Che 214 lecture 03


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Che 214 lecture 03

  1. 1. CHE 214: Biochemistry Lecture Three •NUCLEIC ACIDS •BIOENERGETICS Lecturer: Dr. G. Kattam Maiyoh GKM/CHE 214/LEC 03/SEM 02/2013
  2. 2. d. Nucleic Acids• DNA –deoxyribonucleic acid – Polymer of deoxyribonucleotide triphosphate (dNTP) – 4 types of dNTP (ATP, CTP, TTP, GTP) – All made of a base + sugar + triphosphate• RNA –ribonucleic acid – Polymer of ribonucleotide triphosphates (NTP) – 4 types of NTP (ATP, CTP, UTP, GTP) – All made of a base + sugar + triphosphate• So what’s the difference? – The sugar (ribose vs. deoxyribose) and one base (UTP vs. TTP) GKM/CHE 214/LEC 03/SEM 02/2013
  3. 3. Deoxyribose (like ribose) is a sugar with 5 carbon atoms in a ringOxygen is one of the ring membersIn Deoxyribose, one of the OH groups is missing and replaced with hydrogen,Thus deoxy = - 1 oxygenPhosphate groups are important because they link the sugar on one nucleotide onto the phosphate of the next nucleotide to make a polynucleotide. GKM/CHE 214/LEC 03/SEM 02/2013
  4. 4. Base - pairing• Nitrogenous bases• In DNA the four bases are: – Thymine – Adenine – Cytosine – Guanine• In RNA the four bases are: – Uracil – Adenine – Cytosine – Guanine GKM/CHE 214/LEC 03/SEM 02/2013
  5. 5. DNA and RNA are polynucleotides • Both DNA and RNA are polynucleotides. • They are made up of smaller molecules called nucleotides. Nucleotide • DNA is made of two polynucleotide strands:Nucleotide Nucleotide Nucleotide Nucleotide NucleotideNucleotide Nucleotide Nucleotide Nucleotide Nucleotide • RNA is made of a single polynucleotide strand: Nucleotide Nucleotide Nucleotide Nucleotide Nucleotide GKM/CHE 214/LEC 03/SEM 02/2013
  6. 6. • Nucleic Acids Function – Information Storage • DNA / mRNA – Information transfer / Recognition • rRNA / tRNA / snRNA – Regulatory • microRNA ? GKM/CHE 214/LEC 03/SEM 02/2013
  7. 7. DNA •Information for all proteins stored in DNA in the form of chromosomes or plasmids. •Chromosomes (both circular and linear) consist of two strands of DNA wrapped together in a left handed helix.(imagine screwing inwards) •The strands of the helix are held together by hydrogen bonds between the individual bases. •The “outside” of the helix consists of sugar and phosphate groups, giving the DNA molecule a negative charge. GKM/CHE 214/LEC 03/SEM 02/2013
  8. 8. GKM/CHE 214/LEC 03/SEM 02/2013
  9. 9. The Rule: Complimentarity• Adenine always base pairs with Thymine (or Uracil if RNA)• Cytosine always base pairs with Guanine.• This is because there is only exactly enough room for one purine and one pyrimidine base between the two polynucleotide strands of DNA/RNA. These bases are complimentary to each other GKM/CHE 214/LEC 03/SEM 02/2013
  10. 10. Complimentary Base Pairs A-T Base pairing G-C Base Pairing GKM/CHE 214/LEC 03/SEM 02/2013
  11. 11. GKM/CHE 214/LEC 03/SEM 02/2013
  12. 12. DNA Structure• The DNA helix is “anti-parallel” – Each strand of the helix has a 5’ (5 prime) end and a 3’ (3 prime) end. GKM/CHE 214/LEC 03/SEM 02/2013
  13. 13. DNA Structure 3’ end 5 ‘ endStrand 2 Strand 1(Crick strand) (Watson strand) 5’end 3 ‘ end GKM/CHE 214/LEC 03/SEM 02/2013
  14. 14. DNA Structure• 1 atgatgagtg gcacaggaaa cgtttcctcg atgctccaca gctatagcgc caacatacag• 61 cacaacgatg gctctccgga cttggattta ctagaatcag aattactgga tattgctctg• 121 ctcaactctg ggtcctctct gcaagaccct ggtttattga gtctgaacca agagaaaatg• 181 ataacagcag gtactactac accaggtaag gaagatgaag gggagctcag ggatgacatc• 241 gcatctttgc aaggattgct tgatcgacac gttcaatttg gcagaaagct acctctgagg• 301 acgccatacg cgaatccact ggattttatc aacattaacc cgcagtccct tccattgtct• 361 ctagaaatta ttgggttgcc gaaggtttct agggtggaaa ctcagatgaa gctgagtttt• 421 cggattagaa acgcacatgc aagaaaaaac ttctttattc atctgccctc tgattgtataBecause of the base pairing rules, if we know onestrand we also know what the other strand is.Convention is to right from 5’ to 3’ with 5’ on the left. GKM/CHE 214/LEC 03/SEM 02/2013
