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B/B Section Bank Quick Facts
Terms in this set (64)
Describe isoelectric focusing.
Separation of proteins based on isoelectric point via a stable pH gradient within a gel
How do protein isoforms form?
they are syntehsized from the same gene via alternative splicing of mRNA transcripts (different exons from same gene combined)
What molecule is required for autophosphorylation? How is it controlled in an experiment?
ATP; combine the enzyme with ATP and without the substrate to determine background autophosphorylation levels
What type of cells are osteo-clasts/-blasts? What do they do, respectively?
connective tissue cells (bone cells)
clasts: breakdown/resorb bone
blasts: build bone
What is the dissociation constant (Kd)? How does Kd correspond to affinity?
Kd describes the turnover of a ligand/receptor pair; high Kd = more turnover
lower Kd = higher affinity
Describe the differences between peptide and steroid hormones.
peptide: hydrophilic, soluble in blood, cannot diffuse through membrane
steroid: require transport proteins within bloodstream and are lipophilic
What are examples of steroid hormones?
cortisol, aldosterone, testosterone, estradiol
What is SDS PAGE? How does it separate products?
SDS is a (-) charged detergent that denatures proteins; proteins gain a negative charge due to interactions with SDS that increase with mass
proteins separated by mass
What does reducing conditions mean in reference to SDS-PAGE?
Reducing conditions break disulfide bonds (Cys-Cys) via reduction
protein subunits are generally linked by disulfide bonds
What is native PAGE?
Proteins are not denatured (maintain tertiary or quaternary structure); size and shape important (small proteins still move fastest/furthest)
Name three factors that contribute to tertiary protein structure stabilization.
disulfide bonds, hydrogen bonds, salt bridge (link b/w acidic & basic groups of a protein)
What type of inhibitor does NOT the alter Km/Vmax ratio?
How do the following types of enzyme inhibition alter Vmax and Km?
competitive: Vmax no change, Km incr (E+I->EI)
noncompetitive: Vmax decr, Km no change (E+I->EI+S->ESI; E+S->ES+I->ESI)
uncompetitive: Vmax decr, Km decr (ES+I->ESI)
Uncompetitive inhibitors are most effective in what conditions (regarding inhibitor and substrate )?
uncompetitive inhibitors cannot bind until the ES complex is formed, thus incr [S] -> incr [ES]
What type of peptide sequence would be found in a transmembrane helix of a protein?
unbroken stretches of hydrophobic amino acids!
What is the difference between intrinsic and extrinsic apoptosis?
intrinsic is controlled by mitochondrial factors (Bcl2, Bax)
extrinsic occurs in response to signalling/receptor binding (TNFR, FAS)
What is another name for mRNA? Where is it translated?
transcript = mRNA
translation occurs in the cytoplasm (but does not determine final location of peptide/protein)
What are the complexes (in order) of the electron transport chain?
Include associated electron carriers.
I: NADH-CoQ reductase
II: succinate dehydrogenase + CoQ
III: cytochrome C reductase
IV: cytochrome C oxidase + CytC
Where does the electron transport chain occur?
inner membrane of mitochondria
Name two domains found on a transcription factor.
nuclear localization domain
DNA binding domain
(b/c TF bind DNA in the nucleus)
What mechanism alters the expression of genes resulting in cells of different functions?
nuclear factors (i.e TF) are the only elements that vary in different cells and therefore can confer both temporal and spatial regulation of their target genes
different cells within an organism contain the same DNA sequence (incl genes, promoters, enhancers), the cells regulatory trans-acting elements (nuclear factors) are different and vary based on cell type
What type of amino acids would be found at the interface of a dimer?
hydrophobic amino acids with be at the interface because dimerization is likely to occur in the cytosol (a polar location)
so dimerization reduces exposure of hydrophobic aa to the hydrophilic environment
What methods separate proteins based on their charge?
isoelectric focusing (pH gradient used to separate based on pI)
ion-exchange chromatography (based on net charge of protein)
How does affinity chromatography work?
separates proteins based on their interactions with specific ligands
What key ETC e- carriers are generated in the CAC during the conversion of a-ketoglutarate to oxaloacetate?
What enzyme catalyzes the first step of both gluconeogenesis and glycogenolysis? What is the difference between these pathways?
glycogenolysis breaks down glycogen stores to incr glucose
gluconeogenesis creates glucose from non-carbohydrates (fatty acids, glucogenic aa)
How is catalytic efficiency measured? What results in high catalytic efficiency?
catalytic efficiency = Kcat/Km (thus, lowest Km ~ highest cat. efficiency)
kcat = Vmax/[E] (kcat & Vmax are proportional)
What is cDNA and why is it different than genomoic DNA? Name three enzymes involved in the formation of cDNA.
DNA produced on an RNA template via reverse transcriptase (complementary DNA to RNA)
cDNA only contains exons, genomic DNA have exons & introns
DNA pol, DNA ligase, reverse transcriptase
What type of amino acids can form ionic bonds?
Only charged amino acids (K,R, E, D and maybe H)
What type of molecules feed into the gluconeogenesis pathway?
fatty acids and glucogenic amino acids (non-carbohydrates)
What are the products of glucogenic and ketogenic amino acid catabolism?
catabolism of glucogenic aa produces either pyruvate or intermediates in the CAC
catabolism of ketogenic aa produces acetyl CoA or acetoacetyl CoA
Name three starting materials of gluconeogensis.
lactate, oxaloacetate, and α-ketoglutarate
What happens after glucagon binds it's receptor?
activation of its GPCR
adenylate cyclase and protein kinase A activity increase
level of cAMP increases.
