Ap bio review notes

.pdf

School

Cinco Ranch High School**We aren't endorsed by this school

Course

SCIENCE BIOLOGY

Subject

Biology

Date

Jan 17, 2025

Pages

Uploaded by MegaBraverySeahorse3

(In)Complete AP Biology Study Guide

KEY: Red highlight: idfk aesthetics Bolded and coloured: important points to remember Highlighted: emphasized by the lecturer Bookmarks (for easier navigation)Unit 1: Properties Water, Dehydration Synthesis & Hydrolysis; Carbs and Lipids(Unit Name: Chemistry of Life) Proteins and Nucleic Acids1.1: Structure of Water and Hydrogen Bonding1.2 Elements of Life1.3: Introduction to Biological Macromolecules1.4: Properties of Biological MacromoleculesProteins (review, sort of)The 4 Structure Levels of ProteinsNucleic AcidsUnit 2: Organelles and Cell Size(Unit Name: Cell Structure and Functions) Cellular Organelles: (These are the ones specifically mentioned in Exam Description)The Endomembrane System2.3: Cell SizeMembrane TransportThe Phospholipid BilayerConcentration Gradients (types of transport)Unit 3: Photosynthesis(Unit Name: Cellular Energetics) The Light Reactions (of Photosynthesis)Calvin CycleUnit 3: Cellular Respiration(Unit Name: Cellular Energetics) GlycolysisKrebs cycleElectron Transport ChainFermentationLactic Acid FermentationPhotosynthesis vs. Cellular RespirationUnit 4: Cell Communication Signal Transduction PathwaysTypes of Cell SignalingPhosphorylationThe Process: Part 1 - ReceptionThe Process: Part 2 - TransductionMutations in the PathwayFeedback MechanismsNegative Feedback and Homeostasis

Positive Feedback and HomeostasisUnit 4: The Cell Cycle Mitosis OverviewsMitosis: The ProcessThe G0 CycleRegulation of the Cell Cycle (checkpoints)Interactions between cyclins and cyclin-dependent kinasesExternal Factors that regulate cell cycleDisruptions to the Cell CycleMeiosis: Key OverviewMeiosis 1: Detailed ProcessMeiosis 2: Detailed ProcessesMeiosis and Genetic DiversityNondisjunction in MeiosisUnit 5: Heredity Common AncestryMendel's Law of SegregationMendel’s Law of Independent AssortmentFertilizationRules of ProbabilityChromosomal Inheritance and Environment Effects on PhenotypeUnit 6: DNA Structure and Replication(Unit Name: Gene Expression and Regulation) DNA ReplicationProtein SynthesisDNA vs. RNA StructureNucleotidesDNA StructureProkaryotes Vs. EukaryotesComponents of DNA Replication“Semiconservative”The Role of DNA PolymeraseThe Leading vs. Lagging Strand ProcessSummary: The Process of DNA ReplicationDNA Proofreading and RepairTranscriptionmRNA ProcessingTranslationRetroviruses

Unit 6: Gene Regulation: Prokaryotic and EukaryoticComponents of Gene RegulationEpigenetic (above the genes) ChangesProkaryotes Vs. EukaryotesTranscriptionDNA MethylationmiRNA(Unit Something): Mutations and BiotechnologyMutationsHorizontal AcquisitionSharing DNA: Prokaryotes Vs. EukaryotesTransduction, Transformation, ConjugationBiotechnologyALSO:CHI-SQUARED TESTS

Unit 1: Properties Water, Dehydration Synthesis & Hydrolysis; Carbs and LipidsTopics 1.1-1.4 KEY OVERVIEWS ● How properties of water that result from its polarity and hydrogen bonding affect its biological function ● Composition of macromolecules ● Description of the properties of the monomers and type of bonds that connect the monomers in biological macromolecules Key Terms - Monomers: the subunit that serves as a building block of a polymer - Polymer: a large molecule consisting of many similar or identical monomers linked together by covalent bonds Monomers of: ● Carbohydrates: monosaccharides ● Proteins: amino acids ● Nucleic acids: nucleotides ○ Phosphate group ○ Pentose sugar ○ Nitrogenous base 1.1: Structure of Water and Hydrogen Bonding - The subcomponents of biological molecules and their sequences determine the properties of that molecule Properties of Water ● Water: 2 hydrogen and 1 oxygen bonded together with COVALENT bonds ○ Water is POLAR ○ Forms hydrogen bonds ● The hydrogen bonds between water molecules result in cohesion, adhesion, and surface tension ○ Cohesion: water molecules attached to each other ○ Adhesion: water molecules attached to OTHER things ○ Surface tensions: hydrogen bonds resist being stretched 1.2 Elements of Life Carbon: used to build biological molecules such as carbohydrates, proteins, lipids, nucleic acids ● Used in storage compounds (starch/glycogen) ● Cell formations in all organisms ○ Cell wall; cellulose for plants

Nitrogen: used to build proteins and nucleic acids Phosphorus: used to build acids and certain lipids The 4 Carbon Compounds***Carbohydrates: sugars and starches Lipids: fats and oils Nucleic Acids: nucleotides Proteins: Amino Acids carbon, hydrogen and oxygen The “hydrates” of carbon: twice as much hydrogen as carbon/oxygen in the molecule nonpolar status PHOSPHOLIPIDS: have phosphorus Carbon, hydrogen, oxygen Carbon, hydrogen, oxygen, nitrogen, phosphorus Carbon, hydrogen, oxygen, nitrogen, sulfur 1.3: Introduction to Biological Macromolecules Hydrolysis and Dehydration Synthesis - Used to cleave and form covalent bonds between monomers Dehydration Synthesis ● Monomers are joined by removal of OH (carboxyl) from one monomer and removal of H from another at the site of bond formation Hydrolysis ● Monomers are released by the addition of a water molecule, adding OH (carboxyl) to one monomer and H to the other 1.4: Properties of Biological Macromolecules - Structure and function of polymers are derived from the way their monomers are assembled. Nucleic Acids: ● Biological information is encoded in sequences of nucleotidemonomers. Each nucleotide has structural components: ○ Five carbon sugar (deoxyribose or ribose) ○ Phosphate ○ Nitrogen base (ATGC or U) ● Combine nucleotides through dehydration synthesis

Proteins ● The specific order of amino acids in a polypeptide (primary structure) determines the overall shape of the protein. ○ Amino acids have directionally, with one end being an amino group and the other end being a carboxyl group. Proteins comprise linear chains of amino acids, connected by the formation of covalent bonds ○ The R group of an amino acid can be categorized by chemical properties (hydrophobic, etc). The interaction of these R groups determine structure and function of that region Carbohydrates ● Simple: Monosaccharides and Disaccharides ○ Dehydration synthesis of two monosaccharides makes a disaccharides → glycosidic linkage ● Complex: Polysaccharides ○ Comprised of sugar monomers whose structures determine the properties and functions of the molecules Lipids: Fats, Steriles, Phospholipids ● Nonpolar macromolecules ● Fats: composed of triglycerides (see image below) ○ storage/consumed fats, make up cell membranes ○ Triglycerides: 3 fatty acids (sat or unsat) + a molecule. Dehydration synthesis 3 times to make 3 tails ● Steriles: steroid molecules ○ Four linked carbon rings; cholesterol, for example ○ Maintain cell structure and cell fluidity ● Phospholipids: part of every cell membrane lipid bilayer ○ Contain polar regions that are hydrophilic at the HEAD ○ The tails are hydrophobic**differences in saturation determine the structure and function of lipids** ● Saturated fatty acids: no double bonds ● Unsaturated fatty acids: yes double bonds, more flexible PHOSPHOLIPID BILAYER Phospholipids contain polar regions that interact with other polar molecules (ie. water) and with nonpolar regions that are often hydrophobic. - Phospholipids are a key component of all cell membranes: creates a selectively permeable barrier; heads will face out and tails face in - contain cholesterol and protein **proteins: both peripheral and integral member proteins** RETURN TO BOOKMARKS

Proteins and Nucleic Acids Proteins (review, sort of) ● Molecules needed to build proteins (listed in the orange chart above) ○ ALWAYS has a central carbon ○ Hydrogen connected to the carbon ○ The R chain (defines their properties and functions) ○ Amino functional group ○ Carboxyl functional group Protein Combination and Separation The combination of two amino acids makes a PEPTIDE BOND and multiple combinations of amino acids makes a POLYPEPTIDE CHAINDehydration Synthesis Amino acids are monomers that bond together with a peptide covalent bond to form a polypeptide (polymer) through process of dehydration synthesis Hydrolysis Breaks apart polypeptide chains into individual amino acids The 4 Structure Levels of Proteins PRIMARY STRUCTURE ● Quite literally just a long chain with an amino end and carboxyl end ○ Amino acids are added onto the carboxyl end ● Determined by the sequence order of their constituent amino acids ○ The specific order of amino acids in a polypeptide determines the overall shape of the protein SECONDARY STRUCTURE ● Secondary structure rises through local folding of the amino acid chain into elements such as alpha-helices and beta sheets ○ The alpha helical conformation is a result of hydrogen bonding TERTIARY STRUCTURE ● The overall three-dimensional shapeof the protein, which often minimizes free energy.

