Molecular Bio Lecture Notes PDF

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Moleuclar bio Lecture 6: The Structure of DNA, Organization of the Genome, and the Overview of the Cell Cycle LEC 4 LEC 5: From Gene to Protein 31.01.2025 11:55 Lec 8: Control of Gene Expression Lec 1: Cell Composition and Structure Lecture 2: The Cell Membrane The Metaphase Chromosome PCR Reaction LEC 7: DNA Replication, Transcription, and Translation Structure and Types of RNA The most fundamental function of DNA is to enable accurate growth and duplication, including Friday, October 25, 2024 DNA Vectors CELL SIGNALING LECTURE 3 A semiconservative process occurs because each strand of the DNA helix serves as a template for the Nuclear Envelope Eukaryotic Gene A gene is a fragment of DNA that carries information about one polypeptide and one type of RNA. A The Cell Membrane Lipids Lecture 9: DNA Damage and Repair organelles, chromosomes, and other cellular components. Specific for the species is their number in each cell and their shape/organization. 12:14 The smallest living structure that is able to divide and reproduce itself. Cells contain genetic information Membrane lipids are divided based on their chemical structure: Replication would have needed infinite energy for infinite accuracy. However, variability is good for Morphological features in the metaphase chromosome: length, position, centromere, short & long arm, Thursday, January 9, 2025 Homeostasis synthesis of a new strand, only occurring in the 5' to 3' direction. New nucleotides are joined by a The nuclear envelope is composed of: gene consists of exons (coding), non-coding (introns), and regulatory promoter, enhancer, and silencer that determines their function by producing proteins. Phospholipids evolution. The Four Phases of the Eukaryotic Cell Cycle banding pattern. Polymerase Chain Reaction (PCR) 08:50 Lecture 10: Stem Cells Homeostasis is about the cell maintaining balance by controlling its internal factors to adjust to external phosphodiester bond, which is enzymatic and requires energy. The outer (cytoplasmic) and inner nuclear membranes, with a perinuclear space between them. sequences. There are either prokaryotic or eukaryotic types of cells. The eukaryotic cell cycle typically consists of four phases: Structural components: two sister chromatids, centromere, telomeres, secondary constriction, A process used to duplicate specific DNA genes by utilizing DNA replication mechanisms. Molecular Cloning Stem cells are a specific kind of cell that haven't gained their designated function, therefore being able Replication Proteins The nuclear lamina, which adheres to the inner nuclear membrane. Gene Expression in Eukaryotes Composed of two fatty acids, glycerol, phosphoric acid, and a functional group (ethanolamine, choline, Mutation 1. M Phase (1-hour process) trabant/satellite. factors. Failing to do so will result in disease formation. Nuclear pores, which exchange molecules between the nucleus and cytoplasm. Only 1.5% of DNA consists of coding genes. inositol, or serine). Mutations are changes in the DNA sequence that are unintended and occur due to either internal or Purpose Molecular cloning is a technique that allows scientists to synthesize desired gene sequences. This can to undergo unlimited division and turn into any cell type the body needs. The intracellular fluid tries to match or compensate for stress caused by the extracellular fluid, which Eukaryotic cells can either be single-celled or multicellular, like animals, plants, and fungi. Each animal Sphingolipids ○ Mitosis: The cell's nucleus divides into two. Centromere Their morphological structure consists of a large nucleus, a narrow cytoplasmic ring, and a sparse area. links different cells together. Helicase Gene expression refers to the process where selective segments of DNA are activated to produce cell contains components like the cytoplasm, cytoskeleton, nucleus, endoplasmic reticulum, external factors. ○ Cytokinesis: The cytoplasm splits, forming two separate daughter cells. Contains centromeric DNA and histone proteins, serves as an attachment site for sister chromatids, Detection of specific DNA sequences in a sample involve cloning specific genes, such as promoter regions or other functional DNA segments. Composed of sphingosine (a long-chain amino alcohol), fatty acid, phosphoric acid, and a functional They have the ability to divide after being in their inactive stage and also have increased resistance to Called the MCM 3-7 complex, built up by six identical subunits forming a ring. This protein breaks Nuclear Lamina proteins and RNA molecules. These processes are regulated by intracellular and extracellular signals. mitochondria, Golgi apparatus, lysosomes, and peroxisomes. Mutations also include changes in somatic and germ cells that get passed down to daughter cells. 