Dental Biochemistry Final Exam Flashcards

Terms Definitions
Where do osteoblast originate from in intramembranous ossification?
Mesenchymal fibroblasts. 
How are osteocytes different from osteoblast? 
Osteocytes are osteoblasts trapped in the bony matrix.
What is BMP and its significance?
BMP= Bone Morphogenetic Protein, BMP converts Fibroblasts into Osteocyte when it is [High], when BMP is low = Adipocyte, no BMP = smooth muscle cell. 
High [BMP] gives rise to:
c-Smooth muscle cell
b-Osteocytes are converted from fibroblasts by High BMP. Note High BMP also gives rise to Chondrocytes. 
Low [BMP] gives rise to:
c-Smooth muscle cell
Adipocytes rise from low [BMP]. 
_________ is avascular & forms 1st from  condensed mesenchymal cells.
Endochondral bone 
________ forms directly from mesenchymal cells w/o cartilage template
d-none of the above
b-intramembranous bone forms directly from mesenchymal cells and is vascularized. 
Where are the origins of the cells of the craniofacial complex origination?
Cells derived from Neural Crest and mesodermal cells form the craniofacial complex.
PTH, Vitamin D, and Calcitonin are _______ signals that cause ________.
Endocrine, the affect of inc. bone resportion caused by PTH & Vit. D, and dec. bone resorption caused by Calcitonin. 
Bone Morphogenic protein is a _____ signal
b-paracrine & D-autocrine= BMP
Osteoclasts lineage stem from
a-myeloid stem cells
b-pluripotent hematopoietic Stem Cell
a-myeloid stem cells &
b-pluripotent hematopoietic Stem
_________ secrete HCl and protease causing bone resorption. 
M-CSF, PTH, IL1, & vit.D are all needed to produce:
d-all of the above
Root completion on deciduous teeth is ________ and permanent is ________
a-5months & 2years
b-15 months & 4years
c-19 months & 3years
d-18 months & 3years
d-18 months & 3years
What type of collagen is PDL composed of:
Collagen type 1 and 3 compose PDL. 
Alkaline phosphatase is the hallmark of ____________.
I am a disease typified by craniofacial lesions and deformities. I am...
c-Paget's disease
c-Paget's disease
I am a disease typified by enlarged pulp chambers. I am...
c-Paget's disease
a-Vit. resistant Rickets 
I am a disease typified by loss of primary teeth prematurely. I am...
c-Paget's disease
b-Hypophosphatasia, which cause lack of PDL binding to cementum(b/c no cementum). 
Osteonecrosis of the Jaw (ONJ) is caused by __________.
High dose treatment of Bisphosphonates for cancer t(x).
________ is the protein focus of Dentinogenesis Imperfecta (DGI)
d-dentin sialophosphoprotein
d-dentin sialophosphoprotein
PTH inhibits phosphate and calcium reabsorption at the kidney 
false, only Phophates reabsorption is inhibited, calcium reabs. is stimulated distally. 
calcitonin causes osteoclasts to strink.
In what direction is the protein synthesis on polysomes? 
Polysomes synthesize N terminal first. 
At what end is the start site on the DNA template for polysomes?
The start site is at the 5' end of the mRNA template.
What is a polysome consist of?
Polysomes consist of multiple ribosomes subunits translating an mRNA.
What is the Cental Dogma of protien synthesis?
The Central Dogma states that the movement of information is unidirectional in that it flows from DNA to RNA to Protein only.
What is the triplet code for starting transcription and what amino acid does it code for?
AUG is the start codon for transcription and it codes for Methionine. 
What are the stop triplet codon for protein synthesis?
UAG, UAA, & UGA are the stop codon for protein synthesis. 
What is the triplet codon for Glutamine?
GAG is the codon for the Glutamine.
What is the triplet codon for Val and what is its implication in hemoglobin?
Valine's codon is GUG, and it is implicated in the structurally compromised hemoglobin causing sickle cell; this is classic point mutation of normal codon of GAG which codes for Glutamine.
What type of point mutation causes Hemoglobin S where the Beta chain is mutated?
Mutation of Beta chain in hemoglobin S is caused by missense mutations.
Shortening of DNA is indicative of which type of point mutation?
Nonsense point mutation & frameshift  deletion mutation shortens the DNA chain.  
DNA elongation is caused by what type of mutation?
Suppresor point mutation & Frameshift insertion causes chain elongation. 
What are the components of translation machinery?
The translational components consists of Ribosomes, mRNA, tRNA, Amino acids, Enzymes, and Energy.
What are the components of the ribosomes structure?
The ribosome is composed of Large subunit (consisting of central protuberance) and small subunit. 
50S and 30S subunits is indicative of what type of ribosome?
Prokaryotic ribosome consists of 50S and 30S subunits. 
60S and 40S subunits are from what type of ribosomes?
Eukaryotic ribosomes compose the 60 & 40 subunits. 
Eukaryotic translation consist of what genomic parts?
5' cap, 5'UTR, 3' UTR, only 1 coding region, and 3' poly A of 150 nucleotides is typical of Eukaryotic translation. 
Prokaryotic translation is typified by what?
Polycistronic or more than one ORF/coding region characteristic of prokaryotic translation. 
Tranlational adaptor can be described as?
tRNA, consisting of 3 Loops, loop 2 containing anticodon sequence, and 3' OH amino acid accepting end.
What is the first step in the formation of aminoacyl-tRNA?
The amino acid is 1st activated by reacting with ATP by amino acid synthetase. 
What is the second step of aminoacyl-tRNA formation?
The activated amino acid transferred from aminoacyl-AMP to tRNA.
What and Where is the wobble position on the codon and anticodon machinery?
The wobble postion is the codon region where flexability is allowed in amino acid coding, it is at postion 1 on the anti-codon region and on position 3 on the mRNA. 
What two enzyme are vital for the fidelity of protein synthesis?
Aminoacyl tRNA synthetase is important for activating amino acid and tranfering it to the 3'OH end.
What are the functions and codons for methionine tRNAs?
Methionine tRNAs serve as AUG initiation codon this dubbed N-formyl / F-Met in bacteria, and the other tRNA serve in the internal Met codon. 
What are the stages of translation?
1st-charging of tRNA, 2nd-Initiation, 3rd-Elongaiton, 4th-Termination, 5th-modification.
What stage of translation where both eukaryotes and prokaryotes share the same enzyme?
The first stage of both organisms use Aminoacyl-tRNA synthetase  to charge tRNA. 
Cap dependent scanning is seen in which organism and how is it used?
Cap-dependent scanning is used by 40 S ribosomes of Eukaryotes to find their initation sites. 
What is the synanomous structure in the prokaryote to cap dependent scanning?
The Shine-Delgarno box is what 30 S prokaryotic ribosomes use to find their initiation site for translation. 
IRES differs from Cap dependent how?
Internal ribosome entry site does not use a 5' cap to find scan for AUG, IRES allows for translation initiation in the middle of a messenger RNA. 
What class of pharmaceuticals target prokaryotic 30s ribosomes?
Aminoglycosides are drugs that target the 30s ribosome causing miscoding during elongation, streptomycin is an example of this drug but it inhibits initiation. 
In translation, what steps make up the elongation phase?
The 1st step of Elongation is Amino Acid-tRNA binding, 2nd=Peptidyl Transfer, and 3rd =Translocation. 
What drug class inhibits binding of AA-tRNA to A site?
Tetracyclines inhibits A site binding of AA-tRNA of 30 s ribosome.
In elongation what drug inhibits the peptidyl transferase?
Chloramphenicol targets 50s inhibiting peptidyl transferase. 
In elongation, what drug inhibits translocation?
Translocation is inhibited by Erythromycin/Clindamycin which targets 50s inhibiting translocation. 
Toxins to Eukarotic 60s ribosomes is seen by what toxin?
Ricin's A depurinates 28s rRNA at A residue, at 60s inhibits binding of AA-tRNA to A site.
How is Diphtheria toxin cause toxicity in eukaryotes?
Diphtheria toxin targets eEF2 inhibiting translocation.
What drugs is toxic to prokaryotes and eukaryotes during elongation phase?
Puromycin targets both 50s & 60s ribosomes  causing premature release of nascent polypeptide.
Puromycin imitates which genomic structure & what is its mechanism of toxicity?
Tyrosinyl-tRNA is the anologue that Puromycin imitates causing premature release of nascent polypeptide. 
What does termination phase of protein translation consist of?
Termination consists of termination and release of polypeptide. 
How does termination begin?
Termination is produced by reading termination sequences UAG, UAA, or UGA, 2nd-release factor binds to a stop codon releasing the polypeptide, 3rd-complex dissociates.
What is the energetic cost of tRNA charging?
Amino acid charging of tRNA cost 2ATP. 
How does Initiation energetics compare with the other phases of translation?
Initiation it the most costly of all; several ATP for unwinding & scanning, and 1GTP for Met-tRNA binding. 
How much does it cost to produces 1 amino acid compared to an average protein?
The cost for 1AA is about 4ATPs, however 1 protein costs 1200 ATPs.
IRE-BP bound to IRE indicates what about [Fe+2]?
This indicates that ferritin in not needed thus intracellular [Fe+2] is low. 
Early onset of cataract syndrome and serum ferritin is indicative of what diagnosis?
Hyperferritinemia is the cause of ferritin release into serum, and cataract formation, the cause of these is IRE mutation where ferritin synthesis is de-repressed. 
Protein synthesis is down-regulated at the level of the supply of initiator Met-tRNAi how?
Met-tRNAi is inhibited thus halting protein synthesis by phosphorylating elF2 through kinase activity. 
When is protein synthesis halted by the down regulation of initiator of Met-tRNAi?
Inhibition of protein synthesis via elF2 kinases occurs via HRI in reticulocytes w/o heme, PKR in interferon plus virus infection, ER stress via PERK, and during amino acid starvation via GCN4.
What does elF2 do and what disease is caused by its mutation?
elF2 supplies intiator Met-tRNAi to the 40s subunit leading down the protein synthesis pathway, its mutation leads to Vanishing White Matter (VWM) typified by neurologic deterioration. 
GDP is exchanged for GTP is what process of protein synthesis?
GDP to GTP exchange occurs in the initiation and elongation of amino acid synthesis. 
When ER stress kinase PERK is mutated what diagnosis results?
Mutation of PERK kinase of the ER leads to Wolcott-Rallison syndrome which is characterized by IDDM1 & Growth defects & bone dysplasia.
Kinase activity is shown to inhibit protein synthesis, however kinase activity up-regulates mRNA binding where?
Kinase cascade induced by GF, mitogens, hormones, and cytokines cause phosphorylation of elF4E-4E-BP complex causing the release of 4E-BP, elF4E is phosphorylated and binds to 5'cap and A&G complex leading to scanning and protein synthesis. 
What is the shape of Eukaryotic mRNA?
The functional shape of Eukaryotic mRNA is circular by elF4E, G and poly A Binding protein.
Elongation is regulated by which factor?
SRP recognizes signal peptide and receptor, controls elongation, and targets ER. 
True or false, transcription & translation is coupled in Eukaryotic nucleus?
False Eukaryotic transcription & translation is seperated, Prokaryotic is not.
In which organism is Met-tRNAi binding first then mRNA binding?
This occurs only in Eukaryotes, prokaryotes events occur in the opposite direction. 
Fibril forming collagen is found in which type?
Type 1, 2, and 3 collagen forms fibril forming collagen.
Skin, bone, tendon, blood vessels, and cornea compose which type of collagen?
Type 1 collagen forms skin, bone, tendon, bv, and cornea.
Cartilage, intervertebral disk, and vitreous body forms?
Type 2 collagen. 
The skin of the fetus is composed of what collagen type?
Type 3 collagen forms fetal skin.
What collagen compose basement membrane?
Basement membranes are composed of type 4 collagens. 
During pro-alpha chain assembly, ________ and interchain _________ bonds form at N-terminal propetide extension.
Intrachain, false the disulfide bond forms at C-terminal propeptide extension. 
Collagen is on one gene.
False, collagen genes are spread all over the genome. 
The structure of collagen is composed of amino acids _______, _______, _______.
Collagen is composed of a triple helical amino acid structure intertwined by hydroxyproline, hydroxylysine, and Glycine. 
What two genes are transcribed in the 1st step of collagen synthesis?
Pro-alpha 1 and pro-alpha 2 are the 1st genes transcribed into mRNA.
Which Hydoxylated amino acid residues are glycosylated with glucose and galactose?
Hydroxylysine is the amino acid that is glycosylated w/ glucose & galactose. 
The signal sequence of prepro-alpha-peptide mRNA is removed in the:
c-Golgi aparatus
d-Endoplasmic Reticulum
The Endoplasmic Reticulum is the site of signal seq. removal of prepro-alpha-peptide.
True/False procollagen is cleaved before being secreted from ER?
False, procollagen is 1st secreted from Golgi vacuole, and 2nd N&C terminal propeptides are cleaved in the extracellular matrix.
In linear polymer staggered stacking of collagen fibrils, how is staining produced?
Only in regions with gaps are where heavy staining seen.
Vitamin C and Fe+2 is required by which process in collagen synthesis?
Prolyl hydroxylase requires Fe+2 and Ascorbic acid (Vit. C) as cofactors to hydroxylate proline. 
Hydroxylation of proline requires the cofactors:
a-alpha Ketogluterate
e-all of the above
Hydroxylation by prolyl hydroxylase of proline requires O2, alpha ketogluterate, ascorbate, and Fe+2.
T/F lysyl hydroxylase and prolyl hydroxylase requires the same cofactors?
True, they req. Fe, and Vit. C.
Tell me which is the correct steps of collagen synthesis?
a-, Pro-alpha chain, Hydroxyprolyl residue, Prolyl residue
b-Prolyl residue, Pro-alpha chain, Hydroxylation step
c-Prolyl residue, Hydroxylation step, Pro-alpha chain
c-Prolyl residue,Hydroxylation step, Pro-alpha chain.
Scurvy is considered a mild disease because?
It is mal-nutritionally based and mediated by Ascorbic acid rich foods like citrus foodstuffs. 
OI is a result of what genetic change?
OI results from collagen gene substitutions in COL1A1 or COL1A2 resulting in substitution of Gly to another.
What is the microscopic consequence of genetic mutation of COL1A2 & COL1A1?
OI result due to incorrect folding of collagen's triple helix. 
Ehlers-Danlos Syndrome is cause by and clinically presents?
EDS is a genetic collagen disorder, it is typified by stretchy skin and joint hypermobility. 
T/F elastin is stretchy b/c it has more hydroxylation of it proline and lysine components?
False it has little hydroxyproline and no hydroxylysine.
Mutation in ______ is responsible for Marfan Syndrome:
Fibrillin, is the causitive source of Marfan Syndrome when FBN1 is mutated.
A deletion of chromosome 15 would affect which connective tissue?
Chromesome 15 contains FBN1 which codes for fibrillin, which will vicariously affect elastin. 
Desmosine cross-link is seen seen in which connective tissue type?
Desmosine cross-linking is classical of elastin's elastic properties, this is produced by oxidative deamination by  lysyl oxidase. 
4 Porphobilinogen (3rd reaction of Porphyrin synthesis)
In Porphyrin synthesis' 3rd reaction, tetrapyrrole, 4Porphobilinogen goes into Hydroxymethyl bilane synthase prod. Hydroxymethylbilance 
5/delta aminolevulinate synthase is a protein whose cofactor is ___________ & function is ___________, & inhibited by ______.
cofactor=pyridoxal phosphate, synthase is inhibited y heavy metal ions, & is feedback inhibited by heme/hemin
Catalase functions to do?
Catalase breaksdown peroxidase 
Chlorophyll functions in what process?
Chlorophyll funtions in light absorption
Cytochrome a, b, & c function in what process?
Cytochromes a,b, and c function in electron transport 
Cytochrome P450 does what?
Cytochrome P450 function in hydroxylation.
Heme synthesis is restricted to the mitochondria in what process of its synthesis?
The 1st and last 3 reactions of porphyrin synthesis occur in the mitochondria.
Hydroxymethylbilance (in the 4th reaction) functions?
hydroxymethylbilance goes into uroporphyrinogen synthase which, catalyzes ring closure & isomerization prod. uroporphyrinogen 3 & 4NH3
In Heme degradation the 1st step when Heme goes into Biliverdin reductase what occurs?
The 1st step of Heme degradation does not occur at the enzyme Biliverdin reductase, it occurs at Heme Oxygenase which produces Biliverdin. 
In Porphyrin Synthesis the 1st reaction is ... 
5/delta aminolevulinate synthase catalyzing Glycine & Succinyl CoA producing = 5/delta-aminolevulinic acid (ALA), CO2 and CoA = 1st reaction (rate limiting)
In the liver, bile is immediately preceeded by ________ & which is prod. by _______
Bile is immediately preceeded by Bilirubin diglucuronide produced by Bilirubin Glucuronyl Transferase.
Protophyrin 9 is converted to _________ by what protein?
Protophyrin is converted into heme by ferrochelatase.
Regulation of Heme Synthesis is controlled by _______ @ ______.
accumulation of Heme/Hemin, inhibiting 5 aminolevulinate synthase 
The 2nd reaction of Porphyrin Synthesis is...
