Nucleic Acids PDF

Nucleic Acids 1  NUCLEIC ACID Cells in an organism are exact replicas Cells have information on how to make new cells Molecules responsible for such information are nucleic acids – Found in nucleus and are acidic in nature A nucleic acid is a linear polymer(chain) i...

Nucleic Acids 1  NUCLEIC ACID Cells in an organism are exact replicas Cells have information on how to make new cells Molecules responsible for such information are nucleic acids – Found in nucleus and are acidic in nature A nucleic acid is a linear polymer(chain) in which the monomer units are nucleotides.  Types of nucleic Two Types of Nucleic Acids: DNA: Deoxyribonucleic Acid: Found within cell nucleus – Storage and transfer of genetic information – Passed from one cell to other during cell division RNA: Ribonucleic Acid: Occurs in all parts of cell – Primary function is to synthesize the proteins DNA and RNA 4  Nucleotide Building Blocks Nucleic Acids: Polymers in which repeating unit is nucleotide A Nucleotide has three components: – Pentose Sugar - Monosaccharide – Phosphate Group (PO43-) – Nitrogen containing Heterocyclic Base 5  Nucleotide Building Blocks Pentose Sugar Ribose is present in RNA and 2-deoxyribose is present in DNA Structural difference: ⚫ a —OH group present on carbon 2’ in ribose ⚫ a —H atom in 2-deoxyribose RNA and DNA differ in the identity of the sugar unit in their nucleotides. 6 DNA and RNA p799 DNA and RNA p799  Nucleotide Building Blocks Nitrogen-Containing Heterocyclic Bases There are a total five bases (four of them in most of DNA and RNAs) Three pyrimidine derivatives - thymine (T), cytosine (C), and uracil (U) Two purine derivatives - adenine (A) and guanine (G) Adenine (A), guanine (G), and cytosine (C) are found in both DNA and RNA. Uracil (U): found only in RNA Thymine (T) found only in DNA. 9 p799 3 pyrimidine p799 2 purine p800  Nucleotide Building Blocks Phosphate - third component of a nucleotide is derived from phosphoric acid (H3PO4) Under cellular pH conditions, the phosphoric acid is fully dissociated to give a hydrogen phosphate ion (HPO42-) 13 Figure 22-2 p800  Nucleoside Formation Nucleoside: A compounder formed from a five-carbon monosaccharide and a purine or pyrimidine base derivative. 15  Nucleotide Formation Addition of a phosphate group to a nucleoside – Attached to C5” position through a phosphate-ester bond – Condensation reaction (H2O released) – Named by appending 5’-monophoaphate to nucleoside name 16  17 Copyright © Cengage Learning. All rights reserved Nucleotide Nomenclature  Primary nucleic acids structure Sugar-phosphate groups are referred to as nucleic acid backbone - Found in all nucleic acids Sugars are different in DNA and RNA Copyright © Cengage Learning. All rights reserved 18 The backbone is connected by covalent bonds. The bases are connected by hydrogen bonds. hydrogen bond covalent bond  Primary Structure A deoxyribonucleic acid (DNA) is a nucleotide polymer in which each of the monomers contains deoxyribose, a phosphate group, and one of the heterocyclic bases adenine, cytosine, guanine, or thymine. 20  Primary Structure A ribonucleic acid (RNA) is a nucleotide polymer in which each of the monomers contains ribose, a phosphate group, and one of the heterocyclic bases adenine, cytosine, guanine, or uracil 21  Primary Structure Structure: Sequence of nucleotides in DNA or RNA Primary structure is due to changes in the bases Phosphodiester bond between 3’ and 5’ position 5’ end has free phosphate and 3’ end has a free OH group Sequence of bases read from 5’ to 3’ 23 Comparison of the General Primary Structures of Nucleic Acids and Proteins Backbone: -Phosphate-Sugar- Nucleic acids Backbone: -Peptide bonds - Proteins Copright © Cengage Learning. All rights reserved 24 p805  The DNA Double helix Nucleic acids have secondary and tertiary structure The secondary structure involves two polynucleotide chains coiled around each other in a helical fashion 26  14 THE DOUBLE HELIX bases sugar-phosphate chain Scientist Chargaff found: The amount of adenine in an organism approximately equals the amount of thymine The amount of cytosine roughly equals the amount of guanine. A=T C=G Chargaff’s rules  The DNA Double helix The two polynucleotides run anti-parallel (opposite directions) to each other, i.e., 5’ - 3’ and 3’ - 5’ The bases are located at the center and hydrogen bonded (A=T and G=C) Base composition: %A = %T and %C = %G) – Example: Human DNA contains 30% adenine, 30% thymine, 20% guanine and 20% cytosine 29  10 The bases always pair up in