Decreasing the free energy increases tertiary stability ● Components of a tertiary structure: ○ Hydrogen bonds, disulfate linkage, ionic bonds, hydrophobic interactions QUATERNARY STRUCTURE ● Arises from non-covalent interactions between MULTIPLE polypeptide units ○ Basically, if 2 tertiary structures came together Nucleic Acids Structural Components of Nucleotides ● Nitrogenous Base:has 2 types ○ Pyrimidine has a single ring (Thymine, Cytosine, Uracil) ○ Purine has a double ring on the base (Adenine, Guanine ● Phosphate Group ● Five-carbon sugar:deoxyribose or ribose Dehydration Synthesis Covalent bonds are used between nucleotides to form Nucleic Acids (polymers) - The phosphate group of one nucleotide combines with the hydroxyl end of the previous nucleotide Hydrolysis Basically the opposite. DNA and RNA synthesis Nucleotides are added to the 3’ end of the strand, leading to covalent bonds between nucleotides. ● Antiparallel ⇒double helix ○ Each strand runs in an opposite 5’-3’ orientation ○ 5’ is the phosphate, 3’ is the hydroxyl end ● Binding of the nitrogenous bases ○ Cytosine + guanine with 3 hydrogen bonds ○ Adenine + Thymine with 2 hydrogen bonds Both DNA and RNA: ● Have all 3 components (nitrogenous base, carbon sugar, phosphate group) ● Nucleotides are joined together with covalent bonds ● 5’-3’ ends ● Bases perpendicular to the sugar-phosphate backbone Differences in the two: DNA has: - Double strand - Deoxyribose 5-carbon sugar - Thymine - Antiparallel in directionality RNA has: - Single strand - Ribose 5-carbon sugar - Uracil RETURN TO BOOKMARKS

Unit 2: Organelles and Cell Size Cellular Organelles: (These are the ones specifically mentioned in Exam Description) RIBOSOMES ● Comprised of ribosomal RNA (rRNA) and protein ● Their function: synthesizes protein according to mRNA sequence ● Found in all living things, reflecting common ancestry ○ Proves the theory that everything shares a common ancestor ● Two types of ribosomes: ○ Attached to the Rough ER:makes proteins that are going to be exported from cell ○ Free Ribosomes:makes proteins for the cell to use exclusively ENDOPLASMIC RETICULUM ● Occurs in TWO FORMS: rough and smooth ● Rough is associated with membrane bound ribosomes ○ Small, tiny ribosomes are attached to the ER, which is why it’s called Rough ○ SYNTHESIZES PROTEINS USING THE ATTACHED RIBOSOMES ○ The folded nature of the rough ER compartmentalizes the cell, so it increases efficiency by allowing multiple processes to happen at once ● Smooth ER does NOT have ribosomes bound to it ○ detoxifies certain molecules ○ SYNTHESIZES LIPIDS● Also helps in transporting products of the ribosomes ○ Once finished synthesizing, the ER will transport them to other places in the cellGOLGI COMPLEX ● Membrane bound structure that consists of a series of flattened membrane sacs ○ Also has some vesicles attached to it, to ship out proteins ● Two sides to it: ○ The cis face: where all the incoming proteins go to be modified ○ The trans face (wtf): where all the modified faces go to be “shipped out” ● Functions: correct folding and chemical modification of newly synthesized proteins and packaging for protein trafficking

MITOCHONDRIA ● Responsible for producing ATP, the main energy form used in cellular organisms ○ Powerhouse of the cell Physical Attributes of the Mitochondria ● Have double membranes: allows for compartments for different metabolic reactions + increased surface area ○ Outer membrane is smooth ○ Inner membrane is highly convoluted, forming folds ● The space between the OUTER and INNER: the intermembrane space ● Space inside the inner membrane:the matrix LYSOSOMES ● Membrane enclosed sacs that contain hydrolytic enzymes ○ Hydrolytic enzymes break down any particles that don’t belong in the cell ● Hydrolytic enzymes are important in intracellular digestion, recycling of a cell’s organic materials, and programmed cell death (apoptosis) ○ Responsible for getting rid of any things that have made their way into the cell that need to be broken down/disposed of ● Also responsible for digesting food ○ Merges with vacuoles and uses hydrolytic enzymes to break them down VACUOLE ● Membrane bound sac that plays many differing roles in both plants and animals Plant Cells Maintains turgor pressure in the cell by storing water or molecules in them Surrounded by a “tonoplast” membrane Animal Cells Act as balancers, to main homeostasis and balance within the cell so it doesn’t dry out/drown Store food and waste products until they’re digested or thrown out of the cell CHLOROPLASTS: REFER TO PHOTOSYNTHESIS UNIT DOWN BELOW RETURN TO BOOKMARKS

The Endomembrane System The ER synthesizes proteins, the Golgi packages it, and then the vesicle will export them Other (taken from the Guided Practice) Exocytosis: the fusion of the vesicle with the cell membrane in order to dispose of waste Modification of a protein: done by golgi body by adding sugars and/or phosphates Cilia: the thing that makes the cells move around RETURN TO BOOKMARKS2.3: Cell Size ● Surface area-to-volume ratios affect the ability of a biological system to obtain necessary resources, eliminate waste products, and basically survive. ○ The larger the ratio is, the more efficient the cell is going to be Key Overview (This is a short unit) ● surface area of the plasma membrane must be large enough to adequately exchange materials ○ These limitations can restrict cell size and shape ● Smaller cells typically have a higher surface area-to-volume ratio and more efficient exchange of materials with the environment ● As cells increase in volume, the relative surface area decreases and the demand for internal resources increases ● More complex cellular structures (ie. membrane folds) are necessary to adequately exchange materials with the environment ● As organisms increase in size, their surface area-to-volume ratio decreases, affecting properties like rate of heat exchange with the environment RETURN TO BOOKMARKS

Membrane Transport The Phospholipid Bilayer ● Phospholipids have both hydrophilic and hydrophobic regions that make up the membrane ○ The hydrophilic phosphate regions areoriented towards the aqueous external or internal environments ○ Hydrophobic fatty acid regionsface each other inside the membrane ● Embedded proteins can be hydrophilic, with charged and polar side groups, or hydrophobic with nonpolar side groups ● The fluid mosaic model of cell membranes consist of a structural framework of phospholipid molecules embedded with proteins and others that can flow around the surface of the cell within the membrane ○ Glycoproteins and glycolipids: carbon chains attached to proteinsPermeability ● The structure of the cell membranes result in selective permeability ○ SP is a direct consequence of the membrane structure, described by the fluid mosaic ● Cell membranes separate the internal environment of the cell from the external What Can Pass Through? ● Small Nonpolar molecules can freely pass among the MEMBRANE ○ N2, O2, CO2 ● Hydrophilic substances move across the membrane through EMBEDDED CHANNEL AND TRANSPORT PROTEINS ○ Large polar molecules and ions ○ They’re too big to move through the membrane, so they use proteins ● Polar uncharged molecules pass through membrane in small amounts (ie. H2O)

