Metals in Biochemistry/Biology Lecture Slides PDF

Recommended reading Metals in Principles of bioinorganic chemistry / Stephen J. Lippard, Jeremy M. Berg Mill Valley, Calif. : University Science Books, 1994. Biochemistry/Biology...

Recommended reading Metals in Principles of bioinorganic chemistry / Stephen J. Lippard, Jeremy M. Berg Mill Valley, Calif. : University Science Books, 1994. Biochemistry/Biology Bioinorganic chemistry : inorganic elements in the chemistry of life : an introduction and guide / Wolfgang Kaim, Brigitte Schwederski Chichester : John Wiley, 1994 Introduction Bioinorganic chemistry : a short course/ Rosette M. Roat-Malone Hoboken, N.J. : Wiley-Interscience, 2007 2nd ed Dr Nigel Young Chemistry (School of Natural Sciences) There are many other interesting and suitable texts available within the library – please also explore these. [email protected] 2 Interactive websites There are some very good on-line Libre Texts There is a very good set of interactive websites at covering this material. Copies available on Canvas “The Guided Tours of Metalloproteins” https://chem.libretexts.org/Bookshelves/Inorganic https://sites.chem.utoronto.ca/chemistry/courseno _Chemistry/Supplemental_Modules_and_Websites tes/GTM/main.htm _(Inorganic_Chemistry)/Descriptive_Chemistry/Ele ments_Organized_by_Block/3_d- These allow you to view the different parts of the Block_Elements/1b_Properties_of_Transition_Met metalloproteins and metalloenzymes. als/Transition_Metals_in_Biology Well worth coming back to. https://chem.libretexts.org/Bookshelves/Inorganic _Chemistry/Book3A_Bioinorganic_Chemistry_(Berti ni_et_al.) Resources Assessment Copies of these notes, the material used in the One examination question on the 551553 paper. lectures, supporting material will be available on Representative questions and answers will be made Canvas. available Videos and recordings of the taught sessions will be available. Representative past exam questions and answers. What is the most abundant metal Course Content in the human body? Introduction A. Iron 83% Amino acids and Proteins B. Copper Transition Metal Chemistry C. Zinc Zn metalloenzymes – structural and catalytic functions D. Sodium Fe transport/storage – microorganisms and animals Oxygen transport and storage E. Potassium Oxygen atom transfer reactions F. Magnesium 17% Electron-transfer proteins – copper and iron G. Calcium 0% 0% 0% 0% 0% Pt anti-cancer chemotherapeutics - cisplatin m m r n m nc um pe Iro c iu iu siu Zi p di ss Co l ne So Ca ta ag Po M  What are the second and third most What is the most abundant transition abundant metals in the human body? metal in the human body? A. Iron 50% A. Iron 100% B. Copper B. Copper C. Zinc C. Zinc D. Sodium 25% D. Sodium E. Potassium 17% E. Potassium F. Magnesium 8% F. Magnesium G. Calcium 0% 0% 0% G. Calcium 0% 0% 0% 0% 0% 0% m m m m r r n n m m nc nc um um pe pe Iro Iro c iu c iu iu iu siu siu Zi Zi p p di di ss ss Co Co l l ne ne So So Ca Ca ta ta ag ag Po Po M M What metals does Biology/Biochemistry use? Introduction to metals in biology/biochemistry Element Mass g/ 70 kg Role Calcium 1050 Muscle contraction, bone mineral Potassium 140 Major cation inside animal cells – Role of Ca in biology membrane potential More than 99% of calcium in the human body is found in bone (and teeth) as Sodium 105 Major cation inside animal cells – hydroxyapatite which provides skeletal strength. membrane potential It also acts as a reservoir of calcium for its other important functions such as Magnesium 35 Stability of polyphosphates, muscle contraction, signal transduction pathways, neurotransmitter release from activation of ATP neurons and fertilisation. Iron 4.2 Oxygen transport, redox chemistry Zinc 2.3 10% of all human proteins bind Zn. Structural and catalytic roles Copper 0.11 Redox chemistry – catalysis Manganese 0.02 Many enzymes possess manganese cofactors – bone formation and protection from free radicals Chromium 0.005 Role not fully defined – cofactor for insulin 11 12 Cobalt 0.003 Coenzyme – vitamin B12. 