Biochemistry Concepts and Enzyme Kinetics, Exams of Biochemistry

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Biochemistry Final Assessment Questions and Answers 100% Correct Nonpolar, nonaromatic amino acids (7) - Correct Answer glycine, alanine, valine, leucine, isoleucine, methionine, proline Aromatic amino acids (3) - Correct Answer phenylalanine, tyrosine, tryptophan Polar amino acids, uncharged (5) - Correct Answer serine, threonine, asparagine, glutamine, cysteine Acidic amino acids (2) - Correct Answer aspartic acid, glutamic acid Basic amino acids (3) - Correct Answer lysine, arginine, histidine The surface of a protein is rich with _____ side chains, while the interior is rich with _____ side chains - Correct Answer charged/polar; non-polar/hydrophobic pKa of COOH side chain _____; pKa of NH3 side chain ______ - Correct Answer 2; 9- 10 Equivalents of base added to bring low pH amino acid to first midpoint ([fully protonated] = [zwitterion]); equivalents added to bring amino acid to second midpoint (zwitterion); equivalents added to bring amino acid to third midpoint (zwitterion/fully deprotonated) - Correct Answer 0.5; 1.0; 1.5 Charged amino acids typically have ____ midpoints, uncharged typically have ____ - Correct Answer 3, 2 Peptide bond formation is a ______ reaction - Correct Answer condensation/dehydration; acyl substitution reaction (electrophilic carbonyl carbon attacked by nucleophilic amino group, hydroxyl group is kicked off) Tertiary structure of proteins is determined by - Correct Answer disulfide bonds (can be reduced), salt bridges, H bonding, hydrophobic intx Around which bonds are rotation restricted in amino acids - Correct Answer O=C-N ; - O-C=N+ trigonal planar geometry Hydrolysis of peptide bonds - Correct Answer hydrolytic enzymes- trypsin/chymotrypsin (only cleave at specific points in peptide chains) Proline is not found in ____ of secondary structure, but is found in _____ and ______ - Correct Answer middle of alpha helix/beta-pleated sheet; turns of beta-pleated sheet, beginning of alpha-helix What does the mutant form R48C represent - Correct Answer Arginine (R) at position 48 mutated to Cysteine (C) Kinases are what type of enzyme - Correct Answer Transferase; catalyze the transfer of a phosphate group (ATP) to another molecule Hydrolases include - Correct Answer Phosphatase (cleaves phosphate group from another molecule); peptidases; nucleases; lipases Ligases often require - Correct Answer ATP Cofactors are generally _____ or _____; Coenzymes are ______ - Correct Answer inorganic molecules or metal ions (dietary minerals); small organic groups (vitamins)- NAD+, FAD, CoA Alumunium as a cofactor - Correct Answer dissolves in acidic solution Relationship between Vmax and Kcat - Correct Answer Vmax = [E] Kcat; Kcat is rate of catalysis If [S] >>> Km; If Km is >>> [S] - Correct Answer V = Vmax; V = (Vmax x [S])/Km Y = mx + b form of Lineweaver-Burk Plots - Correct Answer V^-1 = Km/Vmax (S^-1) + Vmax^-1 The rate of product formation by an enzyme-catalyzed reaction would be increased by - Correct Answer enzyme concentration (until saturation) high T (until denaturation) increased substrate concentration WT means - Correct Answer wild-type or naturally occurring Vmax doubles for temp increase of - Correct Answer 10 degrees Celsius Physiologically neutral pH is - Correct Answer 7.4 -changing pH changes enzyme activity Higher Km represents an enzyme with a ____ affinity for substrate because it requires a higher substrate concentration to be half-saturated - Correct Answer lower aldehyde is C number ___ in a sugar molecule - Correct Answer 1; ketone is C number 2 D-fructose - Correct Answer ketohexose D-glucose - Correct Answer aldohexose, C3 -OH points up D-galactose - Correct Answer aldohexose (C4 epimer of glucose) D-mannose - Correct Answer aldohexose (C2 epimer of glucose) sequester means - Correct Answer to remove or isolate D-glyceraldehyde and L-glyceraldehyde are _____ - Correct Answer enantiomers; they must have opposite absolute configurations at every chiral center; not directly to + or - designation sugars that are diastereomers - Correct Answer are in the same family (ketoses or aldoses) and have the same number of carbons; not idential/mirror images special type- epimers, differ at one chiral center D/L designation is based on - Correct Answer location of hydroxide (L- left, D-right) on highest numbered chiral center pyranoses are ____ membered rings; furanoses are _____ membered rings - Correct Answer 6; 5 anomeric carbon - Correct Answer carbonyl carbon (often carbon 1) that