Deoxyribonucleic Acid (DNA) Structure and Function 2024-2025 PDF

DEOXYRIBONUCLEIC ACID (DNA) STRUCTURE AND FUNCTION Mohd Aminudin Bin Mustapha  2 LEARNING OBJECTIVES Describe the theory of DNA structure and functions. Explain the DNA replication process....

DEOXYRIBONUCLEIC ACID (DNA) STRUCTURE AND FUNCTION Mohd Aminudin Bin Mustapha  2 LEARNING OBJECTIVES Describe the theory of DNA structure and functions. Explain the DNA replication process. Detail the process of protein synthesis, including transcription, RNA processing, and translation. Discuss the applications of DNA knowledge in biotechnology.  3 DEOXYRIBONUCLEIC ACID (DNA) In eukaryotes, genetic information is carried by chromosomes. Chromosomes consist of chromatin, which includes DNA. Each chromosome contains many genes that direct cellular activities. Genes carry genetic information that is transmitted from one generation to the next.  4 FREDERICK GRIFFITH’S EXPERIMENTS In 1928, Frederick Griffith's experiments with Streptococcus pneumoniae demonstrated that DNA is the hereditary material. He used two forms of the bacterium: S-strain: Pathogenic/virulent but could be rendered non- pathogenic by heating. R-strain: Non- pathogenic/avirulent.  5 FREDERICK GRIFFITH’S EXPERIMENTS Mice died when injected with a mixture of heat-killed S-strain and living R-strain bacteria, indicating a "transforming principle." Information specifying virulence passed from dead S-strain cells into live R-strain cells.  6 AVERY, MACLEOD, AND MCCARTY EXPERIMENT In 1944, Oswald Avery and his team identified the molecules in the S-strain responsible for transformation. They prepared extracts of the heat-killed S-strain and treated them with enzymes: protease, RNase, and DNase.  7 AVERY, MACLEOD, AND MCCARTY EXPERIMENT Removal of protein and RNA did not affect the transformation ability, but DNA-digesting enzymes destroyed it. This supported the idea that DNA is the genetic material.  8 HERSHEY AND CHASE EXPERIMENT Investigated bacteriophages, viruses that infect bacteria, composed of only DNA and protein. They labeled bacteriophage DNA with radioactive phosphorus (32P) and protein with radioactive sulfur (35S). Only the DNA (32P) entered the bacteria and produced more bacteriophages, confirming DNA as the genetic material.  9 DNA STRUCTURE DNA is a nucleic acid composed of nucleotides. Each nucleotide consists of a 5- carbon sugar (deoxyribose), a phosphate group, and a nitrogenous base (adenine, thymine, cytosine, or guanine).  10 CHARGAFF’S RULE Erwin Chargaff (1947) found that the amount of adenine equals thymine, and the amount of cytosine equals guanine, indicating an equal proportion of purines (A and G) and pyrimidines (C and T). CONTRIBUTIONS TO DNA STRUCTURE Linus Pauling (1951) discovered helix-shaped structures in proteins. CONTRIBUTIONS TO DNA STRUCTURE Rosalind Franklin and Maurice Wilkins used X-ray diffraction to show DNA has a helical structure with nitrogen bases inside and a sugar- phosphate backbone outside.  13 CONTRIBUTIONS TO DNA STRUCTURE James Watson and Francis Crick (1953) proposed the double helix structure of DNA, with antiparallel complementary strands held together by base pairs.  14 STRUCTURE & ORGANIZATION OF GENETIC MATERIAL Genes, specific DNA sequences, code for proteins and RNA molecules. Most of an organism's genome includes non-coding regions. Prokaryotic cells, like Escherichia coli, have a circular, double-stranded DNA chromosome, which is tightly packed and supercoiled. Eukaryotic cells have linear, double-stranded DNA organized with histones into nucleosomes and further compacted in the nucleus.  15 DNA OF PROKARYOTIC CELLS Bacteria, such as Escherichia coli (E. coli), have a chromosome consisting of a circular, double- stranded DNA molecule. This DNA must be tightly packed to fit into the nucleoid, achieved through coiling, compacting, and supercoiling.  