BIOT 100 Summary Notes - Lectures 1-6 PDF

BIOT 100 – Foundations of Biology Summary Notes Lecture 1:  A microscope is an optical instrument used for viewing very small objects.  The human eye can detect objects as small as 100 μm. To view anything smaller than that special magnification tools are needed...

BIOT 100 – Foundations of Biology Summary Notes Lecture 1:  A microscope is an optical instrument used for viewing very small objects.  The human eye can detect objects as small as 100 μm. To view anything smaller than that special magnification tools are needed.  Sizes of the cells:  Eukaryotic Cells: 10 – 100 μm  Animal Cells: 10 – 30 μm  Plant Cells: 10 – 100 μm  Prokaryotic Cells: 0.1 – 10 μm  In terms of increasing size, the order is: 1. Atoms – 0.1 to 0.5 nm (viewed under an electron microscope) 2. Molecules – 0.1 to 100 nm (viewed under an electron microscope; larger molecules can be viewed under a super-resolution fluorescence microscope) 3. Organelles – 0.1 to 10 μm (commonly viewed under a light microscope; an electron microscope may be used to achieve a higher resolution) 4. Cells – 1 to 200 μm (viewed under a light microscope; some larger cells are visible with unaided eyes) Note: You don’t need to know these range of sizes although you do need to know the sizes of Eukaryotic and Prokaryotic cells.  Magnifying glasses and simple microscopes contain a single convex lens.  Convex lens makes the object appear larger.  Concave lens makes the object appear smaller.  A compound microscope uses multiple lenses to generate a higher magnification image.  Important Names and Dates: - In 1590, Hans and Zacharias Jensen developed the first compound microscope. - In 1644, Italian microscopist Giambattista Odierna used a compound microscope to study insects and published a work titled L'Occhio della mosca ("The Eye of a Fly"), which is recognized as the first published microscopic dissection. - In 1665, Robert Hooke used a compound microscope to study insects and plants and published Micrographia. - Dutch microscopist Antonie van Leeuwenhoek developed handheld microscopes with magnification of up to 300-500x. He used them to discover microorganisms (1676), sperm (1677), and bacteria (1683).  Criteria of Microscopes 1. Produce a magnified image of the specimen 2. Separate the details in the image 3. Make the image visible to the human eye, or to a camera  Three main parameters determine the quality of an image in microscopes. 1. Magnification 2. Resolution 3. Contrast  Magnification is an increase in an object’s apparent size.  Resolution is the ability to distinguish between two different objects.  The limit of resolution (LoR) is the smallest distance apart at which two objects can be resolved as separate.  The limit of resolution has an inverse relationship with resolution. As the limit of resolution decreases, the resolution increases.  Contrast is the difference between the object and the background. Types of Microscopes Optical Microscopes Electron Microscopes - Source of illumination is a beam - Source of illumination is a beam of light of electrons - LoR of ~2 x 10-4 μm or 0.2 nm - LoR of ~0.2 μm (Low resolution) (High resolution) - Several different types: - Two primary types:  Simple vs. Compound  Transmission  Confocal  Scanning  Stereoscopic  Fluorescence Note: Not sure if you need to learn this light path but might as well, or at least go through it a few times.  Optical microscopes can be either upright or inverted. Upright Inverted - Objective lenses are above - Objective lenses are below specimen specimen - Light source and condenser - Light source and condenser are below specimen are above specimen  Light travels as waves.  Light slows down when entering a cell from the air and speeds up once it leaves the cell.  Light that has been temporarily slowed by a cell will be out-of-phase relative to light that didn't pass through the cell.  Our eyes perceive these phase differences as variations in brightness of the light waves.  Images are generated as out-of-phase light waves exit specimen, and generate different levels of brightness.  Dense components of the cell slow down light waves passing through it.  Light waves out-of-phase produce different relative levels of brightness.  Stained portions of specimens absorb light of some wavelengths, and allows other wavelengths to pass through it.  