is attacked by nucleophilic oxygen, becomes chiral center alpha anomer designation; beta - Correct Answer alpha-- group is trans to Ch2OH- axial/down beta- group is cis to Ch2OH- equatorial/up Any group on the ___ in the fischer projection will point down - Correct Answer right (D) the ___ anomer is less stable because the -OH group is axial - Correct Answer alpha largest substituent should be in equatorial position aldoses are considered reducing agents because - Correct Answer they can be oxidized to aldonic acids (in open chain formation); free -OH allows this to happen Tollens' reagant and Benedict's reagant are used to detect - Correct Answer reducing sugars a deoxy sugar is missing a hydroxyl group on carbon - Correct Answer 2 (L from anomeric carbon) carbohydrates react with carboxylic acids to form - Correct Answer esters hemiacetals react with alcohols to form ____; in sugars this forms - Correct Answer acetals (gives off water); glycosides- alkoxy group on anomeric hydroxyl group; can be combined to form polysach Sucrose contains a bond between - Correct Answer glucose- alpha-1, 2- fructose Lactose contains a bond between _____ ; Maltose contains a bond between ______ - Correct Answer galactose- beta-1, 4-glucose glucose- alpha-1,4- glucose cellulose is a chain of ____ linked by _____; starch is a chain of _____; glycogen is a chain of _____ - Correct Answer beta-D-glucose molecules; linked by beta-1,4 glycosidic bonds alpha-D-glucose monomers; alpha-1,4 glucose alpha-1,6 glucose bonds (highly branched- also 1,4) glucose has ____ possible stereoisomers - Correct Answer 16 (2^4) plants primarily store starch as ____; which contains _____ bonds; another type of starch is _____; which contains ____ bonds - Correct Answer amylose; alpha-1,4 glucose amylopectin; alpha-1,6 glucose bonds/branching how to convert a fischer projection to a chair - Correct Answer -draw out haworth projection- groups on right go down -draw chair structure with O in back right corner -start on C1 carbon with axial group pointing down, alternate up/down on each C -fill in substituents based on fischer projection branched structures have ____ solubility - Correct Answer higher; reduce intx between adjacent chains, encourage intx with aqueous environment saturated bonds of lipids are solid because - Correct Answer they have greater van der waals forces, more stable overall structure unsaturated bonds makes it difficult to stack, liquids at room temp glycerophospholipids contain - Correct Answer two fatty acids that form ester bonds with the first and second hydroxyl groups of glycerol • a hydroxyl group that forms an ester with phosphoric acid, which forms another phosphoester bond with an amino alcohol shingomyelins are a type of - Correct Answer phospholipid; they contain a phosphodiester bonds major components of oligodendrocytes, Schwann cells ceramide + phosphocholine a sphingosine backbone contains - Correct Answer ceramide is the simplest sphingolipids, single H atom is its head gangliosides contain the ____ group - Correct Answer NANA or sialic acids cerebrosides have one ____ - Correct Answer sugar; globosides have multiple sugars waxes are - Correct Answer long chain fatty acids with long chain alcohols; piiable solids at room temp serve as protection, prevent dehydration cholesterol is a major component of ____ - Correct Answer phospholipid bilayer; mediates membrane fluidity -fluidity depends on temperature -accumulation in arterial walls- atherosclerosis prostaglandins - Correct Answer derive from arachidonic acid, unsaturated paracrine/autocrine signaling molecules regulate synthesis of cAMP- messaging a vitamin is an ; - Correct Answer essential nutriet that must be consumed in diet (not adequately synthesized by the body) vitamin A or carotene is important for - Correct Answer vision, growth/development, immune fxn ex. retinal- light-sensing system vitamin D or cholecalciferol - Correct Answer increases calcium/phosphate uptake (calcium binding sites), bone production consumed or formed in UV light driven rxn in skin cholesterol is a precursor vitamin E or tocopherols/tocotrienols - Correct Answer anti-oxidants mismatch repair - Correct Answer G2 phase- enzymes (MSH2/MLH1)- detect/remove errors in replication Excision endonuclease - Correct Answer cuts and patches helix-deforming lesions such as thymine dimers; makes nicks in phosphodiester backbone AP endonuclease - Correct Answer removes the damaged sequence during base excision repair; not helix-distorting leave behind AP site recombinant DNA - Correct Answer DNA produced by combining