the same way Adenine forms a bond with Thymine Adenine Thymine and Cytosine bonds with Guanine Cytosine Guanine  11 Bonding 2 PO PO 4 4 adenine thymine PO 4 PO 4 cytosine guanine PO 4 PO 4 PO PO 4 4 Copyright © Cengage Learning. All rights 32 reserved  The DNA Double helix DNA Sequence: the sequence of bases on one polynucleotide is complementary to the other polynucleotide Complementary bases are pairs of bases in a nucleic acid structure that can hydrogen-bond to each other. Complementary DNA strands are strands of DNA in a double helix with base pairing such that each base is located opposite to its complementary base. Example : – List of bases in sequential order in the direction from the 5’ end to 3’ end of the segment: – 5’-A-A-G-C-T-A-G-C-T-T-A-C-T-3’ – ’ 33  The DNA Double helix DNA Sequence: the sequence of bases on one polynucleotide is complementary to the other polynucleotide Complementary bases are pairs of bases in a nucleic acid structure that can hydrogen-bond to each other. Complementary DNA strands are strands of DNA in a double helix with base pairing such that each base is located opposite to its complementary base. Example : – List of bases in sequential order in the direction from the 5’ end to 3’ end of the segment: – 5’-A-A-G-C-T-A-G-C-T-T-A-C-T-3’ – Complementary strand of this sequence will be: 3’-T-T-C-G-A-T-C-G-A-A-T-G-A-5’ 34  The DNA Double helix Base Pairing/DNA replication A pyrimidine is always paired with purine ⚫ Fits inside the DNA double strand ⚫ Hydrogen bonding is stronger with A-T and G-C ⚫ A-T and G-C are called complementary bases ⚫ okazaki fragment 35  The DNA Double helix Practice Exercise Predict the sequence of bases in the DNA strand complementary to the single DNA strand shown below: 5’ A–A–T–G–C–A–G–C–T 3’ 36  The DNA Double helix Practice Exercise Predict the sequence of bases in the DNA strand complementary to the single DNA strand shown below: 5’ A–A–T–G–C–A–G–C–T 3’ Answer: 3’ T–T–A–C–G–T–C–G–A 5’ 37  Replication copies the genetic 8.3 information. A single strand of DNA serves as a template for a new strand. The rules of base pairing direct replication. DNA is replicated during the S (synthesis) stage of the cell cycle. Each body cell gets a complete set of identical DNA.  8.3 Proteins carry out the process of replication. DNA serves only as a template. Enzymes and other proteins do the actual work of replication. – Enzymes unzip the double helix. – Free-floating nucleotides form hydrogen bonds with the template strand. nucleotide The DNA molecule unzips in both directions.  8.3 DNA polymerase enzymes bond the nucleotides – together to form the double helix. Polymerase enzymes form covalent bonds between – nucleotides in the new strand. nucleotide new strand DNA polymerase  8.3 Two new molecules of DNA are formed, each with an original strand and a newly formed strand. DNA replication is semiconservative. new strand original strand Two molecules of DNA  8.3 Replication is fast and accurate. DNA replication starts at many points in eukaryotic chromosomes. There are many origins of replication in eukaryotic chromosomes. DNA polymerases can find and correct errors.  8.4 RNA carries DNA’s instructions. The central dogma states that information flows in one direction from DNA to RNA to proteins.  8.4 The central dogma includes three processes. Replication – replication Transcription – transcription Translation – RNA is a link translation between DNA and proteins.  8.4 RNA differs from DNA in three major ways. – RNA has a ribose sugar. – RNA has uracil instead of thymine. – RNA is a single-stranded structure.  8.4 Transcription makes three types of RNA. Transcription copies DNA to make a strand of RNA.  8.4 Transcription is catalyzed by RNA polymerase. – RNA polymerase and other proteins form a transcription complex. The transcription complex recognizes the start of a gene – and unwinds a segment of it. transcription complex start site nucleotides  8.4 Nucleotides pair with one strand of the DNA. RNA polymerase bonds the nucleotides together. – The DNA helix winds again as the gene is – transcribed. DNA RNA polymerase moves along the DNA  8.4 The RNA strand detaches from the DNA once – the gene is transcribed. RNA  8.4 Transcription makes three types of RNA. – Messenger RNA (mRNA) carries the message that will be translated to form a protein. Ribosomal RNA (rRNA) forms part of ribosomes where – proteins are made. – Transfer RNA (tRNA) brings amino acids from the cytoplasm to a ribosome. The transcription process is similar to 8.4 replication. Transcription