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Jaspie - Biochemistry II > V - Proteins > Flashcards

V - Proteins Flashcards

1
Q

Most abundant and functionally diverse molecules in living systems

A

proteins

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2
Q

Linear polymers if amino acids

A

proteins

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3
Q

Set of all the proteins expressed by an individual cell at a particular time

A

proteome

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4
Q

Aims to identify the entire complement of proteins elaborated by a cell under diverse conditions

A

Proteomics

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5
Q

Aims to identify proteins and their post-translational modifications whose appearance or disappearance correlates with physiologic phenomena, aging or specific diseases

A

Proteomics

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6
Q

There are more than 300 amino acids but only ___ are commonly found in mammalian proteins,

A

20

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7
Q

All amino acids have _____, _____ & _____ except for _____.

A

carboxyl group (-COOH), amino group (-NH2), unique side chain (R-group), proline

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8
Q

All three molecular groups in an amino acid are bonded to a central

A

α-carbon

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9
Q

Dictates the function of the amino acid in a protein

A

R-group

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10
Q

Amino Acids: Alipathic Side Chains

A

Glycine, Alanine, Valine, Leucine, Isoleucine

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11
Q

Amino Acids: Hydroxylic Groups

A

Serine, Threonine, Tyrosine

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12
Q

Amino Acids: Sulfur Atoms

A

Cysteine, Methionine

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13
Q

Amino Acids: Aromatic Side Chains

A

Histidine, Phenylalanine, Tyrosine, Tryptophan

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14
Q

Imino Acid

A

Proline

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15
Q

Amino Acids: Basic Groups

A

Lysine, Arginine, Histidine

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16
Q

Amino Acids: Acidic Groups

A

Aspartic acid, Asparagine, Glutamic acid, Glutamine

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17
Q

Side Chains: net charge of zero at physiologic pH, promote hydrophobic interactions, cluster in the interior of the protein

A

non-polar side chains

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18
Q

Amino Acids: has the smallest side chain, used in the first step of heme synthesis, used in purine synthesis, major inhibitory neurotransmitter in the spinal cord

A

Glycine

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19
Q

Glycine + Succinyl CoA

A

δ-ALA (aminolevulinic acid)

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20
Q

Amino Acids: Amino Acids: Carries nitrogen from peripheral tissues to the liver

A

Alanine

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21
Q

Amino Acids: branched-chain amino acids whose metabolites accumulate in Maple Syrup Urine Disease (deficiency in branched-chain α-ketoacid dehydrogenase)

A

Valine, Isoleucine, Leucine

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22
Q

Amino Acids: accumulates in Phenylketonuria

A

Phenylalanine

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23
Q

Deficient enzyme in PKU

A

Phenylalanine Hydroxylase

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24
Q

Accumulating metabolites in PKU

A

phenyllactate, phenylpyruvate, phenylacetate

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25
Q

Causes the musty odor in PKU

A

phenylacetate

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26
Q

Amino Acids: has the largest side chain, precursor for niacin, serotonin (5-HT) and melatonin

A

Tryptophan

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27
Q

Amino Acids: precursor of homocysteine

A

Methionine

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28
Q

Methionine is used in transfer of methyl groups as

A

S-adenosylmethionine (SAM)

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29
Q

Amino Acids: contributes to the fibrous structure of collagen and interrupts α-helices in globular proteins

A

Proline

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30
Q

Side Chains: zero net charge at physiologic pH, presence of side chains that can participate in hydrogen bonds

A

uncharged polar side chains

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31
Q

Amino Acids: contains a sulfhydryl group that is an active part of many enzymes

A

Cysteine

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32
Q

2 cysteine molecules connected by a covalent disulfide bond, abundant in keratin

A

Cystine

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33
Q

Products from Phenylalanine

A

Phenylalanine → Tyrosine → L-Dopa → Dopamine → Norepinephrine → Epinephrine

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34
Q

Precursor for thyroxine and melanin

A

Tyrosine

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35
Q

Amino Acids: phosphorylation site of enzyme modification, linked to carbohydrate groups in glycoproteins

A

Serine

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36
Q

Amino Acids: sites for O-linked glycosylation in the golgi apparatus

A

Serine, Threonine

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37
Q

Amino Acids: have a carbonyl group and an amide group that can also form hydrogen bonds

A

Asparagine, Glutamine

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38
Q

Amino Acids: site for N-linked glycosylation in the endoplasmic reticulum

A

Asparagine

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39
Q

Amino Acids: deaminated by glutaminase resulting in the formation of ammonia, major carrier of nitrogen to the liver from the peripheral tissues