Porphyrin synthesis's 2nd reaction is two 5-aminolevulinate condense in Delta-aminolevulinic acid dehydrase (inhibited by Pb) to produce = porphobilinogen (monopyrrole)
Uroporphyrinogen 3 (The 4th Heme synthesis reaction) functions to produce what?
In the 4th reaction of heme synthesis, Uroporphyrinogen 3 goes to prod. Protoporhyrin 9
What 2 enzymes are in the heme synthetic pathway are inhibited by lead?
Lead inhibits delta Aminolevulinic Acid dehydrase, which prod. Porphobilinogen, & Ferrochelatase which prod. Heme. 
What are Porphyrins?
Porphyrins serve as prosthetic groups for proteins in oxygen transport, heterocyclic ring structures includes 4 pyrrole rings join thru a carbon bridge. In the center lies a metal atom that is chelated to the nitrogen atoms of the pyrrole units, in heme = Fe/chlorophyl = Mg
What enzymatic steps of Heme degradation is restricted to the macrophage?
The 1st (@Heme Oxygenase) and 2nd (@Biliverdin Reductase) steps of heme degradation occur inside the Macrophage to produce Bilirubin. 
What is Hemin?
Free oxidized form of heme, inhibits synthesis and activity of 5-aminolevulinate synthase in primitive RBC and cells w/ other heme protein; activates synthesis of globin peptide by combining w/ an inhibitory protein balancing heme & globin 
What is the significance of Protoporphyrin 9?
Protoporphyrin 9 goes into Ferrochalatase (inhibited by lead) to prod. Heme (Fe2+ protoporphyrin 9)
Fava beans consumed by a person with G6P deficiency would probably cause which type of Jaundice?
G6P deficiency and Fava beans consumption would cause hemolytic anemia leading to hemolytic jaundice. 
Hepatic Jaundice is indicated by:
a-Acute Hemolytic anemia
c-Neonatal physiological juandice
d-Disease like Gilberts disease. 
Disease like Gilbert's disease is indicative of Hepatic Jaundice.
Obstruction of the common bile duct is called?
Post Hepatic Jaundice.
Why does hemoglobin have a square shaped oxygen dissociation curve?
This is false, myoglobin's shape is squared, and hemoglobin is sigmoidal, the reason for the square is b/c myoglobin has greater affinity to oxygen, and curve shape shows the cooperative behavior of hemoglobin. 
In sickle cell valine is substituted for: 
In sickle cell anemia, valine is substituted for glutamate. 
Cementum, Dentin, and Enamel compose what type of tissue?
Cementum, Dentin, and Enamel compose calcified oral tissue.
What calcified oral tissue is composed of 45% inorganic, 33% protein (collagen 1 & 3), 22% water?
Cementum is composed of 45% inorganic, 33% protein, and 22% water.
What is Enamel composed of?
Enamel is composed of (5 %) Ameloblastin, amelogenin,enamelins, Tuftelins, 95% inorganic and less than 1% water.
Pre-odontoblasts, fibroblasts, macrophages, T-lymphocytes are found in what type of oral tissue? 
Pulp tissue contain Pre-odontoblasts, fibroblasts, macrophages, T-lymphocytes.
PDL and fibroblast progenitor cells give rise to what?
Cementoblast are derived form PDL and fibroblast progenitor cells. 
True/False odontoblast come from ectoderm in origin, resides in pulp cavity and die after laying down of pulp?
False odontoblast are mesodermal in origin, do reside in the pulp cavity and live as long as the organism does.
Ameloblast are _______ in orign, and ________ after laying down _________.
ectodermal, die by apoptosis, and enamel. 
________ secrete ________ inwards toward the pre-enamel layer. 
Ameloblast, a organic matrix.
Found in ________, this protein initiates mineralization. 
Osteonectin conducts mineral crystal formation and is produced by osteoblasts and odontoblasts
I am an acidic glycoprotein that binds calcium during calcification, I am?
I am osteonectin.
FGF beta is a pulp protein that is constitutively activated.
False, FGF beta is an active dentin protein only during dentin formation. 
What protein is responsible for circumpulpal mineralization?
     E) All of the above
        F)None of the above
F), Circumpulpal mineralization is controlled by Phosphophoryns, which is from the class of HP highly phosphorylated proteins synthesized by Odontoblasts. 
In an experiment for bone toxicity, what protein could you assay to measure the extent of dentin mineralization?
Sialoprotein is a good marker for dentin mineralization. 
Two enamel proteins which are hydrophobic and hydorphilic are ________ and_________?
Tuftelin is hydrophilic and Amelogenin is hydrophobic.
Tuftelin is all except: 
a-formed shortly during amelogenesis
b-acidic glycoprotein that's phosphorylated
c-Ends mineralization during tooth development
C-, Tuftelin starts mineralization during tooth development. 
This protein directs start & growth of hydroxyapatite crystals & directs cementum, and is used in sex determination.
Amelogenin is the starter protein of hydroxyapatite crystal formation, and is used to determine sex. 
__________ elongates hydroxyapatite crystals and directs mineralization. 
Ameloblastin elongates enamel mineralizatin and directs it. 
Hydroxyapatite binds to:
c-FGF beta
Enamelin binds hydroxyapatite. 
Starch is converted to dextins by beta amylase.
No, alpha-amylase converts starch into dextrins.
True/False, under aerobic conditions does glycolysis of monosaccharides produce lactic acid.
False, only under anaerobic conditions is lactic acid produced from glycolysis of monosaccharides.
How is hyperacetylation executed on the N-terminal of Histones?
Hyperacetylation on N-terminal tails is directed by Activator sequence and is executed by Gbn5 protein
In nuclear receptor family how many zinc finger motif does the centrally located DNA binding domains contain?
The centrally located binding domain of nuclear receptor family genes each contain 2 copies of zinc finger motif.
In nuclear receptor family what domain does N-termini occupy?
The N-termini lies in the activator domains. 
In nuclear receptor family which binding domain does C-terminal fall in?
The C-terminal lies in the binding domain of the Ligands. 
In the hormone dependent gene regulation of glucocorticoid receptor where is the inhibitor molecule bound to and where does the hormone act?
The inhibitor molecule binds to the ligand binding domain and is released when the hormone binds the LBD, allowing the DNA binding domain to bind to the Repsonse element in the nucleus inducing translation. 
In what sequence does the RNA pol II factors form the preinitiation complex?
1) At the TATA box TBP binds, 2)TFIIB binds gene at TATA, 3)TFIIF binds RNA Pol II on gene, 4)TFIIE binds to RNA Pol II, 5)TFIIH binds RNA Pol II completing the Preinitiation complex
What do DNA response elements do?
DNA response elements bind to nuclear receptors, usually to structures with repeat sequences, e.g. GRE, ERE, VDRE, TRE, & RARE
What is an operon?
An operon is a polycistronic genome.
What is happens to the preiniation complex when ATP & NTPs react with it?
When NTPs and ATP react with the Preinitiation complex elongation of Pol II with phosphrylated CTD region and all the general factors are released except for TBP.
What is the function of hormone-receptor complex and name some hormones that act on them?
The hormone receptor  complex functions as a transcription factor and some types are lipid soluble hormes like Cortisol, Retinoic Acid, and Thyroxine. 
What is the location of and effect on alpha amanitin of RNA Pol I?
RNA Pol I is located in the nucleous and has insensitive effect from alpha amanitin
What is the location of and effect on alpha amanitin of RNA Pol II?
RNA PolI is located in the nucleoplasm and has Strongly inhibited effect of alpha amanitin
What is the location of and effect on alpha amanitin of RNA Pol III?
RNA Pol III is located in the nucleoplasm and is inhibitory effect of alpha amanitin at high concentrations 
What is the result of mutation of CBP in the phosphorylation CREB pathway?
Mutation of CBP causes pleiotropic developmental abnormalities called Rubenstein-Taybi syndrome.
What is the successive steps in activation of gene expresion via cAMP and phosphorylation of CREB?
1-Gs protein coupled recptor activates Adenylyl cyclase prod. cAMP,  2-cAMP activates PKA, 3-C protein enters nucleus, 4-C protein activates CREB, 5-CREB binds CRE binding protein and activate CBP/P300 beginning transcription.
What polymerase produce mRNA & snRNA?
Pol II is responsible for the production of mRNA and snRNA.
What polymerases produce rRNA?
Pol I and Pol III produce rRNA.
Where is alpha-amanitin found and of what importance is it for?
Alpha-amanitin is found in the poisonous mushroom Amanita phalloides; it blocks elongation by RNA Pol II.
Where on the histone is deacylation and what directs this mechanism?
Histones are deacylated in N-terminal tails by repressor molecule Rpd3.
What is type of DNA sequences do Restriction Endonuclease target and what are the potential restults?
Restriction Endonuclease target palindrome sequences & cuts can be staggered prod. sticky ends, or blunt prod. flush ends. 
What type of cleavage does the restriction enzyme EcoRI produce?
EcoRI produces sticky ends at the GAATTC palindrome in between the GA nucleotide.
How does bacteria protect themselves from site specific cleavage?
Bacteria protect their own DNA from cleavage by producing site specific methylase.
What is the limit of the polylinker insertion of exogenous DNA into E. coli cell.
Exogenous DNA is limited to 10-15 kbp insertion size into the polylinker of E. coli. 
How is DNA amplified?
DNA amplification is executed through DNA cloning in a plasmid vector via enzymatic insertion.
How is DNA amplified?
Using PCR, DNA is amplified rapidly using DNA template, defined primer pair, dNTPs and DNA polymerase.
During PCR what process takes place during cycle 1 & 2?
Denaturation of DNA, Anealing of primers and elongation of primers take place in Cycle 1 of PCR
What is RT-PCR produce?
RT-PCR is the amplification of cDNA from RNA.
In RT-PCR how is double stranded DNA produced?
Double stranded DNA is produced via PCR amplification after the RNA/DNA duplex is created.
What types of primers can be used in RT-PCR?
Oligo dT, random hexamer, or specific primer can be used in RT-PCR.
What is the Sanger Sequence method?
This is the sequencing of DNA using dideoxynucleotides at a 1% concentration to the normal deoxynucleotides, four seperate tubes are use with normal nucleotides, but individual type ddNTPs for each tube, after the DNA template and primer(radioactive) elongation occurs the synthesis will stop at the ddNTP insertion, after reaction is complete sequence is run on polyacrilimide gel electrophoresis then autoradiography is taken and sequence read. 
How is dideoxynucleotide different from a normal/deoxynucleotide and what is the implication of this difference?
Dideoxynucleotide has a 3' H instead of a 3' OH, this difference causes synthesis termination b/c the triphodiester bond cannot form with H. 
How is the Autoradiogram read in Sanger sequencing?
The autoradiogram is read 5'-3', the smallest fragments/bottom are closer to the primer.
What does DNA microarray do and what is its method?
DNA microarrays are used to detect gene expression, the method starts by 1) using a collection of gene-specific DNA molecules, 2)PCR amplification 3)robotic printing of DNA onto glass, 4) taking labelled mRNA from two seperate samples, one w/red, other w/green fluorchrome, 5)Hybridize & wash, 6) Scan red & green signals and combine images.
How can you go about prenatal testing of unborn's DNA?
Aminocentesis and chorionic villus sampling are used to source DNA from prenate, amnicentesis is more invasive via tesing amniotic fluid.
What is Southern blotting used for and how is the method executed?
Southern blotting is used to detect and measure Nucleic acid(DNA), the steps 1)Cleave DNA w/ restriction enzymes, 2)Run DNA through Gel electrophoresis, 3)transfer to Nitocellulose paper via filter paper and alkaline solution, 4)Hybradize Nitrocellulose DNA transfer with radiographicly labelled DNA or RNA probe. 5)Develop Autoradiograph
commonly used in id sickle cell anemia.
What is Norther blotting used for?
Northern Blotting is used for the detection of mRNA.
What is Western blotting used for and what is its method?
Western blotting is the use of antibody to detect protein, it process starts by 1)Electrophoresis/transfer = SDS polyacrylamide gel is run & transfered to membrane, 2)Antibody Detection = Incubate with Ab1 & wash excess, incubate w/enzyme linked Ab2 & wash excess, 3)Chromogenic detection = react w/ substrate AB2 linked enzyme.
What type of genome tecnhnique use SDS polyacrilimide gel?
SDS polyacrilamide gel is used by Western blot.
What are the steps of PCR for each cycle?
PCR begins with 1)denaturation of double stranded DNA, 2)annealing of primers, 3)elongation of primers.
How is PCR used in id persons?
In assay of tandem repeat identification is possible. 
Apo CII and Apo E are acquired from where?
They are both acquired from HDL, and apo cII binds to lipoprotein lipase to hydrolyze triacylglycerol.
What is the function of Apo E receptors?
Apo E receptors mediate uptake of remnant of chylomicron remnants & cholesterol enters liver cells.
_________ is unique to the nascent chylomicron.
How can you tell if a chylomicron is mature?
It has a apoE and apoC-II added from HDL.
One structural feature of Chylomicron remnants is the lack of Apo E, and ApoB-48.

False, only the lack of Apo C II is indicative of Chylomicron remnant.
_________ functions in reverse transport of cholesterol to liver.
What is a characteristic of nascent VLDL?
VLDL's have apo B100.
What is the process of transforming VLDL to LDL?
VLDL can transform to LDL by transferring apo C-II and apo E to HDL.
What is the site of drug therapy for increasing HDL?
HDL is targeted by increasing apo-A1 synthesis.
HDL to VLDL & LDL transfer of cholesterol is mediated by cholesterol ester transfer protein (CTEP).
And is the target of inhibition to limit high cholesterol.
How is cholesterol converted into cholesterol ester and why?
Cholesterol ester is necessary for storage and this conversion takes place by the enzyme Acyl CoA cholesterol acetyl transferase.
Where are chylomicrons, VLDLs, and HDLs assembled:
a-gut lumen
c-intestine & liver
d-liver and kidney
c- intestine is the site of chylomicron assembly and the liver is the site of VLDL assembly. HDL is assembled in both intestine and liver.
Cholesterol is used by the liver to produce ___________?
Bile Acids.
Proteoglycans consist of 
d-extended glucose
b-glycosaminoglycans/mucopolysaccharides compose Proteoglycans.
Stuctural components of the ECM are usually:
b-Proteoglycans, compose the ECM for the most part. 
_________ is a intracellular proteoglycan that inhibits blood clotting.
How are carbohydrates attached to proteins in glycoproteins?
Carbs are attached to proteins through glycosidic links, either O-glycosidic or N-glycosidic. 
_____________ is a glycosidic link between galactose/glucose & the OH group of hydroxylysine. 
a-N-glycosidic link 
b-O-glycosidic link
b-O-glycosidic link
_____________ is a glycosidic link between N-acetylgalactosamine & serine / threonine.
a-N-glycosidic link 
b-O-glycosidic link
b-O-glycosidic link(another type), form the link between N-acetyl galactosamine & Serine or threonine as seen in blood group and salivary mucins. 
_____________ is a glycosidic link between N-acetylglucosamine & asparagine.
a-N-glycosidic link 
b-O-glycosidic link
a-N-glycosidic link, which exists as High Mannose or complex(i.e. in addition to mannose they contain other sugars like galactose, fucose & sialic acid.
_________ are polyanionic .
c-Glycosaminoglycans, are polyanionic because of carboxyl and sulfate groups.
Where is the carboxyl group on glycosaminoglycans?
a-Alpha carbon
c-D-glucuronic acid
d-L-iduronic acid
C & D, the carboxyl group in glycosaminoglycans are on either D-glucuronic acid or its epimer L-iduronic acid. 
What does the repeating disaccharide motif on the glycosaminoglycan of a proteoglycan look like?
b-galactose-galactose-mannose serine
d-galactose-galactose-xylose-serine, forms the repeating disaccharide motif in glycosaminoglycan of proteoglycans which serves as linker sugar to the serine of the core protein.
Glycosaminoglycans include all except:
a-Hyaluronic acid
b-Chondroitin sulfate
c-Dermatan sulfate 
d-Heparan sulfate
f-keratan sulfate 
all of the above are glycosaminoglycans.
___________ are bound non-covalently to proteoglycan monomers.
a-Hyaluronic acid
b-Chondroitin sulfate
c-Dermatan sulfate 
d-Heparan sulfate
f-keratan sulfate 
a-Hyaluronic acid is bound to proteoglycan monomers w/linker proteins->bottle brush arrangement. 
How does the glycosaminoglycan like chondroitin sulfate differ from Dermatan sulfate?
Chondroitin sulfate has a D-Glucuronic acid attached to N-Acetyl-D-galactosamine vs. Dermatan sulfate which has a L-Iduronic acid attached to N-Acetyl-D-galactosamine.
Keratan sulfate has __________ attached __________.
Keratan sulfate has D-Galactose attached to N-Acetyl-D-glucosamine, which differs from the normal N-Acetyl-D-galactosamine.
_________ is formed on dilichol pyrophosphate then transferred to a protein.  
c-N-linked glycoproteins
d-O-linked glycoproteins   
c-N-linked glycoproteins, are assembled on dolichol pyrophosphate and transferred to a protein. 
How are saccharide units added to glycoproteins?
b, UDP, Nucleoside diphosphate derivatives like UDP-glucuronic acid and GDP-mannose.
