Final Exam Flashcards
What are some common causes of metabolic alkalosis?
Acute alkali administration, vomiting, gastric aspiration, diuretics
What are the functions of prostaglandins/thromboxanes?
- inflammatory mediators (vasodilation) - stimulation of contraction of uterus - platelet aggregation
How is the PDH complex similar or dissimilar to the alpha-ketoglutarate DH complex?
- Each complex has 3 enzyme subunits. Each produces CO2. Substrate for PDH is 3C alpha-keto acid (pyruvate), while substrate for aKGDH is 5C alpha-keto acid (alpha-ketoglutarate). Product for PDH is 2C (acetyl-CoA), while produce for aKGHD is 4C (succinyl-CoA). Regulation of PDH occurs via phosphorylation, while aKGDH is not regulated via phosphorylation. Reactions catalyzed by both are irreversible as a lot of free energy is lost.
What are the degradation products of Tryptophan?
- Acetoacetyl-CoA - Acetyl-CoA - Fumarate
Discuss roles of the CREB, CBP and PKA in transcriptional control
- PKA phosphorylates and regulates many cytosolic proteins, but is also present in activated form in nucleus under high levels of cAMP - Many genes regulated by PKA contain CRE (cAMP responsive element) in their promoter region - PKA influences transcription by phosphorylation of CREB, which then binds CRE - CREB bound to CRE recruits CBP - CBP then recruits EP300 - CBP/EP300 interacts physically with GTFs. Together CBP/EP300 function as HATs, relaxing chromatin and stimulating transcription
Explain how the Philadelphia chromosome affect the health of a carrier
- Philadelphia chromosome = translocation bw c/s 9 & 22- ABL tyrosine kinase is moved from 9 to BCR region on 22.- BCR-ABL protein functions as dominant oncogene causing CML
How do you convert the rectangular hyperbolic V vs. [S] curve into a straight line using the Lineweaver-Burk (double-reciprocal) method. What are the X- and Y-intercepts and the slopes of this plot? How could the Vmax and Km be determined using this plot?
- 1/v = (Km/[S]).(1/Vmax) + 1/Vmax (y = mx + b form) - The x intercept = -1/Km – the negative reciprocal gives you Km - The y-intercept = 1/Vmax – the reciprocal gives you Vmax - Slope = Km/Vmax
Explain how F26BP affects gluconeogenesis. Include details about the enzymes involve, pathways activated and substrates affected.
- Take home message: high concentrations of F26BP inhibit gluconeogenesis, low concentrations of F26BP stimulate gluconeogenesis - F26BP is produced by enzyme PFK2 (produces F26BP from F6P) - Insulin stimulates PFK2 via cAMP leading to increased concentration of F26BP, which causes inhibition of gluconeogenesis via pyruvate carboxylase, PEP carboxykinase and glucose-6-phosphatase - Glucagon inhibits PFK2 via cAMP leading to decreased concentration of F26BP, which causes stimulation of gluconeogenesis via PEP carboxykinase and glucose-6-phosphatase
What is Li-Fraumeni syndrome?
- Dominant heritable condition conferring increased susceptibility to many forms of cancer as a result of dominant negative effect of mutation to TP53 allele - Cells with damaged DNA are free to continue to divide and tumors develop
Describe degradation of GMP vs degradation of AMP to their constituent parts
- General theme is to remove phosphate, then ribose, leaving you with base a.) GMP: - GMP = Guanosine + Pi (ez: 5-nucleotidase) - Guanosine + Pi = Guanine + Ribose-1-P (ez: purine nucleoside phosphorylase) b.) AMP pathway 1: - AMP = IMP + NH4+ (ez: AMP deaminase) - IMP = Inosine + Pi (ez: 5-nucleotidase) - Insoine + Pi = hypoxanthine + Ribose-1-P (ez: purine nucleoside phosphorylase) c.) AMP pathway 2: - AMP = Adenosine + Pi (ez: 5-nucleotidase) - Adenosine = inosine + NH4+ (ez: adenosine deaminase) - Insoine + Pi = hypoxanthine + Ribose-1-P (ez: purine nucleoside phosphorylase)
Explain how epigenetic changes play a role in the development of cancer
- Global hypomethylation of DNA outside of CpG islands is seen in most cancers- Hypomethylation causes genomic instability and therefore elevated transposon activity, resulting in chromosomal abnormalities. This causes cancer.- Hypermethylation of CpG islands in promoter can shut down tumor suppressor genes – sometimes seen in non-familial breast cancers
Explain how ethanol is metabolized? What is its impact on CHO metabolism?
- Alcohol metabolism occurs in the liver by two mechanisms: 1.) two DH reactions (main pathway) and 2.) MEOS: microsomal ethanol oxidizing system: induced by chronic alcohol abuse. - Both DH reactions reduce NAD to NADH, which interferes with CHO metabolism and utilization. - When NADH is high in the cytoplasm, pyruvate and oxaloacetate are converted into lactate and malate respectively via lactate dehydrogenase and malate dehydrogenase respectively. Pyruvate and oxaloacetate are both intermediates in gluconeogenesis and glycolysis. - Lactate levels rise (more than normally) and cannot be processed in the Cori cycle, causing accumulation in blood, leading to metabolic acidosis. Body responds by increasing respiration in order to attempt restoral of acid/base balance. - Failure to complete Cori cycle also leads to epinephrine and glucagon release, which induces a stress response. - NADH inhibits key enzymes of TCA and shunts acetyl-CoA into FA/ketone body biosynthesis leading to a fatty liver over time.
Explain how nitroglycerin can reduce blood pressure.
- Nitroglycerin is converted to NO in the body. When binding to guanylate cyclase in smooth muscle lining blood vessels, it causes them to relax and volume within the vasculature to expand. This causes a reduction in blood pressure.
Explain what reaction(s) the cell can perform when there is a need for NADPH and ATP. Ribose is not required.
How do high levels of NADH prevent gluconeogenesis from proceeding?
- Malate-oxaloacetate shuttle. When levels of NADH are high, it will donate its electrons to oxaloacetate to form malate, which moves into mitochondria and reconverts to oxaloacetate and NADH in the matrix. This ensures low oxaloacetate in the cytosol and inhibition of gluconeogenesis.
What is the committed step in TAG synthesis? What are TAG synthesis precursors used for?
- Committed step is conversion of phosphatidic acid to 1,2 diacylglycerol via phosphatidate phosphatase. - Phosphatidic acid can be shunted into lipid membrane synthesis pathways instead of going down TAG synthesis pathway.
What is the function of lipoxygenase inhibitors? What downstream molecule is being targeted with these inhibitors? What disorder/illness can these alleviate? How?
- These target synthesis of leukotrienes from AA via inhibition of the lipoxygenase enzyme. - Alleviates asthma by reducing smooth muscle contraction.
Which AAs can be used to synthesize succinyl-CoA? How?
- Mnemonic: VOMIT - Valine, odd-chain fatty acids, methionine, isoleucine, threonine - These are converted into propionyl-CoA, which undergoes intermediates to become succinyl-CoA
What is the mechanism of action of tamoxifen?
- Tamoxifen inhibits estrogen action - It is a competitive inhibitor, blocking estrogen binding to its receptor, however ERE dimer still remains dimerized and bound to DNA - Growth of breast cancer is reduced by disrupting this estrogen signaling
Examples of exogenous uncouplers to ETC/ox-phos. Symptoms? Treatment?
- DNP (2,4 dinitrophenol) is a pesticide and poison. It causes sweating, flushing, nausea, inc RR, tachycardia, fever, coma, death in 1-2 days. Treatment with ice baths, oxygen and fluid/electrolyte replacement. - Aspirin in very high doses
Explain the biochemistry of CO (carbon monoxide poisoning).
- CO binds to heme iron at ~ 240 higher affinity than o2 (known as carboxyhemoglobin) - When 2 x CO molecules bind to Hb, R-form stabilizing, meaning T-form unfavored and o2 wants to remain bound and not deliver to tissue. - Treatment is removing individual from CO and administering 100% o2 at high pressure.
Explain how lipids are transported into the mitochondria. Is it in the form of TAGs or FAs?
- FAs are transported into the mitochondria.
Discuss regulation of FA (TAG) synthesis, degradation and mobilization/release
- ) FA synthesis
- Well-fed state:
a. ) insulin: induces expression of acetyl-CoA carboxylase, FA synthase, malic enzyme and G6PD long-term basis
b. ) insulin: activates acetyl-CoA carboxylase and glycolysis (both via phosphoprotein phosphatase, which removes phosphates) – short term basis
c. ) citrate: activates FA synthase
- Starvation
a. ) absence of insulin: levels of acetyl-CoA carboxylase, FA synthase, malic enzyme and G6PD fall
b. ) glucagon: caused cAMP and PKA activity to rise.
c. ) PKA: inactivates acetyl-CoA carboxylase by phosphorylation, inhibits glycolysis - ) FA degradation
- Limiting step = bringing FA into mitochondria via carnitine shuttle / CPTI/II. This is inhibited by malonyl-CoA in well-fed state when FA synthesis is occurring. - ) FA mobilization
- High glucagon/low insulin stimulates mobilization: In fasting state, glucagon raises cAMP levels and activates PKA. PKA activates perilipin and hormone sensitive lipase both by phosphorylation (remember, glucagon acts via phosphorylation). This results in FAs being clipped off glycerols allowing them to become FFAs diffuse out of adipose tissue and move to other tissues. In other tissues they move into mitochondria via CPT I shuttle mechanism which are active as malonyl-CoA is low (this should only be occurring in starved state) and proceed through beta-oxidation.
Describe orotic aciduria
- Rare hereditary condition resulting in UMP synthase mutation - Crystalluria, hypochromic megaloblastic anemia, growth retardation, neurologic abnormalities - Anemia is unresponsive to B12 and folic acid - Treatment with uridine
Common alpha-ketoacid/aminoacid pairs in reactions with alpha-ketoglutarate/glutamate?
- pyruvate/alanine - oxaloacetate/aspartate
Explain patterning. Discuss role of signaling molecules that are necessary for this to occur
- Following specification of axes, patterning takes place. Patterning defines which end of undevelopmed mass of cells is head, which is tail. It segments cells to define which parts become head, thorax, abdomen etc.- Patterning along ant/post axis is determined by homeobox (HOX) genes, which are a family of transcription factors containing a special DNA binding domain called homeodomain. There are 4 HOX clusters on 4 chromosomes- Expression of each of the genes belonging to a cluster correlates with position of respective cell in embryo and with timing of expression. Each cell along axis experiences a different ratio of expression of different HOX genes. Ultimately, the pattern of HOX gene expression determines fate of a cell in segment.
