Lecture Module 6: Chemical Basis of Heredity PDF

Lecture Module 6: CHEMICAL BASIS OF HEREDITY Introduction This module will give you an understanding of the DNA composition and replication that will aid you in connecting to its function as a genetic material. Double-stranded DNA is composed of two antiparallel, interlocked nucleoti...

Lecture Module 6: CHEMICAL BASIS OF HEREDITY Introduction This module will give you an understanding of the DNA composition and replication that will aid you in connecting to its function as a genetic material. Double-stranded DNA is composed of two antiparallel, interlocked nucleotide chains, each consisting of a sugar-phosphate backbone with bases hydrogen bonded with complementary bases of the other chain. Most mistakes during replication are corrected by DNA polymerase during replication or by post-replication repair mechanisms. Other than DNA, you will be engaged in the different kinds of RNA that function in gene regulation. Objectives 1. Explain how DNA became the genetic material 2. Determine factors that contribute to the integrity of the replication process 3. Differentiate in vitro and in vivo replication process The Concept of the Gene Concept of Gene (Splicing) Scientists prefer “Transcription Unit” than “Gene”  Exons – Protein Coding Region or Sequence  Introns – Non-protein Coding Region or Sequence The Concept of the Gene  Promoter – lies upstream of the RNA coding region; serves as an indicator of where and in which direction transcription should proceed. The promoter is not actually transcribed but functions purely as a regulator.  Promoters proceed from the upstream to the downstream direction and contain what is known as the TATA box or the sequence that is recognized and bound by so-called TATA binding protein (TBP). The Concept of the Gene The Concept of the Gene TATA binding protein (TBP) helps position the RNA polymerase machinery and initiates transcription. Promoters work in concert with other types of regulatory sequences known as enhancers, which sometimes lie several kilobases further upstream or downstream from the coding sequence itself, or even within introns. Enhancer regions - serve as binding sites for proteins known as activators. Transcription Factors – proteins that bind to promoters to regulate transcription. Enhancer - short region of DNA that can increase transcription of genes. Repressor - any protein that binds to DNA which regulates gene expression by decreasing the rate of transcription. Activator - any chemical or agent that regulates one or more genes by increasing the rate of transcription. The Concept of the Gene RNA Coding Region – the main component of the transcription unit contains the actual exons and introns. Terminator – sequence of nucleotides at the end of the transcription unit and is transcribed along with RNA coding region, unlike the promoter. Transcription STOPS only after this region has been transcribed. Nucleic Acid Constitute mostly of DNA being about 35% along with histone protein (basic proteins having amino acids such as arginine and lysine in their molecules) which is 55%, thus forming deoxyribonucleoprotein comprising 90% of chromosome. The remaining 10% part is called residual chromosome which contains RNA 12 to 14%, DNA 2 to 3%, and residual protein 83 to 86%. Residual protein (non-histone proteins) is acidic in nature and characterized by the majority of amino acids tryptophan and tyrosine. Non-histone proteins of chromosomes are: Phosphoproteins DNA polymerase RNA polymerase DPN (diphosphopyridine nucleotide) pyro phosphorylase Nucleoside triphosphatase Proteins Basic proteins are histone and protamine (replace histone in nucleus of spermatozoa). Histone is found practically in all types of nuclei and it contains arginine and lysine and little tryptophan or tyrosine. Protamine has 90% arginine and no tyrosine or tryptophan. DNA to Histone ratio is about 1.2: 1 or 1.6: 1 Non-histone or residual protein remains in the chromosome after DNA and histone are removed. Residual protein contains more tryptophan than histone. DNA as Genetic Material DNA is the hereditary material that has now been demonstrated in many prokaryotes and eukaryotes. Cells of one genotype (the recipient) are exposed to DNA extracted from another (the donor), and donor DNA is taken up by the recipient cells. Such a result demonstrates that DNA is indeed the substance that determines genotype and therefore is the hereditary material. Chemical Composition of the DNA DNA has three types of chemical components: Phosphate Deoxyribose Nitrogenous Bases Organization of DNA in Prokaryotic Chromosome and Eukaryotic Chromosome supercoiling Prokaryotes most prokaryotes don’t have proteins called Eukaryotes histones they compress DNA into smaller spaces through supercoiling DNA Replication Replication Fork is the area where DNA replication actually takes place. DNA Helicase is an enzyme that unwinds the double helix by breaking hydrogen bonds between complementary bases. Okazaki fragments are the short lengths of DNA produced by the discontinuous replication of the lagging strand.  