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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

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
____regions interact with water.
Hydrophilic
26
What are the tertiary structure bond types
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
What is the tertiary structure folding
Proteins dont fold randomly. Most proteins use chaperone proteins to assist in folding
28
What are the most famous chaperone proteins
Heat shock proteins
29
What does Iatrogenic refer to
of or relating to illness caused by medical exam or treatment
30
What are prion diseases caused by
improper folding of Prp protein
31
What is Mad Cow Disease
Bovine spongiform Encephalitis
32
What is Scrapie
Spongiform encephalitis found in sheep
33
What is Kuru
human spongiform disease limited to Fore tribe of New Guinea
34
What is Creuzfeldt-Jacob
sporadic, hereditary, acquired
35
What is cystic fibrosis
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
What are the characteristics of quaternary structure
Only found in proteins with more than 1 protein subunit
37
What are some proteins with quaternary structure
1. pyruvate dehydrogenase 2. ribosomes 3. RNA polymerase
38
What is the best way to study proteins?
X-ray crystallography
39
What is protein denaturation
Disrupts weak interactions; destabilizes the structure and becomes less thermodynamically stable
40
Protein denaturation does NOT disrupt ____bonds
covalent (peptide and disulfide)
41
What are some protein denaturants
1. heat 2. pH extremes 3. detergents 4. organic solvents (alcohol, acetone, urea)
42
What is protein hydrolysis
Disruption of primary structure by hydrolysis to single aa by boiling in strong acid or base
43
What are proteases enzymatically?
enzymes that cleave proteins at specific dipeptide sites
44
T/F denatured proteins can be renatured
True
45
AA's critical for proper folding are _____ which means that mutations in codons for these aa are very deleterious (harmful_
invariant
46
Urea ____proteins
denatures
47
BME ____disulfide bonds
reduces
48
Primary structure dictates ____structure
tertiary
49
What two 3D protein structures are important in the progression of Eale's Disease and are current targets for drug design
retinal s antigen and interphotoreceptor retinoid binding protein

MCBM (59 decks)

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