What are modifier genes?
- The individual genetic background modifies the phenotype
Regarding the molecular structure of collagen, describe: a. the importance of amino acid composition and sequence. b. unusual amino acids and their molecular function. c. the importance of vitamin-C and iron in collagen formation.
a. the importance of amino acid composition and sequence. - Collage contains 35% glycine, 11% alanine and modified amino acids known as 4-hydroxyproline and 5-hydroxylysine (previously proline and lysine, but post-translationally modified). - Collage contains the repeating sequence Gly-Pro-Hydroxyproline. Since three polypeptides (in helices) are to come together, it would be important for a smaller residue to be present at the contact points. This is the case, glycine is found here, which has R group of H. b. unusual amino acids and their molecular function. - Collagen has two unusual/modified amino acids known as 4-hydroxyproline and 5-hydroxylysine. Without proline-peptide and peptide-hydroxyproline bonds, helix and triple helix formation would not be possible. Also, strength and rigidity of the molecule would also be compromised. Therefore functional would be lost. Stability is also present in collage as a result of hydrogen bonds formed by hydroxyproline. Lastly, hydroxylysine allows for covalent linkages between helices to form via reactive aldehyde functional groups. c. the importance of vitamin-C and iron in collagen formation. - Ascorbate (vit C) is necessary to catalyze the reaction of proline to hydroxyproline via the prolyl hydroxylase enzyme. This occurs in conjunction with Fe2+ and alpha-ketoglutarate. Ascorbate is required to reduce Fe3+ to Fe2+ in the reaction and allow the enzyme to remain active. Without vit C, enzyme is inactivated and scurvy develops. - Remember hydroxylation in collage allows for normal collagen fibril formation. Without, you have collagen that lacks strength, rigidity and stability.
Effect of lead on heme synthesis
- Lead inhibits porphobilinogen synthase, causing accumulation of ALA - Lead inhibits ferrochelatase, causing accumulation of protoporphyrinogen IX - Causes symptoms similar to the porphyrias
How is the pentose phosphate pathway regulated?
- Glucose-6-Phosphate Dehydrogenase is inhibited by NAPDH. When NADPH is high, G6P can be used elsewhere.
Explain what a competitive inhibitor is?
- A competitive inhibitor is a reversible inhibitor. These compete with substrate to bind at the active site on the enzyme. Increasing substrate concentration will prevent inhibitor binding. Infinite concentration of substrate will abolish inhibition. Inhibitor once removed will not affect enzyme functionality. - These are the most common type of drug
Achondroplasia. Inheritance, defect, frequency
- AD- Caused by defect in FGFR3, gain of function mutation where receptor is constitutively active, exhibits dominant negative effect. Most frequent form of dwarfirsm. Initiation of bone growth leads to short stature. New mutations occur frequently in this disease.- Mutation hotspot
Explain the tumor progenitor cell model
- Tumor progenitor cells arise during development due to epigenetic changes and the action of tumor progenitor genes (TPG)- Then follows a Gatekeeper Mutation (GKM) in a tumor suppressor gene (TSM) or oncogene (ONC) to generate a benign tumor- Finally, epigenetic and genetic plasticity help evolve the benign growth into a metastatic, invasive and drug resistant tumor- Crux of matter: errors in epigenetic programming of stem cells in development lays seed(s) for cancer later in life
Describe the role of HLA haplotypes in the development of type 1 diabetes and other autoimmune disorders
- Think of haplotypes as blocks of genetic information that are inherited together. HLA haplotypes are expressed in a codominant manner. Each parent only transmits one haplotype to the child. Certain HLA haplotypes favor or protect against diseases.- T1D: Contribution of HLA haplotypes to risk for T1D is strong, but not exclusive – only accounting for ~40% of genetic risk. Genetic variation in DR-DQ haplotypes affects risk for T1D. Some DR-DQ haplotypes increases risk and are known as susceptibility alleles. Others decrease risk and are designated protective alleles- Other immune disorders: HLA-B haplotypes determine risk for spondyloarthropathy. HLA-C haplotypes predict risk for psoriatic arthritis.
What is heterozygote advantage? Describe in respect to mutation affecting CFTR, beta-globin and HFE.
- Heterozygote advantage refers to positive selection of heterozygotes as a result of their genotype conferring increased fitness in a particular environment.- CFTR: protects against typhoid fever (population that benefits = European)- Beta-globin/sickle cell: protects against malaria (population that benefits = Mediterranean and African)- Beta-globin/beta-thalassemia: protects against malaria (population that benefits = Meditteranean)- HFE/hemochromatosis: protects against plague (population that benefits = European)
What types of acid-base imbalances are caused by changes in level of CO2?
Respiratory acidosis is caused by higher levels of CO2 resulting in a decrease in blood pH. Respiratory alkalosis is caused by lower levels of CO2 resulting in an increase in blood pH.
Discuss rate of DNA transcription in context of basal transcription complex
- Basal transcription complex = RNA pol II with GTFs - This complex initiates transcription at low rates - High rate requires NF1 binding to CAAT box and SP-1 binding to GC-rich sequences
Define tumor suppressor. How does mutation in these genes contribute to development of cancer?
- Tumor suppressor: inhibit cell growth - Loss of function relieves growth inhibition = non-functioning brake pedal, typically recessive mutations
Explain how to the Robertsonian translocations affect the health of a carrier
- Robertsonion translocation is movement of long and short arms of two chromosomes. Result = one chromosome composed of both the long arms the other composed of both of the short arms. The shorter derivative chromosome does not contain essential genetic information and is typically lost during cell division. Common Robertsonion translocation involves c/s 13 q and 14 q – happens at frequency of 1/1300.
Explain what occurs to the Hb binding curve as pH, 2,3-BPG, temp, CO2 change? Draw it.
Which AAs can be used to synthesize Oxaloacetate?
- Every AAs used to generate pyruvate, then pyruvate into OAA via pyruvate carboxylase - In addition, aspartate and asparagine – Ox with a big ASP (ass)
Cofactor requirement(s) for aminotransferases.
- Vitamin B6 (pyridoxal 5’-phosphate)
How do you determine if R-group on amino acid will be in protonated, deprotonated form and will act as proton donor, acceptor?
- If pH < pKa : acid form predominates : will act as proton donor
- If pH > pKa: basic form predominates : will act as proton acceptor
Action of tetracycline
- 70 S ribosome inhibitor - Specifically blocks A site and prevents tRNA binding
The formation of native protein structure is said to be cooperative. What does this mean? Outline the ‘seeding and nucleation’ model for the progression of prion diseases, Parkinson disease, and Alzheimer disease. What proteins are associated with these disease states?
Cooperative native protein structure indicates that the protein folding cannot be a random process, but instead occurs through favored pathways. This involves the rapid formation of short stable segments of secondary structure, which generate structural motifs which continue to fold into a thermodynamically stable protein structure. The seeding/nucleation model is where a misshaped protein (typically beta-sheets) induces other proteins (during folding) to change confirmation, which has a trickle down/domino effect on other proteins. Parkinson’s: alpha-synuclein is implicated, affect NT release (?) Alzheimer’s: tau and amyloid-beta are implicated, affecting microtubule (?) and neuronal plasticity (?) respectively
How can epigenetic changes contribute to the development of cancers? Example
- Increased methylation silences transcription of a gene, reducing tumor suppressor expression - Decreased methylation activates transcription of a gene, increasing production of oncoprotein - Example: INK4 promoter methylation suppresses transcription, preventing p16ink4 synthesis, allowing for continued phosphorylation of Rb by cyclin-D:CDK4/6 and cell proliferation
What are disorders that prevent proper use of fructose? Explain each
- Essential fructosuria: absence of fructokinase (normally in liver), prevents uptake of fructose. Benign. Fructose can still be used by muscle or become excreted. - Hereditary fructose intolerance: deficiency in aldolase B enzyme. F1P accumulates in liver causing depletion of liver phosphate pools, preventing liver from breaking down glycogen, causing liver to be damaged by accumulation of glycogen, lack of Pi and synthesis of ATP. Pts are required to avoid fructose and sucrose (disaccharide of fructose and glucose)
What is galactosemia?
- There are 3 kinds depending on the enzyme deficiency: Galact-1-P uridyl transferase, galactokinase or UDP-galactose epimerase. - Results in accumulation of galactose1-phosphate in liver and other tissues (CNS, kidney). Newborns present with milk intolerance and signs of liver failure, cataracts and intellectual disability. Also present with jaundice, lethargy and hepatomegaly. Diagnosis is by detection of galactose or galactose-phosphate in urine. Pts must receive a galactose-free diet (no lactose either, which is a glucose, galactose disaccharide).
Name two main sources for mutations affecting chromosome structure
1.) Nonhomologous End Joining during double-strand break repair2.) Unbalanced recombination between non-homologous sequences
Define gain of function.
- Gain of function: Mutated protein may have functions different from its wildtype variant. In this case, the few proteins with novel functions will have an effect no matter how many wildtype versions are present. This mechanism is frequently observed in signal transduction proteins.
What is HIF-1alphabeta and how is it regulated? What is the importance of HIF-1alphabeta in the growth of tumors?
- In normoxic environment, HIF-1alpha (hypoxia-inducible-factor) is hydroxylated by proline hydroxylase, leading to accumulation and destruction of itself - In hypoxic environment, HIF-1alpha associates with HIF-1beta, which regulates expression of VEGF and many other genes, allowing for angiogenesis to proceed. - Result = new blood supply delivers nutrients/oxygen, removes waste to/from tumors
Describe/draw the reactions of glycogen formation (glycogenesis)
What is Burkitt’s Lymphoma? Describe biochemistry that causes it.
- Translocation event moves c-myc gene from normal position on c/s #8 over to c/s #14 - Result = myc gene is now near control elements of antibody HC and continuous production of high levels of Myc occurs in B-cells. B-cells become cancerous
What are population bottlenecks and founder effect and how does it affect the gene pool of a population? Example
- If a large part of a population is wiped out by a catastrophic event, population has to recover from a small founder population of survivors. This bottleneck leads to amplification of rare alleles in the founder’s genotype. - Example: Samuel King immigrated to Eastern PA and founded a large family. He carried a rare recessive mutation in EVC, which cause Ellis Van Creveld syndrome (skeletal dysplasia disorder). This was propagated through founder effect. Consanguineous matings were inevitable in this genetically isolated community and children homozygous for EVC mutation were born. Carrier frequency for EVC is 12.3% in Old Order Amish community in PA, which is only 0.8% in general population
Why are non-competitive inhibitors potentially better drugs than competitive inhibitors? What is the difficulty in manufacturing them?
