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BIOL 112 Course Notes 2013

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Biology (Sci)
BIOL 112
Joseph Dent

BIOL-112 Condensed Notes R. O’Loghlin Bonding  Covalent Bonds o When an atom has an orbital with only one electron in it, it becomes reactive, wanting to fill the space o Strongest bonds o Made up of 2 electrons, one from each atom o The electrons are shared between the two atoms, not always equally, but shared  Hydrogen Bond o Electrostatic interaction between partial negative charge of an atom and the partial positive charge of another atom o Both must be involved in polar covalent bonds o Only occurs between Hydrogen and Oxygen or Nitrogen, or (more rare) Carbon and Oxygen  Ionic Bond o Occur between elements on the far left and far right of the periodic table o Ionic bonds in biology aren’t as strong as the ones in chemistry due to the biological ones usually being individual bonds such as those in the interior of proteins in the absence of water  Polar molecules tend to be hydrophilic, and dissolve in water  Nonpolar molecules are hydrophobic, and are generally made up of c-c or c-h bonds  Hydrophobic interactions o Water forces nonpolar molecules together, because doing so minimizes their disruptive effects on the h-bonded water network o Fairly weak  Van der Waal’s interaction o Nonpolar molecules are also attracted to eachother via weak attractions caused by transient dipoles (temporary) o Strength increases with increasing molecular weight  In order of decreasing strength: o Covalent bond (50-110 kcal/mol) o H-bond and Ionic Bond (Both 3-7 kcal/mol) o Hydrophobic interaction (1-2 kcal/mol) o Van der Waals interaction (1 kcal/mol) Acids & Bases  Acids release/donate ions in solution o Strong acids completely disassociate in solution  Bases accept in solution, or you could say that they release o A strong base completely disassociates in solution  Buffers o Make the overall solution resistant to pH change o Can make a buffer out of a solution of a weak acid and its conjugate base, or a weak base and its conjugate acid o Law of Mass Action  The rate of any given chemical reaction is proportional to the concentration of the reactants Functional Groups  Carboxyl group o Carboxylic acids o –COOH (with double bond between C and one O) o Acetic Acid  Amino group o Amines o –NH2 o Methylamine  Hydroxyl group o Alcohols o –OH o Ethanol  Carbonyl Group o –CO o Aldehyde if the carbonyl group is at the end of the molecule  Acetaldehyde o Ketone if it is in the interior  Acetone o Phosphate group  Organic phosphates  -PO4  ATP o Sulfhydryl Group  Thiols  -SH  Mercaptoethanol Large Molecules  Macromolecules are made the same way in all living things, and are present in all organisms in roughly the same proportions  Proteins, nucleic acids, and lipids can form polymers of multiple molecules o Reaction is called polymerization o Condensation reaction releases a molecule of water for each bond formed o Depolymerisation involved hydrolysis, consuming a water molecules to break a bond  Isomers o Molecules that have the same chemical formula, but different atomic arrangements o Structural isomers  A group is attached to different carbon atoms o Optical Isomers  A group is attached in a different way to the same carbon atom  Optical isomers are non-superimposable mirror images of eachother  Occur whenever a carbon has four DIFFERENT atoms or groups attached to it  Sugars o Carbohydrates (sugars) act as energy storage and building blocks for other molecules o Serve a structural components o Monosaccharides  A single sugar such as glucose o Disaccharides  2 Sugars such as sucrose o Polysaccharides  Many sugars o General carbohydrate formula is CH2O o Glucose has two ring forms  Alpha and Beta glucose  Optical isomer caused by four different groups being bonded to carbons 2-5  DNA o Contains genetic information o Transcribed to RNA, which makes proteins o Nucleotides have additional functions as signalling molecules and energy transducers  Phosphate groups o Joined to the C5 hydroxyl of the ribose sugar  Nitrogenous Bases o Purines  Adenine  Guanine o Pyrimidines  Thymine  Cytosine  Uracil (only in RNA, replaces thymine) o A purine always pairs up with a pyrimidine (chargaff’s law) o Guanine-Cytosine bond is stronger than Adenine-Thymine due to having 3 binding sites rather than 2 o Base pairs are stabilized by hydrogen bonds  Nucleotides o Base connected to C1 of the Sugar o Phosphate connected to C5 o Phosphate group of a nucleotide binds to the 3-prime hydroxyl group of the next  DNA is antiparallel o One strand goes 3 prime to 5 prime, the other is opposite o Polymerization always happens 3 prime to 5 prime  RNA o Main function is to act as an intermediate between DNA and proteins o Often forms 3d structures o RNA