DNA from different sources; can be multiplied cloning procedures require - Correct Answer ligate DNA of interest into a piece called a vector (recombinant vector) bacteria grown in colonies with vector, isolated can express gene of interest or lysted to reisolate the recombinant vectors (processed by restriction enzymes) restriction enzymes - Correct Answer Enzyme that cuts DNA at a specific sequence of nucleotides; recognizes specific double stranded DNA sequences -can yield sticky ends- facilitate recombination with vector DNA (inserted directly) Genomic vs. Expression Libraries - Correct Answer genomic- include exon and intron regions cDNA/expression- include only exons, can be used to reliably sequence specific genes, ID disease-causing mutations, produce recombinant proteins, produce transgenic animals -cDNA prepared from processed mRNA strand by reverse transcription Hybridization of DNA is - Correct Answer joining of complementary base pair sequences telomeres contain - Correct Answer high GC content that prevent DNA unraveling polymerase chain reaction (PCR) - Correct Answer A technique for amplifying DNA in vitro by incubating with: -special primers (complementary to DNA) -DNA polymerase molecules- Thermus aquaticus from bacteria that fxns optimally at these temps -nucleotides (dATP,dTTP,dCTP,dGTP) and dideoxyribonucleotides (ddATP... polymerase can no longer add so these are used at the end) -heat- DNA double helix to denature; repeated cooling and heating cycles allow enzymes to act specifically fragments are separated by size using gel electrophoresis doubles DNA of interest most gene delivery vectors are - Correct Answer modified viruses knockout subject - Correct Answer gene has been intentionally deleted (-/-) transgene - Correct Answer cloned gene introduced to fertilized ova chimera - Correct Answer patches of cells, germ cells derived from each of two lineages DNa mutation cytosine to uracil happens - Correct Answer in the presence of heat fixed by DNA repair enzymes What types of repair mechanisms are active during S phase/G2 phase - Correct Answer mismatch repair What types of repair mechanisms are active during G1 and G2 phases - Correct Answer nucleotide and base excision repair ATP (adenosine triphosphate) - Correct Answer nucleotide of a sugar ribose, nitrogenous base adenine, and a chain of three phosphate groups bonded to it. urea vs. uric acid - Correct Answer urea - from protein NH3, urea cycle uric acid - from N in purines (derivative), requires xanthine oxidase lipid peroxidation - Correct Answer the destruction of polyUNsaturated lipids, leading to membrane damage and increased permeability -radical steals an e- from Ch2- methyl bridge adjacent to double bond NAD+/NADH (nicotinamide adenine dinucleotide/reduced nictoinamide adenine dinucleotide) - Correct Answer an organic molecule that serves as an electron carrier by being oxidized (losing electrons) to NAD+ and reduced (gaining electrons) to NADH -can donate H- (double bond on top ring reduced) Calcium is bound to proteins in the _____ - Correct Answer blood; free calcium is not bound to proteins NADPH - Correct Answer an electron carrier that provides the high-energy electrons needed to make carbon-hydrogen bonds in the third stage of photosynthesis -pentose phosphate pathway- regulator of redox rxns Floppases - Correct Answer Membrane proteins in the ABC transporter family that catalyze movement of phospholipids from the cytosolic leaflet to the extracellular leaflet of a membrane bilayer. -based on backmutation Angiopoietins - Correct Answer required for formation, stabilization of mature blood vessels The ___ strand of DNA is almost identical to the mRNA the ____ strand is complementary and antiparallel - Correct Answer coding (sense) template (antisense) The ____ codon IS transcribed and the _____ codon is NOT transcribed - Correct Answer start, stop codon is not transcribed mRNA takes the information from the nucleus to the ____ - Correct Answer ribosome (through the nuclear pores) each amino acid is activated by a different - Correct Answer aminoacyl-tRNA synthetase requires 2 high-energy bonds from ATP (energy-rich bond), synthetase transfers activate amino acid to the 3' end of the tRNA codons and anticodons are - Correct Answer complementary and antiparallel -remember that nucleic acids are still written 5' to 3' cystic fibrosis is caused by - Correct Answer frameshift mutation- deletion that results in a defective chloride ion channel -blocked passage of salt/water into and out of cells; produce abnormally thick, sticky mucus, gets