Physics Of Life On Scale Of Cell.pdf

Central dogma: - The central dogma of Watson isn’t used while Cricks is. - Crick’s central dogma helps understand the transfer of information. He states that there are 3 major bipolares that transfer information: DNA, RNA and proteins. There are three general transfers, two special transfers and fo...

Central dogma: - The central dogma of Watson isn’t used while Cricks is. - Crick’s central dogma helps understand the transfer of information. He states that there are 3 major bipolares that transfer information: DNA, RNA and proteins. There are three general transfers, two special transfers and four unknown transfers. - Three general transfers are known to occur normally in most cells: - DNA replication - mRNA production > transcription - protein synthesis from mRNA > translation - Two special transfers known to occur in specific conditions like some viruses or laboratory) - RNA replication from RNA - DNA synthesized from RNA > reverse transcriptase - Four unknown cases that is believed to not occur - Protein synthesized directly from DNA - Protein replication from protein - synthesis of RNA using primary structure of protein - synthesis of DNA using primary structure of protein - Replication is necessary for cell division. It occurs simultaneously with transcription. - Transcription converts DNA into mRNA. Pre-mRNA contains introns and exons, intron segments will be spliced out and after modifications, will become mRNA and migrate from the nucleus - Upon leaving the nucleus, mRNA will find the ribosome and transcribe itself to protein. DNA organization and packaging: - First level of folding: DNA around histones - DNA is a double helix that wraps around 8 histone proteins. DNA is negatively charged due to the negatively charged phosphate groups of the backbone. His tones are positively charged due to the high basicity content of the protein. This electrical difference causes histones and DNA to be attracted to each other. - there are 5 major histones: H2A, H2B, H3, H4 and H1. The first four histones are four core histones (H2A, H2B, H3, H4). It’s wrapped around a H2A/H2B dimer, two H3s and two H4s thus form an octomer where DNA wraps around 1.7 times. The DNA wrapped around a histone is called a nucleosome. The H1 binds to DNA at the edge of each nucleosome, keeping DNA and histone complex in place and acts as a stabilizer. - modifications to the histone occur post-translationally and affect gene expression and regulation - Second level folding: Nucleosome coiling - The binding of H1 stabilizes the nucleosome and the nucleosome warps around in a helical fashion called a solenoid. The solenoid further supercoils to make up the chromatin fiber by stacking on top of each other. - Final level of folding occurs when the chromatin fibers condense further - Chromatin fibers that form long loops on a scaffold can become even more compact and attach to non-histone proteins in the nucleus creating metaphase chromosome. Cell Cycle: - The cell cycle consists of Interphase and mitosis, which is Prophase, Metaphase, Anaphase and Telophase. It can also be divided into “action” phases, s and m phase, and “gap” phases, G0, 1 and 2. - Interphase is the state a cell is in in between two successive mitosis. Interphase consists of checkpoints before entering the mitotic cell cycle. These checkpoints are important because they control the accuracy of DNA synthesis and the assembly of microtubules for chromosome movement. If genome is damaged, cell halt progression at these checkpoints or undergo programmed cell death, apoptosis. It’s goal is to prevent mutant cells from replicating and causing cancer. - G0: - when it’s not necessary for cells to divide, they stay in the G0 phase indefinitely. Ex: rbcs and neurons - growth factors and mitogens allow for cell to progress to G1 phase in multicellular organisms - G1: - preparing for S phase - cyclins + CDKS allow for gene transcription, translation and protein production - increase in cell size, organelle formation, energy and protein production - there is one diploid copy of genome, one chromosome - S: [DNA replication] - programmed DNA synthesis leading to the replication of each chromosome to form sister chromatids. Sister chromatids are held together by centromere. This region of DNA is associated with a number of proteins to form kinetochore which is a place that microtubules can attach and form mitotic spindles and control chromosome movement. - Telomeres are the end part of the chromosomes that are specialized repetitive DNA sequences that ensure the integrity of chromosome during cell division and are replicated by telomerases. - Replication of DNA occurs at multiple sites called origins of DNA replication asynchronously. Each chromosome has their own characteristic of replication. - G2: - endonuclease cleave off mismatched DNA - increase in cell size and energy and protein production - Chromosomes only form when cells are dividing - M phase =>Mitosis - starts after