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BIOCHEMISTRY Nucleic Acids BIOB111 CHEMISTRY & BIOCHEMISTRY Session 17 Session Plan • • • • Types of Nucleic Acids Nucleosides Nucleotides Primary Structure of Nucleic Acids • DNA Double Helix • DNA Replication • Types of RNA Stoker 2014, Figure 23-2 p843 Nucleic Acids (NAs) • Cells in a living organism are able to produce exact replicas of themselves. • Cells contain all the information needed to produce the complete organism, they are part of. • Nucleic acids store this information. • Nucleic acids are found in the nucleus & are acidic. • Nucleic acids are polymers of Nucleotides (the monomers). 2 Types of Nucleic Acids • DNA – Deoxyribonucleic acid • Found in the nucleus, stores & transfers genetic info. • Passed from one cell to another during cell division. • RNA – Ribonucleic acid • Found in the nucleus & cytoplasm. • Its primary function is to synthesize proteins. • The hereditary information, required for protein synthesis, is stored in the molecules of DNA in the nucleus & mitochondria (mitochondrial DNA). Chromosomes • The DNA in the nucleus wraps around proteins Histones, joining them together into a fibre, forming Chromosomes. • Chromosome mass is about 15% DNA & 85% proteins. • Cells of different organisms have different numbers of chromosomes in cell nuclei. • The nucleus of human somatic cells contains 23 pairs of chromosomes. Tortora & Grabowski 2003, Figure 3.26, p.85 Nucleotides • Nucleic acids (DNA & RNA) are polymers of Nucleotides. • Nucleotides are the monomer building blocks of NAs, just like monosaccharides are building blocks of polysaccharides & AAs are building blocks of proteins. • • • • A Nucleotide has 3 components: Nitrogen-Containing Base Pentose Monosaccharide Phosphate Group N-containing Bases • Heterocyclic amines • Basic / alkaline (pH > 7) • Derived from: • Pyrimidine • A mono-cyclic base with a ring of 6 atoms (4C + 2N) • Purine • A bi-cyclic base with 2 fused rings (a 5-membered & a 6-membered ring) Pyrimidine & Purine Bases • • • • 3 derivatives of Pyrimidine: Cytosine ( C ) – DNA & RNA Thymine ( T ) – DNA only Uracil ( U ) – RNA only • • • • 2 derivatives of Purine: Adenine ( A ) Guanine (G ) Both are present in DNA & RNA Stoker 2014, Figure 22-2 p790 Pentose Sugars • Pentose monosaccharides • Ribose – in RNA. • Deoxyribose – in DNA. Deoxyribose is lacking O atom on C2’. Phosphate Group • Derived from from phosphoric acid (H3PO4). • The cellular pH leads to full dissociation of the phosphoric acid, producing a hydrogen phosphate ion (HPO42-). • Instead of writing the full ionic version, Biochemistry commonly uses an abbreviation to express the phosphate ion. • Pi = Inorganic Phosphate or Nucleoside • Base + Sugar = NUCLEOSIDE Nucleotide • Nucleoside + Pi attached to C5’ position of pentose sugar via phosphate-ester bond. • Base + Sugar + Phosphate group = NUCLEOTIDE Stoker 2014, Table 22-1 p792 Nucleic Acids • Nucleic acids = polymers of Nucleotides Stoker 2014, Figure 22-3 p793 Structure of Nucleic Acids • Nucleic acids have primary & secondary structure (like proteins). • Primary structure of both DNA & RNA = the sequence of nucleotides. • The primary structure has 2 parts: • 1) Backbone composed of sugars & phosphate groups – constant through entire molecule. • 2) Nitrogen Bases as side chains – sequence of bases is variable & distinguishes 1 molecule of NA from another one. Stoker 2014, Figure 22-4 p794 Structure of Nucleic Acids • Backbone = Phosphate + Sugar (different in DNA & RNA) Primary Structure of Nucleic Acids • The Sequence of Bases attached to the sugar units of the backbone changes & determines the Primary Structure of NAs (like in proteins). • Each non-terminal Pi of the backbone