From DNA to protein, i.e. the central dogma

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1 From DNA to protein, i.e. the central dogma DNA RNA Protein Biochemistry, chapters1 5 and Chapters Chapters 2 5 and will be covered more in detail in other lectures. ph, chapter 1, will be covered in specific lectures Transcription and translation The information flow in the cell. From DNA to RNA and finally to a functional protein From the Nobel e-museum, Jan-Olov Höög 1

2 The basic units in DNA and RNA-nucleotides DNA A C G T RNA A C G U Base pair - Dinucleotide Base pair between the chains Dinucleotide within the chain Jan-Olov Höög 2

3 5 3 The direction of a DNA (RNA) strand is always 5 3. The second strand in DNA is anti-parallel to the first one and harbouring the same sequence. Transcription (RNA-synthesis) The RNA-synthesis appears in the nucleus using DNA as a template. RNA-polymerase is the running enzyme. It will bind to its site in the promoter region in the gene. RNA synthesis Jan-Olov Höög 3

4 RNA processing Polyadenylation 5 -capping Splicing, i.e. introns are deleted Translation Initiation Elongation Termination Jan-Olov Höög 4

5 The components of the translation Ribosome, with small and large subunits incl rrna (4 different) and all proteins (ca. 50) mrna Charged trna NB! Eukaryotic and prokaryotic ribosomes differ 64 codes (tripletes) Degeneracy, i.e. some amino acids are coded by more than one codon AUG (Met) is the initiation codon The code is comma free Three stop codons The code It s crucial for the system to start exactly with the right reading frame Illustration of possible reading frames: AGG TGA CAC CGC AAG CCT TAT ATT AGC A GGT GAC ACC GCA AGC CTT ATA TTA GC AG GTG ACA CCG CAA GCC TTA TAT TAG C Jan-Olov Höög 5

6 trna Peptide bond formation Enzymatic process Peptidyl transferase, one of the proteins in the ribosome Jan-Olov Höög 6

7 Finally posttranslational modification Processing/deletion of the N-terminal Met N-terminal blocking, e.g. acetylation C-terminal blocking, e.g. amidation Processing/deletion of signal peptides, cf. insulin Processing of internal peptides, cf. the C-peptide Modification of certain amino acids, e.g. hydroxylation and glukosylation Protein production The polypetide will be folded into an active structure Jan-Olov Höög 7

8 Proteins The tools of life Biological macromolecules with amino acids as the basic units From greek, proteuo of first order, used for the first time by Jöns Jacob Berzelius 1838 Every cell will synthesize the proteins to be used in the cell Proteins > 51 aar or > 6000 Da Two main protein types Globular proteins the largest group according the number of different proteins Fibrous proteins the largest group according to mass Jan-Olov Höög 8

9 Hemoglobin a globular protein Collagen a fibrous protein An extracellular protein Jan-Olov Höög 9

10 Protein functions Enzymes catalyse chemical reactions, about 400 known reactions are catalysed by enzymes Transport proteins e.g. hemoglobin Storage proteins e.g. myoglobin Structural proteins e.g. collagen Movement proteins e.g. myosin Defence proteins e.g. antibodies (IgG etc) Signal proteins e.g. insulin Receptor proteins - (binds a ligand) e.g. insulin receptor Building units amino acids (1) In proteins there are 20 common amino acids, i.e. they correspond to a genetic codon C is chiral in the amino acids, i.e. it binds four different atoms/groups Solely L-amino acids occur in mammalian proteins Jan-Olov Höög 10

11 The 20 amino acids (2) Amino acids are grouped according to their properties Non polar (hydrophobic) Polar (hydrophilic) Non charged Negative (acid) Positive (basic) Smallest amino acid: Glycine (aminoethane acid) with side chain H. All amino acids are zwitterions at physiologic ph. The 20 amino acids (3) Jan-Olov Höög 11

12 The 20 amino acids (4:1) The 20 amino acids (4:2) Jan-Olov Höög 12

13 Less common amino acids Selenocysteine, the 21st amino acids, coded by UGA Pyrrolysine (the 22nd aa, (not in eukaryotes) coded by UAG) Hydroxyproline in collagen Hydroxylysine in collagen γ-carboxyglutamate in prothrombin Phosphoserine covalent modification β-alanine not in proteins GABA (γ-aminobutyric acid), signal substance Alline found in garlic, anitbacterial The peptide bond Covalent Double bond character (40%) Rigid peptide plan N-terminus (start) C-terminus (end) Jan-Olov Höög 13

14 Protein structure Primary structure order of amino acids Secondary structure folding of the backbone Tertiary structure the overall 3D fold Quaternary structure - the interaction of several polypeptides (subunits) Forces stabilising the protein Hydrophobic interactions Ionic bonds Hydrogen bonds van der Waals forces Disulphide bonds Jan-Olov Höög 14

15 Disulphide bond - covalent Two cysteines form a disulphide bond (bridge) through an oxidation. Secondary structure Three distinct secondary elements can be distinguished. All are stabilised by hydrogen bonds within the backbone. Jan-Olov Höög 15

16 Tertiary structure The tertiary structure is the folding of the entire protein. It s stabilised by hydrophobic interactions, ionic bonds, hydrogen bonds, van der Waals forces and disulphide bonds. All these forces act between the side chains of the amino acids. Quaternary structure The quaternary structure is the structure formed by several polypeptides (subunits). It s stabilised by hydrophobic interactions, ionic bonds, hydrogen bonds, van der Waals forces and disulphide bonds. All these forces act between the side chains of the amino acids. Jan-Olov Höög 16

17 Protein denaturation Degradation of a protein or, specifically, breaking of all noncovalent bonds. Jan-Olov Höög 17