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BIOCHEMISTRY > ME01 - Amino Acids and Peptides > Flashcards

ME01 - Amino Acids and Peptides Flashcards

1
Q

Difference of alpha helix and B sheets

A

ALPHA HELIX
Polypeptide backbone twisted
R groups face outward
Stability due to H bonds between oxygen of the peptide bond carbonyl and H atom of the peptide bond nitrogen

Peptide backbone is highly extended
AA residues form zigzag or pleated pattern
R groups point on opposite direction

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2
Q

What provides the thermodynamic driving force of alpha helices

A

The maximum number of H bonds coupled with Van der Waals forces

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3
Q

Proline and alpha helix

A

Proline lack a Hydrogen atom and could only be stable accommodated within the first turn

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4
Q

Glycine and alpha helix

A

Glycine induces a bend

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5
Q

Types of Beta-Sheet – Parallel and Adjacent

A

Parallel - adjacent segments proceed in the same amino to carboxyl
Antiparallel - opposite directions

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6
Q

Isolating specified protein for determination of physical and functional protein properties

A

Protein Purification

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7
Q

Approaches for Protein Purification

A

pH (isoelectric precipitation)
Polarity (ethanol or acetone precipitation)
Salt concentration (ammonium sulfate salting)

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8
Q

Optimal separation achieved by manipulation of the composition of the 2 phases

A

CHROMATOGRAPHY

Mobile and Stationary Phase

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9
Q

Proteins interacting more strongly with the stationary phase are retained longer

A

True.

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10
Q

Conformation vs Configuration

A

CONFORMATION

  • Spatial relationship between atoms
  • Interconversion does not need bond rupture
  • Retention of configuration
  • Rotation about single bonds

CONFIGURATION

  • Geometric relationship between atoms
  • Interconversion needs breaking of covalent bonds
  • L-amino acids vs D-amino acids
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11
Q

How do you extract soluble proteins

A

Extract using aqueous solutions at physiologic pH and ionic strength

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12
Q

Type of proteins requires detergent solutions

A

Integral membrane proteins

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13
Q

What are the stationary and mobile phase of Column Chromatography?

A

Stationary phase: column containing spherical beads or modified cellulose, acrylamide or silica whose surface has been coated with chemical functional groups

Mobile phase: Liquid type. Percolated and goes through.

Small portions of the mobile phase/eluant are collected

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14
Q

Separation of mixture in columns based on partition of a solute between 2 solvents one of which is immobilized by the substance in the column or paper

A

Partition Chromatography

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15
Q

Also known as gel filtration

A

Size Exclusion Chromatography

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16
Q

What type of Chromatography uses Stoke radius

A

Size Exclusion Chromatography

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17
Q

Separates proteins based on their Stoke radius

A

Size Exclusion Chromatography

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18
Q

Relation of Stoke Radius with Size Exclusion Chromatography

A

Proteins with large Stoke radii remain in the eluent and emerge before the proteins that have a smaller Stokes radii and are able the porous beads

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19
Q

Protein mixture is applied to a column under conditions where protein of interest associates with the stationary phase

A

Absorption Chromatography

Partition coefficient is unity = 1

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20
Q

How are proteins sequentially released and what to use for Size Exclusion Chromatography

A

By disrupting the forces that stabilize the protein-stationary phase complex.
A gradient of increasing salt concentration.

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21
Q

Why is the mobile phase in Size Exclusion Chromatography being gradually altered?

A

So that molecules are selectively released in descending order of their affinity.

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22
Q

Method of protein selection that employs incompressible silica or alumina microbeads as stationary phase and pressures of up to a few thousand psi

A

High_Pressure Liquid Chromatography

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23
Q

HPLC and incompressible matrices

A

Incompressible matrices permit both high flow rate and enhanced resolution

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24
Q

Complex mixtures of lipids or peptides uses what type of chromatography

A

High Pressure Liquid Chromatography

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25
Q

Exploits a hydrophobic stationary phase or aliphatic polymers 3-18 carbon atoms in length

A

Reversed phase HPLC

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26
Q

How are peptide mixtures eluted using HPLC

A

By using a gradient of a weak-miscible organic solvent such as acetonitrite or methanol

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27
Q

Proteins interact with the stationary phase via charge-charge interactions

A

Ion Exchange Chromatography

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28
Q

Concept of Ion Exchange Chromatography

A

Proteins with (+) charge at a given pH adhere beads with negatively charged functional groups such as carboxylates or sulfates (cation exchangers)

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29
Q

Why is it called “Ion-Exchange Chromatography”

A

“Ion-exchange” because proteins compete with monovalent ions for binding

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30
Q

Negatively charged proteins bind to diethylaminoethyl (DEAE) cellulose via replacing the Cl- or CH3COO-. What type of Chromatography is used?

