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BIOCHEM EXAMs > L12 Proteins > Flashcards

L12 Proteins Flashcards

1
Q

Define a protein

A

Proteins are macromolecules made up of amino acid building blocks.

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2
Q

How many common amino acids are in human proteins?

A

20

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3
Q

Amino acids are classified according to what?

A

the chemical properties of the R-group

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4
Q

Name the specific group terms for each arrow

A

Blue = Carboxylic group

Red = Central alpha carbon atom

Green = Side chain

Pink = Amino Group

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5
Q

Nonpolar amino acids are ________.

A

Hydrophobic

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6
Q

List the nonpolar amino acids

A

Alanine (Ala) (A)

Glycine (Gly) (G)

Isoleucine (Ile) (I)

Leucine (Leu) (L)

Methionine (Met) (M)

Phenylalanine (Phe) (F)

Proline (Pro) (P)

Tryptophan (Trp) (W)

Valine (Val) (V)

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7
Q

List the polar (neutral) amino acids

A

Asparagine (Asn) (N)

Cytesine (Cys) (C)

Glutamine (Gln) (Q)

Serine (Ser) (s)

Threonine (Thr) (T)

Tyrosine (Tyr) (Y)

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8
Q

List the negatively-charged polar amino acids

A

Aspartate (Asp) (D)

Glutamate (Glu) (E)

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9
Q

List the positively-charged polar amino acids

A

Arginine (Arg) (R)

Histidine (His) (H)

Lysine (Lys) (K)

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10
Q

There are how many essential amino acids that are not synthesized in the body and have to be supplied in the diet?

List them.

A

8

Isoleucine

Leucine

Lysine

Methionine

Phenylalanine

Threonine

Tryptophan

Valine

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11
Q

The primary structure of a protein is the ________.

A

Amino acid sequence

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12
Q

The secondary structure of a protein is the _______

A

Alpha helix and beta sheet

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13
Q

True or False?

The primary structure is the order in which the amino acids are linked together.

A

True

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14
Q

The amino acids are linked through their _______ by ________ to form a polypeptide chain or backbone.

A

Head groups; peptide bonds

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15
Q

True or False?

The amino end on the first amino acid is added to the carboxyl end of the first one.

A

False

The amino end on the SECOND amino acid is added to the carboxyl end of the first one.

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16
Q

True or False?

The amino terminus of the first amino acid remains unchanged, and polypeptide grows in the carbon to nitrogen direction.

A

False.

the polypeptide grows in the Nitrogen to Carbon direction

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17
Q

The repeating N-C(R)-C subunit remaining after the dehydration reaction is an ________.

A

amino acid residue

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18
Q

Peptide bond have a partial double bond character due to what?

A

Peptide bonds are a resonance structure

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19
Q

Which conformation of a peptide bond is favored?

A

Trans conformation

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20
Q

True or False?

With a planar peptide bond, bond rotation is hindered because peptide bond has resonance.

A

True

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21
Q

True or False?

Bond rotation is only allowed on either side of each peptide bond.

A

True

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22
Q

Peptide bonds form what kind of bonds with side chains?

A

Hydrogen bonds

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23
Q

What determines the secondary structure of a protein?

A

the attractive and repulsive forces among the amino acids

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24
Q

In the coiling of the protein chain, there are how many amino acid residues per turn?

A

3.6

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25
Q

The ______ of a protein alpha helix stick out at right angles from the backbone of the chain.

A

side chains (R groups)

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26
Q

The alpha helix of a protein is stabilized by H-bonds between ___________ and ________of the backbone, which are directed along the axis of the helix.

A

Oxygen on the carboxyl group and Hydrogen on the amino group

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27
Q

What is the beta sheet of a protein?

A

The layering of protein chains one on top of another

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28
Q

What holds the beta sheets of a protein together?

A

the H-bonds of the backbone

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29
Q

How are the side chains situatated in relation to the beta sheets?

