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Nucleic acids Nucleosides & Nucleotides Nucleic Acids DNA & Replication RNA & Transcription Genetic Code & Protein Synthesis Genetic Mutations Recombinant DNA Viruses ©Chemistry for Allied Health: Chap 22 - DNA 21 - 1 Nucleic acids Nucleic acids: – Maintain genetic information – Determine Protein Synthesis DNA = deoxyribonucleic acid – “Master Copy” for most cell information. – Template for RNA RNA = ribonucleic acid – Transfers information from DNA – Template for Proteins ©Chemistry for Allied Health: Chap 22 - DNA 21 - 2 Nucleic Acids In chromosomes (in nucleus) Have genes 1 gene 1 enzyme Enzymes determine external & internal characteristics ©Chemistry for Allied Health: Chap 22 - DNA 21 - 3 NUCLEIC ACIDS Long chains (polymers) of repeating nucleotides. – Each nucleotide has 3 parts: A heterocyclic Amine Base N O HO P OH H HO O O OH H A phosphate unit H H H OH ©Chemistry for Allied Health: Chap 22 - DNA H A sugar H 21 - 4 Nucleotide = phosphate + sugar + base Phosphate Base O O P N Sugar O O O H -N-glycosidic linkage H H H OH H Nucleoside = sugar + base ©Chemistry for Allied Health: Chap 22 - DNA 21 - 5 Nucleic Acids Nucleic Acids = polymers of Nucleotides. base B P S B P S B P S B P phosphate ©Chemistry for Allied Health: Chap 22 - DNA S B B P S P S sugar 21 - 6 THE SUGAR PART • The major difference between RNA and DNA is the different form of sugar used. Ribose C5H10O5 in RNA O HOCH2 H OH H H OH OH H DeoxyRibose C5H10O4 in DNA O HOCH2 H OH H H OH H H The difference is at carbon #2. ©Chemistry for Allied Health: Chap 22 - DNA 21 - 7 The Nitrogenous Bases 5 bases used fall in two classes Purines & N N N N Pyrimidines N N H A double ring A single ring (6 & 5 members) (6 membered) ©Chemistry for Allied Health: Chap 22 - DNA 21 - 8 The Nitrogenous Bases NH2 Purines: N N Adenine (A) O N H N H2N H N H Thiamine (T) In DNA only ©Chemistry for Allied Health: Chap 22 - DNA N N H NH2 O CH3 N N N Guanine (G) O Pyrimidines: H O H O H N N H Uracil (U) In RNA only O N N H Cytosine (C) 21 - 9 Nucleotides deoxyadenosine 5’ monophosphate (dAMP) NH2 N N O O P O Name based on sugar & base names followed by the # of phosphates.. ©Chemistry for Allied Health: Chap 22 - DNA N N O 5' O 4' H H 3' OH H 1' H 2' H 21 - 10 Primary structure NH2 | C O | - O -- P -- O -- CH 2 || O N C HC C CH N N NH2 | C O N O | - O -- P -- O -- CH 2 || O Phosphate bonds link DNA or RNA nucleotides together in a linear sequence. ©Chemistry for Allied Health: Chap 22 - DNA Similar to proteins with their peptide bonds and side groups. N CH C O CH N O || C O O | - O -- P -- O -- CH 2 || O HN C C C N CH H2N N N O || C O HN O | - O -- P -- O -- CH 2 || O C C O CH3 CH N O OH 21 - 11 DNA - Primary Structure ©Chemistry for Allied Health: Chap 22 - DNA 21 - 12 Base pairing and H-bonding H- bonding between purines and pyrimidines.. N H-N N N-H guanine N N cytosine N N-H H 3C H thymine N H | N- H N N adenine N N ©Chemistry for Allied Health: Chap 22 - DNA N 21 - 14 DNA - Secondary Structure Complementary Base Pairing Guanine pairs with Cytosine Position of H bonds and distance match ©Chemistry for Allied Health: Chap 22 - DNA 21 - 15 DNA - Secondary Structure Complementary Base Pairing Adenine pairs with Thymine Position of H bonds and distance match ©Chemistry for Allied Health: Chap 22 - DNA 21 - 16 Hydrogen bonding Each base wants to form either two or three hydrogen bonds. That’s why only certain bases will form pairs. C G T A G C G A ©Chemistry for Allied Health: Chap 22 - DNA C T 21 - 17 Sugarphosphate backbone DNA coils around outside of attached bases like a spiral stair case. Results in a double helix structure. ©Chemistry for Allied Health: Chap 22 - DNA 21 - 18 The double helix The combination of the stairstep sugarphosphate backbone and the bonding between pairs results in a double helix. Distance between bases = 0.34 nm ©Chemistry for Allied Health: Chap 22 - DNA One complete twist is 3.4 nm 2 nm between strands 21 - 19 DNA - Secondary Structure Complementary Base Pairing ©Chemistry for Allied Health: Chap 22 - DNA 21 - 20 • The actual chain is like a coiled spring. – It is something similar to what happens when protein chains form an alpha helix. • It is the sequence (order) of the amines coming off of the backbone that give us all our genetic information – Just like the sequence of words in a sentence give it meaning. – Of the like in words meaning just sentence a give sequence it. (Get my meaning ? ) ©Chemistry for Allied Health: Chap 22 - DNA 21 - 21 • Crick and Watson (1962 Nobel Prize) – Proposed the basic structure of DNA – 2 strands wrap around each other – Strands are connected by H-bonds between the amines. • Like steps of a spiral staircase ©Chemistry for Allied Health: Chap 22 - DNA 21 - 22 Chromosomes Chromosomes consists of DNA strands coiled around protein - histomes. The acidic DNA’s are attracted to the basic histones. ©Chemistry for Allied Health: Chap 22 - DNA 21 - 23 ©Chemistry for Allied Health: Chap 22 - DNA 21 - 24 Chromosomes The normal number of chromosome pairs varies among the species. Animal Man Cat Mouse Rabbit Honeybee, male female Pairs 23 30 20 22 8 16 ©Chemistry for Allied Health: Chap 22 - DNA Plant Onion Rice Rye Tomato White pine Adder’s tounge fern Pairs 8 14 7 12 12 1262 21 - 25 DNA: Self - Replication • When a cell nucleus divides, the bridging hydrogen bonds break (with the aid of enzymes) and the intertwined strands unwind from each other. • The amines left sticking out from each strand are now free to pick up new partners from the plentiful supply present in the cell. P P P P S S S S A T G C amine bases hanging off the nucleotide chain. ©Chemistry for Allied Health: Chap 22 - DNA 21 - 26 Each A picks up a T, each C picks up a G, etc... P P P P S S S S A T G C T P S G P S Eventually, every amine group is reunited with its complimentary amine and the lost partner strand is reformed. They now twine around each other to form the new Double helix. ©Chemistry for Allied Health: Chap 22 - DNA 21 - 27 DNA Replication ©Chemistry for Allied Health: Chap 22 - DNA 21 - 28 Replication of DNA Replication occurs on both halves in opposite directions. ©Chemistry for Allied Health: Chap 22 - DNA 21 - 29 DNA Replication ©Chemistry for Allied Health: Chap 22 - DNA 21 - 30 DNA Replication Okazaki fragments ©Chemistry for Allied Health: Chap 22 - DNA 21 - 31 DNA Replication Okazaki fragments ©Chemistry for Allied Health: Chap 22 - DNA 21 - 32 • It is the linear sequence of paired bases (amines) along the DNA molecule that constitutes the Genetic Code. – Each series of amines that codes for a particular protein is called a Gene. ©Chemistry for Allied Health: Chap 22 - DNA 21 - 33 Flow of genetic information DNA Replication Transcription RNA Translation Protein ©Chemistry for Allied Health: Chap 22 - DNA Flow of information is one way only. 21 - 47 RNA Single strands of nucleotides where ribose is used in the sugar-phosphate backbone. Several secondary structures (types) based on the particular