Proteins Flashcards
(106 cards)
1
Q
Most abundant and functionally diverse molecules in living systems; Linear polymers of Amino Acids
A
Proteins
2
Q
Set of all the proteins expressed by an individual cell at a particular time
A
Proteome
3
Q
Aims to identify the entire complement of proteins elaborated by a cell under diverse conditions
A
Proteomics
4
Q
Structure of Amino Acids
A
1 carboxyl group (-COOH)1 amino group (-NH2)1 unique side chain (R-group)
5
Q
Amino Acids with Alipathic Side chains
A
Glycine (Gly, G)Alanine (Ala, A)Valine (Val, V)Leucine (Leu, L)Isoleucine (Ile, I)
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)
7
Q
Amino Acids with Aromatic Side Chains
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Histidine (His, H)Phenylalanine (Phe, F)Tyrosine (Tyr, Y)Tryptophan (Trp, W)Proline (Pro, P) - Imino Acid
8
Q
Amino Acids with Basic Groups
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Arginine (Arg, R)Lysine (Lys, K)Histidine (His, H)
9
Q
Amino Acids with Acidic Groups and their Amides
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Aspartic Acid (Asp, D)Asparagine (Asn, N)Glutamic Acid (Glu, E)Glutamine (Gln, Q)
10
Q
Net charge of zero at Physiologic pH; promote hydrophobic interactions; Cluster in the interior of the protein
A
Non-polar Side Chains
11
Q
Has the smallest at physiologic pH;Used in the first step of he synthesis
A
Glycine
12
Q
Carries nitrogen from peripheral tissues to the liver
A
Alanine
13
Q
Branched-chain amino acids whose metabolites accumulate in Maple Syrup Urine Disease
A
Valine, Leucine, Isoleucine
14
Q
Accumulate in Phenylketonuria
A
Phenylalanine
15
Q
Deficiency in Phenylalanine hydroxylase
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Phenylketonuria
16
Q
Has the largest side chain; Precursor for Niacin, Serotonin and Melatonin
A
Tryptophan
17
Q
Transfer of methyl group as S-adenosylmethionine (SAM); Precursor of Homocysteine
A
Methionine
18
Q
Not an amino acid; Contributes to the fibrous structure of collagen and interrupts alpha-helices in globular proteins
A
Proline
19
Q
Zero net charge at physiologic pH; presence of side chains that can participate in hydrogen bonds
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Uncharged Polar Side Chains
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
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Cysteine
21
Q
Precursor of Dopamine, Norepinephrine, Epinephrine, Thyroxine and Melanin
A
Tyrosine
22
Q
Phosphorylation site of enzyme modification; Often linked to carbohydrate groups in glycoproteins
A
Serine
23
Q
Sites for O-linked glycosylation in Golgi Apparatus
A
Serine and Threonine
24
Q
Have a carbonyl group and an amide group that can also form hydrogen bonds
A
Asparagine and Glutamine
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Site for N-linked glycosylation in endoplasmic reticulum
Asparagine
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Deaminated by glutaminase resulting in the formation of ammonia; Major carrier of nitrogen to the liver from peripheral tissues
Glutamine
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Positively charged because of the amine group
Basic Amino Acids
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Precursor of Histamine; Used in the diagnosis of folic acid deficiency
Histidine
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Precursor of creatinine, urea and nitric oxide
Arginine
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21st Amino Acid?; found in handful of proteins, including certain peroxidases and reductases; a selenium atom replaces the sulfur of its structural analog, cysteine
Selenocysteine
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All amino acids are chiral EXCEPT
Glycine
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Defined as an atom in a molecule that is bonded to 4 different chemical species allowing for optical isomerism
Chiral Center
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Exact mirror images of each other
Stereoisomers/Optical Isomers/Enantiomers
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All amino acids in proteins
L-configuration
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Bacterial cell walls, antibiotics
D-configuration
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Chemical compound that has a total net charge of zero
Zwitterion
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pH where the zwitterion predominates
pI or Isoloelectric Point
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Which group accepts protons?
Amino group
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Which group donates protons?
