Biochemistry (Block 1-Part 1)

davidwurbel7's version from 2015-04-19 03:45


Question Answer
The average pKa for α-carboxylic acid groups is~2 (1.8 to 2.4)
The average pKa for α-amino groups is ~9.5 (8.8 to 11.0)
Hendersen-Hasselbach equationpH = pKa + log [A-]/[HA]
What are the essential amino acidsPhenylalanine, Valine, Threonine, Tryptophan, Isoleucine, Methionine, Histidine, Arginine, Leucine and Lysine.
pH < PkaProtonated
pH > PkaDeprotonated
pH=Pka50% protonated, 50% deprotonated
The pH at which the net charge on the molecules in solution is zero is called theIsoelectric Point
The histidine side chain is an immidazole ring with a pKa of approximately6
Which amino acid can both accept or donate protons depending on the local pH, hence act as a good buffer.Histidine (ph7)
Which amino acid is considered as an semi-essential amino acidArginine

Amino Acid Properties

Amino AcidsProperties
Asn, Cys, Gln, Gly, Ser, Thr, TyrPolar
Ala, Ile, Leu, Met, Phe, Pro, Trp, ValNonpolar
Arg, His, LysBasic (+)
Asp, GluAcidic (-)
K/Lys/LysineBasic (+)
R/Arg/ArginineBasic (+)
H/His/HistidineBasic (+)
D/Asp/AspartateAcidic (-)
E/Glu/GlutamateAcidic (-)


Question Answer
Build up of β amyloid plaques. Protein aggregates and suffocates cell.Alzheimer’s Disease
Progressive dementia; malnutrition, agitation, withdrawal, hallucinationsAlzheimer’s Disease
TAUB – hyperphosphorylated causes neurfilbular tangles = misfiringAlzheimer’s Disease
Amyloid plaque that accumulates contains Aβ42 having characteristic beta-pleated sheet Alzheimer’s Disease
Protein Misfolding (compromised NS) Abnormal cleavage of Amyloid Precursor Protein on chrom 21 (Down syndrome ass.)Alzheimer’s Disease
Which proteins assist in protein folding.Chaperones & Chaperonins
Protein Misfolding (Compromised NS), Prion induces abnormal protein folding of normal proteinsCreutzfeld-Jakob disease (CJD)
Normal protein is mostly α helices; Prion contains β sheets (45%). Rapidly progressive and always fatal, Rare but fatalCreutzfeld-Jakob disease (CJD)
Somatic cell mutation or rare spontaneous refolding of PrPc to PrPscCreutzfeld-Jakob disease (CJD)
What are the bonds of the Tertiary & Quaternary structureDisulfide bond (covalent), H+ bonds, ionic bonds, van der Waals interaction, hydrophobic interaction
What bonds are located between cysteine residuesDisulfide bonds
What is the most importatn ubiquitin ligases in the ubiquitin–proteasome pathwayE3
What are the bonds of the secondary structureH+ bonds
What is the bacterial equivalent of the human Chaperoneshsp70
What is the bacterial equivalent of the human Chaperoninshsp60
In the protein ubiquitin–proteasome pathway, which amino acid must be marked in order for a protein to be degradadedLysine
Dopamine depletion in the neostriatum due to degeneration of dopaminergic nigrostriatal neurons in substantia nigra pars compacta. This is associated with alpha-synuclein & lewy bodiesParkinson’s disease
What are the bonds of the primary structurePeptide (Covalent) bonds
Which amino acid is considered the helix breakerProline
Alpha-helix or Beta-sheet are associated with what structureSecondary Structure


