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Protein and Nucleic acid > I. PRIMARY STRUCTURE OF PROTEINS > Flashcards

I. PRIMARY STRUCTURE OF PROTEINS Flashcards

1
Q

Unbranched polymers of amino acids linked head to tail, from carboxyl group to amino group, through the formation of covalent peptide bonds.

A

Proteins

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2
Q

Peptide bond formation result in what?

A

release of H2O

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3
Q

the peptide “backbone” of a protein consist of what repeated sequence?

A

-N-Ca-Co

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4
Q

N represents? Ca is the? Co is a?

A

Amide nitrogen, a-carbon atom, Carbonyl carbon

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5
Q

the polypeptide chain is inherently blank since the a-carbon atom of AA is a blank

A

asymmetric, chiral center

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6
Q

All three kind of bonds 9N-Ca-Co) are?

A

single bond

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7
Q

The Co and N atoms of the peptide bond are both in blank

A

Planar sp2 hybridization

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8
Q

The Co and O atoms are linked by a

A

pi bond

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9
Q

peptide bond has a blank double bond character

A

40%

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10
Q

Peptide blank causes the peptide backbone to be blank

A

resonance, relatively polar

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11
Q

The amide N is in a blank while, The carbonyl oxygen is a blank

A

protonated or (+)ly charged form, (-)ly charged form

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12
Q

the presence of these partial charges means that the peptide bond has a blank

A

permanent dipole

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13
Q

the peptide backbone is relatively blank, and protons are gained and lost by the peptide groups only at blank

A

unreactive chemically, extreme ph conditions

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14
Q

types of peptide

A

Peptide, dipeptide, tripeptide, oligopeptide, polypeptide

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15
Q

The peptide bonds of polypeptides and proteins can be blank to liberate the individual AAs

A

hydrolyzed by strong acid

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16
Q

blank is destroyed by acid and must be estimated by other mean to determine its contribution to the total AA composition

A

trp (tryptophan)

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17
Q

The OH containing AAs blank and blank are slowly destroyed

A

ser (serine) and thr (thrionine)

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18
Q

Another complication arises because the B- and Y- amide linkages in blank and blank are acid labile.

A

Asn (Asparagine) and Gln (Glutamine)

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19
Q

Peptide bonds involving blank such as val and ile are only slowly hydrolyzed in blank

A

hydrophobic residues, acid

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20
Q

The side chain blank is released as blank, and all of the Asn and Gln residues of the protein are converted to blank and blank, respectively.

A

amino nitrogen, ammonium free, Asp and Glu

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21
Q

AAs almost never occur in equimolar ratios in proteins, indicating that proteins are not composed of blank of AAs

A

repeating arrays

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22
Q

Collagens contains large proportions of blank and blank, and much of its structure is composed of blank, where blank is any AA.

A

Gly (Glycine) and Pro (Proline), repeating units, x

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23
Q

blank, a class of proteins found associated with the anionic phosphate groups of eukaryotic DNA, are rich in positively charged AAs:

A

Histones, Arg (arginine) and Lys (Lysine)

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24
Q

Molecules composed of one or more polypeptide chains

A

Proteins

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25
Q

Proteins with one polypeptide chain

A

monomeric

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26
Q

Proteins composed of more than one polypeptide chain

A

multimeric

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27
Q

Proteins may contain only one kind of polypeptide

A

Homomultimeric

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28
Q

Proteins composed of several different kinds of polypeptide chain

A

Heteromultimeric

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29
Q

Used to denote the polypeptide composition of multimeric proteins

A

Greek letters and subscripts

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30
Q

Polypeptide chains of proteins typically range in length from about blank to blank

A

100 AAs to around 2000

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31
Q

Titin (Human Cardiac muscle) has blank and a MW of blank

A

26,926 and, 2,993, 497

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32
Q

MW/Mr of proteins can be estimated by blank or blank

A

PAGE, Ultracentrifugation

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33
Q

The E.coli enzyme responsible for blank has a MW of 600,000

A

glutamine synthesis

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34
Q

the analogous enzyme in blank has a MW of 380,000

A

Brain tissue

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35
Q

The AA sequence of proteins is encoded by the blank of DNA

A

nucleotide sequence

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36
Q

AA sequence is a form of blank

A

Genetic information

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37
Q

Because polypeptide chains are unbranched, a polypeptide chain has only two ends which is?

A

Amino-terminal end and Carboxy-terminal end

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38
Q

By convention, the AA sequence is read from the blank of the polypeptide chain through the blank

A

N-terminal end to the C-terminal end

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39
Q

Was the first to determine the sequence of a protein

A

Frederick Sanger

40
Q

6 basic types for determining the AA sequence of a protein

A
  1. Separation of Polypeptide chain
  2. Cleavage of Disulfide bridges
  3. N-terminal analysis and C-terminal analysis
    4-5. fragmentation of the polypeptide chain
  4. Reconstruction of the overall AA sequence
41
Q

Dissociation into component polypeptide chains

A

PH extremes, 8 M urea, 6 M guanidium hydrochloride, High salt concentration

42
Q

Heteromultimers are linked together by blank

A

Interchain S-S bridges

43
Q

S-S reduction must be followed by treatment with blank which modify the SH groups and block disulfide bridge formation.

A

Alkalyting agents

44
Q

Sequential ID of a series of residues beginning at the N-terminus

A

Edman degradation

45
Q

In weakly basic solutions, blank, or Edman reagent, combines with the blank of a protein

A

Phenylisothiocyanate, free amino terminus

46
Q

Blank methods can identify this PTH derivative

A

Chromatographic

47
Q

Cleave AA residues from the C-termini of polypeptides in a successive fashion

A

Carboxypeptidases

48
Q

Carboxypeptidases A

A

bovine pancreas

49
Q

C-terminal peptide bond of all residues except?

