Nucleic Acids Biochemistry PDF

BIOCHEMISTRY Introduction A most remarkable property of living cells is their ability to produce exact replicas of themselves. Cells contain all the instructions needed for making the complete organism of which they are a part. The molecules within a cell that are responsible for these amazing capa...

BIOCHEMISTRY Introduction A most remarkable property of living cells is their ability to produce exact replicas of themselves. Cells contain all the instructions needed for making the complete organism of which they are a part. The molecules within a cell that are responsible for these amazing capabilities are nucleic acids. Friedrich Miescher (1844-1895) discovered nucleic acids in 1869 while studying the nuclei of WBCs. NUCLEIC ACID Types of Nucleic Acids 2 Types of Nucleic Acids found within cells of higher organisms: 1. Deoxyribonucleic Acid (DNA) – nearly all the DNA is found within the cell nucleus. Primary function: Storage and transfer of genetic information 2. Ribonucleic Acid (RNA) – occurs in all parts of a cell. Primary function: Synthesis of proteins  TYPES OF NUCLEIC ACIDS Deoxyribonucleic acid is a molecule composed of two chains that coil around each other to form a double helix carrying genetic instructions for the development, functioning, growth and reproduction of all known organisms and many viruses. Ribonucleic acid (RNA) is typically single stranded and contains ribose as its pentose sugar and the pyrimidine uracil instead of thymine. An RNA strand can undergo significant intramolecular base pairing to take on a three-dimensional structure. There are three main types of RNA, all involved in protein synthesis. Nucleotides: Structural Building Blocks for Nucleic Acids Nucleic acid – is an unbranched polymer containing units called nucleotides. Nucleotide - is a three-subunit molecule in which a pentose sugar is bonded to both a phosphate group and a nitrogen-containing heterocyclic base. Nucleotide Nucleotide Structure. The basic building block of DNA is the nucleotide. The nucleotide in DNA consists of a sugar (deoxyribose), one of four bases (cytosine (C), thymine (T), adenine (A), guanine (G)), and a phosphate. Cytosine and thymine are pyrimidine bases, while adenine and guanine are purine bases. Nucleotides: Structural Building Blocks for Nucleic Acids Pentose Sugars: Either ribose or the pentose 2’-deoxyribose. Nucleotides: Structural Building Blocks for Nucleic Acids Five nitrogen-containing heterocyclic bases are nucleotide components. Nucleotides: Structural Building Blocks for Nucleic Acids Phosphate 3rd component of nucleotide, derived from phosphoric acid, H 3PO4. The DNA Double Helix The amounts of the bases A, T, G, and C present in DNA molecules were the key to determination of the general three-dimensional structure of DNA molecules. Base composition data for DNA molecules from many different organisms revealed a definite pattern of base occurrence. The amounts of A, T, C, and G were always equal, as were the amounts of total purines and total pyrimidines. The relative amounts of these base pairs in DNA vary depending on the life form from which the DNA is obtained. However, the relationships %A = %T and %C = %G Always hold true. Human DNA contains 30% adenine, 30% thymine, 20% guanine, and 20% cytosine. The DNA Double Helix James Watson and Francis Crick (1953) – proposed an explanation for the base composition patterns associated with DNA molecules. Their model involves a double-helix structure that accounts for the equality of bases present, as well as for the other known DNA structural data. The DNA double helix involves two polynucleotide strands coiled around each other in a manner somewhat like a spiral staircase. The bases (side chains) of each backbone extend inward toward the bases of the other strand. The two strands are connected by hydrogen bonds between their bases. Additionally, the two strands of the double helix are antiparallel. One strand runs in the 5’-to-3’ direction, and the other is oriented in the 3’-to-5’ direction. Three Views of the DNA Double Helix Base Pairing Base Pairing Hydrogen-bonding possibilities are more favorable when A – T and G – C base pairing occurs than when A – C and