DNA replication is a highly accurate process, but mistakes can occasionally occur when DNA polymerase inserts a wrong base. Uncorrected mistakes may sometimes lead to serious consequences, such as cancer. Repair mechanisms can correct the mistakes, but in rare cases, mistakes are not corrected, leading to mutations. Error Correction in DNA Replication “Mismatch Repair” Error Correction in DNA Replication In mismatch repair, the incorrectly added base is detected after replication. The mismatch-repair proteins detect this base and remove it from the newly synthesized strand by nuclease action. The gap is now filled with the correctly-paired base RNA as the Genetic Material The central dogma of molecular biology suggests that DNA maintains the information to encode all of our proteins and that three different types of RNA rather passively convert this code into polypeptides. Non-coding RNA in Eukaryotes Non-coding RNA in Eukaryotes HOTAIR is a lncRNA that plays a crucial as an oncogenic molecule in different cancer cells such as breast, gastric, colorectal, and cervical cancers. Ribosomal RNA (rRNA) Small nuclear RNA (snRNA) Small nucleolar RNA (snoRNA) Transfer RNA (tRNA) Micro RNA (miRNA) Small interfering RNA (siRNA) Piwi-interacting RNA (piRNA) Transfer RNA-derived small RNA (tsRNA) Non-coding RNA in Eukaryotes One important subcategory of small regulatory RNAs consists of the molecules known as small nuclear RNAs (snRNAs). These molecules play a critical role in gene regulation by way of RNA splicing. The most abundant of these molecules are the U1, U2, U5, and U4/U6 particles, which are involved in splicing pre-mRNA to give rise to mature mRNA. Non-coding RNA in Eukaryotes Originated from nucleolus which serves as the structure where rRNA processing and ribosomal assembly takes place. Post-transcriptional modification and maturation of ribosomal RNA, small nuclear RNAs, and other cellular RNAs) Small nucleolar RNA (snoRNA) are molecules whose function is to process rRNA molecules, often resulting in the methylation and pseudouridylation (isomerization) of specific nucleosides. Examples: C/D box snoRNAs and H/ACA box snoRNAs Biogenesis and structure of small nucleolar RNAs (snoRNAs). (A) SnoRNA biosynthesis. Most identified snoRNA genes are located in intronic regions of protein-coding genes or long nonBiogenesis and structure of small nucleolar RNAs (snoRNAs). (A) SnoRNA biosynthesis. Most identified snoRNA genes are located in intronic regions of protein-coding genes or long noncoding sequences. They are transcribed by RNA polymerase II (Pol II) and are released from their transcripts after splicing. A small subset of snoRNAs is produced from single genes with independent promoters. (B) SnoRNA structure. C/D box snoRNAs have two conserved sequences, namely box C (RUGAUGA) and box D (CUGA). The upstream of box D'/D is complementary to the target RNAs and guides the 2 -O-ribose methylation. H/ACA box snoRNAs contain conserved H box (ANANNA) and ACA box. They also have two pseudouridylation (NΨ) pockets complementary to the target RNAs to direct their pseudouridine modifications. Non-coding RNA in Eukaryotes MicroRNAs are small regulatory RNAs that are approximately 22 to 26 nucleotides in length. Their existence and functions in gene regulation were initially discovered in nematode C. elegans. Inhibit gene expression by repressing translation. Example: Caenorhabditis. elegans, lin-4 and let-7, bind to the 3' untranslated region of their target mRNAs, preventing functional proteins from being produced during certain stages of larval development Non-coding RNA in Eukaryotes Small interfering RNAs (siRNAs) are yet another class of small RNAs. Although these molecules are only 21 to 25 base pairs in length, they also work to inhibit gene expression. siRNAs were first defined by their participation in RNA interference (RNAi). They may have evolved as a defense mechanism against double-stranded RNA viruses. Small RNAs, including microRNAs, small interfering RNAs, and PIWI-interacting RNAs, assemble with Argonaute (Ago) family proteins into the effector complex called RNA-induced silencing complex (RISC), which mediates sequence-specific target gene silencing. Non-coding RNA in Prokaryotes Bacteria possess a class of small regulatory RNAs. Bacterial sRNAs are ranging from virulence to the transition from growth to the stationary phase. One example of a bacterial sRNA is the 6S RNA found within Escherichia coli; this molecule has been well characterized, with its initial sequencing occurring in 1980. 6S RNA is conserved across many bacterial species, indicating its important role in gene regulation. This RNA has been shown to affect the activity of RNA polymerase (RNAP), the molecule that transcribes messenger RNA from DNA. Riboswitches Gene regulation in both prokaryotes and eukaryotes is also affected by RNA regulatory elements, called riboswitches (or RNA switches). Riboswitches are RNA sensors that detect and respond to environmental or metabolic cues and affect gene expression accordingly. THANK YOU!