V - Proteins Flashcards
Most abundant and functionally diverse molecules in living systems
proteins
Linear polymers if amino acids
proteins
Set of all the proteins expressed by an individual cell at a particular time
proteome
Aims to identify the entire complement of proteins elaborated by a cell under diverse conditions
Proteomics
Aims to identify proteins and their post-translational modifications whose appearance or disappearance correlates with physiologic phenomena, aging or specific diseases
Proteomics
There are more than 300 amino acids but only ___ are commonly found in mammalian proteins,
20
All amino acids have _____, _____ & _____ except for _____.
carboxyl group (-COOH), amino group (-NH2), unique side chain (R-group), proline
All three molecular groups in an amino acid are bonded to a central
α-carbon
Dictates the function of the amino acid in a protein
R-group
Amino Acids: Alipathic Side Chains
Glycine, Alanine, Valine, Leucine, Isoleucine
Amino Acids: Hydroxylic Groups
Serine, Threonine, Tyrosine
Amino Acids: Sulfur Atoms
Cysteine, Methionine
Amino Acids: Aromatic Side Chains
Histidine, Phenylalanine, Tyrosine, Tryptophan
Imino Acid
Proline
Amino Acids: Basic Groups
Lysine, Arginine, Histidine
Amino Acids: Acidic Groups
Aspartic acid, Asparagine, Glutamic acid, Glutamine
Side Chains: net charge of zero at physiologic pH, promote hydrophobic interactions, cluster in the interior of the protein
non-polar side chains
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
Glycine
Glycine + Succinyl CoA
δ-ALA (aminolevulinic acid)
Amino Acids: Amino Acids: Carries nitrogen from peripheral tissues to the liver
Alanine
Amino Acids: branched-chain amino acids whose metabolites accumulate in Maple Syrup Urine Disease (deficiency in branched-chain α-ketoacid dehydrogenase)
Valine, Isoleucine, Leucine
Amino Acids: accumulates in Phenylketonuria
Phenylalanine
Deficient enzyme in PKU
Phenylalanine Hydroxylase
Accumulating metabolites in PKU
phenyllactate, phenylpyruvate, phenylacetate
Causes the musty odor in PKU
phenylacetate
Amino Acids: has the largest side chain, precursor for niacin, serotonin (5-HT) and melatonin
Tryptophan
Amino Acids: precursor of homocysteine
Methionine
Methionine is used in transfer of methyl groups as
S-adenosylmethionine (SAM)
Amino Acids: contributes to the fibrous structure of collagen and interrupts α-helices in globular proteins
Proline
Side Chains: zero net charge at physiologic pH, presence of side chains that can participate in hydrogen bonds
uncharged polar side chains
Amino Acids: contains a sulfhydryl group that is an active part of many enzymes
Cysteine
2 cysteine molecules connected by a covalent disulfide bond, abundant in keratin
Cystine
Products from Phenylalanine
Phenylalanine → Tyrosine → L-Dopa → Dopamine → Norepinephrine → Epinephrine
Precursor for thyroxine and melanin
Tyrosine
Amino Acids: phosphorylation site of enzyme modification, linked to carbohydrate groups in glycoproteins
Serine
Amino Acids: sites for O-linked glycosylation in the golgi apparatus
Serine, Threonine
Amino Acids: have a carbonyl group and an amide group that can also form hydrogen bonds
Asparagine, Glutamine
Amino Acids: site for N-linked glycosylation in the endoplasmic reticulum
Asparagine
Amino Acids: deaminated by glutaminase resulting in the formation of ammonia, major carrier of nitrogen to the liver from the peripheral tissues
Glutamine
Side Chains: negatively charged at physiologic pH because of the carboxylate group, participate in ionic reactions
acidic side chains
Amino Acids: precursor for GABA and glutathione
Glutamate
Side Chains: positively charged because of the amine group
basic side chains
At neutral pH, arginine and lysine are
positively charged
At neutral pH, histidine is
