Bio Temp Notes PDF

Cells are the smallest unit of life. A tissue is a group of similar cells that perform a specific function Several tissues join to form an organ Organs form an organ system Plant kingdom - multicellular, photosynthetic organisms Fungi Kingdom - including molds and mushrooms. Animal Kingdom - m...

Cells are the smallest unit of life. A tissue is a group of similar cells that perform a specific function Several tissues join to form an organ Organs form an organ system Plant kingdom - multicellular, photosynthetic organisms Fungi Kingdom - including molds and mushrooms. Animal Kingdom - multicellular, must ingest and process food Domain → Supergroup → Kingdom → Phylum → Class → Order → Genus → Species Categories of Classification Systematics helps biologists better understand the variety of life on Earth +-----------------------------------+-----------------------------------+ | Amoeba | Protista Kingdom - Unicellular, | | | eukaryotic, lacks a fixed shape | +===================================+===================================+ | Mushroom | Fungi Kingdom - heterotrophic | | | (cannot produce its own food), | | | non-mobile | +-----------------------------------+-----------------------------------+ | Fern | Kingdom Plantae - Multicellular, | | | undergoes photosynthesis, | +-----------------------------------+-----------------------------------+ | Lion | Kingdom Animalia - Multicellular, | | | must consume food (specifically | | | meat due being carnivorous), in | | | order to survive | +-----------------------------------+-----------------------------------+ | Diatoms / phytoplankton? | Protista Kingdom - unicellular, | | | photosynthetic organisms, | | | multicellular, autotrophic | | | | | | Responsible for making natural | | | gas | +-----------------------------------+-----------------------------------+ **Scientific Names** Taxonomists assign each species a two-part, specific name (binomial) **Scientific Name :** Genus name + specific epithet Genus capital; both words italicized *Homo sapiens, Pisum sativum, Felis domesticus* Control Group - Constant variable, not exposed to experimental variable Experimental Variable - Factor tested Responding Variable - Result or change **Hypothesis and Experimental Design** **Hypothesis -** If this new fertilizer increases plant growth (potatoes), then the cost of the plant (potatoes) will decrease **Design an experiment -** Experimental variable - fertilizer Control group - a place where the fertilizer isn\'t being used Experimental group - a place where the fertilizer is being used Responding variable - the change in prices for potatoes **What are model organisms, and why are they important in research?** Model organisms are organisms that are used in experiments. These are important in research because they can be used instead of using a human, they can use human-like organisms and use the research to see how it could affect humans without harming any human. **How does statistical significance help determine if experimental results are reliable?** **Why is it important for scientific studies to be published and reviewed by peers?** It is important for peers to review scientific studies in order to challenge statements and hypotheses made within the study, ensuring that it is reliable and factual information. **Chi Square** **Formula** **Degrees of Freedom** Calculated as the number of outcomes minus one. **Elements that make up 95% of organisms** Oxygen, Carbon, Hydrogen, Nitrogen, Phosphorus, Sulfur **Atom** - smallest part of an element that displays the properties of the element → Made up of : **Protons -** Positively Charged, found inside of the nucleus **Neutrons -** Neutral charge, found in nucleus **Electrons -** Negative Charge, found outside / around the nucleus **The Periodic Table** Elements are different while also being the same (different atom, similar chemical and physical properties) **Vertical Columns = Groups** **Horizontal Rows = Periods** **Electrons** - - - - - **Molecules and Compounds** A **molecule** is a group of two or more atoms held together by **chemical bonds**. A **compound** is a substance which is formed by two or more different types of elements which are united chemically in a fixed proportion. **All molecules are not compounds. All compounds are molecules.** **CHNOPS FORMULA ORDER** **Carbon → Hydrogen → Nitrogen → Oxygen → Phosphorus → Sulfur** **Ionic Bonding** **Ions -** charged atoms that form when electrons are transferred from one atom to another **Examples :** **Na** **→** one electron in its third orbital, tends to be an electron donor. Becomes a positive Na after giving up an electron (e\^-) **Cl →** seven electrons in its third orbital, tends to be an electron acceptor Becomes negative (Cl\^-) after gaining one electron (e\^-) **Covalent Bonding** **Covalent Bond -** when atoms **share** electrons in a way which both atom has a full set of electrons in their outer shell - **Nonpolar and Polar Covalent Bonds** - - - **Properties of Water** **Water has a high heat capacity** **Calorie →** the amount of heat energy needed to raise the temperature of one gram of water 1 degree celsius The hydrogen bonds that link water molecules help water absorb heat without a great change in temperature because the temperature of water rises and falls slowly, organisms are better able to maintain their normal internal temperatures. **Organic Molecules** **Organic Molecules** always include Carbon (C) and Hydrogen (H) Carbons can bond with each other in chains called hydrocarbons **Functional Groups** A specific combination of bonded atoms that always react in the same way **Organic Molecules** **Macromolecules** contain many molecules joined together **Monomers -** repeated subunit of many large organic molecules **Polymers -** Large organic molecules formed by combining monomers Cells use **common reactions** to build or degrade polymers In a **hydration reaction,** a -OH and -H are removed as a water molecule when monomers are joined to build polymers. In a **hydrolysis reaction,** components of water are added when polymers are broken down **Carbohydrates** function as an energy source for