16 DNA OF PROKARYOTIC CELLS DNA supercoiling involves the formation of additional coils in the DNA structure due to twisting forces. This supercoiling is controlled by the enzymes topoisomerase I and topoisomerase II.  17 DNA OF PROKARYOTIC CELLS Some prokaryotes also have plasmids, which are small, circular, or linear DNA molecules often carrying non- essential genes. Most prokaryotes are haploid, possessing only one set of chromosomes and, therefore, only one copy of each gene.  18 DNA OF PROKARYOTIC CELLS Prokaryotic genomes mainly consist of regions containing either genes or regulatory sequences. Regulatory sequences are DNA sections that determine when certain genes and associated cell functions are activated.  DNA OF 19 EUKARYOTIC CELLS Eukaryotic cells have double-stranded, linear DNA molecules tightly compacted in the nucleus. The compaction of DNA in eukaryotic cells is achieved through various levels of organization. Histones are a family of proteins that associate with DNA. Nucleosomes are condensed structures formed when double-stranded DNA wraps around an octamer of histone proteins.  20 TELOMERES Specialized structures at the ends of eukaryotic chromosomes. Protect chromosome ends from nucleases and maintain the integrity of linear chromosomes.  21 DNA REPLICATION The cell cycle includes DNA replication, producing two identical DNA molecules. Three models of DNA replication were proposed: semi-conservative, conservative, and dispersive.  22 MESELSON AND STAHL (1958) They used density gradient centrifugation to observe DNA densities. After one round of replication in the ¹⁴N medium, the DNA consisted of hybrid molecules (one strand of ¹⁵N DNA and one strand of ¹⁴N DNA). After the second round of replication, the DNA consisted of both hybrid molecules and molecules entirely of ¹⁴N DNA. This confirmed the semi-conservative model of DNA replication, where each new DNA molecule consists of one old (parental) strand and one new (daughter) strand.  PROKARYOTIC 24 REPLICATION Single, circular DNA molecule. Replication starts at a single origin of replication. Proceeds bidirectionally around the chromosome. Replicon: DNA segment controlled by an origin.  25 DNA REPLICATION IN PROKARYOTES Essential components include the parental DNA molecule, enzymes, and deoxynucleotide triphosphates.. STEPS OF DNA 26 REPLICATION Initiation: Unwinding begins at a specific nucleotide sequence called the origin of replication. Initiator proteins attach to the DNA and initiate the unwinding process. Helicase enzymes break the hydrogen bonds connecting the complementary base pairs.  27 STEPS OF DNA REPLICATION Initiation: Single-strand-binding proteins stabilize the unwound strands. A replication bubble forms, featuring a Y- shaped replication fork at each end.  28 STEPS OF DNA REPLICATION DNA Replication- Elongation: Leading Strand Two new strands are constructed using the parent DNA as a template. DNA polymerase III facilitates the addition of new nucleotides to form a complementary strand to the parent strand. The strand synthesized continuously in the 5′ to 3′ direction from the parent strand is known as the leading strand.  29 STEPS OF DNA REPLICATION Elongation: Lagging Strand Formed in short segments away from the replication fork in a discontinuous manner. Requires primase to synthesize an RNA primer. After the primer is attached to the parental strand, DNA polymerase III extends the strand by synthesizing DNA fragments called Okazaki fragments.  30 STEPS OF DNA REPLICATION DNA Replication-Termination Takes place once the synthesis of the new DNA strands is finished. The two new DNA molecules separate, and the replication machinery is dismantled.  31 ERRORS DURING DNA REPLICATION A human cell can replicate its entire DNA in a few hours, with an error rate of approximately 1 in 1 billion nucleotide pairs. Errors naturally occur during replication. Base mispairing and strand slippage can cause nucleotide insertions or deletions, leading to mutations, which are permanent changes in the DNA sequence.  