bacteria stuck in eukaryotes ____ searches for the binding site in the promoter region known as _____; _____ help locate and bind to this region - Correct Answer RNA Pol II, TATA Box (-25 from 0- at AUG), Transcription factors (no primer needed) mRNA is derived from - Correct Answer heterogeneous nuclear RNA (hnRNA) Splicing is accomplished by - Correct Answer spliceosome- small nuclear RNA (snRNA) with ribonucleoproteins (snRNPs) excise the 5' and 3' ends of introns the tRNA loaded with MET binds to the ___ site, but incoming aminoacyl-tRNA complex is directed to the _____ site - Correct Answer initial- P site, incoming- A site P site holds growing polypeptide chain _____ enzyme catalyzes the formation of a peptide bond between the incoming amino acid in the A site and the polypeptide in the P site - Correct Answer peptidyl transferase osmotic pressure - Correct Answer pressure that must be applied to prevent osmotic movement across a selectively permeable membrane -water level only rises to the point of hydrostatic pressure (water opposes water) carriers are open to _____ of the cell membrane at any point - Correct Answer one side -can be open or closed conformation Secretion - Correct Answer a process by which substances are produced and discharged from a cell, gland, or organ for a particular function in the organism or for excretion. i.e. secretory vesicles hold material for exocytosis Nernst equation - Correct Answer Note: RT/F = 61.5 at body temp (310 K) z = charge/sign of charge -OUTSIDE to INSIDE outer vs inner mitochondrial membrane - Correct Answer outer- highly permeable (large pores)- passage of ions and small proteins inner- restricted, cristae inc surface area for integral proteins resting membrane potential depends on - Correct Answer differential distribution of ions, active transport/transport method, selective permeability of membrane -most likely to have resting potential that is non-zero so stimuli can be responded to Blood glucose concentration should remain around - Correct Answer 100 mg/dL (5.6 mM) GLUT2 vs. GLUT4 - Correct Answer GLUT2 in liver and pancreatic cells has a high Km (low affinity), blood traveling through hepatic portal vein- goes to storage GLUT4 in skeletal muscle/adipose tissue has a low Km (high affinity), peripheral blood, rate of transport is increased by insulin Glycolysis pathway - Correct Answer Glycolysis net reaction - Correct Answer Glucose + 2Pi + 2ADP + 2NAD+ -> 2pyruvate + 2ATP + 2NADH + 2H+ + 2H2O Rate-limiting enzymes for glycolysis, gluconeogenesis, fermentation, glycogenesis, glycogenolysis, pentose phosphate pathway - Correct Answer glycolysis- **PFK-1 gluconeogenesis- fructose-1,6-bisphosphatase fermentation- lactate dehydrogenase glycogenesis- glycogen synthase glycogenolysis- glycogen phosphorylase PPP- glucose-6-phosphate dehydrogenase Hexokinase vs Glucokinase - Correct Answer -both used to trap glucose Hexokinase: Located in most tissues, except liver and pancreatic B cells Low Km, increased affinity, Low Vmax, decreased capacity NOT induced by insulin Inhibited by Glucose-6-phosphate Glucokinase: Located in Liver and pancreatic B cells High Km, decreased affinity, High Vmax, increased capacity Induced by insulin NOT Inhibited by Glucose-6-phosphate PFK-1 -inhibited by.. -activated by.. - Correct Answer activated- insulin, F2,6-BP (comes from insulin activating PFK-2) inhibited- glucagon The reduction of NAD+ to NADH - Correct Answer can provide energy for ATP synthesis later, as NADH is oxidized Glyceraldehyde-3-phosphate dehydrogenase (G3P-> 1,3 Bisphosphoglycerate) - Correct Answer -produces 1 NADH each rxn which can feed into electron transport chain (from NAD+ and Pi) 3-phosphoglyercate kinase (1,3BPG -> 3-PG) pyruvate kinase (PEP -> pyruvate) - Correct Answer -produces 1 ATP each rxn (4 total, 2 net) from ADP why? high energy intermediates used to generate ATP by substrate-level phsophorylation Pyruvate kinase is stimulated by - Correct Answer fructose 1, 6-bisphosphate, the product of the phosphofructokinase reaction. fermentation is important for - Correct Answer regenerating NAD+ conversion of pyruvate to lactate (to ethanol and CO2) 2,3 BPG - Correct Answer is produced from 1,3BPG via a mutase -binds allosterically to beta chain of hemoglobin A and decreases affinity for oxygen Irreversible steps of glycolysis - Correct Answer 1. hexokinase/glucokinase glucose-> G6P (also into the cell cytoplasm) 3. phosphofructokinase-1** fructose6P -> f-1,6-BP 10. pyruvate kinase phosphoenolpyruvate -> pyruvate gluconeogenesis pathway - Correct Answer -performed by