  15. 15. Chromosomes and Plasmids• Chromosomes are composed of DNA and proteins. – Proteins (histone & histone like proteins) serve a structural role to compact the chromosome. – Chromosomes can be circular, or linear. • Both types contain an antiparallel double helix! – Genes are regions within a chromosome. • Like words within a sentence. GKM/CHE 214/LEC 03/SEM 02/2013
  16. 16. Region (red box) of chromosome XI from the bakers yeast S. cerevisiae. Red and Blue colored boxes are genes Note that either strand may encode a gene, but that all genes start at the 5’ end and finish at the 3’ end. 214/LEC 03/SEM 02/2013
  17. 17. RNA• Almost all single stranded (exception is RNAi).• In some RNA molecules (tRNA) many of the bases are modified (e.g. psudouridine).• Has capacity for enzymatic function -ribozymes• One school of thought holds that early organisms were based on RNA instead of DNA (RNA world). GKM/CHE 214/LEC 03/SEM 02/2013
  18. 18. RNA• Several different “types” which reflect different functions – mRNA (messenger RNA) – tRNA (transfer RNA) – rRNA (ribosomal RNA) – snRNA (small nuclear RNA) – RNAi (RNA interference) GKM/CHE 214/LEC 03/SEM 02/2013
  19. 19. RNA function• mRNA – transfers information from DNA to ribosome (site where proteins are made)• tRNA – “decodes” genetic code in mRNA, inserts correct A.A. in response to genetic code.• rRNA-structural component of ribosome• snRNA-involved in processing of mRNA• RNAi-double stranded RNA, may be component of antiviral defense mechanism. GKM/CHE 214/LEC 03/SEM 02/2013
  20. 20. RNA A - hairpin loop B- internal loop C- bulge loop D- multibranched loop E- stem F- pseudoknotComplex secondary structures can form in linear molecule GKM/CHE 214/LEC 03/SEM 02/2013
  21. 21. mRNA• Produced by RNA polymerase as product of transcription – Provides a copy of gene sequence for use in translation (protein synthesis). – Transcriptional regulation is major regulatory point – Processing of RNA transcripts occurs in eukaryotes • Splicing, capping, poly A addition – In prokaryotes coupled transcription and translation can occur GKM/CHE 214/LEC 03/SEM 02/2013
  22. 22. The Central Dogma of molecular Biology GKM/CHE 214/LEC 03/SEM 02/2013
  23. 23. Bioenergetics GKM/CHE 214/LEC 03/SEM 02/2013
  24. 24. What is Bioenergetics ?•It is the study of the energy relationships and energyconversions in biological systems.•All organisms need free energy to keep themselves aliveand functioning.•The source of energy is just one; solar energy.•Only plants use that energy directly.•What the other organisms use is the chemical energy inthe form of foods.•The very first conversion of solar energy into a chemicalenergy is the sugar molecule. GKM/CHE 214/LEC 03/SEM 02/2013
  25. 25. Respiration• Respiration is important for bioenergetics as it stores the energy to form a molecule ATP; adenosine triphosphate.• This molecule is a link between catabolism and anabolism.• The process of photosynthesis is helpful in understanding the principles of energy conversion i.e. bioenergetics. GKM/CHE 214/LEC 03/SEM 02/2013
  26. 26. • Metabolism refers to all the chemical reactions of the body – some reactions produce the energy stored in ATP that other reactions consume – all biological molecules will eventually be broken down and recycled or excreted from the body GKM/CHE 214/LEC 03/SEM 02/2013
  27. 27. Catabolism and Anabolism• Catabolic reactions breakdown complex organic compounds – providing energy (exergonic) – glycolysis, Krebs cycle and electron transport• Anabolic reactions synthesize complex molecules from small molecules – requiring energy (endergonic)• Exchange of energy requires use of ATP (adenosine triphosphate) molecule. GKM/CHE 214/LEC 03/SEM 02/2013 25-27
  28. 28. ATP Molecule & Energy a b• Each cell has about 1 billion ATP molecules that last for less than one minute• Over half of the energy released from ATP is converted to heat GKM/CHE 214/LEC 03/SEM 02/2011 02/2013 25-28