evolved before cells did  Lipids o Insoluble in water o Aggregate away from water (Hydrophobic Interactions) o Attracted to each other by Van der Waal’s forces o Fats and oils are used for energy storage o Phospholipids used in cell membranes o Carotinoids used in capture of light energy in plants  Fatty Acids o Long carbon chain with a lone hydroxyl at the end o Saturated fatty acids carry the maximum amount of hydrogen atoms  Straight, form part of animal fats o Unsaturated fatty acids have at least one carbon-carbon double bond  Causes kinks that prevent easy packing  Caused by a cis-configuration around the double bond  Part of plant oils  Liquid at rom temp  Triglycerides o 3 fatty acids bound to a glycerol molecule via ester linkages  Phospholipids o Have two hydrophobic fatty acid tails o One hydrophilic head o All attached to a glycerol molecule o Self-assemble into a bilayer due to H-bonding and hydrophobic interactions o Hydrophobic tails stay inside the layer, the hydrophilic heads being on the outside o In the winter, certain fish and plants increase the number of unsaturated fatty acids in their membranes to keep them fluid Proteins  Proteins are polymers of amino acids  Range in size from a few amino acids to thousands o Titin, the largest, is 33000 amino acids in length  Folding is crucial to the function of proteins o Influenced by the sequence of amino acids  The alpha carbon in the amino acid is attached to an amino group, carboxyl group, and R group o R-group determines identity of the amino acid  Peptide linkages are the covalent bonds between two amino acids  Every protein starts with an amino group (NH2), and ends with a carboxyl group (COOH)  The precise sequence of amino acids in a protein is the Primary Structure  Amino acids can be positively charged, neutral, or negatively charged depending on the R-group o Some are polar, but do not carry a charge, such as Serine  These are hydrophilic  Occur with OH and carbonyl R-groups o Some special cases  Cysteine has an SH R-group  Proline forms a ring between the alpha-carbon and the amino group  The amine nitrogen is bound to two alkyl groups  A protein’s secondary structure consists of regular repeated patterns in different regions of the polypeptide chain o Alpha-helix  H-bonds formed by the backbone are parallel to the axis of the helix  Between amino and carboxyl groups  Has a rigid structure  Can insert into plasma membranes  ONLY if the helix ONLY contains hydrophobic amino acid side chains o Coiled coils  Two alpha helices wrapped around each other  Small stripe of hydrophobic amino acids occurring every 4 position  One complete turn is 3.6 amino acids  Fibrous structural proteins consist mainly of alpha helices arranged in coiled coils  Keratin o Beta-pleated sheet  Makes flat plates  R-groups project up and down from the sheet  The strands of the beta sheet can run in parallel or antiparallel direction  Can even come from different polypeptides  Occasionally can be inserted into the plasma membrane (Rare)  Forms a barrel shaped object with R-groups pointing outside  Proline o Alpha helix and Beta sheet breaker  Appears at the end o Doesn’t really fit in either structure because it makes a kink in the peptide  Also because the N carries no H for bonding  Tertiary structure o Tells how the short stretches of alpha helices and beta sheets fold together to make a protein o Determined by:  Location of disulphide bridges  Covalent bond between two cysteines  Location of secondary structure  Ionic interaction between positive and negative charges in the protein  Hydrophobic aggregation of R groups stabilized by Van der Waals forces  Most important factor of tertiary structure  Tries to move interior away from water  Loss of a protein’s normal three-dimensional structure and function is called denaturation o Caused by changes in temperature or pH o Proteins will refold in a test tube  Shows that proteins automatically fold  All folding info is contained within the primary sequence o Denatured proteins in cells do not typically refold because of other partially folded proteins  Chaperones are specialized proteins that keep other proteins sequestered, providing optimal folding conditions Membranes  Phospholipids self-assemble into the lipid bilayer  Cholesterol o Hydrophobic, inserts into membranes causing them to become stiffer  Caused by the rigid ring structure  It is energetically favorable for bilayers to seal/form an enclosed space  Lipid bilayer is fluid, so phospholipids can move around inside the membrane o Lateral diffusion is most common o Flexion o Rotation  Phospholipids and glycolipids are asymmetrically distributed along the membrane with respect to inside/outside  Some proteins bind to specific phospholipids  Transmembrane proteins o Have hydrophobic regions of amino acids that cross the