GoConqr has a new look! Let us know what you think.

Sign up free

Flashcards

BM210 biochemistry

Julia Spychalska English 184 cards

Cards in this deck (184)

  1. 1How many bases per alpha helix turn?10 bases
  2. 2What must the primer have for DNA replication?a free 3'-OH
  3. 3What makes up the lagging strand?short okazaki fragments
  4. 4How are the two replication forks created?When DNA strands separate at an origin of replication
  5. 5What do primers do?initiate DNA synthesis
  6. 6What does telomerase bind to?a DNA repeat sequence
  7. 7Telomerase in DNA replication1. telomerase binds to DNA repeat sequence
    2. telomerase synthesises a 6-nucleotide repeat sequence
    3. telomerase moves 6 nucleotides to the right and begins to make another repeat
    4. primase makes a RNA primer near end of telomere
    5. DNA polymerase synthesises a complementary strand
    6. RNA polymerase is eventually removed
  8. 8transcriptioncoding DNA strand> template DNA strand> mRNA strand
  9. 9RNA synthesis stepsInitiation- RNA polymerase 2 and transcription factors assemble at promoter; RNA synthesis starts. mRNA, tRNA, and ribosomal subunits form a complex.
    Elongation- RNA polymerase 2 moves along template strand as RNA molecule grows in 5' to 3' direction, synthesising polypeptide.
    Termination- RNA molecules completed and stabilised by modifications. The ribosome reaches a stop codon, and all the components disassemble, releasing a completed polypeptide.
  10. 10What is the promoter region?region before the point of RNA synthesis, determines how much RNA is going to be produced.
  11. 11RNA Pol 2ATP dependent and needs to be phosphorylated, allowing it to move along template molecule, resulting in elongation
  12. 12Why are modifications beneficial to RNA molecules?They provide stability
  13. 13What does aminoacyl-tRNA synthase do?link a specific amino acid with a specific tRNA (anticodon)
  14. 14What are the factors required for translation initiation in eukaryotes?initiation factors
    Met-tRNA
    40S ribosomal subunit
  15. 15Elongation of protein1. Aminoacyl-tRNA binds to A site
    2. peptide bond is formed between growing polypeptide chain and new amino acid
    3. elongation factor hydrolyses GTP, driving the mRNA through ribosome. Vacant tRNA moves to P site.
    4. Vacant tRNA dissociates
    5. Repeats until stop codon. Release factor at A site released newly synthesised protein, exits via tunnel.
  16. 16What is the immediate product of Pol 2?pre-mRNA
  17. 17What does capping assess?whether both ends are present before RNA is exported from the nucleus for translation?
  18. 18Capping the 5' end of pre-mRNA1. Loss of phosphoryl group
    2. formation of rare 5'-5' triphosphate linkage with GTP
    3. methylation of terminal guanine
    4. additional methylations
  19. 19pre-mRNA splicing: what recruits splicing proteins?site-specific phosphorylation of Pol-2 at its C terminal
  20. 20At what point is pre-mRNA referred to as mRNA?only after capping and splicing is transcribed
  21. 21What removes eukaryotic pre-mRNA?spliceosome, which is composed of several different subunits known as snRNPS. Each contains small nuclear RNA and a set of proteins
  22. 22What do introns begin and end with?begin with GU and end with AG
  23. 23pre-mRNA splicing reaction1. the specific adenine nucleotide attacks the 5' splice site, the sugar backbone is cut here.
    2. The cut 5' end if the intron covalently binds to the adenine nucleotide, creating a loop.
    3. The OH group at the new 3' end of the exon reacts with the start of the next exons sequence.
    4. The two exon sequences join together, thereby releasing the spliced out intron- a 'lariat'
  24. 24What does the spliceosome do?it is able to capture, splice, and release RNA in a coordinated manner, which requires multiple rearrangements of the spliceosome components.