How are sialic acid units added to glycoproteins?
a-CMP, specifically CMP-NANA add sialic acid to glycoproteins.
T/F N-linked synthesis is direct whereas O-linked synthesis is indirect. 
False, N-linked synthesis uses dolichol pyrophosphate = indirect, O-linked glycoproteins are added directly to glycoproteins. 
Lysosomes degrade _______ in a last on-first off basis.
c-saccaride chains
c-saccaride chains, are degraded by enzymes in lysosomes in an Last on-first off basis.
The lack of mannose 6-phosphate describes what disease?
c-I-cell disease
c-I-cell disease, is prod. when lysosome deficient enzyme does not acquire mannose-6-phosphate which is a targeting signal. 
What is the rational behind the naming of I-cell disease?
Inclusion bodies are seen in fibroblast where lysosomes are defecient in degrading enzyme, thus unable to digest substrate and are engorged; they consequently die in infancy.
The accumulation of Heparan sulfate & Dermatan sulfate due to a deficiency in ______ result in _____ syndrome. 
a-iduronate sulfatase, Sanfilipo's syndrome
b-L-iduronidase, Hunter's syndrome
c-Hydrolase, Hurler's syndrome
d-alpha-L-iduronidase, Hu
d-alpha-L-iduronidase, Hurler's syndrome, results in Heparan, and Dermatan sulfate accumulation. 
Hunter's syndrome is the result of a deficiency in ______ .
a-iduronate sulfatase
a-iduronate sulfatase, an X-linked deficiency leads to Hunters syndrome. 
Sanfilipo's syndrome is a _______caused by a deficiency in one of 3________ or 1________.
Mucopolysachharidoses, Hydrolases, 1N-acetyltransferase. 
T/F, there are many types of MPS, including type V. 
False, there is no MPS type V. 
This MPS is characterized by ß-Glucuronidase deficiency. 
SLY syndrome.
T/F vitamins are required in large amounts in a normal diet.
false, vitamins are organic cmpds required in small amounts. 
What are the fat soluble vitamins and Why?
A, D, E, K are the fat soluble vitamins, their typically contains a ring structure bound to a hydrocarbon, which makes is lipid soluble.  
What are the water soluble Vitamins?
B & C, vitamin B & C compose the 
What vitamin has the highest daily requirement?
a-Vitamin E
b-Ascorbic acid
b-Ascorbid acid/Vitamin C is the highest required daily vitamin intake. 
Vitamin A =? and where is it found 
Vitamin A is found naturally in its alcoholic form, Retinol, then converted to Retinal, then Retinoic acid, which is the photoreceptive chemical that is isomerize by light into 11 cis-retinal 
Which among these molecules are not all-trans.
c-Retinoic acid 
What role does ß-carotene play in vitamin A formation?
a-cofactor for retinol synthesis
b-substrate for retinol synthesis
c-inhibitor of cis-retinal formation
d-stabilize opsin protein
b-substrate for retinol synthesis, ß-carotene is converted into 2retinal (all trans) by Dioxagenase
Vitamin A exists as:
b-Retinoic Acid
d-all of the above
e-none of the above
d, Retinol, Retinal, and Retinoid acid are all the varying forms of Vitamin A
Light causes the transformation of vitamin A to _________.
a-11 cis-Retinol
b-11 cis-Retinoic Acid 
c-11 cis-Retinal
11 Cis-Retinal, is what photoisomerization does to Vitamin A, which is bound to opsin.
A defect in the Dioxagenase in Vitamin A synthesis possibly show what symptom?
a-Daytime Photobleaching 
b-Nightime photobleaching 
d-night blindness
e-Gingiva hyperplasia
C, D, and E, Deficiency of Vitamin A would cause Keratinization, night blindness, and gingival hyperplasia. 
Excess vegetables and liver oil would have what effect on you?
a-increase visual field
b-recupe optical power
C, excess of fish liver & vegetables = excess of Vitamin A which is toxic, as well as Vitamin D. 
Vitamin B1 = ? and is found where?
Vitamin B1 = Thiamine, is  converted to thiamine pyrophosphate serving as cofactor for oxidative phosphorylation.
Thiamine/Vit. B1 is found in 
a-alpha-keto acids formation
b-oxidative decarboxylation
d-conversion of Xylose 5-Phosphate to G3P
all of the above is found using the cofactor of Vitamin B1. 
A deficiency of ___________ leads to 
Polyneuritis, cardiac pathology, edema, Beri Beri. 
b-Vitamin A
c-Vitamin C
d-Vitamin B
e, Thiamine is the vitamin, B1 that when deficient leads to Polyneuritis, cardiac pathology, edema, Beri Beri, and Wernicke Korsakoff syndrome.
A deficiency of ___________ leads to 
atrophy of filliform papillae (seen as satin-like appearance of tongue), angular cheilosis. 
b-Vitamin A
c-Vitamin C
d-Vitamin B
e-Thiamine, in it deficiency affects the oral cavity by causing the sloughing off of filliform papillae which makes the tongue look satin like, and angular cheilosis. 
Thiamine are found in:
a-Milk, liver, green vegetables
b-Legumes, meat 
c-Beans, nuts, fruits, etc
d-Liver, fish, nuts, whole grain cereals
e-Intestinal microorganisms, liver, vegetablesc-
Beans, nuts, fruits, etc, are the source of Thiamine/Vitamin B1.
___________ forms the molecule of Flavin mononucleotide, Flavin adedine dinucleotide.
b-Vitamin A
c-Vitamin C
d-Vitamin B
None of the above, Vitamin B2/Riboflavin forms the cofactor of FMN and FAD.
Vitamin B2/Riboflavin are found in:
a-Milk, liver, green vegetables
b-Legumes, meat 
c-Beans, nuts, fruits, etc
d-Liver, fish, nuts, whole grain cereals
e-Intestinal microorganisms, liver, vegetables
a-Milk, liver, green vegetables
Niacin is seen the formation of _________.
b-NADP, Niacin/Nicotinamide/Vitamin B3 is seen in the NADP cofactor. 
Consumption of legumes and meat would cure Pallegra, dementia and death that is seen in what Vitamin deficiency?
a-Vitamin B5
b-Vitamin B1
c-Vitamin B2
d-Vitamin B3
e-Vitamin B4
d-Vitamin B3, deficiency which lead to Niacin/Nicotinimide deficiency, as seen in a diet too rich in corn.  Oral manifestations also cause ulcerative glossitis. 
___________ serves as the coenzyme for enzymes catalyzing transamination, deamination, and decarboxylation for glycogen phosphorylase.
d-Vit.B6, Pyridoxine forms pyridoxine phosphate.
Microcytic anemia & convulsions are the result of which Vitamin deficiency
d-Pyridoxine, is Vitamin B6, and when deficient cause microcytic anemia, and convulsions. 
A diet of Liver, fish, nuts and whole grains would most likely cure which deficiency disease symptom?
a-Dermatitis, convulsions, microcytic anemia
b-Pellagra & dementia
c-atrophy of filliform papillae, angular cheilosis
d-Beri-beri and Wernicke-Kor
a-Dermatitis, convulsions, microcytic anemia, is cured by Vitamin B6/Pyridoxine rich foods of Liver, fish, nuts and whole grains.
What Vitamin is Biotin classified as, and what is its deficiency cause?
Biotin is called Biotin, and its f(x) is seen in Acetyl CoA Carboxylase, Pyruvate Carboxylase, and Proponyl CoA Carboxylase, its disf(x) causes dermatitis, anorexia, nausea, and muscle weakness, may be caused by consuming large amounts raw eggs.
__________ facilitates covalent linkage of CO2 to lysine side chains of enzymes. 
Carboxylase conducts covalent linkage of CO2 to lysine of side chains of enzymes. 
__________ is a vitamin found in intestinal microorganisms, liver, and vegetables.
Pantothenic Acid is part of ____________ as a cofactor.
b-Vitamin A
d-coenzyme A
d-coenzyme A, where Pantothenic acid forms pantotheine, deficiency causes nausea & fatigue, is synthesized by intestinal bacteria.
______________ is used in to t(x) TB, it has an antagonistic effect on Vitamin B6.
c-Isoniazid t(x) TB and is antagonistic to Vitamin B6/Pyridoxine.
Dihydropteroate Synthetase is inhibited by____________ preventing the production of Folic acid.
c-Sulfanilamide, inhibits Dihydropteroate Synthetase preventing Folic acid.
___________ is a vitamin consisting of Cobalt, is an important cofactor in the conversion of Homocysteine to Methionine via N5 methyltetrahydrofolate going to tetrahydrofolate. 
Cobalamin / Vitamin B12
Methylmalonyl CoA isomerase requires _____________ to produce Succinal CoA 
5-deoxyadenosyl cobalamin
Pernicious anemia & degeneration of spinal cord neurons are caused by __________. 
Cobalamin deficiency cause Pernicious anemia, which is seen in Vegans b/c sources of Vit. B12 =>meat & milk.
What is the best treatment for pernicious anemia
a-Folic acid 
d-A,B, and C
e-A&B, folic acid and vitamin B12 treatment is the best t(x).  
Which vitamins are the anti-oxidant vitamins?
a-Vitamin A, D, & E
b-Vitamin K, E, and Biotin
c-Vitamin E, ß-Carotene, and biotin
d-Vitamin C, E, an ß-Carotene
d-Vitamin C, E, an ß-Carotene are the anti-oxidant vitamins.
___________ regulates Ca at intestine, kidney, and bone.
b-Vit D
c-1,25 dihydroxy vitamin D3
d-UV irradiated 7-dehydrocholesterol in skin
All of the above.
Excess of _________ cause pulp calcification and toxicity. 
Vitamin D
Tocopherol is....
a-analogous to calciferol 
b-when deficient leads to the lysis of erythrocytes.
c-a high poly unsaturated 
b-when deficient leads to the lysis of erythrocytes, is characteristic of Tocopherol/Vitamin E
________ is produced by intestinal bacteria, and is a coenzyme for carboxylation of glutamic side chains.
Vitamin K
4 Porphobilinogen (3rd reaction of Porphyrin synthesis)
In Porphyrin synthesis' 3rd reaction, tetrapyrrole, 4Porphobilinogen goes into Hydroxymethyl bilane synthase prod. Hydroxymethylbilance 
5/delta aminolevulinate synthase is a protein whose cofactor is ___________ & function is ___________, & inhibited by ______.
cofactor=pyridoxal phosphate, synthase is inhibited y heavy metal ions, & is feedback inhibited by heme/hemin
Catalase functions to do?
Catalase breaksdown peroxidase 
Chlorophyll functions in what process?
Chlorophyll funtions in light absorption
Cytochrome a, b, & c function in what process?
Cytochromes a,b, and c function in electron transport 
Cytochrome P450 does what?
Cytochrome P450 function in hydroxylation.
Heme synthesis is restricted to the mitochondria in what process of its synthesis?
The 1st and last 3 reactions of porphyrin synthesis occur in the mitochondria.
Hydroxymethylbilance (in the 4th reaction) functions?
hydroxymethylbilance goes into uroporphyrinogen synthase which, catalyzes ring closure & isomerization prod. uroporphyrinogen 3 & 4NH3
In Heme degradation the 1st step when Heme goes into Biliverdin reductase what occurs?
The 1st step of Heme degradation does not occur at the enzyme Biliverdin reductase, it occurs at Heme Oxygenase which produces Biliverdin. 
In Porphyrin Synthesis the 1st reaction is ... 
5/delta aminolevulinate synthase catalyzing Glycine & Succinyl CoA producing = 5/delta-aminolevulinic acid (ALA), CO2 and CoA = 1st reaction (rate limiting)
In the liver, bile is immediately preceeded by ________ & which is prod. by _______
Bile is immediately preceeded by Bilirubin diglucuronide produced by Bilirubin Glucuronyl Transferase.
Protophyrin 9 is converted to _________ by what protein?
Protophyrin is converted into heme by ferrochelatase.
Regulation of Heme Synthesis is controlled by _______ @ ______.
accumulation of Heme/Hemin, inhibiting 5 aminolevulinate synthase 
The 2nd reaction of Porphyrin Synthesis is...
Porphyrin synthesis's 2nd reaction is two 5-aminolevulinate condense in Delta-aminolevulinic acid dehydrase (inhibited by Pb) to produce = porphobilinogen (monopyrrole)
Uroporphyrinogen 3 (The 4th Heme synthesis reaction) functions to produce what?
In the 4th reaction of heme synthesis, Uroporphyrinogen 3 goes to prod. Protoporhyrin 9
What 2 enzymes are in the heme synthetic pathway are inhibited by lead?
Lead inhibits delta Aminolevulinic Acid dehydrase, which prod. Porphobilinogen, & Ferrochelatase which prod. Heme. 
What are Porphyrins?
Porphyrins serve as prosthetic groups for proteins in oxygen transport, heterocyclic ring structures includes 4 pyrrole rings join thru a carbon bridge. In the center lies a metal atom that is chelated to the nitrogen atoms of the pyrrole units, in heme = Fe/chlorophyl = Mg
What enzymatic steps of Heme degradation is restricted to the macrophage? 
The 1st (@Heme Oxygenase) and 2nd (@Biliverdin Reductase) steps of heme degradation occur inside the Macrophage to produce Bilirubin. 
What is Hemin?
Free oxidized form of heme, inhibits synthesis and activity of 5-aminolevulinate synthase in primitive RBC and cells w/ other heme protein; activates synthesis of globin peptide by combining w/ an inhibitory protein balancing heme & globin 
What is the significance of Protoporphyrin 9?
Protoporphyrin 9 goes into Ferrochalatase (inhibited by lead) to prod. Heme (Fe2+ protoporphyrin 9)
Why does hemoglobin have a square shaped oxygen dissociation curve?
This is false, myoglobin's shape is squared, and hemoglobin is sigmoidal, the reason for the square is b/c myoglobin has greater affinity to oxygen, and curve shape shows the cooperative behavior of hemoglobin. 
Obstruction of the common bile duct is called?
Post Hepatic Jaundice.
Fava beans consumed by a person with G6P deficiency would probably cause which type of Jaundice?
G6P deficiency and Fava beans consumption would cause hemolytic anemia leading to hemolytic jaundice. 
In sickle cell Glutamate is substituted for: 
In sickle cell anemia, Glutamate is substituted by valine, causing sickling. 
Hepatic Jaundice is indicated by:
a-Acute Hemolytic anemia
c-Neonatal physiological juandice
d-Disease like Gilberts disease. 
Disease like Gilbert's disease is indicative of Hepatic Jaundice.
 The active form of nucleotides in biosynthesis is triphosphates. 
false, di & tri phosphates of nucleotides are the active forms. 
Phosphodiester bonds 
How does Hypoxanthine differ from Xanthine?
Xanthine contains 2, 6 Carbonyl groups,which Hypothanthine has only a 6 Carbonyl group. 
Among the nucleotides, which compose the purines?
B & C, Guanine and Adenine make up the purines. 
How does Adenine and Guanine differ?
Adenine has at its carbon 6 position an amino group, vs. Guanine that has a carbonyl group at its 6 position, in addition it has an amino group at its 2 position.  
De novo synthesis of nucleotides come from....
Pentose Phosphate pathway. 
Ribose-5-Phosphate + ATP + PRPP synthase produce...
5-Phosphoribosyl-1-pyrophosphate (PRPP), which is reduced by Glutamine & enters Amidophosphoribosyl Transferase. PRPP synthase is inhibited by AMP, IMP, GMP.
Amidophosphoribosyl Transferase  & PRPP prod. _______?
5-Phosphoribosylamine, this is a major regulatory step., where Amidophophoribosyl Transferase is inhibited by IMP, AMP, and GMP. 
_________ is the precursor for both AMP and GMP. 
D & C, 
All of these are part of purine biosynthesis except:
A-Glutamate is not in the process of purine biosynthesis.
AMP in its feedback inhibition, acts on
a-IMP dehydrogenase 
c-Adenylosuccinate synthetase
c-Adenylosuccinate synthetase is inhibited by AMP in feedback inhibition. 
? is an anti-graft rejection drug, that uncompetitively inhibits Inosine Monophosphate Dehydrogenase.
d-Mycophenolic Acid
d-Mycophenolic Acid inhibits IMP dehydrogenase, used to deprive T & B cells of components of Nucleic Acids. GMP also inhibits IMP dehydrogenase.
_______ & Aspartate -->Adenine
d-Hypoxanthine + Aspartate--> Adenine
Xanthine + Glutamine --->Adenine. 
False, Xanthine + Glutamine -->Guanine. The carbonyl O, b/c NH2.
What enzymes f(x) in the salvage pathway of purine reutilization?
C & D, A-PRT & HG-PRT produce Adenylate, and Guanylate respectively. 
Gout is caused by lost of negative regulation...
PRPP Synthetase & PRPP amidotransferase or PRPP levels are high because of defect in HG-PRT/A-PRT (The Salvage pathway), leading to overprod. of xanthine and then urate. 
What is the result of mutation in ADA (Adenosine Deaminase)?
c-SCIDS is the result of mutation in ADA, Adenosine Deaminase. 
What does Adenosine Deaminase do?
Adenosine is converted into by enzyme Inosine, which is converted into Hypoxanthine. When mutated this incapacitates T and B cells b/c dAMP is high & toxic. 
