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biochemistry > Proteins > Flashcards

Proteins Flashcards

1
Q

Most abundant and functionally diverse molecules in living systems; Linear polymers of Amino Acids

A

Proteins

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2
Q

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

A

Proteome

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3
Q

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

A

Proteomics

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4
Q

Structure of Amino Acids

A

1 carboxyl group (-COOH)1 amino group (-NH2)1 unique side chain (R-group)

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5
Q

Amino Acids with Alipathic Side chains

A

Glycine (Gly, G)Alanine (Ala, A)Valine (Val, V)Leucine (Leu, L)Isoleucine (Ile, I)

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6
Q

Amino Acids with Hydroxylic groups and Sulfur atoms

A

Serine (Ser, S)Threonine (Thr, T)Tyrosine (Tyr, Y)Cysteine (Cys, C)Methionine (Met, M)

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7
Q

Amino Acids with Aromatic Side Chains

A

Histidine (His, H)Phenylalanine (Phe, F)Tyrosine (Tyr, Y)Tryptophan (Trp, W)Proline (Pro, P) - Imino Acid

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8
Q

Amino Acids with Basic Groups

A

Arginine (Arg, R)Lysine (Lys, K)Histidine (His, H)

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9
Q

Amino Acids with Acidic Groups and their Amides

A

Aspartic Acid (Asp, D)Asparagine (Asn, N)Glutamic Acid (Glu, E)Glutamine (Gln, Q)

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10
Q

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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11
Q

Has the smallest at physiologic pH;Used in the first step of he synthesis

A

Glycine

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12
Q

Carries nitrogen from peripheral tissues to the liver

A

Alanine

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13
Q

Branched-chain amino acids whose metabolites accumulate in Maple Syrup Urine Disease

A

Valine, Leucine, Isoleucine

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14
Q

Accumulate in Phenylketonuria

A

Phenylalanine

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15
Q

Deficiency in Phenylalanine hydroxylase

A

Phenylketonuria

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16
Q

Has the largest side chain; Precursor for Niacin, Serotonin and Melatonin

A

Tryptophan

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17
Q

Transfer of methyl group as S-adenosylmethionine (SAM); Precursor of Homocysteine

A

Methionine

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18
Q

Not an amino acid; Contributes to the fibrous structure of collagen and interrupts alpha-helices in globular proteins

A

Proline

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19
Q

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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20
Q

Contains a sulfhydryl group that is an active part of many enzymes; 2 cysteines can be connected by covalent disulfide bond to form Cysteine

A

Cysteine

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21
Q

Precursor of Dopamine, Norepinephrine, Epinephrine, Thyroxine and Melanin

A

Tyrosine

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22
Q

Phosphorylation site of enzyme modification; Often linked to carbohydrate groups in glycoproteins

A

Serine

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23
Q

Sites for O-linked glycosylation in Golgi Apparatus

A

Serine and Threonine

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24
Q

Have a carbonyl group and an amide group that can also form hydrogen bonds

A

Asparagine and Glutamine

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25
Q

Site for N-linked glycosylation in endoplasmic reticulum

A

Asparagine

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26
Q

Deaminated by glutaminase resulting in the formation of ammonia; Major carrier of nitrogen to the liver from peripheral tissues

A

Glutamine

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27
Q

Positively charged because of the amine group

A

Basic Amino Acids

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28
Q

Precursor of Histamine; Used in the diagnosis of folic acid deficiency

A

Histidine

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29
Q

Precursor of creatinine, urea and nitric oxide

A

Arginine

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30
Q

21st Amino Acid?; found in handful of proteins, including certain peroxidases and reductases; a selenium atom replaces the sulfur of its structural analog, cysteine

A

Selenocysteine

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31
Q

All amino acids are chiral EXCEPT

A

Glycine

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32
Q

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

A

Chiral Center

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33
Q

Exact mirror images of each other

A

Stereoisomers/Optical Isomers/Enantiomers

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34
Q

All amino acids in proteins

A

L-configuration

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35
Q

Bacterial cell walls, antibiotics

A

D-configuration

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36
Q

Chemical compound that has a total net charge of zero

A

Zwitterion

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37
Q

pH where the zwitterion predominates

A

pI or Isoloelectric Point

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38
Q

Which group accepts protons?