liver, sometimes kidneys at low levels -activated by glucagon and epinephrine (raise blood sugar) -inhibited by insulin (lower blood sugar) -often in fasting period -4 enzymes used to circumvent reactions arround 3 irvs steps of glycolysis Irreversible steps of gluconeogenesis - Correct Answer 11. pyruvate carboxylase (activate by acetyl CoA from FATTY ACIDS), OAA is intermediate reduced to malate pyruvate-> OAA 10. PEP carboxykinase OAA-> PEP , requires GTP [opposes pyruvate kinase] 3. fructose-1,6-bisphosphatase** removing phosphate from F-1,6-BP to form F-6-P; activated by ATP/glucagon (lowers F-2,6-BP), inhibited by AMP/F-2,6-BP [oppose PFK] 1. glucose-6-phosphatase- only in lumen of ER/liver, G6p -> glucose [opposes hexokinase] Gluconeogenesis is linked to _____ and can only occur in the _____ - Correct Answer fatty acid oxidation, requires acetyl-coA can only occur in the liver glucogenic amino acids vs ketogenic amino acids - Correct Answer -all except leucine and lysine; can be converted into intermediates that feed into gluconeogenesis -ketogenic- can be converted into ketone bodies, alternative fuel source (acetyl co-A is ketogenic) pyruvate can be converted into - Correct Answer -acetyl-coA (pyruvate dehydrogenase complex) -lactate (lactate dehydrogenase)- anaerobic glycolysis -Oxaloacetate (pyruvate carboxylase)- can then be transported through malate- aspartate shuttle to cytoplasm, where it can become PEP (PEP carboxykinase) Galactose metabolism pathway - Correct Answer -lactase hydrolyzes lactose into galactose and glucose (brush-border enzyme of duodenum) -galactokinase phosphorylates galactose into galactose-1P -Galactose-1P turns into glucose-1 phosphate via uridyltransferase and an epimerase -glucose-1-P can turn into glucose-6-P or glycogen fructose metabolism pathway - Correct Answer sucrase breaks down sucrose into glucose and fructose- absorbed into hepatic portal vein to liver production of acetyl coA through other mechanisms - Correct Answer amino acid catabolism- transamination to lose amino group; C skeletons form ketone bodies ketones- typically reverse rxn but can occur -alcohol- alcohol/acetaldehyde dehydrogenase convert alcohol to acetyl-coA; NADH buildup (primarily building fatty acids) Where is each step of ATP formation occurring - Correct Answer glycolysis- cytosol Pyruvate oxidation- mitochondrial matrix TCA cycle- mitochondrial matrix oxidative phosphorylation- inner mitochondrial membrane beta oxidation- mitochondrial matrix (uses carnitine shuttle) why is TCA cycle aerobic - Correct Answer cycle does not directly require O2 -NADH and FADH2 will buildup (without oxidative phosphorylation); this will inhibit cycle Steps of TCA cycle - Correct Answer PDH complex: Pyruvate (3) + COA (2), yield CO2 (1) NADH and acetyl COA (2) Step 1: Acetyl COA (2) + oxaloacetate (4) + H2O, goes to citrate (6) via citrate synthase** Step 2: Citrate (6) to isocitrate (6) via isocitrate Step 3: Isocitrate (6) to alpha-ketoglutarate yield NADH CO2 via isocitrate dehydrogenase (rate-limiting enzyme***) -oxalosuccinate intermediate Step 4: Alpha- ketoglutarate to succinyl COA, yield NADH CO2 via alpha-ketoglutarate dehydrogenase complex** (similar to PDH) Step 5: succinyl COA to succinate (energy release due to hydrolysis of thioester bond), yield one GTP (phosphorylation of GDP) via succinyl-coA synthetase -P of GTP directly transferred to ADP Step 6: succinate to fumarate, yield FADH2 via succinate dehydrogenase -succinate oxidized to fumarate while FAD reduced to FADH2 (connected with complex 2) -occurs at inner membrane Step 7: fumurate to malate via fumarase -hydrolysis of alkene bond Step 8: malate to oxaloacetate, yield NADH via malate dehydrogenase Please, Can I Keep Selling Seashells for Money, Officer? Net reaction of TCA cycle - Correct Answer PDH: pyruvate + CoA-SH + NAD+ -> acetyl-coA + NADH + CO2 + H+ acetyl-CoA + GDP + Pi + 3NAD+ + FAD + 2H2O yields 2CO2 + GTP (ATP) + 3NADH + FADH2 + 3H+ PDH is activated by - Correct Answer dephosphorylation (phosphatase); AMP/ADP inhibited by phosphorylation (kinase); ATP, acetyl-coA, NADH TCA cycle control points - Correct Answer citrate synthase; ATP/NADH/citrate/succinyl-coA allosterically inhibit isocitrate dehydrogenase; ATP, NADH inhibit; ADP/NAD+ activate alpha-ketoglutarate DH complex; ATP, NADH, succinyl-coA inhibit; stimulated by ADP and calcium ions why is oxygen a great final acceptor in the ETC - Correct Answer high reduction potential Complex I- IV of ETC - Correct Answer complex I- NADH-CoQ oxidoreductase -protein with Fe-S cluster and a flavoprotein (with