Confocal microscopes provide a higher-quality image by only allowing light from the desired focal plane to pass through a secondary pinhole.  Stereoscopic microscopes use light reflected from the surface of the object, rather than light transmitted through it.  Typically used for tissue dissections.  Specimen can be thicker as light isn’t being transmitted through it.  Provides a low magnification image.  The electromagnetic spectrum is the range of all types of electromagnetic radiation.  Different types of electromagnetic radiation have different wavelengths.  The human eye contains specialized cells that detect wavelengths within the visible portion of the electromagnetic spectrum. (Note: You don’t need to learn this)  The visible spectrum ranges from ~380-740 nm. (Note: Learn this)  Wavelength and energy level are inversely correlated. Note: Learn what inverse and direct relationships mean.  Fluorescence is the absorbance of a specific wavelength of light, and the emission of a longer wavelength of light.  Emitted light always has a lower energy level than absorbed light.  Fluorophores are fluorescent molecules or proteins that can be excited by lasers.  To visualize proteins in cells, a fluorophore is attached to the protein, and then a laser excites the fluorophore at the correct wavelength.  Fluorescent microscopes detect light emitted from fluorophores at specific wavelengths. Electron Microscopy  Electron microscopes use a beam of electrons as a source of illumination, and have a higher resolution than optical microscopes.  Transmission electron microscopes (TEMs) produce high-resolution (LoR of ~0.2 nm) images of the internal structure of a specimen.  In a TEM, electrons pass through the specimen and contact a detection screen.  The specimen must be specially prepared for use with the TEM.  Electrons can’t penetrate thick specimens, so the specimen must be cut into extremely thin sections (25-100 nm).  To increase contrast, the specimen must be stained with heavy metals.  This increases the electron-scattering ability of dense structures.  Similar to optical microscopes, dense structures prevent the flow of electrons through the specimen, resulting in darker portions of images. (Note: Important, so learn)  Scanning electron microscopes (SEMs) produce high-resolution (LoR of ~10 nm), three-dimensional images of the surface of a specimen.  In a Scanning Electron Microscope (SEM), electrons are scattered off of the specimen's surface, detected by a detector, and used to create an image displayed on a computer screen.  Specimens for SEMs can be much thicker than specimens for TEMs. (Note: Must know this) A potential question from the above image could be: What is the name of this microscope? Answer is SEM. Another potential question for these sets of images could be: What microscope was used to obtain these images? Answer is SEM. So you must know the differences between Optical Microscopes, TEMs and SEMs. Lecture 2: Atomic Structure:  Atoms consist of a nucleus and an outer shell of electrons (e-).  The nucleus is comprised of protons (p+) and neutrons (n0).  Electrons occupy energy levels called electron shells.  The inner-most electron shell has a capacity of two electrons; subsequent shells have capacities of eight electrons.  Electron shells closest to the nucleus fill first, and experience the strongest electrostatic attraction.  The outer-most electron shell is the valence shell.  A chemical bond between two atoms involves the sharing or transfer of valence electrons.  Atoms with unfilled valence shells are unstable and reactive; atoms will full valence shells (e.g., noble gases) are stable and unreactive.  Metals, in groups 1 and 2, lose electrons to form ions, while non-metals, in groups 15-17, gain electrons to complete their valence shell and form ions.  Molecules are groups of two or more atoms of the same element held together by chemical bonds (e.g., H2, N2, O2).  Compounds are pure substances that consist of atoms of two or more different elements in fixed ratios (e.g., H2O, CO2).  Ionic bonds form when electrons are completely transferred from a metal atom to a non-metal atom (e.g., NaCl).  Metal atom loses its electrons and becomes a cation (+ve ion), while the non-metal atom gains the electrons and becomes an anion (-ve ion).  