but neutral side chains
comparing amino acid sequences of proteins
– Usually the first letter of the name
• Acidic – contains carboxyl group as part of side chains
– When more than one amino acid has the same letter,
• Basic – contains amino group as part of side chains the most abundant gets the 1st letter
Non-Polar Amino Acids Non-Polar Amino Acids

Non-Polar Amino Acids

Polar Neutral Amino Acids

 Polar Neutral Amino Acids

Polar Acidic Amino Acids Polar Basic Amino Acids

Essential Amino Acids Chirality and Amino Acids

• Phenylalanine • Threonine • Four different groups are attached to the a-
• Valine • Histidine carbon atom in all of the standard amino acids
except glycine
• Typtophan • Isoleucine
– In glycine R-group is hydrogen
• Methionine • Lysine
• Therefore 19 of the 20 standard amino acids
• Arginine • Leucine contain a chiral center
• Chiral centers exhibit enantiomerism (left- and
right- handed forms)
• Each of the 19 amino acids exist in left and right
handed forms
 Chirality and Amino Acids Acid-Base Properties of Amino Acids
• The amino acids found in nature as • In pure form, amino acids are white crystalline solids
well as in proteins are L isomers • Most amino acids decompose before they melt
• The rules for drawing Fischer • Not very soluble in water
projection • Exists as Zwitterion: An ion with (+) and (-) charges on
– The –COOH group is put at the top, the same molecule with a net zero charge
the R group at the bottom to
position the carbon chain vertically – Carboxyl groups give-up a proton to get negative charge
– The –NH2 group is in a horizontal – Amino groups accept a proton to become positive
position
– Positioning the –NH2 on the left is L
isomer, on the right for D isomer

Amino Acids: Characteristics Amino Acids: Characteristics

• Amino Acids can act as both acids and bases • Isoelectric Point (pI)
– In a free amino acid, carboxyl group and amino – pH at which a particular molecule or surface
group of the general structure are charged at carries no net electrical charge
neutral pH – carboxylate portion negatively – At a pH below pI, they carry a net positive charge
charged and amino group positively charged – At a pH above pI, they carry a net negative charge
– Without charged groups on their side chains, they – For an amino acid, pI can be calculated from the
exist in neutral solution as zwitterions with no net pKa’s of this molecule
charge
– Formula:
• Has equal positive and negative charges

Cysteine: A Chemically Unique Amino

Acid
• Cysteine: the only standard
amino acid with a sulfhydryl
group (-SH grp)
• Cysteine in the presence of
mild oxidizing agents
dimerizes to form a cystine
molecule.
– Cystine – two cysteine
residues linked via a covalent
disulfide bond.
 Amino Acids: Characteristics
• Amino Acids exists in a three-dimensional
structure
– A frequently encountered chiral center in
biomolecules is a carbon atom with four different
groups bonded to it
– Occurs in almost all amino acids
– Non-superimposable mirror-image forms

Aliphatic Amino Acids Aliphatic Amino Acids

Glycine (Gly) – amino ethanoate) Alanine (Ala) – amino propionate Valine (Val) – amino isovalerate Leucine (Leu) – amino isocaproate

Aliphatic Amino Acids Amino Acids with Alcohol

Serine (Ser) – amino b-methyl Threonine (Thr) – amino b-
Isoleucine (Ile) – amino b-methyl valerate propionate methylbutyrate
 Amino acids with Additional Acidic Amino acids with Amides of Acidic
Group Amino Acids
Aspartic Acid (Asp) – amino Glutamic Acid (Glu) – amino Asparagine (Asn) – amino b- Glutamine (Gln) – amino g-
succinate glutarate succinamide glutaramide

Basic Amino Acids Basic Amino Acids

Arginine (Arg) – amino d-
Lysine (Lys) – e-amino caproate guanidine valerate Histidine (His) – amino b-imidazole propionate

Sulfur Containing Amino Acids Sulfur containing Amino Acids

Cysteine (Cys H) – amino b- Cystine (Cys-Cys) – amino b-
mercapto propionate mercapto propionate Methionine (Met) – amino g-methyl mercapto butyrate
 Aromatic Amino Acids Aromatic Amino Acids
Phenylalanine (Phe) – amino b- Tyrosine (Tyr) – amino b-[p-
phenyl propionate hydroxyphenyl] Tryptophan (Trp) – amino b-indol propionate

Secondary Amino Acids Peptide Bonds

Proline (Pro) – 2-carboxy Hydroxyproline (Hypro) – 2- • Under proper conditions, amino acids can bond
pyrollidine carboxy-4-hydroxy-pyrollidine
together to produce an unbranched chain of
amino acids
• The length of the amino acid chain can vary from
a few amino acids to many amino acids
• Such a chain of covalently-linked amino acids is
called a peptide.