G – T base pairing occurs. (a) Two of the three hydrogen bonds can form between A – T and G – C pairs, these combination are present in DNA molecules. (b) Only one hydrogen bond can form between G – T and A – C base pairs. These combinations are not present in DNA molecules. Base Pairing A mnemonic device for recalling observed base-pairing combinations with DNA involves listing the base abbreviations in alphabetical order. Then the first and last bases pair, and so do the middle two bases. DNA: A C G T another way to remember these base pairing combinations is to note that AT spells a word and C and G look much alike. Base Pairing The two strands of the DNA in a double helix are complimentary. This means that if you know the order of bases in one strand, you can predict the order of bases in the other strand. Complementary bases – are pairs of bases in a nucleic acid structure that 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 its complementary base. The following two notations for DNA base sequence have identical meaning. 5’ A – C – G – T – T 3’ 5’ ACGTT 3’ Predicting Base Sequence in a Complimentary DNA Strand Example: Predict the sequence of bases in the DNA strand that is complimentary to the single DNA strand shown. 5’ C – G – A – A – T – C – C – T – A 3’ Solution: because only A forms a complimentary base pair with T, and only G with C, the complementary strand is as follows: Given: 5’ C – G – A – A – T – C – C – T – A 3’ Complimentary strand: 3’ G – C – T – T – A – G – G – A – T 5’ Note the reversal of the numbering of the ends of the complimentary strand compared to the given strand. This is due to the antiparallel nature of the two strands of DNA. CHECK YOUR PROGRESS 1. Which of the following is the correct complementary DNA sequence for the DNA base sequence 5’ C – G – A – A – T 3’? a. 5’ T – A – A – G – C 3’ b. 5’ G – C – T – T – A 3’ c. 3’ G – C – T – T – A 5’ CHECK YOUR PROGRESS 2. Convert each of the following 3’ –to- 5’ DNA base sequences to 5’-to 3’ DNA base sequences a. 3’ ATCG 5’ b. 3’ CACA 5’ c. 3’ AATA 5’ d. 3’ CAAC 5’ e. 3’ GCATAA 5’ DNA Replication Overview DNA replication – is a biochemical process by which the DNA molecules produce exact duplicates of themselves. DNA Replication Overview Chemistry at a Glance: DNA Replication Chromosomes Once the DNA within the cell has been replicated, it interacts with specific proteins in the cell called histones to form structural units that provide the most stable arrangement for the long DNA molecules. These histone-DNA complexes are called chromosomes. Chromosomes are nucleoproteins. Chromosome – is an individual DNA molecule bound to a group of proteins. It is about 15% by mass DNA and 85% by mass proteins. A normal human has 46 chromosomes per cell. Chemical Connections Antimetabolites: Anticancer Drugs That Inhibit DNA synthesis Antimetabolites – are a class of anticancer drugs that interfere with DNA replication because their structures are similar to molecules required for normal DNA replication. 4 Examples of commonly used metabolites 1. 6-Mercaptopurine (6-MP) structurally resemble adenine. 2. Thioguanine 3. 5-Fluorouracil structurally close enough to that of thymine 4. Methotrexate Overview of Protein Synthesis The overall process of protein synthesis is divided into two phases. 1. Transcription 2. Translation DNA Transcription RNA Translation Protein Ribonucleic Acids 4 Major differences exist between RNA molecules and DNA molecules. 1. The sugar unit in the backbone of RNA is ribose, deoxyribose in DNA. 2. The base thymine found in DNA replaced by uracil in RNA. In RNA, uracil, instead of thymine, pairs with (forms hydrogen bonds with) adenine. 3. RNA is a single-stranded molecule; DNA is double-stranded (double helix). Thus RNA, unlike DNA, does not contain equal amounts of specific bases. 4. RNA molecules are much smaller than DNA molecules ranging from 75 nucleotides to few thousand nucleotides. Ribonucleic Acids Types of RNA Molecules RNA molecules found in human cells are categorized into 5 major types, distinguish by their function. 1. heterogeneous nuclear RNA (hnRNA) 2. messenger RNA (mRNA) 3. small nuclear RNA (snRNA) 4. ribosomal RNA (rRNA) 5. transfer RNA (tRNA) Ribonucleic Acids Types of RNA Molecules RNA molecules found in human cells are categorized into 5 major types, distinguish by their function. 