Covalent bonds form when electrons are shared between two non-metal atoms (e.g., Cl2).  A polar covalent bond may form when electrons are shared unequally between two different atoms due to differences in their electronegativity.  Electronegativity is an atom's ability to attract electrons in a chemical bond. It increases from left-to-right and bottom-to-top in the periodic table. Note: You might have to learn these values.  The net polarity of a molecule is the sum of all of the individual bond polarities.  Some molecules can have a net polarity of zero, and are therefore non-polar, despite the fact that they contain polar covalent bonds (e.g., CO2).  Molecules with a net dipole (e.g., H2O) have a positive and negative side. Water contains two intramolecular dipoles that, due to its “bent” geometry, when summed, produce a resultant dipole.  To determine the resultant dipole, add individual dipoles as vectors by connecting the tail of one to the tip of the previous, then draw the resultant dipole from the tail of the first vector to the tip of the last.  A hydrogen bond is a weak attraction between a hydrogen (δ+) atom and an electronegative atom like oxygen (δ-) or nitrogen (δ-). Types of Chemical Reactions  Synthesis reactions involve two atoms or molecules combining. Energy is absorbed as the chemical bond is formed.  Decomposition reactions involve one molecule being broken down. Energy is released as the chemical bond is broken.  99% of the total number of atoms present in cells consist of the elements H, C, N, and O.  Carbon is the most important biological element. It has the ability to form single, double, or triple bonds with other atoms. The total number of covalent bonds that a carbon atom can form is four. States of Matter Solid Liquid Gas Molecules can move Molecules are compact Molecules are far apart around Fixed volume and Fixed volume; dynamic Dynamic volume and shape shape shape Can be slightly Can’t be compressed Can be compressed compressed  Water is the most abundant molecule in cells, comprising at least 70% of total cell mass.  Water has special chemical properties due to its polarity.  The Universal Solvent  Temperature-stabilizing capacity  Cohesiveness  Unique temperature-density profile  Water has the ability to dissolve a large variety of solutes being the universal solvent.  Hydrophilic solutes are water-loving and dissolve easily in water, whereas hydrophobic solutes are water-fearing and do not dissolve readily in water. (Note: Just an example, so you don’t need to learn this.)  The specific heat capacity of water is 1.0 calorie per gram, which is much higher than most liquids.  Specific heat capacity is the amount of heat a substance must absorb to raise its temperature by 1°C.  Water has a high heat of vaporization due to its high capacity for hydrogen bonding.  Heat of vaporization is the amount of energy required to convert one gram of liquid into a vapor.  Water molecules are attracted to one another by hydrogen bonds, which makes water molecules cohesive.  The cohesiveness of water molecules gives water a high surface tension.  Surface tension is the property of the surface of a liquid that allows it to resist an external force.  Water is most dense at 4°C, which causes ice to float, and lakes to freeze from the top down.  Water expands as it freezes into ice.  In liquid water, hydrogen bonds are short and constantly breaking and reforming, while in ice, the bonds spread out, forming a fixed lattice structure with stable distances between molecules.  Acids are proton (i.e., H+) donors, and bases are proton acceptors.  Strong acids donate their protons very readily; weak acids do not donate their protons easily.  The pH (i.e., “power of H+ ions”) is a logarithmic scale that indicates the acidity or basicity of a solution.  A solution’s pH is based on the amount of H+ and OH- ions that are released when this solution ionizes in water. Lecture 3: Macromolecules:  Macromolecules are the most abundant carbon-containing molecules in a living cell.  Polymerization is the process by which small molecules (monomers) combine chemically to produce long chains (polymers).  Polymers grow through condensation reactions, which produce water as a byproduct; this is an anabolic process. Energy must be supplied in order for these reactions to work.   