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Biochemistry > Amino acids ch. 6 and 7 > Flashcards

Amino acids ch. 6 and 7 Flashcards

1
Q

All amino acids except _____ have L forms

A

Glycine

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2
Q

What two things bind to peptide bonds bond

A

O- of one amino acid to NH3+ of another one

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3
Q

Zwitterion

A

Amino group is positively charged and carboxyl group is negatively charged

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4
Q

Cysteine forms what bonds

A

Disulfide

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5
Q

MM form

A

Skeletal muscle

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6
Q

BB form

A

Brain

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7
Q

MB form

A

Cardiac muscle

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8
Q

What protein will be leaked during a myocardial infarction

A

Troponin

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9
Q

Posttranslational modifications

A

Occur after the protein has folded into into a 3D structure

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10
Q

Primary structure

A

Covalent sequence of amino acid residues

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11
Q

Secondary structure

A

Regular, repeating noncovalent structure resulting from H bonding

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12
Q

Tertiary structure

A

Determined by R group interactions, includes hydrogen binding

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13
Q

Quartenary structure

A

Multiple subunits binded through noncovalent interactions

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14
Q

Side chains are ____ to each other and alternate above and below peptide chain

A

Trans

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15
Q

What forms a series of rigid planes in a protein

A

C and N of peptide bonds

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16
Q

What translates mRNA into protein

A

Ribosomes

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17
Q

mRNA is translated in which direction

A

5’ to 3’
N terminal to C terminal

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18
Q

What do the coils and folds from the secondary structure result from

A

Hydrogen bonds

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19
Q

Coiled

A

a-helix

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20
Q

Folded

A

b-pleated sheet

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21
Q

What AA is a helix breaker

A

Proline

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22
Q

Structure of secondary structure

A

Each O of carbonyl attaches to H from NH group,

determined by backbone interaction, Hydrogen bonded

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23
Q

What determines tertiary structure

A

Interactions between R groups, NOT backbone components

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24
Q

What are strong covalent bonds called

A

Disulfide bridges

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25
Q

What do chaperone proteins do

A

Prevent misfolding of protein by shielding the hydrophobic surfaces

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26
Q

Hsp70 proteins

A

Bind to polypeptides that are synthesized on ribosomes

Shields hydrophobic forces to prevent misfolding

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27
Q

Hsp60 proteins (chaperonins)

A

Assist Hsp70 and have ATPase activity

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28
Q

AGEs

A

Advanced glycosylation end products

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29
Q

Denaturants

A

Heat
lower than a pH of 3
Urea

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30
Q

Removal of denaturants can lead to

A

Protein renaturations

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31
Q

Prions

A

Proteins that induce bad conformation of protein

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32
Q

Myoglobin

A

Monomer of globin

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33
Q

Heme has how many rings

A

4 pyrole rings

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34
Q

Proximal histidine blinds to what on heme

A

Fe2+ on side of poryphyrin ring

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35
Q

T state

A

Tense state with LOW affinity for O2

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36
Q

R state

A

Relaxed state with HIGH affinity for O2

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37
Q

Nonpolar, aliphatic amino acids

A

Glycine, Alanine, proline, valine, leucine, isoleucine, METHIONINE, TRYPTOPHAN, PHENYLALINE

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38
Q

Aromatic amino acids

A

Phenylaline, tyrosine, tryptophan

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39
Q

Polar, uncharged amino acids

A

asparagine, glutamine, serine, threonine, CYSTEINE, TYROSINE

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40
Q

Negative charge (acidic)

A

Asparate, glutamate

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41
Q

Positive charge (basic)