A

P (Proline), D (Aspartic acid), E (Glutamic acid), R (Arginine), K (Lysine)

50
Q

Carboxypeptidase B

A

Hog pancreas

51
Q

Carboxypeptidase Y

A

Yeast

52
Q

Specific or non-specific mean

A

partial acid hydrolysis

53
Q

Fragments produced upon cleavage should be blank to yield their sequences through blank and blank

A

small enough, end-group analysis, Edman degradation

54
Q

The most commonly used reagent for specific proteolysis

A

Trypsin

55
Q

Peptide bonds formed by the carboxyl groups of the aromatic AA (F, Y, W) and to a lesser extent L.

A

Chymotrypsin

56
Q

Peptide bonds w/ in the interior of a polypeptide chain

A

Endopeptidases

57
Q

R residue

A

Clostripain

58
Q

K residues

A

Endopeptidases Lys-C

59
Q

D and E residues

A

staphylococcal protease

60
Q

N-term: Blank of the intact protein in an automated blank

A

Edman degradation, Edman sequenator

61
Q

M: Proteolytic fragments generated by blank, followed by blank of the individual fragments

A

CNBr cleavage, Edman sequencing

62
Q

K: Proteolytic fragments from endopeptidases blank, followed by Edman sequencing.

A

Lys-C cleavage

63
Q

E: Proteolytic fragments from blank digestion of catrocollastatin sequenced in the Edman sequenator

A

Staphylococcus protease

64
Q

Exploit the difference in the mass-to-charge (m/z) ratio of ionized atoms or molecules to separate them from each other.

A

Mass spectrometers

65
Q

Blank of a molecule can be used to acquire chemical and structural info

A

m/z ratio

66
Q

Basic operation of a mass spectrometer

A
  1. evaporate and ionize molecules in a vacuum, creating gas-phase ions.
  2. Separate the ions in space and time based on their m/z ratio.
  3. Measure the amount of ions with specific m/z ratios
67
Q

2 most prominent MS modes for protein Analysis

A

Electrospray Ionization (ESI-MS)
Matrix Assisted Laser Desorption Ionization-Time of Flight (MALDI-TOF MS)

68
Q

1st protein sequence database were compiled by blank using chemical sequencing methods.

A

Protein chemist

69
Q

Have unique amino acids

A

protein

70
Q

share a significant degree of sequence similarity and structural resemblance. Perform the same function in different organisms

A

Homologous proteins

71
Q

Proteins from different species that have homologous AA sequence, Arose from a common ancestral gene during evolution

A

Orthologous Proteins

72
Q

Proteins found within a single species that have homologous AA species. Arose through gene duplication.

A

Paralogous proteins

73
Q

Compares nucleotide or protein sequences to sequence database.

A

BLAST (Basic Local Alignment Search Tool)

74
Q

Substitution matrix most often used with BLAST.

A

BLOSUM62 (Block Substitution Matrix)

75
Q

Commonly used program for rapid searching of sequence database.

A

BLAST

76
Q

Assigns a probability score for each position in an alignment based on the frequency with which that substitution occurs in the consensus sequences of related proteins.

A

BLOSUM62

77
Q

The scores are derived using sequences sharing in no more than blank

A

62% identity

78
Q

e-transport protein found in the mitochondria of all eukaryotic organisms

A

Cytochrome c

79
Q

A diagram illustrating the evolutionary relationships among a group of organisms

A

Phylogenetic tree

80
Q

Oxygen binding heme protein of muscle

A

Oxygen-binding Heme Proteins Mb

81
Q

A single peptide chain of 153 AA residues

A

Oxygen-binding Heme Proteins Mb

82
Q

Oxygen transport protein of erythrocytes

A

Hb (Hemoglobin)

83
Q

A tetramer composed of 2 a-chains and 2 b-chains

A

Hb (Hemoglobin)

84
Q

The AA sequence of a- and b-globin chains share blank residues of their approximately blank residues in common

A

64 , 140

85
Q

Mb and the a-globin chain have blank AA sequence identities

A

38

86
Q

129 residues
Hydrolyzes the polysaccharide wall of bacterial cell.

A

lysozyme

87
Q

123 residues
Regulates lactose synthesis in the mammary gland

A

a-lactalbumin

88
Q

Are a consequence of mutations in a gene that have arisen naturally within the population

A

Variants

89
Q

leads to mutant forms of the protein in which the AA sequence is altered at one or more positions

A

gene mutations

90
Q

Functional properties of the protein are unaffected by the AA substitution

A

Neutral mutant form

91
Q

A variety of effects on the Hb molecule are seen in these mutants alteration in

A

Oxygen affinity
heme affinity
stability
solubility

92
Q

The full genetic potential of a cell is contained within its genome

A

Proteome

93
Q

Those genes that are being expressed are defined by the?

A

Transcriptome

94
Q

A more accurate reflection of what a cell is doing at any moment in time is found in the ?

A

Proteome

95
Q

There are only blank or so proteins coding gene in the human genome

A

20,000

96
Q

Bacterial cells contain about blank protein molecules

A

2 million per 10-15

97
Q

Is about 8000 times larger than an E.coli cell, so it would contain as many as blank protein molecules

A

liver cell, 30 billion

Protein and Nucleic acid (6 decks)

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