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MCBM > Protein Structure > Flashcards

Protein Structure Flashcards

1
Q

What is the 3D structure of Proteins

A
  1. Determined by amino acid sequence
  2. determines function of protein
  3. unique for each protein
  4. maintained by non-covalent interactions
  5. Has several recurring motifs
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2
Q

What are the 4 levels of protein architecture

A
  1. Primary: Amino acid sequence + disulfide bond
  2. Secondary: Regular recurring arrangements of adjacent amino acids.
  3. Arrangements of the total protein, the complete 3D structure
  4. Arrangement of multiple protein subunits
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3
Q

The primary structure can be derived from ____sequence

A

gene

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4
Q

The primary structure includes _____ and ____bonds

A

peptide; disulfide

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5
Q

The primary structure can give important clues to probable _____

A

protein function

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6
Q

Contigous regions of a protein with a distinct function or structure is called a

A

domain

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7
Q

Peptide bonds and disulfide bonds are both ____bonds

A

covalent

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8
Q

Peptide bonds are ____and ____

A

planar; rigid

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9
Q

What includes the secondary structure

A
  1. alpha helix
  2. beta sheet
  3. beta turn
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10
Q

What do alpha helices consist of

A
  1. Peptide bonds align along long axis
  2. R groups stick out of sides
  3. each turn -3.6 aa
  4. every 3-4 aa in close proximity and stabilize through H bonding
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11
Q

What are alpha helix destabilizers

A
  1. String of several basic or acidic aa’s
  2. String of several aa with bulky side groups
  3. aa 3-4 residues apart which cannot interact
  4. Proline residues (“helix breakers”)
  5. String of glycine residues
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12
Q

What are the characteristics of beta pleated sheets

A
  1. Extended arrangement of polypeptides
  2. H bonds hold adjacent chains together
  3. Chains may be arranged in parallel or anti parallel fashion.
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13
Q

What are characteristics of Beta turn

A

Contain proline in the cis conformation; requires proline isomerase to convert it

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14
Q

What are characteristics of tertiary structure

A
  1. 3D arrangement

2. Brings distant regions into close proximity

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15
Q

What are the two major groups of tertiary structure

A
  1. Globular

2. Fibrous

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16
Q

What are fibrous proteins

A
  1. Primarily water insoluble
  2. Structural proteins
  3. Simple arrangement
  4. Usually long chains or sheets
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17
Q

What do fibrous proteins consist of

A

Alpha and beta keratin

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18
Q

What are fibrous proteins found in

A

Hair, nails, feathers

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19
Q

What are characteristics of fibrous proteins

A
  1. Classic, right handed a helix
  2. Many hydrophobic aa
  3. 2 stranded superhelix= protofilament
  4. Crosslinks via disulfide links
  5. Permanent wave solution breaks, reforms disulfide bonds
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20
Q

How many types of keratin are found in the skin

A

18

21
Q

What are cytokeratins

A

components of the intermediate filaments of the cytoskeleton

22
Q

What are the characteristics of globular proteins

A
  1. All other proteins
  2. Most enzymes and protein hormones
  3. Secondary structure is more complex
  4. Multiple arrangements of folding into a “spherical” shape
23
Q

How do water molecules arrange themselves

A

in an orderly manner to form “cages” around hydrophobic groups

24
Q

____groups tend to be sequestered internally.

A

Hydrophobic

25
Q

____regions interact with water.

A

Hydrophilic

26
Q

What are the tertiary structure bond types

A
  1. H bonds: an EN atom (usually O or N) acts as a H acceptor
  2. Ionic bonds: Attraction bet oppositely charged atoms
  3. Hydrophobic interactions
  4. Van der Waals: Weak attractions resulting from transient dipole formation.
27
Q

What is the tertiary structure folding

A

Proteins dont fold randomly. Most proteins use chaperone proteins to assist in folding

28
Q

What are the most famous chaperone proteins

A

Heat shock proteins

29
Q

What does Iatrogenic refer to

A

of or relating to illness caused by medical exam or treatment

30
Q

What are prion diseases caused by

A

improper folding of Prp protein

31
Q

What is Mad Cow Disease

A

Bovine spongiform Encephalitis

32
Q

What is Scrapie

A

Spongiform encephalitis found in sheep

33
Q

What is Kuru

A

human spongiform disease limited to Fore tribe of New Guinea

34
Q

What is Creuzfeldt-Jacob

A

sporadic, hereditary, acquired

35
Q

What is cystic fibrosis

A

Caused by defective protein folding
-chloride channel protein (CFTR) is missing a single amino acid (Phe- 508) due to a triplet deletion in the coding sequence of the gene.

36
Q

What are the characteristics of quaternary structure

A

Only found in proteins with more than 1 protein subunit

37
Q

What are some proteins with quaternary structure

A
  1. pyruvate dehydrogenase
  2. ribosomes
  3. RNA polymerase
38
Q

What is the best way to study proteins?

A

X-ray crystallography

39
Q

What is protein denaturation

A

Disrupts weak interactions; destabilizes the structure and becomes less thermodynamically stable

40
Q

Protein denaturation does NOT disrupt ____bonds

A

covalent (peptide and disulfide)

41
Q

What are some protein denaturants

A
  1. heat
  2. pH extremes
  3. detergents
  4. organic solvents (alcohol, acetone, urea)
42
Q

What is protein hydrolysis

A

Disruption of primary structure by hydrolysis to single aa by boiling in strong acid or base

43
Q

What are proteases enzymatically?

A

enzymes that cleave proteins at specific dipeptide sites

44
Q

T/F denatured proteins can be renatured

A

True

45
Q

AA’s critical for proper folding are _____ which means that mutations in codons for these aa are very deleterious (harmful_

A

invariant

46
Q

Urea ____proteins

A

denatures

47
Q

BME ____disulfide bonds

A

reduces

48
Q

Primary structure dictates ____structure

A

tertiary

49
Q

What two 3D protein structures are important in the progression of Eale’s Disease and are current targets for drug design

A

retinal s antigen and interphotoreceptor retinoid binding protein

MCBM (59 decks)

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