and replication both involve complex enzymes and complementary base pairing. The two processes have different end results. – Replication copies all the DNA; transcription copies a gene. – Replication makes one growing RNA gen one copy; e strands transcription can DN make many copies. A Amino acids are coded by mRNA base 8.5 sequences. Translation converts mRNA messages into polypeptides. A codon is a sequence of three nucleotides that codes for an amino acid. codon for codon for leucine (Leu) methionine (Met) The genetic code matches 8.5 each codon to its amino acid or function. three stop codons – – one start codon, codes for methionine A change in the order in which codons are read changes the resulting protein. Regardless of the organism, codons code for the same amino acid.  Amino acids are linked to become a 8.5 protein. An anticodon is a set of three nucleotides that is complementary to an mRNA codon. An anticodon is carried by a tRNA.  8.5 Ribosomes consist of two subunits. – The large subunit has three binding sites for tRNA. – The small subunit binds to mRNA.  8.5 For translation to begin, tRNA binds to a start codon and signals the ribosome to assemble. A complementary tRNA molecule binds to the exposed codon, bringing its amino acid close to the first amino acid.  8.5 The ribosome helps form a polypeptide bond between the amino acids. The ribosome pulls the mRNA strand the length of one codon.  8.5 The now empty tRNA molecule exits – the ribosome. A complementary tRNA molecule binds to the – next exposed codon. Once the stop codon is reached, the ribosome – releases the protein and disassembles. Gene expression is carefully regulated in both prokaryotic and eukaryotic cells.  8.6 Prokaryotic cells turn genes on and off by controlling transcription. A promotor is a DNA segment that allows a gene to be transcribed. An operator is a part of DNA that turns a gene “on” or ”off.”  8.6 Prokaryotic cells turn genes on and off by controlling transcription. An operon includes a promoter, an operator, and one or more structural genes that code for all the proteins needed to do a job. – Operons are most common in prokaryotes. – The lac operon was one of the first examples of gene regulation to be discovered. – The lac operon has three genes that code for enzymes that break down lactose.  8.6 The lac operon acts like a switch. The lac operon is “off” when lactose is not present. – The lac operon is “on” when lactose is present. –  8.6 Eukaryotes regulate gene expression at many points. Different sets of genes are expressed in different types of cells. Transcription is controlled by regulatory DNA sequences and protein transcription factors.  8.6 Transcription is controlled by regulatory DNA sequences and protein transcription factors. – Most eukaryotes have a TATA box promoter. – Enhancers and silencers speed up or slow down the rate of transcription. – Each gene has a unique combination of regulatory sequences.  8.6 RNA processing is also an important part of gene regulation in eukaryotes. mRNA processing includes three major steps.  8.6 mRNA processing includes three major steps. Introns are removed and – exons are spliced together. A cap is added. – A tail is added. –  8.7 Mutations Mutations are changes in DNA that may or may not affect phenotype.  8.7 Some mutations affect a single gene, while others affect an entire chromosome. A mutation is a change in an organism’s DNA. Many kinds of mutations can occur, especially during replication. A point mutation substitutes one nucleotide for another. mutated base  8.7 Many kinds of mutations can occur, especially during replication. A frameshift mutation inserts or deletes a – nucleotide in the DNA sequence.  8.7 Chromosomal mutations affect many genes. Chromosomal mutations may occur during crossing over Chromosomal mutations affect many genes. – Gene duplication results from unequal crossing over. –  8.7 Translocation results from the exchange of DNA segments between nonhomologous chromosomes.  8.7 Mutations can be caused by several factors. Replication errors can cause mutations. Mutagens, such as UV ray and chemicals, can cause mutations. Some cancer drugs use mutagenic properties to kill cancer cells.  