Microbiology Semester 2 Week 8

         Assalamualaikum and hi everyone... how are you all? I hope everyone will be fine as well... On Tuesday, before our class start, my classmates Amyza, and Nisha was presented about a microbe based on topics provided to them. Later on, Dr. Suriana taught us about Microbial Genetics. Basically,  DNA Replication is a process by which a double-stranded DNA molecule is copied to produce two identical DNA molecules. The process of the genetic code duplicated and passed on to each offspring. Must be completed during a single generation time. Elongation and Termination of the Daughter Molecules, as replication proceeds, the newly produced double strand loops down, DNA polymerase I removes RNA primers and replaces them with DNA and when the forks come full circle and meet, ligases move along the lagging strand which begin initial linking of the fragments and complete synthesis and separation of the two circular daughter molecules.

        Transcription is process by which the information in a strand of DNA is copied into a new molecule of messenger RNA (mRNA). mRNA is comparable to a copy from a reference book because it carries the same information as DNA but is not used for long-term storage and can freely exit the nucleus. Although the mRNA contains the same information, it is not an identical copy of the DNA segment, because its sequence is complementary to the DNA template. Transcription is carried out by an enzyme called RNA polymerase and a number of accessory proteins called transcription factors. Transcription factors can bind to specific DNA sequences called enhancer and promoter sequences in order to recruit RNA polymerase to an appropriate transcription site. Together, the transcription factors and RNA polymerase form a complex called the transcription initiation complex. This complex initiates transcription, and the RNA polymerase begins mRNA synthesis by matching complementary bases to the original DNA strand. The mRNA molecule is elongated and, once the strand is completely synthesized, transcription is terminated. The newly formed mRNA copies of the gene then serve as blueprints for protein synthesis during the process of translation. The copying is along the same lines as already explained, (A for T, G for C, C for G) except that a different base called U (uracil) replaces T (thymine).

       On Friday, before our class start, my classmates Sayyi, Shafiqah, Aqilah and I was presented about a microbe based on topics provided to them. I was presented about the Chlorella vulgaris. Later on, Dr Suriana taught us about translation and Gene Regulation. Translation process by which a protein is synthesized from the information contained in a molecule of messenger RNA (mRNA). During translation, an mRNA sequence is read using the genetic code, which is a set of rules that defines how an mRNA sequence is to be translated into the 20-letter code of amino acids, which are the building blocks of proteins. Ribosome is a factory of protein synthesis. Three steps of Translation which is chain initiation is assembly of ribosome, mRNA start codon, and initiator tRNA anticodon. Chain Elongation is ribosome moves codon-by-codon and codon-anticodon pairing results in the
formation of specific amino acids chain, polypeptide. Chain Termination is when the ribosome reaches stop codon, polypeptide is released and translation complex disassembles.

        Gene regulation is mechanisms to increase or reduce production of RNA or protein because energy conservation, environmental adaptation and enzyme activity regulation. Regulation can occur during different stages of gene expression which is transcriptional regulation, translational regulation and post-transcriptional or posttranslational regulation. Regulation of Gene Expression which is gene expression refers to the combined process of transcription and translation of genetic information to a functional protein, not all genes are expressed at any one time, nor are they always expressed at the
same level. Gene expression is tightly regulated, or controlled, so that the cell only makes the gene
products that it needs for efficient growth under its current environmental conditions. An operon is regulatory protein binding region and downstream gene(s). Regulatory proteins called repressors or activators act as off and on switches for transcription, respectively. Negative regulation involves repressor proteins that respond to cell conditions so to actively repress (prevent) RNA Polymerase from beginning transcription of the gene (or operon) by binding onto the DNA at the operator site. Positive regulation of transcription also can occur. Here, environmental conditions in the cell causes an activator protein to bind to the promoter site for a gene (or operon), which enables RNA Polymerase to begin transcription. Operon is a group of genes that consists of Promoter is region where RNA polymerase initiates transcription, Operator is region adjacent to structural genes
that controls their transcription and Structural genes is genes with related functions.