  25. 25What is alternative splicing?In some cases, the function of the spliceosome is regulated so the splicing of exons for a given mRNA can occur in two or more ways. This allows a single gene to encode two or more polypeptides with differences in their amino acid sequences.
    ALLOWS COMPLEX EUKARYOTES TO USE THE SAME GENE TO MAKE DIFFERENT PROTEINS AT THE PROTEOME WHILE MINIMISING THE SIZE OF THE GENOME. (increases number of proteins relative to number of genes)
  26. 26What controls alternative splicing?RNA-associated proteins
  27. 27What are the two different forms of apolipoprotein B? (due to deamination producing a sequence change of mRNA?)Large- synthesised in liver, role in lipid transport
    Small- synthesised in small intestine
  28. 28Self-splciingsome introns can carry out splicing without the spliceosomes but with RNA alone. (do not require any protein)
  29. 29What do mutations in the beta globin gene cause?abnormal splicing of its pre-mRNA
  30. 30how does cellular signalling increase/decrease transcription?by affecting transcription factors (regulators of gene expression)
  31. 31Basal transcription complex: what forms the core promoter?the TATA box and transcriptional start site
  32. 32What is the transcriptional start site?the place in the DNA where transcription actually begins
  33. 33What is the TATA box?a 5'-TATAAA-3' sequence which is usually about 25 bp upstream from a transcriptional start site. It is important in determining the precise starting point for transcription.
  34. 34What is basal transcription?When the core promoter by itself results in a low level of transcription that is termed basal transcription.
  35. 35What are enhancers?they are regulatory elements that play a role in the ability of RNA polymerase to begin transcription, thereby enhancing its rate.
  36. 36neurotransmitters and hormonespeptides- insulin
    small peptides- bradykinin
    amino acids- glutamate
    steroids- oestrogen, testosterone
    vitamins
    fatty acids derivatives- prostaglandins, leukotrienes
    gas- NO
  37. 37agonistsintercellular signals that activate receptors and elicit a physiological response. Ligand with two important properties: affinity; binds to receptor. efficacy; intrinsic activity, induce conformational change in receptor they bind to
  38. 38antagonistligand which blocks the receptor. has affinity but not efficacy. ligands are chemicals which bind to receptor proteins. a ligand without efficacy is an antagonist.
  39. 39How does cellular signalling affect gene expression?Enzyme-linked receptor- epidermal growth factor (EGF) activation of the mitogen-activated protein kinase cascade
    G-protein-coupled receptor- adrenaline activation of adenylate cyclase and cyclic AMP-driven gene expression
  40. 40What happens if EGF binds to EGFR?it activates its kinase activity
  41. 41EGF receptor activation1. receptor dimerization and autophosphorylation
    2. Binding of GRB2 and Sos couples activated EGFR to inactivate Ras
    3. Sos promotes dissociation of GDP from Ras (a monomeric G protein)
    4. GTP binds and Sos dissociates from active Ras, which inactivates effectors
  42. 42Dopamineintracellular signal (agonist)
    binds specifically to dopaminergic receptors, D1 and D2
  43. 43D1 and D2each receptor type binds to dopamine but the consequence of activation of DI is different to that of D2
    D1 via stimulatory GP (Gs) stimulates adenylate cyclase
    D2 via inhibitory GP (Gi) inhibits adenylate cyclase
  44. 44adenylate cyclasean enzyme that makes cAMP which is an intracellular second messenger
  45. 45cAMPsecond messenger which activates protein kinase A, Produced when cell is stimulated
  46. 46cAMP regulates transcriptionactivated PKA phosphorylates CREB, a transcription factor.