neutral (weak base)
Amino Acids: precursor of histamine, used in the diagnosis of folic acid deficiency
Histidine
Ingividuals deficient in folic acid excrete increased amounts of FIGlu in urine particularly after ingestion of large doses of histidine
N-formiminoglutamate Excretion Test
Amino Acids: precursor of creatinine, urea and nitric oxide
Arginine
21st Amino Acid
Selenocysteine
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
Selenocysteine
Non-Polar Amino Acids
Glycine, Alanine, Leucine, Isoleucine, Valine, Phenylalanine, Tryptophan, Methionine, Proline
Polar Uncharged Amino Acids
-OH (Serine, Threonine, Tyrosine), -SH (Cysteine), Amide (Asparagine, Glutamine)
Charged Amino Acids
Acidic (Aspatrate, Glutamate), Basic (Lysine, Arginine, Histidine)
All amino acids are chiral except for
Glycine
An atom in a molecule that is bonded to 4 different chemical species allowing for optical isomerism
chiral center
Molecuels that are exact mirror images of each other
Stereoisomers/Enentiomers/Optical Isomers
Most common configuration of AAs
L-configuration
A chemical compound that has a total net charge of zero
Zwitterion
pH where the zwitterion predominates (AA is uncharged)
Isoelectric Point (pI)
Isoelectric Point (pI)
(pKa before + pKa after)/2
Molecular group that accepts protons
amino group
Molecular group that donates protons
carboxylic acid group
AAs that cannot be synthesized by the body and must come from the diet
Phenylalanine, Valine, Tryptophan, Threonine, Histidine, Arginine, Leucine, Lysine
Conditionally Non-Essential AAs: may be made in the body but usually not enough
Arginine
Conditionally Non-Essential AAs: may be recycled but should eventually be consumed since it is not made at all
Histidine
Linear sequence of a protein’s amino acids
Primary Structure
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
Peptide Bonds
Makes the peptide bond rigid and planar
partial double bond
Cleaves the N-terminal amino acid
Sanger’s reagent, Edman’s reagent
Cleaves the C-terminal amino acid
Hydrazine, Carboxypeptidase
Used to detect covalent modifications in proteins
mass spectrometry
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
Secondary Structure
Secondary Structures: most common, R-handed spiral with polypeptide back bone core, side chains extend outward, 3.6 AA per turn of the spiral
Alpha Helix
Alpha helices are disrupted by
proline, large R-groups, charged R-groups
Secondary Structures: surfaces appear flat and pleated, 2 or more peptide chains parallel to each other, interchain and intrachain bonds
Beta Sheet
Secondary Structures: combinations of adjacent secondary structures such as β-α-β unit, Greek key, β-meander, β-barrel
Motifs (Supersecondary Structures)
Secondary Structures: R-handed spiral, H-bonds parallel to helix, keratin, hemoglobin
Alpha Helix
Secondary Structures: sheets, H-bonds perpendicular to sheets, amyloid, immunoglobulin
Beta-Pleated Sheet
Overall 3D shape of the protein, globular, fibrous, refers to the folding of domains and their final arrangement in the polypeptide
Tertiary Structure
The tertiary structure of proteins are stabilized by
disulfide bonds, hydrophobic interactions, hydrogen bonds, ionic bonds
Fundamental functional and 3D structural units of a polypeptide, formed by combinations of motifs
Domains
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
Chaperones
Can rescue proteins that have become thermodynamically trapped in a misfolded dead end by unfolding hydrophobic regions
Chaperones
Structure of proteins consisting of more than one polypeptide chain, held together by non-covalent bonds
Quarternary Structure
Precipitation of a protein so that it forms ordered crystals that can diffract x-rays
X-ray Crystallography