living organisms \*Play a structural role in woody plants, bacteria, and insects. \*On cell surfaces, involved in cell-to-cell recognition **Monosaccharides -** sugars with 3-7 carbon atoms **Pen**tose refers to a **5** carbon sugar **Hex**ose refers to a **6** carbon sugar, such as **glucose** **Disaccharides -** two **Monosaccharides** joined by a **dehydration reaction** **EX : Maltose, Sucrose, and lactose** **Energy Storage Polysaccharides** **Starch -** storage form of glucose in plants A polymer of glucose molecules with some branching **Glycogen -** is the storage form of glucose in animals **Liver** stores glucose as glycogen In between meals, the liver releases glucose stores in glycogen Highly branched polymer of glucose molecules **Chapter 3** **Prokaryotic Cells -** cells lack a membrane-bound nucleus. **Eukaryotic Cells -** cells possess a membrane-bound nucleus. **Cell Theory** **Anton van Leuuwenhoek -** invented one of the earliest microscopes and observing the first cell **Robert Hooke -** coined the term "cell" All organisms are composed of one or more cells Cells are the basic living unit of structure and function in organisms All cells come only from preexisting cells Cells being small is an advantage for multicellular organisms Nutrients such as glucose can enter the cell Wastes such as CO2 can exit the cell Surface area affects the ability to get materials in and out of the cell As cells increase in volume, the proportionate amount of surface area decreases If a cell **doubles** in size, its surface area increases **fourfold**, while the volume increases **eightfold**. **Prokaryotic Cells** Lack a **membrane-bound** nucleus Cells in domains **Bacteria** and **Archaea** Usually unicellular (single, strings, or clusters) Some bacteria are **Beneficial** Archaea Bacteria Eukaryotes --------------------------- ----------------------------------- ------------------------------------- ------------------------------------- Cell Wall Usually present, no peptidoglycan Usually present, with peptidoglycan Sometimes present, no peptidoglycan Plasma Membrane Yes Yes Yes Nucleus No No Yes Membrane Bound Organelles No No\* Yes Ribosomes Yes Yes Yes, larger than prokaryotic - **Prokaryotic Cell Structure** Prokaryotes are small and come in different shapes Bacillus is a rod-shaped bacteria Coccus is a spherical-shaped bacterium Both can occur as pairs/chains, and cocci can also occur as clusters Spirilla - Long rods twisted into rigid spirals Spirochetes - flexible spirals **Cell Wall** - **Capsule** - **Flagellum** - **Fimbriae** - **Nucleoid** - **Ribosomes** - **Thylakoids** - **Plasma membrane -** phospholipid bilayer with embedded proteins **Cell Wall -** maintains the shape of the cell **Glycocalyx -** a layer of polysaccharides that lies outside the cell wall in some bacteria Aids against drying out and provides resistance against a host's immune system Also helps bacteria attach to almost any surface Called a **Capsule** when it's well organized and not easily washed off. **Inside the Cytoplasm** **Cytoplasm -** semifluid medium inside a cell is the cytoplasm Composed of water,salts, and dissolved organic molecules Contains thousands of ribosomes that synthesize proteins Prokaryotic DNA is located in the **Nucleoid** **Eukaryotic Cells** **Eukaryotic cells -** structurally complex, has a nucleus, possess membrane bound organelles Make up animals, plants, fungi, and protists **Cell Walls** - many eukaryotic cells have cell walls Plant cells could have 2 cell walls **Cellulose** is the **main constituent** of the primary cell wall in plants. **Lignin** is found in secondary cell walls Fungi cell walls - made of chitin **Histone Protein + DNA = Chromatin** **Histone Protein -** a protein that provides structural support for a chromosome **Nucleus** **Nucleus -** a prominent structure, stores genetic material (DNA) - - Contains **chromatin** **Ribosomes** **Protein Synthesis** Use mRNA as template Composed of two subunits (large/small) Subunits consist of rRNA and protein molecules Found in : Cytoplasm, in groups of polyribosomes, attached to endoplasmic reticulum (ER) **Endoplasmic Reticulum** **Rough ER** - - **Smooth ER** - - - - - **Golgi Apparatus** Referred to as the **shipping center** of the cell Collects, sorts, packages, modifies, and distributes materials, such as proteins and lipids **How the Endomembrane System Works** **Lysosomes** Contain hydrolytic digestive enzymes Act as garbage disposals of the cell Break down unwanted foreign substances or work-out parts of cells Bring macromolecules back into the cell **Vacuoles** Large membrane sacs Larger than vesicles & more prominent in plants (Water, sugars, salts, pigments, toxins) **Chloroplasts** The site of photosynthesis in plants and algae **Stroma -** fluid filled space bounded by double membrane Membrane system of sacs called **thylakoids** **Grana -** stacks of thylakoids **Mitochondria** Found in almost all eukaryotic cells Site of cellular respiration Double membrane structure **Matrix -** the inner fluid filled space **Cristae -** formed by invaginations of the inner membrane **CONTAIN THEIR OWN DNA** **The Cytoskeleton** Consists of three interconnecting proteins Actin Filaments Intermediate filaments Microtubules Maintains cell shape Assists in movement of cell and organelles Dynamic - assembled and disassembled as needed **Actin Filaments** Interacts with motor molecules for movement (muscles) Myosin motor molecule in muscle cells **Intermediate Filaments** Support nuclear envelope Help for cell-to-cell junction, such as those holding skin cells tightly together Strengthen human hair **Microtubules** Made of globular tubulin (alpha and beta) assembly Controlled by microtubule organizing center (MTOC) Main MTOC in eukaryotic cells is the **centrosome** **Roles -** - - - **Centrioles** Found in centrosomes of animal cells May be involved in microtubule assembly and disassembly Short cylinders with a (9+0) pattern of microtubule triplets **Cilia and Flagella** Hairlike projections that aid in cell movement Cilia are much shorter than flagella in eukaryotic cells Both are membrane bound organelles (9+2 