Cell Walls (found in plants) ● Cell walls provide a structural boundary as well as permeability barrier for some substances to the internal environment. ○ Usually made up of polysaccharides, esp. Cellulose, to give it structure ○ For plants, prokaryotes and fungi: composed of complex carbohydrates Concentration Gradients ● The selective permeability of membranes allows for the formation of concentration gradients of solutes across the membrane Passive Transport ● The net movement from high concentration to low concentrationwithout direct input of metabolic energy ○ Plays a primary role in the import of metiera and the export of waste ○ Facilitated diffusion!!! ○ Does NOT need ATP Active Transport ● Requires the direct input of low energy to move molecules from regions of low concentration to regions of high concentration ● Hydrolysis of ATP causes shape change in protein, leading to shuffle of proteins in gradient ● Integral proteins allow such substances to pass, along with ATP ○ It moves AGAINSTthe gradient ○ It DOES need ATP ENDO/EXOCYTOSIS ● Require energy to move large molecules into and out of cells. ENDOCYTOSIS ● Cell takes in macromolecules and particulate matter by forming new vesicles derived from the plasma membrane 1. Plasma membraneengulfs the particle 2. Form a vesicle around it and transports into the cell 3. Vesicle fuses with a lysosome that carries digestive enzyme 4. Food is broken down into usable partsEXOCYTOSIS ● Active transport 1. Proteins are produced by the cell (probably by the ribosomes on the ER) 2. Vesicles pinch off from the ERcarrying these proteins and carry them to the golgi apparatus 3. Golgi modifies it 4. Vesicle pinches off from the golgi and travels towards cell membrane 5. Vesicle fuses with the cell membrane and all the contents are released Aquaporins ● Integral membrane proteinsthat allow for the passage of water into the cell ● Very few water molecules can go through the membrane because they’re positively charged ○ Because of that, you must have aquaporinsthat enable water to go through RETURN TO BOOKMARKS

Unit 3: Photosynthesis

Key Overview ● Organisms capture and store energy for use in biological processes ○ Photosynthesis captures energy from the sun and produces sugars ○ Water, Light and Carbon Dioxide creates Oxygen and Sucrose History of Photosynthesis ● Photosynthesis first evolved in prokaryotic organisms ● Scientific evidence supports the claim that prokaryotic photosynthesis was responsible for the production of an oxygenated atmosphere. 6CO2 + 6H20 + Light Energy ⇒C6H12O6 + 6O2 Chloroplasts ● The site of photosynthesis in plants ○ Where solar energy is converted into chemical energy ● Several membrane systems that creates compartments ○ System of compartmentalization allows for organelles to finish their tasks faster Outer Membrane Inner Membrane IntermembraneSpace Thylakoid Membrane

Also a semipermeable membrane that is open to small proteins Regulates the transport in and out of the chloroplast, molecules and ions Space between the inner membrane outer membrane Folded membranes of the thylakoids that are stacked up into “granums” Source of LIGHT REACTIONS Thylakoid Stroma Granum Lumen Absorbs the light in order to be converted into chemical energy Phospholipid bilayer A dense solution, the site of the DARK REACTIONS Stack of thylakoids The Photosynthetic Pigments ● Absorb different wavelengths of light, and are the pigments that convert sun energy. ○ Chlorophyll a ○ Chlorophyll b ○ Carotenoids RETURN TO BOOKMARKSThe Light Reactions (of Photosynthesis) ● Involves a series of coordinated reaction pathways that capture energy present in light to yield ATP and NADPH, which power the production of organic molecules. ○ ATP and NADPH will be used in the Calvin Cycle (Dark Reactions) Photosystem ● Has a collection of pigment molecules (chlorophyll a and b) ● Light harvesting complex ● Reaction center ● Electron transport chain ● Embedded in the thylakoid membrane

Photosystems Photosystem 2 The first photosystem. - Sunlight “excites” the chlorophyll - Light its absorbed by chlorophyll, gets transferred to primary electron acceptor - PEA then passes this down an ETC through a series of molecules embedded in the thylakoid membrane - As it does this, it pumps protons into the thylakoid space as well - Protons come from the water molecules (and actually produces the oxygen molecule) - Thus a PROTON GRADIENT is made (very useful) using photolysis - Adds more energy to a SECOND PHOTOSYSTEM (p1) Photosystem 1 - Picks up energy from P1 and boosts it up to a PEA - These electrons are now transferred directly to proteins in the thylakoid membrane, activating NADPH reductase - Reduces NADP to NADPH - ATP and NADPH are a result from this - This will be used to produce sugar in the Calvin Cycle Highlights of Light Reactions (process summary) ● Light is absorbed by photosystem 2, exciting the electrons ○ It also splits water ○ Electrons that come from water is used to replace chlorophyll a’s lost electrons when they go down the ETC ● Oxygen is diffused out as a byproduct ● Protons are stored in the thylakoid space ○ Electrons are moved the ETC, while moving more protons into thylakoid space ● Protons are used to generate energy that powers the production of ATP ○ This is done by ATP synthase (which produces ATP) ○ ADP is converted into ATP using the protons ● Electrons from photosystem 1 are transferred to NADP reductase to make NADPH ● ATP and NADPH goes to Calvin Cycle RETURN TO BOOKMARKSCalvin Cycle

● The energy captured in the light reactions and transferred to ATP and NADPH powers the production of carbohydrates from carbon dioxide ○ Uses ATP and NADPH to convert CO2 to sugar (glucose) ● Occurs in the stroma ● Three steps: ○ Carbon fixation ○ Reduction ○ Regeneration of RuBP The Process: takes TWO cycles ● Carbon is brought in from the atmosphere and is needed to be fixed into organic molecules ○ The rubisco enzymedoes this job ● Rubisco does this by taking CO2 from the atmosphere and combines it with RuBP to make an organic molecule ○ The molecule is reduced using ATP and NADPH to form G3P ● RuBP is regenerated in order to do it again ● Also known as the C3 pathway RETURN TO BOOKMARKSUnit 3: Cellular Respiration Key Overview ● Cells obtain energy from biological macromolecules in order to power cellular functions ○ Lipis, proteins,carbohydratesare all used to make ATP GLYCOLYSIS ● A biochemical pathway that releases energy in glucose to form: ○ 2 ATP (from ADP) ○ NADH (from NAD+) ○ Pyruvate and inorganic phosphate ● Happens in the cytoplasm of the cell ● 6 glucose molecules are converted into 2 ATP molecules, 2 pyruvate and 2 NADH NAD+ ⇒NADH ● NAD+ combines with 1 proton and 2 electrons to make NADH ● NADH is used to carry these electrons to the electron transport chain PYRUVATE● Is transported from the cytosol to the mitochondrion, where further oxidation occurs ○ Results: 2CO2 and 2 NADH ○ Also makes Acetyl CoA to be used in Krebs Cycle