    CRE (cAMP responsive element, an enhancer) is found in genes that are regulated by cAMP. CREB is bound to CRE (DNA)
    An additional factor, CBP (CREB binding protein), is then recruited to the transcription complex and transcription is initiated
  47. 47protein kinase A (PKA)phosphorylates many target proteins, including some transcription factors
  48. 48RNA polymerase 2transcribes structural genes that encode proteins
  49. 49what are the three types of proteins that play a role in initiating transcription at the core promoter of structural genes?RNA polymerase 2, fiver different proteins called general transcription factors (GTFs), and a large protein complex called mediator
  50. 50Preinitiation complexRNA polymerase 2 and GTFs must come together at the TATA box of the core promoter so transcription can be initiated, A series of interactions occurs between these proteins so RNA polymerase 2 can bind to DNA. the completed assembly of RNA pol 2 and GTFs at the TATA box is called the preinitiation complex
  51. 51transcription in eukaryotes: mediator protein complexmediator is composed of many proteins that bind to each other to form an elliptically shaped complex hat partially wraps around RNA pol 2 and GTFs
    The function of the mediator is to control the rate at which RNA pol can begin to transcribe RNA at transcriptional start site
  52. 52Our genome sequence is X% G or C42%
  53. 53EuchromatinDNA unmethylated
    loosely packed form of chromatin, enriched in genes, often under active transcription
  54. 54HeterochromatinDNA methylated.
    tightly packed form of chromatin, generally genetically inactive and inaccessible to RNA polymerase.
  55. 55DNA methylationusually occurs on the cytosine base and inhibits transcription of eukaryotic genes, particularly when it occurs in the vicinity of the promoter
  56. 56CpGCpG refers to the nucleotides of C and G in DNA that are connected by phosphodiester linkage
  57. 57How does DNA methylation inhibit transcription?1. methylation of CpG islands may prevent an activator from binding to an enhancer element, thus inhibiting initiation of transcription
    2. altering chromatin structure- proteins known as methyl-CpG-binding proteins bind methylated sequences. Once bound to the DNA, the methyl-CpG-binding protein recruits other proteins to the region that inhibits transcription.
  58. 58What do disulphide bonds do to proteins?the polypeptide chain can be cross-linked by disulphide bonds, which form by the oxidation of two cysteines
  59. 59conformational restriction of peptide bonds: why is the trans form strongly favoured?because of steric clashes that arise in the cis R form. Also because R groups are located separately and not close together.
  60. 60alpha helix structure: where is the hydrogen bond?between the hydrogen on the NH and the oxygen on the CO
  61. 61Secondary structure: how do polypeptide chains change direction?with beta turns and omega loops (bigger, irregular structures)
  62. 62interior and exterior of globular proteinsthe interior consists of mainly hydrophobic amino acids.
    The exterior consists of charged and polar amino acids
  63. 63distribution of hydrophilic and hydrophobic amino acids on porinsthe outside of porin is covered in hydrophobic residues, whereas the centre includes a water-filled channel lined with charged and polar amino acids
  64. 64factors that influence protein folding and stabilityhydrogen bonds- bonds form between atoms in the polypeptide backbone and between atoms in different side chains.
    ionic bonds- bonds form between oppositely charged side chains
    hydrophobic effect- nonpolar amino acids in the centre of the protein avoid contact with water.
    van der Waals- weak attractive forces occur between atoms that are optimal distances apart.
    disulphide bridges-a covalent bond forms between two cysteine side chains.