Defect in glucose 6 phosphatase results in ______ & what disease>
Hyperuricemia & Von Gierke's disease. 
Lack of HG-PRT is called:
c-Von Gierke's disease
d-Lesch Nyhan syndrome
D- Lesch Nyhan syndrome results due to a lack of HG-PRT which leads to Hyperuricemia. 
How does the structure of Cytosine & Uracil differ?
a-C-has Two Carbonyl groups, U has one NH2 & Carbonyl group
b-C-has 1 Carbonyl groups, U has 2 NH2 & 1 Carbonyl group
c-C-has Two Carbonyl groups, U has one NH2 & Carbonyl group
d-C-has 1 Carbonyl
D-Cytosine has 1 Carbonyl group and 1 NH2, U-has 2 Carbonyl groups.
What f(x)nal groups does  the structure of Thymine have:
a-1 Carbonyl & 1 NH2
b-2 Carbonyls
c-2 Carbonyls & 1 Methyl 
d-2 Carbonyls & 1COOH 
c-2 Carbonyls & 1 Methyl, describe the functional groups of Thymine. 
2 Carbonyls & 1COOH describe the functional groups on _______.
d-Orotic Acid
d-Orotic Acid has 2 Carbonyls & 1COOH functional groups. 
What are the starter molecules of Pyrimidine biosynthesis?
Glutamine, HCO3, & 2ATP, which enter Cabamoyl Phosphate Synthetase 2, Aspartate Transcarbamylase, and Dihydroorotase dehydrogenase, =>CAD prod. Orotic Acid. 
Where is CPS2 located?
CPS 2 is located in the cytosol. 
What is the fate of Orotic Acid when it leaves CAD?
Orotic Acid enters Orotate Phosphoribosyl Transferase w/ PRPP prod. Orotidine 5' Monophosphate. 
Uridine 5' Monophosphate (UMP) is produced by...
a-Oratate Phosphoribosyl Transferase & Orotic Acid
b-PRPP & Orotidine 5' Phosphate decarboxylase 
c-Orotidine 5' Monophosphate & Oritidine  5' Phosphate Decarboxylase. 
d-Orotic acid & Oritidine
c-Orotidine 5' Monophosphate & Oritidine  5' Phosphate prod. UMP=Uridine 5' Monophosphate. 
On what enzymes are feedback inhibition exerted in the regulation of Pyrimidine biosynthesis?
B,D, & E, CPS2 is inhibited by UTP, as is Aspartate transcarbolymase. Oritidine 5' Phosphate Decarboxylase is inhibited by UMP. 
UTP inhibits CTP2 in:
b- Eukaryotes have UTP inhibit CPS2, not Prokaryotes, however in Prokaryotes UTP inhibits ATC. PRPP & ATP activate CPS2. 
Atoms on pyrimidines come from all except:
b-Ribose 5-Phosphate
e-Glycine is not a contributor to pyrimidine structure, *CO2 comes from Carbonyl Phosphate. 
Megaloblastic anemia is connected to Pyrimidine biosynthesis how?
low activity in Orotidine phosphate decarboxylase & Orotate Phosphoriboxyltransferase cause abnormal growth and megaloblastic anemia.  
What is a non invasive test to determine if megaloblastic anemia is the result of deficient  pyrimidine biosynthesis?
Check the urine for large amounts of oratate it is a positive test for deficient  pyrimidine biosynthesis.
CTP synthetase uses _____ & ________ to produce CTP.
a-Glutamine & UMP
b-Glutamate & UTP
d-Glutamine & UTP
d-Glutamine & UTP, are the substrates that CTP Synthetase converts to CTP. 
What enzymes f(x) in converting RNA to DNA?
Thymidylate Synthase & Ribonucleotide Reductase
Ribonucleotide Reductase is inhibited by______
e-dATP inhibits RR., ATP activates it. 
Thioredoxin is found in the active site of 
a-Thymadylate synthesis
b-Ribonucleotide Reductase
B- RR contains Thioredoxin which has 2 cysteines that are oxidized reducing Ribose, in converting RNA to DNA. 
T/F ADP, GDP, CDP, and UDP are converted into deoxyNucleotides by rNDP Reductase then converted to Triphosphates by reacting w/ATP. 
False, UDP needs to go through a series of reactions, where 5,10 THF converts dUTP->dTTP via Thymadylate Synthetase. This full conversion costs 3 ATPs.
What does 5,10 methylene-tetrahydrofolate do to dUMP with the help of Thymidylate synthase?
a-Reduce dUMP
b-Oxidize dUMP
c-methylate dUMP
d-demethylate dUMP
c-methylate dUMP, is the f(x) of 5,10 methylene tetrahydrofolate prod. dTMP. 
________ & ________ enter Dihydrofolate reductase to produce ____________.
Oxidized Dihydrofolate & NADPH prod. Tetrahydrofolate. Methotrexate is an inhibitor of Dihydrofolate reductase.
5 FU is an anticancer drug that targets:
a-Dihydrofolate reductase 
b-Thymidylate synthase
c-Serine transhydroxymethylase
b-Thymidylate synthase, is targeted by 5FU = Fluorodeoxyuridylate preventing dTMP production. 
When the drug is more toxic to the tumor than host:
b-hot mess
c-selective toxicity
d-Therapeutic dose
c-selective toxicity, is when drug is more toxic to tumor than host. 
How do you calculate the Chemotherapeutic Index?
a-toxic dose/therapeutic dose
b-selective toxicity/toxic dose
c-max tolerable dose/min therapeutic dose
d-max tolerable dose/max therapeutic dose
c-max tolerable dose/min therapeutic dose = Chemotherapeutic index. 
What are the sources of Lipids synthesis?
Ingested triacyglycerols & ingested glucose
What is the fate of ingested triacyglycerols?
1st-emulsified by bile salts in the intestines,
2nd-Digested by Pancreatic Lipase & Colipase, which convert Triacylglycerol into Fatty Acid & 2-Monoacyglycerol(2-MG). 
3rd-FA & 2-MG in Bile salts micelle transporting them to Nasent chylomicrons in the intestine.
4th-Nasent Chylomicron w/apoB, TG & Phospholipids enter lymph, then the blood stream. 
What is the structure of lipoproteins?
Lipoproteins contain phospholipids, cholesterol esters, apoprotein, chlesterol, and triglycerides. 
Acyl carrier protein is part of what process?
b-cholesterol synthesis
c-fatty acid synthesis
d-bilirubin degredation
c-Acyl carrier protein is part of fatty acid synthesis, where Acetyl CoA & 7Malonyl CoA + 14 NADPH + 14 H catalyzed by FAS complex produce Palmitic Acid (C16)
Where does NADP+ get its reducing power needed for palmitoyl CoA synthesis?
NADP+ gets its reducing power from NADH produced in glycolysis,
2-from Hexose Monophosphate shunt pathway where G6P + NADP+ ---> 6-Phosphogluconate + NADPH,
3. 6-Phosphogluconate + NADP+ --> Ribulose-5-phosphate + NADPH.
4. Malate + NADP+ --->Pyruvate + NADPH
Where does the acetyl CoA come from that's used in Palmitoyl CoA synthesis?
Acetyl CoA used in Palmitoyl CoA synthesis from Citrate produced in the TCA of the mitochondria. 
What is needed to produce Malonyl CoA?
Acetyl CoA, CO2, acetyl CoA carboxylase + Biotin, ATP are needed to produce Malonyl CoA. 
Where is the product of the rate limiting step in Fatty acid synthesis?
Production of Malonyl CoA, where Acetyl CoA Carboxylase is the rate limiting step. 
Biotin Carboxylase functions how?
It takes HCO3- and produces CO2. 
T/F, Transcarboxylase = ACC
True, Transcarboxylase is equivalent to Acetyl CoA Carboxylase. 
Beta-Ketoacyl-ACP Synthase takes ________ & _________ forming Acetoacetyl-ACP. 
Acetyl-ACP & Malonyl ACP are combined by Beta-Ketoacyl-ACP Synthase producing Acetoacetyl-ACP.
How is the rate limiting step ACC regulated?
Citrate & Insulin bind to ACC causing it to polymerize = activation. 
How does glucagon inactivate Fatty Synthesis?
Glucagon & Epinephrine causes adenylate cyclase activity inc. cAMP causing phosphorylation of  Acetyl CoA Carboxylase causing inactivation. 
T/F high fat diet has the same effect on FAS and ACC as caloric restriction?
True, both High fat diet & caloric restriction don't induce insulin, thus a decrease the transcription and translation of mRNA for ACC & FAS. 
What enzyme is responsible for fatty acid desaturation?
Fatty acyl CoA desaturase, in the mitochondria with the aid of Cytochrome b5, NADPH dependent Cyt b5 Reductase(FAD) & NADH.
T/F elongation of fatty acids takes place in the mitchondria.
False, fatty acid elongation takes place in the ER, where ß-ketothiolase, enoyl CoA dehyratase, ß-hydroxyacyl CoA dehydrogenase, and enoyl CoA reductase participate in elongation. 
What is the main enzyme of triacyglycerol synthesis?
Activation of phosphatidyl group or the head group with CDP yields?
The formation of phosphatidyl compounds. 
On phosphatidyl compounds Phospholipases selectively hydrolyze:
d-aldehyde groups 
b, ester links are hydrolyzed by Phopholipases on phosphatidyl compounds. 
CDP on either _________ or ________
activates either and promotes ________.
Nucleoside diphosphate on Diacylglycerol or an Alcohol promotes phospholipid synthesis.
This phospholipase acts on phosphatidylinositol releasing arachidonic acid, is rich in pancreatic secretions, requires trypsin & bile for activity, inhibited by glucocorticoids. It is:
a-Phospholipase A1
b-Phospholipase D
c-Phospholipase A2
C, Phopholipase A2 is inhibited by cortisol & is responsible for prod.  precursor of prostaglandins. 
I cleave ester linkages of plant tissue what am I:
a-Phospholipase A2
b-Phospholipase A1
c-Phospholipase D
d-Phospholipase C
Phospholipase D is found primarily in plant tissue. 
I cleave ester links, I am found in liver lysosomes & alpha toxin of bacteria, I'm activated by PIP2 system & serve in 2nd messenger systems when bound to membrane.
I am Phospholipase C.  
Palmitoyl CoA & Serine preceed the formation of:
Sphinganine in the synthesis of sphingomyelin. 
Ceramide + ___________ produce Sphingomyelin. 
e-none of the above
d-Phosphatidylcholine + Ceramide prod. Sphingomyelin. 
Sphinganine + __________ produce Ceramide. 
d-Only the oxidation of Sphinganine by FAD & Fatty acyl CoA prod. Ceramide. 
What is the univeral start off molecules of sphingolipid synthesis?
C- Ceramide can prod. the gambit of different sphingolipids. 
Ceramide + UDP-galactose prod.__________. 
Galactocerebroside is prod. by Ceramide + UDP-galactose. 
Ceramide + ________ prod. Glucocerebroside. 
c-UDP-glucose + Ceramide prod. Glucoscerebroside.
Ganglioside is prod. by 
a-Cerebroside + CMP-NANA & UDP-sugars
b-Ceramide + CMP-NANA & 1UDP sugar
c-Ceramide + UDP-NANA & 2UDP sugars
d-Ceramide + CMP-NANA & 2UDP sugars. 
Ceramide + CMP-NANA & 2UDP sugars will prod. Ganglioside from Globoside, from Ceramide.
Glycolipids that contain Sialic acid = ?
Accumulation of the product of Ceramide + CMP-NANA & 2UDP will lead to ________. 
b-Tay-SACHs Disease
c-Sandhoff's Disease
d-Gaucher Disease
B- Tay Sach's disease, the product of Ceramide + CMP-NANA & 2UDP is Gangliosides (GM2)
Guacher disease results due to accumulation of ___________.
d-the product of Ceramide + UDP-glucose 
d-the product of Ceramide + UDP- glucose, because this product is glucose cerebrosides. 
This is the only X-linked sphingolipid disease, where accumulation of _________ leads to _______ disease. 
Accumulation of ceramide leads to Farber disease. This disease is usually fatal early in life. 
Accumulation of the product of Ceramide and Phosphatidylcholine result in _______.
Ceramide + Phosphatdylcholine produce sphingomyelin, thus accumulation = Niemann-Pick Disease. 
Accumulation of Ceramide + 2UDP-sugars, & symptoms of burning of lower extremity = 
a-Krabbe Disease (Globoid Cell Leukodystrophy)
b-Sandhoff's Disease
c-Farber Disease
d-Fabry Disease
d-Fabry disease where Ceramide + 2 UDP-sugars prod. Globosides, and where burning in lower extremities are a symptom.
In Cholesterol biosynthesis HMG CoA is formed how?
2 Acetyl CoA enter Synthetase enzyme prod. Acetoacetyl CoA, HMG-CoA synthase--->HMG CoA. 
What is the fate of HMG CoA?
Under low cholesterol conditions it is reduced by HMG CoA reductase & 2NADPH producing. Mevalonate. 
What is the fate of Mevalonate?
Mevalonate + 2ATP prod. 5 Pyrophospho-Phosphomevalonate, which is decarboxyated to produce Isopentenyl Pyrophosphate.
Isopentenyl Pyrophosphate is isomerized to become _________ then__________.
Isopentenyl Pyrophosphate is isomerized to become Dimethyl Allyl Pyrophosphate & Geranyl Pyrophosphate.
2 Geranyl Pyrophosphate ---> ________ which is condensed with NADPH to prod. _________
Farnesyl Pyrophosphate, Squalene. 
Cholesterol is synthesized primarily in ________ & ________.
Liver & intestines
How does plasma cholesterol differ from cellular/intestinal?
a-Ether bond at C1
b-Ester bond at C1
c-Ester bond at C3 w/Fatty acid in lipoprotein particles.
d-Ether bond at C17 w/Fatty acid in lipoprotein particles.
c-Ester bond at C3 w/Fatty acid in lipoprotein particles are typical of plasma cholesterol. 
The synthesis of HMG-CoA takes place only the mitochondria. 
False, HMG-CoA synthesis takes place in the Cytosol, Mitochondria, and Peroxisomes. 
Where does the synthesis of Mevalonic acid take place, and what is the significanc of this process?
Mevalonate is produced in the ER, and it is the rate limiting step of Cholesterol synthesis by HMG CoA reductase, which is inhibited by cholesterol. 
Release of PPi in Cholesterol synthesis results in:
a-increased solubility
b-reaction reversibility
c-reaction irreversibility
d-dec in hydrophobicity 
c, release of PPi in cholesterol causes reaction irreversibility, this occurs in peroxisomes. 
sterol responsive element binding protein (SREBP) is 
the transcription factor that regulates cholesterol synthesis, which is a transmembrane protein, has a DNA binding and SCAP domain.
What is the purpose of SCAP in cholesterol synthesis;
a-sense when intracellular cholesterol is low.
b-bind DNA
c-escort SREBP in the Golgi
d-transmembrane escort of SREBO in ER.
All except bind DNA, that is SREBP's job. 
What allows SREBP to enter the nucleus after SCAP takes it to the Golgi Apparatus?
Protease 1 & 2
An increase in the stability of HMG-CoA reductase is seen when
a-Intracellular Cholesterol is high
b-Intracellular Cholesterol is low
c-both a & b
Only when cholesterol is low is the stability of HMG-CoA reductase increase to produce cholesterol through correct folding in the the membrane of the ER. 
HMG-CoA is phosphorylated by _____ leading to ______.
a-inc in ATP & Activation
b-dec in ATP & Activation
c-inc in AMP & Inactivation 
d-insulin & activation
c, phosphorylation occurs by inc. in AMP, and Glucagon that stimulats kinase activity which dec cholesterol synthesis. 
Mevaldyl CoA does ______ to HMGR activity.
Inactivation of HMGR activity is caused by naturally occuring mevaldyl CoA and its synthetic mimics called Statins. 
This drug blocks the absorption of Cholesterol at the intestinal brush border, however does not block the absorption of Triglycerides or soluble vitamins. 
This drug block cholesterol in its synthesis and its intestinal absorption. 
Vytorin (ezetimibe & simvastatin)
Apo CII and Apo E are acquired from where?
They are both acquired from HDL, and apo cII binds to lipoprotein lipase to hydrolyze triacylglycerol.
What is the function of Apo E receptors?
Apo E receptors mediate uptake of remnant of chylomicron remnants & cholesterol enters liver cells.
_________ is unique to the nascent chylomicron.
How can you tell if a chylomicron is mature?
It has a apoE and apoC-II added from HDL.
One structural feature of Chylomicron remnants is the lack of Apo E, and ApoB-48.
False, only the lack of Apo C II is indicative of Chylomicron remnant.
_________ functions in reverse transport of cholesterol to liver.
What is a characteristic of nascent VLDL?
VLDL's have apo B100.
What is the process of transforming VLDL to LDL?
VLDL can transform to LDL by transferring apo C-II and apo E to HDL.
What is the site of drug therapy for increasing HDL?
HDL is targeted by increasing apo-A1 synthesis.
HDL to VLDL & LDL transfer of cholesterol is mediated by cholesterol ester transfer protein (CTEP).
And is the target of inhibition to limit high cholesterol.
How is cholesterol converted into cholesterol ester and why?