KREBS CYCLE● Carbon dioxide is released from organic intermediates ● ATP is synthesized from ADPand inorganic phosphate ● Electrons are transferred to coenzymes NADH and FADH2 ● 2-carbon Acetyl CoA combines with 4-carbon OA Acetate to form citrate ○ 4 molecules of carbon dioxide are produced ○ 6 NADH created,electrons are carried off to the electron transport chain ○ FADH2will also carry electrons ● 2 ATP created ELECTRON TRANSPORT CHAIN ● Transfers energy from electrons in a series of coupled reactions that establish an electrochemical gradient across its membranes ○ Cellular respiration in eukaryotes involves a series of coordinated enzyme-catalyzed reactions that capture energy from biological macromolecules ● When electrons are transferred between molecules in a sequence of reactions as they pass through the ETC, the electrochemical gradient of protons (hydrogen ions)across the inner mitochondrial membrane is established. ● Occurs ON the inner membrane of the mitochondria ● NADH oxidizes and loses its 2 electrons ○ Reverts back to NAD+, and goes back to glycolysis/krebs to do it all again ● ETC reactions occur in chloroplasts, mitochondria, prokaryotic plasma membranes ● Electrons are carried down the chain through a series of embedded proteins that act as primary electron acceptors The Proton Gradient ● The transfer of electrons is accompanied by the formation of a proton gradient across the inner mitochondrial membrane or the internal membrane of chloroplasts, with the membrane(s)

separating a region of high proton concentration from a region of low concentration ● The remaining Hydrogen ions will go against the gradient into the other side ○ This builds a proton gradient in the intermembrane spaceThe ATP Synthase enzyme ● Moves the hydrogen ions from high concentration to low concentration ● The active sites in the enzyme create 34 ATP ● The flow of protons back through membrane-bound ATP synthase by chemiosmosis drives the formation of ATP from ADP and inorganic phosphate ○ Known as oxidative phosphorylation in cellular respiration ○ Photophosphorylationin photosynthesis Fermentation ● Allows glycolysis to proceed in the absence of oxygenand produces organic molecules, including alcohol and lactic acid, as waste products. ○ Makes 2 ATP, 2 pyruvate and 2 NADH ○ There is no electron transport chain ● Does NOT occur in the mitochondria (no oxygen present) The Process ● The Pyruvate loses 2 carbon dioxide molecules to become acetaldehyde ○ Gains back 2 electrons and goes back into glycolysis ○ Causes NAD+ regeneration and makes more ATP ○ End product: 2 Ethanol Lactic Acid Fermentation ● Glycolysis is still the same: ATP, Pyruvate, NO oxygen ● Pyruvate gets back 2 electrons, and forms 2 Lactate ○ This causes NAD+ regeneration, and makes more ATP RETURN TO BOOKMARKSConversion of ADP to ATP (and vice versa)● Releases energy, which is used to power many metabolic processes ○ When the high energy bonds in ADP are broken, energy is released into the cell, to fuel a cellular process

Photosynthesis vs. Cellular Respiration Similarities Photosynthesis - Electrons are sent to the ETC during the light-dependent reactions using a carrier - Existence of a proton gradient in the thylakoid space that passes through enzymes to form ATP Cellular Respiration - Electrons are sent to the ETC during glycolysis and Krebs Cycle using NADH/FADH - H+ proton gradient in the intermembrane space that passes through ATP Synthase to make ATP Some differences in photosynthesis and cell resp. Photosynthesis Terminal electron acceptor is NADP+ Happens in the chloroplast Major function is to produce food Cellular Respiration Terminal electron acceptor is oxygen (mostly) happens in the mitochondria Major function is to produce ATP RETURN TO BOOKMARKSUnit 3(ish): Cell Communication Key Overview ● Cells communicate by generating, transmitting, receiving and responding to chemical signals ● Cells ALSO communicate through direct contact with other cells PARACRINE SIGNALING ● Cells that are near one another communicate through the release of chemical messengers ○ Using ligands that can diffuse through the space between the cells ○ Cells communicate over relatively short distances ● Allows cells to locally coordinate activities with their neighbours ○ Especially important during development, when they allow one group of cells to tell the neighbouring group of cells what “cellular identity” to take on ● Synaptic signaling:example of paracrine signaling, where nerve cells transmit signals .AUTOCRINE SIGNALING ● A cell signals to itself,releasing a ligand that binds to receptors on its own surface ○ Important during development, where it helps cells take on and reinforce their correct identities. (ie. cancer, and its role in metastasis)

ENDOCRINE SIGNALING ● When cells need to transmit signals over long distances,they often use the circulatory system as a distribution network for the messages they send ● Signals are produced by specialized cells and released into the bloodstream ○ Carries the the signals to target cells in distant parts of the body ● Hormones: signals that are produced in one part of the body and travel through circulation to reach far-away targets CELL TO CELL ● Gap junctions: tiny channels that directly connect neighbouring cells ○ Water-filled channels that allow small signaling molecules called “intracellular mediators” to diffuse between the two cells ○ Small molecules are able to move between cells, but large proteins cannot ● The transfer of signaling molecules transmits the current state of one cell to its neighbour. ○ This allows a group of cells to coordinate their response to a signal that only one of them may have received. RETURN TO BOOKMARKSSignal Transduction Pathways ● The process that occurs AFTER a signaling molecule (ligand) from one cell has bound to the receptor on another cell ○ Intracellular signal transduction pathways:the chains of molecules that relay signals inside a cell after its been activated

THE PROCESS - PART 1: RECEPTION ● When a ligand binds to the cell-surface receptor, the inside part of the receptor “changes” ○ Usually means it changes shape, which may make it active as an enzyme or let it bind other molecules ○ The ligand-binding domain of a receptor recognizes a specific chemical messenger, which can be a peptide, chemical, or protein, in a specific 1:1 relationship ■ Eg. g protein-coupled receptor in eukaryotes ● The alpha subunit of a protein binds to the receptor, releasing GDP ○ GTP binds to it ● This activates Adenylyl Cyclase, which sets off Part 2 ● The ligand is the first messenger THE PROCESS - PART 2: TRANSDUCTION ● After the ligand binds, the intracellular domain of the receptor protein changes shape, initiating transduction of the signal ● Second messengers:molecules that relay and amplify the intracellular signal Many signal transduction pathways include protein modification and phosphorylation cascades ● After the process begins, the Kinase enzyme phosphorylates molecules,which phosphorylates another molecule, etc. ● Signaling cascades relay signals from receptors to cell targets, often amplifying the incoming signals, resulting in the appropriate responses by the cell, which includes growth, secretion of molecules, or gene expression.

The environment can elicit a cellular response. ● Signal transduction pathways influence how the cell responds to its environment ● Quorum sensing: Microbes communicate with other nearby cells using chemical messengers to regulate specific pathways in response to population density General Summary ● Step 1: reception; Ligand binds to the receptor protein ● Step 2: signal transduction pathway; molecules communicating with each other, changing and sending signals to each other ● Step 3: Cellular Response: transcription from the DNA that creates desired proteins RETURN TO BOOKMARKSExamples provided on the video: Signal transduction may result in changes in gene expression and cell function, which may alter phenotype or result in apoptosis ● Cytokines regulate gene expression to allow for cell replication and division ● Expression of the SRY gene triggers the male sexual development pathway in animals ● HOX genes and their role in development ● Ethylene levels cause changes in the production of different enzymes allowing fruit to ripen RETURN TO BOOKMARKSMutations in the Pathway ● A change in the structure of any signaling molecule affects the activity of the signaling pathway and can alter the cellular response ○ Mutations in any domain of the receptor protein or in any component of the signaling pathways may affect the downstream components by altering the subsequent transduction of the signal ○ Chemicals that interfere with any component of the signaling pathway may activate or inhibit the pathway figure: on the left, the hedgehog would not create a signal transduction pathway because the inhibition prevents it from going any further. Feedback Mechanisms Negative Feedback and Homeostasis ● Organisms use feedback mechanisms to maintain their internal environments and respond

to internal and external environmental changes. ● Negative feedback mechanisms maintain homeostasis for a particular condition by regulating physiological processes. ○ If a system is perturbed, negative feedback mechanisms return the system back to its target set point. These processes operate at the molecular and cellular levels. Example investigation: blood calcium levels (Bottom circle) - If the blood calcium level falls, then a hormone would be released that takes calcium out of the bone and into the blood.(Upper circle) - Thyroid takes calcium out of the blood and into the bones, to lower the amount of calcium in the blood This is an example of negative feedback maintaining homeostasis within the body. In summary; trying to bring the body back to “normal” when it has reached abnormality Positive Feedback and Homeostasis ● Positive feedback mechanisms amplify responses and processes in biological organisms. ○ The variable initiating the response is moved farther away from the initial set point ● Amplification occurs when the stimulus is further activated, which, in turn, initiates an additional response that produces a system change. Example: Blood Vessel Injury If there is an injury to a cell, molecules are released and trigger previously inactive clotting factors. The now activated clotting factors convert multiple molecules into things that can help with blood clot formation, and the body keeps producing such processes until the injury is healed. In summary; it keeps pushing for abnormality until the desired response is achieved Phosphorylation ● The addition of a phosphate group to one or more sites on the protein, which alters the activity of the protein ○ Typically linked to one of the three amino acids that have -OH in side chains

