Molecular & Cellular Biology 3rd Year Pharmacy Syllabus 2024-2025 PDF

Molecular & Cellular Biology 3rd year Pharmacy Dr. Lina ISMAIIL 2024-2025  Syllabus Molecular Biology A- Molecular Biology B- Cellular Biology 1- General Introduction 1- The...

Molecular & Cellular Biology 3rd year Pharmacy Dr. Lina ISMAIIL 2024-2025  Syllabus Molecular Biology A- Molecular Biology B- Cellular Biology 1- General Introduction 1- The cell: Diversities and universal characteristics 2- Nucleic acids and genomic properties: 2- Internal organization of the cell  DNA Structure 3- Cell cycle  RNA Structure 4- Cell junctions, cell adhesion  Physical and chemical properties of nucleic acids 5- Main cell study techniques  Genomic Organization 6- Cell death From DNA to proteins: 3- Transcription 4- Splicing 5- Translation 6- Control of gene expression 7- Techniques in Molecular Biology  General Introduction The surface of our planet is populated by living organisms that appear extraordinarily diverse (10,000 species). All living things are made of units of living matter called cells. Living things though infinitely: - varied when viewed from the outside - are fundamentally similar inside Same machinery for their most basic functions Molecular Biology / 2024-2025  Definition Cells are the basic building blocks of living things. They are small membrane-bounded compartments filled with a concentrated aqueous solution of chemicals. The simplest forms of life are solitary cells that propagate by dividing in two. Higher organisms are like cellular cities in which groups of cells perform specialized functions and are linked by intricate communication systems Molecular Biology / 2024-2025  Universal features and differences of cells  All cells are enclosed in a plasma membrane across which nutrients and waste materials must pass Molecular Biology / 2024-2025  Universal features and differences of cells  All cells store their hereditary information in the same linear chemical code  All cells replicate their hereditary information by template polymerization Molecular Biology / 2024-2025  Universal features and differences of cells  All cells transcribe portions of their hereditary information into the same intermediary form  All cells translate RNA into proteins in the same way Molecular Biology / 2024-2025  Universal features and differences of cells  All cells use proteins as catalysts Molecular Biology / 2024-2025  Differences between cells Cells come in an astounding assortment of shapes and sizes.  Size and Shape.  Movement and lability.  Metabolism and life style Molecular Biology / 2024-2025  Differences between cells Classification based on rRNA sequences of species Molecular Biology / 2024-2025  Chapter 1 Molecular Biology Chapter 1 : Nucleic acids and genomic properties Molecular Biology / 2024-2025  Molecular Biology Chapter 1 Molecular Biology is the branch of biology that deals with the formation, structure, and function of macromolecules (nucleic acids and proteins) essential to life, and especially with their role in cell replication and the transmission of genetic information. “Molecular biology is a result of the encounter between genetics and biochemistry, two branches of biology that developed at the beginning of the twentieth century.” Molecular Biology / 2024-2025  Chapter 1 Central Dogma The central dogma of molecular biology is a theory stating that genetic information flows only in one direction, from DNA, to RNA, to protein, or RNA directly to protein. Molecular Biology / 2024-2025  Chapter 1 Chemical composition of nucleic acids The nucleic acids are the main molecules carrying the cell’s information. They are polymeric macromolecules formed of a linear chain of monomer units or sub-units called nucleotides. Each nucleotide consists of 3 distinct parts : 1. A sugar formed of 5 carbon atoms called pentose (1'-5') 2. A nitrogenous base is always attached to the C.1' of the sugar 3. A phosphate group H3PO4 is always attached to the C.5' of the sugar. The nomenclature of nucleic acids returns to their acidic nature and their nuclear localization Molecular Biology / 2024-2025  Chapter 1 Chemical composition of nucleic acids 1. The components of a nucleotide The phosphate group They are also known as inorganic phosphate (Pi) or Phosphoric acid H3PO4. In the physiological conditions, the free hydroxyl groups (OH) in the phosphoric acid lose their H+ cations and thus become negatively charged molecules (O-). This gives a negative charge for the nucleotide, then for the nucleic acids. Molecular Biology / 2024-2025  Chapter 1 Chemical composition of nucleic acids 1. The components of nucleotide The sugar It is a 5 carbon atoms sugar numbered from 1' to 5' or pentose (for 5). There are two types of pentose in nucleic acids: 1. The ribose: is the pentose present in the RNA molecules or ribonucleic acids. They have 4 hydroxyl group (OH) at 1', 2', 3' and 5' carbons. 