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USMLE Biochem
USMLE Step 1 Biochemistry
| Question | Answer |
|---|---|
| What changes a cytosine into a uracil? | a Deaminase |
| Which base nucleotides contain an extra amino group? | AdenineCytosine |
| Which base nucleotide has an extra methyl group? | Thymine(THYmine = meTHYl) |
| What are the purines?Pyrimidines? | Purines: Adenine & Guanine (PURe As Gold)Pyrimidines: Cytosine, Uracil & Thymine (CUT the Py) |
| How does Methyltrexate work on DNA? | prevents changing a uracil to a thymine |
| If a sample of DNA has 10% G, how much is the T %? | 10% G + 10% C = 20%therefore 80%/2 = 40% T |
| Which DNA has a higher melting point?Why?Define melting point. | CG bonds They have a triple H-bondMelting point = 50% double-stranded & 50% single-stranded DNA |
| What is the charge of Histones?What 2 AA are histones abundant in? | PositiveArginine & Lysine |
| what causes chromatin to be tightly packaged?Name of this type of chromatin? (active or inactive)If it is not packed tightly, what is it sensitive to? | H-1Heterochromatin - inactivenucleases |
| Endonuclease activation and chromatin fragmentation are characteristic of cell death by apoptosis. What nucleic cell structure would most likely be degraded first in an apoptotic cell? | 10 nm fiber(this is the chromosome without the H-1; fiber b/t a nucleosome) |
| number of origins the prokaryote and eukaryote can begin with regarding DNA replication? | Pro - oneEu - many |
| What is the same structure in DNA and RNA synthesis? | both require a DNA template |
| Something that helps attach nucleotides via a PDE bond to make a new nucleic acid | Polymerase(Polymer = glue) |
| What is needed to begin DNA synthesis?RNA synthesis? | DNA: RNA primerRNA: nothing |
| What has the ability to proofread DNA?How and in what direction? | DNA polymerase III3' -> 5' Exonuclease |
| What recognizes the Origin of replication in a prokaryotic and eukaryotic cell? | Prokaryotic: DNA A proteinEukaryotic: nothing |
| Unwinds DNA in Prokaryotic and eukaryotic cells?What does it require? | Helicase(requires ATP) |
| What stabilizes unwound template strands of DNA? | SSB(Single-stranded DNA-binding protein) |
| What synthesizes RNA primers? | Primase |
| Responsible for synthesis of Leading strand of DNA in the prokaryotic cell? Eukaryotic cell? | Pro: DNA polymerase IIIEu: DNA polymerase Delta |
| Responsible for synthesis of Lagging strand of DNA in the prokaryotic and eukaryotic cell? | Pro: DNA polymerase IIIEu: DNA polymerase Alpha |
| What is responsible for the REMOVAL of RNA primers in prokaryotic cells? In what direction/activity? | Pro: DNA poly I 5' -> 3' exonuclease activity |
| What is responsible for replacement of RNA primer w/ DNA? | DNA poly I |
| Joins Okazaki fragments | DNA ligase |
| Removes positive supercoils ahead of advancing replication forks? | DNA topoisomerase II |
| Synthesis of telomers in prokaryotic and eukaryotic cells? | Pro: not required (circular)Eu: Telomerase |
| What requires an RNA template to direct the synthesis of new DNA? | RNA-dependent DNA polymerase(Reverse Transcriptase) |
| DNA repair have two main enzymes that do all the REPAIR work...what are they? | DNA polymeraseDNA ligase |
| What excises thymine dimers? | Excision endonuclease |
| What phase of cell cycle does a mismatch base problem occur?What phase is it fixed? | Occurs: SFixed: G2 |
| What is used to proofread human DNA? | 3' -> 5' Exonuclease activity of DNA poly Delta |
| What do each of the (3) eukaryotic RNA polymerases make? | RNA poly I: rRNARNA poly II: mRNA, hnRNARNA poly III: tRNA, 5S rRNA |
| What DNA strand should you assume the boards mean if it is not labeled? | Coding strand(strand you will build a template strand from) |
| During RNA synthesis, the DNA template sequence TAGC would be transcribed to produce which of the following sequences? | GCUA(always write in 5'->3' direction) |
| What initiates the promoter in the prokaryotic cell?What may be required to terminate transcription? | intiate: Sigmaterminate: Rho + stem & loop (or UUUUU + stem & loop) |
| What is the initiation codon on the CODING strand of a transcription unit? | ATG(corresponding to AUG RNA) |
| What does the promoter consist of in a prokaryotic cell?What is the "number" of the starting site? | (-35) sequence & (-10) TATAATstarting site: +1 |
| What does the promoter consist of in a eukaryotic cell? (2)What binds the promoter? | (-70) CAAT + (-25 TATA box) Transcription Factors |
| What is the portion just before the initiation codon of a prokaryotic cell called? What recognizes this? | Shine-Dalgarno sequence16S RNA of prokaryotic ribosome |
| What is the term referred to as the creation of a single protein?What type of cell does this? | monocistronicEukaryotic (polycistronic is prokaryotic) |
| 3 posttranscriptional processing steps for eukaryotics | 1. 5' Cap (7-MeG)2. 3' poly-A tail3. removing interons w/ splicesome |