2. S Phase (Synthesis) divides the chromatids into arm sections, has two kinetochores (important for karyokinesis). Gene expression analysis Cloning Process The Role of Homeostasis hydrogen bonds between the nitrogenous bases and is therefore a helicase. This protein also hydrolyzes A network of protein filaments that: There are housekeeping proteins that focus on protecting the DNA and maintaining its function, such as group. Somatic mutations occur in body cells, are not inherited by offspring, and can cause cancer. Diagnostics 1. Generate the backbone of the plasmid radiotherapy and cytostatics. Divided into two subgroups: ○ The phase where the cell replicates its DNA. Kinetochore Mutation detection Multicellular organisms have to coordinate with each other to maintain homeostasis through ATP as it moves along and splits the DNA strand. Gives shape to the cell nucleus. RNA and RNA polymerase, DNA repair enzymes, ribosomal proteins, and enzymes associated with basic Germline mutations occur in oogenesis, spermatogenesis, or embryonic development. They can ○ A plasmid is a DNA sequence found within bacteria. Stem cells can differentiate into different cell types that comprise tissues of: Prokaryotic cells have a cell surface made of the cell membrane, cell wall, mucus, flagella, and pili, while Sphingomyelins: Made of sphingosine, a fatty acid, phosphoric acid, and a functional group. 3. G1 and G2 Phases A shaped layered protein found on both centromeres. Spindle fibers connect to the mitotic spindle and intercellular communication. This must be done at different levels: between cells, within tissues, Provides structural support to chromatin by allowing chromatin domain attachment. metabolic processes. be inherited and cause genetic diseases. Pathogen identification Endodermal origin Topoisomerase Is involved in fragmentation and reconstruction of the nuclear envelope during mitosis. internally containing cytosol, nucleoid, ribosomes, and plasmids. ○ Critical for: Brain matter, neural tissue, and the myelin sheath of nerve endings. ○ The cell monitors both internal and external environments, ensuring conditions are suitable allow movement in metaphase and anaphase. ○ The bacterial plasmid includes: Ectodermal origin between tissues and organs, among organ systems, and across the whole organism. Different types of DNA in cells have their specialized functions: Cells contain either inorganic (do not contain C-H bonds) or organic chemical compounds, which are De Novo Mutations for reproduction and preparing for the next S phase and mitosis. Copying Genes for: § Origin of replication sequence Mesodermal origin Communication There are two different types that focus on removing the torsional stress of the DNA after it has split. Pancreatic beta cells produce insulin found in living organisms. Glycolipids: Made of sphingosine, fatty acid, and one or more sugar molecules (glucose or Types of Chromosomes Genetic engineering § Promoter region Sex cells Intercellular communication is essential for cell survival, division, differentiation, and death. These are Type 1 and Type 2 topoisomerases. Nuclear Pores Pancreatic alpha cells create glucagon Water galactose). Sudden mutations that occur with age or due to physical, chemical, or biological factors. They can Cell Cycle Control System Metacentric – Centromere is found halfway between chromosome ends. Gene cloning § Antibiotic resistance genes RPA is an example, where it binds to single-stranded DNA to prevent hydrogen bonds from forming Composed of three rings, each made of eight elements: Sterols happen in somatic or germline cells, and if they occur during embryo development, they can be Submetacentric – Centromere is located near the center of the chromosome and creates an L B cells (lymphocytes) produce antibodies Water is the main component of every organism, making up 70-80%. It is essential because it is a The cell cycle is regulated by a control system involving proteins that ensure each phase occurs under Functional gene analysis § Restriction sites Stem Cell Division There are two types of communication between cells: electrical and chemical. Chemical communication within the strand and allows DNA polymerase to synthesize a new DNA chain. ○ Cytoplasmic ring, central pore, nuclear ring. Red blood cells synthesize hemoglobin Alcohols belonging to steroids, with cholesterol as an example. inherited. the right conditions (nutrients, molecular signals, etc.). If these conditions are not