Peptide Bonds Peptides

• Peptides are compounds formed by linking small • Dipeptide: bond between two amino acids
numbers of amino acids, ranging from two to • Oligopeptide: bond between ͠10-20 amino acids
several dozen. • Polypeptide: bond between large number of
amino acids
– The bond is formed between the α-carboxyl group of
one amino acid and the α-amino group of the next • Every peptide has an N-terminal end and a C-
one. Water is eliminated in the process, and the linked
terminal end
amino acid residues remain after water is eliminated
– A bond formed in this way is called a peptide bond
– many amino acids (usually more than a hundred) are
linked by peptide bonds to form a polypeptide chain
 Peptide Nomenclature Isomeric Peptides
• The C-terminal amino acid residue keeps its full • Peptides that contain the same amino acids
amino acid name but present in different order are different
• All of the other amino acid residues have names molecules (constitutional isomers) with
that end in –yl. The –yl suffix replaces the –ine or
different properties
–ic acid ending of the amino acid name, except
for tryptophan, for which –yl is added to the • The number of isomeric peptides possible
name increases rapidly as the length of the peptide
• The amino acid naming sequence begins at the N- chain increases
terminal amino acid residue.
– Ala-Leu-Gly has the IUPAC name of Alanylleucylglycine

Peptide Bonds

Biochemically Important Small

Small Peptides: Hormones
Peptides
• Many relatively small peptides are biochemically
active:
– Hormones, Neurotransmitters, Antioxidants
• Small Peptide Hormones:
– Best-known peptide hormones: Oxytocin and Vasopressin
– Produced by the Pituitary Gland
– Nonapeptide (Nine Amino Acid residues) with six of the
residues held in the form of a loop by a disulfide bond
formed between two cysteine residues
Small Peptides: Neurotransmitters Small Peptides: Antioxidant
• This is a tripeptide present in high levels in most cells
• Regulator of oxidation-reduction reactions
• Glutathione is an antioxidant and protects cellular contents
from oxidizing agents such as peroxides and superoxides
– Highly reactive forms of oxygen often generated within the cell
in response to bacterial invasion
• Unusual structural feature – Glu is bonded to Cys through
the side-chain carboxyl group

Proteins Structure Levels

• Naturally-occurring , unbranching polymer of at least • Primary Structure
40 amino acids units
– order in which the amino acids are
– Polypeptide and protein are often used interchangeably
used to describe protein covalently linked together
– The terms polypeptide and protein are often used – one-dimensional first step in
interchangeably used to describe a protein specifying the three-dimensional
– Several proteins with >10,000 amino acid residues are structure of a protein
known
– Common proteins contain 400-500 amino acid residues
– Small proteins contain 40-100 amino acid residues
• More than one peptide chain may be present in a
protein:
– Monomeric: a protein with one peptide chain
– Multimeric: a protein with more than one peptide chain

Primary Structure of a Human

Primary Structure of Proteins
Myoglobin
• Proteins of the same organism always same sequence
(cows, pigs, etc.)
• Different sources: Insulin from pigs, cows, sheep,
humans similar

• Due to differences, insulin may show some reaction

over time
• Now human insulin produced from genetically
engineered bacteria
 Structure Levels Secondary Structure of Proteins
• Secondary Structure • The peptide linkages are essentially planar thus
– arrangement in space of the atoms in the peptide
allows only two possible arrangements for the
peptide backbone for the following reasons
backbone
– For two amino acids linked through a peptide bond six
– α-helix and β-pleated sheet arrangements are two atoms lie in the same plane
most common different types – The planar peptide linkage structure has considerable
rigidity, therefore rotation of groups about the C-N
bond is hindered
– Cis-trans isomerism is possible about C-N bond
– The trans isomer is the preferred orientation

Secondary Structure: Beta-Pleated

Secondary Structure: Alpha Helix
Sheets
• A single protein chain • Completely extended amino acid chains
adopts a shape that
resembles a coiled spring • H-bonding between two different chains –
(helix) inter and/or intramolecular
– H-bonding between same • Side chains below or above the axis
amino acid chains – intra
molecular
– Coiled helical spring
– R-group outside of the helix –
not enough room for them to
stay inside