11  Are metals usually positively or What is the benefit of being negatively charged? positively charged A. positive 100% Stabilisation of negative charges B. negative Ability to bind substrates containing lone pairs of electrons Act as Lewis acids This can lead to reversible binding of substrates Useful in catalysis When H2O is bound to a metal This raises acidity of the H2O as it favours dissociation of H+. 0% Ka can be increased by up to 107 pKa can be changed from 14 to7 e ive iv s it t ga po ne Introduction to metals in biology/biochemistry Introduction to metals in biology/biochemistry What do metals have to offer biological systems? What do metals have to offer biological systems? Positively charged (usually) – may be useful for stabilisation of Variable oxidation states – especially TM’s negative charge, not unique to metals (e.g. R4N+) They are electron-pair acceptors. Two stable oxidation states separated by This leads to an ability to bind substrates containing lone pairs of one unit (difficult to achieve with non- electrons. metals). Lewis acidity Reversible binding of substrates (especially true for TM’s) Vital for electron transfer reactions L L M M e.g. useful in catalysis -L If L is H2O the binding to a metal raises the acidity of H2O i.e. favours H+ dissociation. Ka can be increased by a factor up to 107. Ka can be increased by a factor of up to 107. 15 16 Introduction to metals in biology/biochemistry Introduction to metals in biology/biochemistry Functions of metals in biology. Functions of metals in biology. Nerve cell; high [Na+] outside, low [Na+] Electron transfer – metals offering variable oxidation state. inside. Resting p.d. is -60mV - when Na+ Biological processes are tightly controlled and proceed by ion allowed in the p.d. reverses. regulated flow of electrons. O2 + 4e- + 4H+ 2H2O – controlled reduction of O2. The metal is not doing anything apart from providing + charge. Grp I metal ion is favoured for this. Dioxygen transport. All animals rely on metalloproteins: In the body there are stabilising interactions between metal ions and E.g.haemoglobin iron porphyrin DNA. myoglobin Hemerythrin – Fe2 dimer Structural role – relies on the ability of the metal ion to accept electron Haemocyanins – Cu2 dimer pairs Need reversible binding of the substrate (O2) Transient reduction of the substrate (e.g. to O2− or O22− or partially reduced 17 species) is helpful. Hence transition metals are best. 18 Which of the following have mononuclear iron at the active site? hemoglobin A. hemoglobin 100% (haemoglobin) B. myoglobin C. hemerythrin (haemrythrin) 0% 0% 0% D. hemocyanin (haemocyanin) n n) ) ) in i rin ob i ob n th gl ya l yo ry og oc m m em em ae a a (h (h (h in n n bi hr ni lo ya yt og er oc m m m he he he  Which of the following have myoglobin mononuclear iron at the active site? A. hemoglobin (haemoglobin) B. myoglobin C. hemerythrin (haemrythrin) 0% 0% 0% 0% D. hemocyanin (haemocyanin) n n) ) ) in i rin ob i ob n th gl ya l yo ry og oc m m em em ae a a (h (h (h in n n bi hr ni lo ya yt og er oc m m m he he he Which of the following have a hemerythrin copper dimer at the active site? A. hemoglobin 75% (haemoglobin) B. myoglobin C. hemerythrin 25% (haemrythrin) 0% 0% D. hemocyanin (haemocyanin) n n) ) ) in i rin ob i ob n th gl ya l yo ry og oc m m em em ae a a (h (h (h in n n bi hr ni lo ya yt og er oc m m m he he he  Introduction to metals in biology/biochemistry hemocyanin Functions of metals in biology. Metalloenzymes Hydrolytic enzymes – make use of the Lewis acidity of the metal. Protecting cells from hazardous chemicals – protective metalloenzymes make use of redox chemistry to catalyse disproportionation Cu2+/Cu+ redox couple. 2e− redox enzymes (= 1 electron pair). Multi-electron pair enzymes. Rearrangements. Enzymes that require vitamin B12 as a cofactor. 