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Bio 120 Midterm Notes  Lecture 1  Organism: An assembly of molecules functioning as a more or less stable whole that exhibits the properties of life. Unicellular and multicellular organisms.  Zacharias Jansen: Invented first microscope.  Robert Hooke: Looked at slices of cork and observed the tiny compartments which he named the cellulae from the resemblance of the honeycomb.  Anton Leeuwennhoek: Built a series of single lense microscopes. Discovered diverse protists which he called “little animalcules”. Described sperm cells, blood cells and even bacteria for which he is called “the father of microbiology”.  Robert Brown: Discovered the nucleus.  Mattias Schleiden and Theodore Schwann: Realized that both plant and animals were made of cells.  Rudolph Virchow: created theory of spontaneous generation which is that all cells arise from previously existing cells.  Louis Pasteur: Laid the theory of spontaneous generation to a rest.  Three branches of microscopy: Optical, Electron, and Scanning.  Optical Microscopy: Light microscopes uses light for illumination.  Electron Microscopy: Uses electron beam.  Transmission Electron Microscopy (TEM): Beam of electrons transmitted through sample. Thin slices stained with heavy metals. Used for internal structures.  Scanning Electron Microscopy (SEM): Sample coated with heavy metal. Beam scans surface make a 3D image. External structures.  Magnification: Ratio between the size of an image.

 Resolution: Ability to observe two adjacent objects.  Contrast: How different one structure looks from another.  Fermentation: A metabolic process that converts sugars to acids, gases or alcohol. Ex: Yeast and bacteria ferment sugars. First described by Louis Pasture.  Cells produce a substance called interphase for breaking down substances.  Zymase: Organic molecule with catalytic properties.  Macromolecules: Made up of C atoms with at least some associated H atoms. 4 major categories:  Polymeric: Composed of same or different monomers.  A macromolecule consists of C, H, and O atoms usually with a H:O ratio of 2:1 as in water.  Monosaccharides: Glucose, Fructose, Galactose.  Maltose is a dimmer of glucose.  Starch is a polymer of glucose.  Cellulose is a complex polymer of glucose monomers. Main structural component of the cell wall. Is the largest mass of nutrients on earth.  Amino Acids have two different affinities:   Hydrophobic (nonpolar)-repel water   Hydrophylic (Polar) –Attract water.  Proteins are polymers of amino acids.  DNA: Deoxyribonucleic acid  RNA: Ribonucleic Acid  DNA is a polymer of 4 different deoxynucleotides:   A: Adenine   C: Cytosine   G: Guanosine   T: Thymidine  DNA is a long twisted double strand polymer made of repeating deoxynucleotides. The two strands of DNA are complementary and

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linked by a specific hydrogen bonding between G-C and A-T. Covalent Bonds Hydrogen Bonds base pairing 5` to 3` RNA is a single strand polymer in which deoxyribose is replaced by ribose and thymidine by uracil.  A: Adenine  C: Cytosine  G: Guanosine  U: Uracil Lipids: Molecules that contain hydrocarbons: Fats oils waxes vitemins and most of the non protein membrane of cells. Lipids are hydrophobic molecules (repel water). Phospholipids are amphipathic molecules: Have two different affinities which is hydrophobic at one end and hydrophilic at the other end which attracts water. Phospholipids form membranes.

Bio 120 Midterm Notes Lecture 2  Mitosis: Division of the nucleus.  Cells rely on diffusion to move molecules around. Diffusion is the main way of getting a chemical compound where it is needed. Very rapid over short distances but much slower over long distances.  Red blood cell has a biconcave shape.  Cells cannot increase beyond certain limits for two reasons: Speed of diffusion and surface area/volume ratios.  Microvilli: Tiny finger like extensions from the surface. Don’t add much to the volume but add a lot to the surface area.  Eukaryotes (domain Eukarya): The true nucleus is separated from the surrounding cytoplasm by membranes. Cytoplasm typically contains extensive membrane systems that form organelles.  Prokaryotes (domains Bacteria and Archaea): The nucleoid region has no boundary membrane.  DNA (Deoxyribonucleic Acid): Provides blueprint for the organization, development and function. Harbors genes, which contribute to the characteristics or traits of organisms. A copy of this blueprint is transmitted from parents to offspring.  Selective transport of ions and water-soluble molecules maintains the specialized internal environments required for cellular life. The lipid bilayer is a hydrophobic barrier to water-soluble substances. Selected substances can penetrate cell membranes through transport protein channels.  All cells are surrounded by the plasma membrane. A bilayer made of lipids with embedded protein molecules. Cytoplasm contains the cytosol and cytoskeleton.

