Adobe Systems Department of Biophysics, Medical Faculty, Masaryk University in Brno 1 Lectures on Medical Biophysics Structure of living matter FG23_11ab o3_3 Adobe Systems Lecture outline Water Properties of colloids Structure of proteins Structure of nucleic acids This lecture deals only with selected components of living matter with distinct biophysical properties. Importance of some other components, e.g. electrolytes will be shown in the lecture on bioelectric phenomena. Check on further information in textbooks of biology and biochemistry. Adobe Systems Water o3_3 Molecules of water are strongly polar because of oxygen electronegativity. Moreover, between the oxygen and hydrogen atoms of neighbouring molecules, hydrogen bonds are formed. They join water molecules in aggregates – clusters. Adobe Systems Hydrogen bonds between water molecules FG11_20ab FG11_21 Liquid water Pictures: http://cwx.prenhall.com/bookbind/pubbooks/hillchem3/medialib/media_portfolio/11.html Ice Adobe Systems Colloids Colloids – also known as non-true solutions – the solution consists of solute particles of diameter about 10 – 1000 nm dispersed in the solvent. We can distinguish two types of colloids according to the type of binding forces: ØMicellar colloids (also associative, small particles are bound together by van der Waals bonds) ØMolecular colloids (particles are macromolecules which subunits are bound together by covalent bonds) Weak chemical bonds Hydrogen bonds Hydrophobic interaction van der Waals bonds van der Waals • Also London forces, sometimes not classified as van der Waals bonds Properties of colloids Mechanical: rigidity, elasticity, viscosity – caused by covalent and weak chemical bonds These properties depend on the form of colloid: sol (liquid) or gel (solid). Gel formation = gelatinisation Optical: Light scatter: Tyndall effect (opalescence). Light can be scattered off the colloid particles. Track of a light beam passing through a colloid is made visible by the light scattered by the colloidal particles. Optical activity: Colloidal particles can rotate the plane of polarization of plane-polarised light passing through the colloid Electrical: see lecture on instrumental methods in molecular biophysics Adobe Systems Tyndall effect in micellar and molecular colloids gold4 620095mb_image002 - In solution of gelatin (a protein) http://link.springer-ny.com/link/service/journals/00897/papers/0006002/620095mb.htm - In solution of colloidal gold http://mrsec.wisc.edu/edetc/cineplex/gold/ Adobe Systems Types of Colloids - Biopolymers ̶According to the affinity of the biopolymer to solvent (water) ̶Lyophilic (hydrophilic) - form stable solutions ̶Lyophobic (hydrophobic) - form unstable solutions ̶According to the shape of the biopolymer (the shape is also influenced by the solvent!) ̶Linear (fibrillar – DNA, myosin, synthetic polymers…..also scleroproteins, mostly insoluble in pure water) ̶Spherical (globular – haemoglobin, glycogen … also spheroproteins, mostly soluble in pure water) Adobe Systems Chemical composition of proteins According to the products of hydrolysis: ̶simple (only amino acids in hydrolysate) ̶conjugated (not only amino acids in hydrolysate) ØNucleoproteins ØHaemoproteins ØFlavoproteins ØMetalloproteins ØLipoproteins Ø….. (see Biochemistry) Adobe Systems Structure of proteins ̶Structural units of proteins are amino acids (AA), connected by peptide bond: -RCH-NH-CO-RCH-, which can hydrolyse: -RCH-NH-CO-RCH- + H2O ¬¾® -RCH-NH2 + -RCH-COOH ̶The carboxylic and amino groups can dissociate or protonise. E.g. the glutamic and asparagic acids have one free carboxylic group: -COOH ¬¾® -COO- + H+ ̶AA lysine and arginine have one free amino group, which can protonise: -NH2 + H+ ¬¾® -NH3+ ̶In proteins, 20 different AA can be found which can be divided into AA with polar and non-polar side chain. ̶AA with aromatic ring or heterocycle (phenylalanine, tyrosine, tryptophan) strongly absorb UV light around 280 nm. ̶AA cysteine contains sulphhydryl (thiol) group (-SH), which is oxidised by dehydrogenation and connected with dehydrogenated group of another cysteine residue by covalent disulphidic bridge (bond -S-S-). Disulphidic bridges (in yellow) stabilise the protein structure (bovine ribonuclease A) •http://cwx.prenhall.com/horton/medialib/media_portfolio/text_images/FG04_28a-b.JPG Absorption spectrum of free phenylalanine, tyrosine and tryptophan in UV range •According:http://www.fst.rdg.ac.uk/courses/fs460/lecture6/lecture6.htm Structure of proteins Wavelength (nm) Adobe Systems Structure of proteins ̶Primary (sequence of covalently bound AA residues) ̶Secondary (mutual spatial arrangement of neighbouring links of the polypeptide chain – given mainly by hydrogen bonds) Øa-helix Øb-structure (pleated sheet) Øother ̶Tertiary (spatial arrangement of the polypeptide chain as a whole – given by hydrophobic and hydrogen bonds, stabilised by -S-S- bridges) ̶Quaternary (a way of non-covalent association of individual polypeptide chains (subunits) in whole of higher order) ØHomogeneous – all subunits are identical