| where does transcription and translation occur in the eukaryotic cell? | transcription - nucleustranslation - cytoplasm |
| define:TransitionTransversion | Transition - purine for purineTransversion - purine for pyrmidine |
| Mutation type in DNA that creates a new codon | Missense |
| Mutation type in DNA that creates a stop codon | Nonsense |
| 3 stop codons | UGA (U Go Away)UAA (U Are Away)UAG (U Are Gone) |
| What type of genetic problem is caused by a deletion or addition of a single base? | Frameshift mutation |
| blood problem that is a result of a large segment deletion | alpha-thalassemia |
| blood problem that is the result of a splicing of the donor or acceptor sites (beginning of interons/exons) | beta-thalassemia |
| What is responsible for accuracy of the amino acid selection along with tRNA?what is needed to activate this? | Aminoacyl-tRNA2 high-energy ATP bonds |
| What does the UCG anti-codon code for? | CGA (remember to read anti-codon backwards: 5'->3') |
| What is the bond between two amino acids called? Where does this form? | peptide bond occurs in the ribosome |
| What is the anti-codon for the start codon? | CAU |
| What site in the rRNA does the tRNA bring the AA to? What amount of energy is needed to translate a protein? | A-site (acceptor) 4 GTP |
| Describe the 4 levels of protein shape | Primary - Amino Acids Secondary - folded AA into a-helix or b-sheet Tertiary - 3-D the secondary structures Quarternary - multiple subunits (ex - Hb: 2a2b) |
| Why is there "rough" ER? | N-terminus (NH2) of newly translated protein is hydrophobic, so the rRNA will move to and attach to the ER to complete translation within the ER |
| What does the golgi do to the new protein? | adds sugars to the N-terminus |
| What AA does the golgi add N-oligosaccharides to? O-oligosaccharides? (2)* | N: Asparagine O: Serine and Threonine |
| What does the golgi do if it wants to send the new protein to the lysosomes? | Adds Mannose-6-Phosphate via phosphotransferase |
| Dx: protein creation problem that accompanies the signs of coarse facial features, gingival hyperplasia, joint immobility, growth/psychomotor retardation, cardioresp failure in first decade. What is missing in protein creation? | Dx: I-cell disease Missing: Phosphotransferase (can't send proteins to lysosomes) |
| 2 cells rich in RER | Goblet cells of the GI Ab-secreting Plasma cells |
| What cell organelle is responsible for steroid synthesis? What else is it responsible for? | Smooth ER also responsible for: detoxification of drugs and poisons |
| Covalent modification to proteins by adding 2 negative charges to allow calcium to bind. What important function uses this method? What drug prevents this? | Gamma-carboxylation Clotting factors 2, 7, 9, 10 (Warfarin prevents gamma-carboxy) |
| Most prevalent AA in collagen? Two other common AA in collagen? | Glycine Proline & Lysine |
| Where does hydroxylation of preprocollagen occur? What is hydroxylated? What cofactor is needed for it to occur? | Proline & Lysine are hydroxylated in the ER Vitamin C is required |
| What occurs to collagen after it is hydroxylated? In what part of the cell? What is formed here? Name? | Glycosylated in Golgi Triple helix (Procollagen) |
| Following glycosylation of collagen, what is the next step and alteration of the structure? What is it now called? | Procollagen is secreted from the cell. Then terminal ends are cleaved. Then called: Tropocollagen |
| What is needed to make the tropocollagen into fibrils and stabilizes this structure? (2) | Lysyl Oxidase & Copper |
| (4)* Collagen synthesis deficiencies | SOME: 1. Scurvy 2. Osteogenesis Imperfecta 3. Menkes Dz 3. Ehlers-Danlos |
| Dx: Petechiae, ecchymoses, bleeding gums, poor wound healing, poor bone development Deficiency? | Scurvy Deficiency: hydroxylation of collagen deficiency secondary to lack of Vit-C |
| Dx: Skeletal abnormalities, multiple fractures, blue sclera | Osteogenesis Imperfecta |
| Dx: Hyperextensible, fragile skin, hypermobile joints, vericose veins, arterial and intestinal ruptures Deficiency? | Ehlers-Danlos Deficiency: Lysine hydroxylase collagen deficiency secondary to lack of copper |
| To compare collagen counts of several tissues, what could be measured? | hydroxyproline or hydroxylysine (not Glycine--b/c it's prevalent in other tissues) |
| Dx: 6 month infant has fractured rib; subdural hematoma; thin, colorless, tangled hair; low serum copper; developmental delay. What enzyme is deficient? | Menkes disease Lysyl Oxidase in collagen metabolism, which requires copper |
| What do pseudomonas and diphtheria toxins inhibit in eukaryotic translation? | eEF-2: translocation factor |
| What sequence is found at the 3' end of the tRNA? | CCA then the Amino acid |
| What intermediate is formed by the splicing of the interons out of the mRNA transcripts? What facilitates the splicing? | Lariat-shaped intermediate snRNA ("Snurp") facilitates |