Cholesterol ester is necessary for storage and this conversion takes place by the enzyme Acyl CoA cholesterol acetyl transferase.
Where are chylomicrons, VLDLs, and HDLs assembled:
a-gut lumen
c-intestine & liver
d-liver and kidney
c- intestine is the site of chylomicron assembly and the liver is the site of VLDL assembly. HDL is assembled in both intestine and liver.
Cholesterol is used by the liver to produce ___________?
Bile Acids.
Micelles differ from liposome how?
Liposomes are bilayered and Micelles are single layered.
What is the difference between transmembrane and integral membrane proteins?
Integral membrane proteins are only integrated on one side of the lipid bilayer, vs. Transmembrane which traverse both sides.
The outer leaflet of plasma membrane consist mainly of:
a-phosphatidylcholine, sphingomyelin, and glycolipids
b-Phosphatidylethanolamine, phosphatidylserine, and phosphatidylinositol
c-Phosphatidylethanolamine, phosphatidylserine, cholesterol
a-phosphatidylcholine, sphingomyelin, and glycolipids is the constituent of the outer leaflet. 
The inner leaflet of the plasma membrane consist of Phosphatidylethanolamine, __________, and ___________.
Phosphatidylethanolamine, phosphatidylserine, and phosphatidylinositol compose the inner leaflet of the plasma membrane.
In 2ndary active transport, ________ is used to transport molecules. 
a-Indirect Coupling of ATP
b-Direct coupling of ATP
c-Electrochemical potential difference.
d-none of the above.
In secondary active transport, c-Electrochemical potential difference is used to transport molecules across the cell. 
In the Na/Ca antiporter, how many Na:Ca?
c 3Na in: 1Ca out
Phlorizin is a drug used to inhibit which intestinal transporter:
a-GLUT 2
b-SGLT1 is the Na coupled glucose symporter at the intestinal lumen that is inhibited by Phlorizin. 
Phoretin and Phlorizin inhibit the same transporter.
False, Phloretin inhibits GLUT2 @ the basal surface, Phlorizin inhibits SGLT1 (Na/Glucose symporter)
_______ transports glucose and fructose, whereas _______ transports only fructose. 
GLUT 2 transports both glucose and fructose, whereas GLUT5 transports only Fructose. 
What is the correct order of the plasma membrane with the highest cholesterol content to the lowest?
a-RER ->SER->Golgi->Plama membrane
b-SER -> RER->Plama membrane-> Golgi
c-Plama membrane ->Golgi-> SER-> RER
c-Plama membrane ->Golgi-> SER-> RER, the trend increase as you go further from the nucleus. 
Where on cholesterol is there a Hydroxyl group?
c-Both A&B
B-C3 contains the OH group. 
Which carbon on cholesterol has an 8 carbon side chain?
C17, has the 8 Hydrocarbon tail.
Prostaglandins are synthesized by only a select number of cells, act locally, and have extremely long half-life and are store. 
False/Half-truth, Prostaglandins are produced by every cell of the body, act locally, have an extremely short half-life, and are not stored. 
The action of prostaglandin endoperoxide synthase is ______of ___________ to yield PGH2. 
Prostaglandin endoperoxide synthase oxidatively Cyclizes free arachidonic acid to yield PGH2, which is the 2st step of prostiglandin synthesis. 
Cyclo-oxygenase ____ is inducible and is expressed in most tissues. 
COX 2 is inducible following inflammation and trauma, its found in immunocompetent cells like leukocytes.
T/F COX1 is influenced by steroids, and is influenced by inc cytokines and bacteria. 
False, COX1 is not influenced by steroids, and is not increased by cytokines/bateria. 
Dietary arachidonic acid/(linoleic acid) contribute to all thru COX1 except:
a-blood clotting 
b-Kidney f(x) via PGE2 via inc. blood flow
d-Stomach protection via PGI2 by prod. mucous 
c-pain is not part of the physiological role of COX1. 
all of the following describe PGE2 except:
a-development & reg. of different immune system cells
b-dec. of MMPs & dec. Apoptosis
c-Tumor promotion
d-Stomach f(x)
e-stimulate uterine contractions during labor
b, Matrix Metalloproteases f(x) to increase tumor promotion, it also increase periodontitis. 
PGD2 --->PGJ2 cause tumor _______. 
inhibition, by decreasing MMPs & proliferation, and increase in Apoptosis. 
During blood vessel damage, thromboxanes:
a-cause clotting
b-recruits WBCs
c-stimulate PGI2
d-stimulate constriction of Blood vessels. 
Thromboxanes cause clotting, constricting of blood vessels at site of damage, stimulates PGI2 which causes blood vessel dilation at sites  where clots should not form, but does not recruit WBCs. 
Leukotrienes, a type of PG is related to asthma, how?
Leukotrienes promotes bronchi constriction. 
NSAID such as aspirin works by 
a-irriveribly binding COX 1 & 2
b-binding Arachidonic acid
c-selectively binding linoic acids
a, Aspirin's acetyl group binds serine in COX's 1 & 2's active site blocking arachidonic acids entry. 
a-inhibit COX enzymes 
b-dec PG's & Thromboxanes
c-reduce pain, fever, inflammation
d-all of the above
d, all...
How is the NSAID Tylenol thought to work? 
Tylenol inhibits the activity of COX3 enzymes. 
How is COX2 inhibitors selective for COX2?
COX2 enzymes have a side pocket in its active site, which contain a valine residue at position 523, this is not seen in in COX1. 
Where does Amino acid's nitrogen go?
The Nitrogen Amino acids go to f(x) in Transamination, Glutamate dehydrogen in producing ammonia, and in urea synthesis. 
The carbons of amino acids....
Are used to produce pyruvate in gluconeogenesis, 2-Produce Acetyl-CoA-->FA, Cholesterol, Steroids, 3-Acetoacetate->Ketone bodies, 4-Succinyl-CoA->TCA, 5-2-oxoglutarate (alpha-KG)->TCA
Arginine & Glycine are used to produce:
D-Creatine is produced from SAM reacting with Guanidino acetic acid (by transferring methionine group) which is prod. from arginine & glycine.
Catecholamines are produced from what amino acid:
Phenylalanine is the precursor amino acid of Catecholamines, as well as Thyroid hormones. 
NO is produced from what amino acid:
d-arginine is the precursor of NO. 
T/F, Tryptophan is the amino acid that is used to produce the hormone Serotonin. 
Phenylalanine is the precursor amino acid of S-adenosyl-L-methionine.
False, SAM is based off Methionine
Cysteine is based of which 2 amino acids:
a-arginine & glycine 
b-tryptophan & Phenylalanine
c-methionine & serine
d-methionine & glycine
Methionine & serine are the precursor amino acids of Cysteine. 
dTMP is built on:
a-arginine & serine
b-serine resynthesis
c-methione & serine 
d-methionine resynthesis
D-methionine resynthesis is built into dTMP.
the inability to metabolize Phenylalanine results in?
Phenylketonuria (PKU), which is an inborn error in AA metabolism, where Phenylalanine 4-mononoxygenase is defective in Using Phenylalanine+O2+BH4 to prod. Tyrosine or GTP Cyclohydrolase is defective in prod. BH4 from GTP. 
Transamination uses ________ & aminotransferase.
Oxo-(keto) acid co-substrate to transfer Nitrogen.
When Pyruvate serves as an oxoacid when it recieves a Nitrogen it becomes ________.
Alanine is produced from pyruvate by amino transferase.
When Oxaloacetate serves as an oxoacid when it recieves a Nitrogen it becomes ________.
Aspartate is the amino acid prod. from aminotransferase from Oxaloacetate.
When __________ serves as an oxoacid when it recieves a Nitrogen it becomes glutamate.
d-2-OG is the oxoacid used by aminotransferase to prod. glutamate. 
What is the fate of Glutamate?
Glutamate is produced from transamination of 2-OG, it enters Glutamate Dehydrogenase to produce Ammonia which enters the Urea cycle. 
What is the rate limiting step of the Urea cycle?
The rate determining step of Carbamoylphosphate Synthestase 1 producing Carbamoyl Phosphate from Ammonia and Bicarbonate + 2ATP. CPS1 is upregulated by N-acetylglutamate.
What is the 2nd step of the Urea Cycle?
The production of Citrulline by Ornithine Carbamoyltransferase, which takes Carbamoylphosphate & Ornithine to produce Citrulline. 
The production of Arginosuccinate is found in what step of the Urea Cycle?
Citrulline & Aspartate & ATP combined by Argininosuccinate Synthetase to produce Argininosuccinate, the 4th step of Urea Cycle.
How and when is Urea generated?
Arginosuccinate divides into fumarate & Arginine. Arginase takes Arginine & H2O to produce Urea & Ornithine in step 5 of the Urea Cycle.
How is N-Acetylglutamate produced?
Glutamate reacts with Acetyl CoA via N-AcetylGlutamate Synthase to produce N-Acetylglutamate, which f(x) in an Acute regulatory way. 
Regulation of gene expression of CPS1 gene requires:
b-Acetyl CoA
c-Hepatic nuclear factors (HNFs)
c- HNF's regulate transcription of CPS1 gene, requires tissue specificity. 
Excessive glutamine results in what CNS disease?
Hypreammonemia, which is ammonia toxicity.
The product of Hippuric Acid reflects treatment of __________ by ___________. 
T(x) of Hyperammonemia with Sodium Benzoate results in Hippuric Acid.
T(x) of Hyperammonemia by Sodium phenylbutyrate/acetate produce_________.
Sodium Phenylacetate/butyrate reacts with two NH3 to produce Phenylacetylglutamine.
What clinical manifestation can you expect from mutations in one Urea cycle enzyme e.g. Glutamate Dehydrogenase gene (GLUD1)? 
Hyperammonemia leads to serious liver failure, HI/HA syndrome. 
How does GLUD1 mutation f(x)?
This is a gain of f(x) mutation where glutamate dehydrogenase is not down regulated by GTP resulting in HI/HA, XS GDase in Beta cell-->HI, XS GDase in liver-- xs ammonia (no surplus glutamate to prod. NAG) & down reg. Urea cycle.
Amino Acids the are used to make Pyruvate: GAS ACT = Pyrv
Ace (Acetyl CoA) uses amino acids that have a TILL.
T/F Acetyl-CoA is used in all except:
b-FA synthesis 
c-Cholesterol synthesis 
e-Amino Acid synthesis 
Amino acid synthesis is not used by Acetyl-CoA. 
Phenylalanine & Tyrosine
Decarboxylation of Acetoacetate produces__________
b-Acetyl group
C- Acetone is prod. by decarboxylation of Acetoacetate. 
3-Hydroxybutyrate is produced by...
Ketone reduction of Acetoacetate. 
What is the purpose of Ketone bodies
A-energy for organs when hungry
B-When one can't metabolize glucose
c-nutrient for brain during starvation
d-during insulin shock
B & C, during starvation brain use Ketone bodies for nutrients and during diabetes, where the body can not metabolize glucose.  
Succinyl-CoA is produced by VIT-M
Thus Suc = VIT-M
M-Methionine  prod. Succinyl-CoA
What process of amino acid catabolism uses Vitamin B12?
The production of Succinyl-CoA by VIT-M amino acids by Methylmalonyl-CoA mutase uses Vit. B12
2-OG is prod. by which amino acids?
What amino acid is used in non-invasive test for Folate?
c-Histidine, is used in non-invasive test for folate, b/c if folate works formininoglutamate will form ---> tetrahydrofolate-->5-formiminotetrahydrofolate. If there is a problem w/Folate Histidine will be excreted in Urine.  
Phenylalanine prod. what hormones?
Epi, Norepi, Dopamine, and Thyroid hormones. 
NOS uses all except:
e-GTP derivative BH4 
F, all of the above, NOS use BH4, FAD, FMN, Heme, and NADPH.
Pulp congestion, edema, & necrosis  is caused by what culprit during dental preps?
NO, as well as increased mineralization. 
Does NO signal use Adenylate cyclase?
No, NO signals use Guanylyl cyclase which is soluble converting GTP into cGTP. 
I limit vascular inflammation and limit thrombosis. 
I am NO. 
How is SAM synthesized?
SAM is prod. from methionine + ATP, it serves as methyl donor for Creatine, Epi, Phophatidylcholine, & DNA methylation. 
dTMP requires
a-Free THF
b-5,10 methylene THF
c-Resynthesized Methionine
e-all of the above
e, in the order of c, a, b
Circulating THF exists as...
5-methyl THF, methionine synthase removes the 5-methyl group producing THF. 
What is the fate of a cell that does not receive extracellular signals?
d-die, a cell will die when there are no extracellular signals. 
Peptides & Proteins are examples of:
a-amino acid derivatives
b-Growth factors
Growth factors are peptides and protein hormones. 
PG's & Eicosanoids are examples of:
a-Peptide hormones
b-amino acid hormones
d-fatty acid derivatives
d-fatty acid derivatives hormones are Eicosanoids & PGs 
Amino acid derivative hormones are:
b-Growth factors
Thyroxine & Epinephrine are examples of Amino acid hormones. 
All of these are examples of 2nd messengers except:
a-DAG & Phosphoinositol lipids
c-modified proteins
d-amino acids
d-amino acids
Hormones suffixed with -ine describe:
b-Growth factors
d-Fatty acid derivatives
B, Growth Factors, are hormones ending in -crine.
I have no signal sequence & I am a growth factor of what type:
D-Holocrine has no signal sequence and unknown mechanism. 
Insulin is an example of what type of growth factor?
E-Endocrine, b/c this peptide hormone is secreted from the gland into the blood stream targeting distant cells. 
T/F Hypothalamus has it neurons in the highly vascular terminals of the posterior pituitary. 
False, the neurons of the hypothalamus ends in the anterior pituitary. 
What is the job of the anterior pituitary?
The anterior pituitary is the minion of the Hypothalamus carrying out its (rel.& inhibiting hormones) signals to systemic target organs.
TSH stimulates all except
a-iodine transport
b-thyroid peroxidase
d-none of the above 
e-all of the above
Thyroid hormone regulation is a classic example of:
a-positive feedback loop
b-negative endocrine regulation 
c-neutral feedback
b-negative feedback endocrine regulation is part of thyroid regulation. 
Neurotrophic factors like (NGF, BDNF, and GGF) are what type of growth factor?
c-Neurotrophic factors are paracrine growth factors. 
High binding affinity, induction of cellular proliferation, survival, and differentiation describe what signaling mechanism?
I am a growth factor that affect hematopoietic derived cells. I am...
C-Cytokines affect the humoral & cellular cell of hematopoietic origin. 
What is the range of IL's?
IL-1 to IL-14
I enhance activation of T cells. 
B-IL1, enhance activation of Tcells
 IL2 induces clonal expansion of _______.
c-B cells 
d-T cells 
D-T cells respond to IL-2 by clonal expansion, which would be stimulated by TNF-alpha. 
How does the kidney influence RBC's?
By producing Erythropoietin. 
_________ is a drug t(x) of anemia. 
d-Vit D
c-EPOGEN t(x) of anemia. 
Peripheral neuropathy is casused by...
b-NGF deficiency
b-NGF deficiency b/c loss of NGF prod. cells lead to peripheral neuropathies.
TGF-Alpha uses ________ signaling. 
a-juxtacrine signaling is seen in TGF-alpha signaling. 
EGFR(Her-2) & EGF use ______ signaling and is seen in what disease?
b-Autocrine, Breast cancer
Receptors that stimulate intracellular proteolysis:
What do the insulin receptor and Neurotrophic receptors have in common?
The are receptors with intrinsic enzymatic activity.
T/F kinase activity is restricted to one site on the substrate polypeptide sequence.
False, kinase activity is not restricted to one site on the polypeptide chain or just 1 kinase. 
Kinases are all except:
a-contain consensus amino acids
b-expose domain buried in the protein structure
c-instrumental in formin new SH2 domains
d-Phosphorylate several sequence motifs
d-each kinase works on particular seq. motifs. 
If protein synthesis is inhibited how will early response genes change activity?
The normally inc then dec when protein synthesis takes place, since this won't occur Early response genes will remain activated.
T/F growth factors activate receptor tyrosine kinase activity.
True, once bound ligand induced dimerization occurs, and autophosphorylation of tyrosine residues = activation.  
The autophophorylation on the Receptor Tyrosine Kinsase recruits 
b-Src Homology 3
d-Src Homology 2 is magnetized to the autophosphorylation of tyrosine.The protein has SH2 & SH3 domains. 
SH2 specificity is achieved by A.A. directly N-terminal to pTyr.
False, specificity is achieved by A.A. directly of C-terminal. 
What is the consequence of SH2 proteins binding to RTK?
SH2 domain proteins/GRB2 binds Sos protein which brings Ras & activates it, Ras-GTP activates MAP kinase which translocates to the nucleus activating transcription factors. 
A V12 and N17 Ras mutant leads to .....
a-always active 
b-always inactive
c-dead molecule
c-dead molecule, no effect.
__________ & _______ lead to the JNK pathway.
b-growth factors
d-cell stress
C&D, cell stress & cytokines stimulate the JNK pathway, (ERK pway).
The Ras pathway is the survival pathway.
false, the Ras is the proliferation pathway.
