Biology Notes PDF

Soma means body so somatic is any cell in our body, inner side of our mouth and our stomach Each daughter cell is identical All organisms are composed of one or more cells and the life processes Every cell has a plasma membrane (Eukaryotic Cells and prokaryotic cells...

Soma means body so somatic is any cell in our body, inner side of our mouth and our stomach Each daughter cell is identical All organisms are composed of one or more cells and the life processes Every cell has a plasma membrane (Eukaryotic Cells and prokaryotic cells) Regulates the homeostasis of the cell and other cells The cell had genetic information, DNA or RNA, eukaryotes have a nuclear membrane surrounding a nucleus Metabolism: every single cell, breakdown of molecules so energy can be harvested, transforming energy into other kinds of energy and ATP is synthesized Are viruses living things? They need a host to reproduce Obligated parasites requires a host to complete life cycles and energy or food but they have the ability to transform that energy and metabolize similar to humans Cell membrane Phospholipid bilayer (hydrophilic heads and hydrophobic tails- made up of mostly fatty acids) Protein channels Peripheral proteins Integral proteins Cholesterol ….. Only present in animal cells Glycoprotein Glycoplipid Filaments of the cytoskeleton There dynamics and fluidity The structure and length of the tails are important The fluid plasma membrane is integral There are linear and no double bond Saturated fatty acids versus unsaturated Viscous has less space and less mobility due to lack of presence of double bonds more saturated where as fluid has more space and a double bond Sterol molecules aid in the fluidity of the membrane The amphiphilic structure of the membrane shows how to tightly pack the phospholipid layers Fluidity of fats determined by temperature example butter when cold versus when hot Fluidity important in our cell communication with stereo molecules working as buffers Transporter membrane proteins help transport in and out of the cell Enzyme protein needs an enzyme to transport a substrate Cell surface receptor needs a ligand in order to signal the cell to make a cellular response Cell surface identity marker which is a what is trying to get access to the cell membrane Transmembrane span the entire molecule Lateral movements occur 10^7 times per sec but a flip flop is very rare Fluid mosaic model has molecules that move around Some molecules move freely in and out of the semipermeable membrane by passive transport From high to low concentrations no energy or ATP is needed Simple diffusion versus facilitated diffusion or active transport Aquaporins with water molecules moving through membrane bilayer Semipermeable membrane against the gradient is active transport (low to high) Protons are pumped across by active transport then a proton pump generates an electrochemical gradient with higher concentration of protons with lower concentration of protons outside the cell Antiporter uses the proton electrochemical gradient to move a different molecule outside of its cell against its concentration gradient Uniport only moves one molecule at a time while the symport moves two molecules ata time and the antiport can move multiple molecules at a time Secondary active transport symporter uses concentration gradient to take glucose out of the cell Simple diffusion and facilitated diffusion Osmosis focuses more on the solvent and the solute does not change rather the concentration Outside of the cell is less concentrated and water moves in it is hypotonic Same concentration on outside and inside makes it isotonic Inside the cell is less concentrated and water\ moves out so it is hypertonic Prokaryote vs eukaryote dependent on the presence of a nucleus Prokaryotes are bacteria and archaea Prokaryotes have a flagella and a pili, free ribosomes and a nucleotide Cytoplasm is called the space within a cell and Cytosol is mainly water where cellular structures float Endomembrane system Eukaryotes have membrane bound organelles, complex dna, aerobic and divide by mitosis and meiosis Typically are much larger and both uni and multicellular Prokaryotes are usually unicellular Eukaryotic cell have mitochondria and chloroplasts that harness energy through sunlight and breakdown of chemical compound Double membrane in mitochondria and chloroplasts Organism with better fitness live longer and survive Both are semiautonomous and are able to synthesize some proteins and grow and multiply through fission like prokaryotes Have circular dna similar to prokaryotes How do elements in the plasma membrane modulate? - Process of development is coordinated by cell signaling that then modulated by gene expression - Fertilization, development and eventually living organism - Stem cell has a job to divide and grow more cells - Differentiate cells into specialized functions - Where to find stem cells and why are they important? - ( stem cells can undergo cell division and can become many types of cells) - ( differentiate cells cant undergo cell division and differentiate any further, perform specific functions like muscle cells generate force, neurons that send signals and bone cells that defy