Proteins II

Question 1

______ allows folding of long polypeptide chains onto themselves. What fraction of globular protein’s residues does this structure make up?

Answer 1

• Reverse turns

- 1/3

Question 2

Fibroin in silk has two stacked sheets of interdigitating ___ residues as well as ____/____ residues

Answer 2

• Glycine

- Serine/Alanine

Question 3

In an alpha-helix:
n= ____ (residues/turn)
p= ____ (anxtrums)

Answer 3

• 3.6

- 5.4

Question 4

What is the number of rises/residue in an alpha helix?

Answer 4

1.5 Anxtrums

Question 5

What are the components of a heme group? (2)

Answer 5

• protoporphyrin IX ring

- Iron (Fe2+)

Question 6

Name the 3 globin folded proteins

Answer 6

• hemoglobin
• myoglobin
• lysozyme

Question 7

Retinol must be transported via _____ from the liver to peripheral tissues because it is hydrophobic. What structure does this transporter have?

Answer 7

• RBP (Retinol binding protein)

- Beta-Barrel

Question 8

Disease may occur from ______ replacement of amino acids in a sequence.

Answer 8

Nonconservative

Question 9

Which protein structure forms when all of the Phi and Psi dihedral angles of a polypeptide adopt the same set of values?

Answer 9

Secondary

Question 10

Compared to alpha helices, ______ are not stable by themselves, but only when incorporated into sheets. What is their length compared to an alpha helix?

Answer 10

• Beta strands

- longer (more extended)

Question 11

Name 3 ways Beta-strands can align:

Answer 11

1) Parallel
2) Anti-parallel
3) Mixed

Question 12

In Beta sheets, how do the side chains project -Above and below the plane of the sheet in order to _________. This allows the sheets to stack.

Answer 12

-minimize steric clash

Question 13

Reverse turn types I and II differ in the orientation of the ______ linking residues ___ & ___.

Answer 13

• peptide unit

- 2 & 3

Question 14

______ are located on the surface of proteins and participate in reactions with other molecules. They don’t have regular repeating structure but are well defined structurally.

Answer 14

Loops

Question 15

Tertiary structure is the folding of secondary elements into a specific, unique 3D structure. Tertiary structure schemes include ______, _______, and _______.

Answer 15

• alpha
• beta
• alpha/beta

Question 16

_____ and _____ can be used to determine the structure of tertiary proteins.

Answer 16

• X-ray crystallography

- NMR-spec

Question 17

_____ and ____ comprise super-secondary structures and are small, non-repeating structural units found in proteins.

Answer 17

• folds

- motifs

Question 18

What allows a domain to act as a single entity?

Answer 18

It is a structurally independent folding unit

Question 19

What cofactor is required for Zinc Motif formation?

Answer 19

Zn2+

Question 20

Name the 4 glycolytic enzymes that are alpha/beta folds.

Answer 20

TAPE

1) Triose Phosphate Isomerase (TIM)
2) Aldolase
3) Pyruvate Kinase
4) Enolase

Question 21

_________ are elaborate closed structures of alternating alpha helices and beta strands

Answer 21

TIM Barrels

Question 22

Quaternary proteins are normally ONLY stabilized by ______ (but _____ may be present)

Answer 22

• noncovalent forces

- disulfide linkages

Question 23

In beta-strands, the number of residues/unit (n) is ____ while the pitch (in anxtrums) is _____.

Answer 23

• 2

- 6.8

Question 24

In what direction do side chains radiate from the axis? What does this arrangement minimize?

Answer 24

• outward

- steric hindrance

Question 25

Secondary Protein structure can be folded into 4 forms. What are these forms?

Answer 25

1) Reverse turns 2) Loops 3) Pleated-sheets 4) Helices

Question 26

What is the most common Reverse Turn?

Answer 26

-Beta turn

Question 27

What are the 4 residues required for a functional beta turn require and what kind of bond forms?

Answer 27

- i, i+1, i+2, & i+3 | - Hydrogen bonding between the i and i+3

Question 28

What amino acids are common in beta turns but tend to disrupt alpha helices?

Answer 28

Glycine and Proline

Question 29

The Zinc-Finger motif is about 30 residues long and uses which possible side chains ?

Answer 29

- 2 Cysteins + 2 Histidines | - 4 Cysteins

Question 30

The Zinc-Finger motif binds into a major groove of a ______ via hydrogen bonding, salt bridges, and ______ interactions.

Answer 30

- DNA-Double helix | - Hydrophobic

Question 31

What motif is common in transcription factors (involved in binding DNA and directing transcription).

Answer 31

Helix-loop-helix motif

Question 32

Which portion of the helix-loop-helix motif is involved in dimerization?

Answer 32

the 2nd helix

Question 33

Ig folds consist of 7 to 9 ______ arranged into a greek key topology.

Answer 33

anti-parallel beta strands

Question 34

Cadherins mediate Ca2+ dependent cell adhesion during cell ______ and ______.

Answer 34

- migration | - polarization

Question 35

What type of hetero-tetramer is Hemoglobin?

Answer 35

alpha-2, beta-2

Question 36

Which glycolytic enzyme is a tetramer of four identical subunits. What sites do these tetramers consist of?

Answer 36

- Phosphofructokinase-1 (PFK-1) | - 4 catalytic and 4 regulatory