- Non-competitive inhibitors would perhaps make better drugs since they can inhibit enzyme activity irrespective of the substrate concentration. Would not have to worry about dosing based on substrate concentration. They are difficult to manufacture from the design perspective. Since non-competitive inhibitors bind in a location other than the active site, yet upon binding cause active site to be unable to bind substrate, how can you determine where this other site is?
Synthesis of alanine
From what are Ala and Ser made from?
- Pyruvate and 3-PG
What GTFs are required by RNA Pol II?
- TFIID binds to TATA box, which distorts the DNA helix, acts as signpost and recruits remainder of factors and pol II - Transcriptional initiation complex forms
What is the Pierre Robin Sequence?
- Collagen disorder, generalized growth retardation, neurogenic hypotonia, oligohydramnios leads to ….- Mandibular hypoplasia leads to ….- U-shaped cleft palate and micrognathia (small jaw/chin)
Describe the clinical importance of LDH isozyme profiles.
- There are 5 isozymes of LDH and they are distributed throughout the body in different abundances. - The normal LDH isozyme profile looks at relative abundances of each LDH isozyme and indicates that LDH2 is highest. - After an MI; however, this profile changes and LDH1 (found mostly in the heart and RBCs) becomes elevated. This used to be an important diagnostic tool to determine heart attacks. If LDH5 is evelated, it is diagnostic for acute hepatitis.
What is Crigler-Najjar/Gilbert syndrome? Symptoms.
- Glucuronic acid is a prerequisite for bilirubin excretion. - UGT, which is an enzyme that catalyzes the conjugation of bilirubin with glucuronic acid leads to buildup of bilirubin and syndromes known as Crigler-Najjar/Gilbert. - Jaundice
Discuss checkpoints of cell
- G1/S = restriction point – checking if conditions are favorable for division - G2/M = has DNA been replicated and are conditions still favorable for division - Metaphase/anaphase transition point = are c/s all attached to mitotic spindles
What is the target of the drug trastuzumab (Herceptin) used in the treatment of some breast cancers?
- Binds to EC domain of Her2/Neu and is important inhibitor of tumor growth. - Mechanism? Inhibition of receptor dimerization and activation, induction of apoptosis, stimulation of antibody or complement-mediated cytotoxicity
Types of phospholipases and their functions?
- Phospholipase A1: removal of FAs from C1 of phospholipid - Phospholipase A2: removal of FAs from C2 of phospholipid, usually arachidonic acid - Phospholipase C: removal of phosphate head group from C3 of PIP2 phospholipid creating DAG and IP3
What pyrimidine bases cannot be salvaged?
- Cytosine
What enzyme catalyzes the committed step of purine synthesis and what is its product?
- Formation of PRA is committed step of purine synthesis - PRPP + gln = PRA + glu (ez: amidophosphoribosyltransferase)
Draw a substrate saturation curve and indicate Vmax, Km, Vmax/2.
List a few mucopolysaccharidoses. Describe defect and symptoms. Genetics?
- Hunter’s: defect in iduronate sulfatase, accumulation of dermatan sulfate and heparan sulfate. Symptoms = skeletal abnormalities, mental retardation. X-linked recessive. - Hurler-Scheie: defect in alpha-iduronase, accumulation of dermatan sulfate and heparan sulfate. Symptoms = skeletal abnormalities, mental retardation. Autosomal recessive. - Sanfilippo’s: defect of heparan sulfate degradation. Symptoms = mild physical defects, severe mental retardation. Autosomal recessive.
The blood concentration of alanine and glutamine are higher than the concentration of other AAs. How do these AAs help rid the body of toxic ammonia?
- Alanine and glutamine are released in greatest quantity from muscle - BCAAs transfer their nitrogens to alpha-ketoacids (forming alanine and glutamine) and they travel to the liver where urea is formed
What is acute pancreatitis? Symptoms? Causes? Triggers? Treatment?
- Inflammatory disease of pancreas caused by premature activation of pancreatic digestive zymogens - Symptoms = abdominal pain, vomiting - Causes = pancreatic necrosis - Triggers = alcohol, infections, gallstones - Treatment = supportive via analgesics, fasting, elemental jejunal tube or TPN
Regulation of ribonucleotide reductase
- Allosteric: NTPs and dNTPs activate and inhibit (dATP inhibits) - Transcriptional
What is phenylketonuria. Causes? Pathology? Symptoms? Treatment? Why avoid aspartame if phenylketonuric?
- Mutation in phenylalanine hydroxylase (more common) or DHBtn reductase leads to a elevation of phenylpyruvate, phenylalanine and other metabolites. - Pathology: not fully understood, but: accumulation of phenylalanine competitively inhibits the transport of other AAs across the BB barrier, which might interfere with NT synthesis. Also leads to reduced synthesis and increased degradation of myeline. Phe is also a competitive inhibitor of tyrosinase and intereferes with melanin synthesis - Symptoms: intellectual disability, recurrent seizures, hypopigmentation, eczematous skin rashes - Treatment: limiting dietary Phe (not eliminating, as it is essential), supplementation with tyrosine, treatment before child is 3 weeks of age, lifelong monitoring of plasma phenylalanine - Aspartame is a dipeptide of aspartic acid and methylated Phe derivative. Eating will cause formation of phenylalanine
How can one experimentally distinguish between noncompetitive and irreversible inhibition?
- removal of irreversible inhibitor does not restore enzyme activity; however, removal of non-competitive inhibitor will restore enzyme activity.
What is problematic about unsaturated and branched FAs in beta-oxidation? How are these handled?
- Unsaturated FAs: dbl bonds have to be moved around so enzymes used in beta-oxidation can recognize molecules and process them. a.) If dbl bond bw C3,4, isomerizes to trans-delta2-enoyl CoA b.) If dbl bond bw C4,5, reduced to trans-delta3-enoyl CoA, then isomerized to trans-delta2-enoyl CoA - Branched FAs: result from degradation of chlorophylls a.) requires peroxisomal alpha-oxidation, which starts with hydroxylation and ends with release of CO2
How do problems in gluconeogenesis cause fasting hypoglycemia and metabolic acidosis?
- Pyruvate can be oxidized to acetyl-CoA and moved into TCA or can be oxidized to lactate by lactate dehydrogenase. - When issues occur with gluconeogenic enzymes, much pyruvate can be oxidized to lactate as opposed to taking gluconeogenic pathways, leading to high levels of serum lactate and metabolic acidosis. - For example, when pyruvate carboxylase functions correctly, pyruvate is converted to oxaloacetate and is prevented from forming lactate and is now dedicate to moving through the gluconeogenesis pathway.
What molecules (besides ketogenic/glucogenic) are derived from tyrosine?
- Catecholamines (dopamine, NE, epi) - Thyroid hormones – T3/4 - Melanin
How is ATM activated? Implication
- ATM is activated by replication forks: when RFs are present, DNA replication is present and cell-cycle needs to be halted until this completes - ATM also activated by double-stranded breaks
What is myasthenia gravis and cystic fibrosis. Name the defective ion channels in each.
- Myasthenia gravis: autoimmune disease characterized by muscle weakness and fatigue to the muscles involved with talking, swallowing, facial expression, chewing and eyelid movement. It is the result of self-antibodies targeting nicotinic ACh receptors at the NMJ - Cystic fibrosis: genetic disorder (pop in Caucasians) characterized by multi-organ disease, main manifestation is the accumulation of thick mucous secretions in lungs. Leading to recurrent infections. It is the result of a mutation to a chloride channel, leading to defects in fluid and electrolyte transport.
How do serum lactic acidoses occur as a result of defects to complexes I-IV, administration of DNP, administration of cyanide and lack of oxygen?
- Defects in complexes I-IV would result in “back up” of intermediate substrates / electron carrier molecules, including NADH. This would result in lack of NAD+, which is limited in supply. End result is that pyruvate builds up in the cell and is reduced to lactate via LDH enzyme. Lactate is an acid and therefore a lactic acidosis is occurring here. - DNP, cyanide and lack of oxygen cause the exact same thing to occur.
List endogenous uncoupling proteins. What are their functions?
- UCP1-4. These are found in brown fat, skeletal muscle, brain and other parts of the body and function to increase body temperature.
What is the two hit model? Describe this model in relation to the development of retinoblastoma. What is the normal function of Rb?
- Tumor suppressor genes inhibit proliferation - Damage to both alleles must occur to allow unregulated proliferation as the genes are recessive - This is why it is called two hit model - Individuals inheriting one mutant allele of tumor suppressor gene are at increased risk for certain cancers. If somatic mutation in second allele, tumor growth will occur Retinoblastoma mutation: - Rb protein is phosphorylated by cyclin D-CDK4/6 or cyclin E-CDK2. When phosphorylated, drives cell cycle. - Inherited form: one mutant allele from parent, somatic mutation of second allele in retinal cell leads to retinoblastoma. Tumor tends to develop in infancy - Sporadic form: two separate somatic mutations in a retinal cell or its progeny produces retinal cell in which both copies of functional Rb are lost - Symptoms: Leukocoria = white pupil, represents calcified intraorbital masses
Describe biochemistry behind HPV-induced cervical cancer
- HPV virus produces E6 and E7 proteins that target p53 and Rb respectively leading to ubiqutination
What is Wernicke-Korsakoff syndrome? What are the symptoms?
- It is an advanced thiamin (B1) deficiency that typically occurs in alcoholics. Symptoms include mental confusion, ataxia and loss of eye coordination.
How can oxaloacetate initiate gluconeogenesis?
- Malate-oxaloacetate shuttle. Oxaloacetate can be moved from the mitochondria to the cytoplasm via this shuttle and gluconeogenesis can occur.
LHON
- Most prevalent mitochondrial disorder. Rare at 1/50000- Caused by mutation by ND1 gene (oxphos)- LHON leads to a rapid deterioration of the optic nerve- Exhibits heteroplasmy as mitochondrial disorder
Describe the properties of HbS, the variant of hemoglobin found in sickle cell anemia.
- HbS is an altered Hb structure where a glutamate residue in the beta chain has been substituted for valine. Glu is a acidic hydrophilic AA, which valine is a non-polar, aliphatic AA. As a result, a “sticky hydrophobic pathy” is generated in the betal chains. When in the R-form, it is shielded from water. When in the T-form; however, it is exposed to surface. When in this form, it interacts with other Hb molecules to avoid interaction in polar environment and polymerization of poly Hb is catalyzed. This distores the shape of RBCs. Cells block blood vessels and damage organs.
Why aren’t ketone bodies used in liver or kidney?
- These tissues don’t express acetoacetate:succinyl-CoA transferase to generate the intermediate: acetoacetyl-CoA that generates acetyl-CoA.
What are the products of pyrimidine degradation? How are these secreted?
