Lecture 1a. Introduction to Information System Paradigm PDF

BME454 2024-2025 INTRODUCTION TO THE INFORMATION SYSTEM PARADIGM OF MOLECULAR BIOLOGY Prof. Iman Diab Prof. Doaa Abdelmonsif Professor of Medical Biochemistry & Molecular Biology Alexandria Faculty of Medici...

BME454 2024-2025 INTRODUCTION TO THE INFORMATION SYSTEM PARADIGM OF MOLECULAR BIOLOGY Prof. Iman Diab Prof. Doaa Abdelmonsif Professor of Medical Biochemistry & Molecular Biology Alexandria Faculty of Medicine Molecular biology is the biology of molecules like RNA, DNA and protein, which actively participate in the processes called transcription and translation.  BIOINFORMATICS Bioinformatics involve the technology that uses computers for storage, retrieval, manipulation, and distribution of information related to biological macromolecules such as DNA, RNA, and proteins.  THE CENTRAL DOGMA OF LIFE The central dogma in genetics describes the typical mechanism by which the information saved in DNA sequences fulfills its job: information coded in DNA sequence is passed on to a type of RNA called messenger RNA (mRNA). Information in mRNA is then passed on to proteins. The former step is called transcription, and latter step is called translation.  Transcription is governed by the rule of complementary base pairing between the DNA base and the transcribed RNA base. That is, an A in the DNA is transcribed to a U in the RNA, a T to an A, a G to a C, and vice versa THE CENTRAL DOGMA OF LIFE  CELLS Basic unit of life Different types of c ell: Skin, brain, red/white blood Different biological function Cells produced by cells Cell division (mitosis) 2 daughter cells Eukaryotic c ells Have a nucleus NUCLEUS AND CHROMOSOMES Each cell has nucleus Rod-shaped particles inside Are c hromosomes Always n pairs Different number for species Human(46),tobacco(48) Goldfish(94),chimp(48) Usually paired up X & Y Chromosomes Humans: Male(xy), Female(xx) Birds: Male(xx), Female(xy)  Gene: is a DNA segment (dsDNA) that contained a well- defined genetic information & codes for a specific protein. Genome: means total DNA content of a cell (= total number of genes in one cell).  1. DNA DNA contains the complete genetic information that defines the structure and function of an organism. Proteins are formed using the genetic code of the DNA.  DNA is the short name for deoxyribonucleic acid, which is the molecule that stores the major genetic information in cells. It is formed of nucleotides A nucleotide consists of three parts: a phosphate group, a pentose sugar (ribose sugar), and a base. The bases are of four types: adenine (A), guanine (G), cytosine (C), and thymine (T). A and G are called purines. C and T are called pyrimidines.  The bases of one strand of DNA molecule are connected to those of the other strand by hydrogen bonds. (A = T), (G  C). This base pairing between the opposite strands is very specific and the sequence of bases on one strand is complementary to that of the second strand. An example of a part of DNA strand 2. RNA 1. Messenger RNA (mRNA) It is synthesized in the nucleus by DNA and then carries the message to the ribosomes in the cytoplasm to direct the synthesis of a specific protein. The letters of the message are the nitrogenous bases, the sequence of which is responsible for arranging the amino acids in proper order in the polypeptide chain to be synthesized. Each 3 successive bases in the mRNA are called a “codon” because they code for a specific amino acid. The process of synthesis of mRNA in the nucleus under the directions of DNA is called “transcription”. 2. Transfer RNA (tRNA) It is present in the cytoplasm and may be also known as soluble RNA (sRNA). It functions as carriers for the amino acids and transfer them to the Ribosome. There is, at least, a specific tRNA for each amino acid (around 20 tRNA). 3. Ribosomal RNA (rRNA) It is present in the ribosomes of the cytoplasm. The ribosome is a cytoplasmic nucleoprotein structure. The ribosome particle is formed of at least 4 rRNA molecules complexed with several protein molecules.  Gene: is a DNA segment (dsDNA) that contained a well- defined genetic information & codes for a specific protein. Genome: means total DNA content of a cell (= total number of genes in one cell).  There are three types of genes : 1. Protein-coding genes : these are transcribed into RNA and then translated into proteins. 2. RNA-specifying genes : these are only transcribed into RNA. 3. Regulatory genes : according to a narrow definition, these include only untranscribed sequences.  Three different processes are responsible for the inheritance of genetic information and for its conversion from one form to another : 1. Replication : a double stranded nucleic acid is duplicated to give identical copies. This process perpetuates the genetic information. 2. Transcription : a DNA segment that constitutes a gene is read and transcribed into a single stranded sequence of RNA. The RNA moves from the nucleus into the cytoplasm. 3. Translation : the RNA sequence is translated into a sequence of amino acids as the protein is formed. During translation, the ribosome reads three bases (a codon) at a time from the RNA and translates them into one amino acid  Synthesis of protein under the influence of gene is called gene expression. Expression of this genetic information (gene expression) involves two stages:- - The first stage is transcription to form mRNA. - The second stage is translation of the nucleotide sequence of a mRNA (Codons) into an amino acid sequence of a protein. Gene Expression  TRANSCRIPTION Take one strand of DNA Write out the counterparts to each base G becomes C (and vice versa) A becomes T (and vice versa) Change Thymine [T] to Uracil [U] You have transcribed DNA into messenger RNA Example: Start: GGATGCCAATG Transcribed: CCUACGGUUAC The coding region of eukaryotic genes typically consists of a series of expressed exons with intervening introns.  TRANSLATION Proteins are chains of amino acids. There are 20 types of standard amino acids used in lives. The procedure of translation converts the information from the language of nucleotides to the language of amino acids. The translation is done by a special dictionary: the genetic codes or codon.  GENETIC CODE How the translation occurs Think of this as a function: Input: triples of three base letters (Codons) Output: amino acid Example: ACC becomes threonine (T) Gene sequences end with: TAA, TAG or TGA  EXAMPLE SYNTHESIS A=Ala=Alanine C=Cys=Cysteine D=Asp=Aspartic acid TCGGTGAATCTGTTTGAT E=Glu=Glutamic acid Transcribed to: F=Phe=Phenylalanine G=Gly=Glycine AGCCACUUAGACAAACUA H=His=Histidine Translated to: I=Ile=Isoleucine SHLDKL K=Lys=Lysine L=Leu=Leucine M=Met=Methionine N=Asn=Asparagine P=Pro=Proline Q=Gln=Glutamine R=Arg=Arginine S=Ser=Serine T=Thr=Threonine V=Val=Valine W=Trp=Tryptophan Y=Tyr=Tyrosine