A

The side chains (R groups) are situated at right angles to the sheets.

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30
Q

True or False?

The secondary structure of a protein does not include the hairpin turn.

A

False

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31
Q

How is the hairpin turn formed?

A
  • The polypeptide chain folds back on itself by nearly 180˚
  • A H-bond between the 1st and 3rd peptide bond stabilizes the turn.
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32
Q

What are hydrophobic interactions?

A

The clustering of hydrophobic groups away from water.

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33
Q

What is the tertiary structure of a protein?

A

the overall 3-D arrangement of its polypeptide chain in space

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34
Q

What stabilizes the tertiary structure of a protein?

A

On the outside: polar hydrophilic hydrogen, disulfide bridges and ionic bond interactions, and

On the inside: hydrophobic and van deer Waals interactions between nonpolar amino acid side chains

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35
Q

How is the tertiary structure of a protein formed?

A

The protein twists and turns to minimize the unfavorable interactions and maximize the favorable ones until the most stable shape or conformation is found.

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36
Q

What is a disulfide bond?

A

The sulfur-sulfur linkages between two Cysteine residues which may be far apart from each other in the primary structure but are brought close together as a result of protein folding.

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37
Q

True or False?

Covalent disulfide bond resulted from reduction.

A

False.

Covalent disulfide bond resulted from oxidation

38
Q

What is Bovine pancreatic trypsin inhibitor (BPTI) protein and what makes it so special?

A

One of the most stable proteins known due to the 3 disukfide bonds formed between its 6 cysteine residues.

It is resistant to unfolding reagents, such as urea, and exhibits thermal denaturation below 100 ℃ only in very acidic solutions

39
Q

What is the effect of the 3 disulfide bonds of Bovine pancreatic trypsin inhibitor (BPTI) protein?

A

The effect is partly entropic; –S–S– reduce the number of conformations possible in the unfolded state.

40
Q

In the thermal denaturation of Bovine pancreatic trypsin inhibitor (BPTI) protein, percent of denaturation is a function of _____ at pH 2.1.

A

Temperature

41
Q

At pH 2.1, most proteins would be denatured at _________.

A

room temperature

42
Q

At pH 2.1, the melting temperature (Tm) for reversible denaturation of BPTI is about ______.

A

80 ℃

43
Q

If only one of the disulfide bonds (the one between cysteine residues 14 and 38) has been reduced and carboxymethylated, the Tm is decreased to _______.

A

60 °C

44
Q

True or False?

Even if all the disulfide bonds in BPTI are reduced, the protein is still unfolded at room temperature.

A

True

45
Q

The ionic bonds of the tertiary structure of proteins are also known as ______.

A

Salt bridges

46
Q

What are the ionic bonds of the tertiary structure of a protein?

A

A combination of two noncovalent interactions:

Hydrogen bonds and electrostatic interactions between the carboxylate ion of an acidic residue (Asp, Glu) and the ammonium ion of a basic residue (Lys, Arg, His).

47
Q

Of the tertiary structure of a protein, which bonds are the most important and why?

A

the hydrogen bonds and van der Waals interactions.

Because:

  1. There are more possible opportunities for van der Waals and H-bonding interactions than covalent disulfide bonds (Cys) and ionic bonds (limited number of amino acids).
  2. Proteins are surrounded by water and covalent and ionic bonds will form bonds with water before anything else.
48
Q

As the hydrophilic amino acids form H-bonds with water, the number of ionic bonds contributing to the tertiary structure is _______.

A

Reduced

49
Q

What bonds largely determine the 3-D shape of the protein?

A

Hydrophobic and van der Waals interactions

50
Q

What is the quarternary structure of a protein?

A

A Complex of two or more protein molecules whose subunits are the individual polypeptide molecules.

51
Q

What holds the quarternary structure of a protein together?

A

Van der Waals interactions between the exterior surfaces of proteins.