A

Ion Exchange Chromatography

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31
Q

Proteins elute in inverse order of strength of their interactions with stationary phase?

A

Ion Exchange Chromatography

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32
Q

How do you achieve sequential elution in Ion Exchange Chromatography?

A

pH manipulation. Since it involves ions and charges

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33
Q

Separates via tendency to associate with a stationary phase matrix coated with hydrophobic groups phenyl Sepharose, octyl Sepharose

A

Hydrophobic Interaction Chromatography

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34
Q

Relation of Ionic Strength with Hydrophobic Interaction Chromatography

A

High Ionic Strength enhances adherance of proteins with exposed hydrophobic surfaces to the matrix via hydrophobic interactions

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35
Q

Polarity and Hydrophobic Interaction Chromatography

A

Polarity of mobile phase is decreased gradually lowering salt interaction

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36
Q

What is added to decrease the polarity and weaken hydrophobic interactions?

A

Ethanol or Glycerol

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37
Q

Exploits high selectivity of most proteins for their ligands. What type of Chromatography is used?

A

Affinity Chromatography

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38
Q

How are enzymes purified in Affinity Chromatography?

A

By using immobilized substrates, products, coenzymes or inhibitors

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39
Q

How are bound proteins eluted in Affinity Chromatography?

A

Either by competition with soluble ligand or less selectively by disrupting protein-ligand interactions using urea, guanidine HCl, mildly acidic pH and high salt concentration

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40
Q

Stationary phase of Affinity Chromatography

A

Contain ligands such as NAD+ or ATP analogs

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41
Q

Most powerful and widely applicable affinity matrices are used for – in Affinity Chromatography?

A

Recombinant protein purifications

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42
Q

Recombinant Protein Purification is involved and what type of Chromatography?

A

Affinity Chromatography

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43
Q

Explain Recombinant Protein Purifications

A

Uses an Ni2+ matrix that binds proteins with an attached polyhistidine tag and a glutathione matrix that binds a recombinant protein linked to glutathione S-transferase

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44
Q

Most widely used method for determining protein purity

A

Polyacrylamide Gel Electrophoresis

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45
Q

What is used in Polyacrylamide Gel Electrophoresis?

A

Sodium Dodecyl Sulfate

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46
Q

Concept of Polyacrylamide Gel Electrophoresis

A

Electrophoresis separates charged biomolecules based on the rates at which they migrate in an applied electrical field

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47
Q

What is polymerized and cross-linked to form porous matrix

A

Acrylamide

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48
Q

Denatures and binds to protein at a ration of one molecule per 2 peptide bonds in Polyacrylamide Gel Electrophoresis

A

SDS - Sodium Dodecyl Sulfate

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49
Q

What is used to to reduce or break disulfide bonds in Polyacrylamide Gel Electrophoresis

A

2-Mercatoethanol or Dithiothreitol

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50
Q

What determines the rate of migration in Polyacrylamide Gel Electrophoresis

A

The physical resistance encountered by the polypeptide

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51
Q

Polypeptides and Polyacrylamide Gel Electrophoresis

A

Polypeptides separate based on their relative molecular mass (Mr)

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52
Q

What stain is used when individual polypeptides are trapped in the gel in the Polyacrylamide Gel Electrophoresis

A

Coomassie Blue

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53
Q

Ionic buffers and an applied electric field are used to generate pH gradient within a polyacrylamide matrix

A

Isoelectric Focusing

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54
Q

Explain Isoelectric Focusing

A

Applied proteins migrate until they reach the region of the matrix where the pH at which a molecule’s net charge is 0.