role it plays. RNA is produced by transcription of genes along a strand of DNA. DNA may contain all the information but RNA does all of the work. (Kinda like the architect and the engineer. Or better yet, the teacher and the student. ) ©Chemistry for Allied Health: Chap 22 - DNA 21 - 48 Classes of RNA Messenger RNA - mRNA It carries a copy of the genetic information contained in DNA. Used as pattern to make proteins. ©Chemistry for Allied Health: Chap 22 - DNA 21 - 49 RNA - THE MESSENGER (m/RNA) • DNA in the nucleus of the cell directs the sythesis of an RNA molecule. – The RNA will carry the sequence of amines found on a particular portion of the DNA • Only a portion of a DNA strand is used to make any given RNA. • There needs to be a way to start and stop transcription. • The DNA has systems of promoter and termination base sequences. ©Chemistry for Allied Health: Chap 22 - DNA 21 - 50 RNA synthesis In the first step, RNA polymerase binds to a promotor sequence on the DNA chain. This insures that transcription occurs in the correct direction. The initial reaction is to separate the two DNA strands. ©Chemistry for Allied Health: Chap 22 - DNA 21 - 51 RNA synthesis initiation sequence termination sequence ‘Special’ base sequences in the DNA indicate where RNA synthesis starts and stops. ©Chemistry for Allied Health: Chap 22 - DNA 21 - 52 RNA synthesis Once the termination sequence is reached, the new RNA molecule and the RNA synthase are released. The DNA recoils. ©Chemistry for Allied Health: Chap 22 - DNA 21 - 53 • The messenger RNA (mRNA) move outside the nucleus to the cytoplasm where Ribosomes are anxiously awaiting their arrival. 60 S rRNA rRNA 40 S ©Chemistry for Allied Health: Chap 22 - DNA 21 - 54 • The messenger RNA (mRNA) move outside the nucleus to the cytoplasm where Ribosomes are anxiously awaiting their arrival. 60 S rRNA rRNA 40 S ©Chemistry for Allied Health: Chap 22 - DNA 21 - 55 • The messenger RNA (mRNA) move outside the nucleus to the cytoplasm where Ribosomes are anxiously awaiting their arrival. 60 S rRNA rRNA 40 S ©Chemistry for Allied Health: Chap 22 - DNA 21 - 56 • The messenger RNA (mRNA) move outside the nucleus to the cytoplasm where Ribosomes are anxiously awaiting their arrival. 60 S rRNA rRNA 40 S ©Chemistry for Allied Health: Chap 22 - DNA 21 - 57 Ribosomal RNA – rRNA: Platform for protein synthesis. Holds mRNA in place and helps assemble proteins. 60 S rRNA rRNA 40 S ©Chemistry for Allied Health: Chap 22 - DNA 21 - 58 •The Ribosomes are like train stations –The mRNA is the train slowly moving through the station. 60 S rRNA Codons AUG GCU AUG 5’ UUG 3’mRNA rRNA 40 S ©Chemistry for Allied Health: Chap 22 - DNA 21 - 59 Transfer RNA - tRNA = • relatively small compared to other RNA’s (70-90 bases.) • transports amino acids to site of protein synthesis. HO- A C C A G G A U G U C G G U A C G C G G U C G C G U C G G C U U G C A G G C C U C C G G C C G C U G U A G G C G C U U U C G A G U A C G C G C G G G C G C ©Chemistry for Allied Health: Chap 22 - DNA 21 - 60 Anticodons on t-RNA HO- C Site of amino acid attachment G A U G U C G G U A C G G Three base anticodon site C C A C G G U G C G C G U C G G C U U G C A G G C C U U A G U C G C C C G G C G C U G C G U A C G C G C G A U G U G C ©Chemistry for Allied Health: Chap 22 - DNA A G C G Point of attachment to mRNA 21 - 61 Amino acid codons alanine GCA, GCC, GCG GCU, AGA, AGG arginine AGA, AGG, CGA CGC, CGG, CGU asparagine AAC, AAU aspartate GAC, GAU cysteine UGC, UGU glutamate GAA, GAG