pattern of microtubules) EX : Paramecia move by means of cecilia Cells of the upper respiratory tract use cilia to sweep debris trapped within mucus Sperm cells have flagella **Origin and Evolution of the Eukaryotic Cell** Fossil record suggests first cells were prokaryotes Biochemical data suggests archaea are more closely related to eukaryotes Eukaryotes evolved in stages from prokaryotes **Endosymbiotic Theory -** mitochondria and chloroplasts derived from prokaryotes that were taken up by larger cells - - - Week 3 ====== **Cholesterol** is the one that\'s responsible for keeping the cell intact Too much = too tight, which cant move Plasma Membrane Structure and Function Phospholipid Bilayer with embedded proteins Hydrophilic (water loving) polar heads Face inside and outside of cell - Steroids, such as **cholesterol** in animal cells,stiffen and strengthen the membrane **Peripheral Proteins -** associated with only one side of membrane **Integral proteins -** span the membrane **Glycolipid -** lipids with attached carbohydrates **Glycoproteins** - proteins with attached carbohydrates (considered an ID or identification) **Cell recognition proteins** are glycoproteins - **Channel Proteins -** TRANSPORT (VERY SPECIFIC) Involved in the passage of solutes through the membrane Some may contain a gate that must be opened in response to a signal (to control how much goes in) **Carrier Proteins -** allows the **passage** of a solute by combining with it and helping it to move across the bilipid membrane **Receptor Proteins** (specific shape) All kinds of proteins are **specific** Have a shape that allows a specific molecule to bind - **Enzymatic Proteins** Carry out metabolic reactions directly Helps speed up reactions Act as a catalyst for reactions **Concentration Gradient -** amount of concentration in a place (changes based on where it is, how it is interacting with neighboring solutions) **Everything goes down a concentration gradient** More of a substance on one side of the membrane Going **Down** a concentration gradient - Going **Up** a concentration gradient - - **Aquaporin -** responsible for sorely transfer of water in and out of the cell **Endocytosis -** something getting inside the cell **Exocytosis -** something leaving the cell Endocytosis and Exocytosis are caused through **vesicles** in cytoskeleton **Diffusion** **Diffusion -** movement of molecules from an area of higher concentration to lower concentration Going down the concentration gradient - Solution contains a solute (solid) and a solvent (liquid) Oxygen diffuses through membrane Several factors influence the rate of diffusion - - - - **Osmosis** **Osmosis -** the diffusion of water across a differentially permeable membrane. Diffusion always occurs from higher to lower concentration **Osmotic Pressure** - the pressure that develops in a system due to osmosis - **Isotonic Solution -** The solute concentration is equal inside and outside a cell Animal cell in isotonic solution - **Hypotonic Solution** - A solution has a lower solute concentration than the outside of a cell Animal cell in hypotonic solution - **Hypertonic Solution -** A solution has a higher solute concentration than the inside of a cell Animal cell in hypertonic solution - Transport by carrier proteins **Facilitated transport** needs help (against concentration gradient) **does not** require energy - - - - - **Active transport** needs energy (requires energy while going against concentration gradient) Carrier proteins are required (against concentration gradient) Often called pumps Accumulation inside or outside the cell, combined with carrier protein Energy (ATP) required **In class assignment** Isotonic - an equal concentration of water inside the cell and outside of the cell, meaning no movement of water occurs Hypotonic - an unequal concentration of water; more concentration inside the cell compared to outside the cell, leading to the cell gaining water and bursting. Hypertonic - an unequal concentration of water; more concentration outside of the cell compared to inside of the cell, leading to the cell losing water and shriveling. **Bulk Transport** Macromolecules are transported into or out of cells by vesicle formation Energy is required to form vesicles (called membrane assisted transport) **Exocytosis** Vesicle fuses with plasma membrane as secretion occurs Vesicle membrane becomes apart of the plasma membrane - - - **Endocytosis** Cells take in substances by vesicle formation - - - - - - **Phagocytosis -** large, particulate matter such as "food" molecules, viruses, or whole cells. - **Pinocytosis -** liquids and small particles (same procedure but smaller?) - **Receptor-mediated endocytosis -** type of pinocytosis involving pits coated with receptor proteins for specific molecules - **Cell surfaces in animals** Animal cells have two different types of cell surface features - - Both can connect with the cytoskeleton and contribute to cell-to-cell communication Cytoskeleton = highway **Extracellular Matrix (ECM)** A meshwork of proteins and polysaccharides closely associated with cells that produced them Common structural proteins in ECM - - - **Proteoglycans -** polysaccharides made of amino sugars that attach to proteins in the ECM Attach to a long, centrally placed polysaccharide - - **Types of Junctions** **Adhesion Junctions** Adhesion proteins connect cytoskeletal filaments of adjacent cells **Tight Junctions** Proteins connect plasma membranes of adjacent cells to form impermeable barriers **Gap Junctions** Plasma membrane channels of cells join, allowing communication and strength **Plant Cells** **Cellulose -** main component of cell wall All plant cells have a porous cell wall - - - - **Plasmodesmata -** narrow channels that penetrate the cell wall to connect adjacent cells - - - Week 4 ====== **Energy -** the ability to do work or bring about a change - - Life on earth is dependent on solar energy - **Kinetic Energy** - The energy of motion **Potential Energy -** Stored energy **Types of energy** Chemical energy - stored in chemical bonds Mechanical energy - energy of motion, as in walking **Laws of Thermodynamics** Energy flows