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Exam 1: DHHD 5001 > Proteins (Serwer 1) > Flashcards

Proteins (Serwer 1) Flashcards

1
Q

Proteins of bone and dentin

A
  • Collagen (type 1)
  • Fibronectin
  • Osteocalcin
  • Osteopontin
  • Bone sialoptotein
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2
Q

Major structural protein, 90% of total protein in bone and dentin

A

Collagen (type 1)

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3
Q

Helps direct formation of and needed to maintain collagen matrix in bone and dentin

A

Fibronectin

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4
Q

Minor in amount, but important in bone and dentin

A
  • Osteocalcin

- Osteopontin

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5
Q

Glycoprotein of bone and dentin

A

Bone sialoprotein

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6
Q

Non-collagenous proteins constitute ____% of bone protein, ___% of them coming from serum, and ___% from bone cells. Functions are not well characterized.

A
  • 10-15
  • 25
  • 75
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7
Q

Typical Composition of Bone and Percent by dry weight

A
  1. Hydroxyapatite (50-70%)
  2. Collagen (20-40%, mostly type 1)
  3. Non-collagen proteins (1-2%)
  4. Lipids (3%)
  5. Water (5-10%)
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8
Q

Polymers with 3D structures that promote functions including enzymatic activity and formation of essential structures

A

Proteins

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9
Q

Molecules that consist of repeating subunits

A

Polymers

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10
Q

The repeating subunit of a protein

A

Amino acid

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11
Q

The linkage between amino acids in a protein is _______.

A

An amide linkage

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12
Q

The primary structure of a protein is ________.

A

The sequence of amino acids

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13
Q

Rotation around the peptide bond is restricted by _____.

A

Resonance (partial double bond)

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14
Q

Describe secondary structure

A

3-dimensional, local

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15
Q

The rotation angles of the other two bonds are ________.

A

Sterically restricted

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16
Q

Spiral staircases with amino acid steps

A

Alpha helices

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17
Q

Alpha helices: ___ steps/turn, or interact ___ steps away

A

3.6

4

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18
Q

Alpha helices: ___ nm/residue

A

0.15

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19
Q

Alpha helices: Sidechains project _______

A

Up and out

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20
Q

Alpha helices: _____ handed

A

Right (rotates clockwise)

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21
Q

Alpha helices: ____ and ____ amino acids uncommon

A
  • Pro

- Gly

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22
Q

Alpha helices: The donor-backbone _____ and acceptor-backbone _____ form a ______ bond

A
  • Amide nitrogen
  • Carbonyl oxygen
  • Hydrogen
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23
Q

Fully extended conformations

A

Beta strands

24
Q

Beta strands: The distance between neighboring resides is ____ vs 0.15 nm in alpha helix.

A

0.35

25
Q

Beta strands: Strands pair via donor-acceptor backbone _____ bond like those that stabilize alpha helices.

A

Hydrogen

26
Q

Beta strands: ______ often connects adjacent anti-parallel strands

A

Sharp, four-residue turn (B-turn)

27
Q

Beta strands can align both ____ and ____ to form beta sheets.

A

Parallel and Antiparallel

28
Q

Beta strands: side chains project above and below the sheet in an ______ fashion.

A

Alternating

29
Q

Beta strands: Amino acid resides with _____, _____ chains are most common

A

Bulky, branched

30
Q

_____ B-sheet can wrap as a helix forming a _____

A

Parallel

B-helix

31
Q

Beta strands: variations in proteins

A

B-hairpin

Greek key

32
Q

Collagen Triple Helix is rich in ______ which point to _____ of helix

A

Glycine (smallest amino acid; makes up about 1/3)

Inside

33
Q

The collagen trip helix is a _________ with ____ residue per turn.

A

Stretched, left handed alpha helix

~3

34
Q

The collagen trip helix lacks ____-strand H-bonds

A

Intra

35
Q

NMR spectroscopy requires a ______ of the purified protein (~___mL at high concentration), while X-ray crystallography requires _______ (~__mm in each dimension).

A
  • Soluble solution (0.25)

- Well-ordered crystal (0.1)

36
Q

NMR spectroscopy uses a sample placed in ______, while X-ray crystallography _______.

A
  • Strong magnetic field

- Irradiates the crystal with high intensity x-rays

37
Q

NMR spectroscopy can be applied to proteins of ____, while X-ray crystallography can be applied to proteins of _____.

A
  • Up to 50 kDa

- Any size

38
Q

______ is emerging and done with a frozen sample which has many pictures taken and makes final image.

A

Cryo-electron microscopy

39
Q

Refers to the three-dimensional structure of the entire polypeptide chain

A

Tertiary structure

40
Q

Tertiary structure: The 3D structure is stabilized by ____ bonds, _____ and _____ interactions, and _____ linkages between _____ residues.

A
  • Hydrogen
  • Electrostatic (+ and -)
  • Hydrophobic
  • Disulfide
  • Cysteine (forms cystine)
41
Q

_____ states that tertiary structure is determined by primary structure.

A

Anfinsen Hypothesis

42
Q

____ or ____ unfolds protein and ____ breaks S-S bonds

A

Urea or Guanidine hydrochloride

B-mercaptoethanol

43
Q

Proteins are renatured by removing denaturants by _____.

A

Dialysis

44
Q

Stabilization of tertiary structure is dependent on ____ and ____ interactions

A
  • Hydrophobic

- Electrostatic

45
Q

The arrangement of protein subunits in a multimeric complex

A

Quaternary structure

46
Q

Quaternary structure: the individual polypeptide chains are ____ of the multimeric complex

A

Subunits

47
Q

Quaternary structure: subunits associate into a quaternary structure though the _____ bonds that stabilize tertiary structures of proteins.

A

Same

48
Q

Quaternary structure: the _________ is one of the most well-known and highly characterized multi-protein complexes

A

Hemoglobin heterotetromer

49
Q

Describe the method(s) that could be used to determine the three-dimensional structure of a 35 kDa protein.

A
  • NMR spectroscopy
  • X-ray crystallography
  • Cryo-electron microscopy
50
Q

The partial double bond character of the peptide bond restricts neighboring groups to a single _______ .

A

Plane

51
Q

If an atom-sized gremlin climbed an α-helix as though the α-helix were a staircase and then looked straight up, how far above the gremlin would the next stair be?

A

1.5 nm

52
Q

By how many degrees must you rotate when going from one amino acid to the next in an α-helix?

A

360 degrees/ 3.6 = 100 degrees

53
Q

How does beta-sheet structure differ from that of α-helix? What is meant by parallel and anti-parallel chains?

A
  • Beta is stretched so that the distance between amino acids is greater
  • Parallel chains have the N to C terminus running in the same direction
54
Q

Define tertiary structure.

A

The way in which secondary structures are configured

55
Q

Define denaturation and renaturation as applied to proteins.

A
  • Denaturation is breaking secondary and tertiary structure

- Renaturation is bringing it back

56
Q

What was the fundamental principle tested in the studies conducted by C.B. Anfinsen on protein renaturation?

A

Whether tertiary structure is determined by primary structure

57
Q

In general, what are three roles that a protein can play in a cell?

A

Scaffold, enzyme, structure

Exam 1: DHHD 5001 (14 decks)

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