flavin mononucleotide covalently bonded) to oxidize NADH e- move from NADH (NAD+) to FMN (FMNH2) to Fe-S (Fe-S reduced) to CoQ (CoQH2) -4 protons move into intermembrane space complex II- Succinate-CoQ oxidoreductase -comes from succinate dehydrogenase step -e- move from succinate (fumarate) to FAD (FADH2) to Fe-S (Fe-S reduced) to COQ (CoQH2) -no protons moved complex III- CoQH2 cytochrome c oxidoreductase -cytochromes- proteins with heme groups in which iron is reduced to Fe2+ and re- oxidized to Fe3+ -e- move CoQH2 (COQ) to 2cytochrome c Fe3+ (Fe2+) -Q cycle- 2 e- from CoQH2 (ubiquinol) to CoQ (ubiquinone); reduces two molecules of cytochrome c -4 protons move into intermembrane space complex IV- cytochrome c oxidase -cytochromes a, a3 make up cytochrome oxidase (Cu2+ ions also used) -e- moved from 4 cytochrome c (Fe2+) + 4H+ to O2 (2H2O) final electron acceptor -2 protons move into intermembrane space Is ratio of FADH2/NADH different in fat metabolism? - Correct Answer yes, skips glycolysis (which produces NADH, but no FADH2) electrochemical gradient forms between the intermembrane space and the mitochondrial matrix because - Correct Answer H+ inc in intermembrane space, pH drops; voltage different increases shuttle mechanisms for NADH - Correct Answer 1. glycerol-3-phosphate shuttle- 1.5 ATP for every NADH G3P dehydrogenase in cytosol NADH + DHAP -> NAD+ + G3P -this reduces FAD to FADH2 on the inner membrane, can transfer electrons to Q (QH2) via complex II 2. malate-aspartate shuttle- 2.5 ATP for every NADH -aspartate-> oxaloacetate- transamination -oxaloacetate to malate via malate dehydrogenase; NADH oxidized to NAD+ -crosses inner MM via malate -malate dehydrogenase reverses reaction, producing NADH (passes electrons to ETC via complex I) and oxaloacetate -oxaloacetate -> aspartate- transamination ATP synthase protein complex - Correct Answer -chemiosmotic coupling- delta G is - 220 kJ/mol -protons flow through the Fo ion channel of ATP synthase back into matrix (from intermembrane space)- along gradient -F1 portion utilizes energy to phosphorylate ADP -alternatively, conformational change caused by the gradient -if inc permeability to protons, protons flow through other spaces aside from F0 Uncouplers - Correct Answer compounds that prevent ATP synthesis without effecting the ETC and thus decrease the efficiency of the ETC/oxidative phosphorylation pathway -ADP builds up and ATP synthesis decreases -body sense lack of energy production - increases O2 production and NADH oxidation (form NAD+); body must burn more fuel to maintain the proton-motive force energy from the electrons is released as heat - fever that rises from toxic levels of salicylates (asprin) respiratory control of ATP formation - Correct Answer adequate O2- rate of oxidative phos is dependent on availability of ADP fatty acid catabolism - Correct Answer -beta-oxidation occurs in mitochondria; insulin inhibits, glucagon stimulates -peroxisomal beta-oxidation occurs -branches chain FA- alpha oxidation -omega-oxidation in ER -always activated by attachment to coA (fatty-acyl-coA synthetase) beta oxidation in mitochondria - Correct Answer -occurs within the mitochondria -co-produces FADH2 and NADH which can be used to produce ATP -in muscle/adipose tissue, acetyl-coA formed can enter TCA cycle -in liver, acetyl-coA stimulates gluconeogenesis (activates pyruvate carboxylase) -fasting state- acetyl-coA used to synthesize ketone bodies steps (reverse of fatty acid synthase) 1. oxidation of fatty acid to form double bond by FAD 2. hydration of double bond via H2o to form hydroxyl group 3. oxidation of hydroxyl group to form carbonyl by NAD+ 4. activation, split of beta-ketoacid into shorter acyl coA (continues to be oxidized) and acetyl coA Acetyl CoA vs. Acyl CoA - Correct Answer acyl coA- R group acetyl coA- methyl group beta oxidation of even vs odd chains - Correct Answer even- normal steps- final cycle produce two acetyl-coA molecules odd- produces acetyl coA and propionyl coA (3 C)- converted to methyl malonyl-coA by propionyl-coA carboxylase (uses biotin- vitamin B7); methylmalonyl coA converted into succinyl-coA by methylmalonyl-coA mutase (uses cobalamin- vitamin B12) -succinyl coA in TCA cycle; can be used to produce glucose via gluconeogenesis/malate -in general, additional reductase and isomerase (move and reduce double bond) Malate in gluconeogenesis - Correct Answer Gluconeogenesis is largely but not entirely cytosolic and some enzymes are in the mitochondria. Pyruvate produced is transported to mitochondria where it will undergo conversion to oxaloacetate