A

Arginine, lysine, histidine

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42
Q

Variant region

A

Noncritical region

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43
Q

Hypervariable region

A

Many different amino acid residues tolerated at that region

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44
Q

Conservative substitutions

A

Replace one AA with another one with a similar structure

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45
Q

Invariant region

A

Forms binding sites, same AA sequence between individuals or species

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46
Q

polymorphism

A

Variants of an allele that occurs with a significant frequency

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47
Q

What is PI points

A

Isoelectric point
the pH at which the charge is 0

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48
Q

Superfamily

A

Very large families of homologous proteins

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49
Q

Isozymes

A

Catalyze the same reactions

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50
Q

Isoforms

A

Have same function, but different properties and sequence structures

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51
Q

What hormone is highly conserved between species with no amino acid substitutions

A

Insulin

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52
Q

Structure of insulin

A

One long polypeptide chain, cleaved by protease after disulfide bonds form

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53
Q

What are the invariant residues in insulin

A

cysteine residues

54
Q

When do posttranslational modifications occur

A

After protein folded into 3D form

55
Q

What is altered in a posttranslational modification

A

A specific amino acid

56
Q

What is the B-turn?

A

nonrepetitive, hairpin loop
Found on protein surface

57
Q

What protein structure is flexible and dynamic

A

Tertiary

58
Q

What main interaction is in tertiary proteins

A

Hydrophobic interactions

59
Q

G-actin fold

A

ATP is bound to middle of cleft
Antiparallel

60
Q

NAD+ fold

A

Parallel, domain 1 forms NAD+ bond

61
Q

B-andrenergic structure

A

a-helix goes through membrane in loops

62
Q

cis-trans-prolyl isomerases

A

Converts peptide bond in proline from trans to cis
Makes hairpin turns

63
Q

Protein disulfide isomerases

A

Breaks and reforms disulfide bonds between 2 cysteines

64
Q

Hsp70

A

Shield hydrophobic surfaces to prevent aggregation, prevents it from folding prematurely

65
Q

Hsp60

A

serves as a template for folding, unfolded protein fits into barrel

Has ATPase activity

66
Q

Nonenzymatic glycosylation

A

glucose binds to exposed amino group
leads to irriversible glycosylated protein

67
Q

What causes AGEs

A

Large protein aggregates of glycosylated proteins

68
Q

PrPsc structure

A

More B-sheets

69
Q

Prpc structure

A

No B-sheets, all a-helices

70
Q

What does PrPsc do

A

Lowers activation energy, makes it easier for proteins to refold into PrPsc, leads to multimeric assembly which is RESISTANT to protealytic digestion

71
Q

Multimeric complexes from Prpsc are resistant to

A

Protealytic digestions

72
Q

Prion infections

A

mad cow disease, doctor-induced CJD, Kuru

73
Q

Sporadic or inherited prions

A

Familial CJD

74
Q

Holoprotein

A

With prosthetic group

75
Q

Apopoprotein

A

Without prosthetic group

76
Q

What is heme

A

Prosthetic group

77
Q

Myoglobin

A

Monomeric, globular

78
Q

Hemoglobin structure

A

Tetramer

79
Q

What is the function of heme

A

Oxygen binding site

80
Q

The 4 monomers of hemoglobin are held together by

A

Noncovalent forces

81
Q

Tertiary structure of myoglobin

A

Globulin fold
8 a-helices connected by short coils

82
Q

how many poryphyrin rings in heme

A

4

83
Q

Where does proximal histidine bind to in hemoglobin

A

Fe2+ on one side of porphyrin ring

84
Q

How does oxygen binding in hemoglobin work

A

Proximal histidine binds to Fe2+ on one side of porphyrin ring, causes fe2+ to be pulled above plane