is bonded to 2 sugar molecules via a 3’,5’-phosphodiester bond – one phosphoester bond to C5’ of one sugar & another phosphoester bond to C3’ of the next sugar – both of these bonds originate from one & the same Pi. • • • • The nucleotide chain has a direction. One end – 5’ end – carries a free Pi attached to C5’ of the sugar. The other end – 3’ end – has a free –OH on C3’ of the sugar. By convention, the sequence of bases on a NA strand (DNA or RNA) is read from the 5’ end to the 3’ end. Stoker 2014, Figure 22-5 p795 Segment of DNA Secondary Structure of DNA • The DNA of very animal & plant has a unique base composition but the relationships between the bases are always the same. • %A=%T • %C=%G • Human DNA contains 30% each of A & T & 20% each of C & G. • In 1953, Watson & Crick received the Nobel Price for ‘explaining’ the secondary structure of DNA as a Double Helix, which has now been validated. DNA Double Helix • Double Helix = 2 strands of DNA in their primary structure, wound up around each other like a spiral staircase. • The sugar + Pi backbones of the 2 strands are like banisters of the staircase. • The bases of both strands extend inwards towards the bases of the other strand & are bonded together via Hydrogen bonds. • The 2 strands are anti-parallel = run in opposite directions – one strand runs 5’→3’ & the other 3’→5’ direction. Base Pairing • Always 1 purine base (large) & 1 pyrimidine base (small) are linked together via Hydrogen bonds between each other, forming a pair of bases. • The interior of the Double helix is small & 2 large purine bases would not fit, whereas 2 small pyrimidine bases would be too far apart to form Hydrogen bonds. • When linking together via Hydrogen bonds, the bases form the Secondary structure of DNA & are known as Complementary bases. Complementary Base Pairs • In DNA • A=T • G≡C • In RNA • A=U • G≡C Stoker 2014, Figure 22-7 p798 Stoker 2014, Figure 22-8 p799 Hydrogen Bonding is more favourable between A=T G≡C DNA Double Helix • The Double Helix of DNA = 2 complementary DNA strands. • If the sequence of bases in 1 strand is known, the sequence of bases in the complementary strand can be predicted. • 5’ A – A – T – G – C – A – G – C – T 3’ • 3’ T – T – A – C – G – T – C – G – A 5’ DNA Replication • The process by which a DNA molecule produces an exact duplicate of itself. • This process takes place in the nucleus when the parent DNA divides into 2 daughter DNA molecules, identical to the parent DNA molecule. • Replication uses the same principle of base pairing as encountered in the Secondary structure of DNA double helix. DNA Replication • Both of the 2 strands of DNA forming the double helix serve as Templates for copying. • The enzyme DNA-helicase unwinds the double helix & breaks the hydrogen bonds between the bases (like undoing a zipper). • Replication fork = the point at which the double helix is unwinding & constantly moving. • The 2 strands separate & each of them serves as a template for the synthesis of a new complementary strand. DNA Replication • The bases of the separated strands are not connected by hydrogen bonds anymore – they can now pair with free individual nucleotides present in the nucleus (C≡G & A=T) one at a time & form new hydrogen bonds with the old strand (= the template). • The enzyme DNA-polymerase checks if the pairing of bases is correct & joints the new bases to a new backbone (catalyzes formation of new phosphodiester bonds between nucleotides). • Each of the 2 daughter molecules of double-stranded DNA, formed during replication, contains 1 strand from the original parent molecule & 1 newly formed strand. DNA Replication Stoker 2014, Figure 22-9 p801 DNA Replication • The 2 daughter DNA molecules are synthesized