A

Glutamine

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40
Q

Side Chains: negatively charged at physiologic pH because of the carboxylate group, participate in ionic reactions

A

acidic side chains

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41
Q

Amino Acids: precursor for GABA and glutathione

A

Glutamate

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42
Q

Side Chains: positively charged because of the amine group

A

basic side chains

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43
Q

At neutral pH, arginine and lysine are

A

positively charged

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44
Q

At neutral pH, histidine is

A

neutral (weak base)

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45
Q

Amino Acids: precursor of histamine, used in the diagnosis of folic acid deficiency

A

Histidine

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46
Q

Ingividuals deficient in folic acid excrete increased amounts of FIGlu in urine particularly after ingestion of large doses of histidine

A

N-formiminoglutamate Excretion Test

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47
Q

Amino Acids: precursor of creatinine, urea and nitric oxide

A

Arginine

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48
Q

21st Amino Acid

A

Selenocysteine

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49
Q

Amino Acids: found in a handful of proteins, including certain peroxidases and reductases, inserted into polypeptides during translation but is not specified by a simple three-letter codon, a selenium atom replaces the sulfur in cysteine

A

Selenocysteine

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50
Q

Non-Polar Amino Acids

A

Glycine, Alanine, Leucine, Isoleucine, Valine, Phenylalanine, Tryptophan, Methionine, Proline

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51
Q

Polar Uncharged Amino Acids

A

-OH (Serine, Threonine, Tyrosine), -SH (Cysteine), Amide (Asparagine, Glutamine)

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52
Q

Charged Amino Acids

A

Acidic (Aspatrate, Glutamate), Basic (Lysine, Arginine, Histidine)

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53
Q

All amino acids are chiral except for

A

Glycine

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54
Q

An atom in a molecule that is bonded to 4 different chemical species allowing for optical isomerism

A

chiral center

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55
Q

Molecuels that are exact mirror images of each other

A

Stereoisomers/Enentiomers/Optical Isomers

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56
Q

Most common configuration of AAs

A

L-configuration

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57
Q

A chemical compound that has a total net charge of zero

A

Zwitterion

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58
Q

pH where the zwitterion predominates (AA is uncharged)

A

Isoelectric Point (pI)

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59
Q

Isoelectric Point (pI)

A

(pKa before + pKa after)/2

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60
Q

Molecular group that accepts protons

A

amino group

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61
Q

Molecular group that donates protons

A

carboxylic acid group

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62
Q

AAs that cannot be synthesized by the body and must come from the diet

A

Phenylalanine, Valine, Tryptophan, Threonine, Histidine, Arginine, Leucine, Lysine

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63
Q

Conditionally Non-Essential AAs: may be made in the body but usually not enough

A

Arginine

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64
Q

Conditionally Non-Essential AAs: may be recycled but should eventually be consumed since it is not made at all

A

Histidine

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65
Q

Linear sequence of a protein’s amino acids

A

Primary Structure

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66
Q

Attaches α-amino group of ne AA to the α-carbonyl group of another, very stable, can only be disrupted by hydrolysis through prolonged exposure to a strong acid or base at elevated temperatures, polar, can form hydrogen bonds

A

Peptide Bonds

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67
Q

Makes the peptide bond rigid and planar

A

partial double bond

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68
Q

Cleaves the N-terminal amino acid

A

Sanger’s reagent, Edman’s reagent

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69
Q

Cleaves the C-terminal amino acid

A

Hydrazine, Carboxypeptidase

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70
Q

Used to detect covalent modifications in proteins

A

mass spectrometry

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71
Q

The folding of short (3-30 residues) contiguous segments of polypeptide into geometrically ordered units, regular arrangements of AA that are located near each other in the linear sequence, stabilized by excessive hydrogen bonding

A

Secondary Structure

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72
Q

Secondary Structures: most common, R-handed spiral with polypeptide back bone core, side chains extend outward, 3.6 AA per turn of the spiral

A

Alpha Helix

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73
Q

Alpha helices are disrupted by

A

proline, large R-groups, charged R-groups

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74
Q

Secondary Structures: surfaces appear flat and pleated, 2 or more peptide chains parallel to each other, interchain and intrachain bonds

A

Beta Sheet

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75
Q

Secondary Structures: combinations of adjacent secondary structures such as β-α-β unit, Greek key, β-meander, β-barrel

A

Motifs (Supersecondary Structures)

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76
Q

Secondary Structures: R-handed spiral, H-bonds parallel to helix, keratin, hemoglobin

A

Alpha Helix

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77
Q

Secondary Structures: sheets, H-bonds perpendicular to sheets, amyloid, immunoglobulin

