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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
Proteins with one polypeptide chain
monomeric
26
Proteins composed of more than one polypeptide chain
multimeric
27
Proteins may contain only one kind of polypeptide
Homomultimeric
28
Proteins composed of several different kinds of polypeptide chain
Heteromultimeric
29
Used to denote the polypeptide composition of multimeric proteins
Greek letters and subscripts
30
Polypeptide chains of proteins typically range in length from about blank to blank
100 AAs to around 2000
31
Titin (Human Cardiac muscle) has blank and a MW of blank
26,926 and, 2,993, 497
32
MW/Mr of proteins can be estimated by blank or blank
PAGE, Ultracentrifugation
33
The E.coli enzyme responsible for blank has a MW of 600,000
glutamine synthesis
34
the analogous enzyme in blank has a MW of 380,000
Brain tissue
35
The AA sequence of proteins is encoded by the blank of DNA
nucleotide sequence
36
AA sequence is a form of blank
Genetic information
37
Because polypeptide chains are unbranched, a polypeptide chain has only two ends which is?
Amino-terminal end and Carboxy-terminal end
38
By convention, the AA sequence is read from the blank of the polypeptide chain through the blank
N-terminal end to the C-terminal end
39
Was the first to determine the sequence of a protein
Frederick Sanger
40
6 basic types for determining the AA sequence of a protein
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 6. Reconstruction of the overall AA sequence
41
Dissociation into component polypeptide chains
PH extremes, 8 M urea, 6 M guanidium hydrochloride, High salt concentration
42
Heteromultimers are linked together by blank
Interchain S-S bridges
43
S-S reduction must be followed by treatment with blank which modify the SH groups and block disulfide bridge formation.
Alkalyting agents
44
Sequential ID of a series of residues beginning at the N-terminus
Edman degradation
45
In weakly basic solutions, blank, or Edman reagent, combines with the blank of a protein
Phenylisothiocyanate, free amino terminus
46
Blank methods can identify this PTH derivative
Chromatographic
47
Cleave AA residues from the C-termini of polypeptides in a successive fashion
Carboxypeptidases
48
Carboxypeptidases A
bovine pancreas
49
C-terminal peptide bond of all residues except?
P (Proline), D (Aspartic acid), E (Glutamic acid), R (Arginine), K (Lysine)
50
Carboxypeptidase B
Hog pancreas
51
Carboxypeptidase Y
Yeast
52
Specific or non-specific mean
partial acid hydrolysis
53
Fragments produced upon cleavage should be blank to yield their sequences through blank and blank
small enough, end-group analysis, Edman degradation
54
The most commonly used reagent for specific proteolysis
Trypsin
55
Peptide bonds formed by the carboxyl groups of the aromatic AA (F, Y, W) and to a lesser extent L.
Chymotrypsin
56
Peptide bonds w/ in the interior of a polypeptide chain
Endopeptidases
57
R residue
Clostripain
58
K residues
Endopeptidases Lys-C
59
D and E residues
staphylococcal protease
60
N-term: Blank of the intact protein in an automated blank
Edman degradation, Edman sequenator
61
M: Proteolytic fragments generated by blank, followed by blank of the individual fragments
CNBr cleavage, Edman sequencing
62
K: Proteolytic fragments from endopeptidases blank, followed by Edman sequencing.
Lys-C cleavage
63
E: Proteolytic fragments from blank digestion of catrocollastatin sequenced in the Edman sequenator
Staphylococcus protease
64
Exploit the difference in the mass-to-charge (m/z) ratio of ionized atoms or molecules to separate them from each other.
Mass spectrometers
65
Blank of a molecule can be used to acquire chemical and structural info
m/z ratio
66
Basic operation of a mass spectrometer
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
2 most prominent MS modes for protein Analysis
Electrospray Ionization (ESI-MS) Matrix Assisted Laser Desorption Ionization-Time of Flight (MALDI-TOF MS)
68
1st protein sequence database were compiled by blank using chemical sequencing methods.
Protein chemist
69
Have unique amino acids
protein
70
share a significant degree of sequence similarity and structural resemblance. Perform the same function in different organisms
Homologous proteins
71
Proteins from different species that have homologous AA sequence, Arose from a common ancestral gene during evolution
Orthologous Proteins
72
Proteins found within a single species that have homologous AA species. Arose through gene duplication.
Paralogous proteins
73
Compares nucleotide or protein sequences to sequence database.
BLAST (Basic Local Alignment Search Tool)
74
Substitution matrix most often used with BLAST.
BLOSUM62 (Block Substitution Matrix)
75
Commonly used program for rapid searching of sequence database.
BLAST
76
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.
BLOSUM62
77
The scores are derived using sequences sharing in no more than blank
62% identity
78
e-transport protein found in the mitochondria of all eukaryotic organisms
Cytochrome c
79
A diagram illustrating the evolutionary relationships among a group of organisms
Phylogenetic tree
80
Oxygen binding heme protein of muscle
Oxygen-binding Heme Proteins Mb
81
A single peptide chain of 153 AA residues
Oxygen-binding Heme Proteins Mb
82
Oxygen transport protein of erythrocytes
Hb (Hemoglobin)
83
A tetramer composed of 2 a-chains and 2 b-chains
Hb (Hemoglobin)
84
The AA sequence of a- and b-globin chains share blank residues of their approximately blank residues in common
64 , 140
85
Mb and the a-globin chain have blank AA sequence identities
38
86
129 residues Hydrolyzes the polysaccharide wall of bacterial cell.
lysozyme
87
123 residues Regulates lactose synthesis in the mammary gland
a-lactalbumin
88
Are a consequence of mutations in a gene that have arisen naturally within the population
Variants
89
leads to mutant forms of the protein in which the AA sequence is altered at one or more positions
gene mutations
90
Functional properties of the protein are unaffected by the AA substitution
Neutral mutant form
91
A variety of effects on the Hb molecule are seen in these mutants alteration in
Oxygen affinity heme affinity stability solubility
92
The full genetic potential of a cell is contained within its genome
Proteome
93
Those genes that are being expressed are defined by the?
Transcriptome
94
A more accurate reflection of what a cell is doing at any moment in time is found in the ?
Proteome
95
There are only blank or so proteins coding gene in the human genome
20,000
96
Bacterial cells contain about blank protein molecules
2 million per 10-15
97
Is about 8000 times larger than an E.coli cell, so it would contain as many as blank protein molecules
liver cell, 30 billion

Protein and Nucleic acid (9 decks)

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