membrane o Alpha helices and beta pleated sheets (rare) o Have specific orientations, with an inner part and outer part  Peripheral membrane proteins o Lack hydrophobic regions, are not embedded in the bilayer o Covalently attached to lipids, or bind noncovalently to other transmembrane proteins  Used for signal transduction, molecule transport, energy generation, and cell adhesion  Diffusion o The passive mixing of substances resulting in transport along a concentration gradient o Brownian motion – random movement of molecules due to thermal motions and collisions o Rate is effected by distance, temperature, size of molecule, and steepness of the concentration gradient  Mainly concentration gradient o Hydrophobic molecules diffuse easily through cell membranes o Gases and water cross freely o Large polar molecules and ions cannot cross through diffusion  Osmosis o Diffusion of water across a selectively permeable membrane o Concentration gradient determined by concentration of dissolved solute in the water o Cells shrink in hypertonic solutions  Hypertonic – Inside cell has higher solute concentration than outside o In a hypotonic solution, water will move into the cell, expanding it and possibly bursting  Hypotonic – Inside cell has lower solute concentration than outside  Passive transport – Facilitated diffusion o Two types of membrane proteins  Channel and carrier o Ion channels  Most important channel protein  Can be open or closed (gated)  Specific for one type of ion o Carrier proteins bind the substance to be transported  Changes shape after binding to substrate  Transition between the open out, bound, and open in is random and reversible  Can become saturated when all binding sites are occupied  Rate of diffusion lowers when this happens  Active transport o Requires expenditure of energy o Substances are moved across the membrane against the concentration gradient o Primary active transport  Sodium potassium pump in animals  3 NA ions out, 2 K ions in, uses 1 ATP  Net change of -1, generates membrane potential o Secondary Active Transport  Use established gradients to move substances  Symport  When ions diffuse from outside to in, the energy generated allows the symport protein to move the molecule or substance through  Both molecules move in the same direction  Antiport  Uses the energy generated by an ion diffusing from inside to out to move the molecules through  The molecules move in opposite directions  These are often paired with Primary Active Transporters Cells  Low end estimate of number of cells in the body – 10 trillion  Cells are small because most chemical reactions in cells require diffusion  High surface area to volume ratio is ideal for diffusion  Eggs (one cell) are large because most of the volume is storing food material  All organelles in eukaryotic cells are connected by vesicles that bud off of one compartment and fuse to the next, moving molecules between organelles as needed o Orientation of the membrane is preserved when this happens  The Nucleus o Contains most of the cell’s DNA o Ribosomes are assembled in the nucleolus o DNA is replicated and transcribed into mRNA or rRNA by RNA polymerases o rRNA is not translated, it directly folds into 3D structures  4 rRNAs + about 80 proteins make up a ribosome o In eukaryotes, ribosomes are found free in the cytoplasm, in mitochondria, bound to the ER, and in chloroplasts o Two lipid bilayers form the nuclear envelope  It is perforates with nuclear pores which are selectively permeable to RNA and some proteins  Endoplasmic Reticulum (ER) o Network of interconnecting membranes distributed throughout the cytoplasm o Internal compartment, called the lumen, is a separate part of the cell with distinct protein and ion composition o The ER’s folding generates a huge surface area, larger than the plasma membrane o Continuous with the outer nuclear envelope at certain sites o Rough ER  Has ribosomes attached  They come from the cytosolic pool of ribosomes and are directed to the ER after they have translated the first few amino acids containing a signal sequence that directs them to the ER  Oligosaccharides (3-12 subunits) are attached to the proteins o Smooth ER  Ribosome free segment o All lipids are synthesized in the ER o Enzymes in ER detoxify many substances by adding OH groups  Golgi apparatus o Essentially the sorting and distribution center for the cell o Receives proteins from ER and modifies them o Adds oligosaccharides to membrane lipids o Concentrates, packages, and sorts proteins before they’re sent to their destination o Sugars added to lipids in the Golgi will end up on the outside of the cell membrane  Lysosomes and Endocytosis o Lysosomes are cells that transport material from the Golgi apparatus and secrete it out of the cell through exocytosis  Have a low pH for breaking down and