through an ecosystem **Terrestrial Ecosystem :** - - - - The **first law** of thermodynamics states that energy cannot be changed from one form to another without a loss of usable energy Law of conservation of energy The **second law** of thermodynamics states that energy cannot be canged from one form to another without a loss of useable energy **A leaf cell photosynthesizes** - - Plants and organisms that eat plants use cellular respiration to power cell activities and growth. - - - **Cells and Entropy** **Entropy** refers to the relative amount of disorganization Processes used by cells are energy transformations Every process that occurs in cells increases the total entropy of the universe Cellular processes require an input of energy from an outside source (transport, biosynthesis) Glucose - - - Carbon dioxide and water - - - Unequal distribution of hydrogen ions - - - Equal distribution of hydrogen ions - - - **Energy Transformations and Metabolism** **Metabolism -** the sum of all the chemical reactions that occur in a cell The breaking down and building up of molecules is a large part of cellular metabolism - - **Free energy -** the amount of energy available The change in free energy after a reaction is calculated by subtracting the free energy of the reactants from that of the products **Exergonic Reactions -** spontaneous and release energy - **Endergonic Reactions** - - **ATP: Energy for Cells** **ATP - adenosine triphosphate** - - - - ATP is a nucleotide composed of - - Three phosphate groups - **Function of ATP** **Chemical Work** - **Transport Work** - **Mechanical Work** - **Coupled Reactions -** energy released by an exergonic reaction is used to drive an endergonic reaction ( ATP breakdown is often coupled to reactions that require an input of energy Two main ways to couple ATP hydrolysis to an endergonic reaction: - - - - - - - **Metabolic pathways** - a series of linked reactions - - - **Enzymes -** Typically proteins that function as catalysts to speed up chemical reactions - Participate in chemical reactions, but are not used up by the reaction. Does not determine if reactions go forward Free energy determines which reactions go forward - - ENZYME IS A PROTEIN PROTEINS ARE MADE OF AMINO ACIDS **Energy of Activation** Energy that must be added to cause reactants to react with one another - Enzymes lower the energy of activation - - **Degradation -** enzymatic reaction breaks up substrate into multiple products **Synthesis -** Enzymatic reaction synthesizes a product from multiple substrates **Induced Fit Model** - - - Factors affecting enzymatic speed Enzymatic reactions proceed very rapidly The rate of enzymatic reaction may be influenced by - - - **Temperature and pH** Enzyme activity increases as the temperature rises - - - Decrease of temperature decreases enzyme activity Each enzyme has an optimal pH at which its activity is the highest - - - - **Enzyme Inhibition** Simplest type of enzyme inhibition When product is abundant, it binds to enzyme's active sit and blocks further production When product is used up, it is removed from the active site - More complex enzyme inhibition Product binds to a site other than the active site, which changes the shape of the active site Poisons are often enzyme inhibitors - - **Enzyme Cofactors** Many enzymes require an inorganic ion or nonprotein organic molecule to assist in reaction - - - **Oxidation-reduction reactions and Metabolism** **Oxidation -** the loss of electrons **Reduction -** the gain of electrons Pair of reactions is referred to as redox reactions The term oxidation is used even when oxygen is not involved Na + Cl NaCl. Sodium is oxidized. Chlorine is reduced. Oxidation-Reduction. The terms also apply to covalent reactions involving hydrogen atoms (e\^- + H\^+) - - - - Unit 2 **Cellular respiration -** the release of energy from molecules such as glucose accompanied by the use of this energy to synthesize ATP molecules **Glucose -** high-energy molecule, energy released as it breaks down - - - Cellular respiration involves many individual reactions, each requiring its own enzyme Certain enzymes utilize coenzymes - - - **NAD Cycle** - NAD accepts electrons to become NADH - **Phases of Cellular Respiration** - - - - - - - - - - - - - - - - - - - **Pyruvate** - - - - **Glycolysis -** The breakdown of glucose to two molecules of pyruvate - - - - Glycolysis is the breakdown of glucose to two molecules of pyruvate. This occurs in the cytoplasm while also not requiring oxygen (anaerobic). This process transforms one 6-carbon molecule into two 3-carbon molecules End product of **prep stage** of glycolysis DHAP & D3P NET YIELD OF GLYCOLYSIS 2 ATP 2 H2O 2 PYRUVATE 2 NADH Chemiosmosis - the movement of hydrogen ions across the membrane via ATP synthase. **Generating ATP** First step is glycolysis → end product is 2 pyruvate 2 acetyl CoA Krebs Cycle → 2 Acetyl CoA produces 6 NADH and 2 FADH 2 ATP Electron transport chain → NADH drops off H and goes into proton gradient - **Photosynthesis** **Photosynthesis -** converts solar energy into chemical energy of carbohydrates - - - Oxidation Is Loss of electrons Reduction Is Gain of electrons Chlorophyll has the ability to attract sunlight and harvest energy (Photons) Most photosynthetic organisms contain the pigment **chlorophyll** Photosynthesis occurs in the parts of plants that contain chlorophyll and other pigments - - Water is taken up by roots and transported to leaves by veins CO2 enters through small openings in the leaves named **Stomata** CO2 & water diffuse into cells and enter chloroplast organelles Light energy drives photosynthesis and is absorbed by chlorophyll in chloroplasts **Stoma - single** **Stomata - plural** **Chloroplast Structure** Chloroplast and its fluid-filled interior called stroma are surrounded by a double membrane Thylakoids are a different membrane system within the stroma that form flattened sacs called Thylakoids are stacked together to form grana Thylakoid space is formed by a continuous connection between individual thylakoids Chlorophyll - apart of the thylakoid membrane - Stroma of chloroplast contains enzymes and is where carbon dioxide is reduced to form carbohydrates **Photosynthetic Reaction** **Photo -** capturing solar energy **Synthesis -** producing a carbohydrate **Light Reactions - (**light - dependent) **Calvin Reactions -** (Light independent) Light reactions - occur in the thylakoid membranes - - Calvin cycle occurs in the stroma - - Electromagnetic Spectrum Visible light is divided into wavelengths between 380 and 750 Violet light - Shortest wavelength, highest energy Red light - longest wavelength, lowest energy - - - Green light is reflected and only minimally absorbed (leaves appear green) Other plant pigments become noticeable in the fall when chlorophyll breaks down and the other pigments are uncovered Light reactions → ATP NADPH Consist of two pathways - - Both pathways transform solar energy into chemical energy Only the noncyclic pathway produces NADPH\~ 1. - - - 2. - - 3. - - 4. - 5. - 6. 