PROTEINS

Characteristics of Protein
o A protein is a naturally occurring, unbranched polymer in which the
monomer units are ________________.
o Proteins are the most abundant molecules in the cells after water –
accounting for about 15% of a cell’s overall mass.
o Elemental composition – contains __________, _____________, ___________,
_____________, most also contain ______________.
o The average nitrogen content of proteins is 15.4% by mass.
o Also present are Iron (Fe), phosphorus (P), and some other metals in
some specialized proteins.

Amino Acids: The Building Blocks of Protein

o Amino acid – an organic compound that contains both an _____________
and _______________ group attached to the same carbon atoms.
▪ The position of carbon atom is ___________.
▪ -NH2 group is attached to alpha (a) carbon atom.
▪ -COOH group is attached to alpha (a) carbon.
o R = ____________ – vary in size, shape, charge, acidity, functional groups
present, hydrogen bonding ability, and chemical reactivity.
▪ >700 amino acids are known.
▪ Based on common “R” groups, there are ___ standard amino acids.

o All amino acids differ from one another by their _______________.

o Standard amino acids are divided into four groups based on the properties
of R-groups.
1. Non-polar amino acids: R-groups are non-polar.
- Such amino acids are ____________ – water-fearing (insoluble
in water).
- 9 of the 20 standard amino acids are non-polar.
- When present in proteins, they are located in the _________ of
protein where there is no polarity.
2. Polar-neutral
- Contains polar but neutral side chains.
- 6 amino acids belong to this category.
- Usually located on the __________ of protein.

3. Polar acidic
- Contain ________________ group as part of the side chains.
- Two amino acids belong to this category.
 4. Polar basic
- Contains __________ group as part of the side chain.
- Three amino acids belong to this category.

Nomenclature:
o Common names assigned to the amino acids are currently used.
o Three letter abbreviations – widely used for naming:
▪ First letter of amino acid name is compulsory and capitalized
followed by next two letters not capitalized.
o One letter symbol – commonly used for comparing amino acid sequences
of proteins:
▪ Usually the first letter of the name
▪ When more than one amino acid has the same letter, the most
abundant amino acid gets the 1st letter.
Practice Exercise: Classify the following amino acids based on the polarity of
their R-groups:

a.

b.

c.

d.

e.
Chirality and Amino Acids
o Four different groups are attached to the a-carbon atom in all of the
standard amino acids except ___________.
▪ In __________, R group is H.
o There are 19 of the 20 standard amino acids that contain a chiral center.
o Chiral centers exhibit enantiomer (left and right-handed forms)
o Each of the 19 amino acids exist in left and right-handed forms.
o The amino acids found in nature as well as in proteins are L
enantiomers.
Rules for making the Fischer projection formula for amino acid
structures:
✓ The -COOH group is put at the ________.
✓ The R group is at the __________ to position the carbon chain vertically.
 ✓ The -NH2 group is in a ___________ position.
▪ NH2 on the _______ – L isomer
▪ NH2 on the _______ – D isomer

Acid-Base Properties of Amino Acids:

o In pure form, amino acids are white crystalline solids.
o Exists as _______________: an ion with positive and negative charges on
the same molecule with a net zero charge.
▪ Carboxyl groups give up a proton to get negative charge.
▪ Amino groups accept proton to become positive.
o Amino acids in solution exist in three different species – Zwitterions,
positive ion, and negative ion. Equilibrium shifts with change in pH.
o __________________ – pH at which the concentration of Zwitterion is
maximum – net charge is zero.
- Different amino acids have different isoelectric points.
- At isoelectric point, amino acids are not attracted towards an
applied electric field because they have net zero charge.

Cysteine
o The only standard amino acid with a ______________ group.
o Cysteine in the presence of mild oxidizing agents dimerizes to form a
cystine molecule.
▪ Cystine – two cysteine residues linked via a covalent disulfide
bond.
Peptides
o Under proper conditions, amino acids can bond together to produce an
unbranched chain of amino acids.
o A chain of covalently linked amino acids is called __________.
o The covalent bonds between amino acids in a peptide are called
______________.
o _______________: bond between two amino acids.
o _______________: bond between ~ 3 – 20 amino acids
o _______________: bond between large number of amino acids.
o Every peptide has an N-terminal end and a C-terminal end.

Peptide Nomenclature
o The C-terminal amino acid residue keeps its full amino acid name.
o All the other amino acid residues have names that end in -yl. The -yl
suffix replaces the -ine or -ic acid ending of the amino acid name, except
for tryptophan, for which -yl is added to the name.
o The amino acid naming sequence begins at the N-terminal amino acid
residue.
o Example:
▪ Ala-leu-gly has the IUPAC name of alanylleucylglycine.
General Structural Characteristics of Proteins
o General definition: A protein is a naturally occurring, unbranched
polymer in which the monomer units are amino acids.
o Specific Definition: A protein is a peptide in which at least _____ amino
acid residues are present.
▪ Polypeptide and protein are often used interchangeably to describe
protein.
▪ Common proteins contain 400-500 amino acid residues.
▪ Small proteins contain 40-100 amino acid residues.
o Proteins can have one or more polypeptide chains.
▪ ____________ – protein contains one peptide chain.
▪ ____________ – protein contains more than one peptide chain.
 Protein Classifications Based on Chemical Composition
1. ____________ Proteins
- A protein in which only amino acid residues are present.
2. ____________ Proteins
- Protein that has one or more non-amino acid entities
(prosthetic groups) present in its structure:
• Lipoproteins
• Glycoproteins
• Metalloproteins
Glycoproteins
o Conjugated protein with carbohydrates linked to them.
o ___________ is a glycoprotein.
- Rich in hydroxyproline and hydroxylysine
- Hydroxylysines are linked to glucose, galactose, and their
disaccharides.
o ______________ is also a glycoprotein.
Lipoprotein
o A conjugated protein that contains lipids.
o Major function: help transport lipids through the bloodstream.
o Four major classes of plasma lipoproteins:
a. _______________ – transports dietary TAG from intestine to the liver.
b. ____________________________________ – Transports TAG synthesized
in the liver to adipose tissue.
c. _____________________________ – transports cholesterol to cells
throughout the body.
d. _____________________________ – Transports cholesterol from body
tissues back to the liver for degradation to bile acids.
 Four Types of Protein Structure
1. Primary Structure
- Refers to the order in which amino acids are linked together
in a protein.
- Every protein has its own unique amino acid sequence.

