Biochemistry! " - Bio-Molecules, " - Amino Acids," - Peptides / Proteins "

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1 Biochemistry 2.1) Biomolecules Biochemistry! - Bio-Molecules, - Amino Acids, - Peptides / Proteins Prof. Dr. Klaus Heese Prof. Dr. Klaus Heese Bio-Molecules Interactions Hydrogen Bonds Water molecules modulate molecule interactions / behavior / functions Various non-covalent protein-protein interactions Essential Bio-Energy-related Bio-Molecules 1

2 Amino acids Peptides Proteins THE Bio- Energy Molecule ATP Pentose (5) DNA/RNA ( = AGCT/AGCU) DNA Bio- Energy: Chemical Structure of Hexoses (C 6 H 12 O 6 ) 2

3 Enantiomers - Steroisomers D- /L- forms Bio- Energy: Di-Saccharides Lactose and Sucrose (natural) only synthemc, good for diabemc paments but expensive as gold Lipids Cell Membrane and Cell Metabolism etc The effect of a double bond on the shape of fatty acids Phosphatidylcholine, a typical phosphoglyceride HO- - C- H 2 HO- - C- H H C- OH All phosphoglycerides are amphipathic having a hydrophobic tail (yellow) and a hydrophilic head (blue) in which glycerol is linked via a phosphate group to an alcohol. Either of or both the faxy acyl side chains in a phosphoglyceride may be saturated or unsaturated. In phosphamdic acid (red), the simplest phospholipid, the phosphate is not linked to an alcohol. Essential Cell Membrane Molecules Cross-sectional views of the three structures formed by phospholipids in aqueous solutions The white spheres depict the hydrophilic heads of the phospholipids, and the squiggly black lines (in the yellow regions) represent the hydrophobic tails. Shown are a spherical micelle with a hydrophobic interior composed enmrely of faxy acyl chains; a spherical liposome, which has two phospholipid layers and an aqueous center; and a two- molecule- thick sheet of phospholipids, or bilayer, the basic structural unit of bio- membranes. 3

4 Biochemistry 2.2) Amino Acids Amino Acids Genetic Code read > 3 Prof. Dr. Klaus Heese 20 Proteinogen Amino Acids = amino acids determined in the genetic code Amino Acids with polar side chains Acidic Amino Acids Basic Amino Acids 4

5 Amino Acids AA AA only 1 COOH and 1 NH 2 group smallest unit = glycin only alpha AAs are proteinogen, and here mainly L- alpha- AAs only e.g. beta- Alanin AA e.g. GABA γ aminobutyrate neurotransmixer Amino Acids, Peptides, Proteins D- and L- mirror images of amino acids (AAs) Enantiomers - Steroisomers Amino Acids All α-amino acids, except glycine, chiral ( = at least 1 asymetric C atom) That means, there exist D- and L-form, only L-form is proteinogen! (Fischer ProjecMon) Amino Acids are: Disulfid (S- ) - bridges Cystein + Cystein ---> Cystin (structure / funcmon (enzymes)) (cell (energy) metabolism) Disulfidbridge (cell signalling) 5

6 Non-Essential Amino Acids Essential Amino Acids Phenylketonurie (PKU) - Fölling Disease (lack of Phenylalanin-Monooxygenase) Non-Proteinogen Amino Acids Glu / glutamate GABA Glu Glu/E / E! neurotransmixers γ aminobutyrate Major difference between catecholamines and amino acid neurotransmitters the latter are derived from glucose metabolism and are taken up by glia and neurons Vit.B 6 key synthetic and degradative enzyme (negative feedback inhibition) GABA-T metabolizes GABA to SSADH only if α-ketoglutarate is present to receive the amino group from GABA (to generate then Glu) neurotransmixer Dopamine catecholamine > Parkinson Disease 6

7 Phenylalanine -----> (dietary) (essenmal AA) (Phenylalanine-hydroxylase) (in liver) (usually high conc. in brain TH is saturated by Tyr) Phenethylamine (does cross BBB) (PEA) (L-AADC) (very fast!) (does not cross BBB) (DBH) (PNMT, in adrenal gland regulated by glucocorticoids and NGF) neurotransmixer 5-HT: 1% in brain; In the blood (in platelets) and induces contractions of smooth muscle organs; high concentration in intestinal mucosa where it causes contraction of intestinal smooth muscle (PEA) (essenmal AA) in Neurons (limited, can cross BBB) (rate-limiting step) (L-AADC) (fast) (cannot cross BBB) Phenylethylamine (PEA) is found in abundance in cacao. Because PEA is heat sensitive, much of the PEA in conventional cooked and processed chocolate is missing. PEA is the chemical that we produce in our bodies when we fall in love. This is likely one of the main reasons why love and chocolate have such a deep connection. PEA also plays a role in increasing focus and alertness. Amino acids Acid Base Equilibrium Acid Base Amino acids acid-base systems MtraMon- curve 7

8 Buffers Dissociation of Amino Acids O 2 / CO 2 transport (respiramon) C! Cation (C) Zwitter Anion (A) (hybrid) At isoelectric point (ph IP ) the AA is neutral and in most cases as Zwitter /hybrid form In a similar way each protein has a ph IP where it is neutral (uncharged). Glycine TitraMon - curve of (Hybrid- Ion) IP or IEP (Isoelectric Point) Glycine ph (IEP) or ph (IP) or pi or pip (the value in the basic area will be excluded) Glycine has maximum buffer activity at pk S1 and pk S2 at pk S1 [C] = [Z] and at pk S2 [A] = [Z] Isoelectric point: ph IP = ( pk S1 and pk S2 ) / 2 Glu/E: ph(iep) = pk S1 + pk SR 2 = ( )/2 = 3.22 pk n and pk n+1 refer to the specie with the nexo- charge = 0; means here, the H+ reacmon that makes from the neutral specie a posimve specie and the de- H+ reacmon that makes from the neutral specie a negamve specie. pk R is the pk value of the side group R Also here the buffer ranges are from a physiological point of view (ph around 7) not relevant 8