7. 8. Chemiosmosis - movement of ions down a chemical gradient Final products; ATP, NADPH **Photosynthesis Cycle Simplified** 1. 2. 3. 3 Phases of Calvin Cycle (Stroma) 1. a. 2. b. c. 3. d. Cycle need to happen 6 times to produce 1 glucose molecule C3 (Normal) - 85% of plants carry out C3 photosynthesis \| Mesophyll C4 Photosynthesis - (alters location) Mesophyll cells → bundle sheath cells CAM Photosynthesis - CO2 taken up during the night (carbon fixation at night) and stored until daylight, then undergoes calvin cycle (Changes timing) (mesophyll cell) Week 8 ====== **Somatic Cells** - the body cells that continue to undergo cell division even as an adult **Stem Cells -** unspecialized cells that can develop into many different types of cells in the body, including blood cells, brain cells, and muscle cells **Apoptosis -** programmed cell death, decreasing the number of cells Occurs during development to remove undesired tissue, like the tail of a tadpole Plays a role in preventing cancer **Cell Cycle** **Interphase** (divided into three stages) **G1 -** Stage before DNA Synthesis \| Cell grows and performs normal functions **S Phase -** DNA Synthesis \| DNA Synthesis occurs **G2 Phase -** Stage after DNA synthesis **\|** Cell prepares for mitosis **Mitotic Stage** **Mitosis -** division of the nucleus **Cytokinesis -** Division of the cytoplasm **The Stages of Interphase Deeper Dive** **G1 -** cell doubles its organelles and accumulates material for DNA synthesis - **S** : DNA Replication occurs - **G2** : The cell synthesizes proteins for cell division Check for replication to make sure it is done properly **The mitotic stage** **Mitosis -** the division of the nucleus, follows interphase Sister chromatids separate into daughter chromosomes Distributed to two daughter nuclei **Cytokinesis -** division of the cytoplasm, follows mitosis Two daughter cells that are identical to the mother cell are the result **Apoptosis** Cell passes through typical series of events that brings out cell destruction **Caspases** are responsible for killing the cell / cell destruction **Control of the Cell Cycle** Eukaryotic cells have a complex system for regulating the cell cycle The cell cycle is controlled by **Internal Signals** - - **External signals -** tell the cell whether or not to divide **3 checkpoints control the cell cycle** **G1** → is the DNA damaged? **G2** → is DNA replication complete? **M** → are chromosomes going to be properly distributed? **CRITICAL FOR PREVENTING CANCER DEVELOPMENT** **A DAMAGED CELL SHOULD NOT COMPLETE MITOSIS** **Growth Factors** - signals that set into motion the events associated with entering the cell cycle **Proto-oncogenes and Tumor Suppressor Genes** **Proto-oncogenes (deciding)** - - - **Tumor Suppressor Genes** - - - - Cancer can develop when cells in the body begin to grow uncontrollably due to genetic mutations. Some of these mutations could include proto-oncogenes mutating or tumor suppressor genes malfunctioning. Typically, the spread of cancer can occur due to the cell cycle malfunctioning or deregulating, leading to cells dividing without the typical checks and balances. The uncontrolled growth and spread of cancer cells is what makes cancer so dangerous and difficult to treat. **Carcinogenesis -** development of cancer (multi stage process) - - - - Eukaryotic chromosomes are composed of **chromatin:** a combination of DNA & protein, mostly histones Condensed dna - DNA without histone proteins Maintaining the chromosome number **Diploid (2n) -** cells have a two (a pair) of each type of chromosome - **Haploid (1n)** - Cells have only one of each type of chromosome - **Mitosis -** the division of the nuclear contents in which the chromosome number stays constant - After DNA replication during interphase, each chromosome is composed of two sister chromatids held together by a centromere - - The **spindle fibers** of microtubule fibers brings an orderly distribution of chromosomes to the daughter nuclei Centrosomes organize spindle microtubules - - **Prophase** Nuclear membrane breaks part Centrosomes duplicate; they begin moving opposite to each other Chromatin condenses into chromosomes Spindle fibers begin to form **Prometaphase** Kinetochores appear on each side of the centromere Kinetochores of each chromatid attach to a spindle fiber and extend from the poles to the chromosomes, pulling them to alternate poles to being aligning chromosomes **Metaphase** Chromosomes are aligned at the metaphase plate **Anaphase** Kinetochore spindle fibers shorten, pulling chromosomes closer to the ends **Telophase** Spindle fiber disappears Nuclear membrane reassemble around chromosomes Nucleolus appears in each daughter nucleus Cytokinesis begins (splits cytoplasm and active filaments, stretch the cells apart and eventually split) **Mitosis in Plant Cells** Permits growth and repair as in animal cells Occurs in meristematic tissues that divide throughout life of plant Goes through same phases as animal cells Does not use centrioles or asters **Cytokinesis in Plant Cells** - - - - - **Meiosis** Overview - begins with one diploid parent cell - - - - - - **Fertilization** - - - **First Division** - - - - - **Prophase I** - - - - - **Metaphase I** - **Anaphase I** - **Telophase