Anticancer therapy targeted to __________ is seen in Gleevac
b-TK, Abl
Gleevac targets Tyrosine Kinase; Abl
_________  targets  STAT3 is in anti-cancer therapy.
d-AG490, targets STAT3 in prostate cancer.
________  targets  RTK in anti-cancer therapy.
e-Gefitinib, target and inhibits RTK.
BAY439006 targets  ? in anti-cancer therapy.
a-MAP Kinase
e-TK, Abl
c-Raf is the target of BAY439006 in kidney cancer therapy. 
Nu2048 targets  ? in anti-cancer therapy.
a-MAP Kinase
e-TK, AblV
none of the above, Nu2048 targets intra-nuclear transcription factor Cdk.
Metabolic rate is influenced by all except:
d-physical activity
What is the hypothalamus's role in metabolism?
The hypothalamus regulates eating behavior.
Lesion to the ventromedial area of the hypothalamus results in 
c-high labido
d-low labido
a-hyperphagia or excessive hunger is the result of lesions to the ventromedial area. 
Hypophagia results from______?
Lateral hypothalamus lesions result in decrease eating or hypophagia.
T/F adipocytes secret TNF-alpha?
True, TNF-alpha is secreted by adipocytes to regulate sensitivity of skeletal muscle to insulin.
T/F cardiac muscle uses glucose for fuel. 
False, Cardiac muscle uses only fatty acids & ketone bodies for fuel.
What organ contributes most to digesting proteins?
c-small intestine
The pancreas secretes typsin, chymotrypsin, elastase and carboxypeptidases in the Small intestines, at the brush border is where most digestion takes place.
Ketone bodies come from what fuel source?
Amino acids are the source of ketones, in ketone body formation. 
What is the middle ground of blood glucose level?
What cell produces glucagon and what type of cell is it?
a-D cells
c-Alpha cells
d-exocrine cells
e-endocrine cells
Glucagon is produced by alpha cells, which are endocrine cells.
In what part of the pancreas is digestive enzymes and NaHCO3 produced?
Digestive enzymes and NaHCO3 are prod. by the exocrine cells of the pancreas. 
T/F insulin decreases the exocytosis of glucose permease molecules?
F, insulin increases the exocytosis of glucose permease. 
T/F only in ketone formation is amino acids used for fuel?
False, when Glucagon is released, it in increases Protein breakdown & dec. protein synthesis, this occurs also in adipose tissue. 
Increase in glucose oxidation is seen in:
d-protein synthesis
a-during glycolysis is where glucose oxidation occurs. 
Which of these can cause Coma in diabetes? 
d-lactic acidosis 
All of these can cause diabetic coma.
On a balanced diet what is the insulin:glucagon ratio:
a-2.3 is normal for a balanced diet.
After being hospitalized for having too much fun, I found a glucose IV tracked into my arm. What will my insulin:glucagon ratio be?
Before going to the gym its recommended to ingest protein, how is this significant?
Protein ingestion makes insulin:glucagon ratio jump to 17, which remember is a growth hormone. 
All of these describe insulin except:
a-increased transport of glucose
b-inc. transport of amino acids
c-Stimulation of protein synthesis
d-inhibition of protein degration
e-inc mRNAs for Lipogenic enzymes. 
All of the above describe insulin's actions. 
Cortisol causes all except
a-increased protein breakdown
b-increase lipolysis 
c-increase gluconeogenesis in liver, acting synergistically w/epi & glucagon
d-inhibit cytokine activation/anti-inflammatory  
All are what cortisol's f(x),
Growth hormone is inhibited by:
d-none of the above
Somatostatin inhibits GH
Insulin like growth factors are released from;
b-Anterior pituitary 

IGF are released mainly from the liver.
Growth Hormone is anabolic all its processes. 
False, it is only anabolic in protein synthesis, it is catabolic in glycogen and fatty acids. 
Cortisol synthesis takes place in what tissue and has affects on what organ?
The adrenal glands is the site of cortisol production, and cortisol affects the liver inc. 4 gluconeogenic enzymes.
What is the starting molecule in hormone synthesis?
Cholesterol is the starting molecule in the synthesis of hormones. 
Pregnenolone is a steroid produced from _________ by ________.
a-pregestrone & 3B Dehydrogenase Isomerase.
b-17 alpha-Hydroxy Progesterone & 17 Hydroxylase
c-Cortexolone & 21 Hydroxylase
d-Cholesterol & Desmolase 
d-Cholesterol & Desmolase prod. Pregnenolone. 
3ß Dehydrogenase + __________ produce Progestrone. 
___________ + Progesterone produce 17 alpha-hydroxyprogesterone 
17 Hydroxylase. 
21 Hydroxylase prod. _________ from _________(in the direct cholesterol path). 
Cortexolone from 17 alpha-hydroxy Progesterone.
11 Hyrdroxylse prod. ______ in the direct cholesterol path?
Cortisol is prod. by 11Hydroxylase from Cortexolone. 
Progesterone to 18 Hydroxy Corticosterone  takes ___ ___ & _____ Hydroxylase. 
21, 11, and 18 Hydroxylase to prod. 18 Hydroxy Corticosterone from Progesterone. 
What is the starter steroid in the synthesis of Aldosterone?
d-17 alpha Hydroxy Progesterone
b-Progestrone is the starter molecule in the synthesis of aldosterone. 
How is 18 Hydroxy Cortisosterone converted to Aldosterone. 
Dehydrogenase catalyses this step. 
Where in the body is testosterone produced?
Testosterone synthesis takes place in the Testes, testosterone effects muscle mass. 
Where is estradiol synthesized?
Estradiol is synthesized in the ovary & adrenals, it targets the uterus inc. its proliferation.
How many carbons do adrenal corticosteroids contain?
Adrenal Corticosteroids are steroids with 21 carbon atoms. 
What steroids compose glucocorticoids?
Cortisol & Aldosterone. 
__________ is the only steroid with an aldehyde group @ Carbon 18. 
c-Aldosterone is the only steroid with an Aldehyde group at carbon 18. 
These steroids have 19 carbon atoms
b-adrenal corticosteroids 
c-adrenal androgens 
d-testes androgens
Only Adrenal androgens produce steroids with 19 carbon atoms. 
Produced mainly in the Testes.
C & D Testosterone & Androstenedione are produced in the testes. 
All of the following compose Adrenal androgens except, 
B, Esterone compose Adrenal estrogen an is a steroid w/ 18 carbons. 
This adrenal steroid has an A ring with a 4,5 double bond. 
The only adrenal steroid w/ an A ring w/ 4,5 double bond is Testosterone. 
This steroid has a phenolic ring. 
Estradiol is the only steroid w/ a A ring with a Phenolic ring. 
What is the primary glucocorticoid secreted by the adrenal cortex?
Cortisol is the primary glucocorticoid secreted by the Adrenal Cortex. 
How does stress produce cortisol?
Adenohypophysis->(ACTH+)->Adrenal Cortex->Cortisol
These Hydroxylase are located in the ER
a-17 & 18 Hydroxylases
b-18 & 21 Hydroxylases
c-17 & 21 Hydroxylases
d-11 & 18 Hydroxylases
c-17 & 21 Hydroxylases are located in the ER
11 & 18 Hydroxylase are located:
a- in the ER
b- @ the golgi
c- in the mitochondria
d-in the cytosol
the mitochondria is the site of 11 & 18 Hydroxylases.
Hyper-function of the adrenal glands cause & is called:
a-Cushing's Syndrome
b-Addison's Disease
c-Pineal Cancer
d-None of these
Hyperf(x) of the adrenal cortex cause moonface, virilism, and central obesity due to excess production of Cortisol & androgens=Cushing's Syndrome. 
Addison's disease =
Hypof(x) of adrenal cortex (inadequate mineralocorticoid secretion) this causes bronzing of the skin, gums first. 
Which protein transports sex hormones in the blood. 
SHBG, binds and transports Testosterone & Estradiol.
What molecule is Diethylstilbestrol analogous to?
Estradiol is the sex steroid the Diethylstilbestrol analogous to in binding to the estrogen receptor in the uterus. 
CBP/p300 have anti steroid activity how?
a-bind and restrict steroid entrance to nucleus
b-methylate DNA
c-histone acetyltransferase activity 
c-histone acetyltransferase activity is conducted by CBP/p300 to regulate steroid hormone transcription activity. 
Tamoxifen is an antiestrogen that is most useful in ....
Breast cancer patients who are positive for both estrogen and progesterone receptors. 
I am a hormone that is insoluble in H20, bind cytoplasmic receptors, act in hours, and I affect transcription. 
I am?
a-peptided hormone
c-steroid hormone
d-gas hormone
c-Steroid hormone 
How does Eukaryotic DNA replication address RNA primer removal?
Telomerase fills up 5' end, that was once a Primer. 
PCNA = ?
a-repair factor
c-processivity factor 
d-none of the above
c-processivity factor is PCNA
__________ synthesizes primer RNA and very little DNA.
b-Pol-alpha, synthesizes primer RNA & very little DNA. 
Pol Delta & Sigma are:
b-proofread through exonuclease activity
b-proofread through exonuclease activity, and interact w/PCNA
Terminal Deopxnucleotidyl transferase, viral reverse transcirptase, and viral replication  describe:
What is the equivalent of DNA Pol I in eukaryotes:
c-FEN-1, in Eukaryotes removes RNA primers. 
What is the Eukaryotic equivalent of SSB. 
c-DNA Pol I
b-RPA, is a single strand binding protein.
One strand rich in GGGGs, and CCCC rich in the other, composed of 6-10bp (2k-3K) describe:
Telomere Structure.
Telomerase extends
a-DNA at 5' end
b-degrades RNA primer & extends 3' end
c-Adds Nucleotide at 3' end
d-forms telomere strand from an RNA template
C & D, telomerase Adds Nucleotide at 3' end and forms telomere strand from an RNA template.
How does TdT differ from Telomerase?
Terminal Deoxyribonucleotidyl Transferase (TdT) adds to the 3' end of DNA, and so does Telomerase, however TdT does not need a RNA primer template, TdT does, TdT also can add to ds/ss DNA.  
In Prokaryotic RNA Polymerase, which structure finds a start point.
a-Core enzyme
c-AUG receptor
Holoenzyme is a sigma subunit that finds a starting point. 
_____________ elongates the RNA chain. 
a-Core enzyme
c-AUG receptor
Core enzyme elongates the RNA chain in Prokaryotic RNA Polymerase. 
T/F RNA polymerase elongates in the 5' - 3' direction in the positive supercoil direction. 
DNA synthesis occurs 5' to 3'. 
False, DNA is synthesized by the addition of DNTP to 3' end thus synthesis occurs 3'->5'. 
In what direction is the overall growth of DNA?
although synthesis is 3'-5', overall growth is 5'-3'
Primers for DNA/RNA sythesis must have
a-15 bases H-bonded
b-20 bases H-bonded
c-10 bases H-bonded 
d-5 bases H-bonded
c-10 bases need to be H-bonded for a primer to be functional. 
What is the function of Topoisomerases?
a-synthesize DNA
b-edit DNA
c-convert supercoiled DNA to relaxed form
d-seperate 2 parental strands of DNA
c-convert supercoiled DNA to relaxed form, is the f(x) of topoisomerases. 
Bidirectional replication occurs in:
c-Prokaryotes have bidirectional replication. 
The lagging strand:
a-has synthesis 5'->3'
b-Is begun with Short RNA primer
c-Moves in a moonwalking fashion in synthesis
d-Is slower than the leading strand.
all of the above are correct. 
In bacteria, ______ excises RNA primer & gap is filled. 
a-DNA polymerase III
b-DNA polymerase II
c-DNA polymerase I
e-RNA polymerase I
c-DNA polymerase I excises RNA primer, & fills Gaps between DNA. 
RNA polymerase is elongated by ________?
a-DNA polymerase III
b-DNA polymerase II
c-DNA polymerase I
e-RNA polymerase I
a-DNA polymerase III, elongates RNA primer. 
RNA primers are synthesized from ______.
a-RNA polymerase
b-Primase, synthesizes RNA primer. 
_________ decatenates replicated circles. 
c-Pol I 
e-Topo IV
e-Topo IV, decatenates replicated circles. 
dnaB __________
a-Ori C
b-Joins DNA ends
c-Decatenates replicated circles 
d-DNA synthesis
e-Begins unwinding 
e-Begins unwinding DNA is the job of dnaB. 
OriC is initiated by 
d-dnaA, initiates OriC
What is the replisome assembly composed of
d-Pol II
e-Pol III
A & E, Pol III and primase form the replisome assembly. 
DNA ligase needs _______ to join small DNAs. 
Both NAD or ATP serve as cofactors for DNA ligase. 
Termination of prokaryotic replication occurs at:
c-TUS factor
c-TUS factor, is the termination signal for prokaryotes. 
DNA Pol III has 5' to 3' exonulcease activity.
false, DNA pol I has exonuclease activity, but it is 3' - 5'.
ß-clamp's function....
a-DNA elongation
b-Nucelase activity 
c-Binding protein
d-equivalent to PCNA
d-equivalent to PCNA, ß-clamp is the processivity factor which increase rate and length of DNA>
T/F RNA polymerase elongates in the 5' - 3' direction in the positive supercoil direction. 
In Prokaryotic RNA Polymerase, which structure finds a start point.
a-Core enzyme
c-AUG receptor
b-Holoenzyme, is the sigma subunit that finds the start point. 
___________ elongates the RNA chain of prokaryotic RNA chain. 
Core enzyme elongates the RNA chain in Prokaryotic RNA Polymerase. 
The direction of RNA synthesis is 
c-none of the above
b-5'->3' is the direction of RNA synthesis. 
What are sigma factors and what is their purpose?
Sigma factors are prokaryotic transcription initiation factors that enables specific binding of RNA polymerase to gene promoter w/ A or G. 
Termination of RNA transcription in prokaryotes is ...
a-A & Sigma factor
b-U sequence + Hairpin + Rho factor 
c-G Sigma factor 
b-U sequence + Hairpin + Rho factor is needed for prokaryotic RNA termination. 
The promoter region recognized by RNA polymerase is
a-Pribnow box
b-TATA Box
c--10 sequence 
d--35 sequence 
all of the above, The Pribnow box=TATA box and its at -10.
Where is the start site of prokaryotic RNA transcription
The start of prokaryotic transcription is at the +1 site. 
How does Rifampin work?
Rifampin prevents RNA synthesis, by binding RNA polymerase and distorting its conformation. 
Eukaryotic promoter at TATA box is at:
D, -25 is the TATA Box site in Eukaryotic RNA. 
Eukaryotic RNA polymerase I =
RNA polymerase I = rRNA
Eukaryotic RNA polymerase III =
tRNA = RNA pol III
Eukaryotic RNA polymerase II=
mRNA = RNA polymerase II 
Which RNA polymerase is resctricted to the Nucleoli
RNA pol I/rRNA
CTF, SP1, TFIID are...
a-enhancer binding transcription factors. 
b-Transcription binding factors of Prokaryotes.
c-Transctiption binding factors of Eukaryotes. 
d-None of the above
CTF, SP1, TFIID are transctiption binding factors of Eukaryotes. 
mRNA is postranscriptionally modified by
b-methylguanosine cap
b-methylguanosine cap one of the posttranscriptional modification of mRNA. 
What are the steps of mRNA splicing?
1)-Primary transcript combines w/snRNPs (when folded=spliceosome)
2)-the 2'-OH  of the A at the branch site attacks the 5'-p at the splice donor site of exon 1.
3)-the 3'-OH of exon 1 attacks the 5'-p of exon 2 at the splice acceptor site.
What is the name of the excised intron?
Lariat = excited intron
CCA are added to all
b-tRNA ends are added CCA 
Alpha amanitin inhibits 
Pol II
Actinomycin D & Quinacrine are:
a-enzym specific drugs
b-substrate analogs
c-DNA intercalating agents
c-DNA intercalating agents
Ara - C, and Ara-A are...
Substrate analogs. 
Amino acids are not:
a-optically active
b-have a tetrahedral alpha cardon
c-Naturally occur in the D form
d-None of the above
C-, amino acids naturally occur in it L form not the D. 
Amino acid properties are determined by __________?
The side chains of amino acids determine its properties. 
Alanine(A), Valine(V), Leucine(L), Isoleucine(I), Proline(P), Methionine(M), Phenylalanine(F), and Tryptophan(W) compose what type of Amino Acid?
Alanine, Valine, Leucine, Isoleucine, Proline, Methionine, Phenylalanine, and Tryptophan compose Hydrophobic amino acids.
Hydrophilic Amino acids are composed of __________?
Glycine(G), Serine(S), Threonine(T), Cysteine(C), Asparagine(N), Glutamine(Q), and Tyrosine(Y) compose the hydrophilic amino acids. 
The two acidic amino acids contain _____ groups?
Aspartic Acid(D) and Glutamic Acid(E) compose the acidic amino acids and contain two carboxylic groups each.
Basic amino acids are?
Lysine(K), Arginine(R), and Histidine(H) compose the Basic Amino Acids because the contain more than one Basic group.
What are some rare amino acids?
4-Hydroxyproline, 5-Hydroxylysine, Desmosine, sigma-N-Methyllysine, 3-Methylhistidine, and Isodesmosine.
How do you calculate PI?
PI = pK1 + pK2/2
Where are the regions of buffering of an amino acid?