Structure Levels Four Types of Interactions

• Tertiary Structure • Disulfide Bond: Covalent, strong, between two
– complete three- cysteine groups
dimensional • Electrostatic interaxns: Salt Bridge between
arrangement of all the charged side chains of acidic and basic amino
atoms in a protein acids
– Results from the 4 types – -OH, -NH2, -COOH, -CONH2
of interaxns between • H-bonding between polar, acidic, and/or basic R
amino acid side chains (R groups
groups) that are widely – The H must be attached on O, N, or F
separated from each • Hydrophobic interaxns: Between non-polar side
other chains
 Structure Levels Quaternary Structure of Proteins
• Quaternary Structure • Quaternary structure of protein refers to the
– final level of protein organization among the various peptide chains in
structure and pertains to a multimeric protein:
proteins that consist of – Highest level of protein organization
more than one – Present only in proteins that have 2 or more
polypeptide chain polypeptide chains (subunits)
– chains interact with one – Subunits are generally independent of each other –
another non-covalently not covalently bonded
via electrostatic
– Proteins with quaternary structure are often referred
attractions, hydrogen to as oligomeric proteins
bonds, and hydrophobic
interactions – Contain even number of subunits

3D Shape or Gross Structure 3D Shape or Gross Structure

Globular Proteins
Albumin • Soluble in water and salt solution, has no distinctive amino
acids
Globulin • Sparingly soluble in water, soluble in salt solution
Histones • Basic proteins which are soluble in water and salt solutions
Protamines • Strongly basic proteins of relatively low molecular weight
• Associated with nucleic acid and are obtained from large
quantities of ripe sperm cells of fish
Insulin • Regulatory hormone for controlling metabolism
• Promotes glucose transport into skeletal muscle
Antibody • Proteins involved in immune response
Hemoglobin • Protein involved in oxygen transport
Prolamine • Soluble in 70-80% ethanol , insoluble in water

Globular Proteins 3D Shape or Gross Structure

Fibrous Proteins
• Myoglobin • Hemoglobin Collagen • Major protein in connective tissues in vertebrates
– An oxygen storage – An oxygen carrier molecule • Most abundant of all proteins in mammals
molecule in muscles in blood • Major constituent of skin, tendons, blood vessels,
connective tissues
– Monomer – single peptide – Transports oxygen from
chain with one heme unit lungs to tissues Elastin • Present in tendons, arteries and elastic tissues and
ligaments
– Binds one O2 molecule – Tetramer (four peptide
– Has a higher affinity for chains) – each subunit has Keratin • Contains large amount of sulfur as cysteine
oxygen than hemoglobin a heme group Myosin • Found in muscle tissues
– Oxygen stored in – Can transport up to 4 Fibrinogen • Found in blood, necessary for blood clotting
myoglobin molecules oxygen molecules at time
serves as a reserve oxygen – Iron atom in heme
source for working muscles interacts with oxygen
 Fibrous Proteins 3D Shape or Gross Structure
• Alpha-Keratin • Collagen • Membrane proteins
– Provide protective coating – Most abundant proteins in
for organs humans (30% of total body – are associated with cell membranes
– Major protein constituent protein)
of hair, feather, nails, – Major structural material – Insoluble in water – hydrophobic amino acid
horns, and turtle shells in tendons, ligaments, residues on the surface
– Mainly made of blood vessels, and skin
hydrophobic amino acid – Organic component of – Help in transport of molecules across the
residues bones and teeth
– Hardness of keratin – Predominant structure –
membrane
depends upon -S-S- bonds triple helix
– More –S-S- bonds make – Rich in proline (up to 20%)
nail and bones hard – impt to maintain
structure

Major Categories of Proteins based on

Biological Functions
Function
Function Example • Proteins play crucial roles in most biochemical
Storage and Transport Myoglobin, Hemoglobulin, processes
Transferrin, Ferritin • The diversity of functions exhibited by proteins
Structural Collagen, Elastin, Keratin, Fibrin far exceeds the role of other biochemical
molecules
Muscular Contraction Actin, Myosin
• The functional versatility of proteins stems from:
Biological Catalyst Enzymes
– Ability to bind small molecules specifically and
Metabolic Control Hormones strongly
Protective Immunoglobulin, Fibrinogen, – Ability to bind other proteins and form fiber-like
Thrombin structures
– Ability integrated into cell membranes