A

Amino group

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39
Q

Which group donates protons?

A

Carboxylic acid group

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40
Q

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

A

Essential Amino Acids

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41
Q

Essential Amino Acids

A

PhenylalanineValineTryptophanThreonineIsoleucineMethionineHistidineArginineLeucineLysine

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42
Q

Conditionally Non-essential Amino Acids

A

ArginineHistidine

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43
Q

May be made in the body, but usually not enough

A

Arginine

44
Q

May be recycled, but should eventually be consumed since it is not made at all

A

Histidine

45
Q

Linear sequence of a protein’s amino acids

A

Primary Structure

46
Q

Attach alpha-amino group of one amino acid to the alpha-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 and can form hydrogen bonds; Partial double bond character makes the bond rigid and planar; Generally in trans configuration

A

Peptide Bonds

47
Q

Sequencing of Polypeptides: N-terminal amino acid

A

Sanger’s Reagent (1-fluoro-2,4-dinitrobenzene)Edman’s Reagent (Phenylisothiocyanate)

48
Q

Sequencing of Polypeptides: C-terminal amino acid

A

HydrazineCarboxypeptidase

49
Q

The folding of short (3- to 30- residue) contiguous segments of polypeptide into geometrically ordered units

A

Secondary Structure

50
Q

Kinds of Secondary Structure

A

Alpha-helixBeta-pleated sheets

51
Q

Most common; R-handed spiral with polypeptide backbone core; Side chains extend outward; 3.6 amino acid per turn of the spiral

A

Alpha helix

52
Q

Surfaces appear flat and pleated; 2 or more peptide chains parallel to each other; Interchain and Intrachain bonds

A

Beta sheet

53
Q

Combinations of adjacent secondary structures such as beta-alpha-beta unit, greek key, beta-meander, beta-barrel

A

Motifs or Supersecondary Structures

54
Q

Overall 3-dimensional shape of the protein; Refers to the folding of domains and their final arrangement in the polypeptide

A

Tertiary structure

55
Q

Fundamental functional and 3-dimensional structure units of a polypeptide

A

Domains

56
Q

Specialized group of proteins required for the proper folding of many species of proteins; Prevents aggregation; Can also “rescue” proteins

A

Chaperones

57
Q

Structure of proteins consisting of more than one polypeptide chain; held together by noncovalent bonds

A

Quaternary Structure

58
Q

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

A

X-ray Crystallography

59
Q

Measures absorbance of radio frequency electromagnetic energy by certain atomic nuclei

A

Nuclear Magnetic Resonance Spectroscopy

60
Q

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

A

Molecular Modeling

61
Q

Disruption of a protein’s structure; Unfolded and disorganized; Reversible

A

Denaturation

62
Q

Reasons for Denaturation

A

HeatOrganic solventsMechanical mixingStrong acids and basesDetergentsIons of heavy metals like lead and mercury

63
Q

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

A

Prion Diseases

64
Q

The characteristic senile plaques and neurofibrillary bundles contain aggregates of the protein beta-amyloid

A

Alzheimer’s Disease

65
Q

A complex of Protoporphyrin IX and ferrous iron

A

Heme

66
Q

Heme protein found exclusively in red blood cells; Composed of heme + 4 globin chains

A

Hemoglobin

67
Q

True or False: Hemoglobin is the major transporter of carbon dioxide in blood?

A

FalseMajor (75%) bicarbonate (HCO3)Minor (25%) hemoglobin (carbaminoHb)

68
Q

Hemoglobin Types: Conception up to 1st few months from Yolk sac

A

Embryonal hemoglobin (Hb Gower 1)

69
Q

Hemoglobin Types: First few months to after birth from Liver

A

Fetal Hemoglobin (HbF)

70
Q

Hemoglobin Types: 8th month onwards from Marrow

A

Hemoglobin A (HbA)

71
Q

Hemoglobin Types: Shortly after birth onwards from marrow

A

Hemoglobin A2 (HbA2)