digesting any useful material before excreting the waste  Sites for breakdown of food and foreign material brought into the cell  Phagocytosis  Can eat their host cell if nutrient deprived  Leaves in fall o Endocytosis is when materials are taken into the cell by endosomes, budding inwards into the cell  Mitochondria o Outer plasma membrane and a highly folded inner membrane o Cellular respiration occurs here o Region inside the inner membrane contains many enzymes for respiration  Chloroplast o Carries out photosynthesis o Double membrane  Endosymbiont theory o Mitochondria and chloroplasts are descendants of bacteria taken into a cell by endocytosis o Evidenced by double membrane o They have their own genome o Their own ribosomes as well, to translate their own proteins  Cytoskeleton o Maintains cell shape and polarity o Provides mechanisms for cell movement o Acts as tracks for motor proteins that help move materials within cells  Actin filaments o Long filament surrounding the cell o Gives shape to cells o Mediates cell shape changes, cell migration, and muscle contraction  Intermediate filaments o Found only in multicellular organisms o Rope-like assemblages in cells o Give strength to tissues and nuclei o Progeria is caused by defective nuclear intermediate filaments o Form a coiled coil  Microtubules o Largest of the cytoskeleton subunits o Hollow cylinders made from tubulin o Organize the cell  Provide intracellular skeleton  Determine cell polarity  Function as tracks on which motor proteins can move vesicles and organelles  Move chromosomes during Mitosis and Meiosis  Make up cilia  Cell adhesion o Cell binding to one another o Leads to phagocytosis, DNA exchange, sperm-egg fusion  Cell Junctions o Tight junctions  Separate apical and basolateral membrane domains  Important in the gut o Adherens junctions  Connect two adjacent cells  Does so by connecting actin bundles  Most ancient and important cell-cell junction  Made of transmembrane cadherins o Desmosomes  Provide mechanical strength (skin)  Joins intermediate filaments in one cell to those of another o Gap junction  Makes a small hole between two cells  Made up of proteins called connexins  Small molecules and water soluble ions can flow through o Focal adhesion  Anchors actin filaments to the basal lamina  Most important cell-matrix junction  Made of transmembrane integrins. Several integrins from one cell bind to extracellular matrix molecules  Integrins – receptors that mediate attachment between a cell and the tissues surrounding it o Basal Lamina – Thin mat of extracellular matrix underlying epithelia, surrounding muscles etc Energy  Metabolism is divided into two types of activities o Anabolic reactions  Link simple molecules together to make complex ones  Require energy  Energy storing reactions o Catabolic reactions  Break down complex molecules into simpler ones  Release energy  First Law of Thermodynamics o During any conversion of energy, the total initial energy equals the total final energy o Energy is neither created nor destroyed  Second Law of Thermodynamics o Energy spontaneously disperses from being localized to becoming spread out if it is not hindered from doing so (entropy increases) o Energy conversions only happen if energy disperses in the universe o Dispersing energy is the driving force for energy reactions o Energy transformations always result in a state of higher probability (More disordered)  Free energy (ΔG) = ΔH – TΔS o If Delta G is negative, energy is released and the reaction can proceed o If positive, extra energy will be required for the reaction to occur o Four Types of Reaction  Heat released, Disorder increased(ΔH<0 and Δ S>0)  Always spontaneous  Most catabolic reactions  Heat released, disorder decreases (ΔH<0 and ΔS <0)  Only spontaneous below a certain temperature  Protein folding  Heat consumed, disorder increases(ΔH>0 and ΔS >0)  Only spontaneous above a certain temperature  NaCl dissolving  Heat used, disorder decreases (ΔH>0 and ΔS < 0)  Never spontaneous  Most anabolic reactions  In principle, all reactions are reversible o Adding reactant speeds up forward reaction o Adding product speeds up reverse reaction o Delta G = 0 when both rates equal each other, chemical equilibrium  Standard free energy (Delta G®) applies to 25 degrees Celsius and 1M concentrations of all reactants and products  All living cells use ATP for capture, transfer, and storage of energy o ATP is so useful as the energy currency because its ΔG° is intermediate between what you gain in respiration and what you expend in anabolism  Direction of a reaction can be predicted is delta G is known, but not the rate Enzymes and Glycolysis  A Catalyst is any substance that speeds up a chemical reaction without itself being used up o Most biological catalysts are called enzymes  Enzymes bind