  • Two protein molecules form a dimer such that the two hydrophobic areas face each other rather than be exposed to an aqueous environment.
52
Q

The amino acid sequence of proteins that determines the secondary and tertiary structures is dictated by ___________.

A

the nucleotide sequence of mRNA

53
Q

mRNA sequences are determined by _________.

A

DNA sequences

54
Q

True or False?

Proteins are synthesized in the cytosol.

A

False.

Proteins are synthesized in ribosomes.

55
Q

Certain key amino acids at the proper positions are essential for the _______ of proteins into a functional, unique ________.

A

folding; 3-D conformation

56
Q

True or False?

Out of hundreds of millions of conformational possibilities, ONLY a single conformational form is associated with a functional protein.

A

True

57
Q

What are the 3 thermodynamic factors that influence folding and stability of proteins?

A
  1. Favorable intramolecular enthalpic interactions.
  2. The Unfavorable loss of conformational entropy.
  3. The Favorable gain of solvent entropy from burying hydrophobic groups
58
Q

What is meant by the “unfavorable loss of conformational entropy” in reference to the thermodynamic factors that influence protein folding and stability?

A

The Unfolded state of a protein has many conformations (high entropy) while the folded state of a protein has only a few closely related conformations (low entropy)

59
Q

The Favorable gain of solvent entropy from burying hydrophobic groups influences the thermodynamic factors regulating protein folding and stability because?

A

As hydrophobic side chains cluster in the solvent-inaccessible interior they release ordered solvent molecules from clathrate structures and the folded state is stabilized

60
Q

What are the Favorable intramolecular enthalpic interactions that influence the thermodynamic factors regulating protein folding and stability?

A

The charge-charge interactions (ionic bonds; salt bridges)

The intermolecular hydrogen bonds

The van der Waals interactions that cause the proteins to be densely packed

61
Q

What is the formula for the entropy of protein folding?

A
62
Q

Proteins vary in the extent to which the folded state is favored by _________.

A

enthalpic or entropic factors

63
Q

In the formula Δ G = Δ H − T Δ S

What happens to the value of T Δ S from the unfavorable decrease in conformational entropy?

A

It’s value increases i.e. becomes positive

64
Q

In the formula Δ G = Δ H − T Δ S

What happens to the value of T Δ S from the favorable hydrophobic effect?

A

It’s value decreases, i.e. becomes negative

65
Q

the positive value of T Δ S from the favorable hydrophobic effect and the negative value the value of T Δ S from the unfavorable decrease in conformational entropy causes the NET value of T Δ S to become ______.

A

Positive for folding

66
Q

If the NET value of T Δ S is positive for folding, what is the value of Δ G and Δ H?

A

They are both negative and favorable for folding

67
Q

The stability of myoglobin comes mainly from the _______.

A

hydrophobic effect

68
Q

What must the thermodynamic parameters be for release of Ribonuclease A?

A

Δ G = -46

Δ H = -280

Δ S = -0.79

69
Q

What must the thermodynamic parameters be for release of Chymotrypsin?

A

Δ G = -55

Δ H = -270

Δ S = -0.72

70
Q

What must the thermodynamic parameters be for release of Lysozyme?

A

Δ G = -62

Δ H = -220

Δ S = -0.53

71
Q

What must the thermodynamic parameters be for release of Cytochrome C?

A

Δ G = -44

Δ H = -52

Δ S = -0.027

72
Q

What must the thermodynamic parameters be for release of Myoglobin?

A

Δ G = -50

Δ H = 0

Δ S = +0.17

73
Q

What two enzymes are essential to the hydrophobic effect and what thermodynamic value determines their involvment?

A

Cytochrome C and Myoglobin

It’s their Δ S value that determines if the hydrophobic effect can occur.

74
Q

What is the denaturation of a protein and what does it cause?

A

When a native protein is subjected to heat or change of pH.