- Beta-alanine and beta-aminoisobutyrate - Water soluble and eliminated in urine
Explain the effect of hypomethylation on genome stability
- Hypomethylation reactivates transposable elements (jumping genes) that lead to somatic recombination and genomic instability.
What is Hartnup disease? Symptoms? Treatment?
- Rare genetic disorder affecting transporter of large, neutral amino acid resulting in no absorption of these amino acids across intestinal epithelial cells, also in prox tubule of kidney causing elimination issue - Symptoms? Similar to pellagra, which is niacin deficiency – 4 D’s – diarrhea, dermatitis, dementia, death. - Treatment? Dietary supplementation with niacin
Describe the progression of ribosome assembly
1.) GTP binds eIF2a 2.) GTP:eIF2a becomes bound to Met-tRNA to form ternary complex 3.) 40S:eIF3 binds ternary complex (with eIF1 and eIF1alpha) 4.) mRNA now binds small subunit and pre-initiation complex is formed (with aid of eIF-4a, eIF-4b, eIF-4f, eIF-5 and PAB) 5.) eIF-5b:GTP are added to this complex displacing hydrolyzed GDP:eIF2a and 60 S subunit is recruited and positioned with met-tRNA in P site. Elongation can now ensue
What do protons bind to on Hb?
-His. Causes formation of salt bridge, which stabilizes T-form.
What is allele heterogeneity?
- Different mutations in the same gene cause different phenotypes. Mutations can be gain of function or loss of function
What molecule does FA synthesis begin with? What are the second, third… molecules used?
- FA synthesis begins with acetyl-CoA and then joins with malonyl CoA during round 1 - Round 2-X begins with malonyl-CoA.
Why do T1 diabetic pts often present with DKA whereas type 2 don’t?
- Function of insulin in addition to glucose metabolism is to repress ketone body production and inhibit lipolysis. - In absence as is case with T1 diabetics, large amounts of FFAs are released, ketogenesis ensues and ketoacidosis results. - Lipolysis is seen in T2 diabetics, but not as much as insulin is still available in large amounts and does have somewhat of an effect of repressing lipolysis.
What are the two causes of megaloblastic anemia?
- B12 deficiency - Folate deficiency
Describe problems associated with refeeding and causes of refeeding syndrome. Consider what starvation leads to? How to refeed?
- Starvation: 1.) leads to degradation of digestive enzymes, 2.) depletes intracellular phosphate pools and 3.) depletes potassium stores - Problems: 1.) digestion is impaired and feeding leads to diarrhea and dehydration, 2.) glycolysis starting soaks up phosphate from serum leading to life-threatening hypophosphatemia and 3.) sudden insulin release (insulin moves K into cells) lowers serum potassium further - Watch electrolytes (esp. phosphate and K)
List the enzymes involved in glycogen synthesis. Explain how each is regulated. What are the factors that stimulate and inhibit each.
- Hexokinase: +: insulin; -: G6P - Glucokinase: +: insulin - Phosphoglucomutase: not regulated - UDP-glucose pyrophosphorylase: not regulated - Glycogen synthase: +: insulin; -: glucagon, epinephrine - Branching enzyme: not regulated
In what cells does insulin have a function? What response?
- Muscle: uptake of glucose, production of glycogen - Liver: production of glycogen, production of TAG - Adipose: uptake of glucose
What is Gly made from?
- From serine, which is made from 3-PG
Names of 70S ribosome inhibitors
- Streptomycin - Neomycin - Gentamicin - Tetracycline - Chloramphenicol
What is imprinting? Explain the time and effects of imprinting
- Imprinting is a form of DNA silencing that marks a chromosome as having come from the paternal or maternal parent. Why care? Transcriptional activities of paternal and maternal chromosomes are different.- Imprinting takes place during gametogenesis. Chromosomal regions are silenced by DNA methylation and histone deacetylation. This persists throughout the life of the individual.- Parent-of-origin imprint is erased and rewritten during gametogenesis. Female will reprogram both her chromosomes to make them look like maternal chromosomes. Male reprograms both his chromosomes to make them look like paternal chromosomes
What enzyme(s) require(s) thiamin (B1)?
- Alpha-ketoglutarate dehydrogenase complex and PDH complex.
Li-Fraumeni
- XR- Defects in p53 causes brain tumors and leukemias- Two-hit model
What enzyme is defective in tyrosinemia-I? Symptoms? Treatment
- fumarylacetoacetate hydrolase - symptoms: severe condition affecting liver, kidney and peripheral nerves, fatal at young age if untreated (liver failure) - Dietary management and nitisinone (inhibits coversion of p-hydroxyphenylpyruvate to homogentisate)
What are two major classes and subclasses of drugs?
1.) Reversible inhibitors: removal of inhibitor fully restores enzyme activity a.) competitive: compete with and bind at substrate’s active site b.) non-competitive: binds at site other than active site forming inactive enzyme 2.) Irreversible inhibitors: removal of inhibitor does not restore enzyme activity
What is neurofibromatosis I? What is normal function of the protein?
- Symptoms/signs: café au lait spots, multiple non-malignant peripheral nerve tumors (neurofibromas) and iris Lisch nodules - Result of loss of function mutation in NF1 gene (recessive) that encodes neurofibromin that normally accelerates rate of GTP hydrolysis by Ras, causing it to be in inactive form - Lack of NF1 gene function prolongs Ras signaling increases proliferation through MAP kinase pathway
Outline the changes that must occur before normal cells of the colon can develop into an adenoma and then a carcinoma.
- FAP pts inherit one defective allele from parent - Inactivation/loss of second allele occurs = - Proto-oncogene mutation, typically in Ras and loss of tumor suppressor genes typically TP53 causes adenomas - Additional mutations, gross c/smal changes, increased telomerase leads to carcinoma
Glycogen storage disorders
- AR- Hypoglycemia, accumulation of glycogen
What is the relationship between the magnitude of Km and enzyme/substrate affinity?
- inverse relationship - low Km = high S-E affinity - high Km = low S-E affinity - means some enzyme-substrates interact better than others
Draw function of insulin in regulation of FA (TAG) synthesis.
Name the five most frequent birth defects. Give frequencies
1.) Heart defects – 1/100-2002.) Pyloric stenosis – 1/3003.) Neural tube defects – 1/10004.) Orofacial clefts – 1/700-10005.) Clubfoot – 1/1000
Retinoblastoma
- Autosomal dominant inheritance, expression at cellular level is autosomal recessive- Defects in Rb protein, leads to predisposition and / or development of cancer- Two-hit model
Know some examples of α-neurotoxins and how these compounds exert their effects.
- alpha-conotoxin: produced by cone shell - alpha-cobratoxin: produced by cobra - alpha-bungarotoxin: produced by krait - tubocurarine: produced by plant These cause paralysis by blocking nicotinic ACh receptor on muscle.
What AAs are made from pyruvate and 3-PG?
- Ala, Ser
Why is the formation of cAMP and irreversible reaction?
- Generation of cAMP from ATP via adenylate cyclase produces pyrophosphate (PPi). PPi is hydrolyzed into 2xPi via pyrophosphatase, which drives the formation of cAMP.
Synthesis of cysteine
- s-adenosylhomocysteine is acted on by adenosylhomocysteinase, which generates adenosine and homocysteine - cystathionine beta-synthase and cystathionase are both B6 requiring enzymes
Explain the function of the HOX transcription factors in development
- Following specification of axes, patterning takes place. Patterning defines which end of undevelopmed mass of cells is head, which is tail. It segments cells to define which parts become head, thorax, abdomen etc.- Patterning along ant/post axis is determined by homeobox (HOX) genes, which are a family of transcription factors containing a special DNA binding domain called homeodomain. There are 4 HOX clusters on 4 chromosomes- Expression of each of the genes belonging to a cluster correlates with position of respective cell in embryo and with timing of expression. Each cell along axis experiences a different ratio of expression of different HOX genes. Ultimately, the pattern of HOX gene expression determines fate of a cell in segment.
What are the precursors for gluconeogenesis?
- Lactate, - Amino acids - Glycerol
Where is cholesterol synthesized, what is the rate-limiting step/enzyme, what is the precursor used, in what other pathway is this precursor seen? What enzyme is used to make this precursor? Is this the same enzyme used in the previous pathway? Explain. During what environmental conditions is the precursor made in both pathways?
- Cholesterol synthesis takes place in the liver, intestine and reproductive tissues - Rate-limiting step = HMG-CoA reductase - Precursor = HMG-CoA – seen during synthesis of ketone bodies - Precursor synthesized by cytosolic HMG-CoA synthase isoform that is active in well-fed state. Mitochondrial HMG-CoA synthase isoform synthesizes the precursor when in starving/fasting state.
How does aspirin function?
- It is an irreversible inhibitor of prostaglandin synthase and binds to the active site of the enzyme forming a covalent complex.
Outline salvage of pyrimidine bases
- Orotate/uracil and thymine + PRPP = XMP + PPi (ez: pyrmidine phosphoribosyltransferase) - No cytosine salvage
What is the substrate for NO synthase? What affect does NO have on the vasculature? What enzyme is affected by NO? How is NO signaling turned off?
- NO produced from arginine by the enzyme nitric oxide synthase. It is a gas and diffuses readily in cell, acting locally due to short half-life and conversion into nitrates, nitrites when reacted with o2 and water. - Typical function of NO is to cause relaxation of smooth muscle. - Typical mechanims: ACh is released from nerve terminal, causes activation of NO synthase in endothelial cells, triggering conversion of arginine into NO. NO diffuses to neighbouring smooth muscle cells, binds guanylate cyclase in the cytoplasm, stimulating production of cGMP, which activates cGMP-dependent protein kinase, leading to smooth muscle relaxation. - Inactivation: NO has a short half-life as it is highly reactive with oxygen and water, produced nitrates and nitrites. In addition, cGMP is degraded by phosphodiesterasterases yielding GMP, which are not able to activate cGMP-dependent protein kinases that lead to smooth muscle relaxation.
What is the Bohr effect? What causes it to occur?
- It refers to oxygen’s binding affinity of Hb being inversely related to acidity and concentration of CO2.
- When CO2 concentration is high and acidic environment exists, o2 affinity for Hb is low and therefore Hb is more likely to give up o2 in tissues where this environment exists.
- Causes: H+ binds to histidines foming stabilized T-form salt bridge; CO2 binds to N-terminus forming negatively charged carbamates increasing stabilization of T-form.