The breakdown of polymers occurs via hydrolysis reactions; this is a catabolic process. Carbohydrates: Types of Saccharides 1. Monosaccharides 2. Disaccharides: two sugar molecules 3. Oligosaccharides: short chain of sugar molecules 4. Polysaccharides: long chain of sugar molecules  Monosaccharides are categorized by the location of the carbonyl functional group.  Aldose has carbonyl group at the end of the chain.  Ketose contains an internal carbonyl group.  Under aqueous conditions, carbonyl groups of monosaccharides react with hydroxyl groups (i.e., –OH) on the same chain to form a ring.  Some monosaccharides are structural isomers, meaning they have the same chemical formula, but different atom arrangement.  In glucose, if the hydroxyl groups on C1 and C4 are on the same side, it forms the α-glucose isomer; if they’re on opposite sides, it forms the β- glucose isomer.  Enantiomers are molecules with the same atomic arrangement but opposite 3D conformations (mirror images), and have either D or L configurations, depending on how they rotate polarized light.  Naturally occurring sugar enantiomers are in the D-form, while the L-form can be lab-synthesized. (Note: Remember this!)  Disaccharides are basically two monosaccharides linked together by a glycosidic bond. (Note: Remember the bond name)  Common disaccharides include: (Note: Very important, could be asked in exam)  Maltose: glucose + glucose  Lactose: glucose + galactose  Sucrose: glucose + fructose Example of Sucrose being made  Benedict’s reagent indicates the presence of monosaccharides (and some disaccharides) in a solution through a colorimetric reaction. (Note: Remember the name of the reaction)   Polysaccharides are long chains of monosaccharides. They serve storage and structural roles.  Glycogen is a branched polymer of glucose monomers in animal cells.  It exists as small granules in the cytoplasm and is regulated based on cellular energy needs, being rapidly broken down when energy is required.  Starch is a polymer of glucose monomers. It is found in plant cells, and is used for energy storage.  It is present in the chloroplast.  There are two polymers of starch that exist: amylose and amylopectin. (Note: Starch and Glycogen are important)  Iodine indicates the presence of starch in a solution through a colorimetric reaction.  Amylose is a helical linear polysaccharide that comprises 20-30% of starch polymers, and contains α-1,4 glycosidic bonds.  Amylopectin is a branched polysaccharide that comprises 70-80% of starch polymers, and contains both α-1,4 and α-1,6 glycosidic bonds. (Note: Remember these differences)  Cellulose is a structural polymer found in plant cells, composed of glucose monomers. It is a linear polysaccharide that stacks well, giving it strength. Cellulose is held together by β-1,4 glycosidic bonds.   Enzymes that break down α-1,4 linkages cannot break down α-1,6 or β- 1,4 linkages.  Humans cannot digest cellulose due to its β-1,4 linkages, so it passes through the digestive system as insoluble fiber. However, some animals (like cows and sheep) can digest cellulose because they have symbiotic microbes in their gut that help break it down. (Note: A good summary table, learn it. You won’t have to draw the shapes or the diagrams however you must know how each saccharide looks like.) Lipids  They don’t form polymers.  They are hydrophobic, so they are insoluble in aqueous solutions.  Main types of lipids are:  Triglycerides – energy storage (can be either saturated or unsaturated)  Phospholipids – major component of cell membranes  Steroids – signaling molecules; component of cell membranes  Triglycerides are made up of three fatty acids bound to a glycerol backbone.  Formed by condensation reactions producing three water molecules.  They are catabolized to generate substrates that produce energy.  Fatty acids have a carboxyl group (–COOH) at one end and a long, non-polar hydrocarbon tail at the other. The hydrocarbon tail can be either saturated (no double bonds) or unsaturated (with double bonds).  The structure of fatty acids provides different properties at room temperature (RT).  Saturated fatty acids can be “stacked” closer together, resulting in a higher melting point and a solid state at RT (e.g., animal fats, butter).  