Carboxylic acid group
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Amino acids that cannot be synthesized by the body and must come from diet
Essential Amino Acids
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Essential Amino Acids
PhenylalanineValineTryptophanThreonineIsoleucineMethionineHistidineArginineLeucineLysine
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Conditionally Non-essential Amino Acids
ArginineHistidine
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May be made in the body, but usually not enough
Arginine
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May be recycled, but should eventually be consumed since it is not made at all
Histidine
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Linear sequence of a protein's amino acids
Primary Structure
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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
Peptide Bonds
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Sequencing of Polypeptides: N-terminal amino acid
Sanger's Reagent (1-fluoro-2,4-dinitrobenzene)Edman's Reagent (Phenylisothiocyanate)
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Sequencing of Polypeptides: C-terminal amino acid
HydrazineCarboxypeptidase
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The folding of short (3- to 30- residue) contiguous segments of polypeptide into geometrically ordered units
Secondary Structure
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Kinds of Secondary Structure
Alpha-helixBeta-pleated sheets
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Most common; R-handed spiral with polypeptide backbone core; Side chains extend outward; 3.6 amino acid per turn of the spiral
Alpha helix
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Surfaces appear flat and pleated; 2 or more peptide chains parallel to each other; Interchain and Intrachain bonds
Beta sheet
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Combinations of adjacent secondary structures such as beta-alpha-beta unit, greek key, beta-meander, beta-barrel
Motifs or Supersecondary Structures
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Overall 3-dimensional shape of the protein; Refers to the folding of domains and their final arrangement in the polypeptide
Tertiary structure
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Fundamental functional and 3-dimensional structure units of a polypeptide
Domains
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Specialized group of proteins required for the proper folding of many species of proteins; Prevents aggregation; Can also "rescue" proteins
Chaperones
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Structure of proteins consisting of more than one polypeptide chain; held together by noncovalent bonds
Quaternary Structure
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Precipitation of a protein so that it forms ordered crystals that can diffract x-rays
X-ray Crystallography
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Measures absorbance of radio frequency electromagnetic energy by certain atomic nuclei
Nuclear Magnetic Resonance Spectroscopy
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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
Molecular Modeling
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Disruption of a protein's structure; Unfolded and disorganized; Reversible
Denaturation
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Reasons for Denaturation
HeatOrganic solventsMechanical mixingStrong acids and basesDetergentsIons of heavy metals like lead and mercury
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Fatal neurodegenerative diseases characterized by spongiform changes, astrocytic gliomas and neuronal loss resulting from deposition of insoluble protein aggregates in neural cells
Prion Diseases
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The characteristic senile plaques and neurofibrillary bundles contain aggregates of the protein beta-amyloid
Alzheimer's Disease
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A complex of Protoporphyrin IX and ferrous iron
Heme
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Heme protein found exclusively in red blood cells; Composed of heme + 4 globin chains
Hemoglobin
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True or False: Hemoglobin is the major transporter of carbon dioxide in blood?
FalseMajor (75%) bicarbonate (HCO3)Minor (25%) hemoglobin (carbaminoHb)
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Hemoglobin Types: Conception up to 1st few months from Yolk sac
Embryonal hemoglobin (Hb Gower 1)
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Hemoglobin Types: First few months to after birth from Liver
Fetal Hemoglobin (HbF)
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Hemoglobin Types: 8th month onwards from Marrow
Hemoglobin A (HbA)
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Hemoglobin Types: Shortly after birth onwards from marrow
Hemoglobin A2 (HbA2)
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Hemoglobin Configuration: Low oxygen affinity
T (taut) form
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Hemoglobin Configuration: High oxygen affinity (300x)
R (relaxed) form
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Heme protein found in heart and skeletal muscle
Myoglobin
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Following massive crush injury, myoglobin released from damaged muscle fibers colors the urine dark red
Myoglobinuria
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Hemoglobin curve
Sigmoidal curve
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Myoglobin curve
Hyperbolic curve
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Factors whose interaction with one site of the hemoglobin affects the binding of oxygen to heme groups at other locations
Allosteric Effectors
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P50=pO2 at which Hb is 50% saturatedIncreased affinity=increased pO2Decreased affinity=decreased pO2
NORMAL O2 Dissociation Curve
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Increased P50Decreased affinityIncreased CO2, Decreased pH
Shift to the RIGHT O2 Dissociation Curve
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Decreased P50Increased affinityDecreased CO2, Increased pH
Shift to the LEFT O2 Dissociation Curve
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The deoxy form of hemoglobin has a greater affinity for protons than does oxyhemoglobin
Bohr Effect
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Stabilizes the T structure of hemoglobin by forming additional salt bridges that must be broken prior to conversion to the R state
2,3 Biphosphoglycerate
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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
Methemoglobin
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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
Carboxyhemoglobin
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When blood glucose enters the erythrocytes, it glycosylates the epsilon-amino group of lysine residues and the amino terminals of hemoglobin
Glycosylated Hemoglobin (HbA1c)
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Cutoff of HbA1c
>/= 6.5%
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Level of HbA1c that has been shown to reduce microvascular and neuropathic complications of type 1 and type 2 diabetes
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Disorder characterized by an inherited defect in RBC membrane that renders the erythrocytes spheroidal, less deformable, and vulnerable to splenic sequestration and destruction
Hereditary Spherocytosis
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Disorders caused by either by: Production of a structurally abnormal Hb molecule or Synthesis of insufficient amounts of normal Hb subunits (Rarely both)
Hemoglobinopathies
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Cause: Point mutation in both genes coding for the beta-chain that results in a valine rather than a glutamate
Sickle Cell Disease
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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
Hemoglobin C Disease
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Inadequate synthesis of alpha chains leads to anemia due to beta-chain accumulation and precipitation
Alpha Thalassemia
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Inadequate synthesis of beta chains; Leads to anemia, accumulation of Hb Barts and alpha chain precipitation
Beta Thalassemia
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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
Collagen
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Collagen is rich in
GlycineProline
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Most common type of Collagen
Type I
98
Results from inheritable defects in the metabolism of fibrillar collagen; Type III is most frequently affected
Ehlers-Danlos Syndrome
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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
Osteogenesis imperfecta
100
Hydroxylation of collagen is a post-translational modification requiring Ascorbic Acid
Scurvy
101
A number of genetic disorders affecting the structure of type IV collagen fibers, the major collagen found in the basement membranes of renal glomeruli
Alport's Syndrome
102
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
Menke's Syndrome
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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
Epidermolysis Bullosa
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Connective tissue protein with rubber-like properties, responsible for extensibility and elastic recoil in tissues
Elastin
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Autosomal dominant connective tissue disorder; Mutation in the fibrillin gene
Marfan Syndrome
106
Alpha1-antitrypsin inhibits proteolytic enzymes from hydrolyzing and destroying proteins
Alpha1 Antitrypsin Deficiency