Discuss concept of reduced fitness and new mutations in context of autosomal dominant disorders
- In some autosomal dominant disease, an allele carriers has a reduced chance of reproduction, ie. reduced fitness- Therefore, reduced fitness of the carriers would lead to disappearance of the mutant alleles in populations- However, allele frequencies stay constant as new mutations appear constantly and compensate for the loss of mutant alleles- Low fitness of carriers means high percentage of new mutations- If parents are not affected by dominant disease, affected children could have inherited a new mutation- New mutations are seen in DMD, NF and achondroplasia. Genes implicated in these disorders are large, complex or contain mutation hotspots.
Would a normal cell divide if chromosomes were not correctly attached to the mitotic spindle? Explain
- No - Anaphase of mitosis is delayed until chromosomes attach to mitotic spindle - Correct assembly of mitotic spindle activates anaphase promoting complex (APC) - APC allows degradation of cohesin complexes, which hold sister chromatids together at centromere, sister chromatids can move to opposite poles - APC acquires different subunit and causes degradation of cyclin A or B
Describe heme degradation and excretion
- Heme is cleaved between A and B rings by heme oxygenase, yielding biliverdin - Biliverdin reductase used NADPH to form bilirubin, which is unconjugated (aka indirect) - Becomes bound to albumin and travels to liver where it is conjugated to two UGT molecules and becomes bilirubic diglucuronide. This is form that is excreted in bile - When in gut, BDG is modified into urobiliongen by gut and then spontaneously to urobilins / stercobilins which is found in feces - Some urobilinogen is absorbed back into blood and spontaneously converted into urobilin, which is urinated out.
Biochemical basis for megaloblastic anemia – explain how B12 deficiency leads to functional folate deficiency
- Vitamin B12 deficiency results in deficiency in methionine synthase deficiency and therefore accumulation of N5-methyl THF and concomitant decreased in concentrations of more oxidized forms of THF, therefore Vitamin B12 leads to a functional folate deficiency - N5 N10 methylene is one of these more oxidized forms that would decrease. This is required for DNA synthesis (thymidine) - N10 formyl THF is required for purine synthesis, it is however decreased now too - Therefore lack of THF in oxidation states blocks DNA replication - Result is production of megaloblastic anemia – RBCs with large cytoplasm, but unable to divide
What molecules accumulate with a vitamin B12 deficiency? Explain which reactions these are implicated in?
- 1.) D & L methylmalonyl-CoA (D and L methylmalonate) and 2.) N5-methyl THF - 1.) In process of converting VOMIT AAs to succinyl-CoA - 2.) In converting homocysteine and N5 methyl THF into methionine and THF respectively
Describe synthesis of prostaglandins, thromboxanes and leukotrienes.
1.) Prostaglandins - AA to PGG2 via COX1/2 - PGG2 to PGH2 via PGH synthase - PGH2 is precursor to other prostaglandins via PGD/PGE/PGF synthase enzymes 2.) Thromboxanes - PGH2 to TXA2 via thromboxane synthase - TXA2 to TXB2 via hydrolysis in blood 3.) Leukotrienes - AA to leukotrienes via lipoxygenase and other enzymes
Role of glutathione-S-transferase enzyme family?
- catalyze transfer of glutathione to molecules with reactive electrophiles, generating thioether linkage bw compound and cysteine of glutathione, preventing interaction with other molecules
Describe chromosomal defects in Di George Syndrome
- Deletion in chromosome 22 q. Frequency = 1/4000. Usually a new mutation- Malformations include: congenital heart defect, immunodeficiency, hypoparathyroidism, mental retardation, cleft palate
Function of glutathione
- Intracellular reducing agent: scavenging free radicals and destroying peroxides - Drug detoxification
What is penetrance? What is expressivity?
- Penetrance: percentage of people with disease gene who develop symptoms- Expressivity is the severity of the symptoms
Heme synthesis enzymes affected by lead
- Porphobilinogen synthase - Ferrochelatase
Contrast haploinsufficiency and dominant negative effect in the development of osteogenesis imperfecta subtypes
- Osteogenesis imperfecta-1 is caused by mutations in the collagen I genes.- OI-1 causes deformity of skeleton and predisposes bones to breakage. - Frequency = 1/10000, AD- There are 4 different classes of OI depending on the number of proalpha1 and 2 collagen chains and also if the chains are defective or not. Defect in one chain may disturb the larger structure. This is referred to as dominant negative effect.- Allele heterogeneity is also exhibited in this disease in that the severity depends on the AA exchanged. Type I have brittle bones and blue sclerae without bone deformities. Type II is perinatal lethal. Type III is progressively deforming. Type IV has bone deformities with predisposition to bone fractures.
Explain the role of sorbitol in the pathology of diabetes
- In DM pts, there is more free glucose in the cells than in other pts. This is a result of many things, including the failure of phosphorylation by hexokinase/glucokinase. This turns on aldose reductase, which uses NADPH to general sorbitol, which is used by polyol DH to form fructose, consuming NAD. As a result, antioxidant defenses that rely on NADPH are weakened and NADH is high, so glycolytic capacity is reduced. - Sorbitol also is osmotically active and draws water into cells, distorting cellular/tissue structure
What is THF? What is its function? Where is it derived from?
- THF = tetrahydrofolate - Serves as a carrier of one carbon groups - Derived from folate, vitamin B9, which is found in foliage, green leafy veg, liver, eggs and beans
What are disorders of FA degradation?
- Primary carnitine deficiency - Acyl-CoA dehydrogenase deficiency – eg. VLCAD, LCAD, MCAD and SCAD. MCAD is most common. - Refsum disease – alpha-oxidation deficiency - Peroxisome biogenesis disorders (PBD)
Describe regulation of G1/S transition
- S phase requires active cyclin A-CDK2, which is initially formed as inactive complex with inhibitor called p27kip1 - Late g1: cyclin E-CDK2 is desphosphorylated by phosphatase (Cdc25A) - cyclin E-CDK2 phosphorylates p27kip1 in complex w/ cyclin A-CDK2, cyclin A-CDK2 is activated by being freed from p27KIP2 - It promotes DNA replication by phosphorylating components of ori complexes
Beri-beri. a.) What is it? What is it caused by? b.) What are the symptoms associated with it? c.) What are the two forms of this disorder? d.) What organ/tissue(s) are most affected by this disorder? e.) Do RBCs contribute to this condition? Explain. f.) Which populations are susceptible to this disorder?
- a.) It is a severe thiamin (B1) dietary deficiency. - b.) Neuromuscular symptoms – muscle weakness, muscle atrophy, fatigue, peripheral neuropathy and lactic acidemia. - c.) Dry beri-beri which affects neuromuscular function, does not lead to fluid retention; Wet beri-beri causes peripheral edema and cardiac failure. - d.) It affects the nervous system and musculoskeletal system primarily. - e.) No, as they do not contain mitochondria, where enzymes such as PDH complex and aKGDH that participate in linking glycolysis to TCA cycle and TCA cycle function respectively. - f.) Populations that have high intake of polished rice diets.
Explain why NADH concentration increases while NADPH concentration decreases in alcohol-metabolizing cells.
- The main step to handling ethanol in the liver is through two dehydrogenases (alcohol DH and aldehyde DH), both, which produce NADH. - The other way to handle ethanol is through the higher capacity MEOS system, which as a means to process the alcohol, also oxidizes NADPH.
Give the frequency of chromosomal aberrations, both at conception and at birth
- Structural chromosomal abnormalities (rearrangements, loss and duplications) occur in approximately 0.5 % of pregnancies and 0.2 % of live births
What enzyme is involved in regulating AA catabolism? How does regulation occur?
- Primarily regulated by liver glutamate dehydrogenase (in mitochondria) - Regulation of glutamate DH is by cellular energy charge - High energy (high GTP, high NADH) = inhibition of enzyme - Low energy (high ADP) = activation of enzyme
Describe base excision repair process using the example of the removal of a cytosine residue that has been deaminated to uracil.
- DNA glycosylases recognize diff types of altered bases in DNA and catalyze their hydrolytic removal - Cytosine spontaneously deaminated to uracil - Uracil DNA glycosylase removes uracil base creating AP site - AP endonuclease introduces nick - DNA phosphodiesterase removes remnant sugar and phosphate - DNA Pol and ligase fill in correct base
Explain how LDL receptor production changes in response to cholesterol. Discuss mechanism
- Transcription of LDL receptor gene is upregulated in response to low cellular cholesterol - Result: more LDL receptor production and enhanced cholesterol uptake from blood Low-level transcription - SP1 (zinc-finger protein) binds to GC rich regions in LDL receptor promoter - SP1 requires CRSP protein cofactor to be activated - SP1 and CRSP help pol II and GTFS to assemble at promoter - These are all considered basal transcription factors Up-regulated transcription - Requires basal transcription factors - Also SREBP-1a enters into nucleus as triggered by low cellular cholesterol - SREBP-1a binds to SRE and recruits HAT activity plus some other proteins - Result = enhanced transcription of LDL-receptor gene
Explain the dominant inheritance of familial hypercholesterolemia
- FH is frequent 1/500 person disease, AD- Heterozygotes have 2-fold elevation in LDL levels as there are insufficient receptors to clear LDL from serum. Homozygotes have 4-fold evelated in LDL levels. This is an example of haploinsufficiency, allele heterogeneity- Symptoms: xanthomas
What is meant by term ‘salvage pathways’? What are the sources of substrates for these pathways?
- Conversion of free bases and nucleosides to nucleotides - Sources are: diet, purine/pyrmidine nt degradation products
What is methemoglobin?
-Type of hemoglobinopathy. This is Hb where Fe2+ is oxidized to Fe3+ and has reduced ability to deliver o2 to tissues.
Which molecules are allosteric effectors? What are their signals and affects?
What is Rett Syndrome?
- X-linked dominant disorder mapped to mutations in the gene for methyl-cytosine binding protein MECP2- Mutation leads to loss of transcriptional silencing- Symptoms: autism-like symptoms, repetitive teeth grinding and hand-wringing, motor problems and characteristic gait. Onset age 6-18 months
What gluconeogenic deficiency(ies) seen in human? What is/are the clinical presentation(s)?
- G6PD deficiency: defect that lowers the activity of PPPathway and cells have lower NADPH levels. These levels impair glutathione reduction and deprive RBCs of antioxidant protection. Affected pts are very sensitive to hydrogen peroxide, which are produced in infections (by macrophages), by drugs (eg. Primaquine that is used to treat malaria and pneumocystis pneumonia) and during consumption of fava beans (known as favism) as these cause oxidatie stress and trigger hemolytic crisis and hemolytic anemia. Most prevalent in African and Mediterranean Americans. It is x-linked recessive.
What is the enzyme that commits acetyl-CoA to FA synthesis? What does this reaction do?
