PROTEIN Polar neutral

- Naturally-occurring, unbranched polymer in which
the monomer units are amino acids
- Most abundant substance in cells after water
§ Account for about 15% of a cell’s overall
mass
- Elemental composition: Carbon (C), hydrogen (H),
nitrogen (N), oxygen (O), and sulfur (S)
§ Average nitrogen content is 15.4% by mass
- Contain iron (Fe), phosphorus (P), and other metals in
certain specialized proteins
- Contain polar but neutral side chains
- Six amino acids belong to this category
Polar acidic
- Contain a carboxyl group as part of the side chains
- Two amino acids belong to this category
Polar basic
- Contain an amino group as part of the side chain
- Three amino acids belong to this category

AMINO ACIDS: Building blocks for Proteins Nomenclature

- Contain both an amino (-NH2) and a carboxyl (- - Three-letter abbreviations are used for naming
COOH) group standard amino acids
§ α- amino acids: Amino acids in which the § Abbreviations are the first three letters of the
amino group and the carboxyl group are amino acid’s name
attached to the α-carbon atom o Exceptions: Isoleucine (Ile), tryptophan
o Side chains (R)- Vary in size, shape, (Trp), asparagine (Asn), and glutamine (Gln)
change, acidity, functional groups § One-letter symbols: Used for comparing amino
present, hydrogen-bonding ability, acid sequences of proteins
and chemical reactivity o Usually the first letter of the name
§ >700 amino acids are known o When more than one amino acid has the same
letter, the most abundant amino acid gets the
Standard Amino Acids first letter
- 20 α- amino acids normally found in proteins
- divided based on the properties of R-groups Essential Amino Acids
§ Nonpolar amino acids: Contain one amino - Standard amino acids needed for protein synthesis
group, one carboxyl group, and a nonpolar and must be obtained from dietary sources
side chain - Types of dietary proteins: complete, incomplete,
o Hydrophobic: Not attracted to water and complementary
molecules
o Found in the interior of proteins, Arginine Methionine
where there is no polarity Histidine Phenylalanine
§ Polar amino acids: Hydrophilic Isoleucine Threonine
o Types: Polar neutral, polar acidic, Leucine Tryptophan
and polar basic Lysine Valine
- Not essential for adults but it is required for
growth in children.
Chirality and Amino Acids
- Four different groups are attached to the α- carbon atom
in all of the standard amino acids
§ Exception: In glycine, the R-group is hydrogen
- 19 of the 20 standard amino acids contain a chiral center
- Molecules with chiral center exhibit enantiomerism (left-
and right-handed forms)
- Amino acids found in nature and in proteins are L isomers
§ Exception: Some bacteria
§ Monosaccharides prefer D-isomers
- Rules for drawing Fischer projection formulas for amino
acid structures
§ -COOH group is placed at the top of the projection
formula
- R group is placed at the bottom, positions the carbon chain
vertically
- -NH2 group is placed in a horizontal position
§ NH2 on the left- L isomer
§ NH2 on the right- D isomer
Acid-Base Properties of Amino Acids
- In pure form, amino acids are white crystalline solids
§ Decompose before they melt
- Not very soluble in water
- α- amino acids exist as zwitterions in solution and in
solid waste
§ Zwitterions: Molecules with positive charge
on one atom and negative charge on another,
but have no net charge
§ Carboxyl groups give up protons to produce
a negatively charged species
§ Amino groups accept protons to produce a
positively charge species
- Amino acid forms in solution
§ Zwitterions, positive ion, and negative ion
§ Equilibrium shifts with change in pH
Isoelectric Point (pI)
- pH at which an amino acid exists in its zwitterion
form
- carries zero net charge
- Different amino acids have different isoelectric points
Cysteine: A Chemically Unique Amino Acid
- Standard amino acid that has a side chain that contains
a sulfhydryl group (-SH group)
§ Sulfhydryl group imparts cysteine a unique
chemical property
- Cysteine, in the presence of mild oxidizing agents,
dimerizes to form a cysteine molecule
§ Cystine contains two cysteine residues
linked via a covalent disulfide bond
NATURE OF THE PEPTIDE BOND
Peptide: unbranched chain of amino acids
Ø Dipeptide: compound containing 2 amino acids
Ø Oligopeptide: peptide with 1 to 20 amino acid
residues
Ø Polypeptide: long unbranched chain of amino acids
• Reaction is between the amino group of one amino acid
and the carboxyl group of another amino acid.
Peptide bonds: covalent bonds between amino acids in a
peptide.
• Every peptide has an N-terminal end and a C-terminal
end.
Small peptide hormones
- Best-known peptide hormones: oxytoxin and
vasopressin.
§ Produced by the pituitary gland
§ Hormones are nonapeptides (nine amino acid
residues)
Small peptide neurotransmitters
- Enkephalins are pentapeptide neurotransmitters
produced by the brain.