● Often acts as a “switch on”, but the effect varies among protein ● The transfer of the phosphate group is catalyzed by the kinaseenzyme ○ Cells contain many different kinases that phosphorylate different targets ● The reverse: after a protein has been “activated”, the enzyme phosphatasesswitches them back into non-phosphorylated states RETURN TO BOOKMARKS

Unit 4: The Cell Cycle 4.6: Cell Cycle Key Overview ● Eukaryotic cells divide and transmit genetic information via two highly regulated processes: ○ Mitosis and Meiosis ● Eukaryotic cell division consists of: ○ Mitosis,the division of the genetic material in the nucleus ○ Cytokinesis:the division of the cytoplasm ● Gametes are produced by a variation of cell division called meiosis ○ Meiosisyields nonidentical daughter cells that have only one set of chromosomes, half as many as the parent cell RETURN TO BOOKMARKSMitosis Overviews ● The cell cycle is a highly regulated series of events for the growth and reproduction of cells ○ Consists of sequential stages of interphase (G1, S, G2), mitosis and cytokinesis ● Mitosis is a process that ensures the transfer of a complete genome from a parent cell to two genetically identical daughter cellsFast Facts of Interphase: Summary Interphase - The first part of Interphase (G1) is followed by the S phase, where chromosomes duplicate - G2 is the last part of Interphase MAJORITY OF THE TIME IS INTERPHASE M phase Mitosis distributes the daughter chromosomes to daughter nuclei, and cytokinesis divides the cytoplasm, producing 2 daughter cells How Mitosis produces 2 exact replicas of the parent cell (using the figure on the right)● Purple strand: unduplicated chromosome ○ Chromosome duplicates in the “S” phase ● Once duplicated, a chromosome consists of two sister chromatids, connected along their entire length ○ Each chromatid contains a copy of the DNA molecule in the parent cell ● Molecular and mechanical processes separate the sister chromatids into two chromosomes, distributed into 2 daughter cells ○ Genetically identical!!! RETURN TO BOOKMARKS

Mitosis: The Process ● Mitosis occurs in a sequential series of steps (prophase, prometaphase, metaphase, anaphase, and telophase) G2 of Interphase Prophase Prometaphase The last part of interphase: - A nuclear envelopeencloses the nucleus. - The nucleus contains one or morenucleoli. -Two centrosomeshave formed by duplication - Each centrosomes contain two centrioles - Nuclear envelope begins to disappear - the chromatin fiberscondense into tightly coiled chromosomes.- mitotic spindle begins to form:composed of microtubules, important for moving the chromosomes during the process - Where the spindle fibers begin to form. Some microtubules move the chromosomes to the metaphase plate Two kinds of microtubules: 1. Ones that attach to kinetochores(see img) 2. Non-kinetochore microtubules Metaphase Anaphase Telophase/Cytokinesis - chromosomes are maneuvered to line up right in the middle of the cell (the plate) - spindle is composed of atro fibers, kinetochore and non-kinetochore fibers ( fiber = microtubules) - sister chromatidsare being pulled to opposite sides of the cell, by the spindle fibers - motor proteins help pull these proteins to the opposite sides after the splitting - Non-kinetochore microtubules elongate the cell when they’re pushed into opposing sides - cleavage furrowbegins to separate the two into sister cells - nucleolus and envelope reforms, chromosomes unwinding into chromatin reform

The G0 Cycle● A cell can enter a stage (G0) where it no longer divides, but it can reenter the cell cycle in response to appropriate cues. ○ Nondividing cells may exit the cell cycle or be held at a particular stage in it ● If the cell does not receive the go ahead signal, it will exit the cycle switching to a nondividing state called theG0 phase.Mitosis plays a role in: ● Asexual reproduction: of new cells or new organisms that reproduce ● Growth and development ● Tissue repair: Injuries to a cell can be repaired by replicating the cell in a healthy formRETURN TO BOOKMARKSRegulation of the Cell Cycle ● A number of internal controls or checkpoints regulate progression through the cycle ○ The cell cycle has specific checkpoints where the cell cycle stops until a go-ahead signal is received. G1 checkpoint - for many cells, the G1 is the most important one - checks cell size, growth factors, and the environment **environment: external and internal controls that affect it If passed: Synthesize DNA, prepare to divide and divide successfully If failed: Moves into G0 G2 checkpoint - MPF controls the movement of G2 into the cell cycle by phosphorylating and activating proteins involved with: ● Chromosome condensation ● Nuclear envelope breakdown ● Spindle assembly ● MPF self destruction enzyme (signals the end of G2 checkpt) ^^makes sure all cells are at that state to go more into M M Checkpoint - happens between metaphase and anaphase -if kinetochores remain unattached to spindle microtubules, anaphase will NOT begin - this ensures that you get equal distribution of chromosomes between the two cells Interactions between cyclins and cyclin-dependent kinases purple line: MPF activity - Shows that it peaks at mitosis and drops again at every M checkpoint Red line: cyclin - It “cycles”: builds up prior to mitosis, at its peak, then it declines rapidly RETURN TO BOOKMARKS

Cycle Form Diagram: CDK exists the entire time Cyclin builds up through throughout the entire cycle, until it peaks It combines itself with CDK to form MPF After that, cyclin is degraded,CDK continues to exist and waits for cyclin to regenerate itself in the next cycle External Factors that regulate cell cycle ● Growth factors:proteins released by certain cells that stimulate other cells to divide ○ Eg: platelet derived growth factor stimulates the division of fibroblast cells ● Density dependent inhibition: in which crowded cells stop dividing ○ This gives the currently existing cells a better chance to survive ● Anchorage dependence:where cells are anchored to a substrate in order to divide Cancer cells exhibit neither density dependent or anchorage dependence.Disruptions to the Cell Cycle ● Disruptions to the cell cycle may programmed cell death: apoptosis ● Apoptosis is a type of programmed cell death in which cell components are disposed of in an orderly fashion and without damage to neighboring cells ● It may also result in cancer Cancer Example investigation: p53 transcription factor With P53 Transcription Factor: When DNA is damaged from external factors (UV light, sunburns, etc), transduction pathway activates P53, p53 goes to the nucleus and creates a protein that inhibits the cell cycle from creating damage No damaged cell division. Without P53 Transcription Factor: Damaged DNA from the sun still occurs, so transduction pathways happen again as well, but no P53 activation. That leads to no inhibitory protein, and the damaged cell DNA continues Increased cell division RETURN TO BOOKMARKS

Calculation Based: Chi-Squared Tests Chi squared is the sum of the OBSERVED data minus the EXPECTED data squared, divided by the EXPECTED data. Chi-Squared Tests Formula Critical Value: the number on the table; figure out your degrees of freedom, and ALWAYS use 0.05 - This means that you are 95% sure of it being accurate (if you pick 0.05) Degrees of freedom:number of “choices” that you could possibly have minus 1 If the chi squared value is higher than the critical value on the table, then you reject the null hypothesis. If it’s lower than the critical value, then you accept it RETURN TO BOOKMARKS

Meiosis: Key Overview ● Meiosis is the process that ensures the formation of haploid gamete cells in sexually reproducing diploid organisms ○ Results in daughter cells with half the number of chromosomesof the parent cell. ○ Involves two roundsof a sequential series of steps (meiosis 1 and 2) ● Purpose is to produce genetic variation in gametes RETURN TO BOOKMARKSLike Mitosis… meiosis is preceded by the replication of chromosomes. Takes place in two sets of cell divisions, called meiosis 1 and meiosis 2 Both parents start out as diploid cells, and there is only ONE DNA replication process Unlike Mitosis… Two cell divisions result in four daughter cells, rather than two in mitosis. Each daughter cell has only half as many chromosomes as the parent, so it’s a haploidMeiosis 1 and Meiosis 2: Process Overview ● Meiosis 1 focuses on the separation of homologous chromosomes ● Meiosis 2 ensures that each gamete receives a haploid set of chromosomes that comprises both maternal and paternal chromosomes.