  29. 29. Mechanisms of ATP Generation• Phosphorylation is the addition of phospahate group. – bond attaching 3rd phosphate group contains stored energy• Mechanisms of phosphorylation – within animals • substrate-level phosphorylation in cytosol • oxidative phosphorylation in mitochondria – in chlorophyll-containing plants or bacteria • photophosphorylation. GKM/CHE 214/LEC 03/SEM 02/2013 25-29
  30. 30. Phosphorylation in Animal Cells • In cytoplasm (1) • In mitochondria (2, 3 & 4) GKM/CHE 214/LEC 03/SEM 02/2013 GKM/CHE 214/LEC 03/SEM 02/2011 25-30
  31. 31. Carbohydrate Metabolism--In Review• In GI tract – polysaccharides broken down into simple sugars – absorption of simple sugars (glucose, fructose & galactose)• In liver – fructose & galactose transformed into glucose – storage of glycogen (also in muscle)• In body cells --functions of glucose – oxidized to produce energy – conversion into something else – storage energy as triglyceride in fat GKM/CHE 214/LEC 03/SEM 02/2013 25-31
  32. 32. Fate of Glucosei. ATP production during cell respiration – uses glucose preferentiallyi. Converted to one of several amino acids in many different cells throughout the bodyii. Glycogenesis – hundreds of glucose molecules combined to form glycogen for storage in liver & skeletal musclesi. Lipogenesis (triglyceride synthesis) – converted to glycerol & fatty acids within liver & sent to fat cells GKM/CHE 214/LEC 03/SEM 02/2013 25-32
  33. 33. Glucose Movement into Cells • In GI tract and kidney tubules, Na+/glucose symporters • Most other cells, GluT facilitated diffusion transporters move glucose into cells – insulin increases number of GluT transporters in the membrane of most cells – in liver & brain, always lots of GluT transporters • Glucose 6-phosphate forms immediately inside cell (requires ATP) thus, glucose hidden in cell • Concentration gradient favorable for more glucose to enter GKM/CHE 214/LEC 03/SEM 02/2011 02/2013 25-33
  34. 34. Glucose Catabolism• Cellular respiration – 4 steps are involved – glucose + O2 produces H2O + energy + CO2• Anaerobic respiration – called glycolysis (1) – Results in formation of acetyl CoA (2) is transitional step to Krebs cycle• Aerobic respiration – Krebs cycle (3) and electron transport chain (4) GKM/CHE 214/LEC 03/SEM 02/2011 02/2013 25-34
  35. 35. Historical PerspectiveGlycolysis was the very first biochemistry or oldest biochemistry studied.It is the first metabolic pathway discovered.Louis Pasture 1854-1864: Fermentation is caused by microorganism. Pastuer’seffect: Aerobic growth requires less glucose than anaerobic condition.Buchner; 1897: Reactions of glycolysis can be carried out in cell-free yeastextract.Harden and Young 1905: 1: inorganic phosphate is required for fermentation.2: yeast extract could be separated in small molecular weight essentialcoenzymes or what they called Co-zymase and bigger molecules calledenzymes or zymase.Inhibitor studies: Iodoacetate treatment resulted in the accumulation offructose 1,6biphosphate. Similarly fluoride caused accumulation of 2-phosphoglycerate and 3-phosphoglycerate.1940: with the efforts of many workers, complete pathways for glycolysis wasestablished.
  36. 36. Louis Pasteur (1822-1895)
  37. 37. 6 CH OPO 2− 2 3 5 O H H H 4 H 1 OH OH OH 3 2 H OH glucose-6-phosphateGlycolysis takes place in the cytosol of cells.Glucose enters the Glycolysis pathway by conversionto glucose-6-phosphate.Initially there is energy input corresponding tocleavage of two ~P bonds of ATP.
  38. 38. 6 CH2OH 6 CH OPO 2− 2 3 ATP ADP 5 O 5 O H H H H H H 4 1 4 H 1 OH H OH Mg2+ OH OH OH OH 3 2 3 2 H OH Hexokinase H OH glucose glucose-6-phosphate1. Hexokinase catalyzes: Glucose + ATP  glucose-6-P + ADPThe reaction involves nucleophilic attack of the C6hydroxyl O of glucose on P of the terminal phosphateof ATP.ATP binds to the enzyme as a complex with Mg++.