| With the lac opeon, what is on/off if only glucose is present? Only Lactose? Both? When is Z, Y, A made? | Glucose: Repressor-ON; CAP-OFF Lactose: Repressor-OFF; CAP-ON (Z, Y, A, made) Both: Repressor-OFF; CAP-OFF (glucose causes CAP off and Lactose causes Repressor off) |
| What favors gene expresson--histone acetylases or deacetylases? Why? | histone acetylases - open hisones anything that condenses or bulks chromatin does not favor gene expression |
| Where are enhancers located? | may be upstream, downstream or within interon of gene they control (due to looping) |
| When you see "zinc fingers", "leucine zippers", or "helix-loop-helix", what are they talking about? What are the fingers? | Enhancers (steroid receptors are fingers, while cAMP response elements are zippers) |
| If you have multiple abnormalities with a single gene point mutation, where is the mutatuion? | HOX or PAX gene |
| Dx: childhood obesity and hyperphagia, hypogonadotrophic hypogonadism, small hands and feet, mental retardation, hypotonia Type of genetic problem? | Prader-Willi syndrome Genetic Imprinting (father's gene only) |
| Dx: mental retardation, continuous laughing Type of genetic problem? | Angelman syndrome "Happy Puppet syndrome" Genetic Imprinting (mother's gene only) |
| What does bacteria do to protect its DNA? How does it destroy foreign DNA (bacteriophage)? | it Methylates its DNA Restriction endonucleases |
| What do restriction endonucleases recognize in the sequence? | palindromes |
| Library made from nuclear DNA and is good for seeing all sequences in the cell. Which library is good for seeing proteins (exons) without introns? | Genomic Libraries cDNA Libraries |
| Example of a key tissue for collagen types 1-4 | Bone SCAB: I: bone, Skin II: Cartilage III: Arteries IV: Basement membrane (4 to the floor) |
| What is a key feature to a Dominant genetic problem in pedigree (vs. recessive)? | Dominant - every generation is affected (not in recessive) |
| What is a key feature to Autosomal genetic problem in pedigree (vs. X-linked)? | Autosomal - Male-to-male inheritance (x-linked has no male-to-male) |
| Dx: Lateral displacement of the innercorner of the eye; Pigment abnormalities; congenital deafness; limb abnormalities What gene is the problem? | Klein-Waardenburg Syndrome HOX gene abnormality |
| If cystic fibrosis patient were to be treated with gene therapy, which type of cells should be targeted by the host cells? | Epithelial cells |
| name 5 Autosomal Dominant diseases | FH-MAN Familial Hypercholesterolemia; Huntingtons; Marfans; Acute Intermittent Porphyria; NF-1 |
| What is usually the common problem in the Autosomal Dominant diseases? | Structural protein damage |
| name 4 common Autosomal Recessive diseases | SCriPT Sickle cell; Cystic Fibrosis; PKU; Tay-Sachs |
| What type of genetic diseases affect energy production? (Name 3) | Mitochondrial Diseases: Leber's optic neuropathy; MELAS; MML |
| name 4 X-linked recessive common diseases | Duchennes muscular dystrophy; Lesh-Nylan; G6PD; Hemophilia A & B |
| Paternal relationships b/t man and infant can best be determined by DNA fingerprinting. What about the DNA is analyzed? | Tandem repeats |
| 2 amino acids that are the precursors for catecholamines | Phenylalanine Tyrosine |
| What NT does tryptophan form? What vitamin? | Serotonin Niacin |
| 3 branched-chained amino acids found in Maple Syrup Urine disease? | I Love Vermont: Isoleucine; Leucine; Valine |
| name the (6)* nonpolar, non-aromatic hydrophobic amino acids | VIP GAL: Valine; Isoleucine; Proline Glycine; Alanine; Leucine |
| Only amino acid with a phenol group? | Tyrosine |
| name the 3 aromatic amino acids | Phenylalanine Tyrosine Tryptophan |
| the amino acid that acts as a methyl donor | methionine (SAM) |
| name 3 amino acid that are basic What is the pK of the R groups? | HLA: Histidine (6.5) Lysine (10) Arginine (13) |
| name the 2 amino acids that are acidic What is the pK of the R groups? | Glutamate (4) Aspartate (4) |
| What are the 2 pKs that every amino acid has? | pk (COO-) = 2 pk (NH2) = 9 |
| What is the net charge on the amino acid if the pH is less then the pI? | positive |
| What is the pI? (equation) | average of the pKs: (2+9)/2 = 5.5 for normal AA [average the 2 closest numbers for charged AA] |
| Main extracellular buffer | bicarbonate |
| 10 essential amino acids | PVT TIM HALL: Phe-Val-Thr Trp-Ile-Met His-Arg-Leu-Lys |
| What 2 essential amino acids are required during periods of growth? | Histidine Arginine |
| What is the sign of delta G in a spontaneous reaction? | negative |
| Affect on Km & Vmax: 1) Competitive Inhibitor 2) Non-competative Inh | Competitive: Km= Increase; Vmax= no change Non-competitive: Km= no change; Vmax= Decrease |
| what does the x and y axis measure on Lineweaver-burke plots? | x-axis: -(1/Km) y-axis: (1/Vmax) |
