BIOCHEMISTRY Nucleic Acids
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1 BIOCHEMISTRY Nucleic Acids BIOB111 CHEMISTRY & BIOCHEMISTRY Session 17
2 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
3 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).
4 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).
5 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
6 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
7 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)
8 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
9 Stoker 2014, Figure 22-2 p790
10 Pentose Sugars Pentose monosaccharides Ribose in RNA. Deoxyribose in DNA. Deoxyribose is lacking O atom on C2.
11 Phosphate Group Derived from from phosphoric acid (H 3 PO 4 ). The cellular ph leads to full dissociation of the phosphoric acid, producing a hydrogen phosphate ion (HPO 4 2- ). Instead of writing the full ionic version, Biochemistry commonly uses an abbreviation to express the phosphate ion. P i = Inorganic Phosphate or
12 Nucleoside Base + Sugar = NUCLEOSIDE
13 Nucleotide Nucleoside + P i attached to C5 position of pentose sugar via phosphate-ester bond. Base + Sugar + Phosphate group = NUCLEOTIDE
14 Stoker 2014, Table 22-1 p792
15 Nucleic Acids Nucleic acids = polymers of Nucleotides Stoker 2014, Figure 22-3 p793
16 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.
17 Structure of Nucleic Acids Stoker 2014, Figure 22-4 p794 Backbone = Phosphate + Sugar (different in DNA & RNA)
18 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 P i 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 P i. The nucleotide chain has a direction. One end 5 end carries a free P i 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.
19 Segment of DNA Stoker 2014, Figure 22-5 p795
20 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.
21 DNA Double Helix Double Helix = 2 strands of DNA in their primary structure, wound up around each other like a spiral staircase. The sugar + P i 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.
22 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.
23 Complementary Base Pairs In DNA A = T G C In RNA A = U G C Stoker 2014, Figure 22-7 p798
24 Hydrogen Bonding is more favourable between A = T G C Stoker 2014, Figure 22-8 p799
25 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
26 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.
27 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.
28 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.
29 DNA Replication Stoker 2014, Figure 22-9 p801
30 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.
31 Stoker 2014, Figure p803
32 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
33 Stoker 2014, Figure p803
34 Summary of DNA Replication Stoker 2104, p804
35 Differences between DNA & RNA Pentose Sugar in backbone DNA Deoxyribose RNA Ribose Complementary A = T A = U Base Pairs C G C G Strand Double helix Single strand Size Very large Much smaller (1-100 million nucleotides) (75-few 1,000 nucleotides)
36 RNA Molecule Stoker 2014, Figure p807 Even though the RNA molecule is a single strand it often folds upon itself in certain parts and forms double-helical regions.
37 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 p819
38 Types of RNA Molecules There are 5 types of RNA but only 3 types will be discussed: Messenger RNA Ribosomal RNA Transfer RNA
39 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.
40 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.
41 Transfer RNA trna Stoker 2014, Figure p819 Transport amino acids to the site of protein synthesis (= ribosomes). Contain 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.
42 Readings & Resources Stoker, HS 2014, General, Organic and Biological Chemistry, 7 th edn, Brooks/Cole, Cengage Learning, Belmont, CA. Stoker, HS 2004, General, Organic and Biological Chemistry, 3 rd edn, Houghton Mifflin, Boston, MA. Timberlake, KC 2014, General, organic, and biological chemistry: structures of life, 4 th edn, Pearson, Boston, MA. Alberts, B, Johnson, A, Lewis, J, Raff, M, Roberts, K & Walter P 2008, Molecular biology of the cell, 5 th edn, Garland Science, New York. Berg, JM, Tymoczko, JL & Stryer, L 2012, Biochemistry, 7 th 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, 14 th edn, John Wiley & Sons, Hoboken, NJ. Tortora, GJ & Grabowski, SR 2003, Principles of Anatomy and Physiology, 10 th edn, John Wiley & Sons, New York, NY.
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BIOCHEMISTRY Nucleic Acids
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