by pyruvate carboxylase. Oxaloacetate is then converted to malate and then malate is transported through a malate transporter into the cytosol where it is converted back to oxaloacetate unsaturated fatty acids that can be oxidized to acetyl coA - Correct Answer have at most one trans double bond after adjustment, must be located between carbons 2 and 3 -monounsaturated = enoyl-coA isomerase- rearranges cis dbl bonds at 3,4 once acetyl coA liberated to isolate within first three carbons -polyunsaturated = 2,4-dienoyl coA reductase- converts two conjugated double bonds to just the cis dbl bond at 3,4 common methods of restoring protein activity in cells - Correct Answer transcriptional/translational level it is difficult to get proteins to the mitochondria of living cells because - Correct Answer polar proteins have to get past lipid bilayer of cellular/mitochondrial membranes ketone bodies formed - Correct Answer -transportable acetyl coA -acetoacetate and 3-hydroxybutyrate (reduced acetoacetate) -produce by liver and used by other tissues during starvation -easily metabolized -ketogenesis- mitochondria of liver cells with excess acetyl-coA; HMG-coA synthase, HMG-coA lyase (into acetoacetate) -inc concentrations of acetyl-coA during fasting -ketolysis- acetoacetate activated in mitochondria by succinyl-coA acetoacetyl-coA transferase (thiophorase)- acetoacetyl-coA -liver cannot catabolize ketone bodies, lacks this enzyme -during fasting, stim by low-energy state in muscle/brain tissues proteins are ____ used as an energy source - Correct Answer rarely; used in other functions -proteolysis- pepsin in stomach; trypsin/chymo/carboxypeptidase in pancreas; small intestine (bulk of digestion) dipeptidase/aminopep -absorption- secondary active transp with sodium at luminal membrane, facilitated diffusion at basal membrane -protein catbolized in muscle/liver -lose amino group through trans/deamination- carbon skeleton used for energy Ketogenic and glucogenic amino acids - Correct Answer PhIT amino acids 'fit' into both categories (phenylalanine, isoleucine, threonine, tyrosine, tryptophan) ketogenic- leucine and lysine plus above glucogenic- all but leucine and lysine insulin injections will - Correct Answer increase insulin levels, inc lipid storage, decrease lipid mobilization/breakdown from adipocytes -weight gain conversely, fatty acid breakdown forms ketone bodies due to lack of insulin (can't use glucose for energy)- weight loss urea cycle - Correct Answer mechanism that takes nitrogen across the rumen wall back to the salivary glands in order to preserve nitrogen in the system -occurs in liver -removes excess nitrogen from the body -basic side chains of amino acids feed into the urea cycle the human body is considered a ____ system while the cell is considered an _____ system - Correct Answer open- can exchange energy and matter closed- can only exchange energy; can only come in the form of work (constant P/V though) or HEAT catabolic processes ____ energy; anabolic processes ______ energy - Correct Answer release; break down complex molecules into simpler ones require; build complex molecules from simpler ones modified standard state conditions/equation - Correct Answer H+ = 10^-7 M, pH = 7 delta G is modified value metabolism of fats, carbs/proteins/ketons, ATP, ADP, cAMP releases how much energy - Correct Answer fats- 9 kcal/g carbs/proteins/ketones- 4 kcal/g under standard conditions (excess magnesium) ATP -30.5 kJ/mol ADP ~-30 cAMP ~-50 -ATP hydrolysis energy relies upon pH (protonated, less repulsion with neg charge) overall free energy of reaction is determined by - Correct Answer taking the sum of the free energies of the individual reactions high-energy electron carriers - Correct Answer NADH, NADPH, FADH2, ubiquinone, cytochromes, glutathione, flavoproteins (FAD/FMN)- contain modified vitamin B2 or riboflavin -proteins with prosthetic groups containing Fe-S catecholamines- increase glycogenolysis in muscle and liver, and lipolysis in adipose tissue thyroid hormones- increase BMR and potentiate activity of other hormones (epinephrine) Preferred Fuels in the Well-Fed and Fasting States - Correct Answer Organ : Well-fed : Fasting Liver : well-fed = glucose, amino acids : fasting = fatty acids Resting Skeletal Muscle: well-fed = glucose : fasting = fatty acids, ketones Cardiac muscle : well-fed = fatty acids : fasting = fatty acids, ketones Adipose tissue : well-fed = glucose : fasting = fatty acids Brain : well-fed = glucose : fasting = glucose (K in prolonged fast) RBC : well-fed = glucose : fasting = glucose metabolism