  65. 65post-translational modifications: lack of appropriate protein modificationcan result in pathological conditions
  66. 66post-translational modifications: lack of hydroxylation of protein in collagenresults in scurvy
  67. 67post-translational modification: lack of carboxylation of clotting proteinsresults in haemorrhaging (vitamin K deficiency)
  68. 68histone modifications: methylationmethylation makes amino acid more hydrophobic
  69. 69What do the amino acids side chains of the active site do?stabilise the electron distribution of the transition state
  70. 70How do reactive groups at the enzyme surface catalyse the reaction?1. by donating or withdrawing electrons
    2. by stabilising or generating free radical intermediates
    3. forming temporary covalent bonds (a transition state intermediate)
  71. 71cofactors (inorganic and organic chemicals that assist enzymes during the catalysis of reactions)metal group (e.g. hexokinase Mg2+)
    prosthetic group (heme, lipoic acid)
    coenzyme (NAD)
    holo-enzyme (catalytically active)
    apoenzyme (catalytically inactive)
  72. 72the Michaelis-Menten equationdescribes the dependence of rate reaction on concentration of substrate at steady state (ES formation balanced by its removal) and vast molar excess of substrate over enzyme [S]>>[E]
  73. 73Enzymes with two substrates: the ping-pong reactionone substrate reacts, and modifies enzyme, then second substrate reacts with modified enzyme
  74. 74allosteric inhibitorsincrease the Km and lower the affinity of the enzyme for its substrate
    decrease in the affinity leads to a decrease of enzyme activity
  75. 75how is a hemiacetal formed?by reaction of an aldehyde group with an alcohol group
  76. 76which bond makes sugar reactive?the carbon to oxygen double bond
  77. 77which sugars are good: extrinsic or intrinsic?intrinsic- sugars contained in plant cell walls (good)
    extrinsic- sugars that are free in solution (bad- cause dental plaque)
  78. 78how are sugar alcohols formed?by the reduction of the aldehyde group of glucose to a hydroxyl group
  79. 79polasaccharide reducing and non-reducing endreducing end is where glucose can open up and expose the aldehyde group.
    Non-reducing end can't open up.
  80. 80What is an acetal and how is it involved in the non-reducing end?An acetal is a molecule with two single bonded oxygens attached to the same carbon atom. This prevents opening of the chain to the aldehyde form and renders the modified residue non-reducing.
  81. 81how much cholesterol is in the membrane?60-80% of cellular cholesterol is in the plasma membrane where it makes up 50-60% of all membrane lipid
  82. 82What is cholesterol a precursor of?steroid hormones, bile salts, and vitamin D
  83. 83cholesterol biosynthesis1. synthesis of isopentyl pyrophosphate (via mevalonate)
    2. condensation of six molecules of isopentyl pyrophosphate to form squalene
    3. cyclisation of squalene and further processing to cholesterol
  84. 84what is the major site of cholesterol synthesis?the liver with significant synthesis in the intestines
  85. 85regulation of cholesterol biosynthesisHMG-CoA reductase regulation regulates synthesis (an integral membrane protein in ER): its amount, activity, catalyses the committed step of cholesterol synthesis
  86. 86ways in which HMG-CoA is controlled1. rate of synthesis of HMG-CoA reductase mRNA
    2. rate of translation of HMG-CoA reductase mRNA to protein
    3. rate of degradation of HMG-CoA reductase protein
    4. phosphorylation state of HMG-CoA reductase protein
  87. 87what inhibits rate of translation of HMG-CoA reductase mRNA to protein?non-sterol metabolites derived from mevalonate
  88. 88Rate of degradation of HMG-CoA reductase proteinHMG-CoA reductase membrane domain senses increasing levels of sterols, then interacts indirectly with ubiquitinating enzymes, becomes polyubiquitinated, is extracted from the membrane and then degraded by the proteasome.
  89. 89phosphorylation of HMG-CoA reductasephosphorylation decreases catalytic activity of the reductase, stopping cholesterol synthesis.
    phosphorylation is by AMP-activated protein kinase.
    phosphorylation increases when ATP levels are low.