specific reactant molecules called substrates  Some enzymes require cofactors in order to function o Anything that isn’t an amino acid that is required for enzymes to function properly o Heme in hemoglobin  Enzymes work by lowering the activation energy required for the reaction to occur  Types of catalysis o Orientation  Enzyme’s active site forces the molecules into the right orientation so that the reaction can occur o Strain  The optimal configuration for the substrate is one that induces strain on the molecules  Breaking covalent bonds o Transfer of electrons  Can transfer carboxyl or amino groups to the substrate, providing a charge for the reaction to occur  After the reaction, the provided group is returned to the enzyme  An inhibitor can bind to the active site of an enzyme, blocking the substrate from attaching, effectively deactivating the enzyme o Competitive inhibition  Noncompetitive inhibition is when inhibitor binds to a different site on the enzyme, causing the conformation of the active site to change, no longer able to accept the substrate o Allosteric inhibition  Allosteric regulation is more efficient than competitive inhibition because less inhibitor molecules are required  Positive Allosteric regulation o When the regulator attaches to the enzyme, then it becomes active  Cooperative allosteric transition o Occurs with two or more subunits o The more subunits, the more efficient the inhibitors will be at lowering enzyme activity  Glycolysis o Catabolic pathways are long and complex in order to release energy slowly o Glycolysis for the complete oxidation of a glucose molecule is -686kcal/mol (exergonic) o Half the energy in glucose is collected in ATP, the rest is use to drive reactions  Redox reactions transfer electrons between molecules o A gain of electrons is reduction o Loss of electrons is oxidation o Happen simultaneously o Oxidation of organic molecules decreases number of CH bonds o Methane is most reduced, Carbon Dioxide most oxidized  The Cofactor NAD is an essential electron carrier in redox reactions o After oxidation, energy cannot be immediately stored in ATP  Glycolysis can be divided into two stages o Investment of ATP to activate the sugar, followed by splitting C6 into 2x C3 o Oxidation of C3 giving NADD + H and ATP followed by recovery of initial ATP investment  Phosphate gets added to glucose o Traps it in the cell because of negative charge  Hexokinase turns it into G6P, and so on through a chain of enzyme-assisted reactions  Energy harvesting reactions occur when the C3 compounds are oxidized, reducing NAD+  Substrate level phosphorylation occurs next, forming ATP  Final product of glycolysis is 2 pyruvate molecules  Sequential reactions o If a reaction that you want to move in the forward direction is favoured in the backwards direction, you can couple it with an extremely favorable reaction which uses the products of the first reaction as its reactants, keeping the concentration down, forcing the first reaction to speed up forwards Citric Acid Cycle and Electron Transport Chain  After glycolysis, the pyruvate is oxidized to acetyl CoA o CO2 released  Glycolysis occurs in the cytoplasm, The Citric Acid Cycle in the mitochondrial matrix o Electron transport chain in the inner mitochondrial membrane  Citric Acid Cycle o Completely oxidized the 2-C acetyl group to 2 CO2 molecules with dehydrogenase o Formation of ATP is the only step that isn’t oxidation o Final product is 3 NADH, 1 FADH2, 1 ATP  Per molecule of Acetyl CoA (2 per each glucose molecule) o FAD is needed instead of NAD in the conversion of succinate to fumarate because the redox potential of succinate is much stronger than that of NAD, but not as strong as FAD, and the reactions tend to go towards the higher redox potential  Electron Transport Chain o Uses NADH + H and FADH2 generated during sugar oxidation o Flow of electrons in a series of redox reactions causes the active transport of protons across the inner mitochondrial membrane, creating a proton concentration gradient o NAD doesn’t pass the electrons directly to oxygen, instead going through a series of complexes  NADH can only be oxidized by NADH hydrogenase, which then passes it to the rest of the chain  This is done because energy needs to be released gradually so that it can be captured and utilised o Each NADH + H oxidized in the chain pushes 3 protons across the membrane, FADH pushes 2 o Cyanide kills by binding to the active site of cytochrome c oxidase (Last stop on the chain), blocking the final redox reaction  Pumping of protons in the ET chain followed by ATP synthesis is oxidative phosphorylation  ATP synthesis is reversible, though only occurs in bacteria growing without oxygen  Regulation o Main control point in glycolysis is the kinase that adds a second phosphate  Inhibited by high ATP