met, the cycle may be shape during metaphase and anaphase. Organism modification ○ Restriction sites are locations where the plasmid can be cleaved and later reassembled. occurs when a cell produces a signal to target another cell. solvent, substrate, and product of chemical reactions. Asymmetric division (self-renewal) – Splits into two daughter cells, where one retains properties PCNA is another example of a helper protein. It is a ring-shaped homotrimer made of three subunits. The remaining components form the nuclear basket, allowing selective transport between the Cells can regulate protein sets by: The structure consists of an oxygen molecule bonded to two hydrogen atoms, creating an uneven Structure of Membrane Lipids Spontaneous Mutations delayed or enter a non-dividing state called G0. Acrocentric – Centromere is located near the end of the chromosome, creating a long and a short ○ Restriction enzymes recognize these restriction sites and cleave the plasmid, producing from the mother cell, while the other is differentiated. Methods of Communication With the help of RFC, it binds to the DNA strand so that it can protect the polymerase from falling off nucleus and cytoplasm. Controlling when and how often genes are transcribed Mutations resulting from errors in DNA replication and transcription. These can involve modifications or The system consists of two main controls: arm. Symmetric division – Both daughter cells retain properties from the stem cell, and both are Communication can be local, such as: the template and later releases the polymerase after an Okazaki fragment is synthesized. Controlling the transcription maturation process charge and making the molecule dipolar. The Structure of the Carbon Atom Membrane lipids form a bilayer structure, with a hydrophilic head and hydrophobic tails, making them amphiphilic. loss of nitrogenous bases, DNA polymerase slippage, problems with promoter or regulatory sequences, ○ One produces new components necessary for cell growth. Telocentric – Centromere is located at the end of the chromosome, creating only one long arm. Thermal Cycler sticky ends. 2. Insertion partially differentiated. RFC (Replication Factor C) is a ring-applying protein consisting of five different subunits. It opens the A device used to achieve different temperatures and durations for each stage, as well as to control the Juxtacrine: Requires direct contact between cells via gap junctions, allowing the transfer of Nuclear Matrix Selecting which mRNA will be exported into the cytoplasm A carbon atom contains 6 protons and 6 neutrons, surrounded by two electron shells. The inner shell or even alternative splicing. ○ The other ensures these components are correctly positioned and properly divided. Telomeres ○ The desired gene sample can be obtained from a PCR sample or purchased as a synthetic PCNA trimer using ATP, introduces DNA into the ring, and then closes itself. For the leading strand, this Stem Cell Classification molecules. A signaling molecule on one cell membrane connects to a receptor on another cell. happens once, but for the lagging strand, it must happen multiple times due to Okazaki fragments. A network of fibers inside the nucleus involved in: Regulating the degradation of mRNA has 2 electrons, and the outer shell has 4 electrons. Membrane Proteins Base Modifications The cycle is controlled primarily through cyclic activation and inactivation of key proteins, mainly DNA section at the end of chromosomes. Protected by protein complexes that form a D and T loop. They number of cycles in the PCR process. gene sample. Stem cells are divided based on their potential for differentiation and their source of origin. Specialized receptors help receive, transform, or transmit information. Regulation of DNA replication and gene expression. Selecting mRNA for translation by ribosomes The outer shell allows for easy bonding, especially with other carbon atoms, leading to the creation of via phosphorylation and dephosphorylation. do not encode any genes and protect the cell during division. ○ The gene sample must be prepared using restriction enzymes to ensure the fragments have Different types of errors that happen. They are also classified based on their potency: Paracrine: Works by releasing molecules into the extracellular fluid to target nearby cells. DNA Polymerase Transcription and maturation of pre-RNA. Regulating the rate of protein degradation chains, branches, and ring structures. Membrane proteins are categorized based on how they bind to the lipid bilayer. Base Tautomerization Karyotype PCR Cycle complementary sticky ends. Totipotent / Omnipotent (full potential) Autocrine: A cell