in different ways. • DNA-polymerase can function only in 5’→3’ direction. • However the 2 strands of parent DNA run in opposite directions, therefore only one new strand can continuously grow in 5’→3’ direction = Leading strand. • The other strand – Lagging strand – is synthesized in short segments = Okazaki Fragments (= sequences of about 200 nucleotides with gaps between them), which are eventually joined together by the enzyme DNA-ligase. Stoker 2014, Figure 22-11 p803 DNA Replication • Replication usually occurs at multiple sites within the DNA molecule & proceeds in both directions. • This multiple-site replication enables rapid DNA synthesis. • Note: • Anti-metabolites • Anti-cancer drugs that interfere with DNA-replication in cancer cells, causing them to die. • Examples: 5-fluorouracil (5-FU), 6-mercaptopurine (6-MP), Floxuridine Stoker 2014, Figure 22-12 p803 Summary of DNA Replication Stoker 2104, p804 Differences between DNA & RNA DNA RNA Pentose Sugar in backbone Deoxyribose Ribose Complementary Base Pairs Strand A=T C≡G Double helix A=U C≡G Single strand Size Very large Much smaller (1-100 million nucleotides) (75-few 1,000 nucleotides) Stoker 2014, Figure 22-14 p807 RNA Molecule • Even though the RNA molecule is a single strand it often folds upon itself in certain parts and forms double-helical regions. Secondary Structure of RNA • RNA forms only a single strand, which is the Primary structure. • Secondary structure – portions of the strand fold onto itself, forming loops of double helical regions. • Contains Uracil instead of Thymine. Stoker 2014, Figure 22-19 p819 Types of RNA Molecules • There are 5 types of RNA but only 3 types will be discussed: • Messenger RNA • Ribosomal RNA • Transfer RNA Messenger RNA – mRNA • Carries the genetic information from the DNA in the nucleus to the site of protein synthesis in the cytoplasm. • Its nucleotide sequence is exactly complementary to that of one of the DNA strands. • It is not very stable, it is synthesized when needed & then degraded. • Size varies according to the length of the protein to be synthesized. • The average size is about 750 nucleotides. • Constitutes about 5-10% of overall RNA mass. Ribosomal RNA – rRNA • Combines with specific proteins & forms ribosomes = the site of protein synthesis. • The composition of ribosomes: • Proteins – 35% • rRNA – 65% • rRNA molecules are large. • The most abundant RNA-type, constitutes about 75-80% of overall RNA mass. Stoker 2014, Figure 22-19 p819 Transfer RNA – tRNA • Transport amino acids to the site of protein synthesis (= ribosomes). • Contain 75-90 nucleotides. • Are the smallest of the RNAs. • There is at least one different tRNA molecule for each of the 20 standard amino acids. • The 3D-structure of tRNA is an L-shape but by convention it is represented in 2-D as a clover leaf structure. Readings & Resources • • • • • • • • Stoker, HS 2014, General, Organic and Biological Chemistry, 7th edn, Brooks/Cole, Cengage Learning, Belmont, CA. Stoker, HS 2004, General, Organic and Biological Chemistry, 3rd edn, Houghton Mifflin, Boston, MA. Timberlake, KC 2014, General, organic, and biological chemistry: structures of life, 4th edn, Pearson, Boston, MA. Alberts, B, Johnson, A, Lewis, J, Raff, M, Roberts, K & Walter P 2008, Molecular biology of the cell, 5th edn, Garland Science, New York. Berg, JM, Tymoczko, JL & Stryer, L 2012, Biochemistry, 7th edn, W.H. Freeman, New York. Dominiczak, MH 2007, Flesh and bones of metabolism, Elsevier Mosby, Edinburgh. Tortora, GJ & Derrickson, B 2014, Principles of Anatomy and Physiology, 14th edn, John Wiley & Sons, Hoboken, NJ. Tortora, GJ & Grabowski, SR 2003, Principles of Anatomy and Physiology, 10th edn, John Wiley & Sons, New York, NY.