concentration, activated by high [ADP] o Main control point of the citric acid cycle is the first hydrogenase  High [NAD+] activated, high [NADH + H] inhibits o Electron transport chain is regulated by the H+ gradient  Lower electrochemical gradient, faster electron transport  Fermentation o Electron transport chain and citric acid cycle stop in the absence of oxygen o Some cells continue glycolysis and produce limited amounts of ATP if fermentation regenerated the NAD to keep it going o Occurs in cytoplasm o Reduces pyruvate instead of oxidizing it  Pyruvate replaces oxygen as electron acceptor o Only occurs in muscle cells of humans o Results in 2 ATP per cycle  Cellular respiration produces 32 ATP per molecule of glucose  If inadequate food is available, glycogen stored in muscle and liver are used first o Fats next, but the brain can only use glucose, so it must be synthesized Photosynthesis  Plants make all complex molecules on their own, except ammonium that they get from soil  Photosynthesis occurs in the chloroplasts o Light energy captured in the thylakoid  Difference between NADH and NADPH o Same properties and occur in plants and animals, but are made by separate pathways and independently regulated o NADP used for exclusively anabolic pathways o NAD used exclusively for catabolic pathways o NAD can be converted to NADP if needed  Capture of light energy o Plants absorb light in the visible spectrum because it holds the right amount of energy  IR/Microwaves provide vibrational heat (energy) only  X-rays = damage o Chlorophyll has alternating double bonds which result in delocalized electrons o Plants have two predominant chlorophyll molecules: A and B  Absorb blue and red wavelengths o Other accessory pigments (eg carotenoids) absorb photons between red and blue and then transfer a portion of that energy to chlorophyll o When an electron absorbs light, it becomes excited and reaches a more energetic state  As it descends to its ground state, it releases that energy to a neighboring chlorophyll molecule  Continues along a chain of redox reactions o These reactions occur within the light harvesting complex  Made up of 100 chlorophylls plus carotenoids in the antenna  Only one chlorophyll is attached to the electron acceptor  Antenna is required because individual chlorophyll molecules are excited too rarely  Final step, in the middle of antenna system is a redox reaction  Chlorophyll in the reaction center acts like a sink, its excited state has the lowest energy  Transfer of light energy into chemical energy occurs when the reaction center chlorophyll gives up its excited electron to reduce the first member of the electron transport chain o The Light reactions  Two different systems for transport of electrons in photosynthesis  Cyclic and noncyclic electron transport  Noncyclic electron transport produces NADPH + H, ATP, and Oxygen  Water gives up its electrons to photosystem II, giving off protons and oxygen o Forms an electrochemical gradient, generating ATP  Two photosystems are required because one quantum (photon) of light does not have enough energy to transfer electrons from water to NADP+ and make ATP  Cyclic electron transport only produces ATP  When the plant has enough NADPH and sugars stored, it just uses photosystem I in a cyclic fashion to make ATP  Ferredoxin transports the electrons back to the cytochrome complexes and cycles through photosystem I  The formation of the proton gradient via the electron transport chain, followed by synthesis of ATP is called phosphorylation o Thylakoid region  Carbon Fixation o Rubisco is the most abundant protein in the world o Converts carbon dioxide to solid 3phosphoglycerate o Rubisco is a carboxylase, adding CO2 to RuBP o At low [CO2] and high [O2] it can also be an oxygenase, adding O2 to RuBP  Photorespiration – Not good, uses ATP and NADPH, no beneficial function Cells & the Cell Cycle  Cell theory o All organisms consist of cells o Cells divide to produce new cells o Higher organisms fuse their germ cells to produce a new organism  Chromosomes o Single continuous strand of DNA o Circular (Bacteria) or linear (most other organisms) o When the cell is preparing to divide, chromosomes condense by winding around proteins called histones  DNA winds around the proteins, packing tightly together to form the chromosomes o The number of chromosomes an organism possesses is a characteristic of its species  Bacteria typically have one, humans have 46 (23 pairs) o Eukaryotic chromosomes often come in identical pairs called homologs  Karyotype o A way of organizing and identifying chromosomes o Performed by flattening and staining a cell’s DNA as it is preparing to divide o Chromosomes are paired up according to banding patterns  Before cell division can occur, each chromosome must be replicated to produce two copies of each