Meiosis 1: Detailed Process Prophase 1 Metaphase 1 Takes up about 90% of the time for meiosis Chromosomes begin to condense - These are homologous chromosomes, one set from mom and one set from dad Synapsis: (unlike mit.) chromosomes pair up and twist around each other, aligned gene by gene There are 4 of these, called tetradsHomologous chromosomes line up along the metaphase plate - The same apparatus moves the pairs: microtubules, spindle fibers, asters Microtubules from one pole are attached to the kinetochore of one chromosome of each tetrad, same for the other one. Anaphase 1 Telophase/Cytokinesis 1 Homologous pairs separate and move to opposite sides of the cell One chromosome moves towards each pole, guided by the spindle apparatus Sister chromatids remain attached at the centromere and move as one unit toward the pole Each half of the cell has a haploid set of chromosomes; each chromosome still consists of two sister chromatids. Cytokinesis usuallyoccurs simultaneously,forming two haploid daughter cells Meiosis 2: Detailed Processes Prophase 2 Metaphase 2 No synapsis or mixing of chromosomes. A spindle apparatus forms. In late prophase 2, chromosomes (made up of two chromatids) move towards metaphase plate Homologous chromosomes (or the sister chromatids) line up in the middle of the cell and arranged on the metaphase plate Kinetochores of sister chromatids attach to microtubules extending from opposite poles Anaphase 2 Telophase/Cytokinesis 2 Sister chromatids are separated and move to opposite sides of the cell, now as two newly individual chromosomes. Because of crossing over in meiosis 1, the two sister chromatids of each chromosome are no longer identical.Chromosomes arrive at opposite poles. Nuclei form, and the chromosomes begin decondensing. Result: FOUR haploid cells that have no identical cell. RETURN TO BOOKMARKS

Meiosis and Genetic Diversity ● During meiosis 1, homologous chromatids exchange genetic material via a process called “crossing over” (recombination) which increases genetic diversity among resultant gametes This happens specifically in Prophase/Anaphase 1 Prophase 1 Non-sister chromatids come together in synapsis. Pieces of genetic material on a chromosome crosses over, breaks off and recombines. This exchanges DNA segments - Crossover points: chiasma Each homologous pair has one or more X-shaped regions called “chiasmata” Anaphase 2 The exchange of genes/DNA shows different recombinations of those newly formed chromosomes, proving variety Chromosomes that look like its parent (see 1 and 4 in the figure) parental Chromosomes that are crossed over: (see 2 and 3 in the figure):recombinant Sexual reproduction in eukaryotes involve gamete formation--include crossing over, the random assortment of chromosomes during meiosis, and subsequent fertilization of gametes--serves to increase variation. Three mechanisms to contribute to genetic variation ● Independent assortment of chromosomes ○ Homologous pairs of chromosomes randomlyorient at metaphase 1. How the pairs line up and divide into cells is completely random ○ Each pair of chromosomes sorts maternal and paternal homologues into daughter cells independently of the other pairs. ● Crossing over ● Random fertilization The number of combinations possible when chromosomes assort independently into games is 2n, where n is the haploid number. Nondisjunction in Meiosis ● Nondisjunction in Meiosis I results in failure of homologous chromosomes to separate, and aneuploidy: too many or too few chromosomes in resulting gametes RETURN TO BOOKMARKS

Unit 5: Heredity Unit 5.3 Mendelian Genetics Common Ancestry ● It is believed that all organisms share a common ancestor, which is seen through fundamental processes and features that are shared across all organisms. ● There are FOUR features that support common ancestry: ○ DNA and RNA are carriers of genetic information ○ Ribosomes are found in all forms of life ○ Major features of the genetic code are shared by all modern living systems ○ Core metabolic pathways are conserved across all currently recognized domainsVocabulary: Genotype: the set of alleles carried by an organism Phenotype: an organism’s observable features ● Characters⇒a heritable feature (a gene) which varies. (ie. flow colour) ○ Variant traits are called alleles. A gene can have multiple alleles ● Dominant⇒determines the appearance ● Recessive⇒no noticeable effect ● Hybrid⇒cross of two “true-breeding” ● True breeding ⇒produces offspring with only the same variety as the parent plant Homozygous dominant: two dominant alleles Heterozygous: one dominant one recessive Homozygous recessive: two recessive alleles Mendel's Law of Segregation ● The alleles of a given locus segregate into separate gametes. ○ The 3:1 ratio determines this. It’s based on a model for the inheritance of individual characteristics ● Parents pass along “heritable factors” called genes, which determine offspring traits ○ Each individual has two copies of a given gene ○ If these copies represent different versions (alleles) of the gene, one allele will be the dominant one, hiding the recessive one. RETURN TO BOOKMARKS

Mendel’s Law of Independent Assortment ● Can be applied to genes that are on different chromosomes ● Alleles of two (or more) different genes get sorted into gametes independently of one another. In other words, the allele a gamete receives for one gene does not influence the allele received for another gene Fertilization ● Involves the fusion of two haploid gametes, restoring the diploid number of chromosomes and increasing genetic variation in populations by creating new combinations of alleles in zygotes. ● When a diploid cell contains one chromosome from mom and one chromosome from dad, there are two spots for genetic variation: ○ In interphase, crossing overcauses the cell to create variation ○ When the chromosomes line up in the middle during metaphase,the order and orientation of which they line up is completely random Rules of Probability ● Rules of probability can be applied to analyze passage of single-gene traits from the parent to the offspring. For harder problems, where there are 2 alleles (AaBb) Find the probability of each individual alleles, then multiply the two by each other Example: Probability of ccddfrom CcDd x CcDd Probability of c from Cc: ½ Probability of d from Dd: ½ Probability of c from Cc: ½ Probability of d from Dd: ½ Multiple all numbers together to get 1/16

Chromosomal Inheritance and Environment Effects on Phenotype ● Naturally occurring diversity among and between components within biological systems affects interactions with the same environment ● The same genotype can result inmultiple phenotypesunder different environmental conditions ● Environmental factors influence gene expression and can lead to phenotypic plasticity. ○ Phenotypic plasticity: occurs when individuals with the same genotype exhibit different phenotypes in different environments. ○ Plasticity: a change in gene expression as a result of an environmental experience Here are 3 major examples: SEASONS PH LEVELSPOPULATION DENSITY● Chromosomal inheritance generates genetic variation in sexual reproduction. ○ Segregation, independent assortment of chromosomes, and fertilization result in genetic variation in populations ○ Chromosomal basis of inheritance provides an understanding of the pattern of transmission of genes from parent to offspring RETURN TO BOOKMARKS

Unit 6: DNA Structure and Replication DNA vs. RNA Structure ● DNA, and in some cases RNA, is the primary source of heritable information. DNA Characteristics ● Double stranded ● Deoxyribose sugar ○ The functional group lacks O2 ● Nitrogenous bases: TCAG RNA Characteristics ● Generally single stranded ● Ribose sugars ○ Hydroxyl functional group ● Nitrogenous bases: UCAG Nucleotides ● DNA and RNA are composed of nucleotides: the building block of RNA and DNANucleotides are made of a phosphate group, sugar, and a nitrogenous base: - The Phosphate group covalently bonded to the 3’ or 5’ carbon of the sugar - Nitrogenous Bases held together by hydrogen bonds: A/T, C/G DNA and RNA exhibit specific nucleotide base pairing that is conserved through evolution: (DNA A-T) or (RNA A-U) and (DNA/RNA C-G) ● Purine and Pyrimidine structures are patterns conserved through evolution ○ Purines: Adenine and Guanine, who have double ring structure ○ Pyrimidines: Thymine(Uracil) and Cytosine, who have single ring structureDNA Structure The DNA Molecule has directionality, otherwise known as antiparallel ● The two strands run in opposite directions ● Implies for how the DNA molecule is replicated ● Caused by the the phosphate and sugar bonding and the force exerted by them 5’ End The phosphate group is bound to the carbon at the 5th position on that end, which is why it’s called 5’ end. 3’ End Starting from the 5’ end, the positions alternate until it reaches the open 3’ end This also works in the antiparallel direction RETURN TO BOOKMARKS