2. The deoxyribose: is the pentose present in the DNA molecules or deoxynucleotides acids. The deoxyribose is a ribose where the hydroxyl group linked to C2' has been replaced by a hydrogen atom Molecular Biology / 2024-2025  Chapter 1 Chemical composition of nucleic acids 1. The components of nucleotide The nitrogenous base Are aromatic molecules classified into two classes according to their aromatic rings. We distinguish: 1. The purine bases that contain the purine aromatic ring. This ring contains two different cycles: the pyrimidine ring and the imidazole ring. Molecular Biology / 2024-2025  Chapter 1 Chemical composition of nucleic acids 1. The components of nucleotide The nitrogenous base 2- The pyrimidine bases contain the pyrimidine aromatic ring. This ring is a cycle containing 4 atoms of carbon and 2 atoms of nitrogen. There are 3 pyrimidine bases: thymine (T), uracil (U) and cytosine (C). Molecular Biology / 2024-2025  Chapter 1 Chemical composition of nucleic acids 2. The nucleoside A nucleoside is a compound consisting of a sugar (ribose or deoxyribose) and a nitrogenous base. The sugar binds with its C.1' carbon to a nitrogen of the base by a N-glycosidic connection. Molecular Biology / 2024-2025  Chapter 1 Nomenclature According to the sugar present at the level of a nucleoside, a nitrogenous base will be able to form 2 different nucleosides. - The nucleosides are appointed by adding idine to the original name of a pyrimidine or iosine to the original name of a purine. When the sugar present is the deoxyribose, a Prefix deoxy is added before the nucleoside’s name. As a result, the names of the 4 different nucleosides constituting DNA are: 2' deoxyadenosine (dA), 2' deoxyguanosine (dG), 2' deoxycytidine (dC) and 2' deoxythymidine (dT). Molecular Biology / 2024-2025  Chapter 1 Nomenclature A nucleotide is formed by an esterification between a phosphate group and the OH group linked to the sugar’s C.5' of a nucleoside. The connection thus formed is an ester bond. Nucleotide =nucleoside + P. They are called nucleoside monophosphate - The deoxyribonucleic acids (DNA) are therefore composed of dAMP, dGMP, dTMP and dCMP - The ribonucleic acids (RNA) are therefore composed of AMP, GMP, UMP and CMP. Molecular Biology / 2024-2025  Chapter 1 Nomenclature Nucleosides could sometimes bind to two or three phosphoric acid molecules to form the di and Tri Phosphate nucleoside. These are of great importance in cell metabolism because they constitute the cellular energy substrates Molecular Biology / 2024-2025  Chapter 1 Nomenclature Molecular Biology / 2024-2025  The nucleic acids' simple strand or polynucleotide formation Chapter 1 Molecular Biology / 2024-2025  The nucleic acids' simple strand or polynucleotide formation Chapter 1 Molecular Biology / 2024-2025  The structure of DNA Chapter 1 The structure of DNA was first described by James Watson and Francis Crick in 1953. DNA exists as a double helix, with about ten nucleotide pairs per helical turn. The spatial relationship between the two strands creates furrows in DNA—the major and minor grooves. Each of the two helical strands is composed of a sugar phosphate backbone with attached bases and is connected to a complementary strand by hydrogen bonding. The pairing of the nucleotide bases occurs such that adenine (A) binds with thymine (T) and guanine (G) with cytosine (C). Molecular Biology / 2024-2025  The primary structure of DNA Chapter 1 The order of the nucleotide bases determines the primary structure or sequence of the DNA. DNA is a double-stranded polymer of deoxyribonucleotides joined by covalent phosphodiester bonds. The phosphodiester bonds are bonds that form between the 3′-OH groups of the deoxyribose sugar of one nucleotide with the 5′ phosphate groups of the adjacent nucleotide. Molecular Biology / 2024-2025  The primary structure of DNA Chapter 1 The phosphodiester linkages between individual deoxynucleotides are directional in nature. The 5′ phosphate group of one nucleotide is bound to the 3′ hydroxyl group of the next nucleotide. The two complementary strands of DNA double helix therefore run in antiparallel directions. The 5′ end of one strand is base-paired with the 3′ end of the other strand. This primary structure is stabilized by two types of noncovalent interactions. Molecular Biology / 2024-2025  The primary structure of DNA Chapter 1 Noncovalent interactions One type of noncovalent interaction within DNA includes hydrogen bonds that hold together the two strands of DNA within the double helical structure. Nucleotide bases on one strand form these bonds with nucleotide