Unsaturated fatty acids have “kinks” in the hydrocarbon chain, resulting in reduced compressibility, and a liquid state at RT (e.g., oil, plant fats). (Note: Learn these properties)  Phospholipid is composed of two fatty acids and a negatively-charged phosphate group (i.e., –PO43-) bound to a glycerol backbone.  The fatty acid tails are hydrophobic, and the heads are hydrophilic. Structure of Phospholipid  The phosphate group in phospholipids can be further linked to a variety of “headgroups” like, choline, ethanolamine, serine, and inositol etc.  In aqueous solutions phospholipids arrange themselves as an enclosed bilayer, the hydrophobic tails face inward while the hydrophilic heads face the aqueous environment.  Sudan IV reagent indicates the presence of lipids in a solution through formation of a red layer above the solution.  Sudan IV is a non-polar reagent, and it therefore reacts with non-polar solutes (i.e., lipids)  Steroids are organic compounds with four rings.  An important component of cell membranes that influence membrane fluidity.  Cholesterol is the major sterol (a subset of steroids) in animal cells.  Cholesterol molecules embed themselves in the lipid bilayer with their hydroxyl group close to the polar head group of adjacent phospholipids.  Cholesterol stiffens regions of the hydrocarbon chain and reduces the cell membrane’s permeability to small water-soluble molecules.  The phospholipid bilayer is the primary structural component of the cell membrane. Proteins  Proteins are complex macromolecules essential for nearly all cellular functions, including catalyzing reactions, DNA replication, and responding to signals. They are encoded by genes in the genome and are polymers of amino acids that are linked to form polypeptide chains, with each protein consisting of one or more such chains.  There are 20 types of amino acids, nine of which are essential and must be obtained through the diet, as they cannot be synthesized by the body.  Amino acids have two optical isomers, L- and D-isomers, due to the asymmetry around the central carbon atom (Cα), except for glycine, which lacks this asymmetry.  The biochemical properties of amino acid side chains at a pH of 7.0:  Acidic - Negative charge  Basic - Positive charge  Polar - Uncharged  Non-polar  Amino acids are linked together by peptide bonds, which are produced from a condensation reaction.  There are four levels of protein structure:  Primary: sequence of amino acids  Secondary: interactions between atoms in the polypeptide backbone  α-helices  β-pleated sheets  Tertiary: interactions between atoms in amino acid side chains  Quaternary: interactions between multiple polypeptide chains  Biuret reagent reacts with peptide bonds to indicate the presence of proteins in a solution through a violet colorimetric change. Nucleotides  Components of nucleotides:  The (deoxy)ribose sugar within nucleotides forms important glycosidic bonds with carbons 1, 2, 3, and 5:  Carbon 1 - Binds to the nitrogenous base.  Carbon 2 - Has hydrogen in DNA or hydroxyl (-OH) in RNA.  Carbon 3 - Contains a hydroxyl group that binds the next nucleotide in the DNA or RNA chain.  Carbon 5 - Attaches to the phosphate group, which binds the previous nucleotide in the chain. Difference between Ribose and Deoxyribose is that Ribose is bound to a hydroxyl group at C2.  Two classes of nitrogenous bases exist within cells: 1. Pyrimidines: a single nitrogen-containing ring  Cytosine (C)  Thymine (T)  Uracil (U; found exclusively in RNA) 2. Purines: two nitrogen-containing rings fused together  Adenine (A)  Guanine (G)  DNA is a stable, double-stranded polymer that consists of two helical strands of the nucleotides A, C, T, and G.  DNA encodes proteins that cells need to function.  RNA is an unstable, single-stranded polymer that consists of a single strand of the nucleotides A, C, U, and G.  RNA exists as an intermediate molecule between DNA and protein. (Note: These differences between DNA and RNA are important)  Nucleic acids in one strand of the double-helix hydrogen bond to nucleic acids on the opposite strand; A binds with T, and C binds with G.  Strands are antiparallel; one strand runs in the 5’-to-3’ direction, and the opposite strand runs in the 3’-to-5’ direction. Lecture 4: Membrane Transport  The cell membrane is selectively permeable.  