Major Categories of Proteins based on Major Categories of Proteins based on

Function Function
• Catalytic Proteins: Enzymes are best known for their • Contractile Proteins: Necessary for all forms of movement
catalytic role. – Muscles contain filament-like contractile proteins (actin and
– Almost every chemical reaction in the body is driven by an myosin)
enzyme – Human reproduction depends on the movement of sperm –
• Defense Proteins: Immunoglobulins or antibodies are possible bcoz of contractile proteins
central to functioning of the body’s immune system • Structural Proteins: Confer Stiffness and rigidity
• Transport Proteins: Bind small biomolecules, e.g. – Collagen is a component of cartilage
oxygen and other ligands, and transport them to other – Keratin gives mechanical strength as well as protective covering
locations in the body and release them on demand to hair, fingernails, feathers, hooves
• Messenger Proteins: Transmit signals to coordinate • Transmembrane Proteins: Span a cell membrane and help
biochemical processes between different cells, tissues, control the movement of small molecules and ions
and organs – Have channels – help molecules can enter and exit the cell
– Insulin and Glucagon – regulate carbohydrate metabolism – Transport is very selective – allow passage of one type of
– Human growth hormone – regulate body growth molecule or ion
Major Categories of Proteins based on Major Categories of Proteins based on
Function Composition
• Storage Proteins: Bind (and store) small molecules • Simple Proteins
– Ferritin – an iron-storage protein – saves iron for use in the Composition Example
biosynthesis of new hemoglobin molecules – Made of amino acids Albumin Egg albumin,
– Myoglobin – an oxygen-storage protein present in muscle only serum albumin
• Regulatory Proteins: Often found- embedded in the
exterior surface of cell membranes – act as sites for – general term for Globulin Serum globulin
receptor molecules naturally occurring Prolamine Gliadin, Zein
– Often the molecules that bind to enzymes (catalytic proteins), proteins that yield
thereby controlling enzymatic action Glutein Glutelin
• Nutrient Proteins: Particularly important in the early stages only alpha amino Scleroprotein Collagen,
of life – from embryo to infant acids, or their Elastin, Keratin
– Casein (milk) and Ovalalbumin (egg white) are nutrient proteins derivatives on Histone Histone,
– Milk also provide immunological protection for young mammals
hydrolysis Hemoglobin
Protamine Salmin, sturin

Type Example
Major Categories of Proteins based on Nucleoprotein • Nucleic acids combined with basic proteins such as
histones and protamines
Composition • Upon hydrolysis, yields nucleic acid and histones
• Found in nucleus, microsomes and mitochondria
• Conjugated Proteins: A protein that has one or
more amino acid entities (prosthetic groups) Mucoprotein • Contains large amounts of carbohydrates
present in its structure Glycoprotein • Contains small amounts of carbohydrates
– One or more polypeptide chains may be present Lipoprotein • Conjugated with lecithin, cholesterol and other lipids
– Non-amino acid components – may be organic or • Found in brain, nerve tissues and as structural units of
inorganic prosthetic groups all cells
– Lipoproteins contain lipid prosthetic groups Chromoprotein • Colored proteins
• Hemoglobin and respiratory pigments
– Glycoproteins contain carbohydrate groups
• Contains Mg, Mn, Fe, Zn, Cu, etc.
– Metalloproteins contain a specific metal as prosthetic Metalloprotein
• Tyrosinase, Arginase, Xanthine Oxidase, Ferritin, Alcohol
group
Dehydrogenase
Phosphoprotein • Contains Phosphorus
• Casein in milk, Ovovitellin in egg yolk