72
Q

Hemoglobin Configuration: Low oxygen affinity

A

T (taut) form

73
Q

Hemoglobin Configuration: High oxygen affinity (300x)

A

R (relaxed) form

74
Q

Heme protein found in heart and skeletal muscle

A

Myoglobin

75
Q

Following massive crush injury, myoglobin released from damaged muscle fibers colors the urine dark red

A

Myoglobinuria

76
Q

Hemoglobin curve

A

Sigmoidal curve

77
Q

Myoglobin curve

A

Hyperbolic curve

78
Q

Factors whose interaction with one site of the hemoglobin affects the binding of oxygen to heme groups at other locations

A

Allosteric Effectors

79
Q

P50=pO2 at which Hb is 50% saturatedIncreased affinity=increased pO2Decreased affinity=decreased pO2

A

NORMAL O2 Dissociation Curve

80
Q

Increased P50Decreased affinityIncreased CO2, Decreased pH

A

Shift to the RIGHT O2 Dissociation Curve

81
Q

Decreased P50Increased affinityDecreased CO2, Increased pH

A

Shift to the LEFT O2 Dissociation Curve

82
Q

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

A

Bohr Effect

83
Q

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

A

2,3 Biphosphoglycerate

84
Q

Oxidized form of Hb (Fe3+) that does not bind O2 as readily but increase affinity for CN-; Symptoms of Methemoglobin include cyanosis, anxiety, headache and dyspnea; “Chocolate” cyanosis

A

Methemoglobin

85
Q

Hb bound to carbon monoxide instead of O2; Hb becomes “cherry pink” in color; CO has 200x greater affinity for Hb than O2 and acts as a competitive inhibitor of O2

A

Carboxyhemoglobin

86
Q

When blood glucose enters the erythrocytes, it glycosylates the epsilon-amino group of lysine residues and the amino terminals of hemoglobin

A

Glycosylated Hemoglobin (HbA1c)

87
Q

Cutoff of HbA1c

A

> /= 6.5%

88
Q

Level of HbA1c that has been shown to reduce microvascular and neuropathic complications of type 1 and type 2 diabetes

A
89
Q

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

A

Hereditary Spherocytosis

90
Q

Disorders caused by either by: Production of a structurally abnormal Hb molecule or Synthesis of insufficient amounts of normal Hb subunits (Rarely both)

A

Hemoglobinopathies

91
Q

Cause: Point mutation in both genes coding for the beta-chain that results in a valine rather than a glutamate

A

Sickle Cell Disease

92
Q

Hemoglobin variant that has a single amino acid substitution in the 6th position of the beta-globin chain in which lysine is substituted for glutamate

A

Hemoglobin C Disease

93
Q

Inadequate synthesis of alpha chains leads to anemia due to beta-chain accumulation and precipitation

A

Alpha Thalassemia

94
Q

Inadequate synthesis of beta chains; Leads to anemia, accumulation of Hb Barts and alpha chain precipitation

A

Beta Thalassemia

95
Q

Most abundant protein in the body: A long stiff extracellular structure in which 3 polypeptides (alpha-chains) each 1000 amino acid in length are wound around one another in a triple helix

A

Collagen

96
Q

Collagen is rich in

A

GlycineProline

97
Q

Most common type of Collagen

A

Type I

98
Q

Results from inheritable defects in the metabolism of fibrillar collagen; Type III is most frequently affected

A

Ehlers-Danlos Syndrome

99
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 I

A

Osteogenesis imperfecta

100
Q

Hydroxylation of collagen is a post-translational modification requiring Ascorbic Acid

A

Scurvy

101
Q

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

A

Alport’s Syndrome

102
Q

Characterized by kinky hair and 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

103
Q

The skin breaks and blisters as a result of minor trauma; the dystrophic form is due toMutations 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

104
Q

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

A

Elastin

105
Q

Autosomal dominant connective tissue disorder; Mutation in the fibrillin gene

A

Marfan Syndrome

106
Q

Alpha1-antitrypsin inhibits proteolytic enzymes from hydrolyzing and destroying proteins

A

Alpha1 Antitrypsin Deficiency

biochemistry (7 decks)

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