gravity) - Mscs can differentiate into other types of cells like fat, bones, muscle, tendon and ligament, cartilage and skin - External signals tell the cell to differentiate and neighboring cells and other parts of the cell like the membrane - Cells receive an array of signals that tell them where to go and what to do  - Apoptosis which is a cell programmed death - Transcription factors modulate gene expression and cell communication - Cell communication, the signaling cell releases signal molecules and responding cell has receptor proteins that bind to signaling molecule - It goes through a signal transduction pathway - Extracellular matrix - Adjacent cells Mapk or ErK pathway - Becomes activated when cells undergo cell division set the signal for the cell to become ctivated Raf activates Mek or kinase - Nactivated and genes respond to that activation - Uncontrolled cell division that lead to cancer and a protoctagene - Aecessary for the pathway to be able to signal - Translation that produces protein that promotes cell division - Egf is a pathway that regulates cell division and is mutant in many cancers Receptor always active can lead to cancer and is a common site of mutation ‘ Ras protein lot the, no gtpase activity Raf there is a kinase and phosphorylation and its phosphorylated everyone Kr signal termination Egf receptor activates ras and the map kinase pathway Gtp hydrolysis when the cell activates a set Decrease the gtpase activity of the ras protein Increase the rate of exchange of bound gdp for gtp Greater amounts of active gtp and ras complex with signaling staying on Signal comes from growth factor Endocytosis Our receptor is the endocytosis A molecule Insulin signaling pathway, allows for the york of glucose Receptor activation, response on diagram Signaling ean be terminated by the dephosphorylation of kinases through the action of phosphatases Receptor is endocytosed after binding ligand and cell only respond to signal once Inhibitors can block receptors or other molecules from binding with ligands and 2nd messengers activated Proteins that no longer need to be degraded in the proteasome by a process called ubiquitin mediated proteolysis Kinase and phosphatase regulate protein activity Feedback loops- a downstream component in a linear pathway regulates an earlier component or event in the pathway Positive or negative Positive - same product, keep the signaling on and always activated Negative feedback signaling and response signal travels through the kinases and then to the nucleus, tk2 and tfa the pathway has stopped The signal and everything starts all over again, goes back to the first cell Luciferin binds to the receptor and activate a signaling pathway Produce a protein that causes the flashing, it is gonna flash, Signaling stops the flash turns off but signal is still here but it will signal again to turn on and turn Eventually at night the ligand will dissociated and no more light happens Control of cell cycle, mitosis and meiosis eukaryotes , mitosis is not something that happens too often in the majority of cells, constantly renewing the cells, tissues other tissues don't happen Cells are usually in interphase which is g1, g0 and s phase and g2 phase GPCR PKR ​ G-protein: family of proteins ​ Long term responses with GTPase activity ​ Changes in gene expression ​ Short-term responses, easily reversible ​ Activation of an already existing protein Both GPCR and PKR  ​ Rely on amplification of signal during transduction by kinase cascades (PKR) or massive production of secondary messengers (like cAMP - cyclic AMP) ​ Experience configurational changes when activated ​ Mitogen Activated Protein Kinase (MAPK) pathway ​ Also known as ERK pathway ​ When cells undergo cell division ​ Checkpoint in cell cycle sends signal for MAPK activation → activates genes ​ For cell renewal ​ Overuse of MAPK pathway leads to cancer ​ Raf, MEK → oncogenes. If mutated, can become oncogenic MAPK steps ​ Ligand is growth factor (stimulates growth) ​ When ligand meets receptor, receptor will dimerize ​ The receptor is an enzyme itself. Aactive receptor activates Grb2 ​ Active Grb2 activates Ras, a G-protein → GDP on Ras displaced, GTP binds ​ Active Ras activates Raf, a kinase ​ Via change in configuration in Raf ​ Next is a kinase cascade: Raf → MEK → MAPK → MAPK goes into nucleus and activates transcription factor → gene products (protein) promote cell division ​ Epidermal Growth Factor (EGF) pathway ​ EGF receptor activates Ras and the MAP Kinase pathway ​ EGF and MAPK stimulate cell division ​ Kinase and phosphatase do opposite things ​ Kinase adds a phosphate group ​ Phosphatase removes a phosphate group ​ Cell Cycle is regulated by growth factors ​ Growth factor: tells cell that cell division is necessary (“we need more cells here”) Other ways pathways can be terminated: ​ Receptor endocytosis ​ Receptor inhibition ​ Ubiquitin-mediated proteolysis ​ Feedback loops ​ Receptor endocytosis ​ Steps: ​ Plasma membrane folds inward (invaginates), forms a cavity full of extracellular fluid ​ Plasma membrane folds back on itself until ends of in-folded membrane meet  ​ Vesicle pinched off from the membrane as the ends of the infolded membrane fuse together. Internalized