MTC Week 13 Revision Student 2023 PDF

Week 13 MTC Monday Revision Lecture Overview of the major exam concepts I will not go into specific details University exams are all about showing that you understand Requested Revision Points: these are throughout the lecture 1. Regulation of gluconeogenesis 2. Enzymes Km 3. mRNA calculation 4. K...

Week 13 MTC Monday Revision Lecture Overview of the major exam concepts I will not go into specific details University exams are all about showing that you understand Requested Revision Points: these are throughout the lecture 1. Regulation of gluconeogenesis 2. Enzymes Km 3. mRNA calculation 4. Ketone Bodies Paper 1 • 96 MCQs • MTC: last 24 MCQs • Then 12 STEM questions Know the TCA What does it do? What are the inputs/products? Inputs/Anaplerotic reaction roles lipogenesis Understand the basis of the genetic code Mutation types Understand the different transporter types 3 Na+ out 2 K+ in Know what the Shuttles do G3P and the Malate Aspartate Malate Aspartate Understand protein structure Monomers Hexamers Tetramers Dimers What are the products of beta oxidation: saturated and unsaturated? C-C-C-C-C-C-C-C-C-C-C-C-C-C-C-C-C-C-C-C-C-C 1.5 ATP 2.5 ATP C22 Fatty acid = 11 pairs of C-Cs Hence 11 pairs will become Acetyl CoA, and this goes into the TCA. Each Acetyl CoA will generate 3 NADH, 1 FADH and 1 GTP (ATP equivalent) This equals in ATP = (3 x 2.5 + 1 x 1.5 + 1) x 11 (the pairs) = 110 ATPs 10 Bonds between the pairs must be broken by beta-oxidation This represents 10 NADH and 10 FADH = 10 x 2.5 + 10 x 1.5 = 40 ATPs Hence thus far, 150 ATPs. But we need 2 ATPs to activate the Fatty acid to bind to CoA. 1 NADH = 2.5 ATPs 1 FADH = 1.5 ATPs Thus, total is 148 ATPs Understand Fatty acid synthesis, lipogenesis, lipolysis and their regulation What inputs does it require? What regulates these events? lipases Know glycolysis and gluconeogenesis; regulation of and inhibition What is produced? What is needed? What is regulated? Disease examples: Tumours & red blood cells Know the Urea cycle Urea cycle steps CO2 + water + NH4 gives CP CP + ORN gives Cit Cit + Asp gives AS AS is broken into F and Arg Arg is metabolised to Urea and ORN N-acetyl glutamate synthase Basic chemical structures and bonds (weeks 1-3) Examples: ester, amide, cyano, nitrogen, amino, thioester Know the ETC; how does it work; what do the inhibitors do? DNP 282 CHAPTER 13 | DNA AND ITS ROLE IN HEREDITY Primase Understand DNA replication Lagging strand 3′ Slidi RNA primer RNA primer 5′ 5′ 3′ 3′ 5′ Lagging strand template 1 Primase forms an RNA primer. 3′ 5′ 2 DNA polymerase III adds nucleotides to the new Okazaki fragment only at the 3′ end, continuing until it encounters the primer on the previous Okazaki fragment. DNA polymerase III Okazaki fragment 5′ 3′ 3′ 5′ 5′ 3′ 3′ 5′ DN DNA polymerase I Gap 3′ 3′ 3 DNA polymerase I hydrolyzes the primer and replaces it with DNA. 5′ 5′ 5′ 3′ 13.18 A Polyme by keepi have to r DNA ligase (open) A SLIDIN do DN an enzy Know the steps sub 3′ 5′ 5′ DNA ligase (closed) 3′ 4 DNA ligase then catalyzes the formation of the phosphodiester linkage that finally joins the two Okazaki fragments. 13.17 The Lagging Strand Story In bacteria, DNA polymerase I and DNA ligase cooperate with DNA polymerase III to complete the complex task of synthesizing the lagging strand. DNA r went th polyme meriza substr The new which i protein nut sha the#Km#and#is#an#indicator#of#the#affinity#the#enzyme#has#for Km,#the#higher#the#affinity,#and#vice#versa.#So#an#enzyme#with for#its#substrate.