O2 binds to Fe2+ on the other side

O2 causes Fe2+ to be pulled back into plane of ring

85
Q

What causes cooperativity of O2 binding in hemoglobin

A

Conformational change of tertiary structure when O2 binds

86
Q

Curve for myoglobin

A

Hyperbolic

87
Q

Curve for hemoglobin

A

Sigmoidal

88
Q

P50

A

Half saturated with O2

89
Q

Ligand for NAD+

A

LDH domain

90
Q

Ligand for ATP

A

G-actin

91
Q

Ligand for b2-agrenergic receptor

A

Adrenaline

92
Q

Ka

A

Association constant

93
Q

Ka is what to Kd

A

1/kd or inverse

94
Q

what does high affinity mean

A

Less of the ligand is required to fully occupy the binding site
Tighter binding

95
Q

What is the shape of the curve of the sigmoidal graph

A

S shape

96
Q

Does myoglobin or hemoglobin have a higher affinity for oxygen

A

Myoglobin

97
Q

Why is the P50 of myoglobin so low?

A

It has a high affinity for O2, so it takes less O2 to saturate it halfway

98
Q

At lower levels of PO2, what binds to oxygen better

A

Myoglobin

99
Q

what is the p50 of a high affinity

A

Low p50

100
Q

what does Km tell

A

concentration of substrate required for enzyme to achieve 50% of velocity

101
Q

p50 equals

A

Kd (inverse of Ka)

102
Q

What end defines the beginning of a polypeptide

A

N-terminal

103
Q

What 3 amino acids can be phosphorylated

A

Serine, threonine, tyrosine

104
Q

Nonconservative substitution

A

Replace one AA with one that has a completely different structure

Ex. nonpolar replaced with polar

105
Q

What does the left side of the hemoglobin graph show

A

High affinity

106
Q

What does the right side of the hemoglobin graph mean

A

Low affinity

107
Q

As pH decreases, affinity…

A

Decreases

108
Q

Co2 forms carbamates with the ____ of the b-chain of hemoglobin (Hb)

A

N terminal

109
Q

Strongest bond

A

Covalent bonds

110
Q

Hydrogen bonds are the strongest when

A

Molecules are in a straight line

111
Q

Hydrophobic amino acids

A

Leucine and isoleucine

112
Q

What does hydrophobic regions do when they interact

A

Reduces the size of hydration layer

113
Q

How do polypeptides fold if they have hydrophobic molecules

A

The hydrophobic molecules move towards the inside (hydrophilic stays outside) to avoid contact with the water surrounding

114
Q

What change in amino acids causes sickle cell

A

Glutamic acid to valine

115
Q

Does fetal hemoglobin or adult hemoglobin have a higher affinity

A

Fetal hemoglobin

116
Q

Does fetal hemoglobin or adult hemoglobin have a mutation that can cause sickle cell anemia

A

Adult hemoglobin

117
Q

Higher pH means ___ Co2

A

Lower

118
Q

Lower pH means ____ CO2

A

Higher CO2, more protons

119
Q

acidic pH does what to affinity

A

Decreases

120
Q

What movement does oxygen binding to heme cause

A

It causes conformational change to the subunit that it’s bonded to ionically. The loss of the ionic bond will induce conformational change in the rest of the subunits.

121
Q

Heme group with oxygen does what

A

Pulls Fe into plane of ring

122
Q

Disulfide bridges are required to

A

Maintain the function of insulin

123
Q

Prosthetic group

A

Organic ligand that does not dissociate until protein is degraded (NOT an amino acid)

124
Q

Soluble vs. transmembrane proteins

A

Transmembrane: found in hydrophobic lipid layer

Soluble: found in hydrophilic, water environments

125
Q

What does L form mean

A

NH3+ is on left side of carbon, H is on right

126
Q

What does D form mean

A

H is on left side of carbon, NH3+ is on the right

127
Q

There are 9 different isoforms of what

A

Adenylate cyclase

128
Q

What does adenylate cyclase respond to

A

Adrenaline

129
Q

What type of protein causes prions

A

Anti parallel b-pleated sheets

130
Q

Nonpolar amino acids are also

A

Hydrophobic

131
Q

What structure is the end product of hemoglobin with O2 binding

A

Quartenary

132
Q
A

Biochemistry (13 decks)

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