- Acetyl-CoA carboxylase, which converts acetyl-CoA to malonyl-CoA
Treatment of argininosuccinate lyase deficiency
- As a result of this deficiency – argininosuccinicaciduria - Treat with arginine – supports continued citrulline synthesis and continuation of cycle. Argininosuccinate is water soluble and relatively non-toxic, gets eliminated from kidney as waste - Argininosuccinate carries both nitrogens
Describe vitamin B12 absorption into body and storage
- R-binders in salivary enzymes bind B12 and pass it onto intrinsic factor, produced by stomach parietal cells - Absorbed in ileum through receptor mediated endocytosis - Binds to transcobalamin and is transported to tissues - Preferentially distributed to liver as vit-B12:transcobalamin complex and stored there. Kidney has some B12 stores
List and describe the glycogen storage diseases (GSD). What is occurring in each and what is the clinical presentation?
- GSD-I: aka Von Gierke’s disease: deficiency in G-6-phosphatase. Leads to hypoglycemia and increased glycogen stores in liver. This ez is only found in liver. - GSD-II: aka Pompe’s disease: deficiency in alpha-glucosidase (aka acid maltase). It is required for the degradation of glycogen, which with the deficiency, slowly accumulates in the lysosome. Over time, this process eventually kills affected cells. Death occurs by cardiac or respiratory failure. - GSD-III: aka Cori’s disease: deficiency in debranching enzyme. Glycogen granules grow large because only the non-branched, outer layers of the deposits can be degraded. Presents in early childhood or infancy with hepatomegaly, hypoglycemia and growth retardation. Can also present with muscle weakness. Some pts develop cardiomyopathy. - GSD-V: aka McArdle’s disease: deficiency in glycogen phosphorylase in muscle. Muscle is unable to use glycogen. Leads to greater than normal glycogen stores in muscles. During periods of high glucose demand, ie. exercise, patients experience muscle cramps. - GSD-VI: aka Hers disease: deficiency in glycogen phosphorylase in liver. Presents with mild to moderate hypoglycemia, mild ketosis, growth retardation and prominent hepatomegaly.
Fuel preferences / energy needs of RBCs, muscles, brain, adipose and liver
- RBCs: glucose, anerobic metabolism - Non-cardiac muscle: glucose-anaerobic/aerobic, FFAs - Cardiac muscle: glucose aerobically only, FFAs - Brain: glucose aerobically, ketone bodies after serious period of starvation - Adipose: glucose, TAG – FAs - Liver: FAs, glucose, AAs and lactate
Describe the effects of 5-azacytidine on genome methylation
- Hypermethylation can be reversed by this drug, which is a DNMT inhibitor. Treatment serves to allow for re-activation of silenced tumor suppressor genes
Explain the different types of adrenergic receptors.
- 1.) Alpha receptors a.) alpha-1 subtype: Gq protein coupled = activation of PLC b.) alpha-2 subtype: Gi protein coupled = inhibition of adenylate cyclase - 2.) Beta receptors three subtypes (beta-1,2,3) are Gs protein coupled = activation of adenylate cyclase
What is situs inversus and situs ambiguous, what causes it?
- Both are defects in left/right axis formation- Situs inversus: all organs are complete mirror images in what is normally found (known a situs solitus). Usually asymptomatic- Situs ambiguous describes a more serious condition in which orientation of organs is randomized. This is usually accompanied by heart defects.
Under what conditions will lactic acid fermentation occur in the body? Why? What enzyme is involved? Why is this problematic in the body?
- Concentration of NAD to NADH are tightly monitored. Reason: NAD+ is limited in concentration. NADH must be recycled to NAD+ in order for glycolysis to continue. Lactic acid fermentation takes the electrons from NADH and places them onto pyruvate, generating lactate. This is done by lactate dehydrogenase. - Lactic acid buildup leads to lactic acidosis. Cori cycle tries to circumvent this from occurring.
What are other pathologies related to mutations in collagen?
- Ehlers-Danlos: CT disorder characterized by skin fragility, skin hyperextensibility and joint hypermobility resulting from mutations in collage proteins or proteins required for collage processed. Some benign symptoms, others complicated including bowel and arterial rupture. - Osteogenesis imperfecta: brittle bone diseases characterized by fragile bones, abnormalities in teeth, hearing losss. It can be lethal, otherwise individuals can have normal lifespan with slightly reduced bone mass.
RBC surface antigens. Core? Sugar residues for O, A and B antigen?
- Core: Serine – Gal – GlcNAc – Gal X – Fucose - O: Serine – Gal – GlcNAc – Gal X – Fucose - A: Core – Gal X attached to GalNAc as well as Fucose - B: Core – Gal X attached to Gal as well as Fucose
Describe the 4 main groups of amino acids. What are their characteristics?
a.) non-polar, aliphatic: hydrophobic and chained/branched, found interior aspect of proteins, uncharged Gly, Ala, Val, Leu, Ile, Met, Pro • Gly – no asymmetric carbon (2 Hs) • Pro – ring structure • Met – sulfur-containing AA b.) aromatic: hydrophobic (non-polar rings), often found interior of water-soluble proteins, uncharged Phe, Tyr, Trp • Tyr – has OH group and can be phosphorylated c.) polar, uncharged: hydrogen bond, interior/exterior of proteins Ser, Thr, Cys, Asn, Gln • Ser/Thr – have OH groups that can be phosphorylated • Cys – sulfur-containing AA, forms disulfide bridges with other thiol containing molecules (ie. cystine = 2 cysteines) d.) Ionizable side chained AA – basic/acidic: Acidic: Asp, Glu (net -1 charge at physiological pH) Basic: Lys, Arg, His* (net +1 charge at physiological pH) * His can be basic/uncharged as pKa = 6.0
What is familial adenomatous polyposis? Outline the role of APC in the WNT signaling pathway. How does loss of APC function lead to cell proliferation?
- Hereditary condition due to mutations in APC (adenomatous polyposis coli) gene that encodes tumor suppressor APC. Develop 100-1000s of adenomatous polyps. 100% of untreated FAP pts developed colorectal adenocarcinomas. Prophylactic colectomy is done - APC usually functions to down-regulate WNT signaling pathway - When mutation exists, WNT signaling is activated and expression of cyclin D, Myc and other growth-promoting genes occur - Additional mutations are implicated: oncogenic forms of Ras, may impact p53 function
Describe utilization of glucose by brain, RBCs, brain, liver, muscle and adipose.
- RBCs: glucose through glycolysis to produce lactate (used in liver), G6P into PPP - Brain: glucose through glycolysis to produce acetyl-CoA (oxphos), G6P into PPP. No production of lactate - Muscle/heart: glucose through glycolysis to produce both lactate (used in liver, ? produced in heart) and acetyl-CoA (oxphos), G6P into PPP, G1P as intermediate into glycogenolysis and glycogen synthesis - Adipose tissue: same as muscle/heart, except no lactate production AND acetyl-CoA used for FA synthesis in addition to oxphos. - Liver: glucose through glycolysis to produce pyruvate (to acetyl-CoA to oxphos or FA synthesis), pyruvate to OAA (to gluconeogenesis), G6P to PPP, G1P in glycogenolysis and glycogen synthesis. * no exit of glucose to serum unless from liver.
Impact of diabetes on glucose and FA metabolism.
1.) Glucose: Insulin has no impact on liver, fat and muscles, as a result: - Glucose comes in, remains in serum - Liver receives AA from muscles and performs gluconeogenesis - Fat leaves adipose and enters liver, where ketone bodies are generated 2.) Lipids: insulin does not activate LPL and deactivate HSL, as a result: - Chylomicrons carrying dietary TAG stay in serum and cannot enter adipose via action of LPL - HSL is on and is performing lipolysis, TAGS are degraded into FAs, which enter circulation and travel to liver. FAs are generated in excess of what is needed to generate ketone bodies. As a result, TAGs are synthesized and packaged into VLDL, which become elevated in blood.
How is CDK4/6 activity inhibited
- INK4 proteins inhibit these proteins. - INK4 transcription is stimulated by growth inhibitory factors
What is purpose of vitamin B12 in THF metabolism and keeping functional folate pool?
- Serves to take the most reduced form of THF = N5 methyl THF back to THF form and in the process converts homocysteine to methionine - THF has no other functions in most reduced form, only when in oxidized forms does it have specific functions, including in DNA synthesis
What are point mutations? How might point mutations arise? Distinguish bw silent, missense, and nonsense mutations.
- Exchange of one nt for another - Caused by replication errors, chemical mutagens, radiation, DNA damage repair - Silent: no changes to AA - Missense: change from one AA to another - Nonsense: change from AA to stop codon
How can cholesterol synthesis be inhibited in a clinical setting? Explain how this works.
- Use of statins - Statins inhibit the HMG-CoA reductase enzyme and prevents synthesis of mevalonic acid, a precursor molecule to farnesyl-PP, a precursor to cholesterol.
ETC. a.) What are the components? What are the enzyme complexes involved? Name them b.) What reaction does each component catalyzed? List reduced substrates and oxidized products. c.) What is the sequence of flow through these carriers? Draw and indicate the reactions of each of the complexes. Include movement of protons. What coenzymes and metals do each of the complexes require? d.) Which components are proton pumps? e.) There are other dehydrogenases besides complexes I through IV contained in the mitochondrion. What are they?
- a.) dehydrogenase enzymes (complexes), heme-iron proteins (aka cytochromes), iron-sulfur proteins, CoQ/ubiquinone Dehydrogenase enzymes are: Complex 1: NADH-CoQ reductase Complex 2: Succinate-CoQ reductase Complex 3: CoQH2-cytochrome c reductase Complex 4: Cytochrome c oxidase - b.) Complex 1: NADH + H+ + CoQ = NAD+ + CoQH2 Complex 2: Succinate + CoQ = Fumarate + CoQH2 Complex 3: CoQH2 + 2 cyt c (Fe3+) = CoQ + 2 cyt c (Fe2+) + 2H+ Complex 4: 4 cyt c (Fe2+) + 4H+ + o2 = 4 cyt c (Fe3+) + 2H2o - c.) see picture - d.) Protons are moved to the intermembrane space via complex I, II and IV - e.) Fatty acyl-CoA DH and glycerol-3-P DH. These both reduce CoQ and are not part of the std I-IV complexes
How do the oxygen-binding properties of HbF and HbA1 differ? Why is this important?
- HbA1 refers to the alpha2beta2 Hb tetramer, which is the most common form in adults, account for over 90% of total in blood - HbF is the predominant Hb tetramer present in the 2nd/3rd trimester of development. In contrast to adult Hb, HbF curve is shifted to the left indicating that at a specific o2 pressure, HbF is more saturated than adult Hb. Has higher affinity for o2 than adult Hb. This ensures that the fetus’ high metabolic o2 requirements are met. - This is due to the replacement of a histidine residue with a serine residue in the gamma chain of HbF. As a result, HbF has reduced affinity for 2,3-BPG and is left shifted.