bases on the opposite strand. Adenine forms two hydrogen bonds with thymine, while guanine and cytosine are connected by three hydrogen bonds. This type of base pairing in the interior of the helix stabilizes the interior of the double-stranded DNA because the stacked bases repel each other due to their hydrophobic nature. The hydrogen bonds between bases can be made and broken easily, allowing DNA to undergo accurate replication and repair. Molecular Biology / 2024-2025  Chapter 1 DNA secondary structure DNA consists of two complementary chains that are precisely cross-linked by specific hydrogen bonding between purine and pyrimidine bases. Chargaff’s rules:  The amount of adenine equals that of thymine: [A] = [T].  The amount of guanine equals that of cytosine: [G] = [C].  The amount of the purine bases equals that of the pyrimidine bases: [A] + [G] = 28  The amount of the purine bases equals that of the pyrimidine bases: [A] + [G] = [T] + [C]. Molecular Biology / 2024-2025  Chapter 1 DNA secondary structure The result is a ladder structure.  The upright portions are the sugar phosphate backbones,  The connecting rods are the paired nitrogenous bases, AT or GC. The ladder is twisted into a double helix with approximately 10 base pairs for each complete turn of the helix. The two DNA strands run in opposite directions, that is they are antiparallel, and the 5’ end of one strand is the 3’ end of the other Molecular Biology / 2024-2025  Spatial conformation of DNA Chapter 1 Structural variation in DNA reflects free rotation about the C-1’–N-glycosyl bond Because of steric constraints, purines in purine nucleotides are restricted to two stable conformations with respect to deoxyribose, called syn and anti. Pyrimidines are generally restricted to the anti conformation because of steric interference between the sugar and the carbonyl oxygen at C-2 of the pyrimidine Molecular Biology / 2024-2025  Spatial conformation of DNA Chapter 1 Molecular Biology / 2024-2025  Chapter 1 DNA secondary structure DNA is a right-handed double helix composed of deoxyribonucleotides. It can take up different forms of structural conformations based on different factors, some are: - salt concentration, - presence of chemically altered bases, - hydration level, - sequence of DNA, - presence of polyamines in the solution, - direction and quantity of supercoiling. Molecular Biology / 2024-2025  Chapter 1 DNA secondary structure The A form is favored in many solutions that are relatively devoid of water Molecular Biology / 2024-2025  Chapter 1 DNA tertiary structures A palindrome is a common type of DNA sequence o A palindrome is a word, phrase, or sentence that is Palindrome spelled identically read either forward or backward; o ROTATOR and NURSES RUN. o “radar” “Madam, I’m Adam,” The term is applied to regions of DNA with inverted repeats of base sequence having two-fold symmetry over two strands of DNA. Such sequences are self-complementary within each strand and therefore have the potential to form hairpin or cruciform (cross-shaped) structures When the inverted repeat occurs within each individual strand of the DNA, the sequence is called a mirror repeat Molecular Biology / 2024-2025  Chapter 1 DNA tertiary structures Molecular Biology / 2024-2025  Chapter 1 Unusual DNA tertiary structures H-DNA A particularly exotic DNA structure is found in polypyrimidine or polypurine tracts that also incorporate a mirror repeat. The H -DNA structure features the triple -stranded form Two of the three strands in the H-DNA triple helix contain pyrimidines and the third contains purines. In the DNA of living cells, sites recognized by many sequence-specific DNA-binding proteins are arranged as palindromes, and polypyrimidine or polypurine sequences that can form triple helices or even H-DNA are found within regions involved in the regulation of expression of some eukaryotic genes Molecular Biology / 2024-2025  Chapter 1 Unusual DNA tertiary structures H-DNA A- A sequence of alternating T and C residues can be considered a mirror repeat centered about a central T or C. B- These sequences form an unusual structure in which the strands in one half of the mirror repeat are separated and the pyrimidine containing strand (alternating T and C residues) folds back on the other half of the repeat to form a triple helix. The purine strand (alternating A and G residues) is left unpaired. This structure produces a sharp bend in the DNA. Molecular Biology / 2024-2025  Chapter 1 DNA structures Molecular Biology / 2024-2025  Chapter 1 Supercoiling of DNA Negative DNA supercoils Positive DNA supercoils is energetically favored makes opening the helix gives "superhelices" which more difficult facilitate unwinding of the doublehelix for