| How does affinity relate to Km? | low Km = high Affinity |
| amino acid precursor to GABA | Glutamic Acid |
| amino acid precursor to Heme | Glycine |
| the amino acid that is the precursor for: Creatine Urea Nitric Oxide | Arginine |
| adds a phosphate to a substance | Kinase |
| 2 serine kinases | cAMP cGMP |
| which receptor type has no g-protein and results in smooth muscle relaxation? Second messenger? | cGMP Protein kinase G |
| What phosphorylates in the insulin/glucagon world? Which needs ATP? | Glucagon - phosphorylates (needs ATP) Insulin - de-phosphorylates |
| removes a phosphate from a substance | Phosphatase |
| What bug affects ADP-ribosylation at Gs receptors? What bug affects it at Gi? What do they both cause in the cell? | stimulates Gs- Cholera (stimulates the stimulator) inhibits Gi- Pertussis (inhibits the inhibitor) Both cause: Increase in cAMP |
| What two Vitamins can be used in dehydrogenase reactions? | Riboflavin (B2) Niacin (B3) |
| Vitamin that makes CoA? | Pantothenic Acid (B5) |
| What (4)* things does the liver produce in a well-fed state? | G-TAB: GLYCOGEN Triglyerides ATP Bile (from cholesterol) |
| What is the first step in a well-fed state for the following tissues: liver, RBC, brain, muscle, fat? | GLYCOLYSIS |
| 2 actions of RBC in a well-fed and fasting state? | 1) glycolysis (for ATP) 2) Lactate production |
| What tissues use insulin receptors: GLUT 1 and 3? | RBC Brain |
| What tissues use receptor: GLUT 2? | Liver |
| What tissues use receptor: GLUT 4? | Muscle Adipose |
| Once there is enough energy in liver during well-fed state, what 2 substances build-up? What is done with them? | Glucose & Acetyl-CoA Glucose - added together to be stored as glycogen Acetyl-CoA - added together to become fatty acids (then transported to adipose via VLDL) |
| What does adipose do during well-fed states? | takes in glucose and fatty acids to make ATP and fat |
| What (4)* substances enter the liver during a well-fed state? Where is each from? | Goes to Liver And Grows: Glucose - food (blood) Lactate - RBC Amino Acids - food (blood) Glycerol - Chylomicrons (food) |
| What does the liver give to tissues during fasting states? To what tissues? | Glucose - RBC & Brain Ketone bodies - muscle |
| What does muscle get during the fasting state? (2) From where? | Ketone bodies - liver (once enough ATP is made and Aceytl-CoA builds-up) Fatty acids - Adipose (carried on albumin) |
| What does the muscle provide to the liver during fasting states? For what? (2) | Amino Acids 1. to make Pyruvate (then glucose) 2. for Urea cycle |
| 2 sources (& preliminary substances) to make pyruvate b/t meals for the liver to make glucose | RBC - lactate muscle - Alanine |
| What 2 ways can the GLUT-4 receptor move to the surface of muscle? | 1) Increased Insulin 2) Exercise |
| What are the 2 anaerobic steps of substrate level phosphorylation in glycolysis? | 1,3BPG --> 3PG (via Phosphoglycerate kinase) PEP --> Pyruvate (via Pyruvate kinase) |
| What are two essential items needed to make ATP from NADH? | 1) Oxygen 2) Mitochondria (for ETC) |
| What 2 steps of glycolysis use ATP? | First and third step: Glucose --> G6P (via Hexokinase/Glucokinase) F6P --> F-1,6-BP (via PFK-1) |
| What is the rate-limiting step of glycolysis? Net ATP? | PFK-1 2 ATP (net) |
| How does the RBC replenish NADH? With what essential enzyme? If enzyme was not there, what would occur? | Pyruvate --> Lactate (Enzyme: Lactate DH) changes NAD+ --> NADH for glycolysis (lactate goes to liver) If Lactate DH not there, RBC would die |
| What enzyme of glycolysis is only in the liver and is induced by insulin? Level of affinity of this enzyme? | Glucokinase Low affinity = High Km = high Vmax |
| How is PFK-1 controlled? Which form is active (dephosphorylated or phosphorylated)? | Insulin (dephos) stimulates PFK-2 for: F6P --> F-2,6-BP to make PFK-1 Glucagon (phosphorylates) inhibits PFK-2 |
| What (3)* metabolic events occur in the mitochondria? | Fatty acid oxidation Acetyl-CoA production TCA cycle |
| What (5)* metabolic events occur in the cytoplasm? | Glucose Found Here Protects Steroids: Glycolysis Fatty acid synthesis HMP shunt Protein synthesis (RER) Steroid synthesis |
| What (3)* metabolic events occur in both the mitochondria and the cytoplasm? | Heme synthesis Urea cycle Gluconeogenesis |
| What 2 shuttles take NADH from the cytoplasm to the mitochondria? How many ATP does each yield? Which yields a FADH2 instead of the NADH in the mito? | Malate/OAA Shuttle - 3ATP G3P Shuttle - 2ATP (creates FADH2) |
| If a patient has cataracts early in life, what is the underlying metabolic problem? What toxic substance accumulation causes this? | Galactose metabolism Toxic: Galacititol |
| Dx: young patient with hepatosplenomegaly, cataracts, mental retardation. Which enzyme presents sx at birth? Which in early childhood? | Galactosemia: Galactose-1-P uridyltransferase = at birth; Galactokinase = early childhood |
