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Physiology Exam 1 > Medical Biochemistry Lecture 4 > Flashcards

Medical Biochemistry Lecture 4 Flashcards

1
Q

Primary Structure

A

protein adopt specific three-dimensional conformations

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2
Q

Native fold

A

has a large number of favorable interactions within the protein

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3
Q

What does protein. structure have?

A

the lowest Gibbs free energy

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4
Q

True or False: This structure can fulfill a specific biological function

A

True

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5
Q

Hydrophobic effect

A

water makes the best hydrogen bonds with itself and is disrupted by other molecules
-Hydrophobic groups aggregate, hiding their entire surface from water, which creates a structured salvation layer around the molecule

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6
Q

Van der Waals (London dispersion)

A

-attractive force due to induced dipoles in all atoms
-important to the stability in the interior of the protein

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7
Q

hydrogen bonds

A

-Interaction of N-H and C=O if the peptide bond leads to local regular structure such as alpha helices and Beta sheets
-Maximized in protein structure, allow polar molecules to traverse interior protein

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8
Q

Ionic interactions

A

-long range strong interactions between permanently charged groups
-salt-bridges, especially buried in the hydrophobic environment strongly stabilize proteins

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9
Q

Disulfide Bridge

A

-mostly in secreted proteins
-generally not found in reducing environment of cell

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10
Q

What are the four levels of protein structure?

A

Primary, Secondary, Tertiary, Quaternary

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11
Q

Peptide bond

A

partial double bond

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12
Q

Resonansance in peptide bonds allows a what configuration because of steric hindrance

A

trans

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13
Q

Is rotation around the peptide bond permitted?

A

no

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14
Q

Is rotation around connected on the alpha carbon permitted

A

yes

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15
Q

bulky R groups generally are on what sides?

A

opposite

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16
Q

phi

A

angle around alpha carbine: amide nitrogen bond

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17
Q

psi

A

angle around the alpha carbon-carbonyl carbon bond

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18
Q

In a fully exited polypeptide, both phi and psi are what degrees

A

180

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19
Q

The peptide are _____
but bulk-R groups on adjacent alpha carbons can interfere

A

planar

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20
Q

What two possible conformations can peptide bonds exist?

A

trans highly favorable except for proline( which can be found 6 percent in cis conformation in beta turns)

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21
Q

Secondary structures

A

local spatial arrangement of the polypeptide backbone

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22
Q

Secondary structure of alpha helix

A

-stabilized by H-bond between new\arby residues
-25% of amino acids in this conformation(highly variable between proteins)

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23
Q

Secondary structure of beta sheets

A

stabilized by H-bond between adjacent segments that may be far away

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24
Q

Random coli

A

irregular arrangement of the polypeptide chain

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25
Q

alpha helix

A

the helical backbone is held together by hydrogen bonds between an amide hydrogen of one amino acid and a carbonyl oxygen four amino acids away, maximizing bonds

26
Q

What hand helix is 3.6 residues (5.4) per turn giving a twist?

A

right

27
Q

Peptide bond are aligned roughly parallel with

A

helical axis

28
Q

another characteristics of the alpha helix

A

sides pot out and roughly perpendicular with the helical axis

29
Q

What is the inner diameter

A

4-5 A

30
Q

What residues align nicely on top of each other

A

1 and 8

31
Q

Peptide bond has a strong dipole movement with

A
  • carbonyl, + amide
32
Q

where does negatively charge residues occurs

A

near the positive end of the helix dipole

33
Q

All polypeptides sequences adopt an alpha helical structures

A

False: Not all polypeptide sequences adopt an alpha helical structures

34
Q

Small hydrophobic residues such as what are strong helix formers

A

Ala and Leu

35
Q

What amino acid serves as a helix breaker and why?

A

Pro because the rotation around the N-C alpha bond is impossible

36
Q

What other amino acids serves as a helix breaker and why?

A

Gly because the tiny R group supports other conformations

37
Q

Attraction or repulsive interactions between side chains 3-4 amino acids apart will affect

A

formation

38
Q

Why is non polar side chains along each alpha helix can be arranged?

A

their side chain groups contact another helix

39
Q

coiled coil

A

this allows side groups to pack neatly only when the alpa helices interact at 18 degrees from parallel. If alpha helices remained parallel, could stain contact for only few residues

40
Q

Multiple coils

A

helical bundle

41
Q

What can an alpha helix supercoiling be

A

tertiary or quaternary

42
Q

Beta sheets

A

the planarity of the peptide bond ad tetrahedral geometry of the alpha carbon create a pleated sheet-like structure

43
Q

How are the side chains in beta sheets?

A

alternating in up and down direction

44
Q

How are beta sheets in proteins?

A

twist in a right-handed manner

45
Q

Whare the two orientation of beta sheets?

A

parallel and antiparallel

46
Q

Parallel Beta sheets

A

the H-bonds strands run in the same direction; bent H-bonds(weaker)

47
Q

Antiparallel B-sheets

A

the H-bonds stands run in opposite direction, linear H-bonds (stronger)

48
Q

When does beta turns occurs?

A

frequently when the strands of the B sheet changes direction

49
Q

How is 180 degree accomplished in a B turn?

A

over 4 amino acids

50
Q

How is the turn stabilized?

A

H-bond from carbonyl oxygen to amide proton three residues down the sequence

51
Q

What are common in B turns?

A

Proline(cis) in position 2 or a flexible glycine in position 3

52
Q

Tertiary structure

A

overall spatial arrangement of atoms in a protein

53
Q

How is tertiary structure stabilized?

A

numerous weak and strong interactions between amino acids side chain, often far apart in the primary sequence

54
Q

What are the two major class of tertiary structure?

A

fibrous and globular(water or lipid soluble)

55
Q

what do proteins have?

A

motifs(folds)

56
Q

What is the strongest influence on protein folding?

A

Burial of hydrophobic(non polar) side chains into the core of the polypeptide’s structure

57
Q

What happens in aqueous solution regarding the hydrophobic core?

A

proteins with a large number of non polar side groups will tend to internalize the non polar residues and be more stable than proteins containing mostly polar groups

58
Q

True or False: Polar bonds can H-bond with water, and thus a smaller free energy would be gained from packing polar groups vs non polar groups

A

True

59
Q

Change is G is more positive than non polar packing

A

False

60
Q

Why do some alpha helices have alternating polar and non polar amino acids

A

to improve packing of helical bundles

61
Q

Transmembrane proteins have a long stretches of how many non polar amino acids to cross the membrane?

A

20

Physiology Exam 1 (6 decks)

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