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Properties of amino acids Primary structure: Sequence of amino acids within the peptide chain. Peptide bonds Amino-terminal end Carboxy-terminal end The α-helix II ¾ The peptide bond causes a dipole which becomes stronger by the regular arrangement ¾ Consequence: Positively charged Nterminal end Negatively charged Cterminal end Atome: rot, Sauerstoff; schwarz: Kohlenstoff; blau: Stickstoff; weiß; Wasserstoff. Biochemie/Proteine_28 3 Carbohydrates ¾ The simplest compound with the gross fomula (CH2O)n is formaldehyde: n=1 ¾ H2C=O has little in common with usual concept of sugars ¾ Smallest carbohydrates are the trioses ¾There are two trioses: Glyceraldehyde and dihydroxyacetone ¾ Represent major classes of monosaccharides ¾ Glyceraldehyde is an aldehyde: Aldoses ¾ Dihydroxyacetone is a keton: Ketoses ¾ Tautomer structures ¾ Can interconvert through an instable intermediate: Enediol Mathews, van Holde & Ahern, 2000 Ring structures Example: ribose, a pentose ¾ Can form either a five-membered furanose ring ¾ Or a six-membered pyranose ring ¾ Reaction: formation of hemiacetals from the acldehyde group ¾ In each case, two enantiomeric forms, α or ß are possible Nucleophilic attack Mathews, van Holde & Ahern, 2000 Hexose rings Pyranose ring conformations ¾ Chair (more stable) ¾ Boat (less stable) Mathews, van Holde & Ahern, 2000 Same monomers, different polymers: h Starch (α-1,4 bonds) h Cellulose (ß-1,4 bonds) h Glycogen (α-1,4 and α-1,6 bonds) Starch (Stärke) Cellulose ß-1,4 -1,4 Cellobiose Influence of binding form on secondary structure Cellulose is the most abundant biopolymer on earth Glycogen Branched polysaccharide: The linkages between glucose residues are of two types, α-1,4 and α-1,6 Glycogen in liver cells Storage polymer composed of glucose in animal liver Murein: Poly-N-acetyl glucosamine – the construction material for bacterial cell walls Smooth and rough colonies of B. anthracis Sugars and blood groups The ABO blood group antigens The O oligosaccharide does not elicit antibodies in most humans The A and B antigens are formed by addition of GalNAc or Gal, respectively, to the O oligosaccharide Each of the A and B antigens can elicit a specific antibody In this figure, R can represent either a protein molecule or a lipid molecule Mathews, van Holde & Ahern, 2000 Phospholipids Hydrophobic Bonds („hydrophobic interactions“) ¾ Non-polar molecules mixed with water do not dissolve (e.g. oil slick on water). Why? ¾ Water is held together by hydrogen bonds. If nonpolar molecule is inserted into water, would have to break the ordered lattice of water molecules held together by H bonds. ¾ But this would require energy – it canott happen spontaneously. Instead, nonpolar molecules (or parts of molecules) will aggregate to avoid water. ¾ A similar situation occurs in parts of many proteins. ¾ The Hydrophobic Bond is very weak (ca. 2,5 J Mol-1), rather a lower energy state than would occur if these molecules were dissolved in water. Functions of membranes Fluid mosaic model Diagram of the structure of the cytoplasmic membrane; the inner surface (In) faces the cytoplasm and the outer surface (Out) faces the environment. ¾ The matrix of the unit membrane is composed of phospholipids, with the hydrophobic groups directed inward and the hydrophilic groups toward the outside, where they associate with water. ¾ Embedded in the matrix are proteins that have considerable hydrophobic character in the region that traverses the fatty acid bilayer. ¾ Hydrophilic proteins and other charged substances, such as metal ions, may be attached to the hydrophilic surfaces. ¾ Although there are some chemical differences, the overall structure of the cytoplasmic membrane shown is similar in both prokaryotes and eukaryotes Brock, 10th ed. Pyrimidine bases Sugar binding sites Purine bases Sugar binding sites Structure of the bases of D N A and RNA. The letters, C, T, U, A and G are used to designate the individual bases. In attaching the base to the 1‘ carbon of the sugar phosphate, pyrimidine bases are bonded through N-1 of the ring and purine bases through N-9 of the ring Structural formulas of nucleic acid sugars. The name „deoxy“ comes because here an O is lacking ¾ The formulas can be represented in two alternate ways, open chain and ring. ¾ The open chain is easier to visualize, but the ring form is the commonly used structure. ¾ Note the numbering system on the ring. This is a nucleoside This is a nucleotide 5‘ end 3‘ end 5‘ end 3‘ end Primary structure of nucleic acids: base sequence G-C: 3 hydrogen bonds Secondary structure of nucleic acids: Base pairs 2 hydrogen bonds The tertiary structure of nucleic acids Franklin's X-ray diagram of the B form of sodium thymonucleate (DNA) fibres, published in Nature on 25 April 1953, shows "in striking manner the features characteristic of helical structures"5. „Her photographs are among the most beautiful X-ray photographs of any substance every taken." — J. D. Bernal, 1958. From the Nobel prize winning publication in Nature Quarternary structure of DNA: supercoiling Relaxed and supercoiled DNA Melting and denaturizing of DNA ¾ A=T pairs are more easily separated than G≡C pairs ¾ Therefore, denaturation starts with A=T pairs ¾ High G≡C proportion: higher melting point RNA: ribonucleic acid – single stranded •Backbone: Ribose, Phosphoric acid •Bases: A,G,C,U • single stranded •80-85% of bacterial RNA is in ribosomes • Ribosomes: Protein synthesis • Information encoded on DNA is translated into protein via RNA during protein synthesis Three major types of RNA • messenger RNA (mRNA) • transfer RNA (tRNA) • ribosomal RNA (rRNA) → Two types of function • genetic - carries genetic information of DNA (mRNA) • structural e.g. -structural role in ribosome (rRNA), - amino acid transfer (tRNA), - catalytic (enzymatic) activity (ribozymes) PD Dr. Bettina Siebers The UV damage to DNA Ultraviolet (UV) photons harm the DNA molecules of living organisms in different ways. In one common damage event, adjacent bases bond with each other, instead of across the “ladder.” This makes a bulge, and the distorted DNA molecule does not function properly. (Illustration by David Herring) http://web.indstate.edu/thcme/micro/bactGen/thy_dmr.gif ATP Components of the important nucleotide, adenosine triphosphate (ATP) The energy of hydrolysis of a phosphoanhydride bond (shown as squiggles) is greater than that of a phosphate ester and will have significance in Chapter 5 (Section 5.8) [Brock, 10th ed.] NAD+/NADH Coenzyme Required for redox reactions Example: Reduction of pyruvate Although not used in the electron transport chain, Coenzyme A is a major cofactor which is used to transfer a two carbon unit commonly referred to as the acetyl group. The structure has many common features with NAD+ and FAD in that it has the diphosphate, ribose, and adenine. In addition it has a vitamin called pantothenic acid, and finally terminated by a thiol group. The thiol (-SH) is the sulfur analog of an alcohol (-OH). The acetyl group (CH3C=O) is attached to the sulfur of the CoA through a thiol ester type bond. Acetyl CoA is important in the breakdown of fatty acids and is a starting point in the citric acid cycle www.elmhurst.edu/~chm/vchembook/images/594CoA.gif