Protein Structure and Folding + Physiological Activities of Proteins

Question 1

There are four structures of proteins and they are:

Answer 1

1- Primary structure: linear sequence of amino acids

2- Secondary structure: regions of regularly repeating conformations of the peptide chain, such as a-helices and b-sheets

3- Tertiary structure: describes the shape of the fully folded polypeptide chain (3D structure of the entire polypeptide chain)

4- Quaternary structure: arrangement of two or more polypeptide chains into multi-subunit molecule

Question 2

Type of bond present between polypeptides

Answer 2

Peptide bond

• does not rotate
• most are in trans configuration (99.95%) because the cis configuration (0.05%) is sterically unfavorable (unstable) as the R groups are close to each other hence steric clashes

Question 3

is there a rotation around C-N bond ?

Answer 3

No, its restricted due to the double bond nature of the resonance hybrid form (peptide bond)

Question 4

The pitch, rise, and turn of alpha-helix

Answer 4

Pitch: 0.54nm
Rise: 0.15nm
Turn: 3.6

Question 5

β strands and β sheets

Answer 5

β strands: almost fully extended polypeptide chain
β sheets: multiple β strands arranged side by side

β strands are stabilized by H.B between C–O and -NH on adjacent strands

Question 6

Parallel and Anti-Parallel β strands

Answer 6

Parallel β sheets - strands run in the same N- to -C terminal direction

Anti-Parallel β sheets - strands run in opposite N- to -C terminal directions
in Anti-Parallel β sheets the H.B are nearly vertical and so they are more stable than Parallel β sheets

Question 7

Loops and Turns

Answer 7

they connect α helices and β strands and allow a peptide chain to fold back on itself to make a compact protein structure

Question 8

Super secondary structures (motifs) part 1

Answer 8

Question 9

Super secondary structures (motifs) part 2

Answer 9

Question 10

Classes of Proteins

Answer 10

1- Fibrous proteins: Highly elongated protein molecules that are dominated by a single type of secondary structure such as a-helix or b-sheet.
Examples: a- and b- keratin, silk fibroin and collagen.

2- Globular proteins: Are highly folded protein molecules with single or more than one secondary structure.
Examples: Heat shock proteins, myoglobin, hemoglobin and Cytochrome C

Question 11

α-Keratin (coiled coil)

Answer 11

• Found in Hair, Horn, nails, feathers, etc.
• α-Keratins present in higher mammals and b-Keratins present in birds and reptiles.
• Rich in Cys residues, form intermolecular -S-S- bridges between adjacent polypeptide chains.

Question 12

Silk Protein (b-keratin)

Answer 12

• All -b-sheet
• Insects produce various types of silks to fabricate their nests, cocoons, webs
• Primary structure
• The b-strands of silk fibroin stack-up on one another to form a microcrystalline array in which Gly residues are all arranged on one side and Ala and Ser residues arranged on the other side.

Question 13

Collagen

Answer 13

• Most abundant and insoluble vertebrate protein.
• Main protein in connective tissue, cartilage, tendon and fibrous matrices - Skin and blood vessels.
• A single collagen molecule consists of 3 polypeptide chains.

Question 14

Globular proteins

Answer 14

• Usually water soluble, compact, roughly spherical
• Hydrophobic interior, hydrophilic surface
• Globular proteins include enzymes, carrier and regulatory proteins

Question 15

Domains

Answer 15

• Main polypeptide chain folds into three distinct domains
• Independently folded
• Domain size: ~25 to ~300 amino acid residues
• Domains are connected to each other by loops, bound by weak interactions between side chains
• Domains illustrate the evolutionary conservation of protein structure

Question 16

Polypeptide Domains: Rossmann fold

Answer 16

Michael Rossmann showed that babab motifs provide for the binding of dinucleotides such as NAD and NADP. Accordingly, this motif is know as Rossmann fold.

Some of the motifs act as active sites and some as immunological recognition sites

Question 17

Hemoglobin

Answer 17

• quaternary structuredue to the presence of four protein chain subunits
• four subunits, each having one polypeptide chain and one heme group

Question 18

Hemoglobin S

Answer 18

results from a change in asingle amino acid, or protein building block. This causes mutated proteins to more easily clump together inside red blood cells, forming long, stiff fibers. These fibers make red blood cells more fragile and contort them into the sickle-like shape characteristic of the disorder.

