PROTEINS
Lesson 6
TOPIC OUTLINE
Characteristics
Amino Acids
Peptides
Protein Structure
Protein Hydrolysis
Protein Denaturation
Classifications of Proteins
CHARACTERISTICS OF PROTEIN
• Naturally-occurring, large and complex molecules that
play many critical roles in the body*
• Most abundant substance in cells after water
• Account for about 15% of a cell’s overall mass
• Elemental composition - C, H, N, O, and S*
AMINO ACIDS
• Contain:
⚬ an amino (—NH2)
⚬ a carboxyl (—COOH) group
⚬ an R side chain
• 700 amino acids are known
AMINO ACIDS
• Alpha (α) amino acid— amino and carboxyl group are
attached to the a-carbon atom
• Beta (ß) amino acid—carboxylic acid groups and amine
groups on secondary carbon atoms
STANDARD AMINO ACIDS
STANDARD AMINO ACIDS: NONPOLAR
• Contain one amino group, one
carboxyl group, and a nonpolar
side chain
• Hydrophobic
• Found in the interior of proteins
STANDARD AMINO ACIDS: POLAR
• Contain one amino group, one carboxyl group,
and a polar side chain
• Hydrophilic
• Three types:
⚬ Polar neutral
⚬ Polar acidic
⚬ Polar basic
STANDARD AMINO ACIDS:
POLAR NEUTRAL
• Contain polar but neutral
side chains (not charged)
STANDARD AMINO ACIDS:
POLAR ACIDIC
• Contain a carboxyl group as
part of the side chain
• Each side chain is acidic
• Can donate a proton
• Negative charge
STANDARD AMINO ACIDS:
POLAR BASIC
• Contain an amino group as part
of the side chain
• Each side chain is basic
• Can accept a proton
• Positive charge
STANDARD AMINO ACIDS: NOMENCLATURE
• Three-letter abbreviations are used for naming standard
amino acids
⚬ Example: Lysine (Lys) and Arginine (Arg)
⚬ Exceptions: Isoleucine (Ile), tryptophan (Trp),
asparagine (Asn), and glutamine (Gln)
STANDARD AMINO ACIDS: NOMENCLATURE
• One-letter
symbols
• Used for
comparing amino
acid sequences
of proteins
• Dr. Margaret
Oakley Dayhoff
ESSENTIAL AMINO ACIDS
• Standard amino acids needed for protein synthesis
• Must be obtained from dietary sources
• There are 10 of them:
phenylalanine
valine
threonine
tryptophan
isoleucine
methionine
Mnemonic: PVT. TIM HA*LL
histidine
arginine*
leucine
lysine
AMINO ACIDS AND CHIRALITY
Exception: Glycine -->
R-group is hydrogen
19 of the 20 standard amino
acids contain a chiral center
AMINO ACIDS AND CHIRALITY
• Amino acids found in nature
and in proteins are Lisomers
• Rules for drawing Fischer
projection:
⚬ Top: COOH group
⚬ Bottom: R group
⚬ Horizontal: NH2 group
AMINO ACIDS: ACID-BASE PROPERTIES
• α-amino acids exist as zwitterions (solid state & solution)
• Zwitterions: molecules that has at least two functional
groups— one having a positive charge and the other
having a negative charge, with an overall charge of zero
AMINO ACIDS: CYSTEINE & ITS UNIQUENESS
• Standard amino acid with a side chain containing a
sulfhydryl group (—SH group)
• Cysteine, in the presence of mild oxidizing agents,
dimerizes to form a cystine molecule
AMINO ACIDS: CYSTEINE & ITS UNIQUENESS
PEPTIDES
•
•
•
•
Peptide: Unbranched chain of amino acids
Dipeptide - Compound containing two amino acids
Oligopeptide - Peptide with 10 to 20 amino acid residues
Polypeptide: Long unbranched chain of amino acids
NATURE OF PEPTIDE BONDS
• Length of the amino acid chain can vary from a few amino
acids to hundreds of amino acids
• Peptide bonds: Covalent bonds between amino acids