  90. 90how is cholesterol transported in the membrane?in body fluids in lipoprotein particles
  91. 91What are the five classes of steroid hormones? (derivatives of cholesterol)progestogens, glucocorticoids, mineralocorticoids, androgens, oestrogens
  92. 92Genetic variation: markera gene or DNA sequence with a known location on a chromosome that can be used to identify individuals or species
  93. 93Contigset of overlapping DNA segments that represent the consensus region of DNA (order of most frequent residues)
  94. 94genetic variation: phasethe gametic phase represents the originals allelic combination that an individual received from its parents. (therefore a particular association of alleles at different loci on the same chromosome)
  95. 95haplotypea group of genes in an organism that are inherited together from a single parent
  96. 96SNPsingle-nucleotide polymorphisms
  97. 97Microsatellitesshort tandem repeats (STR)
    simple sequence repeats (SSR)
    2-7 base pairs
  98. 98minisatellitesvariable number tandem repeats (VNTR)
    8 to >50 base pairs
  99. 99polymorphic DNA sequences : CNVcopy number variant (CNV)
    0,1,3 or more copies of a large stretch of DNA sequence
  100. 100highly repetitive DNAsatellite DNA
    found in long tandem strings
    near telomeres
    around the centromeres (middle of chromosomes)
  101. 101Satellite DNAalpha satellite DNA (alphoid)
    functions in the centromere of chromosomes
    each repeat unit contains smaller repeat units, between 4 and 32 base pairs
  102. 102RFLPs: restriction fragment length polymorphismbacterial enzymes that act as primitive immune system
    restrict a specific phage (viral) DNA sequence
    used by researchers as a molecular tool.
    restriction fragment sizes are altered by changed in or between enzyme recognition sites.
  103. 103polymorphisms permit DNA fingerprintingtechniques used to distinguish the unique combination of polymorphisms present in individual from another
    first applied by alec jeffreys
    originally used minisatellites
    used in crime, paternity tests
  104. 104Amelogenin gene locus (AMEL)a gene encoding a protein in tooth enamel
    AMELX gene on X chromosome and AMELY on Y chromosome
    PCR used to amplify segment of DNA
  105. 105partial linkagecrossover. meiotic recombination between X and Y.
    frequency of recombinants proportional to physical distance apart.
  106. 106genetic engineering/cloning: EcoRIrestriction enzyme that cut the DNA at specific sequences (GAATTC)
    The cut ends have overhangs which allows them to reform in the presence of ligase enzyme
  107. 107human chromosomes size rangefrom 55X10^6 bp to 250x10^6 bp
  108. 108human genome project phasesphase 1: produce high resolution chromosomal maps (position genetic markers and genes, create libraries of BAC clones for sequencing)
    phase 2: sequence each BAC DNA
    phase 3: assemble all sequences to produce final draft and annotate to identify genes
  109. 109Genome sequencing approachesIHGSC: clone-by-clone approach
    disadvantages: slow process and expensive
    Advantages: very effective at getting over regions of highly repetitive DNA sequences. Able to retrieve clones faster.
    CELERA: shotgun sequencing. Blast genome into small fragments sequence each one and then use the power of computers to reassemble to sequence.
  110. 110How many genes in our genome?20K - 25K
  111. 111FOXP2a gene involved in human speech and language disorders.
  112. 112why have some haplotypes increased so rapidly?they contain advantageous gene variants.
    strong selection from environment means that they provided increased fitness
    increase offspring= increased frequency in population
  113. 113When does absorptive state occur?when ingested nutrients enter the blood from GI.
  114. 114When does the post-absorptive state occur?when the GI tract is empty of nutrients and the body's own stores must supply energy.
  115. 115enzymes in small intestine- pancreatic amylase disaccharidases: Absorption of monosaccharides and water.
    -trypsin, chymotrypsin: Absorption of short peptides and amino acids
  116. 116enzymes in stomachpepsin cleaves peptide bonds.
    gastric lipase.
  117. 117Glycolysissequence of reactions that metabolises one molecule of glucose to two molecules of pyruvate with the concomitant net production of two molecules of ATP
  118. 118phosphoryl shift in anaerobic glycolysismovement of a phosphoryl group from oxygen to an alcohol oxygen in the same molecule.
    Alcohol hydrogen is removed and binds to the formerly phosphorous-bound oxygen
  119. 119how is NAD+ regenerated?through the metabolism of pyruvate. without it glycolysis will stop.
    lactate formation regenerates NAD+
  120. 120the reaction of pyruvate dehydrogenase multi-enzyme complex-decarboxylation of pyruvate (3C) to a 2-carbon alcohol
    -oxidation of the alcohol to an acid (acetic acid), with reduction of NAD+ to NADH
    -esterification to coenzyme A> acetyl CoA> TCA cycle
  121. 121role of the glycolytic pathway1. degradation of glucose to generate ATP
    2. provision of building blocks for synthetic reactions, e.g. fatty acids.