| Dx: lethargy, vomiting, liver damage, hyperbilirubinemia, hypoglycemia, jaundice, renal proximal tubule problems. What enzyme is deficient? | Fructose Intolerance Enz: Aldolase B |
| What are the (5)* cofactors used for Pyruvate Dehydrogenase? | TLC For Nipples: Thiamine (B1) Lipoic Acid Coenzyme A (B5) FADH2 (B2) NADH (B3) |
| What does Pyruvate DH change pyruvate into? | Acetyl CoA |
| Overall net reaction of the TCA cycle? What makes the ATP in this reaction? | Acetyl CoA --> 2 CO2 3NADH + FADH2 + GTP = 12 ATP (2x everything per one glucose) |
| Which enzyme in the TCA cycle is in the inner mitochondrial membrane versus the matrix of the mitochondria? | Succinate Dehydrogenase |
| What enzyme has the same 5 cofactors as Pyruvate DH? | Alpha-Ketogluterate DH |
| In order, what are the 8 steps in the TCA cycle? | Can I Keep Selling Sex For Money Officer? Citrate-->Isocitrate--> (alpha)Ketogluterate--> Succinyl CoA-->Succinate--> Fumarate-->Malate-->OAA |
| What does a Pyruvate DH deficiency lead to? What can it be due to? How is it treated? | Lactic Acidosis (from backup of substrates) Seen in Alcoholics (thiamine deficiency) Tx: Ketogenic acids (Lysine & Leucine) |
| What part of the TCA cycle is also part of the ETC? What does it provide to the ETC? | Succinate Dehydrogenase (Complex II) Provides: FADH2 |
| What part of the TCA cycle deals with Fatty Acid synthesis? | Citrate |
| What part of the TCA cycle deals with Heme synthesis? | Succinyl CoA |
| What part of the TCA cycle deals with the Urea cycle? | Fumarate |
| What parts of the TCA cycle deals with Gluconeogenesis? | OAA & Malate |
| What is the rate limiting step of the TCA cycle? What does it depend on? | Isocitrate DH depends on NADH levels |
| What enzymes in the TCA produce the energy? (5)* | KIM SUCkS: Ketoglutarate DH - NADH Isoglutarate DH - NADH Malate DH - NADH Succinyl CoA - GTP Succinate DH - FADH2 |
| What does Complex I use in ETC? What drug class inhibits Complex I? | NADH Barbiturates |
| What 3 reactions add FADH2 to Coenzyme Q? Which is considered Complex II? | TCA (Succinate DH) [Complex II] Glycerol-P shuttle Beta-oxidation (Fatty Acyl CoA DH) |
| Which Complex in the ETC uses Oxygen? Another name for thtis complex? What else is needed for this Complex? What 2 compounds inhibit this Complex? | Complex IV (Cyto a/a3) copper Cyanide & CO |
| Where is the ATP made in the ETC? What inhibits this? | ATP Synthase Inhibitor: Oligomycin |
| What is a common Uncoupler? How does it work? | Aspirin Brings H+ across the proton gradient, which inhibits the creation of ATP and increases Oxygen consumption |
| What is the rate limiting step in Glycogen creation? | UDP-Glucose --> Glycogen (via Glycogen Synthase) |
| In which type of muscle fiber is glucose converted to Lactate? In which type is it completely oxidized? | to Lactate: White (fast) fibers completely oxidized: Red (slow) fibers |
| What converts Glycogen back into Glucose 1-P? What stimulates it in the liver and muscle? (2 each) | Glycogen Phosphorylase Stimulated by: Liver: Glucagon and Epinephrine Muscle: AMP and Epinepherine |
| What are the (4)* main Glycogen storage diseases? (in order I, II, III, V) | Very Poor Carbohydrate Metabolism: Von Gierke Pompe Cori McArdles |
| Dx: Glycogen storage disease that causes severe hypoglycemia, hepatomegaly, hyperlipidemia & hyperuricemia What is the deficient enzyme? | Von Gierke's (Glucose-6-Phosphatase) "LU Von Geirke is 6" [LU = hyper Lipidemmia and Uriceia] |
| Dx: Glycogen-like material in inclusion bodies, cardiomegaly, muscle weakness and death by age 2 What is the deficient enzyme? | Pompe's (Lysosomal-alpha-1,4-glucosidase) |
| Dx: Glycogen storage disease that is similar, but milder then Type I. What is the deficient enzyme? | Cori's (Alpha-1,6-Glucosidase) [Cori is A-16 yo-Girl] |
| Dx: Increased glycogen in muscle, painful cramps, myoglobinuria w/ exercise What is the deficient enzyme? | McArdle's (Muscle Glycogen Phosphorylase) |
| What are the 3 irreversible steps in Glycolysis? | Glucokinase PFK-1 Pyruvate Kinase |
| What are the (3)* ways Gluconeogenesis circumvents the irreversible glycolysis steps (in order)? | Pathway Produces Fresh Glucose: Pyruvate Carboxylase/PEPCK F-1,6-Bisphosphatase Glucose-6-phosphatase |
| What are the (3)* cofators for Carboxylase reactions? | ABC enzymes: ATP Biotin CO2 |
| What is the rate-limiting enzyme in Gluconeogenesis? | PEPCK |
| What enzyme converts Pyruvate to OAA? How does this OAA get to the cytoplasm to create Glucose? | Pyruvate Carboxylase Malate/OAA shuttle |
| What is an easy test to see if patient has a glycogen storage disease? | inject patient with glycerol; if patient does not increase blood glucose, there is a G6P deficiency |
| Cycle that Transfers excess reducing agents from RBC and muscle to the liver, allowing the muscle to function anaerobically What do the muscle and RBC distribute to the cycle? | Cori Cycle RBC and Muscle give: Lactate |