o Chromatids are joined in the middle by a centromere (conglomeration of proteins) o These paired up chromatids are called mitotic chromosomes  Segregating the replicated chromosomes during cell division is where most of the cell’s resources are devoted o Organisms need at least one of each chromosome, as they each carry essential genetic material o Organisms typically need EXACTLY one of each chromosome  Down Syndrome results from an extra copy of chromosome 21  Steps in cell division o S Phase  Consists of the replication of the chromosomes (DNA) o Mitosis (M phase)  Process by which somatic cells make identical copies of themselves o OR Meiosis  Process by which germ cells make non-identical copies of themselves o Cytokinesis (Optional stage)  Dividing the cytoplasm and organelles between daughter cells  The cell cycle o When cells aren’t dividing (Most of the time), and haven’t performed DNA synthesis (S phase) yet, they’re in the Gap 1 (G1 phase) of the cell cycle o There is a checkpoint in between the G1 and S phase that checks for external chemical signals from other cells  E.g. Cyclin E becomes active in response to hormone signals during mammalian pregnancy, which results in proliferation of breast cells needed for lactation o Followed by the S phase  DNA synthesis o Followed by the second Gap phase (G2), which has another checkpoint  G2 checkpoint makes sure that all DNA has been replicated before allowing the cell to divide  This checkpoint can be disabled by treating a cell with caffeine  Treating a cell with hydroxy urea will prevent DNA replication (Skips S phase)  Treating a cell with both results in a cell with only one set of chromosomes entering mitosis, where the daughter cells will be destroyed due to not containing necessary genetic material  Proteins involved in regulation of the Cell Cycle o Cdk4 and Cyclin D are important mitotic regulator proteins o Cyclin D is synthesized in G1 when the cell is ready to replicate DNA o Cyclin D binds to the active site of a Cdk4 molecule, activating it  Sends signals to the cell telling it to enter the S phase, then breaks down, restarting the process o There are many other proteins involved in the cell cycle, these were just obvious ones used as an example  Most cells of your body are not dividing, and have no plans to divide any time soon o Cells that are not dividing are usually arrested in the G1 phase, waiting for external chemical signals to tell the cell to divide  Cancer results from unregulated cell division o If the G1-S checkpoint of a cell is defective, a cell can continuously divide in an unregulated manner o If Cyclin E is always active, or over abundant, a cell will repeatedly divide as if during pregnancy Mitosis and Meiosis  First noticeable part of mitosis is the condensing of the chromatin to form the chromosomes o Prophase  Microtubule organising centers (centrosomes) migrate to the poles of the nucleus o Start forming dense fibers which will form the spindle  Prometaphase o Nuclear envelope breaks down o Tubules are now free to interact with the chromosomes o Microtubules grow and shrink, hooking onto the chromosomes  Some do not join with chromosomes, but become rigid and overlap, stabilizing the cell  Known as polar microtubules  Kinetochores on the centromeres bind to the microtubules o Chromosomes arrive on the metaphase plate  Metaphase o All chromosomes have been captured by at least one microtubule from each centrosome o The microtubules pull the chromosomes to align them along the metaphase plate o Sister chromatids are bound to kinetochore microtubules on opposite spindles  Anaphase o Centromeres holding the identical chromatids together separate o The kinetochore microtubules begin shortening, pulling the sister chromatids to opposite sides of the cell o Makes sure that each daughter cell will receive one of each chromosome  Telophase o Nuclear envelope reforms o Chromosomes reach the poles o Chromatin becomes diffuse  Cytokinesis o In animals – Actin and myosin form a purse string that constricts and divides the cell  Contracts much like in muscle cell o In plants – Vesicles fuse to make cell membrane and cell plate, which becomes a new cell wall o Some cells don’t bother to divide their cytoplasm  Muscle cells have many nuclei (Syncytial) because they undergo mitosis without cytokinesis  Ploidy o N = a set of chromosomes that includes exactly one of each homologue o Multiples of N are named  N = haploid  2n = diploid o In humans, somatic cells are diploid, gametes are haploid  Meiosis o Meiosis I  Early prophase I  DNA begins condensing  Centrosomes begin moving towards poles  Mid prophase I  Homologues start to pair up, forming tetrads o Called synapsis – The pairing of homologous chromosomes (2x2 homologs)  Late prophase I
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