Define primary structure, secondary structure, tertiary structure, and quaternary protein structure.
a. Primary structure: the amino acid sequence of the polypeptide chain b. Secondary structure: a segment of polypeptide chain that has regular repeating structure. Results from H-bonding between the C=O and H-N groups of the polypeptide backbone. Alpha-helices and beta-pleated sheets. c. Tertiary structure: the 3D structure resulting from the interaction of various secondary structures and non-ordered regions of the polypeptide chain, results from disulfide bridges (covalent) and hydrogen bonding, ionic interactions (salt bridges) an hydrophobic forces (all non-covalent) d. Quaternary structure: protein molecules that have more than one subunit, each with tertiary structure, have overall quaternary structure. The subunits associate through same forces found in tertiary structures
How does beta-oxidation differ in peroxisomes from other tissues?
- Beta-oxidation in peroxisomes involves preferential catabolism of LCFAs and produces hydrogen peroxide instead of FADH as seen in beta-oxidation in other tissue. Peroxisomes use oxidase enzyme
Explain how F26BP affects glycolysis. Include details about the enzymes involve, pathways activated and substrates affected.
- Take home message: high concentrations of F26BP stimulate glycolysis; low concentrations of F26BP inhibit glycolysis - F26BP is produced by enzyme PFK2 (produces F26BP from F6P) - F26BP activates PFK1 leading to increased production of F16BP - F26BP inhibits fructose bisphosphatase leading to increased production of F16BP - Insulin stimulates PFK2 via cAMP leading to increased concentration of F26BP, which stimulates PFK1, inhibits bisphosphatase and stimulating glycolysis - Glucagon inhibits PFK2 via cAMP leading to decreased concentration of F26BP, which means that PFK1 is inhibited, bisphosphatase is stimulated and glycolysis is inhibited - AMP stimulates PFK2, causing increased concentrations of F26BP, which stimulates PFK1, inhibits bisphosphatase and stimulated glycolysis
What molecules are derived from tryptophan?
- Serotonin - Melatonin - Niacin
Describe and explain graphically with 1/V vs. 1/[S] plots and pictorially with drawings: • irreversible inhibition
- Graphically indistinguishable from a non-competitive inhibition graph.
Why do some porphyrias cause photosensitivity?
- Porphyrins are conjugated systems, which absorb UV and visible light. - The light energy must be discharged upon being absorbed, so it is discharged into the tissues and generates ROS. As a result photosensitivity of skin occurs
Explain process of beta-oxidation. Include enzymes, substrates, cofactors and products.
Describe reactions that form triacylglycerols.
What is the role of phospholipids in prevention of respiratory distress syndrome in premature infants?
- Surface of lung epithelium is covered with secretion that prevents alveolar membranes from sticking together (surfactant) - This surfactant is rich in phospholipids, particularly dipalmitoyl phosphatidylcholine (sometimes called dipalmitoyl lecithin). - This surfactant is produced at about 31 weeks gestation. - Infants born prematurely have a lecithin/sphingomyelin ratio below 2, indicating they have insufficient amounts of surfactant, which puts them at risk for respiratory distress syndrome (RDS). - Artificial surfactant mixtures treat premature infants. - Also they are given corticosteroid growth hormones to stimulate lung maturation.
How does methotrexate function to inhibit thymidylate synthase?
- Methotrexate is an antifolate medication - Remember, N5-N10-methylene THF is needed to convert dUMP to dTMP
How does methylation silence transcription?
- Methylation of DNA occurs on cytosine residues in CpG islands- After methylation occurs, methylcytosine binding proteins bind methylcytosine.- MBPs interact with repressors of transcription leading to transcriptional block and HDACs that lead to chromatin condensation
CF. Inheritance, defect, frequency
- AR- Defect that impairs trafficking of CFTR chloride channel to cell surface causing pulmonary problems and pancreatic malfunction. CF pts have 2-5 times amount of NaCl in sweat. Severity varies (allele heterogeneity, modifier loci): pancreatic sufficient or insufficient- 1/2000
Describe how the receptor tyrosine kinases HER2 and ErbB1 can be converted into constitutively active forms that function as oncoproteins
- HER2 (aka Neu): point mutation allows activation of kinase in the absence of ligand - ErbB1: deletion of ligand bind domain results in constitutive activation of kinase domain
What is the malate-aspartate shuttle? Where does it occur? Draw it.
- It is a shuttle mechanism to move electrons from NADH in cytoplasm to the mitochondrion. It occurs in liver and heart.
Why is gluconeogenesis not a reversal of glycolysis? Explain. Explain what reactions occur to circumvent this issue.
- Glycolysis has 3 irreversible reactions: hexokinase, phosphofructokinase 1 and pyruvate kinase. In order for glucose to be synthesized, ie. gluconeogenesis, 4 new enzymes not seen in glycolysis are seen: Pyruvate carboxylase, PEP carboxykinase, Fructose-1,6-bisphosphatase and glucose-6-phosphatase.
Name 3 antineoplastic agents that are inhibitors of DNA replication and repair
- Cytarabine - Cyclophosphamide - Doxorubicin
Outline salvage of pyrimidine nucleosides.
- Uridine / cytidine + ATP = UMP / CMP + ADP (ez: uridine-cytidine kinase)
Fructose 1,6 bisphosphatase deficiency
- AR- Fasting hypoglycemia
Describe how a mutation in the amino acid sequence could affect protein structure and/or function. Give several examples.
A change in amino acid sequence will lead to different interactions and therefore different folding (see 14). Different structure will confer different function. The original purpose of the protein can no longer be served. Examples of diseases where misfolded proteins are implicated: • CJD: inherited or spontaneous • Kuru: infectious • vCJD: infectious Above diseases lead to spongiform encephalopathies (neurodegeneration, brain becomes spongy) • Parkinson’s: loss of dopaminergic neurons, formation of Lewy bodies (aggregates of alpha-synuclei protein seeds more) leads to tremor, bradykinesia, postural instability • Alzheimer’s: neurological condition leading to dementia from plaque/fibrillary structures in brain containing amyloid-beta and tau proteins that seeds more
Describe homocystinuria. Causes? Symptoms? Treatment?
- Grossly evelated homocysteine (plus other metabolites of this) accumulat in body and are seen in urine - Most commonly due to cystathionine beta-synthase mutation - Symptoms: dislocation of optic lens, osteoporosis, lengthening and thinning of long bones, thromboembolism, intellectual disability - Treatment: low methionine diet with cysteine supplements, pyridoxine or betaine supplements
Describe ways by which ATM/ATR kinases can prevent cell cycle progression in the face of DNA damage.
1.) ATM is activated by double-stranded breaks 2.) ATR is activated by UV light and certain DNA-damaging drugs - Both kinases stabilize p53 - P53 upregulates p21cip1 - p21 inhibits activates a kinase that prevents cdc25a and cdc25C from activating cyclin A/E-CDK2 (S phase) and cyclin A/B-CDK1 (M phase) respectively. - ATM and ATR also activate a checkpoint kinase that prevents cdc25a and cdc25C from activating cdc25a and cdc25C from activating cyclin A/E-CDK2 (S phase) and cyclin A/B-CDK1 (M phase) respectively
What roles do chromatin remodelling complexes, histone acetyltransferases (HATs), histone deacetylases (HDACs) and DNA methylation play in controlling the availability of genes for transcription?
1.) chromatin remodeling complexes: use ATP to change nucleosome structure temporarily to allow or inhibit transcription 2.) HATs: acetylate lysine residues in histones, reduce net pos charge of protein, weakens histone:DNA interaction, facilitates transcription 3.) HDACs: remove acetyl groups from histone, increasing net pos charge of protein, strengthens histone:DNA interaction, inhibits transcription 4.) DNA methylation: methyl groups added to cytosine, found in silent regions of genome, binds proteins that recruit HDACs to DNA, promoting condensation and inhibiting transcription
Molecular action of insulin
- Binds to IR in PM of target cells - IR = kinase, phosphorylates itself then IRS - Phosphorylation cascade ensues, but at level of enzymes, dephosphorylation occurs via phosphatase - Cell undergoes dramatic changes in protein activation, protein localization and gene transcription
Which enzymes of gluconeogenesis are regulated? What factors inhibit and stimulate these enzymes? Which is the main regulated step? Which are reversible/irreversible?
- Pyruvate carboxylase: +: acetyl-CoA; -: insulin - PEP carboxykinase: +: glucagon via cAMP; -: insulin, AMP - Fructose-1,6-bisphosphatase: +: citrate; -: F26BP, AMP (main regulated step) - Glucose-6-phosphatase: +: glucagon; -: insulin
What are the 2 sources of cytosolic NADPH?
- PPP via G6PD - Conversion of malate to pyruvate via malic enzyme
What is Smith-Lemli-Opitz Syndrome?
- Impairment of Shh signaling secondly to defect in cholesterol biosynthesis. - This is an autosomal recessive disorder affecting 1/20-50K- Leads to multiple severe congenital malformations
Describe and explain graphically with 1/V vs. 1/[S] plots and pictorially with drawings: • noncompetitive inhibition
What molecule is the temporary ammonium ion carrier in the body?
- glutamine
What inhibits thymidylate synthase?
- 5-fluorouracil - Methotrexate
Defect in Shh mutation
- Midline defects such as holoprosencephaly = failed or incomplete separation of forebrain early in gestation
Describe de novo synthesis of pyrimidines
1.) Synthesis of uridine nucleotides (three* enzymes below are part of CAD multifunctional protein) - Gln + bicarb + ATP = carbomyl phosphate + ADP + glu (ez: *carbomyl phosphate synthetase II) - Carbomyl phosphate + Asp = N-carbamoyl aspartate + Pi (ez: *asp transcarbamoylase) - N-carbamoyl aspartate = dihydroorotate (ez: *dihydroorotase) - Dihydroorotate + NAD = orotate + NADH (ez: dihydroorotate DH) - Orotate + PRPP = OMP + Pi (ez: ^orotate phosphoribosyltransferase) - OMP = UMP + Co2 (ez: ^OMP decarboxylase) Notes: three beginning ezs are part of *CAD multifunctional enzyme, last two are part of ^UMP synthase multifunctional enzyme 2.) Synthesis of cytosine nucleotides - UMP is converted to UTP via nucleoside-5-monophosphate kinases and nucleoside diphosphate kinases - UTP + glut + ATP = CTP + gln + ADP + Pi (ez: CTP synthase) 3.) Synthesis thymine nucleotides - Note: TMP, TDP or TTP are never synthesized (never get ribose forms), only make dTMP, dTDP and dTTP - dUMP + N5,N10-methylene THF = dTMP + THF
What is the name of the molecule that synthesizes rRNA?