  122. 122sites of control in the glycolytic pathwayenzymes catalysing irreversible reactions are potential sites of control.
    Hexokinase, phosphofructokinase, AMP, pyruvate kinase.
  123. 123fructose 2,6-bisphosphategenerated by phosphofructokinase 2
    it is a regulatory molecule
  124. 124phosphofructokinase 2responsible for synthesis and hydrolysis of fructose 2,6-bisphosphate to phosphofructokinase
    phosphofructobisphosphatase is a 55kDa protein composed of an N-terminal regulatory domain, a kinase domain, and a phosphatase domain
  125. 125glycogen anabolism (synthesis)Initiation- catalysed in an autocatalytic manner by glycogenin.
    Elongation- catalysed by glycogen synthase in concert with the branching enzyme
  126. 126glycogen synthase (GS)main enzyme in glycogen polymerisation- can only add to an existing chain of at least 8 glucose residues (elongation stage)
  127. 127regulation of glycogen synthaseregulated by covalent modifications and allosteric mechanisms
    -Glycogen synthase is phosphorylated by PKA and glycogen synthase kinase A
    -phosphorylation converts active a form to inactive b form
    However, b is still active when a high level of allosteric enzyme activator glucose-6-phosphate is present
  128. 128What is the immediate precursor for glycogen synthesis?uridine diphosphate glucose (UDP-glucose), an activated form of glucose
  129. 129Why is branching so important?-it increases the solubility of glycogen
    -it creates a large number of terminal residues
    -terminal residues are the sites of action of glycogen phosphorylase and glycogen synthase
    -branching increases the rate of glycogen synthesis and degradation
  130. 130Fatty acid synthesis: which protein is bound to the intermediates?an acyl-carrier protein (ACP)
  131. 131Fatty acid synthesis: how does the chain grow?the fatty acid chain grows by the addition of 2C units derived from acetyl CoA.
  132. 132Fatty acid synthesis: what is the activated donor?malonyl-ACP
  133. 133Fatty acid synthesis: what is the transfer to ACP driven by?a decarboxylation reaction releasing carbon dioxide
  134. 134spiral pathwaycondensation pathway driven by release of carbon dioxide. Acetyl ACP reacts with a malonyl ACP. final product is butyryl ACP
  135. 135why is fat high energy?because it is very reduced
  136. 136where are triacylglycerols (TG) synthesised?liver, adipose tissue, intestinal tract
  137. 137Glycogenolysisglycogen breakdown into glucose in liver and secreted into blood.
  138. 138four enzymes in glycogenolysisglycogen phosphorylase, transferase, alpha-1,6-glucosidase, phosphoglucomutase.
    One degrades glycogen
    Two remodel glycogen so that it remains a substrate for degradation.
    One to convert the product into a metabolisable form.
  139. 139Phosphorolysisaddition of orthophosphate to yield glucose 1-phosphate (phosphorolysis)
    does not consume any ATP
    Reaction catalysed by glycogen phosphorylase, which cleaves off glucose residues.
  140. 140What are the two major essential polyunsaturated fatty acids?linoleic acid and linolenic acid
  141. 141What are the three types of fat in our diet?triacylglycerols- 3 fatty acids attached to glycerol.
    phospholipids- 2 fatty acids and a head group attached to glycerol
    cholesterol- 4 ring hydrocarbon.
  142. 142common phospholipid headgroupsphosphocholine, phosphoethanolamine, phosphoserine, phosphoinositol
  143. 143what are the different lipases in the stomach, mouth, and intestine?mouth- lingual lipase
    stomach- gastric lipase
    intestine- pancreatic lipase and phospholipase
  144. 144why are lipoproteins needed to transport lipids around the body?because they are hydrophobic and insoluble in aqueous environments.