The buffering region is seen around the pKs of the amino acids.
What is the primary structure of amino acids?
 The primary structure of amino acids is
a sequence of amino acids joined together by peptide bonds.
Describe the peptide bond?
It is between N and C, and is double bond in nature. 
Beta pleated sheets, and Alpha Helix describe what about amino acids?
The secondary structure of single interamino acid structure is seen as Beta pleated sheet, and or Alpha Helix. 
What are elements of tertiary structure of proteins?
a-Disulfide bonds
b-Hydrogen bonds
c-Salt bridges
d-hyrophilic interactions
e-none of the above
f-all of the above except d
f, Disulfide bonds, Hydrogen bonds, Salt bridges and hydrophobic interactions between separate amino acids are elements of tertiary structure of amino acids.
In a triple helix amino acid, what is the stabilizing force?
The stabilizing force of a triple helix amino acid is found in the hydrogen bonding of Glycine on one chain and proline of another with 1Hydrogen bond per triplet.
Type 5 collagen is found in what tissues?
Cornea, placenta, bone, and heart valve is composed of Type 5 collagen. 
Endothelial & epithelial membranes are composed of ________ collagen.
Type 4 collagen compose Endothelial & epithelial membranes.
Type 3 collagen....
Is found in intestinal and uterine wall tissue.
Nucleus pulposus and hyaline cartilage are made up of _________ collagen.
Type 2 collagen. 
bone, tendon, fibrocartilage, dermis and cornea compose....
Type 1 collagen. 
How does one purify a protein from a cell?
a-disrupt cells
b-solubilize the protein
c-Gel filtration on Sepharose beads 
d-Ion exchange chromatography
e-Affinity chromatography 
f-All of the above
e-non of the above 
f-all the above
What process uses the size of protein to discriminate them.
Gel filtration, and SDS PAGE utilizes protein size to separate them.
In gel filtration fractionation of protein by size, you expect _______ molecules to pass 1st. 
Large molecules pass 1st, as they pass quickly. 
________ is used for For determining the the subunit composition and molecular weight of the subunit.
Chymotrypsin hydrolyzes ___________?
Hydrophobic side chains are hydrolyzed by chymotrypsin. 
Trypsin hydrolyzes:
a-Hydrophobic side chains
b-Lysine only
c-Arginine only
d-A,B, and C
e-B & C
Lysine and arginine side chains are only hydrolyzed by trypsin.
Chymotrypsin and trypsin are used in what analysis process?
a-Sanger DNA sequencing 
b-Edman degradation
d-Gel Filtration
B, Edman degradation utilizes chymotrypsin, and trypsin hydrolysis in sequencing amino acid
What is normal blood glucose concentration?
100 mg/dL or 1g/L
Hypoglycemia will result in a individual with blood glucose below ________.
Below 45mg/dL will result in hypoglycemic shock(coma).
What blood glucose concentration will result in diabetes & its diseases?
A persistent blood glucose level above 125 mg/dL will result in diabetes. 
The correct sequence of insulin processing is:
a-Proinsulin + signal peptide, C-peptide + insulin, preproinsulin
b-Preproinsulin, C-peptide + insulin, Proinsulin + signal peptide
c-Preproinsulin, proinsulin + signal peptide + C-peptide + insulin.
C- Preproinsulin, proinsulin + signal peptide (N-terminal) + C-peptide + insulin
How does insulin react with its receptor?
Insulin causes dimerization & aggregation of the receptor.
 What is the consequence of the receptor dimerization & aggregation of the insulin receptor?
The insulin receptor when dimerizes autophosphorylates effector proteins. 
Anti glucagon effects include all but:
a-inc in protein tyrosine kinase
b-Phosphoprotein phosphatase dec
c-phosphodiesterase is inc
d-GTPase is inc
d- Phosphoprotein phosphatase increase in insulin receptor activation which has anti-glucagon effects. 
Insulin recruits GLUT 1 to the plasma membrane.
False GLUT4 is stimulated by insulin to move to the plasma membrane. 
Once insulin binds to its receptor it stays there until enough glucose has been absorbed and is released from the receptor.
False, insulin undergoes receptor internalization and degradation, which leads to desensitization. 
Plasma insulin in response to oral glucose has ____ phases of synthesis.
b-2 phases of synthesis is seen in insulin synthesis. 
What is the reason behind the 1st  phase of insulin synthesis?
The 1st phase is caused by insulin secretion initiated by inc ATP/ADP ratio w/i the cell which close ATP sensitive K channels causing depolarization of the cell. This voltage change opens Ca channel, influxing Calcium causing release of insulin packaged into secretory vesicle in the golgi = Short 1st phase.
How do the two phases of insulin synthesis differ?
Phase 1= ATP dependent K and Ca induced is short. 
Phase 2=cytosolic long chain fatty acyl CoA, using Diacyl glycerol & PKC signaling, induction is prolonged. 
Diabetes is classified in ______ ways. 
4, gestational, other, Type 2, and Type 1.
Which type of diabetes is autoimmune destruction of Beta cells?
Type 1, insulin is absent here. 
After sending unheeded messages to take up glucose, I just gave up.
What cell am I?
beta cell in diabetes type 2, where insulin resistance leads to Beta cell failure. 
What type of diabetes commonly cause keto acidosis?
Type 1 Diabetes commonly cause keto acidosis. 
Which of these are most probable sites of insulin resistance in diabetes?
a-prereceptor where insulin receptor antibodies
b-decrease # of insulin receptors
c-post receptor, where defects in signal transduction, dec IRS-1 level
d-glucose transport
c-post receptor is the site of insulin resistance, where defects in signal transduction, defects in tyrosine phosphorylation, red. IRS-1 level, dec phosphatidylinositol 3 kinase, dec pyruvate dehydrogenase or glycogen synthase.
High hemoglobin A1c or hbA1c = 
High glucose concentration (hyperglycemia) which is common in diabetic patients, isulin should be administered here.  
An hbA1c of 7%  says what about the diabetic status of this patient?
hbA1c of 7% = poor control of diabetes. 
How does lack of insulin result in acidosis?
Lack of insulin induces glucagon to stimulate increased lipolysis-->increased ketogenesis-->Ketonemia-->Acidosis--> Compensetory hyperventilation. 
What is the mechanism of dehydration in diabetics?
Inc gluconeogenesis & Dec glucose uptake-->Hyperglycemia-->glycosuria-->osmotic diuresis--->dehydration. 
_______ & _______ lead to ketone body formation how?
Diabetes & Starvation lead to excess Fatty acid oxidation, 2Acetyl CoA combine to form Acetoacetyl-CoA-->ß-Hydroxy-ß-methyl Glutaryl-CoA=(HMG-CoA)-->Acetoacetate--->Acetone + CO2 and/or D-ß-hydroxybutyrate.
All of these are major long term complications of diabetes except:
e-Diabetic foot
f-Diarrhea & impotence
g-exema is not a complication of diabetes. 
In periodonatal Disease the patient posses plaque, tartar, ______ & ___.
a-inc alveolar bone length
c-reduced bone level
d-increased gingival pocket
c&d, increased gingival pocket.
t/f, pregnancy can cause periodontal disease?
In periodontal disease attachment loss & probing depth is attributable to:
a-poor hygeine
c-degree of disease
B, genetics is the main player of periodontal attachment loss & probing depth in periodontal disease. 
_______ stimulates Osteoclast progenitor with_________ & _______ to become _______.
Osteoblasts / stromal cell,  M-CSF & RANKL, Osteoclast. 
1.5 - 2 ATP is the biochemical worth of what reduced co-enzyme?
a-NADH & H+
B, FADH2 = 1.5-2ATP
Fatty acid oxidation takes place:
D, mitochondria is the site of Fatty acid oxidation. 
How does electrons enter the mitochondria from the cytosol. 
Electrons carried by NADH are transferred to the mitochondria by electron shuttles, i.e. glycerol phosphate shuttle and malate-apartate shuttle. 
How does the glycerol phosphate shuttle work?
In the cytosol, 1) glycerol 3-phosphate dehydrogenase  catalyzes reduction of Dihydroxyacetone phosphate by NADH, 2)-Glycerol Phosphate catalyzes transfer of electrons from Glycerol 3-Phosphate to FAD. 3)-Reduced FAD is oxidized by complex 2 in the electron transport chain. 
How does the Malate-Aspartate shuttle work?
1-Oxaloacetate is converted to Malate by Cytosolic malate dehydrogenase & NADH + H+, Malate enters the mitochondrial matrix reacting with NAD+ & Mitochondrial malate dehydrogennase producing NADH+ H+ and Oxaloacetate, NADH &  H+ enter the electron-transport chain. Oxaloacetate leaves the matrix by entering Amino transferase with Glutamate to produce Alpha-ketoglutarate & Aspartate which can both leave the matrix.
How much energy does anaerobic glycolysis produce?
Anaerobic glycolysis produces 2 ATP and 2 molecules of Lactic acid. 
Hydrolase activity is seen in what organelle?
d-plasma membrane
Lysosomes are the sites of hydrolase activity. 
Oxidation of very long fatty acids occur in the mitochondrion. 
False, long fatty acids are oxidized in peroxisomes, i.e. perioxidation. 
Protein synthesis occurs in what organelle?
The ER is the site of protein synthesis and xenobiotic metabolism.
The complete oxidation of glucose to CO2 = ?
2 ATP, 2GTP, 10NADH, and 2FADH
The golgi is the site of ________ & _________.  
Glycosylation & sulfation
What is the bioenergetic worth of Reduced coenzyme = NADH?
NADH = 2.5 - 3 ATP
The mechanism of irreversible inhibitors are through _________. 
Covalent binding at the active site of enzyme is the mechanism of Irreversible inhibition of enzymes. 
In drug design competitive inhibitors increases both Km and Vmax.  
False, only Km is increased by competitive inhibition not Vmax. 
para-aminobenzoic acid (PABA) is used in function as a coenzyme in the conversion of certain chemical intermediates to purines. What is PABA's competitive inhibitor.
PABA is inhibited by Sulfanilamide which is its anti-metabolite.
Adenine is competitively inhibited by?
Anti-cancer therapy through competitive inhibition of dihydrofolate reductase is produced by.....
Methotrexate is the competetive with 5,6,7,8-Tetrahydrofolate in inhibiting Dihydrofolate reductase. 
Collagenase competitive inhibition for the control of periodontal disease is performed through what drug?
Doxycycline competitively inhibits collagenase.
Mozenavir & Tipranavir are drugs given to ______?
Treat HIV, through competitive inhibition of HIV protease.
Xanthine oxidase is the enzyme made famous by its participation in gout, its inhibited by:
E, Allopurinol inhibits xanthine oxidase competitively. 
The Km on the graph of an enzyme that is competitively inhibited would _________?
increase to the right in a normal graph, but will become more negative in the linweaver-burke plot.
In a noncompetitive inhibition, how would the graph Vmax and Km look?
In a noncompetitive inhibition, only Vmax is shifted, in the normal plot it is shifted downward(dec) in the Y-axis, in the lineweaver-burke plot 1/Vmax is shifted upward on the y axis. Km & 1/Km remains the same. 
Flouride is a ____________ inhibitor of enolase.
Flouride is a non-compeptitive inhibitor. 
Non-nucleoside drugs are inhibitors of what type of HIV RT?
Non-nucleoside drugs are non-competitive inhibitors of RT. 
Penicillin is an example of a non-competitive inhibitor.
False, Penicillin & Amoxicillin is an irreversible inhibitor of glycopeptide transpeptidase where the reactive peptide  bond on the Beta-lactam ring causes the covalent bond of irreversibility. 
Augmentin is composed of what drugs, what do they do?
Amoxicillin and Clavulinic acid compose Augmentin, Amoxicillin is an irreversible inhibitor of glycopeptide transpeptidse, and Clavulinic acid irreversibly inhibits Beta-lactamase.
Elastase is significant how?
It is the protein that is pivital in Emphysema that is inhibited irreversibly no more by deficient Alpha 1 antitrypsin. 
Aceytcholinesterase is irreversibly inhibited by________?
Sarin (Nerve gas) irreversibly inhibits acetylcholinesterase. 
5-Fluorouricil is an irreversible inhibitor of:
b-glycopeptide transpeptidase
c-dihydrofolate reductase
d-thymidylate synthetase
d, thymidylate synthetase is one target for anti-cancer therapy where 5-Fluorouracil irreversibly binds it.
Chronic Periodontitis is treated by 
d, minocycline is an enzyme inhibitor used clinically to treat chronic periodontitis. 
True/False Ribozymes are proteins?
False, Ribozymes are non-protein enzymes. 
What enzyme lowers the activation energy of respiration and how?
Carbonic Anydrase lowers the activation energy of respiration in the lungs by converting bicarbonate and H+ to CO2 & H2O. In repsiring tissue CA converts CO2 & H2O into bicarbonate and H+.
What reaction does Carbonic Anhydrase catalyze in respiratory tissue?
CA catalyzes CO2 and H2O into HCO3+ and H+.
How does specific activity differ from turnover number of enzyme?
both calculate mole of substrate converted too product by specific activity = per unit time/mg protein, and turnover # = per mole of active site.
What is a holoenzyme composed of?
Holoenzyme is active form of an apoenzyme that has bound its coenzyme. 
How do coenzyme and cofactors affect the inactive enzyme to make them active?
Coenzymes and cofactors alter the conformation around the active site of the enzyme activating it. 
What is the activation energy?
Activation energy is the energy required to convert 1 mole of substrate to the activated complex.
_________ is the sole determinant whether the reaction will proceed in the direction written.
Free Energy, is negative for spontaneous reaction.
Standard free energy change can be used to_________?
Determine Keq., is zero when Keq=1, and neg. when Keq < 1. 
How do you calculated the free energy?
Free energy = Standard Free Energy + 2.303RT x log[P]/[S]
Proteolytic cleavage of _____  leads to active enzymes.
Proenzymes/zymogens, e.g. pepsinogen to pepsin, & coagulation cascade; fibrinogen ->fibrin. 
A covalent modification of a protein that may increase or decrease its activity is _______
Phosphorylation by Kinases or dephosphorylation by Phosphatases covalently modify proteins. 
PKA activation by cAMP is an example of:
a-Covalent modification
b-Protein-protein interaction
c-proteolytic cleavage
d-none of the above
Protein-protein interaction is seen in PKA activation by cAMP. 
__________ is an enzyme that is inhibited by end product. 
Allosteric enzymes are enzymes that usually begin a cascade of reactions where end product neg. feedbacks by allosterically inhibiting the enzyme. 
Which is not correct about allosteric enzymes?
a-can be down regulated by allosteric inhibitors @ constant [S]
b-follows MM kinetics
c-contain 1 polypeptide chains
d-none of the above
b-allosteric enzyme does not follow MM kinetics.
What enzyme show allosteric behavior?
Hemoglobin is classic allosteric enzyme, which shows positive cooperativity, and sigmoid kinetics. 
A high plasma concentration of Asn/Apsaragine is seen in what condition?
High plasma Asparagine is seen in Leukemia patients. 
Km is a property of the concentration of E & S.
False, Km is the property of only ES complex.
Km is a ratio of _____? 
The mechalis constant is a ratio of the rate constants of            K1
                            E + S ---> ES ---> P
                                    <---        K3
Where k2 + k3/k1 =Km=[S] @ 1/2 Vmax
The efficiency of catalysis is measured by what ratio?
Efficiency of catalysis = Vmax/Km
The Enzyme-Substrate complex is describe by.....
The Michaelis-Menten Equation describes the formation of ES complex, where the maximal velocity when enzyme is saturated with substrate times Substrate concentration divided by the Michaelis constant plus Substrate.
Vmax is directly proportional to:
c-ES complex
D, Vmax is directly proportional to the concentration of Enzyme concentration. 
What are the steps of enzyme, substrate relation?
Enzyme + Substrate leads to Enzyme-Substrate complex leading to Enzyme + Product.
What happens in the brain and liver when ATP is at 1.0mM?
In the liver glucose will be oxidized at 25%, in the brain 100%.
What is the Lineweaver-Burke plot?
Lineweaver-Burke plot describes the behavior of E-S complex like the mechalis menton equation, however its inverted. 
The equations = 1/v =(Km/Vmax)(1/[S]) + 1/Vmax
What is the wrong characteristics of enzyme kinetics?
a-enzyme activity increase with the concentration of substrate.
b-enzyme activity increases with concentration of substrate to a point then acts independent of [S].
c-Enzyme activity increase as
E, only Enzyme activity increases with concentration of substrate to a point then acts independent of [S].
Where is the Km & Vmax in the Lineweaver-Burke plot?
Vmax, or rather where 1/Vmax is located on at the X-intercept at the 1/S value of O. 
1/Km is located where the Y-intercept is 0.
Excess oxidation of fatty acids during starvation & diabetes = 
Formation of ketone bodies.
The need for oxidation of fatty acid does not begin:
a- when running more than 100 yards.
b-extended aerobics
c-by Heart muscle
d-during starvation
e-by diabetics w/low glucose metabolism.
f-when brain ATP is low
F-when brain ATP is low. 
What is fatty acid oxidation?
Fatty acid oxidation is the mobilization of fatty acids and there activation in the cells, transporting them to mitochondria and oxidation, excess oxidation =ketone bodies.