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55
Q

The one who determined the amino acid sequence of Insulin

A

Frederick Sanger

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56
Q

Separated both chains by reducing disulfide bonds and cleaved with trypsin, chymotrypsin and pepsin.

A

Sanger Amino Acid Sequencing

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57
Q

Who introduced Edman’s reagent?

A

Pehr Edman. Other term for Edman’s reagent is phenylisothiocyanate

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58
Q

Phenylthiohydantoin (PTH) derivative can be removed under mild conditions to generate a new amino terminal residue

A

EDMAN Amino Acid Sequencing

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59
Q

What is necessary to circumvent post translational modifications and to render a proteins alpha-amino group unreactive to Edman’s reagent

A

Cleavage

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60
Q

Steps for EDMAN Amino Acid Sequencing

A

Cleavage
Peptides are purified by reversed phase HPLC
Sequencing

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61
Q

Provides a partial amino acid sequence

A

EDMAN Amino Acid Sequencing

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62
Q

Oligonucleotide primers modeled are used to ID the gene and amplify it using PCR

A

Hybrid Approach

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63
Q

STEPS in Hybrid Approach

A

ID the gene

Oligonucleotide sequence is determined to infer the primary structure of the encoded polypeptide

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64
Q

Enhances the speed and efficiency of primary structure analysis

A

Hybrid Approach

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65
Q

Only a few segments of the primary structure should be determined by what approach

A

Edman’s approach

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66
Q

Order of which amino acids are added in DNA sequencing

A 
Proteolytic processing
Methylation
Glycosylation
Phosphorylation
Proline and Lysine Hydroxylation
Disulfide bond formation
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67
Q

Replaced Edman’s sequencing

A

Mass Spectrometry

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68
Q

How is post translational modification identified in Mass Spectrometry

A

Via Mass increments

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69
Q

Bias in Mass Spectrometry

A

Discriminates molecules based solely on mass

70
Q

A sample in vacuum is vaporized under conditions where protonation can occur, imparting positive charge

A

Mass Spectrometry

71
Q

The force of ions with identical net charge is proportionate to their mass in Mass Spectrometry, T or F.

A

True.

72
Q

Molecules with identical net charge have velocities inversely proportional to their mass. T of F

A

True.

73
Q

Type of Mass Spec suited for large protein masses.

A

Time-of-flight mass specs

74
Q

Types of Mass Specs that permitted determination of large polypeptide masses

A

Matrix-assisted laser-desorption (MALDI)

Electrospray dispersion

75
Q

Peptides inside the mass spec are broken down into smaller units by collision with natural helium

A

Collision-induced dissociation

76
Q

Peptide bond are more labile than carbon-carbon bond

A

True

77
Q

Molecular mass of each amino acid is unique except for

A

Leucine and Isoleucine

78
Q

Used to screen blood samples from newborn (Newborn Screening)

A

Tandem Mass Spec

79
Q

Used for abnormalities in metabolites (phenylketonuria, ethylmalonic encephalopathy and glutaric acidemia type I)

A

Tandem Mass Spec

80
Q

Genomics uses what approach

A

Hybrid Approach

81
Q

How many residues are needed to identify the correct open reading frame (ORF)

A

4-5 residues

82
Q

What is Peptide mass profiling

A

A peptide is digested and introduced into the mass spec

83
Q

A computer program is used to find an ORF whose predicted protein product would produce a set of peptides whose masses match the ones in the mass spectrometry

A

Genomics

84
Q

Aimd to id the entire complement of proteins elaborated by a cell under diverse conditions

A

Proteomics

85
Q

Proteins whose appearance/disappearance are associated with a specific physiologic condition or disease

A

Proteomics

86
Q

Utilizes robotic automation

A

Proteomics

87
Q

Alternative and complementary approach that utilizes mRNA that encodes proteins

A

DNA Chips

88
Q

Gene arrays are more sensitive

A

True

89
Q

Compact, Spherical with axial ratios

A

Globular Proteins

90
Q

Axial Proteins >10

A

Fibrous Proteins

91
Q

Lipid protein

A

Lipoproteins

92
Q

Carbohydrate protein

A

Glycoprotein

93
Q

Tightly-associated metal ions

A

Metalloproteins

94
Q

Structure - Amino Acid Sequence

A

Primary Structure

95
Q

Structure - Folding of 3-30 amino acid residues forming geometrically ordered units

