BCH101

Macromolecules:
Proteins
Proteins
 Proteins

Proteins with strikingly different properties and activities are produced by

joining a common set of 20 amino acids in many different combinations
and sequences
From the common building blocks- different organisms can make such
widely diverse products as enzymes, hormones, antibodies, transporters,
light-harvesting complexes in plants, the flagella of bacteria, muscle fibers,
feathers, spider webs, rhinoceros horn, antibiotics, and myriad other
substances that have distinct biological functions
Enzymes are the most varied and specialized
Catalysts of almost all cellular reactions, enzymes are one of the keys to
understanding the chemistry of life
Fundamental chemical properties of amino acids
 Peptides and Oligopeptides

• Oligopeptides can be formed by adding amino acids one after other

• Small peptides can have distinct biological functions: aspartame
• Many vertebrate hormones are small peptides
• Proteins: generally contain fewer than 2,000 amino acid residues
Four levels of protein structure
Four levels of protein structure
 Four levels of protein structure

• Description of all covalent bonds (mainly peptide bonds and disulfide

bonds) linking amino acid residues in a polypeptide chain is its
primary structure.
• The most important element of primary structure is the sequence of
amino acid residues.
• Secondary structure refers to particularly stable arrangements of
amino acid residues giving rise to recurring structural patterns,
through interactions among the peptide backbone atoms, not
involving R groups.
• Tertiary structure describes all aspects of the three-dimensional
folding of a polypeptide, formed through interactions among the R
groups.
• When a protein has two or more polypeptide subunits, their
arrangement in space is referred to as quaternary structure.
 Higher order structures in protein

• Theoretically, a protein can assume a virtually uncountable number

of spatial arrangements, or conformations.
• Protein structures are stabilized by non-covalent interactions and
forces
• Protein segments can adopt regular secondary structures such as
the α helix and the β conformation
• Tertiary structure describes the well-defined, three-dimensional
fold adopted by a protein
• Tertiary structure is determined by amino acid sequence
Primary structure of Protein
 Overview of Protein Structure

Native structure of a protein:

• The possible conformations of a protein or protein segment
include any structural state it can achieve without breaking
covalent bonds.
• one or a few, among thousands that are possible, generally
predominate under biological conditions
• Most thermodynamically stable one (lowest energy state)
dominates at a given set of conditions
• Why multiple possible stable native conformations?:
The need for multiple stable conformations reflects the changes
that must take place as they bind to other molecules or catalyze
reactions
 Secondary structure
• The term secondary structure refers to any chosen segment of a
polypeptide chain and describes the local spatial arrangement of its
main-chain atoms, without regard to the positioning of its side chains or its
relationship to other segments.
• A regular secondary structure occurs when each dihedral angle, ϕ and ψ,
remains the same or nearly the same throughout the segment
• α helix and β sheets are common and stable secondary structures
• Both of these secondary structures are held together by hydrogen bond between
CO and NH groups of peptide bonds
• An α helix is formed when a region of a polypeptide chain coils around itself, and
H bond is formed between CO and NH groups of peptide bond separated by four
amino acid residues
• In a β sheet, hydrogen bonds connect two parts of a polypeptide chain lying
side by side.
• Secondary structures without a regular pattern are sometimes referred to as
undefined or as random coils
 Dihedral angles

• Rotation about the N—Cα (ϕ) and Cα—C (ψ) bonds are possible
• Angle of rotation can be varied
• In a specific secondary structure, all ϕ and ψ angles are the same.
• There are idealized values of the ϕ and ψ angles for each type of secondary
structures.
 α helix

• The simplest arrangement the polypeptide chain can assume

that maximizes the use of internal hydrogen bonding from the
C=O and N—H bonds in the peptide backbone
• It is a right-handed helical structure in which the polypeptide
backbone is tightly wound around an imaginary axis and the R
groups of the amino acid residues protrude outward.
• The repeating unit is a single turn of the helix, which extends
about 5.4 Å along the long axis, each helical turn includes 3.6
amino acid residues
• Allows R-group interaction pairing.
• The backbone atoms of the amino acid residues in the α helix
have a characteristic set of dihedral angles that define the
conformation of the α helix, can vary slightly.
• about one-fourth of all amino acid residues in proteins are
found in α helices
 α helix

1
2
3
4

5
6
7

8
α helix
 Why is α helix so stable?

Why does the α helix form more readily than many other possible
conformations?
• optimal use of intrahelical hydrogen bonds
• hydrogen bond between the N-H hydrogen atom first amino acid and
the C=O oxygen of the fourth amino acid
• Even at the ends of an α-helical segment, the three or four groups that
cannot participate in this helical pattern of hydrogen bonding are
either exposed to the surrounding solvent, where they
hydrogen-bond with water, or other parts of the protein may cap the
helix to provide the needed hydrogen-bonding partners.
 The β sheets
• In β-conformation, the backbone of the polypeptide chain is extended into a zigzag
rather than helical structure. More extended conformation of polypeptide chains.
• The zigzag polypeptide chains can be arranged side by side to form a structure
resembling a series of pleats.
• Uses a characteristic set of dihedral angles
• The adjacent polypeptide chains in a β-sheet can be either parallel or anti
parallel (having the same or opposite amino-to-carboxyl orientations).
• The repeat period for parallel conformation= 6.5 Angstrom
• The repeat period for antiparallel conformation= 7 Angstrom
• Example: Silk fibroin and fibroin of spider webs (contains Gly and Ala)
The β strand and β sheets
 Parallel vs anti-parallel sheets