  145. 145oxidation of fatty acids (beta oxidation)1. activation- to form a thioester bond with CoA
    2. oxidation- 2H removed > double bond C=C
    3. hydration- water added across double bond
    4. oxidation C-OH converted to C=O
    5. thiolysis (acetyl-CoA cleaved from activated end)
  146. 146how does CoA activate fatty acids?the thiol group of coenzyme A forms a high energy thioester bond with the carboxylic acid group of the fatty acid.
  147. 147what is carnitine?acyl-carrier that transports the fatty acyl chains across the mitochondrial membrane as most acyl-CoA cannot cross
  148. 148ATP production per round of beta oxidationNADH- 2.5 ATP
    FADH2- 1.5 ATP
    Acetyl-CoA- 10ATP
    Palmitate needs 7 cycles, producing 108ATP, however 2ATP are used to activate fatty acid.
    TOTAL= 106 ATP
  149. 149Degradation of unsaturated fatty acids requires two additional enzymes1. for one C=C bond, cis-D 3-Enoyl CoA isomerase
    2. for two C=C bonds, cis-D 3-Enoyl CoA isomerase PLUS 2,4-dienoyl CoA reductase
  150. 150What happens if fat metabolism predominates?there is a shortage of oxaloacetate, because it is used for gluconeogenesis (to make glucose), Not enough oxaloacetate causes an excess of acetyl-CoA as it cannot link oxaloacetate.
    Acetyl-CoA is converted to ketones, which can cross the blood brain barrier.
  151. 151Where is glucose 6-phosphate located?in liver and kidneys (tissues that maintain blood glucose levels)
    Located in the membrane of the ER
  152. 152what are the cofactors of fructose 1,6-bisphosphateMg2+, Mn2+, and Zn2+
  153. 153pyruvate carboxylase-localised in the mitochondrium
    -carries a biotin as a prosthetic group
    -biotin functions as a carrier for activated CO2
    -a carboxybiotin-enzyme intermediate is formed
    -the activated carboxyl group is transferred to pyruvate to form oxaloacetate
    -Acetyl CoA is an allosteric activator
  154. 154what is required for gluconeogenesis?an oxaloacetate produced by pyruvate carboxylase in the mitochondrium needs to be transported to the cytosol
  155. 155how can mitochondrial oxaloacetate become cytosolic?1. reduction to malate
    2. transmission to aspartate
    3. conversion to phosphoenolpyruvate PEP (mitochondrial PEPCK)
  156. 156how is oxaloacetate reduced to malate?by malate dehydrogenase linked to NADH.
    -malate is transported across the mitochondrial membrane
    -malate is oxidised by cytosolic NAD+, linked malate dehydrogenase
  157. 157How can oxaloacetate be converted to aspartate?If there is a lot of NADH in the cytoplasm (e.g. when lactate is being used as gluconeogenic substrate; lactate dehydrogenase)
  158. 158why is a carboxylation and a decarboxylation required to form a phosphoenolpyruvate from pyruvate?addition of a phosphoryl group to pyruvate is an energetically highly unfavourable reaction =+31 kj mol
    carboxylation and decarboxylation leads to +0.8kj mol.
    decarboxylations often drive reactions that are otherwise highly endothermic.
  159. 159What must peripheral tissues do in order to participate in the cori/ glucose-alanine cycles?they must release either lactate as the end product of glucose metabolism or alanine and not oxidise glucose completely to CO2 and H2O
  160. 160which amino acids can supply carbon skeletons for gluconeogenesis?all except leucine and lysine
  161. 161gluconeogenesisthe breakdown products of triglycerides and proteins, namely glycerol, fatty acids, and amino acids, can be used for energy either directly or indirectly by their conversion in the liver to glucose.
  162. 162why can glucose not be synthesised from acetyl CoA?so that gluconeogenesis does not take place from even chain fatty acids or ketogenic amino acids.