Glycoproteins Immunoglobulins
• Conjugated proteins with carbohydrates linked to them: • Glycoproteins produced as a protective response
– Many of plasma membrane proteins are glycoproteins
– Blood group markers of the ABO system are also glycoproteins
to the invasion of microorganisms or foreign
– Collagen and Immunoglobulins are examples molecules – antibodies against antigens
• Collagen – glycoprotein • Immunoglobulin bonding to an antigen via
– Most abundant protein in human body (30% of total body variable region of an immunoglobulin occurs
protein)
– Triple helix structure through hydrophobic interactions, dipole-dipole
– Rich in 4-hydroxyproline (5%) and 5-hydroxylysine (1%) – interaxns, and hydrogen bonds
derivatives
– Some hydroxylysines are linked to glucose, galactose, and their
disaccharides – help in aggregation of collagen fibrils
 Lipoproteins Derived Proteins
• These are conjugated protein that contains lipids in • are obtained when proteins are altered by
addition to amino acids
• Major function: help suspend lipids and transport them chemical or physical methods
through the bloodstream
• Four major classes of plasma lipoproteins: • differ only slightly from source original
– Chylomicrons: Transport dietary triacylglycerols from intestine proteins, & are formed by means of the action
to liver and to adipose tissues
– Very-low density lipoproteins (VLDL): Transport triacylglycerols of heat, acids, alkali, water, enzymes, &
synthesized in the liver to adipose tissue mechanical shock
– Low-density lipoproteins (LDL): Transport cholesterol
synthesized in the liver to cells throughout the body
– High-density lipoproteins (HDL): Collect excess cholesterol from
body tissues and transport it back to the liver for degradation to
bile acids

Derived Proteins Derived Proteins

• Primary Protein Derivatives • Secondary Protein Derivatives
– are proteins that have undergone slight intramolecular – substances formed during the progressive hydrolysis
rearrangement through the hydrolytic action of certain of proteins
physical & chemical agents 1. Proteoses
Proteans • are proteins that have undergone slight intramolecular • (highest molecular weight group)
rearrangement through the hydrolytic action of certain 2. Peptones
physical & chemical agents
• Fibrin from Fibrinogen, Myosan from Myosin • (lower molecular weight than proteoses)
Metaproteins • are products of further action of acids & akalies 3. Peptides
• Acid and Alkali albuminates • (small hydrolytic fragments 2-20 amino acids)
Coagulated • are insoluble products resulting from either the
Proteins action of heat or alcohol
• Coagulated albumin, cooked meat

Hydrolysis of Proteins Protein Denaturation

• Reverse of peptide Bond formation • Partial or complete disorganization or protein’s tertiary
structure
• Results in the generation of an amine and a • Cooking food denatures the protein but does not change
carboxylic acid functional groups protein nutritional value
• Digestion of ingested protein is enzyme-catalyzed • Coagulation: Precipitation (denaturation of proteins)
hydrolysis – Egg-white – a concentrated solution of protein albumin – forms
• Free amino acids produced are absorbed into the a jelly when heated because the albumin is denatured
• Cooking:
bloodstream and transported to the liver for the – Denatures proteins – makes it easy for enzymes in our body to
synthesis of new proteins hydrolyze/digest protein
• Hydrolysis of cellular proteins and their – Kills microorganisms by denaturation of proteins
resynthesis is a continuous process – Fever: >104degF – the critical enzymes of the body start getting
denatured
 Diseases involving Proteins Protein Misfolding Disorders
• Protein-misfolding diseases • Many diseases result from mutant proteins that
• Protein deficiency diseases evade quality control processes of the cell, fold
abnormally and ultimately form aggregates.
• Amino Acid metabolism disorders
• These misfolded protein aggregates can impair
cellular functions and are associated with many
neurodegenerative diseases.

Protein-Energy Malnutrition
• Kwashiorkor • Marasmus
– deficiency of dietary protein – often seen under the age of 1
in the presence of normal to and is associated with
high carbohydrate intake inadequate intake of both
– “the sickness of weaning” as protein and calories
it is often seen following – The body’s own energy stores
weaning after birth are utilized, resulting in
emaciation

Amino Acid Metabolism Disorders Amino Acid Metabolism Disorders

• Phenylketonuria • Maple Syrup Urine Disease
– Deficiency in phenylalanine hydroxylase – AKA Branched chain ketoaciduria
– Phenylketone spills in the urine – Metabolic disorder affecting branched-chain amino
– Causes Seizures and intellectual disability acids (Leucine, Isoleucine, Valine)
• Alkaptonuria – Deficiency in α–keto acid dehydrogenase
– Black Urine Disease – Causes sweet urine odor, lethargy, seizure
– Rare inherited genetic disorder of tyrosine • Homocystinuria
metabolism – Metabolic disorder of methionine
– Deficiency in homogentisate 1,2-dioxygenase which – Deficiency in crystathionine β-synthase
participates in tyrosine degradation – Causes nearsightedness, abnormal blood clots, retinal
– Causes black urine when exposed to air detachment