I** - - - **Interkinesis** - - **Meiosis II - Replicates** **Human Life Cycle** (mitosis and meiosis required) Haploid (sperm cell) and haploid (egg) fuse **Zygote** has a diploid (2n) number of chromosomes - **Spermatogenesis and Oogenesis in Humans** - - **Spermatogenesis** Process begins at puberty and continues throughout life Primary spermatocytes (2n) divide in meiosis I to form two secondary spermatocytes (1n) Secondary spermatocytes divide in meiosis II to produce four spermatids (1n) **Oogenesis** Begins in the ovaries of a female fetus - Resumes at puberty One primary oocyte continues the process of meiosis during each menstrual cycle Primary oocyte (2n) divides in meiosis I to produce one secondary oocyte (1n) and one polar body (1n) - If the secondary oocyte (1n) is fertilized, meiosis II will proceed If it isn't fertilized, it disintegrates **Patterns of Gene Inheritance** **Genetics -** explains the process of inheritance and why there are variations between offspring from one generation to the next **Gregor Mendel -** father of genetics In plants and humans, chromosomes come in pairs called homologous chromosomes One member of the pair is inherited from the father, and one from the mother Homologous pairs have certain characteristics - - - - **Law of Segregation -** mendel had no knowledge of chromosomes, but he decided, based on his observations, that the following were true: - - - - - **Phenotype -** an individual's actual appearance - **Genotype -** alleles carried by the chromosomes that are responsible for a given trait **Inheritance of a Single Trait** - - - In the case of a single trait, there are three possible combinations of the two alleles - If the two alleles are the **same** (homo), the individual is said to be **homozygous** If the two alleles are **different** (hetero), the individual is said to be **heterozygous** **FF** **Homozygous dominant** **Freckles** -------- -------------------------- ----------------- **Ff** **Heterozygous** **Freckles** **ff** **Homozygous recessive** **No freckles** There is a sunflower, sunflower two traits (yellow dominant) (orange recessive) When these two organisms cross and produce a new sunflower, how many sunflower babies will be yellow? **Gamete Formation** Genotype has two alleles for each trait, whereas the gamete has one allele for a trait - - When solving genetics problems - - SC Sc Cs cs ---- ------ ------ ------ ------ SC SSCC SSCc SsCC Sscc Sc SSCc SScc SsCc Sscc Cs SsCC SsCc ssCC Ccss cs SsCc Sscc ssCC ccss S = Black s = White C = curly c = straight Black + Curly - 9/16 Black + Straight - 3/16 White + Curly - 3/16 White + Straight - 1/16 9 : 3 : 3 : 1 **Pedigree** - a chart of family\'s history with regard to a genetic trait - - - **Autosomal Recessive Disorders** Two recessive alleles are required to display an autosomal recessive disorder **Tay-Sachs disease** - - - - **Cystic fibrosis (CF)** - - - **Phenylketonuria (PKU)** - - - **Sickle-cell disease** - - - Immediate symptoms include clogging of blood vessels and breakdown of red blood cells Other symptoms include poor circulation, anemia, and low infection resistance Internal hemorrhaging leads to further complications **Autosomal Dominant Disorders** **Marfan Syndrome** - - - - **Huntington\'s Disease** - - - - - **Osteogenesis imperfecta** - - - - - **Codominance** Occurs when alleles are equally expressed in a heterozygote - - - **Rh Factor** - **Polygenic Inheritance** Occurs when a trait is governed by two or more genes (each with two sets of alleles) Dominant alleles have a quantitative effect on the phenotype, and these effects are additive The result is a continuous variation of phenotypes An example of this is skin color **Skin color** Skin color is the result of pigmentation produced by melanocyte cells More than 100 different genes influence skin color - When two individuals with the genotype AaBbCc reproduce with one another, their offspring may range in skin color from verydark to very light. The phenotype distribution follows a bell- shaped curve (characteristic of a polygenic trait) **Environmental Influences** Environmental factors such as nutrition or temperature can influence the expression of genetic traits Polygenic traits are especially influenced by environment - - - - Exam 3 ====== **DNA Structure** **DNA -** deoxyribonucleic acid - genetic material **Nature of the Genetic Material** 1931 - discover of the genetic role of DNA begin with research by Frederick Griffith Worked with streptococcus pneumoniae, bacteria that cause pneumonia in animals - - **Experiment** By the 1940s scientists recognized that genes are located on chromosomes, and that chromosomes contain both proteins and nucleic acids. Debate arose about whether DNA or protein was the genetic material 1944, Oswald Avery and his co investigators reported that DNA was the transforming substance. **Results of Avery and his co colleagues** - - - - **Alfred Hershey and Martha Chase** Demonstrated that DNA is the genetic material, not proteins Two Experiments - - -  - **Structure of DNA** James Watson and Francis H. C. Crick determined the structure of DNA in 1953 DNA is a chain of nucleotides Each nucleotide is a complex of three subunits - - - **Four possible bases in DNA** Two **Purines** with a double ring - - Two **Pyrimidines** with a single ring - - DNA is a polynucleotide **Strand** with a backbone of alternating phosphate and sugar groups - **Structure of DNA cont.** Two polynucleotide strands make up a DNA **double helix** The strands are held together by hydrogen bonds between the bases - - - - - Unwound DNA helix resembles a ladder - - Two DNA strands are antiparallel-oriented in opposite directions - - - - - **DNA Replication** - the process of copying one DNA double helix into two identical double helices. - 1. 