• Every peptide has an N-terminal end and a C-terminal end
PEPTIDE NOMENCLATURE
Rules:
• C-terminal amino acid keeps its full name
• All the other amino acid have names that end in -yl
• -yl suffix replaces the -ine or -ic acid ending of the amino
acid name
⚬ except for tryptophan (-yl is added to the name)
• Amino acid naming sequence begins at the N-terminal
amino acid residue
PEPTIDE NOMENCLATURE
Name this short peptide chain
PEPTIDE NOMENCLATURE
Gly-Ala-Ser
glycylalanylserine
ISOMERIC PEPTIDES
• Contain the same amino acids but present in different
order with different properties
• Number of possible isomeric peptides increases rapidly as
the length of the peptide chain increases
BIOCHEMICALLY IMPORTANT SMALL PEPTIDES
Small Peptide Hormones
• Best-known— oxytocin & vasopressin
• Produced by the pituitary gland
• Hormones are nonapeptides (nine amino acids)*
BIOCHEMICALLY IMPORTANT SMALL PEPTIDES
Small Peptide Neurotransmitters
• Enkephalins— pentapeptide neurotransmitters
produced by the brain
• Bind receptor sites in the brain to reduce pain
Leuenkephalin
Tyr-Gly-Gly-Phe-Leu
BIOCHEMICALLY IMPORTANT SMALL PEPTIDES
Small Peptide Antioxidant
• Glutathione (Glu–Cys–Gly)— Tripeptide present in
high levels in most cells
• Regulates oxidation–reduction reactions
• Protects cellular contents from free radicals*
PROTEIN STRUCTURE
• Common proteins: 400–500 amino acids
• Small proteins: 40–100 amino acid
• More than one polypeptide chain may be in a protein
⚬ Monomeric: contain one polypeptide chain
⚬ Multimeric: contain two or more polypeptide chains
￭ Homomultimer: one kind of chain
￭ Heteromultimer: two or more different chains
(ex: hemoglobin)
PROTEIN STRUCTURE
•
•
•
•
Primary
Secondary
Tertiary
Quaternary
FOLDING- the physical process by which a protein chain is translated
to its native 3D structure to become biologically functional
PRIMARY STRUCTURE OF PROTEINS
• Order in which amino acids are linked together in a
protein via peptide bonds
• Frederick Sanger: first protein (insulin) in 1953
PRIMARY STRUCTURE OF PROTEINS
• Order in which amino acids are linked together in a
protein via peptide bonds
• Frederick Sanger: first protein (insulin) in 1953
PRIMARY STRUCTURE OF PROTEINS
• Every protein has its own unique amino acid sequence
PRIMARY STRUCTURE OF PROTEINS
SECONDARY STRUCTURE OF PROTEINS
• Arrangement in space adopted by the backbone portion
of a protein
• Types:
⚬ Alpha-helix (a helix)
⚬ Beta-pleated sheet (b pleated sheet)
SECONDARY STRUCTURE OF PROTEINS
Alpha-helix (a helix)
• Twist of the helix forms a
clockwise, spiral
• The O from the C=O bond and
the H from the N—H bond
form a hydrogen bond
(oriented parallel to the axis of
the helix)
SECONDARY STRUCTURE OF PROTEINS
Beta Pleated Sheets
• Two protein chain segments in the
same or different molecules
• The O from the C=O bond and the
H from the N—H bond form a
hydrogen bond (oriented lateral to
the axis of the pleated sheets)
TERTIARY STRUCTURE OF PROTEINS
• Overall 3D shape of a protein
• Results from the interactions between amino acid side
chains that are widely separated from each other
• Types of stabilizing interactions observed
⚬ Covalent sulfide bonds
⚬ Electrostatic attractions (salt bridges)
⚬ Hydrogen Bonds
⚬ Hydrophobic attractions