26 Protective enzymes Hydrolytic enzymes make use of Lewis acidity of metal make use of redox chemistry of Cu(II)/Cu(I) Carboxypeptidase Zn Cleaves C-terminal amino acids from proteins Superoxide Cu, Zn 2O2- +2H+  H2O2 + O2 dismutase Carbonic anhydrase Zn H2O + CO2  H2CO3  H+ + HCO3- Catalase Cu 2H2O2  2H2O + O2 Alkaline Zn Hydrolysis of phosphate esters phosphatase removes superoxide and peroxide 27 28 Two electron (i.e. one pair) redox enzymes Multi-electron pair enzymes Cytochrome c Fe, Cu O2 + 4H+ + 4e-  2H2O Cytochrome P-450 Fe Oxidation of hydrocarbons to enzymes alcohols oxidase Tyrosinase Cu Ortho-hydroxylation of phenolic substrates Sulfite oxidase Mo SO32-  SO42- Oxygen evolving Mn 2H2O  O2 + 4H+ + 4e- complex (OEC) (in photosystem II) Liver alcohol Zn CH3CH2OH + NAD+  CH3CHO + dehydrogenase NADH + H+ Catechol Fe Oxidation of catechols to 1,6- dioxygenase dicarboxylic acids Nitrate reductase Mo NO3-  NO2- Nitrogenase Mo, Fe N2 + 6H+ + 6e-  2NH3 Ribonucleotide Fe Ribose  deoxyribose (DNA reductase biosynthesis) Factor F-430 Ni 4H2 + CO2  CH4 + 2H2O Nitrite reductase Fe NO2- + 8H+ + 6e-  NH4+ + 29 30 hydrogenases 2H2O Rearrangements Enzymes that require vitamin B12 Glucose Fe D-glucose  D-fructose Methionine Co Homocysteine  isomerase synthase methionine Aconitase Fe4S4 Citrate = isocitrate (Kreb’s cycle) Diol Co 1,2-diols  aldehydes dehydratase Ribonucleotide Co Ribonucleotides  reductase deoxyribonucleotides 31 32  Metals in Biochemistry/Biology To understand the roles of transition metals in biology, we need to look at two components Introduction the organic superstructure usually made up of amino acids and proteins Dr Nigel Young the metals Chemistry (School of Natural Sciences) surrounded by ligands [email protected] What are the most important classes What ligands does biology use? of biological ligands? phosphates Proteins made up of long chains of amino acids water Macrocyclic ligands sulfides DNA/RNA carbonates nucleobases Also lipids carbohydrates coenzymes (vitamins)  Ligands Ligands are just the groups attached to the metals Metals in They can be charged or neutral Biochemistry/Biology Each ligand can contain one atom connected to the metal, or more than one. Monodentate ligands have one donor atom attached Some metal binding groups (ligands) of importance in biology Bidentate have two donor atoms Tetradentate have four donor atoms Dr Nigel Young Hexadentate have six donor atoms Chemistry (School of Natural Sciences) In general each donor atom donates a pair of electrons [email protected] to the metal Which of the following are Which of the following are monodentate ligands? bidentate ligands? A. A 50% A. A 60% B. B B. B 40% C. C C. C 40% D. D D. D E. E E. E 10% 0% 0% 0% 0% 0% B B C C D D A A E E  Example of tetradentate ligand 8 7 Example of hexadentate ligand O 9 6 10 5 1 2 N O OH 22 11 4 1 2 2 12 3 N 1 OH 1 1 HO N 2 1 NH 23 21 HN 13 2 HO 2 O 14 1 1 24 N 15 19 20 O 16 17 18 EDTA porphyrin Some metal-binding groups of importance in biology OH N N N N N O H N H H N Mg H N N N N N Me OH R porphyrin O Example of hexadentate ligand MeO2C O protoporphyrin IX chlorin ring of chlorophylls (iron complex is called haem) O HN - O O Mo O O S N N N N H N S H Ni H HN N N N N O H2N N N O PO32- H corrin (e.g. cobalt complex in vitamin B-12) molybdenum cofactor in oxo transfer proteins (probable structure) O nickel(II) hydroporphyrin of Factor F430 (ring substituents omitted for clarity) O H H N N HO O OH OH O O OH O O O O O NH OH OH enterobactin  Amino Acids and Proteins See also separate documents on Canvas Metals in Amino acids.pdf Biochemistry/Biology Protein Structures.pdf Amino acids Dr Nigel Young Chemistry (School of Natural Sciences) [email protected] How many naturally occurring The twenty common amino acids amino acids are there? A. 12 50% Alanine (Ala, A, 89, 71) Arginine (Arg, R , 174, 156) Asparagine (Asn, N, 132, 114) Aspartic acid (Asp, D, 133, 115) B. 16 