Question 19

Protein Folding

Answer 19

• occupy a low-energy conformation that makes the native structure most stable
• Many proteins can fold spontaneously to this low-energy conformation
• Folding is extremely rapid, the native conformation is generally reached < 1 second

-During folding the polypeptide collapses in upon itself due to the hydrophobic effect

• An intermediate “molten globule” forms with elements of secondary structure
• The backbone is rearranged to achieve a stable native conformation

Question 20

Molecular chaperones

Answer 20

increase rate of correct folding and prevent the formation of incorrectly folded intermediates

Chaperones can bind to unassembled protein subunits to prevent incorrect aggregation before they are assembled into a multisubunit protein

Question 21

HSPs

Answer 21

• Most chaperones are heat shock proteins (synthesized as temperature increases)
• Hydrolysis of several ATP molecules is required
• HSPs expressed during the normal growth process of cell cycle consecutively, but also get induced in cells during various stress conditions produced by cellular insult, environmental changes, temperature, infections, tumors etc.

Question 22

Roles of chaperones in quality control of the proteome.

Answer 22

1- Newly synthesized proteins emerging from the ribosome are either released as unfolded proteins
2- or folded by ribosome-associated chaperones
3- Unfolded and misfolded proteins also arise from various cellular stresses.
4- Some unfolded, misfolded, and non-native proteins require the activity of chaperones to be remodeled into active, native proteins, while others refold spontaneously.
5- Non-native proteins that accumulate tend to form aggregates, although some chaperones are able to provide protection against aggregation.
6- Other chaperone systems reverse the aggregation process by solubilizing aggregates and returning the unfolded polypeptides to the pool of non-native proteins.
7- Some unfolded and misfolded proteins that cannot be rescued by molecular chaperones are targeted for degradation by chaperones that translocate unfolded polypeptides to compartmentalized proteases or the eukaryotic proteasome.

Question 23

Protein Denaturation

Answer 23

Disruption of native conformation of a protein, with loss of biological activity

Question 24

NMR

Answer 24

(nuclear magnetic resonance) is used to analyze protein structure in solution

Question 25

Diseases caused by Protein Mis-folding

Answer 25

• Alzheimer’s Disease
• Mad-Cow Disease
• Parkinkson’s disease
• Cystic Fibrosis
• Cancer and Protein Misfolding

Question 26

X-ray crystallography

Answer 26

used to determine the three-dimensional conformation of proteins

Question 27

Protein structure and stabilization are caused by three effects/forces

Answer 27

• Hydrophobic effect: Nonpolar side chains associate with each other causing a polypeptide chain to collapse to a molten globule
• Van der waals: contacts occur between nonpolar side chains and contribute to the stability of proteins
• charge charge interactions: between oppositely charged side chains in the interior of a protein also may stabilize protein structure

(Intermolecular forces)

Question 28

Structure of each:
Myoglobin
Hemoglobin

Answer 28

(Mb) - monomeric protein that facilitates the diffusion of oxygen in vertebrates
(Hb) - tetrameric protein that carries oxygen in the blood

Question 29

Heme

Answer 29

Consists of a tetrapyrrole ring system called protoporphyrin IX complexed with iron
Heme of Mb and Hb binds oxygen for transport

Question 30

His-93 and His-64 are complexed with..

Answer 30

His-93 is complexed to the iron atom and His-64 forms H.B with oxygen

Question 30

His-93 and His-64 are complexed with..

Answer 30

His-93 is complexed to the iron atom and His-64 forms H.B with oxygen

Question 31

Hemoglobin subunits

Answer 31

Hb is an a2b2 tetramer (2 a globin subunits, 2 b globin subunits)
Each globin subunit is similar in structure to myoglobin
Each subunit has a heme group
The a chain has 7 a helices, b chain has 8 a helices

Question 32

Oxymyoglobin vs Deoxymyoglobin

Answer 32

Oxymyoglobin - oxygen bearing myoglobin
Deoxymyoglobin - oxygen-free myoglobin

Question 33

O2 binding curves

Answer 33

Mb-O2 binding curve is hyperbolic, indicating a single equilibrium constant for binding O2

Hb-O2 binding curve is sigmoidal, and reflects the binding of 4 molecules of O2, one per each heme group