 Origin of Eukaryotic Cells: Two prokaryotic cells join. One from the domain bacteria and the other from the domain archaea. Likely gave rise to the complex organelles specialized for energy metabolism.  All eukaryotic Cells have energy transforming organelles: Mitochondria and chloroplasts. Mitochondria ascended from aerobic bacteria. Chloroplasts descended from cyanobacteria.  Cytoplasm: Mixture of cytoskeleton filaments, dissolved molecules, and water enclosed within the cell membrane and the organelles. Cellular activities include metabolic pathways, glycolysis, and cell division.  Cytoskeleton: The skeleton and muscle of the cell. Movement, shape, and stability. It gives the cell shape. 3 types of fibers:  Microfilaments: Fine thread like protein fibers. Composed of the contractile protein called acin. Association with meiosis contract muscle carry out movements. Cell contraction and cytokinesis.  Microtubules: Tubes composed of subunits of protein tubulin, alpha and beta. Form the spindle fibres for seperating chromosomes during mitosis in flagella, and provides locomotion.  Intermediate Filaments: Tensile strength of the cell.  Nucleus: Holds DNA. Genes are organized into chromosomes.  Prokaryotic Cells: Three most common shapes: Spherical, rodlike, and spiral.

 Prokaryotic Chromosome: Ribosomes are free in the cytoplasm which assemble amino acids into proteins. Cell wall is coated with glycocalyx composed of polysaccharides. When the glycocalyx is loosely associated with the cells, it is a slime layer. When firmly attached it is a capsule.  Flagella: The bacterial flagellum. Moves the cell.  Hairlike pili attach the cell to surfaces or other cells. A special sex pilus joins bacteria during mating.

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Bio 120 Midterm Notes Lecture 3  The nucleus is separated from the cytoplasm by the nuclear envelope which consists of two membranes.  Nuclear Envelope: Network of protein filaments (lamins) which reinforces the nuclear envelope in animal cells. Other proteins reinforce the nuclear envelope in protists, fungi, and plants.  Nuclear Pore Complex: Formed of many types of proteins called the nucleoporins. Embedded in the nuclear envelope are the paths for the assisted exchange of large molecules such as proteins and RNAs.  Nuclear Localization Signal: Many proteins move from the cytosol into the interior of the nucleus. They are targeted with a sequence of 7-41 amino acids. Mainly basic amino acids lysine and arginine.  Transport of Nuclear Proteins: Cargo molecules associated with a transport protein that act chaperone. Shuttle the cargo through the pore. Prevents the transport of material not meant to cross the nuclear membrane. Small molecules simply pass through unassisted.  Nucleoplasma: The liquid or semi-liquid substance within the nucleus. Most of the space inside the nucleus is filled with chromatin.  Chromosome: One complete DNA molecule. Human cells have 46 chromosomes. One complete molecule with its associated proteins.  Chromatin: a collection of eukaryotic DNA. Molecules with their associated proteins.  Euchromatin: Relaxed regions of the chromosome. Most active portion of he genome within the cell nucleus. High gene concentration under active transport.  Heterochromatin: Highly compacted regions of chromosomes. Metaphase chromosome. Transcriptionally inactive.

 Nucleoli: A nuclear structure formed around the genes coding for ribosomic RNA (rRNA). Site of ribosomal subunits synthesis. rRNA exit the nucleus through the nuclear pore complexes and in thee cytoplasm form ribosomes.  Ribosomes: Large and complex structure composed of one or more ribosomal (rRNA) molecules and a variety of proteins. Serves as the site of protein synthesis. Consists of two major subunits: -The small subunit reads the mRNA.-The large subunit joins amino acids to form polypeptide chain.  Proteins made on free ribosomes in cytosol may: remain in cytosol, pass through the nucleus pores into the nucleus or become parts of the mitochondria, chloroplasts, the cytoskeleton, or other cytoplasmic structures.  Proteins that enter the nucleus become parts of chromatin, line the nuclear envelope.  Endoplasmic Reticulum: Extensive interconnected network (reticulum) of membranous channels and cisternae. Two forms the rough ER, and the smooth ER.  Functions of the ER: Active transport of cellular materials. Some proteins are passed to the golgi complex for packaging as vesicles. Formation of nuclear membrane during cell division.  Rough ER: Many ribosomes attached on its outer surface. Proteins made on ribosomes enter the ER lumen where they fold into there final form. Produce glycoproteins. Proteins are then delivered to other regions of the cell.  Smooth ER (SER): Connected to the nuclear envelope. No ribosomes attached to their surfaces. Function of the Smooth ER is to synthesize lipids that become part of cell membranes. Most membrane lipids are synthesized in cytosolic leaflet of smooth ER from fatty acid building blocks.  Lipids in the ER membrane can diffuse laterally to the nuclear envelope. Lipids can be transported to golgi, lysosomes, vacuoles, or plasma membrane.

