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Objectives
Classify proteins according to function,
solubility and composition
Illustrate how amino acids are linked to form
the four levels of structure in proteins
Identify the various forces of attractions that
stabilize each level of protein architecture

Proteins Classification of Proteins

From the Greek word proteios meaning first of Accdg. to COMPOSITION
rank
Most abundant biomolecule in the cell
SIMPLE Proteins
Yield only amino acids upon hydrolysis

CONJUGATED Proteins
Simple proteins + non-protein substances

Classification of Proteins Classification of Proteins

Accdg. to COMPOSITION Accdg. to BIOLOGICAL FUNCTION
CONJUGATED Proteins
Biological catalysts
Nucleoproteins (nucleic acid + protein)
Transport proteins
Glycoproteins (carbohydrate + protein)
Nutrient and storage proteins
Lipoproteins (lipid + protein)
Defense proteins
Phosphoproteins (phosphate groups + protein)
Contractile proteins
Hemoproteins (heme + protein)
Structural proteins
Flavoproteins (flavin nucleotide + protein)
Regulatory proteins
Metalloprotein (metal ion + protein)

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Classification of Proteins
Accdg. to BIOLOGICAL FUNCTION
ENZYMES
Catalyze biological
reactions
TRANSPORT PROTEINS
Bind or carry specific
molecules or ions from
one organ to another
Classification of Proteins
Accdg. to BIOLOGICAL FUNCTION
CONTRACTILE or MOTILE
PROTEINS
Allow cells and organisms to
contract, change shape or
move about
Classification of Proteins
Accdg. to BIOLOGICAL FUNCTION
REGULATORY PROTEINS
Regulate physical or cellular
activities
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Classification of Proteins
Accdg. to BIOLOGICAL FUNCTION
NUTRIENT and STORAGE
PROTEINS
Mobilized by the body to
derive building blocks or
energy
DEFENSE PROTEINS
Defend organisms against
invasion by foreign substances
Classification of Proteins
Accdg. to BIOLOGICAL FUNCTION
STRUCTURAL PROTEINS
As supporting filaments,
cables or sheets for strength
and protection of biological
structures
Classification of Proteins
Accdg. to SHAPE
GLOBULAR PROTEINS
Polypeptide chain coiled into
compact spherical shape
Soluble in water
Mobile within cells
eg. amylase, hemoglobin
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Classification of Proteins Classification of Proteins

Accdg. to SHAPE Accdg. to SOLUBILITY

FIBROUS PROTEINS 1. ALBUMINS soluble in water and dilute solutions

Polypeptide chains arranged (eg. Ovalbumin, lactalbumin of milk)
side-by-side in long filaments
2. GLOBULINS soluble in dilute salt solutions but
Insoluble in water not in water (eg. Myosin)
Mechanically strong
3. PROLAMINS soluble in 70-80% alcohol solutions
Structural and protective
(eg. Zein-corn storage protein)
function
eg. collagen 4. GLUTELINS soluble in dilute alkali/acidic
solutions (eg. Rice glutelins)

DEFATTED SEED SAMPLE

0.5 M NaCl, 1 h at 4C

RESIDUE EXTRACT

70% ethanol, 1 h at 4C Dialyze vs. water at 4C

LEVELS OF PROTEIN
ARCHITECTURE
PROLAMIN RESIDUE GLOBULIN ALBUMIN
(supernatant) (precipitate)
0.05 M NaOH, 1 h at 4C

GLUTELIN
OSBORNE FRACTIONATION of SEED
(supernatant) STORAGE PROTEINS

Hierarchy of Protein Structure Primary Structure

Amino acid sequence

Linear order of amino acids from the N-
terminus to the C-terminus
Dictates the structure and function of the
protein

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Secondary Structure Secondary Structure

Spatial arrangement of amino acid residues
that are near one another in the linear
sequence
Common regular folding patterns of the
polypeptide backbone
Main interaction: HYDROGEN BONDS between
peptide bonds
Secondary structures include: -helix,
-pleated sheets, collagen helix
Spatial arrangement of amino acid residues
that are near one another in the linear
sequence
Common regular folding patterns of the
polypeptide backbone
Main interaction: HYDROGEN BONDS between
peptide bonds
Secondary structures include: -helix,
-pleated sheets, collagen helix

