2. Protein Structure, Folding

Question 1

Primary, secondary, tertiary and quaternary structures of proteins

Answer 1

(pic)
Primary structure- AAs linked by peptide bonds
Secondary structure-H bonds btwn main chain CO and NH gps
Tertiary structure-folding into 3D structure
Quaternary structure-interaxn btwn diff subunits

Question 2

Primary structure

Answer 2

Covalent linkage of the α-carboxyl (COO-) group of one amino acid with the α-amino (NH3+) group of the next amino acid
Amide linkage known as the peptide bond
Involves condensation with the liberation of water
Breaking a peptide bond requires the addition of water (hydrolysis)

Question 3

Peptide bond

Answer 3

Has a partial double bond nature

Has hydrophilic properties-water soluble

Question 4

Peptide unit

Answer 4

A peptide unit consists of the Cα and C=O group of one amino acid and the NH and Cα of the next amino acid, all in the same plane
The R groups are in trans configuration (so less stereo constraint)
Each peptide unit can partially rotate around the N-Cα bond (Φ-phi) and the Cα-C bond (Ψ-psi)
Such rotation gives some flexibility to protein chains

Question 5

Reading AA sequence

Answer 5

Free amino end of the peptide chain (N-terminal) is on the left
Free carboxyl end of the peptide chain (C-terminal) is on the right
All amino acid sequences are read from the N-terminal to the C-terminal

Question 6

Secondary Structure (2 types- rigid)

Answer 6

α helix
-linked by H bonds btwn carbonyl carbons and NH gps of same chain

β pleated sheet
-stacked polypeptide chains that are linked by H bonds btwn chains (not same chains, but adjacent chains)

Flexible irregular structure – random coil
-Random coils occur btwn alpha helices, or btwn alpha helices and beta sheets

Question 7

α Helix

Answer 7

Main chain C=O and N-H groups, that are four residues apart, hydrogen bonded to each other
Intrachain H bond
Founded by Linus Pauling

A rigid, rod-like structure
Average length: 12 residues (range: 5-45)
-Residue=AA in polypeptide chain
Forms spontaneously 
Peptide unit planes are parallel to the axis of the helix
3.6 amino acid residues per turn 
R groups (side chains) extend outward
Right-handed

Question 8

β Pleated Sheet

Answer 8

(pic)
Laterally packed β strands
5-8 residues long, extended config
Hydrogen bonds between adjacent strands
R groups above and below the plane of the pleated sheet

Adjacent strands in either antiparallel or parallel orientation

-Antiparallel
C-N on top, N-C on bottom (opp orientations)
Alternate wide and narrow spacing between hydrogen bonds

-Parallel
Even spacing between hydrogen bonds
Sim orientations (N-C on top and bottom)

Question 9

β Bend or Turn

Answer 9

Allows a tight U turn, reversing direction
Helps to form a compact structure
Generally composed of:
-Glycine – has the smallest R group
-Proline – causes a kink in the polypeptide chain (Pro is called a Helix Breaker)

Question 10

Super Secondary Structures

Motifs

Answer 10

(pic)
Combinations of secondary structure elements
Form the interior (core region) of globular proteins
Connected by loop regions at the surface of the protein
Eg beta-alpha-beta; hairpin (betas); alpha-alpha; folds of alpha-beta-etc to get Greek key

Question 11

Tertiary Structure

Answer 11

Refers to the overall folding of a polypeptide chain
Combination of secondary structure elements (motifs) into domains

Stabilized by interactions between R groups (side chains)
Hydrophobic interactions
Hydrogen bonds
Ionic bonds (btwn 2 charged gps)
Disulfide bonds (btwn cysteines)
Metal ion complexes (bring two AA’s together)

Question 12

Domain Structures

Answer 12

(pic)
α Domain- alpha helices linked by random coil structures
(eg Myoglobin, Hemoglobin)

β Domain (β-can)- beta sheets with random coils
(eg Green Fluorescent Protein)

B-sheet – cleaved protease w carboxyl end (eg carboxypeptidase)

β-barrel eg Triose-p isomerase-enzyme in carb metabolism in glycolysis

B-a-b loops come together to make ab barrel (eg pyruvate kinase)

Question 13

Hydrophobic Interactions

Answer 13

interactions between the nonpolar molecules eg btwn R groups of isoleucine and leucine

Question 14

Ionic bonds

Answer 14

aka electrostatic bonds

complete transfer of valence electron(s) between atoms and is a type of chemical bond that generates two oppositely charged ions

Question 15

Disulfide Bonds

Answer 15

S-S bond, or disulfide bridge, is a covalent bond derived from two thiol groups (eg Insulin)

Denaturation by reducing agents:
Cysteine + (2 H) reducing agent –> 2 cys

Question 16

Metalloproteins

Answer 16

(pic)
Protein that contains a metal ion cofactor
Brings otherwise far aa’s together
Eg Zinc finger domain (Steroid hormone receptors) and copper binding domain (plastocyanin)

Question 17

Quaternary Structure

Answer 17

(pic)
Quaternary structure involves multiple polypeptide chains (subunits)
The subunits may be identical or different
Eg hemoglobin (2α, 2β)- ea subunit in Hb has heme, which binds oxygen
Eg insulin (hexamer- 6 polypeptide units) (has zinc ion in middle)

Subunits held together by non-covalent interactions
Hydrogen bonds
Electrostatic (ionic) 
Hydrophobic
Metal ions

Subunits may function independently or cooperatively
-eg Hemoglobin has 4 subunits that bind/release oxygen in a cooperative fashion

Question 18

Types of Protein Folding

Answer 18

Spontaneous Protein Folding (Some proteins fold into their native conformation spontaneously)

Assisted Protein Folding
Other proteins require the assistance of helper proteins called chaperones or heat shock proteins
This process uses the energy from ATP
Don’t need to know specific names of chaperones or heat shock proteins

Question 19

Structure and Function are Interrelated

Answer 19

Incorrect shape/Misfolding of proteins causes defective function often leading to disease states
Two examples of protein misfolding are prion disease and amyloidosis

Other causes of disease

• Over-abundance of protein
• Deficiency/absence of protein

Question 20

Misfolding - Prion Disease

Answer 20

(pic)
Known as Cruetzfeldt-Jakob disease in humans, Scrapie in sheep and Mad Cow disease in cattle
Caused by misfolding of PrP (a helical) into PrPSc (more β sheets) which aggregates
PrPSc induces normal PrP to change its conformation to the rogue form

Question 21

Misfolding - Amyloidosis

Answer 21

Native monomer -> misfolding -> b-sheet oligomers -> amyloid fibrillar aggregates
Misfolded proteins tend to assume β sheet structures, oligomerize (aggregates) and form aggregates known as amyloid fibrils in brain, kidneys, etc.
Amyloid fibrils are seen in several diseases eg Alzheimer’s, Parkinson’s, Huntington’s, ALS (amyotrophic lateral sclerosis), frontotemporal lobar degeneration