Cysteine (Cys, C, 121, 103) Glutamatic acid (Glu, E, 147, 129) Glutamine (Gln, Q, 146, 128) Glycine (Gly, G, 75, 57) C. 18 33% Isoleucine (Ile, I, 131, 113) Leucine (Leu, L, 131, 113) Lysine (Lys, K, 146, 128) D. 20 Histidine (His, H, 155, 137) E. 22 17% Phenylalanine (Phe, F, 165, 147) Methionine (Met, M, 149, 131) Proline (Pro, P, 115, 97) Serine (Ser, S, 105, 87) F. 24 Threonine (Thr, T, 119, 101) Tryptophan (Trp, W, 204, 186) Valine (Val, V, 117, 99) 0% 0% 0% Tyrosine (Tyr, Y, 181, 163) 12 16 18 20 22 24  Henderson-Hasselbalch equation HA HA HA 𝑝𝐾 = 𝑝𝐻 + log 𝑝𝐻 = 𝑝𝐾 − log log = 𝑝𝐾 − 𝑝𝐻 𝐴 𝐴 𝐴 This tells us that pKa = pH when log[HA]/[A−] = 0, i.e. when [HA] = [A−], or when the concentration of the acid HA is equal to the concentration of its conjugate base A−. We need to remember that pKa is a fundamental property of the acid, whereas pH is something we can adjust. Using the Henderson-Hasselbalch equation we can see that when pH < pKa, log[HA]/[A−] has to be > 0, so [HA] > [A−], i.e. the protonated form, HA, will be present pH > pKa, log[HA]/[A−] has to be < 0, so [HA] < [A−], i.e. the deprotonated form, A−, will be present pKa for –COOH is ca. 2.2 and pKa for -NH3+ is ca. 9.5 Therefore at physiological pH (ca. 7) the amino acids are present as zwitterions containing COO− and NH3+  The pKa values of the side chains also allow us to Arginine predict the form of these present at Alanine (Ala, A, 89, 71) (Arg, R , 174, 156, pka 12.48) Asparagine (Asn, N, 132, 114) Aspartic acid (Asp, D, 133, 115, pKa 3.65) physiological/biological pH. From the considerations above a pKa of less than 7 will result in a deprotonated carboxylic acid, and a Cysteine Glutamatic acid Glutamine (Gln, Q, 146, 128) Glycine (Gly, G, 75, 57) pKa of greater than 7 will result in a protonated (Cys, C, 121, 103, pKa 8.35) (Glu, E, 147, 129, pKa 4.25) group such as amine, hydroxyl, thiol. O OH NH2 Isoleucine (Ile, I, 131, 113) Leucine (Leu, L, 131, 113) Lysine Histidine (Lys, K, 146, 128, pKa 10.79) (His, H, 155, 137, pKa 6.00) The amino acids that commonly function as ligands are the thiolate of cysteine, the imidazole of Methionine (Met, M, 149, 131) Phenylalanine (Phe, F, 165, 147) Proline (Pro, P, 115, 97) Serine (Ser, S, 105, 87) histidine, the carboxylates of glutamic and aspartic acid, and the phenolate of tyrosine. O O O O OH O OH Threonine (Thr, T, 119, 101) Tryptophan (Trp, W, 204, 186) Valine (Val, V, 117, 99) O NH2 NH2 Tyrosine aspartate glutamate (Tyr, Y, 181, 163, pKa 10.13) O O O H N OH OH S OH NH2 NH2 NH2 N O tyrosine cysteine histidine  Which amino acid typically ligates metal ions through an imidazole side- chain? The amino acids that commonly function as ligands 40% 40% are the thiolate of cysteine, the imidazole of A. alanine histidine, the carboxylates of glutamic and aspartic B. aspartate acid, and the phenolate of tyrosine. C. glutamate Less frequently encountered are the hydroxyl D. tyrosine 20% groups of serine and threonine, the thioether of methionine, the carboxamide groups of glutamine E. phenylalanine and asparagine, the amino group of lysine and F. histidine possibly the guanidine group of arginine. G. cysteine 0% 0% 0% 0% 0% H. methionine ne e e e te ne e ne s in in at in rta ei ni di an m on ro st la sti pa a al hi cy ty yla ut hi as et gl en m ph Which amino acid(s) typically ligates histidine metal ions through carboxylate side chains? 67% A. alanine B. aspartate C. glutamate D. tyrosine E. phenylalanine 17% 17% F. histidine G. cysteine 0% 0% 0% 0% 0% H. methionine ne e e e te ne e ne s in in at in rta ei ni di an m on ro st la sti pa a al hi cy ty yla ut hi as et gl en m ph  Which amino acid typically ligates metal ions through a functionalised aromatic side-chain? 