Question Answer
FBN1 gene is located on what chromosome15
Panacinar emphysema or COPD can be a result asα1-Antitrypsin deficiency
Cigarette smoke directly inactivates ______ by oxidizing essential methionine residues to sulfoxide formsα1-Antitrypsin
What inhibits number of proteolytic enzymes including elastasesα1-Antitrypsin
Two allysine residues can undergoAldol condensation
Copper requiring lysyl oxidase catalyzes the oxidation of some of the lysine to produce ___________ to help strengthen the collagen molecule.Allysine
What forms cross-links in elastin catalyzed by lysyl oxidaseAllysines
A genetic condition characterized by a mutation in gene coding for type IV collagen and leads by kidney disease, hearing loss, and eye abnormalities.Alport Syndrome
What is required as a coenzyme for prolyl hydroxylase and lysyl hydroxylase in collagen formation.Ascorbic acid
What type of collagen is found in skin, tendon, vascular ligature, organs, bone, corneaCollagen I
What type of collagen is found in cartilage and vitreous humorCollagen II
What type of collagen is found in reticular fibersCollagen III
What type of collagen is found in the basement membrane or basal laminaCollagen IV
Gly-X-Y repeats can be found inCollagen Structure
Skin changes vary from thin and velvety to skin that is either dramatically hyperextensible ("rubber person" syndrome) or easily torn or scarred. Patients develop characteristic "cigarette-paper" scars. Ehlers-Danlos syndrome (EDS)
Collagen disorder, mitral valve prolapse and hernias, mild to moderate scoliosis, and degenerative arthritis. Commonly associated with loose or hypermobile joints and hyperelasticEhlers-Danlos Syndromes
Mutations in collagen genes and lysine hydroxylase geneEhlers-Danlos Syndromes
Hypermobile joints, dislocations, varicose veins, ecchymoses, arterial, intestinal rupturesEhlers-Danlos Syndromes
Mutation in COL5A1 and COL5A2 (type V collagen) Ehlers-Danlos Syndromes II (mild)
Mutation in COL1A1 and COL1A2 (type I collagen)Classic Ehlers-Danlos Syndromes (EDS I—severe)
Mutation in TNXB gene, which encodes tenascin X.Hypermobile Ehlers-Danlos syndromes (EDS III)
Mutation in COL3A1 (type III collagen) & defect in the enzyme lysyl hydroxylaseVascular Ehlers-Danlos syndromes (EDS IV)
Mutation in gene coding for type IV collagen leads to what diseaseAlport Syndrome
Auto immune dysfunction where the immune system attacks the basement membranes of the glomeruli and the alveoli.Goodpasture’s Syndrome
What bonds are hydroxyprolines involved in which stabilize the triple helix of collagenHydrogen Bonds
α1-Antitrypsin is synthesized mainly in theLiver
Mutation in the α1-AT gene, results in the substitution ofLysine for Glutamic Acid
Skeletal, Heart & Eye issuesMarfan Syndrome
A disease caused by mutations in the Fibrillin-1 (FBN1) gene, a key component of connective tissue on chromosome 15Marfan Syndrome
Ocular abnormalities (myopia and detached lenses)Marfan Syndrome
Cardiovascular diseases. Dilation of ascending aorta (90%) frequently leads to aortic rupture or congestive heart failureMarfan Syndrome
Characterized by skeletal abnormalities (thin, elongated limbs, pectus excavatum, pectus carinatum), hypermobile jointsMarfan Syndrome
Arachnodactyly (spider fingers), Positive Walker-Murdoch & Steinberg signsMarfan Syndrome
Triad of long limbs, dislocated lenses (superotemporal subluxation) and aortic root dilatation Marfan Syndrome
Deficient cross-linking secondary to functional copper deficiencyMenkes Disease
Depigmented (steely) hair, arterial tortuosity, rupture, cerebral degenration, osteoporosis, anemiaMenkes Disease
A disorder of copper transport caused by mutations in the copper-transporting ATPase gene (ATP7A).Menkes Disease
X-linked recessive trait, Lysyl oxidase enzyme is affected which leads to a defect in cross-linkingMenkes Disease
What degrades elastin of alveolar walls and other tissue proteins.Neutrophil elastase
Lobstein Syndrome is a genetic bone disorder a.k.aOsteogenesis Imperfecta
Single base substitutions mutations in type 1 collagen genesOsteogenesis Imperfecta
Skeletal deformities, fractures and tainted scleraOsteogenesis Imperfecta
Dental abnormalities (dentinogenesis imperfecta), the teeth may have a characteristic amber, yellowish brown, or translucent bluish gray color because of a deficiency of dentin that is rich in type I collagen.Osteogenesis Imperfecta
Mutations in either the proα1 chain gene or the proα2 chain gene of type I procollagen (the COL1A1 and COL1A2 genes). GLY-X-Y (Can be defect in Gly to any other amino acid)Osteogenesis Imperfecta
A severe decrease in bone mass (osteopenia) that makes bones brittle. The appearance of "popcorn-like" deposits of mineral in x-rays of the ends of long bones is an ominous sign. The disorder is frequently associated with blue sclera.Osteogenesis Imperfecta
Petechia, echymoses, poor wound healing, poor bone developmentScurvy
Perifollicular hemorrhages in the skinScurvy
In advanced cases, swollen, bleeding gums are a classic finding. Alveolar bone resorption results in loss of teeth.Scurvy
Deficient hydroxylation secondary to ascorbate acid deficiencyScurvy
Vitamin C deficiency is associated withScurvy
Swollen, bleeding gums, joints, loose teeth, pinpoint hemorrhages around hair folicles (petechiae), gums, nails, soreness and stiffness of joints & lower extremities, slow wound healing, anemia, fatigueScurvy
Fibrillin-1 directly binds a latent form of _____ keeping it sequesteredTGFβ
What is the co-factor needed for prolyl hydroxylase and lysyl hydroxylase during biosynthesis of collagen catalize by hydroxylation in the lumen of the RER.Vitamin C/Ascorbic Acid