9 Titration Curve of a basic amino acid such as Lysine (Lys/K) the only AA with a pk in physiological range Titration Curve of Histidine IP e side-chain (pk R ) Determination of NH 2 -group in AAs: boiling AAs with NaOH, NH 3 gas forms and reacts on wet ph paper with the water. The OH - is then coloring the ph paper (e.g. blue) Amino Acid Identification using Ninhydrin practical application: finger prints α- Amino Acids react with Ninhydrin forming the blue violet red- brown dye. The AA will be decarboxylated and oxidized to form an aldehyde with 1 less C- atom > finger print 9

10 Amino acids Peptides Biochemistry 2.3) Peptides / Proteins Proteins Prof. Dr. Klaus Heese synthesis direcmon of the protein in ribosoms plain, plane, layer, plakorm, planar Ramachandran Diagram Not allowed 10

11 Cysteine in Proteins Tertiary structure is the overall three-dimensional shape of a polypeptide results from interactions between amino acids and R groups Hyrdogen bond HO CH CH 22 O H O C H 3C H 3C CH CH CH 3 CH 3 Hydrophobic interackons and van der Waals interackons PolypepMde backbone Disulfid- bridges Cystein + Cystein ---> Cystin Disulfidbridge CH 2 CH 2 S S CH 2 Disulfide bridge O CH 2 NH O C CH 2 Ionic bond hxp://en.wikipedia.org/wiki/homocysteine hxp://en.wikipedia.org/wiki/cysteine 11

12 Biological Important Peptides Glu Cys Gly - H Tri- pepmde: CysMne (shown here in its neutral form), two cysteines bound together by a disulfide bond. The thiol group (- SH) is easy to be oxidized to form disulfide bridges to a 2 nd Glutathion molecule under cleavage of H. This is an important Redox- system in the blood and muscles. practical application: hairdresser / coiffeur Disulfide (S-S) bridges between the hairs need to be cleaved Insulin (controls blood glucose level) This is the acmvamon reacmon to form Ammoniumthioglykat Cleavage of S-S bridges by Ammoniumthioglykat After the hairdresser has made the new hairstyle, the S-S bridges will be recovered with H 2 O 2 12

13 9/6/15 S- S in RedOx ReacMons ROS or ROI Postulated mechanism whereby NO causes cytotoxicity or cytoprotection in nervous tissue (still a ROS) (SOD) (GPO) either or (GRD) -Calmodulin ROS or ROI lead to DNA disruption, mutation, activation of proteases ----> cell death Post-translational modifications of Amino Acids Biological Important Peptides Ring-form peptide hormone with intra-molecular disulfide bridge, causing contraction of mscles in mammary gland and uterus. peptide hormone, only 2 AAs are different to Ocytocin, causes water reabsorption in kidney; and blood-pressure increase. Significance of Peptides Synthesized as proteins/pepmdes based on DNA codons MulM- funcmons: as hormones Proteins & Structure AnM inflammamon anm- viral AnMbioMc Opioid pepmdes Epo (ErythropoeMn) / sports 13

14 α-helix β-sheet: 2 amid bonds! 3 amid bonds! 2 amid bonds! 3 amid bonds! The Tertiary Structure of Proteins The Quaternary Structure of Proteins The tertiary structure describes the spatial arrangement of a protein e.g. as alpha-helix or beta-sheet using also disulfide-bridges, ion-bonds, Van-der-Vaals forces, etc In the quaternary structure several protein chains form a globular structure by arranging themselves around ions such as Fe 2+, Mg 2+, etc Biochemistry 2.4) Amino Acids, Peptides, Proteins & Diseases Protein structure (folding / misfodling) and diseases: Abnormal protein structures in the pathogenesis of various neurodegeneramve diseases: > Alzheimer s disease (Aβ pepmde and Tau protein) Parkinson s disease (α- Synuclein protein) HunMngton s disease (HunMngMn protein) Prion disease (Prion) Prof. Dr. Klaus Heese All these brain diseases are about protein folding problems 14

15 Amino Acids - Carbon content: XTX- coded hydrophobic AAs: F 0.45 I L M V Non- XTX- coded hydrophobic AAs: G A 0.3 P C W Basic knowledge about the characterismc features of amino acids, pepmde bonds etc: > Further readings, not for exam: just to show the significance of this knowledge: Thymine distribu/on in genes provides novel insight into the func/onal significance of the proteome of the malaria parasite Plasmodium falciparum 3D7. Palanisamy B, Ekambaram R, Heese K. BioinformaMcs Mar 1;30(5): Lead discovery and in silico 3D structure modeling of tumorigenic FAM72A (p17). Pramanik S, Kutzner A, Heese K. Tumor Biology Jan, 36(1): D structure, dimeriza/on modeling, and lead discovery by ligand- protein interac/on analysis of p60 transcrip/on regulator protein p60trp. Pramanik S, Kutzner A, Heese K. Molecular InformaMcs 2015 July, in press. 15