targets itself by releasing molecules into the intracellular fluid, which then bind Characteristics: Transport of ribosomes into the cytoplasm. Expression is mainly done by transcription and translation. The transcription machinery includes RNA Organic Components Integral Membrane Proteins When nitrogenous bases get a tautomeric form, meaning they are isomers with a different proton Mitosis Complete set of chromosomes in a somatic cell. PCR consists of three main stages: 3. Isolation ○ Can turn into all types of cells that create an organism, including sex cells. to its own receptors. polymerase and transcription factors that bind to gene promoters. The transcription process can be ○ Before combining the vector (plasmid backbone) and the gene sample (insert), the mixture There are four families of small organic molecules: saccharides, fatty acids, amino acids, and Embedded within the membrane, reinforced by the lipid tail by connecting to the hydrophobic part of position or double bond. Characteristic of all individuals of the same species, same sex, and good health. They can go through the ○ Can also turn into extra-embryonic structures like the fetal membrane or placenta. Communication can also be distant, such as: Requires a DNA template. Nucleolus turned on and off. nucleotides. These are usually found in the cytosol. the amino acid. The hydrophilic side of amino acids points inward, allowing polar molecules to pass Mitosis is essential for cell division, requiring both replicated DNA and duplicated centrosomes. same aberrations. Karyotypes can distinguish autosomes (same chromosomes between sexes) or 1. Denaturation must be purified to remove restriction enzymes and any residual fragments. Endocrine communication: Hormones travel through the bloodstream to stimulate target cells. Can only read in the 5' to 3' direction. Examples: Centrosomes help form the mitotic spindle, which assists in pulling apart the nucleus. ○ Includes the zygote and cells created from fertilization, as well as blastula cells (clusters of Mainly composed of RNA and proteins. Types of Expression Regulation Carbohydrates through. Time: 30 seconds – 5 minutes 4. Assembly Needs a primer to start replication. Ketone into enol allosomes (heterosomes). cells). Neuronal (synaptic) communication: The nervous system uses electrical signals within neurons, Occupies 25% of the nuclear volume during interphase. There are two classes of regulatory sequences: Carbohydrates consist of saccharides containing C, H, and O atoms. They include monosaccharides, Monotopic: Attached to one side of the membrane. Stages of Mitosis Temperature: 92–96°C ○ The sticky ends of the vector and insert allow them to bind together. Pluripotent (multi-potential) which convert to chemical signals at synapses. This is especially important for long-distance This protein operates in two modes: Disappears during prophase and is reconstructed in telophase. 1. Cis-type sequences occur on the same chromosome as the gene being regulated. disaccharides, and polysaccharides. The longer the chain, the less soluble it becomes. Transmembrane: Spans the entire lipid bilayer. Amine into imine 1. Interphase Karyogram Hydrogen bonds between the DNA strands break, making each strand available for reading. ○ Ligase is used to seal the structure, creating recombinant DNA. signaling. The chemicals used are called neurocrines and can be divided into: 1. Polymerization: Synthesizes new DNA strands. These isomers can form nontraditional base pairings, leading to mutations. Arranges the chromosomes in homologous pairs (from mother and father). The order is based on their The goal is to denature the genomic DNA. ○ Can turn into all cells except sex cells or extra-embryonic structures. 2. Trans-type sequences occur on a different chromosome than the gene being regulated. Carbohydrates serve as energy sources, storage (as starch or glycogen), and structural components Polytopic: Crosses the membrane multiple times. ○ The cell increases in size, replicates its DNA, and duplicates its centrosome. ○ The mixture may contain by-products such as incorrectly assembled or undigested plasmids. ○ Form the blastula that develops in the first week of the embryo. ○ Neurotransmitters: Have a fast effect by diffusing across the synaptic cleft. 2. Editing for proofreading: If an incorrect nucleotide is introduced, the enzyme changes shape, Nuclear Chromatin Cis Regulatory Sequences (such as cellulose, ribose) or protein modifiers. Non-Penetrating Integral Membrane Proteins Oxidative Deamination 2. Prophase size and location of centromeres. Strings and colors are used for recognition. 