##An#example#of#an#enzyme#with#a#low#Km#is catalyzes#the#reaction## Be able to use Km when comparing enzymes Glucose#+#ATP#⇒#glucose\6\phosphate#+#ADP### Km = 0.05 and#has#a#low#Km#for#glucose#and#therefore#a#high#affinity#fo Hexokinase 1 (RBCs) has a high affinity for glucose. which#catalyzes#the#same#reaction#as#hexokinase,#has#a#low# • Hence a Low Km = 0.05 mM therefore# requires# relatively# high# glucose# concentrations# to later# chapter# how# glucokinase# is# used# as# a# means# of# detec Glucokinase/Hexokinase IV (liver) Catalyzes the same reaction. Has a low affinity for glucose and therefore requires relatively high part#of#a#mechanism#in#controlling#insulin#secretion#from#the glucose concentrations to function. • Hence has a higher Km = 5-6 mM # Hexokinase# and# glucokinase# differ# in# another# way# –# t Km = 5-6 HKI: low glucose concentrations: Hexokinase#cannot#only#catalyze#the#phosphorylation#of#glu High affinity for substrate fructose,# it# can# mistake# fructose# for# glucose# and# ph HKIV: higher glucose concentration (promiscuous#little#enzyme!!).#In#comparison,#glucokinase,#w Low affinity for substrate its# hexose# substrate,# is# very# specific# for# glucose# an phosphorylation# of# fructose# (or# any# other# hexose).# So# hex specificity#while#glucokinase#has#high#substrate#specificity.# Week 12 New therapies and cancer targets Calculation question mass moles = molecular weight So just plug in the numbers, and solve for ‘X’: • Molarity This is how many moles you want 1 mol = Xg This is the unknown mass of sugar you want (in grams) 342 g/mol 1 mol x 342.3 g/mol = X g X = 342.3 g i.e. One mole of sugar is 342.3 g (so the molecular weight tells you how many g are in 1 mole!) This is the known molecular weight of sucrose (“sugar”) 2 x 6 STEM questions • Stem 1: TCA cycle/regulation and associated reactions (week 7 content) • Stem 2: Glycolysis, linking reaction and gluconeogenesis (week 6-8 content) 25-26 options for each stem and 6 questions Paper 2 4 x Case based Questions How can you measure enzyme activity? Practice KFPs week 6 and 7 Know about protein structure Monomers Hexamers Tetramers Dimers Be able to calculate protein from mRNA, and the reverse Open reading frame is the length of mRNA sequence that encodes a protein. Start with a start codon (AUG) and ends with a stop codon (UGA, UAA, UAG) By example 9. A hexameric protein composed of identical monomeric subunits has a molecular mass of 260 kDa. What is the minimum length of mRNA needed to encode the protein assuming the average molecular mass of a protein amino acid is 110 Da? Hexamer (6 subunits) = 260,000 daltons Mass of 1 subunit is then 260,000/6 = 43,333 Number of amino acids per sub unit is then 43,333/110 Da = 394 The open reading frame includes a start (methionine) and stop codon (nothing: no amino acid). Thus the number of nucleotides in the ORF = (394 x 3) +3 bps = 1182 + 3 = 1185 Calculation question mass moles = molecular weight So just plug in the numbers, and solve for ‘X’: • Molarity This is how many moles you want 1 mol = Xg This is the unknown mass of sugar you want (in grams) 342 g/mol 1 mol x 342.3 g/mol = X g X = 342.3 g i.e. One mole of sugar is 342.3 g (so the molecular weight tells you how many g are in 1 mole!) This is the known molecular weight of sucrose (“sugar”) How is glycogen metabolism regulated? Insulin and glycogen Mechanistically, done by the phosphorylation of glycogen synthase and glycogen phosphorylase. glycogen(n residues) + Pi ⇌ glycogen(n-1 residues) + glucose-1-phosphate. Understand Fatty acid synthesis, lipogenesis, lipolysis: regulation by Insulin and glucagon lipases Fed state SUMMARY Insulin increase Glycolysis Glycogenesis Lipogenesis Protein production In presence of oxygen Produce ATP via the TCA and ETC RBCs (erythrocytes) always produce lactate Lactate recycled by the liver No oxygen: Anaerobic glycolysis: only 2 ATPs With oxygen: Aerobic glycolysis: 32 ATPs AMPK activity depends on the energy levels in the cell Fasting/starving state Glucagon increase Gluconeogenesis Glycogenolysis Lipolysis Beta oxidation Ketone body production Protein breakdown Increased Urea generation Links between