-Helix -Helix
Rises by 5.4 / turn Stabilized by H-bonds
between C=O and
Each turn has ~3.6
NH in the polypeptide
amino acid residues
backbone that are 3-4
~1.5 rise between residues apart.
amino acid residues
Usually found mostly in
Can be right-handed globular proteins
(counterclockwise) or
left-handed (clockwise)

-Helix -Pleated Sheet

R groups are protruding Backbone of the
outward of the helical polypeptide chain is
backbone extended into a zigzag
Bulky side chains are rather than a helix
less commonly found in Zigzag polypeptide
alpha-helices chains are lying side by
Gly and Pro destabilizes side and held together
the helical structure by hydrogen bonds
Pleated due to
alternating position of
-carbon

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-Pleated Sheet
Can be PARALLEL
N C
N C
N C
Collagen Helix
Three separate polypeptide
chains are super-twisted about
each other
~3 aa residues per turn
Superhelical twisting is right-
handed
Repititive amino acid sequence:
Gly-Pro-Hyp (hydroxyproline)
Tertiary Structure
Overall 3D arrangements
of all atoms in the
protein
Results from folding into
specific 3D shapes and
unique binding sites
Highest level of protein
architecture common to
all biologically active
proteins
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-Pleated Sheet
or ANTI-PARALLEL
N C
C N
N C
Non-Helix and -Sheet Regions
Hinges, turns, coils
Gives flexibility
Connects secondary structures
Tertiary Structure
Stabilized by the following interactions:
1. HYDROPHOBIC INTERACTIONS
Overall tendency of side chains of non-polar
residues to collect in the interior of the protein
2. HYDROGEN BONDING
Between side groups or between peptide bonds
3. ELECTROSTATIC INTERACTION
Charged side chains (e.g. COO of aspartate
and glutamate, and -NH3+ of lysine)
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Tertiary Structure Tertiary Structure

4. DISULFUDE BONDS/BRIDGES
Formed by two cysteine residues
An actual covalent bond

Tertiary Structure Structural Motifs

The Chemistry of Perm Hairstyling
Also called supersecondary structures
Combinations of 2o structures in specific
geometric arrangements
Indicative of a particular 3D architecture
and associated with specific function

R.A. ammonium thioglycolate O.A. H2O2

Structural Structural Motifs

Motifs LEUCINE ZIPPER
(coiled coil)
Made up of mostly
hydrophobic amino acids
Two helices can associate
through hydrophobic
interactions

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Structural Motifs Structural Motifs

HELIX-loop-HELIX ZINC FINGER LOOP BARREL

Quaternary Structure Quaternary Structure

Can have homo-multimers or
Describes the organization of subunits hetero-multimers
(polypeptide chains with 3 structure) in
a protein with multiple subunits Hetero-multimers: composed of
(multimeric) more than one different
polypeptides
Subunits are held together by non-
covalent interactions Homo-multimers: composed of
multiple copies of a single
Multimeric/Oligomeric proteins are more polypeptide
stable than dissociated subunits

Quaternary Structure Protein Folding

Folding of the protein gives its three dimensional
shape which is critical in the function of that
Oligomeric protein (eg. formation of the binding site)
protein made The manner by which proteins fold is dictated by
up of 4 its amino acid sequence.
polypeptide
chains and a Proteins fold into specific conformation that
heme grp results to a minimized free energy of the
molecule molecule becomes more STABLE

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Protein Folding Protein Folding

In aqueous environment, the polypeptide chain
folds in such a way wherein hydrophobic side
chains are buried in the interior and polar side
chains are on the surface

Hydrophobic groups

Hydrophillic groups

Protein Folding Misfolded Proteins

Folding of proteins can be stable or with the aid Misfolded proteins must be targeted for
of molecular chaperones degradation.
Accumulation of misfolded proteins are the
causes of some diseases:
Alzheimers
Parkinsons
Mad Cow

Campbell, 2009

Protein Denaturation
Alteration of the secondary, tertiary and
quaternary structure of proteins

PROTEIN DENATURATION

Campbell, 2009

The primary structure of the protein is preserved

peptide bond is not easily disrupted

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Protein Denaturation
May result into reduction or complete loss of
biological activity of the protein
Accomplished by the following agents of
denaturation
Physical agents: heat, extremes of pH
Chemical agents:
strong acids and bases
Heavy metal cations (Pb2+, Hg2+)
Alkaloidal reagents (trichloroacetic acid)
Organic solvents (ethanol, acetone)