Solutes with high permeability:  Small  Uncharged  Non – Polar  Solutes with low permeability: Large  Charged (i.e., ions)  Polar  Passive transport: down the electrochemical gradient; no energy is required.  Simple diffusion: solutes travel directly through the lipid bilayer.  Facilitated diffusion: protein facilitates passage of solute.  Active transport: against electrochemical gradient; requires energy.  Facilitated diffusion of solutes with low membrane permeability down their concentration gradient involves transport proteins.  Transporters bind solute and undergo conformational change.  Channel proteins form a continuous pore with open and closed states.  Diffusion is the passive movement of a substance down its electrochemical gradient.  The net movement of water is osmosis, which is a type of diffusion. It occurs when the membrane is semi–permeable (i.e., permits the flow of water, but not of solute).  Aquaporins are channel proteins that facilitate osmosis by transferring water across the cell membrane.  Tonicity depends on the relative concentration of membrane-impermeable solutes across a membrane.  Hypotonic: lower concentration of solutes compared to another solution.  Hypertonic: higher concentration of solutes compared to another solution.  Isotonic: same concentration of solutes in both compartments.  The tonicity of cells relative to their extracellular environment determines the direction of osmosis.  E.g., water flows from the left compartment to the right compartment to equalize [solute] in both compartments.  Coupled transport is when the transport of one solute can provide energy to co- transport a second.  Uniporter: transports only one solute across the membrane.  Symporter: transports two solutes in the same direction (e.g., Na+ and glucose symporter in intestinal cells).  Antiporter: transports two solutes in different directions (e.g., Na+ and K+ ATPase pump).  The breakdown of ATP into ADP and inorganic phosphate catalyzes energetically unfavourable reactions.  The sodium-potassium pump (Na⁺/K⁺ pump) uses ATP to transport three Na⁺ ions out of the cell and two K⁺ ions in, contributing to a negative resting membrane potential and enhancing the electrochemical gradient for Na⁺ and K⁺ ions.  Endocytosis (cellular import of materials):  Phagocytosis: It is the process by which a cell uses its plasma membrane to “engulf” a foreign particle.  Pinocytosis: The cell takes in extracellular fluid, a process sometimes called "cell drinking," forming small vesicles.  Receptor-Mediated Endocytosis: The cell membrane uses receptors to selectively take in specific molecules. These receptors gather in coated pits, leading to the formation of coated vesicles inside the cell.  Exocytosis (cellular export of materials): The cell secretes intracellular substances to the outside, typically in vesicles that fuse with the plasma membrane.  Cells import extracellular materials by endocytosis, and secrete intracellular materials by exocytosis.  Phagocytic cells of the immune system engulf foreign particles, such as pathogenic bacteria, to combat infection.  Relies on interactions between antibodies surrounding a pathogen and receptors on the surface of phagocytic cells.  Lipofection uses a lipid complex to deliver DNA into cells through endocytosis.  Lipids form a bilayer around the DNA, allowing it to fuse with the cell membrane. The DNA is then released from the endosome and transported to the nucleus, where it can be transcribed. Lecture 5: Organelles  Organelles are subcellular compartments within eukaryotic cells. Each organelle has a specialized structure and function.  Cytoplasm refers to all contents within a cell outside of the nucleus, and consists of :  Cytosol, a gel-like substance  Organelles  Approximately have of the cytoplasm is occupied by organelles.  The nucleus contains most of the cell's DNA in the form of chromosomes and also houses the nucleolus. Chromosomes combine with proteins to create condensed chromatin. The nucleolus is responsible for ribosome biogenesis.  The nucleus is enclosed by a nuclear envelope made of two lipid bilayers (an outer and inner membrane). It contains nuclear pores that allow the transport of materials, such as proteins and mRNA, in and out of the nucleus. The outer membrane is continuous with the endoplasmic reticulum membrane, and the envelope is reinforced by the nuclear lamina, a protein mesh that strengthens it and anchors nuclear pores.  