A

Beta-Pleated Sheet

78
Q

Overall 3D shape of the protein, globular, fibrous, refers to the folding of domains and their final arrangement in the polypeptide

A

Tertiary Structure

79
Q

The tertiary structure of proteins are stabilized by

A

disulfide bonds, hydrophobic interactions, hydrogen bonds, ionic bonds

80
Q

Fundamental functional and 3D structural units of a polypeptide, formed by combinations of motifs

A

Domains

81
Q

Specialized group of group of proteins required for the proper folding of many species of proteins, prevent aggregation, thus providing an opportunity for the formation of appropriate secondary structural elements and their subsequent coalescence into a molten globule

A

Chaperones

82
Q

Can rescue proteins that have become thermodynamically trapped in a misfolded dead end by unfolding hydrophobic regions

A

Chaperones

83
Q

Structure of proteins consisting of more than one polypeptide chain, held together by non-covalent bonds

A

Quarternary Structure

84
Q

Precipitation of a protein so that it forms ordered crystals that can diffract x-rays

A

X-ray Crystallography

85
Q

Measures the absorbency of radiofrequency electromagnetic energy by certain atomic nuclei, groups of nuclei have particular absorbency patterns

A

Nuclear Magnetic Resonance Spectroscopy

86
Q

Molecular dynamics programs can be used to stimulate the conformational dynamics of a protein and the manner in which factors such as temerature, pH, ionic strongth or AA amino acid substitutions influence these motions

A

Molecular Modeling

87
Q

Disruption of a protein’s structure

A

Denaturation

88
Q

Means of Protein Denaturation

A

heat, organic solvents, mechanical mixing, strong acids or bases, detergents, ions of heavy metals (lead & mercury)

89
Q

Fatal neurodegenerative diseases characterized by spongiform changes, astrocytic gliomas and neuronal loss resulting from the deposition of insoluble protein aggregates in neural cells

A

Prion Diseases

90
Q

Prions: normal protein, rich in α-helices

A

PrPc

91
Q

Prions: pathologic conformation, rich in β-sheets

A

PrPsc

92
Q

The caharcteristic senile plaques and neurofibrillary bundles of the protein β-amyloid which undergoes conformational transformation from a soluble α-helix rich state rich in β-sheets and prone ti self aggregation, mediated by Apo-E

A

Alzheimer’s Disease

93
Q

A complex of protoporphyrin IX and ferrous iron (Fe2+), electron carrier in cytochromes, active site of the enzyme catalase that breaks down hydrogen peroxide, reversibly binds oxygen in myoglobin and hemoglobin

A

Heme

94
Q

Heme protein found exclusively in red blood cells, composed of heme and 4 globin chains

A

Hemoglobin

95
Q

Major transporter of CO2 in the blood

A

HCO3 (75%), carbaminohemoglobin (25%)

96
Q

Hemoglobin: ζ2ε2, conception until the first few months, yolk sac

A

Embryonal Hemoglobin (Gower 1)

97
Q

Hemoglobin: α2γ2, first few months to after birth, liver

A

Fetal Hemoglobin (HbF)

98
Q

Hemoglobin: α2γ2, 8th month onwards, marrow

A

Hemoglobin A (HbA)

99
Q

Hemoglobin: α2δ2, shortly after birth onwards, marrow

A

Hemoglobin A2 (HbA2)

100
Q

Binds up to 4 molecules of oxygen, exhibits positive cooperativity, sigmoidal curve

A

Hemoglobin

101
Q

Hemoglobin binds to O2 with increasing affinity

A

Positive Cooperativity

102
Q

Hemoglobin: low oxygen affunity

A

T (taut)

103
Q

Hemoglobin: high oxygen affinity (300x)

A

R (relaxed)

104
Q

Heme protein found in the heart and skeletal muscles, reservoir of oxygen, oxygen carrier that increases the rate of transport of O2 within the muscle cell, hyperbolic curve

A

Myoglobin

105
Q

Consists of a single polypeptide chain composed of polar and non-polar AAs, contains histidine for O2 binding, released from damaged muscle fibers and turns the urine dark red, can be detected in plasma following MI

A

Myoglobin

106
Q

O2 Carriers: 1 polypeptide

A

Myoglobin

107
Q

O2 Carriers: carries 1 O2

A

Myoglobin

108
Q

O2 Carriers: hyperbolic curve (saturation)

A

Myoglobin

109
Q

O2 Carriers: storage

A

Myoglobin

110
Q

O2 Carriers: heart, muscle

A

Myoglobin

111
Q

O2 Carriers: 4 polypeptides

A

Hemoglobin

112
Q

O2 Carriers: carries 4 O2

A

Hemoglobin

113
Q

O2 Carriers: sigmoidal curve (cooperativity)