the cell proceeds through he G2 checkpoint. The Mediation of Cell Cycle: - Cell cycle is controlled by cycling, CDKs and tumor suppressors. - cyclins: proteins that bind to cyclin dependent kinases, activating them - cyclin dependent kinases: enzymes that are kinases, which phosphorylation proteins to activate or deactivate them. - tumor suppressors: - inhibiting cyclins can inhibit the cell cycle progression - ex: p53 is a tumor suppressor that indirectly regulates CDKs. p53 is a protein that can arrest the cell cycle if there is DNA damage - ex: cyclin D in the G1 phase binds to CDK4 and 6 leading to the phosphorylation of Rb and inactivating it. Rb is bound to the transcription factor E2F and the phosphorylation causes it to loosen it’s grip on E2F. This allows E2F to activate the transcription of cyclin E gene. Cyclin E binds to CDK2 and completely phosphorylates Rb causing E2F to unbound. Cyclin E also phosphorylates p27 kip1, which is an inhibitor of cyclin D, and tags it for degradation. Degradation of this protein promotes the expression of cyclin A as well as E2F promoting the transcription of A by removing the CCRE represor from the promoter. The cell enters the S phase. There is also a negative feedback loop since cyclin A phosphorylates E2F and deactivates it form removing represor molecule. - cyclin A activate 2 CDKs: 2 and 1. 2=> s phase. 1=> M phase. S phase => nucleus => DNA replication only occurs once per cell cycle => prevents excessive replication complexes - cyclin E initiates pre-replication inititation complex that is needed for DNA replication and forms at the origin of replication. Cyclin A+CDK2 complex replaces cyclin E and increases the replication complex terminated. Cyclin a+cdk1 complex aids in the activation and stabilization of Cyclin B+cdk1 complex. cyclin A-CDK1 complex induces mitotic exit. Cyclin B mitotic cyclin, maturation promoting factor, MPF. High concentration => enter M phase DNA Repair in Cell Cycle: - G1: - nucleotide excision repair: repairs the nucleotides - S: - mismatch repair: insertion, deletion, and mis-incorporation - base excision repair throughout cell cycle Cell Cycle Checkpoint: - G1: oversees cell growth and DNA damage - G2: has the cell replicated correctly, is it growing well - Metaphase: are the chromosomes lined up and attached to correctly - regulators are proteins that regulate the cell cycle. Positive regulators move the cell cycle forward while negative regulators keep it from progressing. - ex: positive- cyclin +CDK, negative: p53 - G1 inhibition: - inhibition of the cell cycle occurs when Rb, p107 or p130 binds to E2F transcription factors and prevent progression from G1 to S. If E2F is inhibited there is no cyclin E production which prevents the cell from progressing to S phase. - p53 will stimulate p21 which inhibits CDK, which stimulates Rb. - p53 and Rb are tumor suppressors and when inhibited, they cause tumors which may cause cancer - G1 stimulation: - GF bind to tyrosine kinases which stimulates the cell cycle to progress to S phase - Growth factor example: insulin, EPO, PDGF and EGF - if its not possible to repair DNA damage => apoptosis - G2 inhibition: - p53 stimulates checkpoint 1 and 2 which are also stimulated by ATM => prevent progression - G2 stimulate: - cyclin B +CDK1 phosphorylates transcription factors and stimulates entry into the mitotic phase Mitosis and Meiosis: - Mitosis is the replication of somatic cells while meiosis is the replication of germ cells - Mitosis has a constant chromosome number after replication while in meiosis that number decreases to half - In meiosis 2 there is no DNA synthesis Epigenetics: - Occurs in somatic cells - Epigenetics are modifications that alter the DNA activity’s without altering the nucleotide structure. They are reversible and can be caused by personal behaviors and environmental factors. - It occurs as gene expression, which genes are turned on and off - DNA methylation: - Methyl groups are added to cytosine of DNA. Inactive genes are methylated and active genes are demethylated. - The methyl groups are added by DNA methyltransfarases usually to C (CpG island) - promoter regions are not methylated - allows for the differentiation of genes by methylating certain genes to be inactivated and not expressed - DNA is demethylatd through Human TET, which adds a hydroxy group to methyl cytosine which can be reversed back to cytosine - cancer changes methylation and demethylation patterns. For example hyper-methylation of promoter region can cause a tumor suppressor gene to be not produced - numerous functions: DNA repair, DNA transcription/replication start, gene repression/activation, apoptosis, etc. - Histone modification: - If DNA is too tightly wrapped around histone, gene activation low, if loosely wrapped around, gene activation high. - Histones have a tail and a fold region. The tail is where modifications occur - Acetylation - lysine or arginine residues get acetylated- basic amino acids with positive charge - Acetyl group is added by histone acetyl transferase from acetyl CoA - DNA and histones are bound through electrostatic attraction of the positive NH of lysine in histones and the negative phosphate group on DNA. Acetylation of lysine replaces positive charge with negative causing electrostatic repulsion and the loosening of DNA from the histone. - Acetylation makes DNA more accesible to modifiers -> euchromatin have acetylated residues - Histone deacetylases remove acetyl groups - Phosphorylation - Methylation - Histone methyltransfarases add methyl groups to usually arginine and lysine - usually found in the heteróclito matin structure because it causes the tails of hitones to condense - Ubiquination - Sumoylation Embryo development: - When a sperm fertilizes an egg, a zygote is created. The zygote divides rapidly turning into a blastocytes. The blastocytes develop further and take on human characteristics and become an embryo. - differentiation occurs in the embryonic stages Cell Differentiation: - Cell differentiation occurs by modification of the genome to silence and activate genes. - Stem cells are undifferentiated cells that can differentiate and specialize to a certain cell types - Adults also have mesenchymal stem cells that have limited self-renewal and differentiation capabilities compared to embryonic stem cells Mechanical Stimuli on Biological processes: - Mechanobiology: a field that describes the mechanisms by which mechanical loads regulate biological processes. - Computational models are developed to propose and test rules that may govern the effects of mechanical loading on cells and tissues. - Functional stimuli: compression for the formation and maintenance of bone, tension for connective tissue and a combination of both for cartilage. - Ex: a surface has a distinct structure loaded on it called the domain. The stem cells reside outside the domain but disperse inside. Inside the domain cells undergo mitosis and proliferation and stem cells migrate within the domain (stem cell commitment). Then the cells differentiate depending on where they are. Cells where there is more pressure on the domain cause the formation of tougher bones. - Raux: cells are in constant competition for their own functional stimulus which determines tissue type - Pauwle: (he added stress and strain to the description) Proposed that cells feel mechanical stimuli as elongation and hydrostatic pressure. He suggested that elongation was a stimulus for connective tissue and hydrostatic pressure was stimulus for cartilage formation. Elongation is a result of tension, compression and shearing while hydrostatic pressure is for negative and positive pressure - Perren and Cordey: They proposed the mechanism for the cell specialization after fractures, called the interfragmentary strain theory. A tissue that ruptures under a certain strain level can’t be formed in a region that has a greater strain level. The cell that can resist the most strain is granulocytes, therefore after fractures, they are the first types of cells to inhibit the area. The garanulation tissue stiffens the mechanical environment and cartilage starts to form. When cartilage fully is present inside the gap they are ready for bone generation. - first granulation tissue forms, callus ossifies, modeling occurs then remodeling occurs. - Prendergast: Described how fluid can amplify cellular deformation and the relative velocity between phases as a stimulus for differentiation. He proposed that the mechanical stimuli (velocity and strain) could stimulate the replacement of one cell population by another. Stimuli important for constant adaptation of tissues. - Carter: Devleved deeper into Pauwels theory and suggested a specific combination of mechanical invariants and the different times of loading is the triggering factos that stimulates tissue differentiation. - Biphasic poroelastic constitutive model: mathematical equation that calculates the the solid stress and solid fluid - Diffusion coefficient is dependent on tissue phenotype Experimental Instruments used in single molecule imaging and manipulation techniques: - Single DNA imagine using Atomic Force Microscopy: - Detects nucleosome distribution in chromatin and dependence of higher order structure of chromatin - structural and conformational information on chromatin - Single DNA fluorescence imaging; - Direct information about the compaction of DNA and nucleosome formation dynamics - Means of single DNA manipulations and applications - glass fiber - atomic force microscope - optical tweezer - magnetic tweezer pS3 10730/20 why · central dogma revers mRNA all phases C 1: S : - > Transcriptrace DNA is How anymore ? used not dogma is central pre organises RTPCR DNA - cell in : syntrate mirosis synthase T Gzi pre mitotic ; M chronatin (in) - DNA prin packed ? is How ? mitotic & control sites ( - micosis, mitosis Csomatic) Gurm) when surn are chromosomes wont alls ↳ Wher meiosis => to 2nd mitosis in cell divide - no DNA synthesis ? chromosome