32 CORRECTING ERRORS DURING DNA REPLICATION DNA polymerase I and II have proofreading capabilities, recognizing and correcting errors in newly synthesized DNA strands. Mismatch repair involves a group of proteins that identify and fix deformities in newly synthesized DNA featuring mispaired bases. Errors that remain after DNA polymerase proofreading or mismatch repair become mutations once cell division occurs.  33 GENETIC CODE The sequence of bases in DNA forms the genetic code. A triplet of bases controls the production of a specific amino acid in the cytoplasm. The sequence and order of amino acids determine the type of protein produced. A gene may contain thousands of bases. CENTRAL DOGMA OF GENETICS Genetic information flows from DNA to RNA to protein within each cell. This flow of information is unidirectional and irreversible.  35 PROTEIN SYNTHESIS Transcription RNA Processing Translation  36 TRANSCRIPTION Synthesis of RNA molecules using DNA strands as templates to transfer genetic information from DNA to RNA (similar to DNA replication). Begins at the promoter DNA (TATA box) and ends at the terminator DNA (stop). RNA polymerase produces the RNA molecule by separating the DNA strands and linking RNA nucleotides together. The pre-RNA molecule is released when transcription is complete.  RNA 37 PROCESSING Maturation of pre-RNA molecules occurs in the nucleus. Introns are spliced out by spliceosomes, and exons are joined together. The mature RNA molecule then leaves the nucleus for the cytoplasm. Introns are non-coding DNA sequences between exons, which are expressed DNA sequences that code for amino acids.  38 TRANSLATION Initiation Elongation Termination  39 TRANSLATION - INITIATION Brings together mRNA, a tRNA with the first amino acid, and the two ribosomal subunits. A small ribosomal subunit binds with mRNA and a special initiator tRNA carrying methionine, which attaches to the start codon. Initiation factors bring in the large subunit, positioning the initiator tRNA in the P site.  TRANSLATION - ELONGATION 40 Consists of a series of three-step cycles adding each amino acid to the preceding one. An elongation factor assists H- bonding between the mRNA codon at the A site and the corresponding tRNA anticodon. This process continues codon by codon, adding amino acids until the polypeptide chain is complete.  TRANSLATION - TERMINATION 41 Occurs when one of the three stop codons reaches the A site. A release factor binds to the stop codon, hydrolyzing the bond between the polypeptide and its tRNA in the P site, freeing the polypeptide and disassembling the translation complex.  42 APPLICATIONS OF DNA TECHNOLOGY Medicine Diagnosis of infectious diseases and genetic disorders. Human gene therapy, targeting heart disease and cancer. Production of pharmaceutical products such as growth hormones, insulin, and vaccines. APPLICATIONS OF DNA 43 TECHNOLOGY Forensics DNA fingerprinting using simple tandem repeats (STRs) found in satellite DNA. Analysis of five small genome regions known for variability.  44 APPLICATIONS OF DNA TECHNOLOGY Environmental Genetically engineered organisms for heavy metal extraction and sewage treatment. Research on organisms to degrade chlorinated hydrocarbons and other toxic chemicals. Bioremediation for cleaning oil spills and waste dumps.  45 APPLICATIONS OF DNA TECHNOLOGY Agricultural Transgenic organisms with increased productivity, pest resistance, and disease resistance. "Pharm" animals and "golden rice" enriched with beta-carotene.  POLYMERASE CHAIN REACTION (PCR) 46 A method to amplify specific DNA segments, making numerous copies. PCR can produce billions of copies of a target DNA sequence in a few hours. Invented in 1984, PCR is now integral to molecular biology.  47 PCR AND DISEASE Primers can be created to bind and amplify specific alleles or mutations. Used in genetic counseling and diagnostic tests for genetic diseases. Diseases diagnosed with PCR include: o Huntington's disease o Cystic fibrosis o Human immunodeficiency virus (HIV)