A

Hemoglobin

114
Q

O2 Carriers: transport

A

Hemoglobin

115
Q

O2 Carriers: allosteric effects are present

A

Hemoglobin

116
Q

Factors whose interaction with one site of the hemoglobin affects the binding of oxygen to heme groups at other locations, effect may be positive or negative, myoglobin is not affected

A

Allosteric Effectors

117
Q

Shifts the O2 Dissociation Curve to the right

A

CO2, acidity, 2,3-BPG, exercise, temperature

118
Q

The deoxy form of hemoglobin has a greater affinity for protons than does oxyhemoglobin

A

Bohr Effect

119
Q

Stabilizes the T structure of hemoglobin by forming additional salt bridges that must be broken prior to conversion to the R state, synthesized by erythrocytes

A

2,3-BPG

120
Q

Oxidized form of Hgb (Fe3+) that does not bind to O2 as readily but has a high affinity for CN, cyanosis, anxiety, headache, dyspnea, chocolate cyanosis (muddy brown), 85% O2 Sat.

A

Methemoglobin

121
Q

Hgb bound to carbon monoxide instead of O2, cherry pink

A

Carboxyhemoglobin

122
Q

Hemoglobin: CO

A

Carbohyhemoglobin

123
Q

Hemoglobin: CO2

A

Carbaminohemoglobin

124
Q

Hemoglobin: cherry pink

A

Carboxyhemoglobin

125
Q

Hemoglobin: muddy brown

A

Methemoglobin

126
Q

Hemoglobin: When blood glucose enters erythrocytes, it glycosylates the

A

ε-amino group of lysine residues and the amino terminals of hemoglobin (HbA1c)

127
Q

Disorder characterized by an inherited (intrinsic) defect in the RBC membrane that renders erythrocytes spheroidal, less deformable and vulnerable to splenic sequestration and destruction

A

Hereditary Spherocytosis

128
Q

Hereditary Spherocytosis: Mutations

A

spectrin, band 4.1, band 3

129
Q

Hereditary Spherocytosis: Diagnosis

A

osmotic fragility test

130
Q

Hereditary Spherocytosis: Treatment

A

splenectomy for symptomatic patients

131
Q

Point mutation in both genes coding for β-chain that results in a valine rather than a glutamate, homozygous recessive disorder

A

Sickle Cell Disease

132
Q

Polymerization and decreased solubility of the deoxy form of Hgb, distortion of the RBC membrane, misshapen, rigid RBCs occlude capillaries

A

Sickle Cell Disease

133
Q

Amenia, tissue anoxia, painful crises, protective against malaria

A

Sickle Cell Disease

134
Q

Sickle Cell Disease: Treatment

A

hydration, analgesics, antibiotics if with infection, transfusions, hydroxyurea

135
Q

Hemoglobin variant that has a single amino acid substitution in the 6th position of the β-chain in which lysine is substituted for glutamate, homzygous patients present with mild hemolytic anemia

A

Hemoglobin C

136
Q

Inadequate synthesis of the α-chains, leads to anemia due to β-chain accumulation and precipitation, symptoms appear at birth because α-chains are needed for HbF and HbA

A

Alpha Thalassemia

137
Q

Alpha Thalassemia: 1 defective gene

A

silent carrier

138
Q

Alpha Thalassemia: 2 defective genes

A

Alpha Thalassemia Trait

139
Q

Alpha Thalassemia: 3 defective genes

A

Hb H DIsease

140
Q

Alpha Thalassemia: 4 defective genes

A

Hydrops Fetalis

141
Q

Alpha Thalassemia: Chromosome

A

Chrom. 16

142
Q

Inadequate synthesis of β-chains, leads to anemia, accumulation of Hb Barts, α-chain precipitation, symptoms appear after birth sins Hbf does not have β-chains

A

Beta Thalassemia

143
Q

Beta Thalassemia: 1 defective gene

A

Beta Thalassemia Minor

144
Q

Beta Thalassemia: 2 defective gene

A

Beta Thalassemia Major

145
Q

MOst abundant protein in the body, long stiff extracellular structure in which 3 polypeptides (α-chain) each 1000 AA in length are wound around one another in a triple helix, stabilized by hydrogen bonds, 28 distinct types made up of 30 distinct polypeptide chains

A

Collagen

146
Q

Most Common Collagen Type

A

Type 1

147
Q

Collagen is rich in

A

Glycine, Proline

148
Q

X portion of collagen

A

Proline (facilitates kinking)