Prokaryotes Vs. Eukaryotes Similarities ● Both contain plasmids: double stranded, circular molecules● Chromosomes have dynamic structure for cell processes, some regions can be loosened, others stay condensed Differences Prokaryotes They have circular chromosomes. Eukaryotes They have linear chromosomes. Packing of Eukaryotic DNA:it’s so densely packed that it’s largely inaccessible to the machinery responsible for transcribing genetic information ● Acts as a way of regulating gene expression Histones:proteins that pack chromatin in eukaryotes; chemical modifications to histones change chromatic organization.DNA Replication ● DNA Replication ensures continuity of genetic info ○ synthesized 5’ to 3’ direction!! Components of DNA Replication ● Semiconservative: one strand serves as template for new strand ● Enzymes that direct DNA replication: ○ helicase (unwinds DNA strands) ○ topoisomerase (relaxes supercoiling one front of replication fork) ○ DNA polymerase (add nucleotides to synthesize new strands, needs RNA primers to initiate DNA synthesis) ○ Primase (facilitates construction of RNA primers) ○ Ligase (joins fragments in lagging stands, Okazaki Fragments) ○ Single Stranded Binding Proteins(stabilize unwound template strands) RETURN TO BOOKMARKS“Semiconservative” Breaking off hydrogen bonds between bases, separation of parental strands into templates for complementary strands. This ensures that the DNA replication is identical. This model predicts that when a double helix replicates, each daughter molecule will have one new strand and one old strand.

The Role of DNA Polymerase DNA Polymerase I vs. III Polymerase I responsible for removing RNA primers on okazaki fragments and replacing with DNA nucleotidesPolymerase III responsible for adding DNA nucleotides to RNA primersThe Leading vs. Lagging Strand Process Leading Strand DNA Polymerases add nucleotides only to the free 3’ end of a growing strand ● therefore, a new DNA strand can elongate only in the 5’ to 3’ direction DNA polymerases cannot initiate synthesis of a polynucleotide. They can only add nucleotides to an already existing chain base-paired with the template the initial nucleotide strand is a short RNA primer, laid down by RNA Primase. The enzyme, primase, starts an RNA chain from a single RNA nucleotide and adds RNA nucleotides one at a time using the parental DNA as a template. ● The new DNA strand will start from the 3’ end of the RNA primer. Enzymes called DNA polymerasescatalyze the elongation of new DNA at a replication fork. Lagging Strand Along one template strand of DNA, the DNA polymerase synthesizes a leading strand continuously, moving towards the replication fork. To elongate the leading strand, DNA polymerase must work in the direction away from the replication fork. ● The lagging strand is synthesized as a series of segments called okazaki fragments After formation of okazaki fragments, DNA polymerase ONE removes RNA primers and replaces the nucleotides with DNA. !! Remaining gaps are joined together by DNA ligaseRETURN TO BOOKMARKS

Summary: The Process of DNA Replication 1. Helicaseunwinds the parental double helix. 1. Molecules of single-stranded binding proteinstabilize the unwound template strands. 2. Theleading strandis synthesized continuously in the 5’ to 3’ direction by DNA polymerase III 3. Primasebegins synthesis of the RNA primer for the okazaki fragments 4. DNA Polymerase I removes the primer from the fragment end, replacing it with DNA nucleotides added one by one to the 3’ end 5. After the last addition, the backbone is left with a free 3’ end. DNA Proofreading and Repair Polymerase proofreads newly made DNA, replacing any incorrect nucleotides with the correct ones Mismatch repair:other enzymes correct errors in base pairing Nucleotide extension repair:nuclease cuts out and replaces damaged stretches of DNA Error rate after proofreading is low but not 0. ● mutations may be passed onto next generations ● Leads to genetic variation ⇒natural selection RETURN TO BOOKMARKS

Protein Synthesis RETURN TO BOOKMARKSOverview ● Genetic information flows from a sequence of nucleotides in DNA to a sequence of bases in an mRNA molecule to a sequence of amino acids in a protein ○ Transcription ⇒mRNA processing ⇒Translation! Types of RNA molecules (useful in learning the sequences) ● The sequence of RNA bases, together with the structure of the RNA molecule, determines the RNA function mRNA carry info from DNA to ribosometRNA bind specific amino acids & have anti-codon sequences that base pair with mRNA, recruited to the ribosome during translation to generate the primary peptide sequence based off of the mRNA sequence rRNA functional building blocks of ribosomes Transcription Transcription is where DNA strands are turned into RNA strands for translation to use. RNA polymerases use a single template strand of DNA to form a complementary RNA strand ● DNA template strand: non coding strand, minus strand, antisense strand ● mRNA strand: coding strand, plus strand, sense strand RNA polymerase synthesizesmRNA in the 5’ to 3’ direction, readsDNA template in 3’ to 5’ direction*** mRNA Processing: Enzyme Regulated Modifications of mRNA transcript: ● The change from pre mRNA to mature mRNA occurs in eukaryotic cells, where the mRNA transcript is modified into mature mRNA ● Addition of a poly-A-tail & GTP cap ● Removal of introns, splicing and retention of exons in nucleus ○ Tip to Remember: Introns stay inside nucleus, Exons are expressed ● Alternative splicing: excision of introns and retention of exons can result in different versions of the resulting mRNA molecule

Translation Translation is where RNA is turned into proteins for the cell to use. ● Initiated when rRNA in ribosome interacts with mRNA at the start codon ● Codons: Sequence of nucleotides on mRNA read in triplets ○ Each codon encodes a specific amino acid, many amino acids are encoded by more than one codon (LOOK AT CHART BELOW!) ● Each ribosome has an Arrival, Polypeptide, & Exiting spot Translation involves energy and sequential steps: initiation, elongation, & termination Initiation tRNA brings the correct amino acid to the correct location specified by the mRNA codonElongation Amino acid is transferred to a growing polypeptide chain. Process continues along mRNA until a stop codon is reached Termination Release Factor: process terminated by release of newly synthesized polypeptide/ protein RETURN TO BOOKMARKSProkaryotes vs. Eukaryotes ● Translation on ribosomes occur in both cells Prokaryotes Translation of the mRNA molecule occurs at the same time it is being transcribed Eukaryotes Translation occurs also on the rough endoplasmic reticulum, on top of ribosomes Common ancestry THIS IS IMPORTANT supposedly ● Nearly all living organisms use the same genetic code, which is evidence for common ancestry

Retroviruses Normal Flow: DNA, RNA, Protein Retrovirus: RNA, DNA, RNA, Protein● Alternate flow of information: RNA to DNA, made possible by reverse transcriptase (enzyme) ○ Reverse transcriptase:copies viral RNA genome into DNA, which integrates into the host genome and becomes transcribed and translated for the assembly of viral progeny STEPS FOR RETROVIRUS SYNTHESIS: 1. plasma membrane of virusfuseswith that of the cell (virus enters cell) 2. virus containsprotein capsids, RNA, & reverse transcriptasewhich it dumps into the cytoplasm of the host cell 3. Reverse transcriptase makes DNA strand, which forms a complementary strand 4. Double stranded viral DNA is inserted into the genome of host cell 5. Host cell duplicates viral DNA & proteins, which then leave the cell to infect more cells RETURN TO TOP