How is fat mobilized from adipose?
Glucagon binds to its receptor on adipose cells stimulating---> Adenylate cyclase producing cAMP-->PKA--->activating Hormone Sensitive Lipase to Phospho-HSL hydrolyzing Triglyceride producing Glycerol & Fatty acid which is release into blood. 
How is fatty acid removed from albumin to get inside cellular mitochondria?
Fattyacyl CoA synthetase uses ATP & CoA to cleave Fatty Acid - FABP complex producing Fattyacyl-SCoA which enters mitochondria from cytosol. 
Oxidation of fatty acids occur in the:
b-Inner mitochondrial membrane
d-outer membrane
c-fatty oxidation of fattyacyl-CoA occurs in the Matrix.
Where happens when Fatty acyl CoA meet Carnitine Palmitoyl Transferase (CPT1)?
Fatty acid is converted into Fatty Aylcarnitine in the intermembranous space.
Where is Fatty acyl CoA is produced?
In the outer mitochondrial membrane lies Acyl CoA synthetase takes ATP + CoA + Fatty acid producing Fatty acyl CoA in the cytosol and is transferred into the intermembranous space. 
What process does it take for Fatty acylcarnitine to traverse the inner mitochondrial membrane and enter the the matrix?
Fatty acylcarnitine reacts with Carnitine acylcarnitine translocase which translocates it to the matrix.
In the matrix, Fatty acylcarnitine reacts with ____________ in the inner mitochondrial membrane producing Fatty acyl CoA, releasing Carnitine. 
Carnitine palmitoyl transferase 2 (CPT2). 
How many ATPs are produce for each cycle of ß-oxidation of Fatty acids?
2 ATP for FADH2 & 3ATP for NADH = 5ATP/cycle of ß-oxidation.
The production of 8 acetyl coA is produced in ___________ cycles.
7 cycles of ß-oxidation produces 8 acetyl CoA. 
Carnitine deficiency is results in...
Lipid deposits in muscles and fatigue. 
Hereditary fatty acid disease leading to extreme fatigue, perspiration, vomiting, coma, and death. 
Medium chain fatty acyl CoA dehydrogenase (MCAD)
CPT2 is the rate limiting enzyme in fatty acid oxidation and is inhibited by Propionyl CoA. 
False, CPT1 is the rate limiting enzyme and is inhibiting by Malonyl CoA. 
In Fatty acid regulation Hormone Sensitive Lipase activity is increased by:
B & C, Epi and Glucagon increase HSL activity. 
What is gp120?
Envelope protein on HIV connected to gp41; binds host CD4 antigen 
What are the Inner layer HIV proteins?
p17 Matrix protein & p24 Capsule protein
Where is p24 capsule protein located in HIV?
Surrounds reverse transcriptase and RNA molecule
Gag encodes ________, __________, _________.
Matrix, Capsid, Nucleocapsid proteins 
Pol encodes _________, _________, ___________?
Protease, Reverse Transcriptase, and Integrase protein
Env encodes _________, __________, ___________?
Encodes GP160, which encodes Gp120 & Gp41
Non-structural Genes in HIV are?
HIV genome produce...
Encodes 9 ORF, 15 proteins
TAT protein serves as?
TAT  f(x) as an anti-terminator of transcription.
NEF does what?
NEF down regulates CD+ antigens & induces cytokines. 
CCR5 is a protein used by macrophage to do...
CCR5 is employed by macrophage -tropic HIV in early stages (unclear) 
CXCR4 (fusin) function in what way?
CXCR4 is a G-protein-coupled receptor promoting infection fusion of CD4+ T cells.
CCR2 is a receptor that?
CCR2 is a Co-receptor, where mutation results in long term survival of HIV patients.  
CCR5 is ?
binds to chemokines-RANTES, MIP1a, MIP1b, suppressing HIV's ability to infect cells, two copies of defective gene confers immunity from HIV infection; single results in delayed AIDS progression
Heperan Sulfate in HIV functions as?
A macrophage proteoglycan the binds Gp 120
CD91 ?
Antigen on Macrophage that interacts w/HSP acquired by HIV
What are DC-SIGN proteins?
DC-SIGN on macrophages recognises and binds to mannose type carbohydrates, a class of Pathogen associated molecular patterns PAMPs commonly found on viruses, bacteria and fungi. This binding interaction activates phagocytosis
Galactocerebroside Receptor is used by HIV how?
Galactocerebroside Receptor are used to infect non CD4 cells in brain and intestine. 
RT Inhibitor Drugs - Nucleoside?
Competitive inhibitors, DNA chain terminators = AZT, DDI, 3TC 
RT Inhibitors Drugs - Non Nucleoside?
non competitve inhibitors = Nevirapine, Delavirdine, and efavirenz
NonNucleoside (Viramine, BIRG-587)
NonNucleoside (Rescriptor)
NonNucleoside (DMP266, Sirstiva) 
Azido -2,3 dideoxythymidine?
Nucleoside class, (Zidoudine, Retrovir)
Nucleoside class (Didanosine, Videx)
Nucleoside class (Lamivudine, Epivir)
AZT mechanism?
AZT is phosphorylated b/c AZT-triphosphate, 2nd its incoporated into viral genome & blocks synthesis b/c 3' phosphate ester can't be formed
Protease Inhibitors work on HIV how? 
they act as analogs binding to active site of viral protease. 
HIV Protease Inhibitors? 
Saquinavir (SQ), Ritonavir, HAART, 
Nucleotides come from which glycolytic intermediate?
Glucose 6 Phosphate
Fructose 6 phosphate forms what compounds?
Amino sugars, glycolipids, and glycoproteins are formed from F6P.
Lipids are derived from _________?
a-amino sugars
b-Glyceraldehyde 3 Phosphate
d-dihydroxyacetone phosphate
Dihydroxyacetone phosphate form lipids.
_____________ forms amino acids & pyrimidines.
a-dihydroxyacetone phosphate
b-fructose 6-phosphate
d-glucose 6-phosphate
c-Phosphoenolpyruvate composes amino acids and pyrimidines. 
In glycolysis, serine is derived from Glyceraldehyde 3 phosphate.
False, 3-phosphoglycerate precedes serine.
alanine is derived from what glycolytic product?
Pyruvate is converted to alanine. 
Oxaloacetate is the source of ....
aspartate, purines, and pyrimidines. 
Succinyl CoA forms __________.
Heme & chlorophyll are derived from Succinyl CoA. 
Glutamate and purines are derived from alpha-ketoglutarate.
True, alpha-ketogluterate forms glutamate and purines.
Fatty acids are derived from succinyl CoA. 
False, citrate are the originators of fatty acids.
Pyruvate Carboxylase produces...
Oxaloacetate is produced by pyrvate carboxylase & CO2.
Pantothenate is a vitamin precursor that forms what carrier molecule?
Coenzyme A is formed from Pantothenate, it carries Acyl. 
pH = 
pKa + log [conjugated base]/[acid] 
or -log[H+]
Phopholipids are similar to triglycerides except for containing a polar head.
False in addition to containing a polar phosphate head, phospholipids contain two fatty acids bound to glycerol backbone.
Phosphatidate is the group carried by what carrier molecule?
Citidine diphosphate diacylglycerol is the carrier molecule of Phosphatidate. 
Proteins are ingested from food to use what?
Proteins are a source of amino acids. 
Pyruvate binding to ___________ to form Oxaloacetate is an example of ___________ reaction. 
Carbon Dioxide, Ligation reaction via Pyruvate carboxylase. 
Riboflavin = vitamin B2 is a precursor to what carrier molecule?
FADH2 and FMNH2 is formed from Vitamin B2, both of which carry electrons.
Stearic, oleic, and palimitic acids consists of 18 carbons.
False, Stearic and Oleic acids contain 18 carbons with Oleic acid containing 1 double bond. Palmitic acid contains 16 carbons.  
Sucrose is broken down into?
Glucose and Fructose (5carbon).
T/F D-Glucose is a reducing sugar.
True, D-glucose is a reducing sugar. 
T/F phosphorylation inactivates glycogenesis?
True, phosphorylation inactivates glycogenesis
True/False as Bicarbonate concentration increases pH dec.
False, as  Bicarbonate concentration increase like during a meal to about 30mM, the pH rises to 7.46. 
True/false insulin operates through phosphorylation mechanism?
False, Insulin operates through dephosphorylation mechanisms activating glucogenesis. 
Uridine diphosphate glucose is the carrier protein of ___________?
Glucose, is the carrier molecule of UDP glucose.
Vitamin B1 / Thiamine is the precursor of what carrier molecule?
Thiamine pyrophosphate is the carrier molecule of aldehyde which is formed from Vitamin B1/Thiamine. 
What are some reducing sugars?
Maltose, D-glucose, and lactose are reducing sugars. 
What does a peptide bond consist of?
The peptide bond consists of CO-NH.
What does Folate vitamin precursor form?
Tetrahydrofolate is the activated form of vitamin folate, it carries one Carbon. 
What does S-Adenosylmethionine serve as?
S-Adenosylmethionine is a carrier protein for a methyl group. 
What enzymes execute hydrolytic reactions and where are they performed?
Hydrolytic reactions are performed by peptidases at the site of peptide bonds on the C-N site.
What is considered the futile cycle?
The futile cycle is when both synthetic and degradative occur at the same time, this causes wasteful hydrolysis of ATP. 
What is glycogen composed of?
Glycogen is a polysaccharide of glucose which bonded by alpha 1-4, and alpha 1-6 links. 
What is Lactose composed of?
Glucose + galactose = lactose
What is the buffer in the oral cavity?
Bicarbonate is the buffer in the oral cavity, its concentration is 1.3mM
What is the catabolic fate of glucose under aerobic conditions?
Glucose under aerobic conditions is catabolicaly converted to Pyruvate. 
What is the composition of Maltose?
Glucose + Glucose = Maltose
What is the composition of Triglycerides?
Triglycerides are composed of glycerol backbone attached to 3 fatty acid chains. 
What is the fate of Pyruvate during non-strenuous exercise?
Because non-strenuous exercise is aerobic, pyruvate would be converted into Acetyl CoA. 
What is the fate of Pyruvate during strenuous exercise?
During strenuous exercise under Anaerobic conditions Pyruvate is converted to Lactate.
What is the pH of saliva during non meals around 2mM?
pH around 2mM is 6.3.
What type of enzyme prosecutes the Addition & Removal of functional groups to double bonds?
Lyases execute the addition and removal of functional groups to double bonds, e.g. Aldolase in taking Glyceraldehyde 3-phosphate & Dihydroxyacetone phosphate to produce Fructose 1,6-bisphosphate.
when [A-] = [HA] ....
pH = pKa
When ________ is high _______ pathways are inhibited.
When ATP concentration is high, degradative pathways are inhibited. 
When oral pH rises due to dental plaque how does the buffering system react?
Carbonic anhydrase 6 produced by the acinar cells of the parotid glands converts bicarbonate to neutralizes the acid by producing CO2 and H2O. 
• transformation of nutrients 
• excretion of waste products 
• energy transformations 
• synthetic and degradative processes
are summed up in what process?
What is the amount of calaries does the hydrolysis of ATP yield?
The Standard change in Free energy that hydrolysis yields is 7300 calories.
-0.32 volts is the standard redox potential of:
b-1/2 O2/H2O
NAD+/NADH has a standard redox of -0.32 volts, Oxygen is much less at +0.82 volts.
Where does oxidative phosphorylation take place and what are it's 1st step?
Ox Phos takes place in the inner membrane. In oxidative phosphorylation,
1-NADH reduces FMN of NADH-CoQ reductase complex giving it 2e-, 4H+ go from matrix goes to the intermembrane space. The electrons are transfered w/i the complex from FMN to Fe-S, these electrons are transferred to CoQ. 
Oxidative phosphorylation Alternative 1st step is?
At Succinate-CoQ Reductase complex, where Succinate reduces this complex producing Fumarate, and transferring 2e- to FAD then Fe-s then CoQ. FADH2 also reduces this complex prod. 2e-. 
How does the FADH2 reduction of Succinate-CoQ reductase complex differ than that of Succinate reduction?
Succinate reduction transfers electrons from FAD->Fe-S->CoQ, however FADH2 transfers electrons straight to Fe-S.  
What does CoQ do with the electrons it's received from Fe-S from Succinate, FADH2, or NADH?
CoQ when it receives the 2e- from the electron carriers will pick up 2H+ from the matrix before moving to the next stop of this chain, which is at the CoQH2-cyt c reductase complex. 
What occurs at the CoQH2-cyt c reductase complex?
This is the 2nd step, where At the CoQH2-cyt c reductase complex CoQ delivers the 2e- to Cyt b, this causes it to release 2H+ from the matrix into the intermembrane space, the electrons are then transferred through Fe-S to Cyt c1, which transfers it to Cyt C.
Why does CoQ pick up 2H+?
It picks 2H+ b/c only neutral molecules can move freely w/i the inner membrane, it releases these 2H+ once its reached the CoQH2-cyt c reductase complex.
What does Cyt c do with the 2e-?
This is the 3rd step, where Cyt c transports the 1e- to the Cytochrome c oxidase complex, specifically to Cu subunit.
How many electrons can Cyt c carry?
In the 3rd step of Ox phos, _______ transfers electrons to Cyt a. 
Cu subunit transfers electrons to Cyt a, Cyt a transfers 2e- to Cyt b-Cyt a3 complex this causes 2H+ to shoot out of the complex from the matrix. 
The transfer of electrons to Cyt b-cyt a3 is the ________ step at the Cyt c oxidase complex?
The transfer electrons to Cyt b-cyt a3 is the 2nd to last step before, Cyt b-cyt a3 transfers 2e- to 1/2 O2 & H2 to produce H2O.
What happens to the all the H+ that has been building on the intermembranous space?
Some will combine with OH produced by the OH/HPO4 antiport, most will go to drive the ATP synthase enzyme (3H+) down its concentration gradient.
_________ takes ADP & HPO4 & _________to produce ____________.
ATP synthase take ADP & HPO4 & 3H+ to produce ATP & OH in the matrix, which is shuttled out the ATP/ADP antiporter. 
Antimycin A inhibits:
a-complex 2
b-complex 3
c-complex 1
d-complex 4
Complex 3 is inhibited by Antimycin A.
Complex 4 is inhibited by Oligomycin. 

False, carbon monoxide and cyanide inhibits
complex 4. 
Binds and inhibits ATP synthase aka Complex 5. 
Rotenone inhibits CoQH2-cyt c reductase complex. 
False CoQH2-cyt c Oxidase complex is complex 4 which is inhibited by CO & CN-.
Rotenone inhibits NADH-CoQ complex aka Complex 1.

Complex 3 =?
CoQH2-cyt c reductase complex is complex 3 which is inhibited by Antimycin A.
What affect would poisoning your arch enemy with Atractyloside do?
Atractyloside inhibits ATP:ADP Translocase/antiporter preventing ATP synthesis. 
How does brown adipose make heat?
It uses an uncoupler of Ox Phos which uses 2,4 dinitrophenol & thermogenin which dissipates proton gradient on inner membrane thus preventing ATP synth, but allowing energy release as heat.
Lebers Hereditary optic neuropathy & Leigh syndrome are....
Caused by hereditary defect in ox. phos which results in lactic acidosis & muscle & nerve pathology. 
This process provides reduced NADP for synthetic reactions and reduces glutathione?
Pentose Phosphate Pathway.
I have alpha 1-4, & branch points at alpha 1-6 at every 8-12 alpha 1-4 links.
I am Glycogen, I have glucosyl residues joined by glycosidic links. 
Amylo 1-4->1-6 Transglucosylase  form?
Branch points are formed by this branching enzyme.
The transfer of glucose from UDP-glucose to glycogen forms:
a-alpha 1-6 links
c-alpha 1-4 links
C- Alpha 1-4 links, which is executed by Glycogen synthase. 
Glucose 6 Phosphate becomes Glucose 1 Phosphate by ______.
Phosphoglucomutase catalyzes the reversible product of G1P. 
Which of these two proteins are inactivated by kinase activity?
a-glycogen synthase
c-glycogen phosphorylase 
d-UDP-glucose pyrophosphorylase
A & B Glycogen synthase is halted by kinase phosphorylation (due to Epi/Glucagon)  preventing formation of new glycogen, however it activates glycogen cleavage by glycogen phosphorylase cleavage.
PFK2 usually inhibits gluconeogenesis but when PKA is high due to glucagon, its not. 
Ca in muscle stimulates _____ during contration.
Glycogen phosphorylase is activated via Ca binding to the calmodulin subunit of Phosphorylase kinase causing glycogen degradation.
During strenuous exercise how is glycogen broken down?
AMP produced during anoxia & ATP depletion activates glycogen phosphorylase. 
What are the oxidative reactions of the Pentose Phosphate Pathway?
G6P to 6-Phosphogluconate to Ribulose 5-Phosphate, catalyzed by NADP+, G6P Dehydrogenase & 6 Phosphogluconolactone hydrolase, and NADP+, 6 Phosphogluconate dehydrogenase.
Phospentose epimerase converts  ___________ into Xylulose 5-phoshate. 
Ribulose 5-Phosphate, which precedes Glyceraldehyde 3 Phosphate by Thiamine Pyrophosphate & Transketolase. 
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