149
Q

Y portion of collagen

A

hydroxyproline or hydroxylisine

150
Q

Formed in fibroblasts or in the osteoblasts of bone and chondroblasts of cartilage, secreted into the extracellular matrix

A

Collagen

151
Q

Collagen monomers aggregate and become cross-linked to form

A

Collagen Fibrils

152
Q

Collagen: pro α-chain + signal peptide

A

PrePro α-chain

153
Q

Collagen: signal peptide removed

A

Pro α-chain

154
Q

Collagen: lysine and proline are hydroxylated

A

Procollagen

155
Q

Collagen: 3 procollagen chains form the triple helix

A

Triple Helix Procollagen

156
Q

Collagen: secreted from the cell

A

Triple Helix

157
Q

Collagen: triple helix with propeptide removed

A

Tropocollagen

158
Q

Collagen: lysine cross-links, parallel, staggered

A

Collagen Fibrils

159
Q

Collagen: bone

A

I

160
Q

Collagen: skin

A

I

161
Q

Collagen: tendon

A

I

162
Q

Collagen: dentin

A

I

163
Q

Collagen: fascia

A

I

164
Q

Collagen: cornea

A

I

165
Q

Collagen: late wound repair

A

I

166
Q

Collagen: cartilage

A

II

167
Q

Collagen: vitreous body

A

II

168
Q

Collagen: nucleus pulposus

A

II

169
Q

Collagen: skin

A

III

170
Q

Collagen: blood vessels

A

III

171
Q

Collagen: uterus

A

III

172
Q

Collagen: fetal tissue

A

III

173
Q

Collagen: granulation tissue

A

III

174
Q

Collagen: basement membrane/basal lamina

A

IV

175
Q

Results from inheritable defects in the metabolism of fibrillar collagen, collagen is most frequently affected

A

Ehlers-Danlos Syndrome

176
Q

Hyperextensible skin, tendency to bleed, hypermobile joints, high risk for berry aneurysms

A

Ehlers-Danlos Syndrome

177
Q

Brittle bone syndrome, mutation in collagen genes result to bones that easily bend and fracture, most common form is autosomal dominant with abnormal collagen type

A

Osteogenesis Imperfecta

178
Q

Multiple fractures, blue sclerae, hearing loss, dental imperfections

A

Osteogenesis Imperfecta

179
Q

Hydroxylation of collagen is a post-translational modification requirin ascorbic acid. deficiency causes decreased cross-linking of collagen fibers

A

Scurvy

180
Q

Sore spongy gums, loose teeth, poor wound healing, petechiae on skin and mucous membranes

A

Scurvy

181
Q

A number of genetic disorders affecting the structure of type IV collagen fibers, the major collagen found in the basement membranes of the renal glomeruli, hematuria, ESRD

A

Alport’s Syndrome

182
Q

Kinky hair, growth retardation, reflects a dietary deficiency of the copper required by lysyl oxidase which catalyzes a key step in formation of the covalent cross-links that strengthen collagen fibers

A

Menke’s Syndrome

183
Q

The skin breaks and blisters as a result of minor trauma, the dystrophic form is due to mutations affecting the structure of type VII collagen which forms delicate fibrils that anchor the basal lamina to collagen fibrils in the dermis

A

Epidermolysis Bullosa Dystrophica

184
Q

Connective tissue protein with rubber-like properties, responsible for extensibility and elastic recoil in tissues

A

Elastin

185
Q

Rich in proline and lysine but little hydroxyproline and no hydroxylysine

A

Elastin

186
Q

Precursor tropoelastin is deposited into an irregular fibrillin scaffold cross-linked by desmosine

A

Elastin

187
Q

Elastin is found in tissues where elastic recoil is needed like in

A

lungs, large arteries, elastic ligaments, vocal cords, ligamentum flavum

188
Q

Autosomal dominant connective tissue disorder, mutation in fibrillin gene

A

Marfan Syndrome

189
Q

Taller, thinner, dolichostenomelia, arachnodactyly, ascending aortic dilatation and dissection

A

Marfan Syndrome

190
Q

Deficiency in the enzyme that inhibits proteolytic enzymes from hydrolyzing and destroying proteins, elastase destroys the alveolar walls resulting in emphysema

A

α1 Trypsin Deficiency

191
Q

Many different genetic types, triple helix, (Gly-X-Y)n repeating structure, presence of hydroxylysine, carbohydrate containing, intramolecular aldol cross-links, presence of extension peptides during biosynthesis

A

Collagen

192
Q

One genetic type, Intramolecular desmosine cross-links

A

Elastin

Jaspie - Biochemistry II (15 decks)

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