2. DNA replication is **semiconservative** - - **Stages of DNA replication** Because strands are antiparallel and DNA polymerase can only add new nucleotides to one chain, DNA synthesis occurs in the opposite directions - - DNA ligase connects Okazaki fragment and seals breaks in the sugar-phosphate backbone The two double helix molecules are identical to each other and to the original DNA molecule **Gene Expression** The process of using a gene sequence to synthesize a protein - - - **Transcription** - - **Translation** - - - 1. a. b. c. 2. d. e. f. 3. g. h. i. RNA polymerase binds to promoter region Helicase unwinds DNA Elongation - RNA polymerase adds nucleotides Transcription begins with an RNA polymerase, binding to the promoter region, and then helicase unwinds a portion of the DNA strand. The following step is elongation, which is the process of mRNA synthesis. This process involves RNA polymerase moving along the DNA template strand, adding the complementary RNA nucleotides to the DNA nucleotides. The final step is termination, which occurs until the RNA polymerase (elongation) meets a stop codon, ultimately stopping the Transcription process. The mRNA strand is complete and detaches from the DNA strand. **Processing of mRNA** - - - - A guanine cap is added to the 5' end A poly-A tail is added to the 3' end The mature mRNA molecule is ready **Translation** - - **The Genetic Code** Triplet code: each three-nucleotide unit of an mRNA molecule is called a **codon** - - - Three are stop codons (UAA, UGA, UAG) that signal termination **AUG = Start Codon \| codes for methionine?** The genetic code is universal in all living things Purpose of each codon is meant to find their own amino acid **Transfer RNA** - - - - Order of mRNA codons determines the order in which tRNA brings in amino acids **Codon (mRNA) =** CGG **Anticodon (tRNA) =** GCC **Amino Acid (protein) =** Arginine **Ribosomes and Ribosomal RNA** **Ribosome -** Initiation Elongation Termination **Control of Gene Expression** Each cell type contains its own specific protein combination to distinguish it from other cells - - - - The activity of selected genes accounts for the specialization of cells Gene expression is controlled in a cell, and this control accounts for its specialization **Control of Gene Expression in Prokaryotes** E Coli. can use various sugars as a source of energy and carbon - - - An **Operon** is a cluster of genes usually encoding for proteins related to a certain metabolic pathway, along with the short DNA sequences that coordinately control their transcription Control Sequences - -  - - The lac operon in E. coli includes three genes that code for enzymes needed for lactose metabolism and are under the control of one promoter and one operator. **When lactose is absent:** A repressor protein binds to the operator. RNA polymerase cannot transcribe the three genes of the operon (genes are not expressed). The lac repressor is encoded by a regulatory gene located outside the operon. **When lactose is present:** Lactose binds with lac repressor. The repressor is unable to bind to the operator. RNA polymerase is able to transcribe the genes. Lactose-digesting enzymes are produced. The lac operon is considered an inducible operon. Only activated when lactose induces its expression. Repressible operons are usually active until a repressor turns them off. **In prokaryotes,** a single promoter serves several genes that make up a transcription unit or operon. In eukaryotes, each gene has its own promoter. Eukaryotes employ a variety of mechanisms to regulate gene expression. Affect whether the gene is expressed, the speed with which it is expressed, and how long it is expressed There are two different scenarios for eukaryotes. When lactose is present, the lactose binds with the lac repressor, making the repressor unable to bind to the operator. Consequently, RNA polymerase is able to transcribe the genes, producing lactose-digesting enzymes. When lactose is not present, the repressor protein is able to bind to the operator, preventing the production of lactose-digesting enzymes and the transcription of the genes by the RNA. **Levels of Gene control** Eukaryotic gene expression is controlled at different levels - - - - - - - - - - - - - - - - - - - - - - - **Gene Mutations and Cancer** A **gene mutation** is a permanent change in the sequences of bases in DNA Effects can range from changing expression of a gene to complete inactivity of a protein Germ-line mutations occur in sex cells and can be passed to subsequent generations (23rd chromosomes)/ - **Somatic Mutations,** which are not passed on to the next generation, can also lead to cancer development (1-22 chromosomes) **Causes of Mutations** Spontaneous mutations arise due to abnormalities in normal biological processes Induced mutations result from environmental influences **Errors in DNA Replication** DNA replication errors are a rare mutation source Proofreading by DNA polymerase usually minimizes errors in the new strands - Typically, there is one error per one billion nucleotide pairs replicated **Mutagens** **Mutagens** are environmental influences that can cause mutations - DNA repair enzymes constantly monitor and repair any irregularities, generally keeping the mutation rate due to mutagens low **Transposons -** jumping genes DNA sequences that move within and between chromosomes, often altering neighboring gene expression in new location (usually by increasing/decreasing gene expression The presence of white kernels in corn is due to a transposon within a gene for a pigment-producing enzyme (indian corn) Charcot-Marie-Tooth disease is a rare neurological disease in humans and is caused by a transposon (Mariner) - **Point Mutations** → involve a change in a single DNA nucleotide - **Possible outcomes** May have no effect at all May produce an incomplete protein (STOP codon) May cause change in a specific amino acid MAy produce an abnormal protein - **Effect of Mutations on Protein Activity** **Frameshift Mutations** → one or more nucleotides are either inserted or deleted from DNA The result can be a completely new sequence of codons and a nonfunctional protein **Nonfunctional Proteins** A single non functioning protein can have a dramatic effect on the phenotype, because enzymes are often a part of metabolic pathways. PKU (Phenylketonuria) and albinism **Mutations can Cause Cancer** - - - P53 is a major tumor suppressor gene that is more frequently mutated in human cancers than any other known gene - - Most cancers