| What enzyme changes lactate to and from pyruvate? | Lactate DH |
| What is the function of the HMP shunt? What are the 2 important enzymes in this reaction? | to regenerate NADPH and Ribose 5-P Enzymes: G6PDH Transketolase (TPP) |
| What are the 3 main roles of NADPH? | Liver: Biosynthesis (FA, Cholesterol, DNA) RBC: Protect against ROS Neutrophil: NADPH oxidase (kill bugs) |
| What are the 2 essential Fatty acids? What is their nomenclature? | Linoleic = C18:2(9,12) Linolenic = C18:3(9,12,15) |
| What cells have telemorase activity? (2) | Embryonic (germ) cells Cancer cells |
| What strand is identical to the mRNA (except T for U)? What strand is Complementary and antiparallel to the mRNA (except T for U)? | Identical: Coding Strand Complementary: Template Strand |
| What drug inhibits all transcription in prokaryotes and eukaryotes? | Actinomycin D |
| What is 3 bases and antiparallel to mRNA w/ U instead of T? where is this attached? | Anti-codons attached to tRNA |
| (2) steps of Collagen formation that occurs in the RER? What Dz can occur from a deficiency in these steps? | 1. Removal of the "Pre" from Prepro-alpha to make Pro-alpha 2. Hydroxylation of the Pro-alpha with Vitamin C Dz: Scurvy (Vit-C deficiency) |
| (2) steps of Collagen formation that occurs in the Golgi? What Dz can occur from a deficiency in these steps? | 1. Glycosylation 2. Triple Helix formation to make Procollagen Dz: Osteogenesis Imperfecta |
| (3) steps of Collagen formation that occurs in the ECM? What (2) Dz can occur from a deficiency in these steps? | 1. cleavage of peptide ends to make Tropocollagen 2. Tropocollagen into fibrils w/ Lysyl Oxidase and copper 3. Fibrils to Collagen Fibers Dz: Ehlers-Danlos (Lysine hydroxylase deficiency) Menke's Dz (Copper digestion insufficiency) |
| Drug that is against Pertussis by inhibiting the translocation of peptidyl-tRNA on 50s ribosome | Erythromycin |
| What effect does Exotoxin A of Pseudomonas have on the human cells? | inhibits translocation factor: eEF-2 |
| Define: 1. Plasmid 2. Vector 3. Phage | Plasmid: circular DNA in bacteria Vector: carrier for human DNA to insert into a plasmid Phage: Larger vector |
| What type of Genetics: NO male to male; no male to female; if mother has it, all kids have it | Mitochondrial inheritance |
| With Southern blot, how does the DNA align? (2) | DNA (negative charge) moves to the positive Larger fragments at top and smaller at bottom |
| What does it measure? 1.Southern blot 2. Northern blot 3. Western blot Which is good to answer questions about gene expression? About the amount of antigens or antibodies? To determine specific restriction fragments? | Southern = DNA (restriction fragments) Northern = RNA (gene expression) Western = Proteins (Antibodies/Antigens) |
| Type of receptors: 1. Gs 2. Gi 3. Gq What does each do? | Gs = Beta receptors (stimulates Adenyl cyclase to inc cAMP) Gi = Alpha-2 receptors (Inhibits Adenyl cyclase to dec cAMP) Gq = Alpha-1 receptors (Stimulates Phospholipase C in PIP2 receptor system) |
| Which receptor is associated w/ Protein Kinase C? | IP3 (Gq) |
| Which receptor is assoc w/ Protein Kinase A? | cAMP (Gs and Gi) |
| What is the G-receptor for Vasopressin? Glucagon? | Gq - IP3 system Gs/Gi - cAMP system |
| MCC of deficiency in: Thiamine | Alcoholism |
| MCC of deficiency in: Folic Acid (2) | Alcoholism Pregnancy |
| MCC of deficiency in: Cyanocobalamin (B-12) | Pernicious Anemia |
| MCC of deficiency in: Pyridoxine | Isoniazid therapy |
| What NT is always released w/i the eyes (in the dark) causing constant depolarization? What channels respond to light causing the cell to hyperpolarize? | Glutamic Acid cGMP-PDE Na+ gated channels close |
| What vitamin is used to introduce Calcium to binding sites of several calcium-dependent proteins? With which mechanism? What drug inhibits this? | Vitamin K Gamma-carboxylation of Glutamate Warfarin inhibits it |
| Bleeding time difference and PT difference b/t a deficiency in: Vit-C and Vit-K | Vit C: Increased bleeding time normal PT Vit K: normal bleeding time Increased PT |
| If tissue is hypoxic, what enzymes will be increased in the blood? | Any Glycolysis enzyme (not Lactate DH) |
| MC genetic deficiency that causes hemolytic anemia | Pyruvate Kinase Deficiency |
| What amino acid is assoc w/ the Malate-OAA shuttle? | Aspartate |
| What enzyme in glycolysis is activated after a big meal? What activates it? | PFK-2 Activated by Insulin |
| What thiamine-dependent enzyme is essential for glucose oxidation in the brain? | Pyruvate DH |
| After an overnight fast, what enxymes of what metabolic process would be insignificant? | Glycolysis enzymes (b/c liver is producing glucose, not storing it) |
| What enzymes in the TCA cycle produce items but not NADH? (2) | Succinates: Succinyl CoA Synthase = GTP Succinate DH = FADH2 |