vesicle is processed by the cell Ub-Mediated Proteolysis ​ Ubiquitin (Ub): small protein that gets attached to the disposable protein. Ubiquitin targets a protein for proteolysis ​ Degradation at proteosome: cellular “toilet” and site of protein degradation (after Ub tagging) ​ Signaling can be terminated by several means ​ Deactivation of kinases through the action of phosphatases ​ Receptor is endocytosed after binding ligand-> cell only responds to that signal once ​ Inhibitors can block receptors or other molecules from binding with ligands or 2nd messengers activating ​ Kinase and phosphatase activity regulate protein function, if there are kinases there are also phosphatases ​ Make sure to understand roles of kinases, phosphatases, and the role of ubiquitin ​ If proteins are not needed but may be used later, they can be turned off by phosphatase ​ If those proteins are no longer needed they can be ubiquitinated ​ A downstream component in a linear pathway regulates an earlier component or event in the pathway ​ There are positive and negative feedback loops ​ Positive feedback loops, same product keeps activating the signaling ​ Negative feedback loops, signaling response terminates signaling ​ Luciferin in fireflies is an example of negative feedback loops (and an oscillation pathway), when it is produced the firefly flashes, but a phosphatase is also produced causing the signaling to stop and the firefly to “turn off” Control of Cell Cycle, Mitosis and Meiosis: ​ Cancer is a way in which the cell cycle becomes unregulated, leading to uncontrolled cell division ​ Learning objectives: ​ Describe mitosis and meiosis and know the kind of biological processes with which they are associated ​ Compare and contrast mitosis and meiosis ​ Describe how cell division is regulates ​ Explain role of cyclins and CDKs in progression of the cell cycle ​ Evaluate the importance of cell cycle checkpoints for the normal cycle of cell division, and recognize consequences of mutations that affect these checkpoints ​ Know how different failures in cell cycle regulation may lead to cancer  ​ Useful vocab: ​ Chromosome ​ Gene ​ Locus ​ Alleles ​ Sister Chromatids ​ Homologous Chromosomes ​ Ploidy, Haploid and Diploid ​ Chiasmata ​ Crossing Over ​ Recombination ​ Centromere ​ Kinetochore ​ Centrosome ​ Centrioles ​ Microtubules ​ Spindle Fibers ​ Every cell in your body that can divide goes through the cell cycle ​ Interphase is the longest phase of cell cycle ​ Interphase contains four phases in itself, G1 phase, S phase, G2 phase, and G0 phase ​ G0 is essentially a stage in which the cycle does not actively divide, or is terminally differentiated ​ This means the cell still metabolizes and lives, but it does not divide (neurons and red blood cells) ​ In some cases cells may exit G0 to divide ​ In diagrams, G0 is typically kept outside the cycle (mitosis) ​ During Interphase, the chromatin is much like a tangle, or bowl of spaghetti in the nucleus ​ For cell division, this spaghetti must condense, forming the structure on the right in the diagram above ​ Humans have 23 pair of chromosomes ​ 22 of these pairs are somatic, one pair is known as the sex chromosome ​ Each pair is homologous ​ Haploid number is the number of unique chromosomes (23 in humans) ​ Diploid number us the number of copies of unique chromosomes (for example, there are two copies of each chromosome in the figure above, so the diploid number is 2) Centromeres/ Chromatids ​ Each (arm) of a chromosome is a chromatid ​ Sister chromatids are identical Kinetochores ​ Microtubules attach to chromosomes, specifically on kinetochores ​ The most remarkable difference between prokaryotes and eukaryotes is that prokaryotes lack a true nucleus and organelles ​ Though eukaryotes are larger in size than prokaryotes, size itself is not a good distinction between these two cell types Mitochondria ​ Harness energy from chemical compounds (breakdown of sugar through cellular respiration) Chloroplasts: ​ Harness energy from sunlight (photosynthesis) and transforms energy into chemical energy ​ Special organelles (mitochondria and chloroplasts) have their own circular DNA, have a double membrane, have ribosomes, and can synthesize some of their own DNA, can divide independently of the cell ​ Resemblance with certain bacteria lead scientist Lynn Margulois to propose the Endosymbiosis Theory The Evolution of Organelles ​ Video available on lecture slides Endosymbiosis Theory Evidence ​ Mitochondria and chloroplasts are ​ Semi-atonomous, grow and multiply independently from the cell by fission, like prokaryotes ​ Have a double membrane and their own circular DNA and ribosomes and synthesizes some of their proteins ​ They resemble and have similar DNA to certain type of bacteria ​ As development advances, cells become differentiated/specialized (become skin cells, eye cells, etc…) and unable to express certain genes What is a Stem Cell? ​ A stem cell is a cell type whose “job” is to decide to make more cells or to differentiate into cells with specialized functions ​ Why are stem cells relevant for cell function? ​ Where do you find stem cells? ​ Stem cells and differentiated cells have exactly the same genes but are expressed differently (genes can be on/off for each cell type) ​ Stem cells and differentiated cells are two extremes (stem cell has ability to differentiate into any type of cell in the body and can express all genes, differentiated cells are specialized, having a specific structure and function within the body, some genes are off) ​ Potency → how many genes can be expressed ​ Starting with one genome → cell continuous to divide and differentiate (some genes turn off) but genome is still the same ​ Genome is still the same but gene expression changes, genetic code (instructions) still the same ​ External signals - either from neighboring cells or from other parts of the organism ​ Cells receive signals that tell them what to do, behave, and, where to go  ​ Cell membrane is amphipathic ​ Fluidity is vital for cell communication ​ Fluidity can be altered by temperature - Changes in the fatty acid chain that can fix fluidity: length of chain, adding double bonds, adding sterol molecules  ​ At high temperatures, membrane becomes more fluid so more saturated fatty acids is required to balance the fluidity ​ At low temperatures, membrane becomes less fluid, so more unsaturated fatty acids is required to balance the fluidity ​ Sterol molecules acts as a buffer to increase/decrease fluidity ​ Animal: Cholesterol ​ Plant: Sitosterol ​ Bacteria: Hopanoids Membrane proteins ​ Integral membrane proteins span the entire membrane ​ Peripheral membrane proteins attach to the external or internal side of the membrane Fluid Mosaic Model ​ Membrane is made up of a variety of proteins that have different functions and play a part in homeostasis of a cell Small and nonpolar molecules are easily able to diffuse through the membrane. The rest of the molecules in the answer choices require a transporter to pass through the membrane. Small and nonpolar molecules are easily able to diffuse through the membrane. The rest of the molecules in the answer choices require a transporter to pass through the membrane. * Water can pass through the membrane but with specialized transporters called aquaporins. Since liposomes have similar characteristics to the plasma membrane, it can fuse with the membrane and deliver the drug to the interior of a cell. Types of transport ​ Passive Transport - doesn’t require ATP, goes down its concentration gradient (high to low concentration) ​ Simple diffusion - doesn’t require carriers and channels ​ Facilitated diffusion - requires carriers and channels ​ Aquaporins - transporters designated for water only, doesn’t require ATP ​ Active Transport - requires ATP, goes against its concentration gradient (low to high concentration) ​ Primary active transport - directly uses ATP Ex. Na-K pump Using ATP, the conformation of the carrier changes and pushes Na+ out to the exterior of the cell. -Na-K pump is an antiporter ​ Secondary active transport - indirectly uses ATP ​ The first molecule moves through the carrier with the help of ATP and establishes a proton or electrochemical gradient ​ Gradients by themselves have potential energy  ​ The second molecule can use those gradients and can go out of the cell either against or towards the concentration gradient ​ The second molecule can move in two different ways: ​ Symporter: Both molecules move in the same direction. Second molecule moves against its concentration gradient. ​ Antiporter: Both molecules move in opposite directions. Second molecule can move either with or against its concentration gradient. Cell Theory ​ All organisms are composed of cells ​ Cells are the smallest living things ​ Characteristics of living cells: ​ Plasma membrane ​ Defines cell ​ Separates from external environment ​ Compartmentalization (only in Eukaryotes) ​ Communication ​ Genetic information ​ Instructions to grow, function, and reproduce ​ Metabolism ​ Obtain and transform energy from environment to produce ATP ​ Are viruses considered living organisms? ​ NO: viruses do not metabolize/break down energy on their own ​ Since they are not alive, viruses do not die ​ Viruses have DNA or RNA, and a protein capsid. Cell Structure ​ Cell membrane is composed of phospholipids ​ Phospholipids contain hydrophobic and hydrophilic ​ Hydrophobic: “hates” water ​ Hydrophilic: “loves” water ​ Amphipathic: both hydrophilic and hydrophobic ​ Phospholipids are amphipathic ​ In water, phospholipids spontaneously arrange themselves: ​ Hydrophilic head (polar) of the phospholipid interacts with the water ​ Hydrophobic tail (nonpolar) of the phospholipid arranges itself facing each other avoiding the water ​ Behavior of phospholipids in water: ​ Micelle: if hydrophilic is more prominent than hydrophobic ​ Structure of plasma membrane may change based on type of bonds in the phospholipid ​ Unsaturated = contains a double bond ​ Saturated = no double bonds ​ Unsaturated hydrocarbons can cause more fluidity in membrane because: ​ More double bonds = more “kinks” in the hydrocarbon = more space between hydrocarbons ​ Cholesterol - only found in animal cells ​ Plants have sitosterol ​ Membrane fluidity can be affected by temperature ​ If temp is hot, the membrane might be kept more rigid to counteract the temperature ​ If temp is too cold, the membrane fluidity may increase