glutamine CAA, CAG glycine GAA, GCC, GGG GGU histidine CAC, CAU isoleucine AUA, AUC, AUU leucine CUA, CUC, CUG CUU, UUA, UUG ©Chemistry for Allied Health: Chap 22 - DNA lysine AAA, AAG methionine AUG phenylalanine UUC, UUU proline CCA, CCC CCG, CCU serine UCA, UCC UCG, UCU AGC, AGU threonine ACA, ACC ACG, ACU tryptophan UGG tyrosine UCA, UCU valine GUA, GUC GUG, GUU 21 - 62 Protein Synthesis 1: Activation Each AA is activated by reacting with an ATP The activated AA is then attached to particular tRNA... (with the correct anticodon) activated AA anticodon ©Chemistry for Allied Health: Chap 22 - DNA fMET C G A 21 - 63 NH2 Aa + N N O O P O ©Chemistry for Allied Health: Chap 22 - DNA N O N 5' O 1' 4' H H H H 2' 3' H OH adenosine 5’ triphosphate (ATP) 21 - 64 Translation AUG Initiation factors 5’ GCU AUG UUG mRNA 3’ Psite A site 40S ribosome unit ©Chemistry for Allied Health: Chap 22 - DNA 21 - 65 Translation fMET U A C AUG Initiation factors 5’ GCU AUG UUG mRNA 3’ Psite A site 40S ribosome unit ©Chemistry for Allied Health: Chap 22 - DNA 21 - 66 Translation fMET 60S U A C AUG 5’ GCU AUG UUG mRNA 3’ Psite A site 40S ribosome unit ©Chemistry for Allied Health: Chap 22 - DNA 21 - 67 Translation Ala fMET 60S C G A U A C AUG 5’ GCU AUG UUG mRNA 3’ Psite A site 40S ribosome unit ©Chemistry for Allied Health: Chap 22 - DNA 21 - 68 Translation peptide bond forms fMET Ala U A C C G A AUG GCU AUG UUG mRNA 3’ 5’ ribosome unit ©Chemistry for Allied Health: Chap 22 - DNA 21 - 69 Translation peptide bond forms fMET Ala U A C C G A AUG GCU AUG UUG mRNA 3’ 5’ ribosome unit ©Chemistry for Allied Health: Chap 22 - DNA 21 - 70 Translation Amino Acid peptide bond Met Ala Z Z Z C G A GCU UUC UUG mRNA 3’ 5’ ribosome unit ©Chemistry for Allied Health: Chap 22 - DNA 21 - 71 Translation peptide bond forms Met Ala ??? C G A ? ? ? GCU UUC UUG mRNA 3’ 5’ ribosome unit ©Chemistry for Allied Health: Chap 22 - DNA 21 - 72 Termination After the last translocation (the last codon is a STOP), no more AA are added. “Releasing factors” cleave the last AA from the tRNA The polypeptide is complete ©Chemistry for Allied Health: Chap 22 - DNA 21 - 73 Codons There are two additional types of codons: Initiation AUG (same as methionine) Termination UAG, UAA, UGA A total of 64 condons are used for all amino acids and for starting and stopping. All protein synthesis starts with methionine. After the polypeptide has been made, an enzyme removes this amino acid. ©Chemistry for Allied Health: Chap 22 - DNA 21 - 74 Amino acid codons alanine GCA, GCC, GCG GCU, AGA, AGG arginine AGA, AGG, CGA CGC, CGG, CGU asparagine AAC, AAU aspartate GAC, GAU cysteine UGC, UGU glutamate GAA, GAG glutamine CAA, CAG glycine GAA, GCC, GGG GGU histidine CAC, CAU isoleucine AUA, AUC, AUU leucine CUA, CUC, CUG CUU, UUA, UUG ©Chemistry for Allied Health: Chap 22 - DNA lysine AAA, AAG methionine AUG phenylalanine UUC, UUU proline CCA, CCC CCG, CCU serine UCA, UCC UCG, UCU AGC, AGU threonine ACA, ACC ACG, ACU tryptophan UGG tyrosine UCA, UCU valine GUA, GUC GUG, GUU 21 - 75 Recombinant DNA Circular DNA found in bacteria E.Coli plasmid bodies Restriction endonucleases cleave DNA at specific genes Result is a “sticky end” Addition of a gene from a second organism Spliced DNA is replaced and organism synthesizes the new protein ©Chemistry for Allied Health: Chap 22 - DNA 21 - 87 Recombinant DNA Bacterium Remove gene segment DNA Plasmid sticky ends Cut gene for insulin Replace in bacterium ©Chemistry for Allied Health: Chap 22 - DNA 21 - 88