100% A. alanine B. aspartate C. glutamate D. tyrosine E. phenylalanine F. histidine G. cysteine 0% 0% 0% 0% 0% 0% 0% H. methionine ne e e e te ne e ne s in in at in rta ei ni di an m on ro st la sti pa a al hi cy ty yla ut hi as et gl en m ph Which amino acid(s) typically ligates tyrosine metal ions through a sulfur atom? 25% 25% 25% 25% A. alanine B. aspartate C. glutamate D. tyrosine E. phenylalanine F. histidine G. cysteine 0% 0% 0% 0% H. methionine ne e e e te ne e ne s in in at in rta ei ni di an m on ro st la sti pa a al hi cy ty yla ut hi as et gl en m ph  Some metal-binding groups of importance in biology OH N N N N N O H N H H N Mg H N N N N N Me OH R porphyrin O cysteine MeO2C O methionine protoporphyrin IX (iron complex is called haem) chlorin ring of chlorophylls O HN - O O Mo O O S N N N N H N S H Ni H HN N N N N O H 2N N N O PO32- H corrin (e.g. cobalt complex in vitamin B-12) molybdenum cofactor in oxo transfer proteins (probable structure) O nickel(II) hydroporphyrin of Factor F430 (ring substituents omitted for clarity) O H H N N HO O OH OH O O OH O O O O O NH OH OH enterobactin Proteins Made up of amino acids Metals in How connected to each other Biochemistry/Biology Peptide bonds Proteins Dr Nigel Young Chemistry (School of Natural Sciences) [email protected] Protein structures Primary protein structure primary Amino acids are joined together by peptide bonds secondary Primary structure is order of amino acids in the tertiary polypeptide or protein backbone. quartenary Secondary protein structure This describes the three dimensional orientation of the proteins. Controlled by Hydrogen bonds Between carbonyl oxygen of one amino acid and amino hydrogen of a different amino acid  Two distinct structural types which are represented by coils and arrows. The coils are called α-helices, The arrows are called β-sheets, or β-pleated sheets. α – helix One of the two common motifs in the secondary structure of proteins. Every N-H group in the protein backbone hydrogen bonds to a C=O group also in the backbone, but located four residues earlier in the protein sequence. This forms a right-handed helical structure, where each turn of this helix contains 3.6 amino acids. The R groups of the amino acids which define the primary structure point out from the helix, meaning that they are able to interact with for example metals. β-sheet The β-sheet, or β-pleated sheet is the second The R groups of the amino acid residues protrude important structural motif found in the secondary alternately above and below the plane of the β- structure of proteins. sheet. β-sheets consist of β-strands connected laterally by The β-strand is typically 3 to 10 amino acids long. hydrogen bonds between two (or more) The arrows point from the amino (N-terminus) polypeptide chains. towards the carboxyl (C-terminus) residues. The amide hydrogen of one amino acid is located opposite the carboxy oxygen of another one. This forms a twisted, pleated sheet.  The individual strands may either be parallel, where they point in the same direction (i.e. the N- and C- anti-parallel parallel termini match up) or antiparallel, pointing in opposite directions (i.e. the N-terminus from one strand is located next the C-terminus of the other). The anti-parallel arrangement produces the strongest inter-strand stability because the hydrogen bonds formed are planar Tertiary structure This is the overall structure When protein folding takes place, the hydrophobic Largely determined by interactions R groups from the non-polar amino acids lie within of the R groups of the amino acids. the protein interior resulting in hydrophobic interactions. hydrogen bonding The hydrophilic R groups are on the outside. ionic bonding dipole-dipole interactions London dispersion forces Covalent bonding (disulfide bridges between two cysteines.  Quartenary structures Some proteins, such as hemoglobin, form from several smaller proteins or polypeptides, and it is the interaction of these sub-units that results in the quaternary structure. Myoglobin is just one unit, but hemoglobin has four sub-units https://openstax.org/books/biology-2e/pages/3-4-proteins#fig-ch03_04_09