Measures the absorbency of radiofrequency electromagnetic energy by certain atomic nuclei, groups of nuclei have particular absorbency patterns
Nuclear Magnetic Resonance Spectroscopy
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
Molecular Modeling
Disruption of a protein’s structure
Denaturation
Means of Protein Denaturation
heat, organic solvents, mechanical mixing, strong acids or bases, detergents, ions of heavy metals (lead & mercury)
Fatal neurodegenerative diseases characterized by spongiform changes, astrocytic gliomas and neuronal loss resulting from the deposition of insoluble protein aggregates in neural cells
Prion Diseases
Prions: normal protein, rich in α-helices
PrPc
Prions: pathologic conformation, rich in β-sheets
PrPsc
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
Alzheimer’s Disease
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
Heme
Heme protein found exclusively in red blood cells, composed of heme and 4 globin chains
Hemoglobin
Major transporter of CO2 in the blood
HCO3 (75%), carbaminohemoglobin (25%)
Hemoglobin: ζ2ε2, conception until the first few months, yolk sac
Embryonal Hemoglobin (Gower 1)
Hemoglobin: α2γ2, first few months to after birth, liver
Fetal Hemoglobin (HbF)
Hemoglobin: α2γ2, 8th month onwards, marrow
Hemoglobin A (HbA)
Hemoglobin: α2δ2, shortly after birth onwards, marrow
Hemoglobin A2 (HbA2)
Binds up to 4 molecules of oxygen, exhibits positive cooperativity, sigmoidal curve
Hemoglobin
Hemoglobin binds to O2 with increasing affinity
Positive Cooperativity
Hemoglobin: low oxygen affunity
T (taut)
Hemoglobin: high oxygen affinity (300x)
R (relaxed)
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
Myoglobin
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
Myoglobin
O2 Carriers: 1 polypeptide
Myoglobin
O2 Carriers: carries 1 O2
Myoglobin
O2 Carriers: hyperbolic curve (saturation)
Myoglobin
O2 Carriers: storage
Myoglobin
O2 Carriers: heart, muscle
Myoglobin
O2 Carriers: 4 polypeptides
Hemoglobin
O2 Carriers: carries 4 O2
Hemoglobin
O2 Carriers: sigmoidal curve (cooperativity)
Hemoglobin
O2 Carriers: transport
Hemoglobin
O2 Carriers: allosteric effects are present
Hemoglobin
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
Allosteric Effectors
Shifts the O2 Dissociation Curve to the right
CO2, acidity, 2,3-BPG, exercise, temperature
The deoxy form of hemoglobin has a greater affinity for protons than does oxyhemoglobin
Bohr Effect
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
2,3-BPG
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.
Methemoglobin
Hgb bound to carbon monoxide instead of O2, cherry pink
Carboxyhemoglobin
Hemoglobin: CO
Carbohyhemoglobin
Hemoglobin: CO2
Carbaminohemoglobin
Hemoglobin: cherry pink
Carboxyhemoglobin
Hemoglobin: muddy brown
Methemoglobin
Hemoglobin: When blood glucose enters erythrocytes, it glycosylates the
ε-amino group of lysine residues and the amino terminals of hemoglobin (HbA1c)
Disorder characterized by an inherited (intrinsic) defect in the RBC membrane that renders erythrocytes spheroidal, less deformable and vulnerable to splenic sequestration and destruction
Hereditary Spherocytosis
Hereditary Spherocytosis: Mutations
spectrin, band 4.1, band 3
Hereditary Spherocytosis: Diagnosis
osmotic fragility test
Hereditary Spherocytosis: Treatment
splenectomy for symptomatic patients
Point mutation in both genes coding for β-chain that results in a valine rather than a glutamate, homozygous recessive disorder
Sickle Cell Disease
Polymerization and decreased solubility of the deoxy form of Hgb, distortion of the RBC membrane, misshapen, rigid RBCs occlude capillaries
Sickle Cell Disease
Amenia, tissue anoxia, painful crises, protective against malaria
Sickle Cell Disease
Sickle Cell Disease: Treatment