The central dogma of molecular biology states that genetic information flows in one direction: from DNA to RNA to protein.  DNA is “transcribed” into messenger RNA (mRNA) in the nucleus, which is then processed and exported into the cytoplasm.  Ribosomes “translate” messenger RNA (mRNA) into a polypeptide.  Some ribosomes circulate freely in the cytoplasm, while others are attached to the rough endoplasmic reticulum.  The ribosome moves along the mRNA strand and synthesizes a polypeptide chain.  The endoplasmic reticulum (ER) consists of both rough and smooth components, each with different structure and function.  The rough endoplasmic reticulum contains ribosomes embedded in it, and synthesizes membrane proteins and secretory proteins.  The smooth endoplasmic reticulum synthesizes and metabolizes lipids.  After protein synthesis in the rough ER, membrane and secretory proteins are transported to the Golgi apparatus for further processing.  The Golgi apparatus is a series of membrane stacks called cisternae.  The Golgi apparatus modifies membrane and secretory proteins, and targets them to their correct cellular location.  A vesicle is a small, liquid-filled sac enclosed within a lipid bilayer that transports materials within cells.  Transport vesicles shuttle cargo between organelles.  Secretory vesicles bud off of the Golgi apparatus and transport secretory cargo or membrane proteins to the plasma membrane.  Endocytic vesicles are formed when cargo enters the cell by endocytosis  Secretory and membrane proteins are translated by ribosomes on the rough ER surface, processed in the Golgi apparatus, and exported.  The cytoskeleton is a network of protein filaments that has numerous different functions within cells:  Structural support  Changes in cell shape  Intracellular transport of vesicles, organelles, and proteins  Chromosome alignment and segregation during cell division  Cell movement (Note: Not very important, skip if you want. But it won’t hurt to study em)  Microfilaments are helical polymers of the protein actin, and are highly concentrated at the cell cortex. They facilitate changes in cell shape.  Microtubules are long, hollow cylinders of the protein tubulin, and have one end attached to a microtubule-organizing center. They are used for Intracellular transport, cell division, cell movement  Intermediate filaments are rope-like fibres of protein that extend across the cytoplasm, as well as reinforce the nuclear envelope. They provide mechanical strength.  Mitochondria have two lipid bilayers, and synthesizes ATP in the inner membrane.  The inner mitochondrial membrane folds inwards to form cristae.  Lysosomes are small acidic vesicles that contain acid hydrolase enzymes that degrade macromolecules to recycle their components.  Lysosomes degrade signaling molecules, food particles, pathogens, and damaged organelles.  Peroxisomes are vesicles that produce hydrogen peroxide (H2O2), and use it in peroxidation reactions to oxidize substances (e.g., alcohol).  The plasma membrane consists of a phospholipid bilayer that contains embedded cholesterol and proteins, with numerous cellular functions:  Provide a selectively-permeable barrier  Regulate transport of solutes and macromolecules  Respond to extracellular signals  Interact with the cytoskeleton (Note: Not very important, skip if you want. But it won’t hurt to study em)  Proteins in the lipid bilayer that span the entire bilayer are integral (e.g., channel proteins); proteins that don’t are peripheral (e.g., signaling proteins)  Carbohydrate (i.e., polysaccharide) groups can be covalently attached to both lipids (glycolipids) and membrane proteins (glycoproteins). Carbohydrate groups are involved in cell signaling. (Note: Ehh I don’t think this is very important; you can probably skip this) Lecture 6: Cell division  Cells replicate their genomes and organelles prior to undergoing cell division, which produces a subsequent generation of cells.  Nuclear DNA encodes all of the genes necessary for cells to synthesize organelles, function, grow, and proliferate.  