§ Bind receptor sites in the brain to reduce
pain.
- Best-known enkephalins
Ø Met-enkephalin: Tyr-Gly-Gly-Phe-Met
Ø Leu-enkephalin: Tyr-Gly-Gly-Phe-Leu
Small peptide antioxidant
- Glutathione (Glu-Cys-Gly): Tripeptide present in
high levels in most cells.
§ Regulates oxidation-reduction reactions
§ Antioxidant that protects cellular contents
from oxidizing agents such as peroxides and
superoxides.
PROTEIN
General definition: Naturally-occurring, unbranched
polymer in which the monomer units are amino acids.
Specific definition: Peptide in which at least 40 amino acid
residues are present.
- The terms polypeptide and protein are used
interchangeably.
- Several proteins have> 10,000 amino acid residues
More than one polypeptide chain may be present in a protein.
Ø Monomeric: proteins which contains one polypeptide
chain.
Ø Multimeric: proteins which contains two or more
polypeptide chains.
PROTEIN CLASSIFICATION BASED ON CHEMICAL
COMPOSITION
Simple protein: protein in which only one amino acid residues
are present.
Conjugated protein: protein that has one or more non-amino-
acid entities (prosthetic groups) present in its structure.
May be classified further based on the nature of prosthetic
group(s) present
§ Lipoprotein contains lipid prosthetic groups
§ Glycoprotein contains carbohydrate groups
§ Metalloprotein contains a specific metal as its
prosthetic groups
TYPES OF STRUCTURES
1) PRIMARY STRUCTURE: Order in which amino acids
are linked together in a protein.
- Every protein has its own unique amino acid sequence
- Primary structure of a specific protein is the same
within the organism
§ Structures of certain proteins are similar
among different species of animals (e.g.,
Insulin from pigs, cows, sheep, and humans
are similar but not identical)
- Amino acids are linked to each other by peptide
linkages
DIFFERENCE IN ANIMAL AND HUMAN INSULIN
- Immunological reactions gradually increase over
time.
2) SECONDARY STRUCTURE
- Arrangement in space adopted by the backbone
portion of a protein
- Types: Alpha-helix (α-helix) and the beta-
pleated sheet (β pleated sheet)
- Alpha-helix structure: A single protein chain
adopts a shape that resembles a coiled spring
(helix)
§ Coil configuration maintained by hydrogen
bonds
§ Twist of the helix forms a right-handed, or
clockwise, spiral
- Hydrogen bonds between C=O and N-H entities
are orientated parallel to the axis of the helix
 - All of the amino acid R groups extend outward
from the spiral
§ There is not enough room within the
spiral
- Beta-pleated sheet structure: Two
extended protein chain segments in the same or
different molecules
§ Held together by hydrogen bonds
o H-bonding between chains-
inter and/or intramolecular
3) TERTIARY STRUCTURE
- Overall 3-D shape of a protein
- Results from the interaction between amino acid
side chains (R groups) that are widely separated
from each other
- Types of stabilizing interactions observed
§ Covalent disulfide bonds
§ Electrostatic attractions (salt bridges)
§ Hydrogen bonds
§ Hydrophobic attractions
4) QUATERNARY STRUCTURE
- Organization among the various peptide subunits in a
multimeric protein
§ Highest level of protein organization
§ Contain even number of subunits
§ Found in proteins that have two or more
polypeptide chains (subunits)
o Subunits are independent of each
other and not covalently bonded to
each other
PROTEIN HYDROLYSIS
- Reverse of peptide bond formation
§ Results in the regeneration of an amine and
carboxylic acid functional groups
§ Protein digestion- Enzyme-catalyzed
hydrolysis
o Free amino acids produced are
absorbed into the bloodstream and
transported to the liver for the
synthesis of new proteins
fully § Hydrolysis of cellular proteins to amino
acids is an ongoing process, as the body
resynthesizes needed molecules and tissue
PROTEIN DENATURATION
- Partial or complete disorganization of a protein’s
characteristic three-dimensional shape
§ Occurs due to disruption of its secondary,
tertiary, and quaternary structural
interactions
- Coagulation: Precipitation out of biochemical
solution of denatured protein (e.g., Egg white is a
concentrated solution of protein albumin, which
forms a jelly when heated)
PROTEIN CLASSIFICATION BASED ON SHAPE
1) Fibrous proteins: protein molecules with elongated shape
- One dimension is much longer than the others
- Generally insoluble in water
- Have a single type of secondary structure
- Tend to have simple, regular, and linear structures
- Aggregate together to form macromolecular
structures (e.g., hair, nails, etc)
α- Keratin
- Provide protective coating for organisms
- Major protein constituent of hair, feather, nails,
horns, and turtle shells
- Mainly made of hydrophobic amino acid residues
Collagen
- Most abundant protein in humans (30 % of total
body protein)