- RNA pol I, some Pol III
Distinguish between carbomyl phosphate synthetase I and carbomyl phosphate synthetase II? Clarify what their substrates are and where each activity is found in the cell?
1.) CPS I: - Found in mitochondria of liver, synthesizes carbomyl phosphate for urea cycle - Substrates: bicarb, 2ATP, ammonium; Products: carbomyl phosphate, ADP, phosphate 2.) CPS II: - Found in cytosol of liver, synthesizes UMP - Substrates: bicarb, 2ATP, gln; Products: carbomyl phosphate, ADP, glu
Write the Michaelis-Menten equation. Define what each of the variables are.
- v = (Vmax [S])/(Km + [S]) - v = rate of ez catalyzed reaction - Vmax = maximum reaction rate (reached when every ez molecule is bound to substrate). Depends only on ez concention. - [S] = substrate concentration - Km = Michaelis-Menten constant (k2+k3)/k1 – it is the substrate concentration at which v=Vmax / 2 . Km is independent of enzyme concentration, reflects physical properties of enzyme.
An inability to generate THBtn would impact synthesis of which of the following molecules? A.) histamine B.) NE C.) Thyroid hormone
- B.) NE (remember, tyrosine in thyroglobulin molecule, not free tyrosine)
Explain what a non-competitive inhibitor is?
- A non-competitive inhibitor is a reversible inhibitor. These bind at sites on the enzyme other than the active site, forming inactive enzymes (E-I form or E-S-I). Increasing the concentration of the substrate does not influence inhibitor binding. It is reversible if the inhibitor can be removed. Enzyme will work after inhibitor removal.
Describe and explain graphically with 1/V vs. 1/[S] plots and pictorially with drawings: • competitive inhibition
Which reactions in glycolysis use ATP, produce ATP and produce NADH? What is the net production of ATP from 1 molecule glucose?
- use of ATP: hexokinase (produce G6P from glucose) and phosphofructokinase (produce F16BP from F6P) - produce ATP: phosphoglycerate kinase (produce 3PG from 13BPG) and pyruvate kinase (produce pyruvate from phosphoenolpyruvate) - produce NADH: glyceraldehyde phosphate DH (produce 13BPG from dihydroxyacetonephosphate) - net ATP: 2 - net NADH: 1
What is the function of farnesyl PP?
- converted into dolichol-PP for protein glycosylation - converted into coQ for electron transport - used for prenylation (post-translational) of proteins which influence water solubility of proteins
Pyruvate. a.) What is the fate of pyruvate? b.) What enzyme converts pyruvate to acetyl-CoA? c.) What enzyme converts pyruvate to oxaloacetate? d.) What determines whether pyruvate is used to form acetyl-CoA or oxaloacetate?
- a.) lactate, oxaloacetate, acetyl-CoA and alanine - b.) PDH complex - c.) pyruvate carboxylase - d.) pyruvate carboxylase is allosterically activated by acetyl-CoA. When there is sufficient amount of acetyl-CoA and therefore little need to divert more pyruvate into acetyl-CoA, pyruvate carboxylase converts pyruvate to oxaloacetate.
A defect in tyrosine hydroxylase would impact synthesis of all except? A.) dopamine B.) epinephrine C.) melanin
- C.) melanin
Describe how Phe, Tyr are degraded
Describe metabolism of glucose, AAs and FAs in well-fed state
Explain how the genetic and the environmental influences on complex disease can be estimated
- Twin and adoption studies (MZ vs DZ twins)- Concordant trait = trait shared by both twins- Discordant trait = trait not shared by both twins- Diseases with significant genetic component will show higher concordance rate in MZ twins than in DZ twins using crude measure known as heritability H2- H2 = (concordance MZ – concordance DZ) x 2- High heritability = trait is determined predominantly by genetic factors
Synthesis of aspartate
Describe the synthesis of pyruvate from AAs.
Synthesis of serotonin
Synthesis of glutamine
What are the effects of insulin, glucagon and epinephrine on glycolysis, glycogenolysis and glycogenesis in liver and muscle? Tabulate.
Explain the process of FA desaturation. Why is this necessary? Where does it occur?
- Many lipids in body are not saturated. - Desaturation of FAs occur in endoplasmic reticulum as shown here:
What are branched-chain amino acids? Metabolism / Pathway of BCAA degradation? Products?
- BCAA = LIV mnemonic = leu, iso, val - Metabolism: muscle has high levels of BCAT (branched-chain AA aminotransferase), which forms branched-chain alpha-ketoacids that are released into blood. BCKDH (branched-chain alpha-ketoacid DH) complex decarboxylates these BCAA in liver - Valine (see picture) - Isoleucine produces acetyl-CoA and propionyl-CoA, it is ketogenic and glucogenic AA - Leucine produces acetyl-CoA and acetoacetate, it is ketogenic AA only
Draw the glycolytic pathway. Include all the enzymes, where ATP is made or used and where reducing equivalents are produced.
Describe role of chylomicron, where synthesized, association with apoproteins, source of apoproteins, destination of contents and formation / fate of chylomicron remnant.
Describe the synthesis of FAs.
Synthesis of proline
Describe metabolism of early fast.
Asparagine synthesis
Explain mechanism that brings acetyl-CoA to cytoplasm from mitochondrion that preceeds FA synthesis?
Describe role of VLDL, IDL and LDL. Include where each are synthesized/formed, association with apoproteins, source of apoproteins, destination of contents and fate of lipoprotein.
Synthesis of serine
What is the glycerol phosphate shuttle system? Where does it occur? Draw it.
- It is a shuttle mechanism to move electrons from NADH in cytoplasm into the mitochondrion. It occurs in brain and muscle.
Explain what reaction(s) the cell can perform when there is a need for ribose, but not for NADPH. ATP is not required.
Main source of glutamate is the diet. How else is it synthesized in the body?
- Transamination via aminotransferase enzyme (ALT / AST) - Deamidation of glutamine via glutaminase
Describe how arachidonic acid is synthesized and inserted into phospholipids.
Describe the synthesis of cholesterol from farnesyl PP.
Which molecules are inducers of covalent modifications (aka phosphorylations)? Signals and affects?
Synthesis of tyrosine
What molecules are regulators of gene expression? Signals? Affects?
Describe synthesis of succinyl-CoA from AAs.
Explain why balanced chromosomal alteration often cause infertility of otherwise health carriers. Explain the inheritance of balanced alterations.
- Carriers of balanced alterations ~ 0.2% of live births are not aware of their condition as there is typically no impact on the carrier - Their genetic abnormality does; however, shows at reproduction when they lead to the production of aberrant gametes. See image below
Describe role of HDL. Include where synthesized, association with apoproteins, source of apoproteins, destination of contents and fate of this lipoprotein.
Describe the synthesis of farnesyl PP.
Describe synthesis of OAA from AAs
Describe/draw the synthesis of glucose from non-CHO precursors (gluconeogenesis).
Explain what reaction(s) the cell can perform when there is a need for NADPH and glucose. ATP is not required.
Draw function of glucagon presence (insulin absence) in regulation of FA synthesis.
Describe synthesis of ketone bodies
Acetyl-CoA. a.) What is its structure? b.) What is its metabolic importance? c.) What is its source? Where does it come from?
- a.) see picture - b.) It is an important intermediate and precursor molecule for TCA, FA biosynthesis, ketone body formation and cholesterol biosynthesis (leading to steroid hormones, bile acids and vit D production) - c.) It is produced as a result of glycolysis, beta-oxidation and AA deamination/oxidation. It is requires presence of vitamin B5.
Describe/Draw how fructose is degraded.
Outline synthesis of T3/4. What precursor molecule is used?
- Synthesized from tyrosine residue on thyroglobulin, after synthesis of the molecules, proteolysis releases them as free T3/4
Outline synthesis of catecholamines. Where does each reaction occur?
Explain what reaction(s) the cell can perform when there is a need for both NADPH and ribose. ATP is not required.
Describe synthesis of alpha-ketoglutarate from AAs
Describe creatine synthesis.
Describe reactions of urea cycle. Where is each reaction taking place?
Describe/Draw the oxidative/non-oxidative phase reactions of the pentose phosphate pathway.
Synthesis of melatonin
Explain the process of FA elongation from a 16 carbon molecule. Why is this necessary? Where does it occur?
- Cytoplasm has FA synthase that synthesizes FAs to 16 carbons = palmitate (16:0), which is a saturated molecule. - Many lipid structures in the body are longer than 16 carbons - Elongation occurs in mitochondrial as shown here:
Synthesis of glycine
- PLP = active form of B6
Describe/draw the reactions of glycogen degradation (glycogenolysis).
TCA cycle. a.) What are the 2 major functions of the TCA cycle? b.) What is the overall balanced reaction of the TCA cycle? c.) Draw the reactions of the TCA cycle. Include enzymes, cofactors. d.) What is the fuel for the TCA cycle? e.) Which reaction(s) liberate CO2? f.) Which reaction(s) liberate NADH? g.) Which reaction(s) liberate FADH2? h.) Which reaction(s) involve substrate-level phosphorylation? i.) How many ATPs/ATP-equivalents are produced from a molecule of acetyl Co-A? From pyruvate? From glucose? j.) Explain mechanisms for TCA cycle regulation. What enzymes are regulated?
- a.) Serves to generate ATP and to generate biosynthetic precursors. - b.) CH3COSCoA + 2H2O + 3NAD+ + FAD + GDP + Pi = 2CO2 + 3NADH + 3H+ + FADH2 + CoASH + GTP - c.) see picture - d.) Acetyl-CoA - e.) isocitrate to alpha-ketoglutarate; alpha-ketoglutarate to succinyl-CoA - f.) isocitrate to alpha-ketoglutarate; alpha-ketoglutarate to succinyl-CoA; malate to oxaloacetate - g.) succinate to fumarate - h.) succinyl-CoA to succinate - i.) since 3 ATPS per NADH and 2 ATPS per FADH - 12 per acetyl CoA, 15 from pyruvate (considering PDH reaction) and 30 from glucose - j.) Regulation of the TCA cycle occurs through regulation of isocitrate dehydrogenase and alpha-ketoglutarase dehydrogenase complex. Isocitrate dehydrogenase activity increases when conc of ADP are high and decreases when NADH conc are high. Alpha-ketoglutarate dehydrogenase complex activity decreases when concentrations of succinyl-CoA and NADH are high.
Draw the Lineweaver-Burk plot and indicate what each intercept, slope and axes mean. Indicate what navigating around the graph means.
Synthesis of methionine
