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EOM Test 1 > Proteins: Higher Orders Of Structure > Flashcards

Proteins: Higher Orders Of Structure Flashcards

1
Q

What is secondary structure and what are the two common forms?

A

Secondary Structure refers to a local spatial arrangement of the polypeptide backbone

A-helix
B-Sheet

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2
Q

What is the structure of the a-helix?

A

Coil held in shape by H-bonds between amide and carbonyl groups of AAs

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3
Q

How does AA sequence affect helix stability?

A

Small hydrophobic residues are strong helix formers (Ala and Leu)
Proline is a helix breaker
Gly is a helix breaker
Attractive or repulsive interactions between side chains 3-4 AAs apart

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4
Q

Describe the structure of a B-pleated sheet

A

Polytpeptide chains arranged side by side
Can be parallel or anti parallel in orientation
H-bonds stabilize the chains

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5
Q

What is the difference in H-bonding between B-sheets and a-helixes?

A

B-sheets: H-bonds are perpendicular to the polypeptide backbone

A-helix - H-bonds are parallel tot he backbone

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6
Q

Describe the structure of B-turns

A

A 180 degree turn accomplished over 4 amino acids

Pro and gly occur frequently in B-turns

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7
Q

Why are 6% of peptide bonds involving proline in the cis configuration?

A

These proline residues are mostly involved in B-turns

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8
Q

What is cyclophilin?

A

A proline isomerase

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9
Q

What is tertiary structure?

A

The entire three-dimensional conformation of a polypeptide. How secondary structures form domains

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10
Q

What is a domain?

A

Section of a protein sufficient to perform a particular chemical or physical task.

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11
Q

What forces stabilize a protein’s tertiary structure?

A 
Hydrophobic interactions
Hydrophilic interactions
Salt Bridges
H-bonds
Disulfide bonds
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12
Q

What are the pros and cons of using X-Ray Crystallography to determine protein structure?

A

Pros - no size limits, well-established

Cons-Difficult for membrane proteins, can’t see hydrogen’s

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13
Q

What are the pros and cons of using NMR to determine protein structure?

A

Pros - no need to crystallize, can see many H’s

Cons - difficult for insoluble proteins, works best for small proteins

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14
Q

What is the Quaternary structure of a protein?

A

Formed by combination of two or more tertiary subunits.

Stabilized by same forces as tertiary.

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15
Q

What is the role of Chaperons in protein folding?

A

Responsible for segregating hydrophobic regions of proteins into the interior of the protein.

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16
Q

Name 6 ways proteins can be denatured

A 
Temperature
PH
Organic Solvents
Heavy Metals
Chaotropic agents (e.g. detergents/urea)
Agitation/whipping
17
Q

What two residues are post-translationally modified and involved in the inter-molecular cross-linking of collagen?

A

Lysine and Proline

Modified to hydroxyLys and HydroxyPro

18
Q

What is the role of prolyl Hydroxylase?

A

Adds hydroxyl groups to prolyl residues

Facilitates intra-chain H-bonding

19
Q

What is Lysyl oxidase and what is its role?

A

A Copper continent Extracellular enzyme that catalyzes the cross-linking of collagen fibrils.

Oxidatively deaminates lysine to Hydroxylysine, forms cross links with other lysine residues.

20
Q

What is Elastin?

A

Fibrillar protein found lungs, arteries, elastic ligaments, skin and bladder

21
Q

What is desmosine and what is its purpose?

A

Desomsine is a cross-link formed in elastin

Lysyl oxidase catalyzes the formation of this cross-link between three lysine residue side chains.

22
Q

What is the function and role of a-1 antitrypsin?

A

Inhibits several proteases including elastase.

Protects from emphysema and COPD.

23
Q

What proteolytic pathway degrades extracellular and cell surface proteins?

A

Endosome-Lysosome pathay

24
Q

What proteolytic pathway degrades cytoplasmic, nucleic, and ER proteins?

A

Upiquitin-proteasome pathway

25
Q

What is the axial ratio of fibrous proteins? Globular?

A

Fibrous - >10

Globular - < 3

26
Q

Where is fibrillar collagen synthesized in connective tissue? Bone? Cartilage?

A

Connective - fibroblasts

Bone - Osteoblasts

Cartilage - chondroblats

27
Q

What four cofactors are required for the prolyl hydroxylase reaction?

A

A-ketoglutarate

Oxygen

Iron

Ascorbate (Vitamin C)

28
Q

What happens as a result of ascorbic acid deficiency?

A

Formation of a stable triple helix is impaired.

Results in Scurvy
-skin discoloration and gum and teeth problems

29
Q

What is the cause of Menke’s disease?

A

Copper deficiency, leads to premature birth and nervous system deterioration. Affected individuals usually don’t live past 3

30
Q

What is Lathyrism and its cause?

A

Consumption of sweet pea seeds inhibit lysyl oxidase.

Characterized by skeletal and vascular problems

31
Q

What is Ehlers-Danlos syndrome?

A

Heterogenous group of connective tissue disorders that result from heritable defects in the metabolism of fibrillar collagen molecules

32
Q

What is tropoelastin?

A

The basic soluble unit of Elastin.

EOM Test 1 (17 decks)

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