alanine and glucose Links between the Urea and TCA Paper 4 all MTC 22.5 marks all up 12 questions Know: Pentose phosphate pathway (week 7) Pentose Phosphate Isomerase Diseases associated with dysfunction of the PPP Ribose-5-P Glycolysis/gluconeogenesis and its regulation: Galactose: know and why Urea cycle; steps; disrupted function in disease? N-acetyl glutamate synthase Bioc 460 - Dr. Miesfeld Fall 2008 taken up by the liver Figure 18. where aminotransferase enzymes transfer the amino group to αketoglutarate to form glutamate. Amino acids derived from the degradation of cellular proteins are also deaminated to generate glutamate. The glutamate is imported into the mitochondrial matrix where it is metabolized by the enzyme glutamate dehydrogenase to produce NH4+ which is used to make the urea cycle precursor carbamoyl phosphate. In addition, some of the glutamate is converted to aspartate by the aspartate aminotransferase reaction and fed into the urea cycle as the second source of nitrogen. Glutamine, which carries excess two nitrogen atoms to the liver from peripheral tissues, is deaminated by the enzyme glutaminase to generate NH4+ and glutamate. The NH4+ is used to make carbamoyl phosphate directly, and the glutamate, is deaminated by glutamate dehydrogenase to liberate a second molecule of NH4+ for carbamoyl synthesis. Urea is synthesized in the liver and transported through the blood to the kidneys where it is concentrated and excreted in urine. As shown in figure 19, five enzymatic reactions are required for urea synthesis, two of which occur inside mitochondria and three others in the cytosol. It can be seen that two of the reactions require ATP hydrolysis (reactions 1 and 3), resulting in the expenditure of four high energy phosphate bonds for every mole of urea produced. The urea cycle was discovered in 1932 by Hans Krebs and a medical student who worked in his lab, Kurt Henseleit. Understand Fatty acid synthesis, lipogenesis, lipolysis and their regulation What inputs does it require? lipases Understand the purpose of ketone body synthesis Inputs, outputs When and why? Fasting metabolism (overnight): KB: ketone bodies Starvation: KB: ketone bodies Understand Transcription and translation How is mature eukaryotic mRNA made Steps of translation Application to PCR, RT-PCR Splicing Uses antisense strand to make Sense RNA strand ETC, coupling and electron transport into the mitochondria BACK YOURSELF FOR THE EXAM READ THE QUESTIONS SLOWLY ANSWERS THE EASY ONES FIRST with clear HAND writing!!!!! KNOW the PATHWAYS and their REGULATION Projects with my lab and TUH Clinicians (MBBS Honours Year projects) 1. Liver cancer in North Queensland: collecting HCCs, making organoids (3 dimensional primary tumour cultures) Performing next generation sequencing of non-tumour and tumour; validating drugs targets and gene function. 30 patients per year. Genomics; liquid biopsy. 2. Understanding Sarcopenia in North Queensland Indigenous Patients. Collecting primary muscle tissue from surgery patients, making primary muscle cultures. Perform next generation sequencing and proteomics to characterise key genes and molecules. 200 patients for this study Coworkers: Dr Craig McFarlane; A/Prof Matt Field and A/Prof Ulf Schmitz (bioinformaticians) Surgeons: A/Prof Pankja Saxena and Dr Matan Ben David, Gastroenterologist Dr Rozemary Karamatic The after MTC experience 4 pm today: Belgium and Dutch Beer, great metabolism!!! 5.5% 8% 10% Semester II: group leader, conference travel, SYD, BNE, Singapore Publish or perish, Funding applications Uni Admin Some fishing The picture I show my colleagues down south Best of luck with your studies!!! Hard work = Success!!! You are here once. Success: remember luck plays a big part. Do not waste your time. Make your time and career fulfilling. Helping others is a good way to achieve this.