Replication of DNA molecules DNA polymerase enzyme can only function in the 5’-to-3’ direction Therefore one strand (leading strand ) grows continuously in the direction of unwinding The lagging strand grows in segments (Okazaki fragments) in the opposite direction The segments are latter connected by DNA ligase DNA replication usually occurs at multiple sites within a molecule (origin of replication) 74  8.3 Two new molecules of DNA are formed, each with an original strand and a newly formed strand. DNA replication is semiconservative. new strand original strand Two molecules of DNA Replication of DNA molecules 76  Replication of DNA molecules Chromosomes Upon DNA replication the large DNA molecules interacts with histone proteins to fold long DNA molecules. The histone–DNA complexes are called chromosomes: ⚫ A chromosome is about 15% by mass DNA and 85% by mass protein. ⚫ Cells of different kinds of organisms have different numbers of chromosomes. ⚫ Example: Number of chromosomes in a human cell 46, a mosquito 6, a frog 26, a dog 78, and a turkey 82 77  Replication of DNA molecules Chromosomes Chromosomes occur in matched (homologous) pairs. Example: The 46 chromosomes of a human cell constitute 23 homologous pairs 78  Types of RNA Molecules Transfer RNA (tRNA): Delivers amino acids to the sites for protein synthesis – tRNAs are the smallest (75–90 nucleotide units) 79  Transcription : RNA synthesis Transcription: A process by which DNA directs the synthesis of mRNA molecules –Two-step process - (1) synthesis of hnRNA and (2) editing to yield mRNA molecule 80  Transcription : RNA synthesis Gene: A segment of a DNA base sequence responsible for the production of a specific hnRNA/mRNA molecule – Most human genes are ~1000–3500 nucleotide units long 81 Transcription : RNA synthesis –Genome: All of the genetic material (the total DNA) contained in the chromosomes of an organism –Human genome is about 20,000–25,000 genes 82  Transcription : RNA synthesis Post-Transcription Processing: Formation of mRNA Involves conversion of hnRNA to mRNA Splicing: Excision of introns and joining of exons ⚫ Exon - a gene segment that codes for genetic information ⚫ Intron – a DNA segments that interrupt a genetic message The splicing process is driven by snRNA 83  Transcription : RNA synthesis Transcriptome: All of the mRNA molecules that can be generated from the genetic material in a genome. – Transcriptome is different from a genome – Responsible for the biochemical complexity created by splice variants obtained by hnRNA. 84  Genetic code The base sequence in a mRNA determines the amino acid sequence for the protein synthesized The base sequence of an mRNA molecule involves only 4 different bases - A, C, G, and U Codon: A three-nucleotide sequence in an mRNA molecule that codes for a specific amino acid – Based on all possible combination of bases A, G, C, U” there are 64 possible codes 85  Mutagens Mutations are caused by mutagens A mutagen is a substance or agent that causes a change in the structure of a gene: – Radiation and chemical agents are two important types of mutagens – Ultraviolet, X-ray, radioactivity and cosmic radiation are mutagenic –cause cancers – Chemical agents can also have mutagenic effects E.g., HNO2 can convert cytosine to uracil Nitrites, nitrates, and nitrosamines – can form nitrous acid in cells Under normal conditions mutations are repaired by repair enzymes 86  Nucleic acid & Viruses Vaccines Inactive virus or bacterial envelope Antibodies produced against inactive viral or bacterial envelopes will kill the active bacteria and viruses 87  Recombinant DNA & genetic engineering Recombinant DNA: DNA molecules that have been synthesized by splicing a sequence of segment DNA (usually a gene) from one organism to the DNA of another organism. 88  Recombinant DNA & genetic engineering Genetic Engineering (Biotechnology): A process in which an organism is intentionally changed at the molecular (DNA) level so that it exhibits different traits. 89  Recombinant DNA & genetic engineering Benefits First genetically engineered organism are bacteria (1973) and Mice (1974) Insulin producing bacteria - commercialized in 1982. ⚫ Bacteria act as protein factories 90  Recombinant DNA & genetic engineering Benefits Many plants have now been genetically engineered and numerous beneficial situations have been created. ⚫ Disease resistance – increased crop yield ⚫ Drought resistance – consumption of less water ⚫ Predator resistance – less insecticide use ⚫ Frost resistance – resist changes in temps below freezing. ⚫ Deterioration resistance – long shelf-life. 91  Seatwork I. Predict the sequence of bases in the DNA strand complementary to the single DNA strand shown below: 1)5’ G-A–A–T–G–C–A–G–C–T-G-G-A 3’ 2) 5’ C-C-T-T-G-G-A-A-C-G-T-A-G-C-A 3’ II. Interpret the genetic code matches each codon to its amino acid. 1)UUA 2)CCU 3) UCC 4)GAG