hydration, analgesics, antibiotics if with infection, transfusions, hydroxyurea
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
Hemoglobin C
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
Alpha Thalassemia
Alpha Thalassemia: 1 defective gene
silent carrier
Alpha Thalassemia: 2 defective genes
Alpha Thalassemia Trait
Alpha Thalassemia: 3 defective genes
Hb H DIsease
Alpha Thalassemia: 4 defective genes
Hydrops Fetalis
Alpha Thalassemia: Chromosome
Chrom. 16
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
Beta Thalassemia
Beta Thalassemia: 1 defective gene
Beta Thalassemia Minor
Beta Thalassemia: 2 defective gene
Beta Thalassemia Major
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
Collagen
Most Common Collagen Type
Type 1
Collagen is rich in
Glycine, Proline
X portion of collagen
Proline (facilitates kinking)
Y portion of collagen
hydroxyproline or hydroxylisine
Formed in fibroblasts or in the osteoblasts of bone and chondroblasts of cartilage, secreted into the extracellular matrix
Collagen
Collagen monomers aggregate and become cross-linked to form
Collagen Fibrils
Collagen: pro α-chain + signal peptide
PrePro α-chain
Collagen: signal peptide removed
Pro α-chain
Collagen: lysine and proline are hydroxylated
Procollagen
Collagen: 3 procollagen chains form the triple helix
Triple Helix Procollagen
Collagen: secreted from the cell
Triple Helix
Collagen: triple helix with propeptide removed
Tropocollagen
Collagen: lysine cross-links, parallel, staggered
Collagen Fibrils
Collagen: bone
I
Collagen: skin
I
Collagen: tendon
I
Collagen: dentin
I
Collagen: fascia
I
Collagen: cornea
I
Collagen: late wound repair
I
Collagen: cartilage
II
Collagen: vitreous body
II
Collagen: nucleus pulposus
II
Collagen: skin
III
Collagen: blood vessels
III
Collagen: uterus
III
Collagen: fetal tissue
III
Collagen: granulation tissue
III
Collagen: basement membrane/basal lamina
IV
Results from inheritable defects in the metabolism of fibrillar collagen, collagen is most frequently affected
Ehlers-Danlos Syndrome
Hyperextensible skin, tendency to bleed, hypermobile joints, high risk for berry aneurysms
Ehlers-Danlos Syndrome
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
Osteogenesis Imperfecta
Multiple fractures, blue sclerae, hearing loss, dental imperfections
Osteogenesis Imperfecta
Hydroxylation of collagen is a post-translational modification requirin ascorbic acid. deficiency causes decreased cross-linking of collagen fibers
Scurvy
Sore spongy gums, loose teeth, poor wound healing, petechiae on skin and mucous membranes
Scurvy
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
Alport’s Syndrome
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
Menke’s Syndrome
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
Epidermolysis Bullosa Dystrophica
Connective tissue protein with rubber-like properties, responsible for extensibility and elastic recoil in tissues
Elastin
Rich in proline and lysine but little hydroxyproline and no hydroxylysine
Elastin
Precursor tropoelastin is deposited into an irregular fibrillin scaffold cross-linked by desmosine
Elastin
Elastin is found in tissues where elastic recoil is needed like in
lungs, large arteries, elastic ligaments, vocal cords, ligamentum flavum
Autosomal dominant connective tissue disorder, mutation in fibrillin gene
Marfan Syndrome
Taller, thinner, dolichostenomelia, arachnodactyly, ascending aortic dilatation and dissection
Marfan Syndrome
Deficiency in the enzyme that inhibits proteolytic enzymes from hydrolyzing and destroying proteins, elastase destroys the alveolar walls resulting in emphysema
α1 Trypsin Deficiency
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
Collagen
One genetic type, Intramolecular desmosine cross-links
Elastin