      

  

Microbiology Semester 2 Week 7

         
           Assalamualaikum and hi everyone... how are you all? I hope everyone will be fine as well... On Tuesday, before our class start, my classmates Aina, Amira and Adriana was presented about a microbe based on topics provided to them. The program is known as Pecha Kucha. Aina talked about Karlodinium veneficum, Amira talked about Haematococcus phuvalis, and Adriana talked about Clostridium noyvi. Later on, Dr. Suriana taught us about introduction of systematic prokaryotes again because on friday before mid sem break, many students are absent to the class. Dr. Suriana also taught us about small-subunit rRNA-based classification of prokaryotes. Molecular method for systematics which is molecular methods have been introduced, based on sequencing of genes that can be used as “evolutionary clocks,” i.e., that provide information on evolution in the prokaryote world, the principle of molecular taxonomy and of phylogenetic tree reconstruction is based on the concept that biological macromolecules can be used as evolutionary chronometers that measure evolutionary change and thanks to the availability of new techniques i.e sequencing of the genes encoding the small-subunit (16S) ribosomal RNA. Discovery of small-subunit ribosomal RNA sequence which is Carl Woese, in the late 1970s, hypothesized that ribosomes were ancient, conserved structure, better way to check is by looking at the genetic sequence. He studied various ribosomal RNAs: 5S, 16S and 23S, and finally chose 16S as  molecule to study the evolution of life.

           Properties of rRNA as phylogenetic marker is common ancestry, genetic stability, appropriate size and presence of independently evolving domains. The phylogenetic tree is do not provide an answer to the question of the nature of the universal ancestor of all life forms on Earth,  do not infer from these trees whether the Archaea are a more ancient group than the Bacteria, or whether the prokaryotes formed an ancestral stage that led to the development of the primitive eukaryotic cell, mitochondria found in most eukaryotic cells have an ancestry that can be traced back to the Proteobacteria and origin of the chloroplasts in algae and higher plants, is within the Cyanobacteria. Differences between Bacteria and Archaea is the morphologically, the Archaea and the Bacteria are very similar, and also at the level of the cell ultrastructure, there are no obvious differences between typical representatives of both groups.

         Differences is in the nucleotide sequences of ribosomal RNAs, structure of the cell wall, type of lipids in the membrane, the properties of the transcription mechanism of DNA to form RNA, the details of operation of the protein synthesis machinery of the ribosome, sensitivity to different antibiotics. Identification of prokaryote isolates not a simple procedure, not straightforward conventional way using the dichotomous identification keys, latest approach using polyphasic approach to taxonomy – morphological characters (cell shape and size, the Gram-reaction, cell inclusions, presence and nature of the surface layers, including extracellular capsules). Polyphasic approach morphological characters  – (cell shape and size, the Gram-reaction, cell inclusions, presence and nature of the surface layers, including extracellular capsules), information on motility  – (presence of flagella, their number and the way they are inserted into the cell, gliding movement), the mode of nutrition and energy generation, the cells’ relationship to molecular oxygen, temperature, pH, and tolerance towards and requirement for salt.

             On Friday, before our class start, my classmates Subatra, Nadhirah and Harissa was presented about a microbe based on topics provided to them. The program is known as Pecha Kucha. Subatra talked about Ceriporiopsis subvermispora, Nadhirah talked about Penicillium chrysogenum, and Harissa talked about Agaricus bisporus. Later on, Dr. Suriana taught us about microbial genetic. The genome is all genetic instructions (genes) for development of cellular structures, metabolic functions, and their regulation (organization of which, when, where, and how much). Genes are located within chromosomes (linear or circular) or plasmids, as specific regions of DNA (or RNA for some viruses). Gene a certain segment of DNA that contains the necessary code to make a protein or RNA molecule.