| Which is the only enzyme in the TCA that deals w/ substrate level phosphorylation? | Succinyl CoA Synthase |
| Which direction do H+ flow in the ETC? In which complexes? In which complex is the flow the opposite direction? Which side does O2 -> H20? On which complex? | Mitochondrial matrix -> cytoplasm: Complexes I, III and IV Opposite direction: ATP synthase O2 -> H20: mitochondrial matrix on Complex IV |
| What does Nitroprusside break down into? What complex in ETC does it affect? | Cyanide Complex IV |
| What glycogen storage Dz has debranching enzymes? | Cori's Dz |
| If FA beta-oxidation is occurring in the liver, what does pyruvate do? | Carboxylates to OAA for entry into Gluconeogenesis |
| What do G6PDH deficient patients have resistence to? | Malaria |
| What do the bilirubin levels in the blood and urine look like w/ hemolytic jaundice (from G6PDH deficiency)? | Direct = normal Indirect = increased Urinary = absent |
| What type of bonds are there in alpha-helix and beta-sheet proteins? | Peptide bonds that participate in H+ bonding |
| What property of water most contributes to its ability to dissolve compounds? | Hydrogen bonds |
| What tissue has the highest concentration of Cystine? | Keratin |
| What gives strength to the IgG structure? What can break these bonds? | Disulfide bonds Urea (and reducing agents) |
| What is constant (the same) in each class of immunoglobulins? | Constant regions of the heavy chains |
| How many antigen binding sites does each immunoglobulin have per molecule? | 2 |
| Which FA is cardio-protective? | Linolenic (omega-3) |
| When is a FA considered "saturated"? | when it has NO double bonds |
| Name and give the nomenclature for the FA that is the precursor to Prostaglandins, thromboxanes and Leukotrienes | Arachidonic Acid: C20:4(5,8,11,14) |
| What is a good way to remember the placement of the double bonds for unsaturated FA? (3) | 1. Double bonds occur every 3 carbons 2. "L's" start w/ 9 3. Arachidonic C20:4 - take 20/4 = 5. This starts at 5 |
| Accumulation of what in the liver triggers it to make fat? What is needed? | Acetyl CoA Need Energy (ATP) |
| In the mitochondria, there are (2) pathways to make fat depending on the fed or fasting state. What is the path for each to get to Citrate? | Fed (insulin): Pyruvate -> PDH -> Acetyl CoA -> Citrate Fasting (glucagon): Pyruvate -> P Carboxylase -> OAA -> Citrate |
| What from the mitochondria leaves the TCA cycle to enter the cytoplasm for fat synthesis? What does it then turn into? | Citrate Aceytl CoA |
| What is the essential enzyme to transform Acetyl CoA to Malonyl CoA? What else is needed? How many Acetyl CoA are needed to make one Palmitate? | Acetyl CoA Carboxylase ATP/Biotin/CO2 8 Acetyl CoA are needed for 1 Palmitate (7 cycles) |
| What enzyme and substance is needed to convert Malonyl CoA to Palmitate (16:0)? (2) | FA Synthase (2) NADPH |
| How many molecules of NADPH are needed for one Palmitate? | 14 NADPH (2 x 7 cycles) |
| To transport FA from liver, what do you need to do to the molecule? What is needed for this? | Convert it to a TG Need: Glycerol-3-P |
| (2) enzymes that are induced/activated by insulin in FA synthesis | PDH Acetyl CoA Carboxylase |
| What is needed for every Carboxylase enzyme? | Biotin |
| (2) ways to make TG in the liver | 1. Glucose enters liver: Glucose -> DHAP + Glycerol-3-P DH -> Glycerol-3-P + 3 FA CoA -> TG 2. Glycerol enters liver: Glycerol + Glycerol Kinase -> Glycerol-3-P + 3 FA CoA -> TG |
| What in Adipose allows for the removal of FA from TG carried by chylomicrons and VLDL? With what "key"? | Lipoprotein Lipase Key: ApoC-II |
| What is the only Apoprotein left on LDL? What is its use? | ApoB-100 used as a key to LDL receptors in cell membranes to endocytose the LDL for cholesterol usage |
| What are the (2) Apoproteins on HDL? Use of each? | ApoE - Key to liver ApoA-1 - Key to stimulate LCAT |
| What does the LCAT receptor of peripheral tissues do? | Adds a FA from the periphery to HDL for it to take back to the liver |
| What are the main ingredients of the plaque on the vessel walls? (3) What is this called? | "Fatty Streak" formation: Cholesterol Foam cells (sick macros) Smooth muscle (migrated) |
| What membrane transport shuttle is used in Beta-oxidation of FA? | Carnitine shuttle |
| (2) main enzymes in B-oxidation of FA? Which is the rate limiting step? | Carnitine Acyl Transferase (rate-limiting across shuttle) Fatty Acyl CoA DH |
| What is the end product of b-oxidation? | Acetyl CoA |
| When is the only time FA can go back into glucose? What does it make in this case? | When it is a FA w/ an odd number Makes: Succinyl CoA |
| What (2) enzymes are used in the breakdown of odd-chained FA? What is needed with each step? | Propionyl CoA Carboxlase (biotin) Methylmalonyl CoA Mutase (Vit B-12) |
| What is the difference b/t a TG and a glycerophospholipid? | glycerophospholipid has Inositol or choline attached |