1. heterogeneous nuclear RNA (hnRNA) – is RNA formed directly by DNA transcription. Post-transcription processing converts the hnRNA to messenger RNA. 2. messenger RNA (mRNA)- is RNA that carries instructions for protein synthesis (genetic information) to the sites of protein synthesis. 3. small nuclear RNA (snRNA) – is RNA that facilitates the conversion of heterogeneous nuclear RNA to messenger RNA. It contains 100 – 200 nucleotides. 4. ribosomal RNA (rRNA)- is RNA that combines specific proteins to form ribosomes the sites of protein synthesis. 5. transfer RNA (tRNA)- is RNA that delivers amino acids to the sites of protein synthesis. They are the smallest of the RNAs possessing only 75-90 nucleotide units. Ribonucleic Acids The most abundant type of RNA in a cell is ribosomal RNA (75% - 85% by mass). Transfer RNA constitutes 10% - 15% of cellular RNA: messenger RNA and its precursor, heterogeneous nuclear RNA, make up 5% - 10% of RNA material in a cell. Additional role of RNA: it plays a part in the process of blood coagulation near a wound. RNA that is released from damaged cells associated with the wound helps activate two enzymes needed for blood coagulation process. The process of DNA transcription occurs in the nucleus as does the processing of hnRNA to mRNA also occurs in the nucleus. The mRNA formed in the nucleus travels to the cytoplasm where translation (protein synthesis) occurs. Ribonucleic Acids The process of DNA transcription occurs in the nucleus as does the processing of hnRNA to mRNA also occurs in the nucleus. The mRNA formed in the nucleus travels to the cytoplasm where translation (protein synthesis) occurs. Transcription: RNA Synthesis Transcription – is the process by which DNA directs the synthesis of hnRNA/mDNA molecules that carry the coded information needed for protein synthesis. Gene – is a segment of a DNA strand that contains the base sequence for the production of a specific hnRNA/mRNA molecule. Genome – is all of the genetic material (total DNA) contained in the chromosomes of an organism. genomics – is the study of the structure and function of genome. Transcription: RNA Synthesis Steps in the Transcription Process 1. A portion of the DNA double helix unwinds, exposing a sequence of bases (gene). The unwinding process is governed by the enzyme RNA polymerase rather than by DNA helicase (replication enzyme). 2. Free ribonucleotides, one nucleotide at a time, align along one exposed strand of DNA bases, the template strand, forming new base pairs. 3. RNA polymerase is involved in the linkage of ribonucleotides, one by one, to the growing hnRNA molecule. 4. Transcription ends when the RNA polymerase enzyme encounters a sequence of bases that is “read” as a stop sign. The newly formed hnRNA molecule and the RNA polymerase enzyme are released, and the DNA then unwinds to re-form the original double helix. Transcription: RNA Synthesis Transcription: RNA Synthesis In DNA – RNA base pairing, the complementary base pairs are DNA RNA A ----- U G ----- C C ----- G T ----- A RNA molecules contain the base U instead of T. Transcription: RNA Synthesis Translation: Protein Synthesis Translation is the process by which mRNA codons are deciphered and a particular protein molecule is synthesized. The substances Mutations A mutation is an error in the base sequence in a gene that is reproduced during DNA replication. Such errors alter the genetic information that is passed on during transcription. 2 Common Types of Mutation 1. Point mutation – is a mutation in which one base in a DNA sequence is replaced by another base. Such mutation is often called a substitution mutation. Original DNA T A G C A C C has replaced G Point Mutated DNA T A C C A C Mutations 2. Frameshift mutation – is a mutation that inserts or deletes a base in a DNA molecule base sequence. Mutagen – is a substance or agent that cause a change in the structure of a gene. Radiation and chemical agents are two important types of mutagens. Chemical agents like nitrous acid (HNO2) is a mutagen that causes deamination of heterocyclic bases. HNO2 can convert cytosine to uracil.