Question Answer
HbA1c monitors glucose levels over16 weeks duration
Myoglobin’s PO2 (P50) =2.8 mm Hg
hemoglobin PO2 (P50) =26 mm Hg
Fetus hemoglobin (HbF) α2γ2 predominates from 6 weeks of fetal life and gradually starts falling from30 weeks
How long after birth will HbA take over HbF6-weeks
Carbon dioxide is bound to amino groups of globin part of hemoglobin formingCarbaminohemoglobin
What binds with heme of hemoglobin, forming very bright red compound, which may cause the skin to appear pink in death, instead of white or blue.CO
2,3- BPG _______the oxygen affinity of hemoglobin.Decreases
Increase in 2,3-BPG, Increase in PCO2, Decrease in pH (increased H+ ion concentration)-AcidosisFactors shifting oxygen-hemoglobin dissociation curve to the right
Decreased 2,3-BPG, Decrease in PCO2, Increased pH (decreased H+ ion concentration), Presence of COFactors shifting oxygen-hemoglobin dissociation curve to the left
On complete saturation, hemoglobin binds to how many oxygenFour O2
When does HBA changes to HbA1cGlycosylation of Hemoglobin
Hemoglobin α2β2HbA (normal adult hemoglobin)
Hemoglobin α2δ2HbA2 (a minor adult hemoglobin)
Hemoglobin α2γ2HbF (fetal hemoglobin)
Which hemoglobin does not interact with 2,3-BPG, hence has higher affinity for oxygen.HbF (α2γ2 )
Addition of _________ into storage media prevents 2,3-BPG from decreasingInosine
The curve for myoglobin rises sharply and then takes a platue state (flattens) at lower PO2 (which is referred asHyperbolic Curve
In hemoglobin and myoglobin, _______serves to reversibly bind oxygen.Heme
______ is an iron dependent moleculeHeme
Pproximal histidine interacts directly with Fe2+ of heme.His F8
Distal histidine does not directly interact with heme, but help stabilize the binding of oxygen to the ferrous iron.His E7
Two polypeptide chains within the dimer (αβ) are held together predominantly byHydrophobic Interactions
In the presence of oxygen (oxy form, R or relaxed form), the interaction between (αβ)1- (αβ)2 isLess tight and have more freedom of movement of the dimers.
Where does erythropoiesis takes place at 6 Weeks of prenatal life until birthLiver & Spleen (minor)
Where does erythropoiesis takes place from birth to adulthoodLong Bones
What functions as reservoir of oxygen in red muscle fibersMyoglobin
On complete saturation, myoglobin binds to how many oxygenOne O2
Interaction between the dimers, (αβ)1- (αβ)2, is predominantly byPolar bonds (hydrogen bonds and salt bridges (ionic interactions))
Hemoglobin curve rises slowly and steadily and reaches a platue state (flattens) at high PO2 which is referred asSigmoidal Curve
Cooperativity phenomenon takes place at 90-100 mmHG in the hemoglobin, which makes oxygen-dissociation curve of hemoglobinSigmoidal
In the absence of oxygen (deoxy form, T or taut form), the interaction between (αβ)1- (αβ)2 isTight and constrains the movement of the dimers.
Where does erythropoiesis takes place at 15 days – 6 Weeks of prenatal lifeYolk Sac