TERTIARY STRUCTURE OF PROTEINS
QUATERNARY STRUCTURE OF PROTEINS
• The association of several
peptide chains into a
closely packed arrangement
• Subunits are independent
of each other and not
covalently bonded to each
other
• Contain even number of
subunits
STRUCTURE OF PROTEINS
PROTEIN HYDROLYSIS
Reverse of peptide bond formation
PROTEIN DENATURATION
• Partial or complete disorganization of a protein's 3D shape
• Coagulation- change in protein structure* brought about by
heat, mechanical action, acids, or enzymes
Cooking denatures proteins
A fever of above 41°C is dangerous
CLASSIFICATION OF PROTEINS
• Based on Shape
• Fibrous Proteins
• Globular Proteins
• Membrane Proteins
• Based on Function
BASED ON SHAPE: FIBROUS PROTEIN
α-Keratin
• Provide protective coating for organisms
• Major protein constituent of:
BASED ON SHAPE: FIBROUS PROTEIN
α-Keratin
• Mainly made of
hydrophobic amino
acid residues
• Individual molecules
are almost wholly
alpha (α) helical
BASED ON SHAPE: FIBROUS PROTEIN
Collagen
• Most abundant protein in humans
• Major structural material in:
BASED ON SHAPE: FIBROUS PROTEIN
Collagen
• Organic component of:
• Predominant structure
is Triple-helix
BASED ON SHAPE: GLOBULAR PROTEIN
Hemoglobin
• Oxygen-carrier
molecule in
blood
• Tetramer
composed of
two α and two ß
subunits
BASED ON SHAPE: GLOBULAR PROTEIN
Myoglobin
• Oxygen-storage
molecule in muscles
• Monomer composed of a
single peptide chain and
one heme unit
• Higher affinity for
oxygen than hemoglobin
BASED ON SHAPE: MEMBRANE PROTEIN
• Proteins found on
the cell membrane
• Insoluble in water*
• two broad
categories
⚬ integral
(intrinsic)
⚬ peripheral
(extrinsic)
BASED ON FUNCTION
• Functional versatility of proteins stems from their
ability to:
⚬ Bind small molecules specifically and strongly
⚬ Bind other proteins and form fiber-like structures
⚬ Integrate into cell membranes
CLASSIFICATION OF PROTBASED ON FUNCTION
Catalytic Proteins
• Accelerate chemical
reactions
• Most end in –ase
BASED ON FUNCTION
Defense Proteins
• Important component of
the body's immune system
• Known as
immunoglobulins or
antibodies
• Found in the blood, lymph,
and vascularized tissues
BASED ON FUNCTION
Transport Proteins
• Bind to small biomolecules, transport them to other
locations in the body, and release them as needed
⚬ Channel Proteins
⚬ Carrier Proteins
BASED ON FUNCTION
Contractile Proteins
Structural Proteins
• Necessary for movement
• dictate stiffness & rigidity
• Examples: Actin and myosin • maintain cell shape
⚬ ex: collagen & keratin
BASED ON FUNCTION
Storage Proteins
• Bind and store small molecules
Regulatory Proteins
• found embedded in the exterior surface of cell
membranes
• Act receptors for molecules
• Bind to enzymes (catalytic proteins) and control enzymatic
action
BASED ON FUNCTION
Nutrient Proteins
• Important in the early stages of life
• Examples:
⚬ Casein (found in milk)
⚬ ovalbumin (found in egg white)
BASED ON FUNCTION
Buffer Proteins
• part of the system by which the acid–base balance within
body fluids is maintained
Fluid-Balance Proteins
• maintain fluid balance between blood and surrounding
tissue
• Proteins in the blood are called albumin and globulin
• Blood proteins have the ability to attract and keep fluid in
the bloodstream