begin as an abnormal cell growth that is **benign**, or not cancerous, and usually does not grow larger Additional mutations may occur and the growth may become **malignant**, meaning that it is cancerous and possesses the ability to spread **Characteristics of Cancer Cells** **Cancer cells are genetically unstable** - - - - **Cancer cells do not correctly regulate the cell cycle** - - - **Cancer cells can escape the signals for cell death** - - - - - **Cancer cells can survive and proliferate elsewhere in the body** - - - **Germ-line mutations** - A gene change in a body\'s reproductive cell (egg or sperm) that becomes incorporated into the DNA of every cell in the body of the offspring **Somatic mutations** **Induced mutations** **Spontaneous mutations** - heritable changes in the sequence of genetic material **Point mutations** - a change in single DNA nucleotide sequence, potentially producing an incomplete protein (STOP CODON), a change in a specific amino acid, or the production of an abnormal protein (EX: Sickle Cell disease) **Frameshift mutations** - the insertion or deletion of nucleotide bases, potentially creating a new sequence of codons and a nonfunctional protein **Week 13/14** **Biotechnology** - the use of natural biological systems to create a product r achieve some other end (enabled by DNA knowledge) Scientists can modify genomes through genetic engineering to improve an organism\'s characteristics, make biotechnology products, or treat cancer and genetic disorders **Genome -** cloned genes are used to alter the genome of viruses or cells - **GMO (Genetically Modified Organism)** has a modified genome; usually with DNA technology **Cloning →** production of identical copies of an organism, cell, or DNA through asexual means. - Uses of gene cloning - - - **Recombinant DNA Technology** **Recombinant DNA (rDNA)** Contains DNA from two or more sources To make rDNA, a **vector** is needed → a piece of DNA that foreign DNA can be added to - - - Two enzymes needed to introduce foreign DNA into vector DNA **Restriction Enzyme →** to cleave vector DNA - - - **DNA Ligase →** will seal the foreign DNA into the opening in the vector DNA created by the restriction enzyme After the cutting, a gap is created in which pieces of foreign DNA can be placed if there is complementary pairing. Foreign DNA and vector DNA are cleaved with same restriction enzyme - - **DNA Sequencing →** the procedure that determines the order of nucleotides in a segment of DNA Helps identify the specific alleles and sequences - - **The polymerase Chain Reaction** - - - PCR is a chain reaction since the target DNA is duplicated repeatedly **DNA Analysis** - - - - **Short tandem repeat (STR)** is now currently used STRs are the same short sequence of DNA bases that recur several times **STR profiling** - **CRISPR -** a relatively new advance in DNA technology, targeting specific DNA sequences for replacement or removal - - **CRISPR -** used as an immune defense system against viruses, targeting specific sequences of nucleotides for editing in any organism. **Cas9 -** Identification of nucleotide sequences in genomic DNA of viruses, inactivating it - **PCR -** the process of creating copies of a segment of DNA **Gel electrophoresis -** the method used to separate combined DNA,RNA, or proteins. Molecules separated are pushed by an electric current through a gel that contains small pores **Genetically modified bacteria** Bacteria that live on plants have been altered from frost-plus to frost-minus bacteria - **Transgenic Bacteria** Can be selected for their ability to degrade a particular substance Ability can be enhanced by bioengineering - Foreign genes can be introduced into Immature plant embryos Protoplasts → plant cells with cell wall removed - - - **Genetically modified Animals** Technology has been developed to insert genes into the eggs of animals It is possible to microinject foreign genes by hand or by vortex mixing **Vortex Mixing:** - - When the eggs are fertilized, transgenic offspring are produced - **Gene Pharming** - - - - - - **Cloning Process** - - - **Gene Therapy** - Various methods of gene transfer have been used - - - **SCID (Severe combined immunodeficiency)** - - Gene therapy treatment steps: Remove bone marrow stem cells from body Infect cells with a virus that carries the normal gene that codes for the enzyme, ADA Return cells to patient with the hope they will divide, expressing the normal gene for ADA **Ex Vivo Gene Therapy** **Treatment of familial hypercholesterolemia** - - - **In Vivo Gene Therapy** - - **Treatment** The gene needed to cure cystic fibrosis is sprayed into the nose or delivered to the lower respiratory tract by an adenovirus vector or by using liposomes Increasingly relied upon as a part of cancer treatment - - - **RNA Interference** RNA interference, or RNAi - **Sequencing the Genome** Discovery of single nucleotide polymorphisms (SNPs) - - - The HGP (Human Genome Project), along with identification of RNAs in cells, led to the determination that humans have approximately 20,000 genes - - Most genes are expected to code for proteins Noncoding or "junk DNA" may have important functions **Genome Architecture** Nearly 98% of the human genome is DNA that does not directly code for amino acid sequences Some is transcribed into rRNA or tRNA - The rest of the genome consists of a variety of sequences - Genome architecture Transposable elements (or transposons) - - - Repetitive DNA elements - - **Gene -** A genomic sequence, of DNA or RNA, directly encoding functional products, either RNA or protein - - - **Functional Genomics** Compare genomes of organisms Identify similarities between the sequence of human bases and those of other organisms - - Understand the function of the various genes discovered within each genomic sequence and how these genes interact Uses DNA microarrays to tell which genes are turned on in a specific cell or tissue at a certain time or under certain conditions **Proteomics** A study of the structure and function, and interactions of cellular proteins - - **Bioinformatics** - - - **BLAST** → stands for basic logical alignment search tool - - -