A

Secondary Structure

96
Q

Structure - Assembly of secondary structure into larger functional units

A

Tertiary Structure

97
Q

What is the Quarternary Structure

A

Polypeptide unts of oligomeric proteins and spatial arrangements

98
Q

Provides both molecular fingerprint for ID and information to determine the clone the gene that encodes it

A

Primary Structure

99
Q

Acid strength

A

pKa

100
Q

Net charge of pKa

A

Sum of all the (+) and (-) charged groups present - depends on the pKa values

101
Q

Polarity and Environment

A

Polar env’t favors charged form

Nonpolar env’t favors uncharged

102
Q

pH midway between pKa values of an isoelectric species

A

pI

103
Q

pI is isoelectric

A

Molecule has equal number of (+) and (-) charges

104
Q

Amino acids do not absorb visible light and are colorless. T or F

A

True

105
Q

Proteins that absorb high wavelength

A

Tyrosine, Phenylalanin, Tryptophan

106
Q

Smallest aa found in peptide bend

A

Glycine

107
Q

Hydrophobic Proteins

A 
MVP TTAIL
Methionine
Valine
Phenylalanine
Tryptophan
Tyrosine
Alanine
Isoleucine
Leucine
108
Q

Amino acids with BASIC side chains

A

HArgLys
Histidine
Arginine
Lysine

109
Q

Amino acids with ACIDIC side chain

A

Aspartic Acid

Glutamic Acid

110
Q

Amino Acids with polar but uncharged side chains

A 
Ser Gln, Thrash'n
Serine
Glutamine
Threonine
Asparagine
111
Q

Amino Acids with Special Cases

A

Cysteine
Glycine
Proline

112
Q

Where is free rotation possible on Secondary Structure

A
  1. Ca to Co

2. Ca to N

113
Q

Why is partial double bond character of Co to a-N requires carbonyl carbon

A

Prevent rotation

114
Q

Carbonyl Oxygen and a-Nitrogen remain coplanar

A

Prevent rotation

115
Q

Angle about the Ca- N

A

Phi (o)

116
Q

Angle about the Ca-Co

A

Psi (y)

117
Q

Most o(phi) and y(psi) are not allowed due to steric hindrances except

A

Glycine

118
Q

Why is Proline restricted in the secondary structure

A

Due to absence of Ca -N

119
Q

Most common secondary structure

A

a-helix and B-sheets

120
Q

Joining two units of secondary structure

A

Loops and Bends

121
Q

4 aa residues - Carbonyl oxygen of the first residue forms a hydrogen bond with the amino-group hydrogen of the fourth residue

A

B turn

122
Q

Examples for B turn

A

Proline and Glycine

123
Q

Regions that contain residues beyond the minimum number necessary to connect adjacent region of secondary structure

A

Loops

124
Q

Serve key biologic function

A

Loops

125
Q

Describe LOOPS

A

Lack apparent structural regularity

In enzymes, bridge domains which bind substrates and contain aa residues that participates in catalysis

126
Q

Stabilizes loops

A

H bonding, Salt bridges and Hydrophobic forces

127
Q

Provide oligonucleotide-binding portion of DNA-binding proteins such as repressors and transcription factors

A

Helix-Loop-Helix Binding

128
Q

Intermediate between 2 and 3 structure

A

Supersecondary structures

129
Q

Accessible sites for antibody recognition and binding

A

Epitopes

130
Q

Where do loop and bends reside

A

On protein surfaces

131
Q

Not all proteins are ordered

A

True

132
Q

Often at extreme amino or carboxyl terminal

A

Disordered regions

133
Q

Refers to the entire 3D conformation of polypeptide

A

Tertiary Structure

134
Q

Helices, sheets, bends, turns and loops

A

3-D spatial behavior

135
Q

Protein structure sufficient to perform a particular chemical or physical task such as substrate or ligand binding

A

Domains

136
Q

Functions of Tertiary Structure

A

Anchor protein to a membrane

Interact with a regulatory molecule modulating its function

137
Q

Examples of Single Domains

A

Triose phosphate isomerase

138
Q

Examples of Two Domains

A

Protein Kinases

139
Q

What is rich in B sheets and binds ATP

A

Amino terminus

140
Q

What is rich in a-helices and binds peptide/protein structure

A

Caboxyl terminus

141
Q

Where do the groups that catalyze phosphoryl transfer reside in?