 - Major structural material in tendons, ligaments,
blood vessels, and skin
- Organic component of bones and teeth
- Predominant structure: Triple-helix
§ Glycine and proline help maintains the
structure of the triple-helix
2) Globular proteins: protein molecules with peptide chains
folded into spherical or globular shapes
- Water-soluble substances- Hydrophobic amino acids
residues are in the protein core
Hemoglobin
- An oxygen-carrier molecule in blood
§ Transports oxygen from lungs to tissues
- Tetramer (four polypeptide chains)
§ Each subunit contains a heme group
o One molecule can transport up
to four oxygen molecules at
time
o Iron atom in heme interacts with
oxygen
Myoglobin
- Oxygen-storage molecule in muscles
- Monomer
§ Consists of a single peptide chain and
one heme unit
§ One molecule carries one O2 molecule
- Has a higher affinity for oxygen than hemoglobin
- Oxygen stored in myoglobin molecules serves as
a reserve source for working muscles when
oxygen demand exceeds its supply
3) Membrane proteins: proteins associated with cell
membranes
- Insoluble in water- Hydrophobic amino acid residues
are on the surface
PROTEIN CLASSIFICATION BASED ON FUNCTION
- Proteins play crucial roles in biochemical processes
- Diversity of functions exhibited by proteins exceed
the role of other biochemical molecules
- Functions versatility or proteins stems from their
ability to:
§ Bind small molecules specifically and
strongly
§ Bind other proteins and form fiber-like
structures
§ Integrate into cell membranes
1) Catalytic proteins
- Known for their role as “catalysts”
§ Almost every chemical reaction in the body
is driven by an enzyme
2) Defense proteins
- Central to functioning of the body’s immune system
§ Known as immunoglobulins or antibodies
3) Transport proteins
- Bind to small molecules, transport them to other
locations in the body, and release them as needed
4) Messenger proteins
- Transmit signals to coordinate biochemical processes
between different cells, tissues, and organs (e.g.,
insulin, glucagon, and human growth hormone)
5) Contractile proteins
- Necessary for all forms of movement (e.g., actin and
myosin)
- Human reproduction depends on the movement of
sperm, which is possible because of contractile
proteins
6) Structural proteins 12) Fluid-balance proteins
- Confer stiffness and rigidity - Maintain fluid balance between blood and
- Collagen is a component of cartilage surrounding tissue
- α- keratin gives mechanical strength and protective
covering to hair, nails, feathers, and hooves GLYCOPROTEINS: contain carbohydrates or carbohydrate
derivatives in addition to amino acids
7) Transmembrane proteins - E.g., Proteins in cell membrane and blood group
- Control the movement of small molecules and ions markers of ABO system
through the cell membrane
- Have channels to help molecules enter and exit the Collagen
cell - Structural feature: 4-hydroxyproline (5%) and 5-
- Selective, allow passage of only one type of molecule hydroxylysine (1%)
or ion - Carbohydrate units are attached by glycosidic
linkages to collagen at its 5-hydroxylysine
8) Storage proteins residues
- Bind (and store) small molecules - Direct the assembly of collagen triple helices into
- Ferritin: iron-storage protein which saves iron for collagen fibrils
use in the biosynthesis of new hemoglobin molecules
- Myoglobin: oxygen-storage protein present in muscle GLYCOPROTEINS: IMMUNOGLOBULINS
- Produced as a protective response to the invasion of
9) Regulatory proteins microorganisms or foreign molecules
- Found embedded in the exterior surface of cell - Serve as antibodies to combat invasion of the body by
membrane antigens
- Act as sites for receptor molecules § Antigen: Foreign substance, such as a
- Bind to enzymes (catalytic proteins) and control bacterium or virus, that invades the human
enzymatic action body
10) Nutrient proteins § Antibody: Biochemical molecule that
- Important in the early stages of life, from embryo to counteracts a specific antigen
infant - Bonding of an antigen to variable regions of
- Examples: Casein (found in milk) and Ovalbumin immunoglobulins occurs through hydrophobic
(found in egg white) interactions, dipole-dipole interactions, and hydrogen
- Milk provides immunological protection for bonds
mammalian young
LIPOPROTEINS
11) Buffer proteins - Conjugated proteins that contain lipids and amino
- Part of the system by which the acid-base balance acids
within the body fluids is maintained - Help suspend lipids and transport them through the
bloodstream
- Classes of plasma lipoproteins
§ Chylomicrons: Transport dietary
triacylglycerols from intestine to the liver
and to adipose tissue
§ Very-low density lipoproteins (VLDL):
Transport triacylglycerols synthesized in the
liver to adipose tissue
§ 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