Biochemistry Chapter 6 Proteins: Three Dimensional Structure

What is a primary structure of a protein?

Its linear sequence of amino acids

What is secondary structure of a protein?

the local spatial arrangement of a polypeptide's backbone atoms without regard to the conformations of its side chains

What is tertiary structure of a protein?

the 3D structure of an entire polypeptide, including its side chains

Many proteins are composed of two or more what?

polypeptide chains/subunits

What does a proteins quarternary structure refer to?

The spatial arrangement of its subunits

What do proteins secondary structures include?

helices, sheets, and turns

What group has a rigid, planar structure as a consequence of resonance interactions, giving peptide bond double-bond character?

Peptide group

What is trans conformation of peptide groups?

In which successive C alpha atoms are on opposite sides of the peptide bond joining them

What is the cis conformation of peptide groups?

Less stable than the trans-conformation because of steric interference between neighboring side chains

What amino acid is the only exception that cis conformations are less stable?

Proline: 10% of Proline residues in proteins follow a cis peptide bond

How can the conformation of the backbone (main chain) be described?

By the Torsion Angles around the bond (Cα-N)- Φ and the bond (Cα-C) ψ of each residue

What are sterically constrained of the polypeptide backbone?

Conformational freedom and the torsion angles

Rotation around the Cα-N and Cα-C bonds to form certain combinations of and Φ and
ψ angles will cause what?

The amide hydrogen, the carbonyl oxygen, or the substituents of
Cα of adjacent residues to collide and make those combinations impossible

What does the Ramachandran Diagram indicate?

Allowed conformations of polypeptides

Most combinations of Φ and ψ represent what?

Forbidden conformations

In a Ramachandran Diagram Blue-shaded regions indicate what?

sterically allowed Φ and ψ
angles

In a Ramachandran Diagram green-shaded regions indicate what?

the more crowded Φ and ψ angles

In a Ramachandran Diagram Yellow circles represent what?

conformational angles of secondary structures, EXCEPT GLY & PRO

What residues do polypeptide chains assume conformations that are
forbidden to other residues?

Glycine( GLY)

What are common regular secondary structures?

Both α helix and β sheet

What is a coil that has favorable hydrogen bonding pattern and Φ and ψ values that fall within allowed regions of the Ramachandran plot?

α helix

How many residues per turn does a right handed α helix have?

3.6

What pitch does a right handed α helix have?

5.4

What is the average length of α helices of proteins?

12

How are backbone hydrogen bonds arranged?

Such that the
peptide bond (C=O) of the nth residue points along the helix axis toward the peptide N-H group of the (n+4) residue.
This results in a strong hydrogen bond

How do amino acid side chains project from the helix to avoid steric interference ?

Projects outwards and downwards

How is the core of the helix packed?

tightly

What kind of bond does β sheet utilize?

Hydrogen bonding

How does hydrogen bonding occur in β sheets?

hydrogen bonding
occurs between neighboring
polypeptide chains rather than within one as in α helix

In antiparallel sheet neighboring
hydrogen-bonded polypeptide
chains run in what direction?

Opposites

In parallel sheet, the hydrogen-bonded chains extend in what direction?

Same direction

What kind of appearance does β sheets have?

a rippled or pleated appearance

Successive side chains of a polypeptide chain in a
β sheet extend to where?

opposite sides of the sheet with a two residue
repeat distance of 7.0 Å

How many proteins do β sheets carry?

2 to as many as 22
polypeptide strands, with an average of 6 strands.

Each stand of β sheet may contain up to how many residues?

UP to 15 residues but the average of 6 residues

Which is less stable? Parallel sheets or antiparallel sheets?

Parallel sheets are less stable than antiparallel sheets
β Sheets contain mixtures of parallel and antiparallel
strands and exhibit right-handed twist

What is a Twist in sheets?

a consequence of interactions between chiral L-amino acid residues in polypeptide chains and
distorts sheet's inter-chain hydrogen bonds

What is the geometry of a β sheet comprised of?

A compromise between
optimizing the conformational energies of its polypeptide
chains and preserving its hydrogen bonding.

What do turns connect?

units of secondary structures

What is the connection of two antiparallel strands?

Small loop

What is the link between tandem parallel strands?

must be a crossover connection that is out
of the plane of the sheet

What can the connecting link be?

extensive containing helices

How are α helices or the β strands of sheets are
sometimes joined?

by bends that change their direction

What are proteins classified as?

fibrous or globular, depending on their
morphology.

What doe fibrous proteins have?

a protective, connective, or supportive role in living organisms
Ex: keratin and collagen

They have a repeated secondary structure

What is α Keratin?

Coiled coil

What is Keratin?

a mechanically durable and relatively unreactive protein that
occurs in all higher vertebrates (hair, horn, nails, feathers) two keratin
polypeptides helices twist around each other to form a left-handed coil
(coiled coil structure)

What are Coiled coil dimers packed into ?

protofilaments, two protofilaments
constitute a protofibril, Four protofibrils constitute a microfibril, which
associates with other microfibrils to form a macrofibril.

What is Keratin rich in?

Cys
residues, which form
disulfide bonds, crosslinking
adjacent
polypeptide chains

Collagen is what kind of Helix?

Triple Helix

When does collagen occur?

occurs in all multicellular animals, and is the most abundant
vertebrate protein.