Proteins II

Question 1

Levels of Protein Structures

Answer 1

Primary (1°) Secondary (2°) Tertiary (3°) Quaternary (4°)

Question 2

“Supersecondary” structure between

Answer 2

2º and 3º

Question 3

the linear sequence of amino acids, and the disulfide bonding pattern, in a polypeptide chain written from N-terminus to C-terminus going left to right. E.g. Met-Asn-Pro is a tripeptide.

Answer 3

1° structure:

Question 4

Proteins can evolve via

Answer 4

genetic mutation

Question 5

Nucleotide replacements can be ________ (e.g., leu to ile) or __________

Answer 5

conservative, non-conservative

Question 6

forms when all the phi and psi dihedral angles of a contiguous stretch of polypeptide adopt the same set of values

Answer 6

2° structure

Question 7

Regular local folding of a short stretch of polypeptide into one of several specific structural forms of secondary proteins:

Answer 7

• Various helices
• Various pleated sheets
• Reverse turns
• Loops (do not have regular, repeating structure)

Question 8

Side chains radiate outward from helix axis Minimizes steric hindrance; allows for protein-protein and protein-ligand interactions (contains hydrogen bonds

Answer 8

The alpha-helix

Question 9

The b-strands are not stable by themselves, but only when incorporated into

Answer 9

sheets

Question 10

Strands can align in either a _____ or an ______manner; mixed sheets are also common

Answer 10

parallel, antiparallel

Question 11

In alpha helix - n (# residues/turn) = ____ p (pitch) = _____ rise/residue = _____

Answer 11

3.6 5.4 Å 1.5 Å

Question 12

In beta strands and beta sheets: n = _______ p = _____

Answer 12

n = 2 residues/unit p = 6.8 Å

Question 13

Silk fibroin

Answer 13

400 kDa protein that has an extensive antiparallel beta sheet structure.

Question 14

REVERSE TURNS

Answer 14

allow a long polypeptide chain to fold back on itself

Question 15

Nearly ___of residues in globular proteins are involved in reverse turns.

Answer 15

1/3

Question 16

What is the most common reverse turn?

Answer 16

the beta-turn

Question 17

Number of residues required to complete a turn in a beta turn

Answer 17

four

Question 18

1st residue hydrogen-bonds to _____ in a beta turn

Answer 18

the 4th

Question 19

common in b-turns but tend to disrupt the a-helix

Answer 19

Gly & Pro

Question 20

the folding of a continuous sequence of 2° elements into a specific and unique three-dimensional architecture.

Answer 20

Protein Tertiary Structure

Question 21

Only about 30 residues long. Uses side chains of 2 His and 2 Cys (or 4 Cys) residues residues to coordinate Zn2+ ion

Answer 21

The Zinc-Finger DNA Binding Motif Occur via H-bonds, salt-bridges and hydrophobic interactions.

Question 22

A feature of some transcription factors (eg., MyoD) that bind DNA and direct transcription, especially during development Forms dimers: 2nd helix involved in dimerization Some similarities to leucine zipper motif

Answer 22

The Helix-Loop-Helix Motif(a type of “supersecondary” structure)

Question 23

How many Ig domains are present with the antibody (Ig) molecule with each domain containing an Ig fold?

Answer 23

12

Question 24

Fold consists of a ___layer sandwich of _____ antiparallel beta-strands arranged in two beta-sheets with a ______ topology

Answer 24

2, 7-9, Greek key

Question 25

largest protein structural family in human genome, with 765 members

Answer 25

Ig “superfamily”

Question 26

proteins with Ig domains:

Answer 26

Titin; fibroblast growth factor receptor (FGFR), a tyrosine kinase; Cadherins, molecules that mediate ca2+ dependent cell-cell adhesion involved in cell polarisation and migration, have one or more Ig-like folds

Question 27

Stores O2 in the muscle

Answer 27

Myoglobin

Question 28

Transports O2 (and CO2, H+) in the blood.

Answer 28

Hemoglobin

Question 29

An elaborate closed barrel structure that contains alternating segments of a-helices and b-strands

Answer 29

The alpha/beta or TIM barrel fold (an alpha/beta domain protein) TRIOSEPHOSPHATE ISOMERASE (TIM) and other glycolytic enzymes (aldolase,enolase, pyruvate kinase) have domains that fold into this structure

Question 30

Topology of 8 antiparallel B-strands linked by Beta-turns

Answer 30

Beta-Barrel Structure: Retinol Binding Protein (a beta domain protein) ex. Retinol (vitamin A) a plasma carrier (RBP)

Question 31

The particular arrangement of two or more polypeptides in association stabilized by non-covalent forces only Each component polypeptide is called a subunit of the oligomer.

Answer 31

Protein Quaternary Structure Each polypeptide has its own 3° fold; each folds into a specific arrangement that functions as a single unit.

Question 32

Some Oligomeric Proteins

Answer 32

Some Oligomeric Proteins

Question 33

• Mammalian enzyme: Allosterically inhibited by ATP, citrate;
• activated by AMP, Fru-2,6-BP
• KEY CONTROL POINT FOR GLYCOLYSIS

Answer 33

Phosphofructokinase-1

•Tetramer of four identical subunits