The soluble form of globular proteins undergoes coagulation to give fibrous proteins which are insoluble in water, causing loss in the biological activity of the protein

75
Q

The process of directing and targeting the folding of intermediate polypeptides to the fully folded structures is aided, in some instances, by proteins known as _________.

A

molecular chaperones (also called chaperonins)

76
Q

Chaperones bind reversibly to _________ and prevent their ___________________.

A

unfolded polypeptide segments; misfolding and premature aggregation

77
Q

What are heat-shock proteins?

A

A major class of chaperones that are synthesized in both prokaryotic and eukaryotic cells in response to heat shock or other stresses.

78
Q

How do heat-shock proteins (HSP) help cells in response to heat shock or other stresses?

A

They stabilize nascent (freshly generated in a reactive form.) polypeptides and also are able to re-conform denatured forms of polypeptides

79
Q

How do heat-shock proteins (HSP) produced?

A

They increase their expression when the cells which contain them are exposed to high temperatures or other stresses.

  1. Stress conditions dennature proteins
  2. Denatured proteins are detected.
  3. HSPs are produced.
  4. HSPs refold denatured proteins
80
Q

What non-stressful conditions produce heat-shock proteins?

A
  1. monitoring the cell’s proteins by carrying old proteins to the cell’s “recycling bin” (proteasome)
  2. helping newly synthesised proteins fold properly
81
Q

What is unique about glycine with respect to other natural amino acids?

A

It has no side chain

82
Q

What are the characteristics of a peptide bond?

A

a) It is PLANAR
b) It is capable of forming a hydrogen bond.
c) The TRANS configuration is favored. CIS IS UNFAVORED
d) Single bond rotation is NOT permitted between nitrogen and the carbonyl group BC ITS PLANAR; ROTATION IS ONLY ALLOWED AT SIDE CHAIN

83
Q

True or False?

The ability of peptide bonds to form intramolecular hydrogen bonds and the steric influence of amino acid residues are important to secondary structure.

A

True

84
Q

Interactions between ________ are important in protein tertiary structure.

A

Amino acid residues

85
Q

What is the strongest form of intermolecular bonding that could be formed involving the residue of the amino acid valine?

A

van der Waals interactions BC ITS HYDROPHOBIC

86
Q

__________ refers to the arrangement of different protein subunits in a multiprotein complex.

A

Quaternary structure

87
Q

What is the strongest form of intermolecular bonding that could be formed involving the residue of the amino acid serine?

A

hydrogen bond DUE TO -OH GROUP

88
Q

What is the strongest form of intermolecular bonding that could be formed involving the residue of the amino acid arginine?

A

ionic bond BC OF + CHARGED NITROGEN

89
Q

What is the strongest form of intermolecular bonding that could be formed involving the residue of the amino acid glutamic acid?

A

Ionic bond

90
Q

What is the strongest form of intermolecular bonding that could be formed involving the residue of the amino acid tyrosine?

A

Hydrogen bond

91
Q

Proinsulin, the precursor of insulin, is one peptide chain that contains three disulfide bonds. Protease cleavage releases a middle segment of the peptide chain, which leaves two peptide chains held together via two disulfide bonds. Which one of the following is most accurate?

A

Figure A

The question text states that proinsulin is one peptide chain (Figure B and Figure D are wrong).

It further states that insulin is two peptide chains (Figure C is wrong).

Note that solid lines are used to represent peptide chains and dashed lines represent disulfide bonds.

92
Q

What bonds/interactions are responsible for maintaining quaternary structure of a protein?

A. The same bonds/interactions responsible for the tertiary structure

B. Polar covalent bonds between alpha carbons

C. The same bonds/interactions responsible for the primary structure

D. The same bonds/interactions responsible for the secondary structure

A

A. The same bonds/interactions responsible for the tertiary structure

BIOCHEM EXAMs (10 decks)

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