• Hydrogen bonds form between backbone atoms of adjacent segments of

polypeptide chain within the sheet
• R groups of adjacent amino acids protrude from the zigzag structure in
opposite directions, creating the alternating pattern seen in the side view
• The adjacent polypeptide chains in a β-sheet can be either parallel or
anti parallel (having the same or opposite amino-to-carboxyl
orientations).
• The repeat period for parallel conformation= 6.5 Angstrom, whereas the
repeat period for antiparallel conformation is 7 Angstrom
• The inter-strand hydrogen bonds are essentially in-line in the antiparallel
β sheet, but are distorted or not in-line for the parallel variant.
• antiparallel β sheets are found twice as frequently as parallel β sheets.
 β Turns
• In globular proteins, which have a compact folded structure, some amino acid
residues are in turns or loops where the polypeptide chain reverses direction
• These are the connecting elements that link successive runs of α helix or β
conformation
• Particularly common are β turns that connect the ends of two adjacent segments
of an antiparallel β sheet
• The structure is a 180° turn involving four amino acid residues, with the carbonyl
oxygen of the first residue forming a hydrogen bond with the amino-group
hydrogen of the fourth
• The peptide groups of the central two residues do not participate in any
inter-residue hydrogen bonding
 Tertiary structure

• Tertiary structure is the folding of the polypeptide chain as a result of

interactions between the side chains of amino acids that lie in regions of
primary sequence.
• Covalent disulfide bonds from between closely aligned cysteine residues form
the unique Amino Acid cystine.
• Nearly all of the polar, hydrophilic R groups are located in the surface, where
they may interact with water
• The nonpolar, hydropobic R groups are usually located inside the molecule
• tertiary structure includes longer-range aspects of amino acid sequence.
• Amino acids that are far apart in the polypeptide sequence and are in different
types of secondary structure may interact within the completely folded
structure of a protein, through weak interactions
 Hydrophobic effects has the most stabilizing effect
• Hydrophobic amino acid side chains tend to cluster in a protein’s interior,
away from water
• The amino acid sequences of most proteins include a significant content
of hydrophobic amino acid side chains (especially Leu, Ile, Val, Phe, and
Trp).
• These are positioned so that they are clustered when the protein is folded
• forms a hydrophobic protein core.
• This more than counterbalances the large loss of conformational entropy
as a polypeptide is constrained into its folded conformation.
 Polar Groups Contribute
Hydrogen Bonds Protein Folding
• any polar or charged groups in the protein interior usually have suitable
partners for hydrogen bonding or ionic-interactions
• One hydrogen bond seems to contribute little to the stability of a native
structure, but but the presence of hydrogen-bonding groups without
partners in the hydrophobic core of a protein can be very destabilizing
• Hydrogen bonds between groups in a protein form cooperatively
• hydrogen bonds often have an important role in guiding the
protein-folding process
 Ion Pairs in protein folding

• The interaction of oppositely charged groups that form an ion pair, or salt
bridge, can have either a stabilizing or destabilizing effect on protein
structure
• Salt bridges, especially those that are partly or entirely buried, can provide
significant stabilization to a protein structure
• Ionic interactions limit structural flexibility and confer a uniqueness to a
particular protein structure
 van der Waals Interactions work in unison in
folding

• Individually, van der Waals interactions contribute little to overall protein

stability
• Work only over a very small distance, 0.3 to 0.6 nm.
• in a well-packed protein, or in an interaction between a protein and another
protein or other molecule at a complementary surface, the number of such
interactions can be substantial.
• Combination of all these interactions contribute substantially in protein
folding
 Two rules followed by all protein structure

1) Hydrophobic residues are largely buried in the protein interior,

away from water

2) The number of hydrogen bonds and ionic interactions within the

protein is maximized, thus reducing the number of unpaired
hydrogen-bonding and ionic groups
 Tertiary structure of Myoglobin
• Myoglobin contains a single polypeptide chain of 153 amino acid residues of known
sequence and a single iron protoporphyrin, or heme, group
• Myoglobin is particularly abundant in the muscles of diving mammals such as whales,
seals, and porpoises
• how the polypeptide chain is folded in three dimensions:
• Eight relatively straight segments of α helix interrupted by bends
• structure that is largely stabilized by the hydrophobic effect
 Motifs
• Recognizable folding pattern involving two or more
secondary structures
• Example: β-α-β loop and β barrel
 Domain
• A part of a polypeptide chain that is independently stable or could undergo movements as
a single entity with respect to the entire protein
• A polypeptide chain often folds into two or more domains, sometimes with different
functions.
• domain from a large protein will retain its native three-dimensional structure even when
separated (for example, by proteolytic cleavage) from the remainder of the polypeptide
chain
• Change is one domain can cause changes in the adjacent domain, essentially propagating
the change
 Quaternary structure
• Association of different, folded polypeptide chains.
• binding of small molecules may affect the interaction between subunits, causing a
large effect on overall protein’s function
• separate subunits take on separate but related functions, such as catalysis and
regulation
• A multisubunit protein can also be referred to as an oligomer or multimer
 The Function of a Protein Depends on
Its Amino Acid Sequence

• Unique sequence leads to specific structure, structure leads to specific functions

• Amino acid sequences within a protein are not at all random
• Dictated by DNA sequence
• Functional importance of primary structure
• Proteins with different functions always have different amino acid sequences
• Change in amino acid sequence leads to diseases due to production of altered
proteins
• There is a close link between protein primary structure and function is evident,
evident from the sequence homology of functionally similar proteins.
The Function of a Protein Depends on
Its Amino Acid Sequence: GLUT4