Gene Regulation: Prokaryotic and Eukaryotic Overview Regulatory sequences are stretches of DNA that interact with regulatory proteins to control transcription Components of Gene Regulation ● Promoter: DNA sequence where RNA polymerase binds and start transcription, proceeding downstream (right) ● Control Elements:regulatory elements, DNA sequences located near (proximal) or far (distal) from the promoter ○ distal control elements grouped together are enhancers ● At other end of gene, there is a poly-A signal sequencein the last exon of the gene; it is transcribed into an RNA sequence that signals where the transcript is cleaved and the poly-A-tail is added ● mRNA processing (UTR buffers mark where coding segment should be started) Epigenetic (above the genes) Changes Inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence - Can affect gene expresses through reversible modifications of DNA or histones - Do not alter DNA sequence, rather via chromatin modifications - Can be passed to future generations - Eukaryotic DNA packed by histone proteins- can be tightened (less access) or loosened (more access to genes) - Amino acids in histone tails may be chemically modified: acetyl groups can be added to make chromatin less compact and DNA available for transcription RETURN TO BOOKMARKS

Regulation of Gene Expression: Prokaryotes Vs. Eukaryotes Prokaryotes operons are transcribed in a single mRNA molecule. There are 2 types: repressible (on until switched off, trp operon) inducible(off until switched on, lac operon) Operon:functionally related genes that can be coordinately controlled by “on off” switch, also known as the operator - Includes entire stretch of DNA including operator, promoter, and genes they controlEukaryotes operons not used in eukaryotes Genes may be influenced by the same transcription factors to coordinately regulate expression Genes co-expressed are scattered over different chromosomes Often occurs in response to chemical signals from outside the cell, either steroid or protein hormones that activate transcription factors - Steroid hormones act directly - protein hormones via a signal transduction pathway Promoters:DNA sequences upstream of transcription start siteExample of Gene Regulation: Lactose No Lactose Present In the absence of lactose, the repressor switches off the operonby binding to the operator. Lactose Present When lactose is present, and the bacteria needs to break down to digest it, allolactose (an isomer of lactose) acts as an inducer by binding to the repressor and inactivates it. This means it can not block the operator, and RNA polymerase can bind to it and begin to transcribe the proteins needed to digest lactose. RETURN TO BOOKMARKSTranscription

The steps of regulation of transcription: 1. DNA control elements in enhancersbind to specific transcription factors & mediator proteins 2. Bending of DNA enables activators to contact proteins at the promoter,initiating transcription 3. A transcription initiation complex is formed DNA Methylation DNA methylation is the process through which a methyl group is added to DNA nucleotides. ... DNA methylation can stably alter the gene expression of a cell, which may direct processes like stem cell differentiation and genomic imprinting. ● Addition of methyl groups to certain bases in DNA, usually cytosine ● Generally reduces transcription ● Methylation pattern inherited Alternative RNA splicing: excision of introns and retention of exons can result in different versions of the resulting mRNA molecule RETURN TO BOOKMARKSmiRNA: ● A microRNA (abbreviated miRNA)is a small non-coding RNA molecule (containing about 22 nucleotides) found in plants, animals and some viruses, that functions in RNA silencing and post-transcriptional regulation of gene expression. ○ Degrades mRNA if bases are completely complementary. If the match is less than complete, then the translation is blocked. Mutations and Biotechnology Mutations ● Mutations are the main cause of genetic variation ● Some genotypic mutations cause changes in phenotype (ex. Mutated CFTR protein, cystic fibrosis)

● Alterations in DNA can lead to changes in type or amount of protein produced ● DNA mutations can be positive, negative, or have no consequence; effect is determined by environmental conditions (usefulness of a mutated phenotype determined by natural selection) ● Changes in chromosome number often result in new phenotypes(ex. sterility caused by triploidy or increased vigor of other polyploids) ○ Changes in chromosome number also cause human disorders with developmental limitations (ex. Down syndrome) Horizontal Acquisition: ● Horizontal Acquisition is the transmission of DNA between different genomes ● Distinguished from the transmission of genetic material from parents to offspring during reproduction, which is known as vertical gene transfer ○ Occurs: eukaryotes, prokaryotes, and between chloroplasts, nucleus, & mitochondrion Sharing DNA: Prokaryotes Vs. Eukaryotes Prokaryotes: (details below) There are 3 ways that prokaryotes share or transfer their DNA: Transformation:introduces DNA to bacterial cell via plasmid (can be used for genetic engineering) (outside environment to bacteria) Transduction: viral transmission of genetic information Conjugation: cell to cell (bacteria) transfer of plasmid via conjugation pilus Eukaryotes subcellular pathways and cell signaling Transposition: (the removal and the) transfer of a segment of DNA from one site to another of the same or different chromosome - Effects: can interrupt genes, disrupt regulation, increase likelihood for recombinationRETURN TO BOOKMARKSTransduction, Transformation, Conjugation (source:Khan Academy) Transformation Transduction Conjugation

a bacteriumtakes in DNA from its environment, often DNA that's been shed by other bacteria. If the DNA is in the form of a circular DNA called a plasmid, it can be copied in the receiving cell and passed on to its descendants. virusesthat infect bacteria move short pieces of chromosomal DNA from one bacterium to another "by accident." The viruses that infect bacteria are called bacteriophages. Bacteriophages commandeer a cell's resources and use them to make more bacteriophages. DNA is transferred from one bacterium to another. After the donor cell pulls itself close to the recipient using a structure called a pilus, DNA is transferred between cells. In most cases, this DNA is in the form of a plasmid.Donor cells typically act as donors because they have a chunk of DNA called the fertility factor (or F factor). This chunk of DNA codes for the proteins that make up the sex pilus. It also contains a special site where DNA transfer during conjugation begins Biotechnology Gel Electrophoresis: DNA (-) placed in wells in agarose gel Electric charge (- to +) DNA is repealed from (-) end and attracted to (+) end ● Smaller fragments of further/faster ● DNA is cut prior with restriction enzymes (remember blunt v. sticky ends)DNA Sequencing: genetic engineering technique that determines order of nucleotides in DNA and used to analyze DNA ● can identify organisms or be used for forensic identification Gene Cloning: Nucleus of somatic cell taken from desired animal Nucleus fused with an egg cell Creates a clone of desired animal RETURN TO BOOKMARKS7.1-7.2 Introduction to Natural Selection (NOT ON THE EXAM) Natural Selection: a process in which individuals that have certain inherited traits tend to survive and reproduce at higher rates than other individuals, because of those traits.

7.1 KEY TAKEAWAYS: ● Evolution is characterized by a change in the genetic makeup of a population over time and is supported by multiple lines of evidence ● Natural selectionis the mechanism of evolution, proposed by Charles Darwin OBJECTIVES ● You should be able to describe the causes of natural selection ● You should be able to explain how natural selection affects populations Practice Questions 1. Parental pairs with specific beak depth of 5 mm had the highest repro success 2. Each strain adapts to specific host species 3. The S Aureus strain 3 has the highest percentage of hemoglobin binding BIG OVERVIEW Components needed for natural selection mechanism (proposed by Darwin) ● Variation ○ Differences in phenotypes that exist in a population ● Reproduction ○ Both variations reproduce ○ More offspring will be produced than the environment can hold, which leads to.. ● Competition ○ For food, mates, nesting sites and to be able to escape predators ● Fitness ○ Thus, the variation with more successful traits are more likely to survive and keep producing ● Evolution ○ As the unsuccessful died off and the successful rises, the adaptations become common Starting population ⇒overproduction ⇒variation and competition ⇒adaptation ⇒differential survival ⇒differential reproduction Sources of variation in a population a. Mutations: random changes to DNA sequences b. Sexual reproduction: organisms that reproduce have the mixing of alleles, and these new arrangements of alleles in every offspring means new combinations, new phenotypesNatural selection acts on phenotypic variations in populations. Environments can change and apply new selective pressures to populations TIPS ON ANSWERING QUESTIONS Describing a trend based on a graph - Point out specific parts of the graph (ie. groups with 6 mm of x had the highest rate of y)

- Give short answers!! No need for long explanations “Identify” a certain number of things - ONLY IDENTIFY THAT MANY! DO NOT GO OVER THE ASSIGNED NUMBER CALCULATION QUESTIONS “Calculate total efficiency” - If you have ___ amount of energy, but you only use ____ amount, then the amount that you actually used was the efficient part - Divide the amount that you ACTUALLY used by the amount available