Classes of Proteins

Question 1

The Classes of Proteins:

Answer 1

Based on structure and solubility, proteins
can be grouped into three large classes:

.1.Fibrous Proteins
2. Globular Proteins
3. Membrane Proteins

Question 2

Fibrous:

Answer 2

proteins in this class are
elongated molecules with well-defined
secondary structures and function primarily
in a structural role, i.e. they hold things
together.

a- and b-keratins, fibroin, collagen, elastin

Question 3

Globular:

Answer 3

most of
the catalytic work is
done by this class
of protein so named
because of their
compact 3-D fold.
* Synthesizing, transporting, metabolizing,
catalyzing, etc

Question 4

Fibrous Proteins contain…

Answer 4

polypeptide
chains organized parallel along a single
axis, producing long fibers or large sheets.

• They are mechanically strong, play
  structural roles in nature;
• Difficult to dissolve in water;
• a-Keratins, Fibroin and Collagen are
  examples of fibrous proteins

Question 5

The properties of fibrous proteins typically…

Answer 5

impart strength and/or
flexibility to the structures in which they are found.

Simple repeating unit of a given secondary structure.

Question 6

Fibrous proteins are..

Answer 6

insoluble in water, due to a high percentage of
hydrophobic amino acids associated with them.

Composed of supramolecular complexes, wherein the hydrophobic
surfaces pack against each other, and are thus excluded from water.

Question 7

a-Keratin are found in…

Answer 7

hair, fingernails, claws, horns, beaks, and a large fraction of animal skin.

Question 8

a-Keratin sequence consists…

Answer 8

of 311-314 residue alpha helical rod segments
capped with non-helical N- and C-termini

Question 9

Primary structure of helical rods consists

Answer 9

of 7-residue repeats, which
promote association of helices
b-keratins are found in silk and consist of gly-ala repeat sequences;

• Ala is small and can be packed within the sheets

Question 10

The keratins: a-keratins are…

Answer 10

major proteins of hair
and fingernails and a large fraction of animal skin.

Question 11

Individual molecules contain

Answer 11

long sequences over 300 residues that are wholly a-helical.

Pairs of these molecules twine about one
another in a left-handed coiled-coil structure.
(amino acid side chains interdigitate).

Question 12

In hair, two coiled…

Answer 12

coils further twist
together to form a 4 molecule protofibril.

8 protofibrils combine to make a microfibril
that is the basis of hair structure

Question 13

The keratins (a) properties:

Answer 13

They are stretchy and flexible, but can be hardened by the introduction of
disulfide cross-links within the several levels of fiber structure. (12% CYS)

Question 14

Structure of a-keratin

Answer 14

Found in hair, wool, nails, claws, quills, horns, hooves, and
the outer layer of skin.

Question 15

a-keratins are found in

Answer 15

hair and nails. Nails have
more disulfide cross-links than hair, therefore are
less flexible than hair.

Question 16

The process of introducing a “permanent wave” into
human hair involved

Answer 16

reduction of the disulfides,
rearrangement of the fibers and re-oxidation to “set
the waves”.

Question 17

b-keratins, as their name implies

Answer 17

contains the
much more extended b-sheet structure. Thus, they
are much less flexible than helical a-keratins.

• b-keratins are found in structures like the feathers
  and scales of birds and reptiles.

Question 18

Another b-sheet protein is
Fibroin…

Answer 18

found in the fibers
spun by silkworms and spiders.

Silkworm fibroin contains long
regions of antiparallel b-sheet
interrupted by periodic
compactly folded regions

Question 19

The b-sheet regions comprise multiple..

Answer 19

repetitions containing Gly, Ser and
Ala residues such that they pack on top of one another making them
strong, inextensible yet flexible.

This is because bonding between the sheets involves only weak van der
Waals interactions between the side chains, which provide little resistance
to bending.

Question 20

Silk is composed of…

Answer 20

fibroin proteins, which
are composed mainly
of stacked antiparallel
b-sheets.

Question 21

In antiparallel sheets…

Answer 21

hydrophobic side chains
will typically be on just
one face of the sheet,
while hydrophilic side
chains will reside on the
other.

Question 22

Globular proteins are more…

Answer 22

numerous than
fibrous proteins in cells. Globular proteins can
be classified according to the type and
arrangement of secondary structure

Question 23

Globular Proteins: Richardson’s classification

Answer 23

-Antiparallel alpha helix proteins

-Parallel or mixed beta sheet proteins

-Antiparallel beta sheet proteins

• Metal-and disulfide-rich proteins

This classification is too simple to reflect the
function and evolutionary origins of proteins.

Question 24

Packing of Globular Proteins: 1/2

Answer 24

*Secondary structures pack closely to one another and
also intercalate with extended polypeptide chains

*Most polar residues face the outside of the protein and
interact with solvent

• Most hydrophobic residues face the interior of the protein
  and interact with each other

Answer 25

*van der Waals’ volume is about 72-77% of the total protein volume; about 25% is not occupied by protein
atoms. These cavities provide flexibility in protein
conformation and dynamics.

• Random coil or loops maybe of importance in protein
  function (interacting with other molecules, enzyme
  reactions)

Question 26

Atomic motions:

Answer 26

are random and within short
distances (~0.5Å). These motions are arise from
kinetic energies and are a function of temperature.

Question 27

Collective motions:

Answer 27

refer to motions of a group of
atoms as a single unit. Usually longer distance and
slower.

Question 28

Conformational changes:

Answer 28

involve motions of
domains or segments in proteins. May occur in
response to stimuli.

Question 29

Protein structures are…

Answer 29

dynamic

Question 30

Levinthal’s Paradox:

Answer 30

a new folding view is needed

Consider a protein with 100 amino acids

Question 31

Levinthal’s paradox illustrates

Answer 31

that proteins
must only sample through limited
conformations, or fold by “specific pathways”.

Much research effort is devoted to searching
for the principles of the “specific pathways”.

Question 32

Folding Pathways (hypothesis)

Answer 32

• protein folding is
  initiated by reversible and rapid formation of
  local secondary structures

-Secondary structures then form domains
through the cooperative aggregation of
folding nuclei.

-Domains finally form the final protein through
“Molten globule” intermediates.