2. Secondary Structure
- Arrangement of backbone of atom in space
- The two most common types are: alpha-helix and beta-
pleated sheet).
▪ Alpha-Helix
- A single protein chain adopts a shape that resembles a coiled
spring (helix).
- H-bonding between same amino acid chains—
________________ bonding.
- Coiled helical spring.

▪ Beta-pleated Sheet
- H-bonding between two different chains—inter and/or
intramolecular bond.
3. Tertiary Structure
- The overall three-dimensional shape of protein.
- Results from the interactions between amino acid side
chains (R groups) that are widely separated from each other.
- In general, 4 types of interactions are observed.
e. Disulfide Bond: covalent, strong
f. Electrostatic interactions: salt bridge between charged side
chains of acidic and basic amino acids.
g. H-bonding between polar, acidic, and/or basic R groups.
- For H-bonding to occur, the H must be attached to ___, ___,
or ____.
h. Hydrophobic interactions: between ______________ side chains

4. Quaternary Structure
- Refers to the organization among the various peptide chains
in a multimeric protein.
- Highest level of protein organization.
 - Present only in proteins that have 2 or more polypeptide
chains (subunits).
- Proteins with quaternary structure are often referred to as
___________________ proteins.
- Contain even number of subunits.

Protein Classification Based on Shape

1. Fibrous Proteins: proteins with elongated shape
- ________________ in water
- Single type of secondary structure
- Tend to aggregate together to form macromolecular
structures, e.g. hair, nails.
2. Globular Proteins: protein molecules with peptide chains folded into
spherical or globular shapes.
- Generally water _______________.
- Functions as enzymes and intracellular signaling molecules.
Fibrous Protein: Keratin
- Provide protective coating for organs.
- Major protein constituents of hair, feather, nails, horns, and
turtle shells
- Hardness of keratin depends upon __________ bonds.
Fibrous Protein: Collagen
- Most ______________ proteins in humans (30% of total body
protein)
- Major structural material in tendons, ligaments, blood
vessels, and skin
- Predominant structure—triple helix
- Rich in proline—important to maintain structure.
Globular Protein: Myoglobin
- Oxygen storage molecule in muscles.
- Monomer – single peptide chain with one heme unit.
- Binds ______ O2 molecule.
- Has a higher affinity for oxygen than hemoglobin.
Globular Protein: Hemoglobin
- Oxygen carrying molecule in blood.
- Transports oxygen from lungs to tissues.
- Tetramer – four peptide chains
- Can transport up to _____ molecules of Oxygen at a time.
Classification of Protein Based on Function
 1. Catalytic Proteins
- Enzymes are best known for their catalytic role.
- Almost every chemical reaction in the body is driven by an
enzyme.
2. Defense Proteins
- Immunoglobulins or antibodies are proteins involved in the
body’s immune system.
3. Transport Proteins
- Binds small biomolecules and transport them to other
locations in the body and release them on demand.
4. Messenger Proteins
- Insulin and glucagon—regulate carbohydrate metabolism.
- Human Growth hormone—regulate body growth.
5. Contractile Proteins
- Actin and myosin
- Necessary for all forms of movement
6. Structural Proteins
- Collagen is a component of cartilage.
- Keratin gives mechanical strength as well as protective
covering to hair, nails, etc.
7. Transmembrane proteins
- Help control the movement of small molecules and ions in
the cell membrane.
8. Storage Proteins
- Ferritin – an iron storage protein
- Myoglobin – an oxygen storage protein in the muscle.
9. Regulatory Proteins
- Often found embedded in the exterior surface of cell
membranes.
- Molecules that bind to enzymes, thereby turning them “on”
and “off”, and thus controlling enzymatic action.
10. Nutrient Protein
- Particularly important in the early stages of life—from
embryo to infant.
- Casein and albumin
- Milk also provides immunological protection for young
mammals.
Protein Hydrolysis and Protein Denaturation
Protein Hydrolysis
o ____________ of peptide bond formation
 o Results in the generation of an amine and a carboxylic acid functional
group.
o Digestion of ingested protein is enzyme-catalyzed hydrolysis.
o Free amino acids produced are absorbed into the bloodstream and
transported to the liver for the synthesis of new proteins.
Protein Denaturation
o Partial or complete disorganization of protein’s tertiary structure
o Cooking food denatures the protein but does not change protein
nutritional value.
o _______________ – denaturing agent
o Cooking or applying heat kills microorganisms by denaturation of
proteins.
o Fever >104oF or >40oC – the critical enzymes of the body start getting
denatured.