A

Reside in a loop positioned at the interface of the 2 domains

142
Q

Defines the polypeptide composition of a protein and the spatial relationships between subunits or protomers

A

Quaternary Structure

143
Q

Single polypeptide Chain

A

Monomer

144
Q

Two polypeptide Chain

A

Dimer

145
Q

2 copies of the same polypeptide

A

Homodimer

146
Q

2 copies of different polypeptide

A

Heterodimer

147
Q

Elements of quarternary structure in terms of genes

A

A2B2Y2

148
Q

Non covalent factors stabilizing tertiary and quarternary structure

A

Hydrophobic interactions drive hydrophobi aa side chains into interior
Hydrogen bonds
Salt bridges

149
Q

Covalent factors stabilizing tertiary and quarternary structure

A

80-120 kcal/mol per bond

Disulfide bridges

150
Q

Steps for Xray Crystallography

A
  1. Protein is precipitated to form crystals
  2. Crystals are mounted into quartz capillaries and irradiated with monochromatic x rays of 0.15 nm to confirm protein nature
  3. Crystals are frozen in liquid nitrogen
  4. Diffraction patterns are recorded.
  5. Data is analyzed and summates wave functions
151
Q

Measures the absorbance of radio frequency electromagentic energy by certain atomic model

A

Nuclear Magnetic Resonance Spectroscopy

152
Q

A function of both the functional group within which it resides and the proximity of other NMR-active nuclei

A

Frequency or chemical shift in NMR Spectroscopy

153
Q

Analyzes proteins in aqueous solution therefore conformation accompanying ligand binding or catalysis is possible

A

NMR Spectroscopy

154
Q

Less than or equal to 30 kDA in size is analyzable uses this kind of Spec

A

NMR Spectroscopy

155
Q

Computer technology determining the 3D protein structure

A

Molecular modeling

156
Q

3-D structure of protein is used as a template to build a model of the probable structure of a related protein

A

Homology modeling

157
Q

Cell organelle that participates in folding process

A

Ribosomes

158
Q

Extreme high concentrations of protein in cells

A

Affects kinetic of protein folding

159
Q

Protein conformation vs Protein folding

A

Protein conformation is energetically favored.

Protein folding occurs in a stepwise fashion.

160
Q

Stage in Protein Folding : Newly synthesized polypeptide emerges from the ribosomes and short segments fold into secondary structural units

A

First Stage

161
Q

Stage in Protein Folding where forces that drive the hydrophobic regions into the interior of the protein away from solvent drive the partially folded polypeptide into a molten globule

A

Second stage

162
Q

Proteins that undergo spontaneous folding

A

Denatured proteins (treated with chaotropic agents like detergents)

163
Q

Proteins that assist in folding of over half of mammalian proteins

A

Chaperones

164
Q

Bind to short hydrophobic aa shielding them from a polar solvent

A

Hsp 70

165
Q

Differ in sequence and acts later in folding together with Hsp 70

A

Hsp 60

166
Q

Provides a donut-shaped central cavity which shelters polypeptide

A

Hsp 60

167
Q

Diseases of Protein Folding

A

Prion Diseases, Alzheimers disease, Beta-Thalassemia

168
Q

Configuration of PrPc normal protein into an abnormal PrPSc

A

Prion Disease

169
Q

Feature of Prion Disease

A

Beta-pleated sheet stacking

Amyloid plaques which then cause CJD, Kuru, MCD, BSE, Scrapie and other prion-related diseases

170
Q

Composed of misfolded tangles in proteins

A

Azheimer’s Disease

171
Q

What is Tau in Alzheimer’s Disease

A

Tau is misfolded tangle in protein which is responsible for maintaing microtubule organization of the nerve cells

172
Q

Causes of Alzheimer’s Disease

A

Plaques and Misfolded Tangles

BIOCHEMISTRY (25 decks)

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