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MCBM Exam 1 > 3-D Structure of Proteins > Flashcards

3-D Structure of Proteins Flashcards

1
Q

What is the primary organization of proteins?

A

Amino acid sequence + disulfide bonds

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2
Q

What is the secondary organization of proteins?

A

Regular recurring arrangements of adjacent amino acids

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3
Q

What is the tertiary organization of proteins?

A

Arrangement of the total protein, the complete 3D structure

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4
Q

What is the quaternary organization of proteins?

A

The arrangement of multiple protein subunits

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5
Q

When a protein is denatured, what bonds aren’t broken?

A

Disulfide bonds

Peptide bonds

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6
Q

What is a domain, with regards to proteins?

A

A contiguous region with a distinct function

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7
Q

What are some examples of protein domains?

A

DNA binding
Transmembrane
Calcium binding

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8
Q

Peptide bonds and disulfide bonds are both which type of bond?

A

Covalent

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9
Q

Peptide bonds are ___ and ___.

A

Planar and rigid

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10
Q

Which amino acid acts as the “oxidative stress sensor”?

A

Cysteine

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11
Q

What are the 3 major secondary structure types in proteins?

A

Alpha helix
Beta pleated sheet
Beta turn

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12
Q

In alpha helices, where do the peptide bonds align?

A

Along the long axis

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13
Q

In alpha helices, where are the R groups?

A

Sticking out of the sides

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14
Q

Each turn in alpha helices uses about how many amino acids?

A

About 3.6

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15
Q

How are alpha helices stabilized?

A

Lots of hydrogen bonding

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16
Q

Which amino acid is generally a “helix breaker”?

A

Proline

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17
Q

What things are alpha helix destabilizers?

A
  • A string of several basic or acidic amino acids
  • A string of several amino acids with bulky side groups
  • Amino acids 3-4 residues apart which cannot interact
  • Proline residues
  • A string of glycine residues
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18
Q

How are beta pleated sheet chains arranged?

A

May be in parallel or anti-parallel fashion

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19
Q

What is beta pleated sheet?

A

Extended arrangement of polypeptides

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20
Q

What hold the adjacent chains together in beta pleated sheet?

A

Hydrogen bonds

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21
Q

Beta turns contain which amino acid?

A

Proline

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22
Q

In which conformation is proline found in beta turn?

A

The cis conformation

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23
Q

What converts proline from the trans to the cis conformation?

A

Proline isomerase

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24
Q

What are the two major groups of protein tertiary structure?

A

Globular

Fibrous

25
Q

Are fibrous proteins primarily water soluble or insoluble?

A

Water insoluble

26
Q

Which group of proteins (globular or fibrous) are structural proteins?

A

Fibrous proteins

27
Q

How are fibrous proteins usually arranged?

A

In long chains or sheets

28
Q

What are classic examples of right-handed alpha helix?

A

alpha and beta keratin

29
Q

Where is alpha and beta keratin found?

A

Hair
Nails
Feather
etc.

30
Q

What type of amino acids are found in alpha and beta keratin?

A

Many hydrophobic amino acids

31
Q

What is a protofilament?

A

2-stranded superhelix

32
Q

How do alpha and beta keratin crosslink?

A

Via disulfide links

33
Q

To create a perm, what bonds are broken and then reformed?

A

Disulfide bonds

34
Q

How many types of keratin are there in the skin?

A

At least 18

35
Q

Cytokeratins can be diagnostic for what?

A

Tumors

36
Q

Most enzymes and protein hormones are what type of protein?

A

Globular proteins

37
Q

Which structure is more complex in globular proteins than in fibrous proteins?

A

Secondary structure

38
Q

What shape do globular proteins take on, due to the multiple arrangements of folding?

A

“spherical”

39
Q

What are the 4 bond types found in the tertiary structure?

A

Hydrogen bonds
Ionic bonds
Hydrophobic interactions
Van der Waals forces

40
Q

What occurs in an H+ bond?

A

An electronegative atom (Usually O or N) acts as a Hydrogen acceptor

41
Q

What is an ionic bond?

A

Attraction between oppositely charged atoms

42
Q

What are hydrophobic interactions?

A

Forces that hold nonpolar regions together

43
Q

What are van der Waals forces?

A

Weak attractions resulting from transient dipole formation

44
Q

What proteins assist in folding or assembling subunits of a new protein?

A

Chaperone proteins

45
Q

What are the most famous chaperone proteins?

A

Heat shock proteins

46
Q

What causes prion diseases?

A

Improper folding of PrP protein

47
Q

What is Scrapie?

A

Spongiform encephalitis found in sheep

48
Q

What is kuru?

A

Human spongiform disease found in the Fore tribe of New Guinea

49
Q

What is Creutzfeldt-Jacob disease?

A

Sporadic, hereditary degenerative neurologic disease

50
Q

What causes cystic fibrosis?

A

Defective protein folding

51
Q

Which protein is missing an amino acid leading to cystic fibrosis? Which amino acid is missing?

A

Chloride channel protein is missing Phe-508

52
Q

When is quaternary structure found in proteins?

A

Only if the protein has more than one protein subunit

53
Q

What are some huge proteins with quaternary structure?

A

Pyruvate dehydrogenase
Ribosomes
RNA polymerase

54
Q

What is the best way to study protein structure?

A

Via x-ray crystallography

55
Q

What things will denature the secondary-quaternary structure of proteins?

A

Heat
pH extremes
Detergents
Organic solvents (alcohol, acetone, urea)

56
Q

How can the primary protein structure be broken?

A

Boiling in a strong acid or base

57
Q

What things can cleave proteins at specific dipeptide sites?

A

Proteases

58
Q

What chemical can be used to reduce disulfide bonds?

A

Beta-Mercaptoethanol (BME)

59
Q

Tertiary structure is dictated by what?

A

Primary structure

MCBM Exam 1 (7 decks)

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