  163. 163lipolysisenzymes within fat cells hydrolyse triglycerides into fatty acids and glycerol, both of which enter the bloodstream. The fatty acids diffuse into cells, where they are used as an alternate energy source to glucose.
  164. 164What is the irreversible link from glycolysis to the TCA cycle?pyruvate dehydrogenase
    The acetate unit within pyruvate is activated by linking it to coenzyme A, so that it can then undergo further reactions.
  165. 165energy output per acetyl CoA3 NADH, 1 FADH2, 1 GTP
  166. 166TCA cycle regulation: pyruvate dehydrogenase-activated by ADP and pyruvate
    -inhibited by ATP, acetyl CoA and NADH
  167. 167TCA cycle regulation: isocitrate dehydrogenase-allosterically activated by ADP
    -inhibited by ATP and NADH
    Accumulation of citrate> moves to cytoplasm and inhibits PFK> halts glycolysis
  168. 168TCA cycle regulation: alpha ketoglutarate dehydrogenase-feedback inhibition by succinyl CoA and NADH
    -inhibited by high levels of ATP
  169. 169TCA cycle regulation: citrate synthase in bacteriainhibited by ATP
  170. 170location of oxidative phosphorylationeukaryotes- mitochondria, inner membrane
    prokaryotes- plasma membrane
  171. 171concept of oxidative phosphorylation1. electrons from NADH and FADH2 flow through complexes in the inner mitochondrial membrane
    2. this drives export of proteins (H+) to the intermembrane space to result in a proton gradient
    3. the H+ gradient is used by ATP synthase to make ATP (ADP is phosphorylated)0
  172. 172What blocks coenzyme A?rotenone
  173. 173What blocks complex 3?antimycin A
  174. 174what blocks complex 4?cyanide, axide, carbon monoxide
  175. 175ATP synthase: conformations 1-3Conformation 1: ADP and Pi bind with good affinity.
    Conformation 2: ADP and Pi bind so tightly that ATP is made.
    Conformation 3: ATP (and ADP and Pi) bind very weakly, and ATP is released.
  176. 176ATP synthase: how does the proton-motive force drive the rotation?protonation and de-protonation of aspartic acid.
    -the pump has an arginine amino acid that hands off hydrogen ion to aspartates on the rotor. Aspartate typically are negative, but since the rotor is surrounded by membrane lipids, it would be very unfavourable. So, the rotor only turns when the aspartates have a hydrogen attached, neutralising their charge.
  177. 177why is the energy yield from oxidative phosphorylation less than expected?because the transport processes dissipate some of the H+ gradient.
  178. 178glucose metabolism: liver-increased glucose uptake
    -increased glycogen synthesis
    -inhibition of gluconeogenesis
    -inhibition of glycogen breakdown
  179. 179glucose metabolism: skeletal muscle-increased glucose uptake
    -increased glycogen synthesis
    -inhibition of glycogen breakdown
  180. 180glucose metabolism: adipose tissue-increased glucose uptake
    -increased fatty acid/triglyceride synthesis
  181. 181effects of PKA on metabolism-directly phosphorylates and inactivates glycogen synthase, blocking glycogen synthesis
    -activates glycogen phopshorylase, leading to increased glycogen breakdown
    --activates a key enzyme activity involved in gluconeogenesis, leading to increased glucose production.
  182. 182ways of studying cell cycle progression1. examine growing cell microscopically
    2. stain cells with DNA binding fluorescent dyes
    3. use of flow cytometer measurement
  183. 183What suppresses CDK activity?inhibitory phosphorylation and CDK inhibitor proteins (CKIs)
  184. 184how can tumour tissue be detected on scans?by its unusually high uptake of radioactively labelled fluorodeoxyglucose (FDG), due to active glucose uptake and metabolism.

Information

Description
Flashcards on BM210 biochemistry, created by Julia Spychalska on 08/12/2017.
Views
0
Rating

Feedback

What is it about?

What do you think of the new look?

How do you like it?