  39. 39. Glycolysis of Glucose & Fate of Pyruvic Acid• Breakdown of six-carbon glucose molecule into 2 three-carbon molecules of pyruvic acid – 10 step process occurring in cell cytosol – produces 4 molecules of ATP after input of 2 ATP – utilizes 2 NAD+ molecules as hydrogen acceptors• If O2 shortage in a cell – pyruvic acid is reduced to lactic acid so that NAD+ will be still available for further glycolysis – Lactic acid rapidly diffuses out of cell to blood – Liver cells remove it from blood & convert it back to pyruvic acid GKM/CHE 214/LEC 03/SEM 02/2011 02/2013 25-39
  40. 40. 10 Steps of Glycolysis GKM/CHE 214/LEC 03/SEM 02/2013GKM/CHE 214/LEC 03/SEM 02/2011 25-40
  41. 41. GKM/CHE 214/LEC 03/SEM 02/2013
  42. 42. Formation of Acetyl Coenzyme A• Pyruvic acid enters the mitochondria with help of transporter protein• Decarboxylation – pyruvate dehydrogenase converts 3 carbon pyruvic acid to 2 carbon fragment (CO2 produced) – pyruvic acid is oxidized so that NAD+ becomes NADH• 2 carbon fragment (acetyl group) is attached to Coenzyme A to form Acetyl coenzyme A which enter Krebs cycle – coenzyme A is derived from pantothenic acid (B vitamin). GKM/CHE 214/LEC 03/SEM 02/2013 25-42
  43. 43. GKM/CHE 214/LEC 03/SEM 02/2013
  44. 44. Krebs Cycle (Citric Acid Cycle) • Series of oxidation- reduction & decarboxylation reactions occurring in matrix of mitochondria • It finishes the same as it starts (4C) – acetyl CoA (2C) enters at top & combines with a 4C compound – 2 decarboxylation reactions peel 2 carbons off again when CO2 is GKM/CHE 214/LEC 03/SEM 02/2013 formed
  45. 45. THE TCA The names of the various enzymes in the previous slide are indicated in the figure below GKM/CHE 214/LEC 03/SEM 02/2013
  46. 46. Products of the Krebs Cycle• Energy stored in bonds is released step by step to form several reduced coenzymes (NADH & FADH2) that store the energy• In summary: each Acetyl CoA molecule that enters the Krebs cycle produces yields; – 2 molecules of CO2 • one reason O2 is needed – 3 molecules of NADH + H+ – one molecule of ATP – one molecule of FADH2• Remember, each glucose produced 2 acetyl CoA molecules GKM/CHE 214/LEC 03/SEM 02/2011 02/2013
  47. 47. The Electron Transport Chain • Involves a series of integral membrane proteins in the inner mitochondrial membrane capable of oxidation/reduction • Each electron carrier is reduced as it picks up electrons and is oxidized as it gives up electrons • Small amounts of energy is released in small steps • Energy used to form ATP by chemiosmosis GKM/CHE 214/LEC 03/SEM 02/2013
  48. 48. Chemiosmosis • Small amounts of energy released as substances are passed along inner membrane • Energy used to pump H+ ions from matrix into space between inner & outer membrane • High concentration of H+ is maintained outside of inner membrane • ATP synthesis occurs as H+ diffuses through a special H+ channel in inner membrane GKM/CHE 214/LEC 03/SEM 02/2013
  49. 49. Steps in Electron Transport• Carriers of electron transport chain are clustered into 3 complexes that each act as proton pump (expel H+)• Mobile shuttles pass electrons between complexes• Last complex passes its electrons (2H+) to a half of O2 molecule to form a water molecule (H2O) GKM/CHE 214/LEC 03/SEM 02/2013
  50. 50. Proton Motive Force & Chemiosmosis• Buildup of H+ outside the inner membrane creates + charge – electrochemical gradient potential energy is called proton motive force• ATP synthase enzyme within H+ channel uses proton motive force to synthesize ATP from ADP and P GKM/CHE 214/LEC 03/SEM 02/2013
  51. 51. Summary of Cellular Respiration • Glucose + O2 is broken down into CO2 + H2O + energy used to form 36 to 38 ATPs – 2 ATP are formed during glycolysis – 2 ATP are formed by phosphorylation during Krebs cycle – electron transfers in transport chain generate 32 or 34 ATPs from one glucose molecule • Points to remember – ATP must be transported out of mitochondria in exchange for ADP • uses up some of proton motive force – Oxygen is required or many of these steps can not occur GKM/CHE 214/LEC 03/SEM 02/2013