What enzyme catalyzes the rate-limiting step in glycogen breakdown (glycogenolysis)?
Glycogen phosphorylase (adds phosphate)
NB: phosphatases remove phosphate via hydrolysis
Describe the bonds in glucose polymers in the liver (glycogen).
glycosidic bonds between glucose molecules
α(1→4) linkage linearly
α(1→6) linkage at branch point.
What are the reactants and products of succinyl-CoA synthetase?
succinyl-CoA --succinyl-CoA synthetase--> succinate + GTP
What are free radicals? What are free radical scavengers? Give an example of each.
FR: an uncharged molecule (typically highly reactive and short-lived) having an unpaired valence electron (i.e. O₂ --> 2O°); byproducts of oxygen metabolism that cause oxidative stress
FRS: mitigate the effects of reactive oxygen species (N-acetyl cysteine (NAC)
What is siRNA? What does it do? How does it do it?
siRNA = small interfering RNA
dsRNA that interferes or silences RNA translation
binds and promotes degradation of specific mRNA blocking protein production
What is lipoic acid?
lipoic acid, a cofactor for the enzyme pyruvate dehydrogenase which catalyzes the conversion of pyruvate to acetyl-CoA
(A-CoA is used in FA synthesis and TCA)
What enzyme catalyzes the conversion of glucose 6-phosphate to 6-phosphogluconolactone? What pathway does this occur in?
glucose 6-phosphate dehydrogenase
Pentose Phosphate Pathway
How does the DNA sequence of the coding strand compare to the related mRNA transcript?
The nucleotide sequence of both the coding strand and the mRNA are complementary to the template strand.
coding DNA seq = mRNA seq (T--> U)
What are three lab techniques to analyze gene expression?
What is southern blotting?
A technique that uses DNA probes to detect the presence of specific DNA sequences
What are the e- acceptors and donors in lactic acid fermentation?
pyruvate is reduced by NADH to produce lactate
pyruvate = acceptor, NADH = donor
What is the difference between prokaryotic and eukaryotic cell membranes?
EUK: contain phospholipids, glycoproteins, and cholesterol
PRO: contain proteins and phospholipids (cell walls can contain peptidoglycan)
What is the amino acid precursor of serotonin?
Increasing the volume of air involved in gas exchange results in...
enhanced O₂ uptake and CO₂ removal, thereby increasing blood pH
What is differential pressure (regarding the respiratory system)? How do the two types of pressure compare to atmospheric pressure?
difference between intrapulmonary (inside lung) pressure and intrapleural (outside lung) pressure.
Intrapulmonary pressure = atmospheric pressure (lung is open to the outside, so has same pressure as outside)
Intrapleural pressure = less than atmospheric pressure --> prevent lung from collapsing. During breath intake, intrapleural pressure decreases even further, causing the lung to expand.
When does ∆G = 0?
Gibbs Free Energy = 0 when Keq = 1 because
∆G = -RTln(Keq) --> ln(1) = 0 --> ∆G = 0
What is lipophilicity?
It is a measure of the solubility of a substrate in a membrane (lipophilic = fat loving)
Ex: lipophilic drugs move easily through the membrane
What function does BSA serve?
protein that mobilizes and stablizes proteins and lipids in serum;
improve catalytic rates by stabilizing the transition state
What type of bond links monosaccharides in an oligosaccharide?
a special type of acetal linkage known as a glycoside bond
What is the charge of His at pH 7?
neutral, His becomes protonated at pH less than 6 (pKa = 6-6.5)
What does a lipase do?
Lipase uses water (hydrolysis) to break triacylglycerol (fatty acids) to diacyclglycerol to monoacylglycerol (two processes)
Which type of bond is formed by glycogen synthase upon release of UDP?
an α-1,4-glycosidic bond; glycogen synthase is the main chain linkage of glycogen; UDP release means that only glucose was added
What do glucocorticoids do related to muscles?
glucocorticoids act on skeletal muscle causing the breakdown of muscle proteins
What are three common symptoms of diabetes mellitus?
In diabetic patients, high blood glucose results in excretion of excess sugar into the urine, hence sweet-tasting urine.
Similarly, the catabolism of fatty acids and proteins results in weight loss and feelings of fatigue respectively.
What is the average molecular weight of an amino acid?
average molecular weight of an amino acid is 110 Da
What does the Hill Coefficient measure? What does it mean when >1, =1, or <1?
measures cooperativity (as seen in sigmoidal curves; i.e. hemoglobin)
H > 1 = cooperativity
H = 1 = no cooperativity
H < 1 = negative cooperativity
What organ releases hormones to control blood glucose levels? What are the hormones and their affect?
the pancreas releases insulin or glucagon to lower or raise BGL, respectively
What is a signal sequence domain?
signal sequence domains are protein domains required for proteins that are directed toward secretory pathways
What is the result of glucagon binding its GCPR?
activation of its coupled G protein (dissociation of bound GDP and exchange for GTP on the α subunit)
increase in activities of the adenylate cyclase and PKA
increase cAMP levels
What is a phosphatase and how does it function?
Phosphatase is a type of hydrolase that hydrolyzes the bond between a molecule and phosphate group, resulting in the formation of inorganic phosphate
What are three control experiments that can be used to validate siRNA experiments?
measure and observe decrease protein levels after siRNA treatment
confirm siRNA does not interfere with expression of other unrelated proteins
confirm non-specific siRNA does not interfere with the expression of FASN or mtKAS
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