replication, recombination and transcription Molecular Biology / 2024-2025  Chapter 1 Supercoiling of DNA Topoisomerases are enzymes with both nuclease and ligase activity. These proteins change the amount of supercoiling in DNA. Topoisomerases are required for many processes involving DNA, such as DNA replication and transcription They are divided into type I and type II enzymes They are targets of o antineoplastic drugs (etoposide) o antibacterial drugs (fluoroquinolones) Molecular Biology / 2024-2025  Chapter 1 Supercoiling of DNA Topoisomerase I transiently cleaves one strands of DNA Type II topoisomerases make transient (1) cleavage of one DNA strand; double stranded breaks and allow the (2) passage of a segment of DNA passage of another duplex across the through the break break. (3) resealing the break Molecular Biology / 2024-2025  Modification of DNA structure Chapter 1 Molecular Biology / 2024-2025  Chapter 1 RNA structure RNA consists of a single polynucleotide chain Linear polymer of ribonucleotides linked by phosphodiester bonds RNA occurs in multiple copies and various forms Cells contain up to eight times as much RNA as DNA. Molecular Biology / 2024-2025  Chapter 1 RNA structure RNA is sensitive to alkaline hydrolysis RNA is destroyed by Rnase Molecular Biology / 2024-2025  Chapter 1 An RNA chain can therefore folds into a particular shape, this ability to fold into complex three- dimensional shapes allows some RNA molecules to have precise structural and catalytic functions. Molecular Biology / 2024-2025  Chapter 1 Types of RNA Molecular Biology / 2024-2025  Chapter 1 mRNA Messenger RNA (mRNA) serves to carry the information or “message” that is encoded in genes to the sites of protein synthesis in the cell, where this information is translated into a polypeptide sequence. In prokaryotes, a single mRNA may contain the information for the synthesis of several polypeptide chains within its nucleotide sequence Molecular Biology / 2024-2025  Chapter 1 mRNA Eukaryotic mRNAs  encode only one polypeptide,  are synthesized in the nucleus in the form of much larger precursor molecules called heterogeneous nuclear RNA, or hnRNA.  hnRNA molecules contain noncoding regions called intervening sequences or introns because they intervene between coding regions, which are called exons.  Introns interrupt the continuity of the information specifying the amino acid sequence of a protein and must be spliced out before the message can be translated.  In addition, eukaryotic hnRNA and mRNA molecules have a run of 100 to 200 adenylic acid residues attached at their 3-ends, so-called poly(A) tails. This polyadenylylation occurs after transcription has been completed and is believed to contribute to mRNA stability. Molecular Biology / 2024-2025  Chapter 1 Prokaryotic mRNA is polycistronic, meaning multiple protein products are coded by each mRNA molecule. Molecular Biology / 2024-2025  Chapter 1 Eukaryotic mRNA is monocistronic, meaning each mRNA contains the coding sequence for one protein. Molecular Biology / 2024-2025  Chapter 1 rRNA Ribosomes, the supramolecular assemblies where protein synthesis occurs, are about 65% RNA of the ribosomal RNA type. Ribosomal RNA (rRNA) molecules fold into characteristic secondary structures as a consequence of intramolecular hydrogen bond interactions The different species of rRNA are generally referred to according to their sedimentation coefficients Ribosomes are composed of two subunits of different sizes Molecular Biology / 2024-2025  Chapter 1 Eukaryotic ribosomes are somewhat larger than prokaryotic ribosomes Molecular Biology / 2024-2025  Chapter 1 Ribosomal RNAs characteristically contain a number of specially modified nucleotides, including pseudouridine residues, ribothymidylic acid, and methylated bases Molecular Biology / 2024-2025  Chapter 1 tRNA Transfer RNA (tRNA) serves as a carrier of amino acid residues for protein synthesis. The tRNAs are the smallest RNAs (size range—23 to 30 kD) and contain 73 to 94 residues, a substantial number of which are methylated or otherwise unusually modified All tRNA molecules possess a 3-terminal nucleotide sequence that reads -CCA, and the amino acid is carried to the ribosome attached as an acyl ester to the free 3-OH of the terminal A residue A special sequence of three bases (the anticodon) forms base pairs with complementary bases (the codon) in the mRNA. Molecular Biology / 2024-2025  Other RNA types Chapter 1 Small nuclear RNA : snRNA Found in the nucleus of eukaryotic cells contain from 100 to about 200 nucleotides, some of which, like tRNA and rRNA, are methylated or otherwise modified. found in stable complexes with specific proteins forming small nuclear ribonucleoprotein particles, or snRNPs Molecular Biology / 2024-2025