Question 34

A change from one conformation of a molecule to another involves _________.
a. rotation about bonds only
b. breaking and reforming of covalent bonds
c. inversion about a center of symmetry
d. all of the above

Answer 34

a. rotation about bonds only

Question 35

The native ________ is the single shape a protein adopts under physiological conditions.
a. configuration
b. conformation
c. primary structure
d enantiomer

Answer 35

b. conformation

Question 36

Structural proteins that typically assemble into large cables or threads to provide mechanical support to cells or organisms are classified as _________ proteins.
a. fibrous
b. enzyme
c. globular
d. -strand

Answer 36

a. fibrous

Question 37

Alpha-helices belong to ____________ level of structure of a protein
a. primary
b. secondary
c. tertiary
d. quaternary

Answer 37

b. secondary

Question 38

What does it mean to say a protein is oligomeric?
a. In vivo it establishes equilibrium between two or more active conformations.
b. It has more than fifty amino acids.
c. The active protein involves the association of two or more polypeptide chains.
d. The protein has multiple -helices.

Answer 38

c. The active protein involves the association of two or more polypeptide chains.

Question 39

____________ is a technique used to analyze the macromolecular structure of proteins in solution.
a. X-ray crystallography
b. SDS-PAGE
c. affinity chromatography
d. NMR

Answer 39

d. NMR

Question 40

NMR is often used for the determination of ______________ of proteins in solution.
a. the molecular weight
b. the isoelectric point
c. the tertiary structure
d. the pKa

Answer 40

c. the tertiary structure

Question 41

Which is evidence that structures for proteins determined by X-ray crystallography represent the structures in solution?
a. Their similarity to structures determined by NMR.
b. The protein crystals are soluble in water.
c. The proteins must align in a regular pattern to form a crystal.
d. Only one conformation is ever possible for a protein so it is irrelevant whether the protein is in a crystal or in solution.

Answer 41

a. Their similarity to structures determined by NMR.

Question 42

Which statement is not true about the peptide bond?
a. The peptide bond has partial double-bond character.
b. The peptide bond is longer than the typical carbon-nitrogen bond.
c. Rotation is restricted about the peptide bond.
d. The carbonyl oxygen and the amide hydrogen are most often in a trans configuration with respect to one another.

Answer 42

b. The peptide bond is longer than the typical carbon-nitrogen bond.

Question 43

What feature does a Ramachandran plot display?
a. Allowed angles of phi and psi for a polypeptide backbone.
b. amino acids present in a protein-helix.
c. The hydropathic index of amino acids.
d. The variation of pH versus volume of base added during titration to determine the pKa.

Answer 43

a. Allowed angles of phi and psi for a polypeptide backbone.

Question 44

Which represents the backbone of a protein?
Note: R = amino acid side chain
N = nitrogen
C = alpha carbon
C = carbonyl carbon
a. R1R2R3R4R5……….
b. Repeating units of N-C
c. Repeating units of N- C-C
d. Repeating units of C-C

Answer 44

c. Repeating units of N- C-C

Question 45

Ramachandran determined the “allowed” values of the phi and psi angles primarily by considering ______________.
a. pKa values of the amino acids
b. the hydropathic index of amino acids
c. steric hindrance
d. hydrogen bonding effects

Answer 45

c. steric hindrance

Question 46

What is true about the rotation about bonds in a protein backbone?
a. The rotation is free about all bonds in the backbone, except for the bond between the nitrogen and the alpha carbon in proline residues.
b. The bond between the carbonyl carbon and nitrogen is restricted. Other bonds are free to rotate depending only on steric hindrance or the presence of proline residues.
c. All bonds in the backbone have restricted rotation and partial double-bond character.
d. The rotation is free only about the peptide bond. The other bonds are restricted by steric hindrance and the presence of proline residues.

Answer 46

b. The bond between the carbonyl carbon and nitrogen is restricted. Other bonds are free to rotate depending only on steric hindrance or the presence of proline residues.

Question 47

The conformation of the backbone of a polypeptide is described completely by the angle(s) of rotation about which bond(s)?
a. the peptide bond only
b. N-C C only
c. N- C, C-C and C-N bonds
d. N- C and C-C bonds only

Answer 47

d. N- C and C-C bonds only