in liver - Correct Answer roles- maintain constant Bglucose, synthesize ketones (when fatty acids are oxidized- lipolysis) after meal -glucose first used to replenish glycogen -remaining converted to acetyl co-A and used for fatty acid synthesis (VLDL) between meal -liver releases glucose metabolism in adipose tissue - Correct Answer after meal glucose uptake (insulin) fatty acid release from VLDL/chylomicrons- re-esterified for storage fasting hormone-sensitive lipase- fatty acids released metabolism in skeletal muscle - Correct Answer resting muscle after meal-glucose uptake- glycogen stores/amino acids for protein synthesis fasting- use fatty acids/ketone bodies active muscle -creatine phosphate transfers P to ADP for short-lvied source of energy -anaerobic glycolysis -oxidation of glucose/fatty acids at first, then just fatty acids metabolism in cardiac muscles - Correct Answer myocytes prefer fatty acids- b- oxidation parallel skeletal muscle during extended periods of exercise metabolism in brain - Correct Answer consumes lots of glucose uses lots of O2- exclusively uses aerboic metabolism of glucose fatty acids cannot cross blood-brain barrier, not used at an energy source between meals, relies on blood glucose via hepatic glycogenolysis or gluconeogenesis (do not store glucose or energy fuels!!) primary factor in the gradual change of body mass over time is _____ - Correct Answer lipids normal BMI- 18.5-25 overweight- 25-30 obese- 30+ ketogenic diet - Correct Answer -high in ketone bodies -metabolism of hydroxybutyrate only converts one NAD+ to NADH (rather than four from glycolysis/PDH) -higher NAD+/NADH ratio, inc NAD+ availability -can be helpful for seizures/brain-based diseases -less depletion of NAD+ regulation of enzymes of glycogen metabolism by insulin/glucagon is through - Correct Answer dephosphorylation, phosphorylation RQ indicating lipid metabolism, amino acid metabolism, carb metabolism - Correct Answer lipids- 0.7 amino acids- 0.8-.9 carbs- 1.0 denaturation of proteins disrupts - Correct Answer secondary and tertiary structure in isoelectrophoresis, what pH is ideal to separate two molecules? - Correct Answer pH equivalent to isoelectric point of either molecule; when pH = PI the molecule does not move; when pH is below PI, it will be protonated (cation) and move toward cathode; when pH is above PI, it will be deprotonated (anion) and move toward anode juxtacrine vs paracrine signaling - Correct Answer paracrine- secretions nearby cells juxtacrine- direct cell to cell contact Gel Electrophoresis Steps - Correct Answer Restriction enzymes cut DNA into specific lengths Add DNA to wells in a gel run a current through the gel DNA moves towards positive end shortest fragments- chain is terminated earliest (at positive end) represent 5' end; read bases + to - end ETC is inhibited by - Correct Answer ATP; proton gradient formation Steps where ATP is used/produced in glycolysis - Correct Answer used: 1. hexokinase -1 3. PFK -1 produced: 7.bisphosphoglycerate ->3-phosphoglycerate +2 per 10. pyruvate kinase (PEP to pyruvate) +2 per Cells with lots of mitochondria _____ glucose - Correct Answer consume Guanine and Cytosine - Correct Answer 3 hydrogen bonds both have carbonyl and 2 nitrogen groups on pyrimidine Adenine and Thymine - Correct Answer 2 hydrogen bonds adenine does not have carbonyl on pyrimidine, thymine has two carbonyls thymine, uracil - Correct Answer uracil is missing a methyl group histones associate with DNA through - Correct Answer salt bridges between + lysine residues and - phosphate acetylation- disrupts ionic intx and makes DNA more accessible Reading Gel Electrophoresis Results - Correct Answer PAGE- non-denaturing; shows proteins that are separate as separate SDS-PAGE- denaturing; will reduce up to secondary structure; each constituent is a separate line in the lanes monomeric vs multimeric proteins hetero vs homo - Correct Answer multimeric can have quaternary structure; multiple polypeptide chains (monomeric- just one chain) hetero- different polypeptide chains- 2 distinct bands homo- identical polypeptide chains- shows up as 1 band peptide bond hydrolysis is - Correct Answer thermodynamically favorable but kinetically unfavorable (will not happen without high temp) requires H2O total yield of a purification step - Correct Answer find total activity = total protein x specific activity specific activity = ratio of activity of protein/total mass of protein desired HPLC is a good technique for - Correct Answer individual amino acids and dipeptides Catalytic efficiency - Correct Answer Kcat/Km