Genetic material exists as a series of pairs of chromosomes, with cells receiving one copy of each chromosome from each parent.  Ploidy (n) is the number of chromosome sets in a cell.  Cells with one copy of each chromosome are haploid (n) cells, and cells with two copies of each chromosome are diploid (2n).  Chromosomes have a short arm “p” and a long arm “q” that are separated by a centromere. Chromosomes normally exist as chromatids.  A typical cell cycle lasts ~24 hours, and consists of two phases: interphase (~23 hours) and mitosis (~1 hour).  Interphase: cells grow, replicate DNA, and prepare for cell division  Mitosis: chromosomes separate and cells divide  Interphase:  G1(gap 1): the end of mitosis until the start of DNA replication  S: DNA replication  G2(gap 2): the end of DNA replication until the start of mitosis  DNA replicates semi-conservatively; each daughter DNA molecule consists of one new strand, and one strand from the parent molecule.  The complementarity of each strand of a DNA double-helix allows one strand to serve as a template for replication of the opposite strand.  DNA replication involves three main steps: Initiation, where the double-helix unwinds and RNA primers are synthesized; Elongation, involving the movement of replication forks and synthesis of the leading and lagging strands; and Termination. Enzymes in DNA Replication  DNA helicase: “unwinds” the DNA double-helix into two single strands.  Single-stranded binding proteins: stabilizes single-stranded DNA.  DNA primase: complexes with DNA polymerase α to generate RNA primers as starting point for synthesis.  DNA polymerases: synthesizes a new DNA strand complementary to a template strand.  Polymerase α: begins synthesis of short complementary DNA strand following RNA primer on lagging strand.  Polymerase δ: synthesizes Okazaki fragments and replaces RNA primers with deoxyribonucleotides.  Polymerase ε: synthesizes leading strand.  DNA ligase: fills in “nicks” between Okazaki fragments.  DNA helicase unwinds the double helix in both directions, allowing the replication forks to move outward from the origin of replication.  Single-stranded binding proteins bind to and stabilize single-stranded DNA after the two strands have been separated by DNA helicase.  Synthesis of RNA primers occurs in the 5’-to-3’ direction, meaning DNA primase moves along the template strand in the 3’-to-5’ direction.  DNA polymerase has 5’-to-3’ polymerase activity, and can synthesize complementary DNA strands using an existing template.  DNA polymerase also possesses 3’-to-5’ exonuclease activity, which allows it to remove incorrectly-paired nucleotides.  The high fidelity of DNA polymerase, in addition to its proofreading capabilities, result in relatively few mutations during replication.  Because DNA polymerase only synthesizes DNA in the 5’-to-3’ direction, there is a lagging strand that is synthesized discontinuously. Each replication fork contains both leading (i.e., continuously-synthesized) and lagging strands.  The lagging strand is synthesized in short Okazaki fragments, and the “nicks” between these fragments are joined by DNA ligase.  DNA replication terminates when two replication forks come into contact with one another.  Mitosis is the segregation of the duplicated chromosomes equally into the two daughter cells, and consists of several phases.  Cytokinesis is the division of the cytoplasm of the parent cells equally into the two daughter cells.  Prophase is characterized by: (1) condensation of the replicated chromosomes and (2) formation of the mitotic spindle.  The mitotic spindle is a series of microtubules that extend outward from the microtubule-organizing centre (a.k.a. the centrosome).  Prometaphase is characterized by: (1) breakdown of the nuclear envelope and (2) attaching of the mitotic spindle to the kinetochores.  During metaphase, chromosomes are aligned at the equator of the mitotic spindle.  During anaphase, kinetochore microtubules shorten and sister chromatids separate and are pulled towards each end of the cell.  Telophase is characterized by: (1) daughter chromosomes arriving at spindle poles and de-condensing, (2) nuclear envelope reassembly, and (3) contractile ring formation.  During cytokinesis, a contractile ring of actin microfilaments “pinches” the cell in half to create two daughter cells.