ØHeterogeneous – subunits of two or more kinds • • •Podle: http://cwx.prenhall.com/horton/medialib/media_portfolio/text_images/FG04_10.JPG protein structure Rise per residue Adobe Systems b-structure (pleated sheet – antiparallel model) http://www-structure.llnl.gov/Xray/tutorial/protein_structure.htm betas.gif (5742 bytes) Adobe Systems Triple helix of collagen http://cwx.prenhall.com/horton/medialib/media_portfolio/text_images/FG04_34.JPG FG04_34 •Podle: http://cwx.prenhall.com/horton/medialib/media_portfolio/text_images/FG04_01.JPG protein structures Adobe Systems Structure of nucleic acids (NA) ̶Mononucleotide (the structural subunit of NA) is formed by: ØPyrimidine (C, U, T) or purine (A, G) nitrogen base ØSugar (ribose or deoxyribose) ØPhosphoric acid residue ̶ ̶DNA: up to hundreds thousands of subunits. M.w. 107 – 1012. Two chains (strands) form antiparallel double helix. ̶RNA: Øm-RNA (mediator, messenger) Øt-RNA (transfer) Ør-RNA (ribosomal) Ø(viral RNA, microRNA …… ?) •http://cwx.prenhall.com/horton/medialib/media_portfolio/text_images/FG19_13_90035.JPG double helix formation Adobe Systems B-DNA http://cwx.prenhall.com/horton/medialib/media_portfolio/text_images/FG19_15aC.JPG FG19_15aC Adobe Systems A-DNA – dehydrated, B-DNA – commonly present under physiological conditions, Z-DNA – in sequences rich on CG pairs Adobe Systems Superhelical structure of circular DNA •Podle http://cwx.prenhall.com/horton/medialib/media_portfolio/text_images/FG19_191C.JPG superhelix Adobe Systems Structure of chromatin http://cwx.prenhall.com/horton/medialib/media_portfolio/text_images/FG19_23_00742.JPG, http://cwx.prenhall.com/horton/medialib/media_portfolio/text_images/FG19_25_00744.JPG FG19_23_00742 FG19_25_00744 Transfer RNA for valine – schematic t-RNA from yeasts ↓ http://cwx.prenhall.com/bookbind/pubbooks/hillchem3/medialib/media_portfolio/text_images/CH23/FG23_ 14.JPG, http://www.imb-jena.de/cgi-bin/ImgLib.pl?CODE=4tra IMB Jena Image Library Thumb Nail: 4TRA trna Amino acid binding site Valine „Clover leaf structure“ Ribosomal RNA Next picture was published in: Science 11 February 2011: Vol. 331 no. 6018 pp. 730-736 in the article: Crystal Structure of the Eukaryotic 40S Ribosomal Subunit in Complex with Initiation Factor 1 (Julius Rabl, Marc Leibundgut, Sandro F. Ataide, Andrea Haag, Nenad Ban) Description (for those interested in it): Architecture of the 40S. (A) Front and back views of the tertiary structure of the 40S showing the 18S rRNA as spheres and colored according to each domain (5′ domain, red; central domain, green; 3′ major domain, yellow; 3′ minor domain, blue; ESs, magenta), and the proteins as gray cartoons (abbreviations: H, head; Be, beak; N, neck; P, platform; Sh, shoulder; Bo, body; RF, right foot; LF, left foot). (B) Secondary structure diagram of the Tetrahymena thermophila (a protist)18S RNA …showing the rRNA domains and the locations of the ESs. (C) Ribosomal proteins of the 40S are shown as cartoons in individual colors; rRNA is shown as gray surface. The 40S is shown as in (A). (D) View of the quaternary interactions between ES6 and ES3 at the back of the 40S. The RNA is displayed as a cartoon with the proteins omitted for clarity. ES6 helices are colored in a gradient from light to dark magenta and labeled from A to E... ES3 is highlighted in pink, and the rest of the 18S rRNA is colored in gray. (E) The position of helix h16 in bacterial 30S [left…] and in 40S. Adobe Systems http://www.sciencemag.org/content/331/6018/730/F1.large.jpg Adobe Systems MicroRNA (source: Wikipedia) MicroRNA or miRNA are single strand non-coding RNAs with a typical length of 21-23 nucleotides which take a part in regulation of gene expression. miRNAs are produced by transcription from DNA genes, but they are not translated into proteins. https://upload.wikimedia.org/wikipedia/commons/thumb/c/c4/MiRNA_processing.svg/250px-MiRNA_processi ng.svg.png •After modification by nucleases called „Drosha“ and „Pasha“ the pre-miRNA enters the cytoplasm where can interact with the endonuclease called „Dicer“ forming miRNA. It is bound into the RISC complex (RISC = RNA-induced silencing complex). Just the RISC is able to silence the gene expression, which is known as RNA interference. Adobe Systems Conformation changes and denaturation of biopolymers ̶Changes in secondary, tertiary and quaternary structure of biopolymers are denoted as conformation changes. ̶They can be both reversible and irreversible. ̶‘native’ state of a biopolymer: its functional state. Otherwise the biopolymer has been ‘denatured’. Adobe Systems Denaturation factors ̶Physical: ØIncreased temperature ØIonising radiation ØUltrasound Ø….. ̶Chemical: ØChanges of pH ØChanges in electrolyte concentration ØHeavy metals ØDenaturation agents destroying hydrogen bonds – urea Ø….. ̶Combination of above factors: ionising radiation or ultrasound act directly and/or indirectly (chemically via free radicals) Adobe Systems Author: Vojtěch Mornstein Content collaboration and language revision: Carmel J. Caruana, Viktor Brabec Last revision September 2024