| What are the (2) main ingredients in Sphingolipids? Precursor to all sphingolipids? | Serine (not glycerol) + FA Precursor: Sphingosine |
| Sphingolipids extra ingredients for: 1. Sphingosine 2. Cerebrosides 3. Gangliosides | 1. Sphingo = CHOLINE 2. Cerebro = SUGAR 3. Ganglio = SIALIC ACID and complex sugars |
| Deficient Lysosomal enzyme: Gaucher's Dz | Glucocerebrosidase |
| Deficient Lysosomal enzyme: Niemann-Pick | Sphingomyelinase |
| What is the actual enzyme that causes the increased amount of Galactose to be converted into Galactitol to cause Cataracts? | Aldose Reductase |
| What are the enzymes for the (2) sources of ammonia that enter the Urea cycle in the liver? | Both break down Glutamate: Glutaminase in the GI Glutamate DH in liver |
| What vitamin is essential for aminotransferase reactions? | Vitamin B-6 |
| If blood glutamate is increased in the blood, what is the possible problem? | Deficiency in Urea cycle |
| What are the steps in the Urea cycle? (8)* | Careless Crappers AlSo ARe Frivolous About Urination Outside: Carbamoyl Phosphate -> Citruline + Aspartate -> Argininosuccinate - Fumarate -> Arginine - UREA -> Ornithine |
| Which step in the Urea cycle is inside the mitochondria? | Carbamoyl Phosphate |
| What is the enzyme deficiency with the following Sx? blood glutamine increased, BUN decreased, cerebral edema, lethargy, convulsions, Uracil and Orotic acid increase in blood and urine | Ornithine Transcarbamoylase (OTC) |
| What reactions and AA enter at the Succinyl CoA part of the TCA? (5)* | VOMIT SUCks: Valine; Odd-chain FA; Methionine; Isoleucine; Threonine |
| (2) enzymes in the body that need Vit B-12 | Methylmalonic CoA Mutase Homocysteine Methyl Transferase |
| What are the (2) Ketogenic AA? Where do they enter the TCA cycle? | Leucine Lysine enter at Acetyl CoA |
| What (2) AA enter the TCA cycle at Fumarate? | Phenylalanine Tyrosine |
| If you see zinc in heme, what enzyme is inhibited? | Ferrochelatase |
| Steps in Heme Synthesis (6)* | GAP UP Here: Glycine + Succinyl CoA -> Aminolevulinic Acid (ALA) -> Porphobilinogen -> Uroporphyrinogen-III -> Protoporphyrin -> Heme |
| What enzyme is deficient in Acute Intermittent Porphyria? | Uroporphyrinogen Synthase |
| Dx: Painful abdomen; Pink urine (Port-wine urine); Polyneuropathy; Psychological disturbances | 4 P = Porphyria |
| Porphyria that also causes blistering of the skin from photosensitivity | Porphyria Cutanea Tarda |
| Dx: Patient is given a barbituate and begins projectile vomiting, confusion, abdominal pain, paranoia. | Acute Intermittent Porphyria |
| (3)* causes of Increased Indirect Bilirubin | HCG: Hemolysis; Crigler-Najjar syndrome; Gilbert's syndrome |
| (2) conditions that increase Direct Bilirubin | Hepatic damage Bile duct obstruction |
| What are the (2) required AA for Pyrimidine synthesis? | Glutamatine Aspartic Acid |
| Blocking THF creation would lead to not being able to make what? What (3) drugs do this? What is the side effect of all of these drugs? | Thymidine (dTMP) Drugs that block DHF reductase: METHotrexate (cancer); TriMETHoprim (PCP); PyriMETHamine (toxoplasmosis) Side effect: Bone marrow Suppression |
| What are the (3)* important enzymes in the conversion of UMP to dTMP (in order)? Which Anti-cancer med targets each? | Right Here The Funky Drugs Mingle: Ribonucleotide Reductase (Hydroxyurea) Thymidylate synthase (5-FU) DHF reductase (Methotrexate) |
| What is Orotic Acid involved in? | Pyrimidine synthesis |
| What is the additional AA that is used to make purines? | Glycine |
| What enzyme in Purine synthesis is the rate-limiting step? What (2) drugs inhibit this step? | PRPP Amidotransferase Drugs ("Purin"): AlloPURINol (Gout); 6-MercaptoPURINe (cancer) |
| What intermediate in purine synthesis is different from guanine and adenine by one amino group and is also an intermediate in the breakdown of purines? | Hypoxanthine |
| Lack of the salvage pathway of purines leads to what syndrome? What is the missing enzyme? What is an unusual sign of this syndrome? | LNS = Lacks Nucleotide Salvage: Lesch-Nyhan syndrome HGPRTase Sign: Self-mutilation |
| Adenosine Deaminase deficiency causes a lack of what product? | Inosine |
| Dx: 48-yo man w/ recessive condition is at high risk for deep vein thrombosis and has had replacement of ectopic lenses; no evidence of anemia. Enzyme that is deficient? What AA would be in excess? | Homocysteinuria Enzyme: Cystathionine Synthase AA: Methionine |
| Dx: Man has dark pigment of cartilage and arthritis, and dark urine What enzyme is deficient? | Alkaptouria Enzyme: Homogentisate Oxidase [AL KAPT a HOMe] |
| How do you treat Cystinuria? | Alkalinize the urine w: Acetazolamide |
| Precursor to Ketone body formation | HMG-CoA |
| (4)* genetic Dz w/ Trinucleotide repeats | Try HUNTING for MY FRIED X (eggs): Huntington's; Myotonic Dystrophy; Friedreich's Ataxia; Fragile X |
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