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 Functions of the Smooth ER: Regulation of osmosis. Regulation of intracellular calcium concentration, Glycogenolysis occur in the SER. Sending glucose into the lumen of the ER.  Detoxification in the SER: Toxins result in increased activity of detoxification enzymes.  Cisternae: A stack of flattened membranous sacs.  Golgi Complex: Tags proteins for sorting to their final destinations. The membrane of the vesicle fuses with the plasma membrane and becomes part of the plasma membrane.

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Bio 120 Midterm Notes Lecture 4 Mitochondria and plastids

 Cells that are not very metabolically active have very few mitochondria. Our mitochondria come from our mother.  Semiautonomous Organelles: Can grow and reproduce themselves. But they are not completely autonomous. They depend on other parts of the cell for their internal components.  Mitochondria: Mitochondria have two membranes surrounding an inner compartment, the mitochondrial matrix. The outer membrane covers the organelle. The inner membrane is expanded by folds called cristae. Reason they fold is for better use of the surface.  Two compartments within the mitochondrion:  The intermembrane space and the mitochondrial matrix. This structure has important connotations for energy conversion. A heavily folded inner membrane that is much larger than the outer membrane. Provides a large surface area on which to conduct chemical reactions.  Primary role of mitochondria: Convert chemical energy stored into covalent bonds. Sugars, fats and amino acids store a large amount of energy. The breakdown of these molecules into simpler molecules releases energy in the form of ATP. Proteins use ATP to carry out their functions. Muscle connection, uptake of nutrients, cell division.  Cellular Respiration: Is the process by which energy-rich food molecules are broken down to water and carbon dioxide by mitochondrial reactions. Energy is captured in the form of ATP. Requires oxygen. Breathing supplies oxygen for mitochondrial reactions.  Glycolisis: Splitting 6 carbon sugar.

 In humans our mitochondria consume as much as 80% of the oxygen we breathe.  Endosymbiosis and the origin of mitochondria: Symbiotic bacteria took up permanent residence within other cells. Evidence for this is that mitochondria have their own DNA (nucleoid).  Semiautonomous Organelles Division: A form of asexual reproduction and cell division. Some protozoa and organelles within eukaryotic organisms divide by binary fission. Bacteria cells don’t divide by mitosis. But by binary fission.  The mitochondria has its own independent genome. The mitochondria split by fission.  Organelles found in plant cells but not animal cells: Plastids, Central vacuole, cell walls.  Plastids: DNA genomes and the molecular machinery for gene expression and the synthesis of proteins on ribosomes.  Chromoplasts or colored plastids: Synthesize and store yellow, orange, and red pigments. In autumn give leaves their yellow orange and red colours.  Gerontoplast: Control the dismantling of the photosynthetic apparatus during senescence.  Leucoplasts colourless that differentiate in:   Amyloplasts: Store starch and detect gravity.   Elaioplasts: Store fat.   Proteinoplasts: Store and modify proteins.  Chloroplasts: Contain the green pigment chlorophyll, green colour. Found in nearly all species of plants and algae. Three membranes, an outer boundary membrane and an inner boundary membrane which completely encloses an inner compartment the stroma. The thylakoids within the stroma (fluid interior). Consisting of flattened closed sacks.  Thylakoids: Consists of a membrane surrounding a Lumen. Contain chlorophyll that absorbs light energy and converts it to chemical energy in photosynthesis. Site of light dependent reactions of photosynthesis.

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 Central Vacuoles: Occupy 90% of the cells volume in plants. Contains transport proteins that move substances into and out of the central vacuole. Store salts, organic acids, sugars, storage proteins, pigments, and waste products. Pigments concentrated in the vacuoles produce colours of many flowers. Contain enzymes that break down biological molecules. Contain molecules that provide chemical defenses against pathogenic organisms.  Cell Walls: Support individual cells. Contain the pressure produced in the central vacuole. Protect cells against bacteria and fungi. Consist of cellulose fibers. The walls of cells beside together are held together by a layer of polysaccharides (pectin) called the middle lamella. Primary and secondary cell walls are perforated by plasmodesmata.  Plasmodesmata: Plasma membrane lined channels that connect cytosols of adjacent cells. Allow ions and small molecules to move directly from one cell to another through the cytosol.