2. Annealing (Primer Attachment) 5. Transformation ○ Neurohormones: Have a slower effect as they diffuse into the bloodstream. removes the incorrect nucleotide, and then resumes polymerization. Short-range cis-regulatory sequences include promoters, enhancers, and silencers. An exchange of an amino (-NH₂) group for an oxygen, changing bases like: ○ The blastula creates three germ layers that will develop into every tissue. The form of chromatin during interphase. Fatty Acids Placement according to the cell membrane: ○ Chromosomes condense into two closely associated sister chromatids. Time: 15 seconds – 1 minute ○ The recombinant plasmid is inserted into a bacterium, such as Escherichia coli, allowing the Multipotent (few potentials) Examples of Signaling Molecules Polymerase α / Primase Composed of DNA, histone proteins, non-histone proteins, and ribonucleic acids with other ions. Long-range cis-regulatory sequences can act from distances of over thousands of base pairs, regardless Fatty acids are chains of carbon atoms connected to a carboxyl group (acid). Shorter chains tend to be Outer monolayer Adenine to hypoxanthine ○ The mitotic spindle begins to form as centrosomes move apart. Central Dogma Temperature: ~55°C (varies) plasmid to replicate and produce a sufficient quantity. Primase acts as the starting point by synthesizing a short RNA nucleotide sequence. Then, DNA of their position or orientation relative to the promoter. Guanine to xanthine 3. Prometaphase DNA replication – Making an exact copy of DNA. ○ Can turn into all cell types within their germ layer: DNA is originally 2 meters long and becomes 10,000 times shorter during metaphase due to more fluid. Saturated fatty acids only have single bonds, while unsaturated fatty acids have double Inner monolayer Temperature is lowered so that primers can form hydrogen bonds at designated spots on the DNA 6. Selection of Functional Bacteria Signal Molecule Origin Type of Molecule Actions Polymerase α (alpha) adds 20-30 nucleotides to the primer. Regulatory Sequences The regulatory sequences don’t work on their own but need to be activated by Cytosine to uracil ○ The nuclear envelope starts breaking down. § Ectoderm – Sensory epithelium, nervous system histone and non-histone proteins. bonds. Internal membrane between the two monolayers Transcription – Produces a single-stranded pre-mRNA. strands. ○ Antibiotics are used to eliminate non-functional or undesired bacteria, ensuring only those Hormones Polymerase δ (delta) and Polymerase ε (epsilon) focus on different parts of replication: transcription regulatory proteins, which can either activate gene transcription or repress it to inhibit Lipids These changes lead to different pairings and mutations (except guanine to xanthine). ○ Chromosomes attach to the mitotic spindle via kinetochores. Translation – Process of translating the mRNA to create a protein. carrying the recombinant plasmid survive. § Endoderm – Respiratory system, pancreas, liver There is a forward primer and a reverse primer that attach to opposite sides of the DNA strands. Delta prefers the lagging strand, creating Okazaki fragments. Chromatin Types transcription. Lipids are fatty acids with an ester group and are connected to alcohols, making them nonpolar and Peripheral Membrane Proteins 8-oxoguanine is an oxidized form of guanine and will bind to adenine, forming a mutation. 4. Metaphase Reverse transcription – Reading the mRNA to create DNA. Too low a temperature causes non-specific primer binding. 7. Verification § Mesoderm – Dermis, skeletal and cardiac muscle Epinephrine Adrenal gland Derivative of amino Increases heart rate, blood pressure, and 1. Euchromatin Connected on both sides of the membrane via ionic bonds, hydrogen bonds, or Van der Waals forces. Models for Action at a Distance Activator (repressor) proteins bind to enhancer/silencer sequences, Unipotent (one potential) (Adrenaline) acid (Tyrosine) metabolism (fight-or-flight response) Epsilon prefers the leading strand, synthesizing it continuously. ○ Loosely packed, genetically active, and lightly stained. insoluble in water, such as glycerol. Depurination and Depyrimidination ○ Chromosomes align at the equator of the spindle. The temperature can vary depending on the number of nucleotides used. More GC bonds require ○ DNA sequencing and PCR can be used to verify the plasmid’s structure and confirm ○ Can only differentiate into one specialized cell type. Both read from 5' to 3' and have exonuclease activity in the 3' to 5' direction for proofreading. ○ Accounts for 92% of the genome during interphase. which are far from the gene promoter. A loop is formed so that the enhancer/silencer comes into Simple lipids inclu