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Transcript
Nucleic acids • Informational macromolecule • Deoxyribonucleic acid (DNA) is the genetic material • Ribonucleic acid (RNA) – Messenger RNA (mRNA) carries information from DNA to the ribosomes – Ribosomal RNA (rRNA) and transfer RNA (tRNA) are involved in protein synthesis – RNAs involved in regulation of gene expression and processing and transport of RNAs and proteins Nucleic acids • DNA and RNA are polymers of nucleotides • Nucleotides consist of – Purine and pyrimidine bases • Purines: adenine (A) and guanine (G) • Pyrimidines: cytosine (C) and thymine(T) • RNA has uracil (U) in place of thymine – 5 C sugar (5’ phosphorylated) • D-Ribose (RNA) • D-2’deoxyrobose (DNA) – Phosphate: 1-3 phosphate at 5’C of sugar Nitrogenous bases • Structures are meaningful • Reactive centers? Base pairing: Hydrogen bonding Hydrogen bonding btw complementary bases is the basis for double stranded DNA structure Backbone • Sugar phosphodiester forms the backbone • Ribose for RNA • 2’-deoxyribose for DNA • Nucleoside=covalent bonding of C1 of sugar and a base • Naming: Guanosine, Adenosine, cytidine and Thymidine, Uridine • Nucelotide= Nuceloside+5’phosphate (1-3) • Naming: – Adenosine monophosphate (AMP) – Adenosine diphosphate (ADP) – Adenosine triphosphate (ATP) • Can you name the others? Adenosine Adenosine monophosphate (AMP) Adenosine diphosphate (ADP) Adenosine triphosphate (ATP) Phosphodiester bond formation • DNA polymerases catalyze the rxn • uses complementary dNTPs • dehydration reaction between • 3’-OH of new strand and • 5’-phosphate of incoming dNTP • synthesis is 5’3’ • covalent bond is called phosphodiester • there is always a 5’-phosphate and a 3’-OH that gives the DNA its polar sense (5’3’) • complementary strands are antiparallel Phosphodiester bond formation • DNA polymerases catalyze the rxn • uses complementary dNTPs • dehydration reaction between • 3’-OH of new strand and • 5’-phosphate of incoming dNTP • synthesis is 5’3’ • covalent bond is called phosphodiester • there is always a 5’-phosphate and a 3’-OH that gives the DNA its polar sense (5’3’) • complementary strands are antiparallel DNA is an antiparallel helix • Geometry of bases and their spacial arrangement to form Hbond cause helix structure of dDNA • In B-form right handed dDNA • pairing bases stack in the centre • backbone intertwined • creates minor and major grooves • 0.34 nm (3.4 A) rise per base pair • one full helix turn houses 10 nucleotides Major groove 34 A 20 A Central dogma • Complementary base pairing allows one strand of DNA to act as a template for synthesis of a complementary DNA or RNA strand • DNA is transcribed to pass genetic information to RNA • The information in RNA is present in a triplet code where every three bases stands for one of the 20 amino acids • Translation: mRNA codes for protein • This flow of information from DNA to protein is called “central dogma” in cell biology Information flow: DNAmRNAProtein Central dogma and mutations GAGGUG • The DNA contains the instructions for the sequence of amino acids in each protein • The order of amino acids in a protein determines its shape and function • Errors or faults, ie mutations, in the DNA can change the amino acid sequence and function of the encoded protein • Sickle cell anaemia is due to one nucleotide change affecting hemoglobin reduced O2 carrying capacity Proteins • Proteins are the most diverse of all macromolecules • Each cell contains several thousand different proteins • Proteins direct virtually all activities of the cell • Functions of proteins include: Enzymes Structural components (e.g. keratin, collagen) Motility (e.g. actin) Regulatory (e.g. transcription factors) Transport (e.g. Na+-K+-ATPase) Receptors (e.g. insulin receptors) Transport and storage of small molecules (e.g. O2) Transmit information between cells (protein hormones), Defense against infection (antibodies) Amino acids • Polymers of 20 different amino acids. • Each amino acid consists of the α carbon bonded to a carboxyl group (COO−), an amino group (NH3+), a hydrogen, and a distinctive side chain (R) Amino acids • Amino acids are grouped based on characteristics of the side chains: – Nonpolar side chains – Polar side chains – Side chains with charged basic groups – Acidic side chains terminating in carboxyl groups Nonpolar amino acides • • • • 10 aa have nonpolar R-groups (hydrophobic) Simplest is glycine (R=H) 2 contain S and two have cyclic side chains Nonpolar aa tend to be burried in the hydrophobic core of proteins Polar amino acides • 5 aa have polar R-groups; either –OH or NH2 (hydrophilic) • Partial charge; H-bond formation with water • Polar aa tend to appear on the surface of proteins Charged amino acids • • • • 3 aa have positively charged NH2 groups (basic) Full charge; H-bond and ionic bond Like Polar aa tend to appear on the surface of proteins Might take part in catalytic core of enzymes Charged amino acids • 2 aa have negatively charged –COO- group (acidic) • Full charge; H-bond and ionic bond • tend to appear on the surface of proteins or enzyme catalytic core Peptide bond formation • Polypeptides: chains of amino acids joined by peptide bonds • Number of aa’s varied • oxytocin – 9 aa, • insulin – 51 aa, titin (connectin)– 34,350 aa’s • Average 400-500 aa • One end of a polypeptide terminates in an α amino group (N terminus) • other end is an α carboxyl group (C terminus) Protein structure • Sequence of amino acids in a protein is determined by the order of nucleotide bases in a gene (Primary structure) • One can deduce aa sequence from the sequence of nucleotides in the gene (or mRNA) • 3-D conformation is critical to proteins function • What determines the 3-D structure of proteins? Protein secondary structure Christian B. Anfinsen (1957) • 3-D structure is a result of interactions between the amino acids • Christian Anfinsen denatured ribonuclease (RNase) by heat treatment; breaks H-bonds • If the treatment was mild, the proteins would return to their normal shape at room temperature • This would mean that the information for folding the protein is in its primary sequence (how could he test?) Protein secondary structure • Secondary structure: regular arrangement of amino acids within localized regions • There are 2 types of secondary structure: - The polypeptide can coil in a spiral helix shape The polypeptide can fold to form a β pleated sheet (parallel or antiparallel) • Both are held together by hydrogen bonds between the CO and NH groups of peptide bonds Protein Tertiary structure Observation: • Similarly disrupting the disulfide bonds (S-S) using chemical denaturing agents (eg. βmercaptoethanol) denatures proteins (-SH forms) • Incubation under oxygen refolded the RNase back to its functional conformation (ie enzyme gained capacity to degrade RNA) • indicates a higher level of structure important for function that relies on covalent S-S bridge (tertiary structure) Protein Tertiary structure • Tertiary structure: folding of secondary structural elements to form a 3-D arrangement RNase • 2° elements connected by loops and less ordered aa’s • interactions btw the side chains of amino acids in different regions of protein stabilizes the 3° structure - Covalent bonds (S-S bridge) - Hydrophobic and hydrophilic interactions • In most proteins this results in domains, the basic units of tertiary structure Insulin Protein Quaternary structure • Quaternary structure consists of interactions between different polypeptide chains • In multi-subunit enzymes • Hemoglobin, for example, is composed of four polypeptide chains Protein structure: Summary Campbell & Reece, 2002 Can you meet these objectives? • Distinguish among nucleosides, nucleotides and nucleic acids? • Explain the structure of DNA? • List some functions of proteins in cells? • Describe and distinguish between amino acids? • Discuss the levels of protein structure and organization of proteins?