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Bio 120 Midterm Notes Lecture 5 Cell Cycles  Cell Cycle: Series of cellular events leading to division and duplication (replication). It produces two daughter cells.  How many mg of DNA g1, how much is in DNA G2. Answer is double.  Mitosis: divides replicated DNA equally and precisely in somatic cells.  Meiosis: A process gametes cell division. Required for sexual reproduction in eukaryotes, such as animals, plants, and fungi. The number of sets of chromosomes is reduced to half the original number. Typically from two sets (diploid) to one set (haploid).  Cytokinesis: Is the process in which the cytoplasm of a single eukaryotic cell is divided to form two daughter cells. Usually initiates during the late stages of mitosis, splitting a mitotic cell in two.  Chromosomes: Nuclear units of genetic info. Chroma is the colour. Soma is the body. In eukaryotic cells are individual. Formed by linear DNA with associated proteins.  Replicated chromosomes are called chromatids.  Ploidy: The number of sets of chromosomes in the nucleus of a cell.  Haploid Number: The number of chromosomes in a gamete.  Diploid Zygote: Is two two gametes with twice this number (2n)  Karyotype: The number and appeatance of chromosomes in the nucleus of eukaryotic cell. Complete set of chromosomes in a species.  Cytogenetics: Study of karyotypes.  Sex Chromosomes: The sex chromosomes of diploid cells may be considered as haploid chromosomes. Since haploid is also a term used to define a set of chromosomes with only one copy in the cell. Humans contain 46 chromosomes. For humans diploid species would have 23.  Interphase: Enters initial period of cytoplasmic growth (G1 Phase).

 Helicases: Bind and separate double-stranded DNA into single strands allowing each strand to be copied.  Prophase: Chromosomes condense into compact rod like structures. Spindle forms in the cytoplasm.  Centriole: Cylindrical structure composed mainly of tubulin. Not present in plant cells.  Centrosome: Formed by an association of a pair of centrioles.  Microtubules Organizing Centre (MTOC): Found in eukaryotic cells when microtubules emerge. Have towo main functions Organization of eukaryotic flagella and cilia and organization of mitotic and meiotic spindle apparatus, which separate the chromosomes during cell division.  The Spindle: Polymerized elastic structure composed of hundreds proteins and microtubules. Segregate chromosomes.  Kinetochores attach microtubules to attach chromosomes.  Prometaphase: Nuclear envelope breaks down, Spindle enters former nucleus area, Microtubules from opposite spindle poles attach to two kinetochores of each chromosome.  Spindle Connections at Prometaphase: Colchicine inhibit spindle formation and arrest cells at pro-metaphase.  Metaphase: Spindle is fully formed, Chromosomes align at spindle midpoint, moved by spindle microtubules.  MTCO: Microtubules-organizing complex (centre)  Kinetochore Microtubules: Connect chromosomes to spindle poles.  Nonkinetochore Microtubules: Extend between spindle pores without connecting to chromosomes. At spindle midpoint microtubules from one pole overlap with those from opposite pole.  Kinetochore Movement: Polymerized Elastic Structure composed of hundreds proteins. Forming microtubules. Segregate Chromosomes Kinetochores attach microtubules to chromosomes. Depolymerization of microtubules generate tension at kinetochores.  Animal spindle Formation: Centrosome divides, the two parts move apart. Microtubules form early spindle.

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 Plant Cell with no centrosome Formation: Spindle forms from microtubules and assemble in all directions surrounding nucleus.  Chromosome Segregation: Equal distribution of daughter chromosomes to each of two cells resulting from cell division. DNA replication followed by equal separation of chromosomes.  Anaphase: Aligning chromosomes at the equater (Ends) and poising them for segregation to daughter cells.  Telophase: Chromosomes decondense, return to extended state typical of interphase.  Cytokinesis in animal cells: Furrowing which is a band that splits the two cells. Also known as a cleavage furrow.Forms a plasma membrane.  Cytokinesis in plants: Cell plate forms which seperates the daughter cell creating a new membrane and wall.

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Bio 120 Midterm Notes Lecture 6

 Genetic Recombonation: Process by which two DNA molecules exchange genetic information. Results in the production of a new combination of alleles.  Alleles: Is one of two or more versions of a gene.  Principle of Independent Assortment: Describes how different genes independently separate from one another when reproductive cells develop.  Synapsis: The process of pairing the homologous chromosomes. Pairing is brought in a zipper like fashion.  Chiasmata: Non-sister chromatids may cross over at these points.  Paternal chromosomes from male parents.  Maternal from female parents.  Humans have 23 chromosomes.  Prometaphse: Nuclear envelope breaks down.  No DNA replication occurs during interkinesis.  Fertilization fuses nuclei of egg and sperm.  Zygot cell produced by fertilization restores parental chromos...