Exam 1 Notes PDF - Prin Of Biology II (University of Kentucky)

lOMoARcPSD|46808047 Exam 1 Notes Prin Of Biology II (University of Kentucky) Scan to open on Studocu Studocu is not sponsored or endorsed by any college or university Downloaded by Kara Richie ([email protected]) ...

lOMoARcPSD|46808047 Exam 1 Notes Prin Of Biology II (University of Kentucky) Scan to open on Studocu Studocu is not sponsored or endorsed by any college or university Downloaded by Kara Richie ([email protected])  lOMoARcPSD|46808047 Types of Macromolecules: Processes of life dependent on four major organic molecules: Proteins Nucleic Acids Carbohydrates Lipids Molecules are mostly large polymers-made of repeated simpler units (monomers/subunits) connected by covalent bonds Proteins: Function: performing critical reactions in the cell and providing structure and support Monomer subunit: amino acid subunits Type of bond: peptide bonds- carboxyl and amino group Additional Notes: - must be folded correctly to be functional Nucleic Acids: Function: serves as energy carrier molecules and carries genetic information in nucleotides Monomer subunit: nucleotide monomers Type of bond: phosphodiester bonds Additional Notes: Downloaded by Kara Richie ([email protected])  lOMoARcPSD|46808047 - GTP/ATP: primary energy currency for cellular respiration and photosynthesis Carbohydrates (sugars): Function: energy for metabolism Monomer subunit: monosaccharides- linear/cyclic molecules containing 5-6 atoms Type of bond: glycosidic Additional Notes: - monosaccharides formed w/ glycosidic bonds form complex carbs- disaccharides and polysaccharides -those complex carbs formed from single or multiple monosaccharides Lipids: Downloaded by Kara Richie ([email protected])  lOMoARcPSD|46808047 Shared feature of lipids: hydrophobic components Function of fats: energy storage Function of steroids: in animal plasma membranes, utilized as signaling membranes Function of phospholipids: major component of cell membranes Downloaded by Kara Richie ([email protected])  lOMoARcPSD|46808047 Additional Notes: - not polymers but all contain hydrophobic components - fats are nonpolar molecules (3 fatty acids linked to glycerol) -steroids composed of carbon atoms to fused rings -phospholipids consist of glycerol linked to a phosphate group and two hydrocarbon chains Metabolism and Enzymes: Metabolism: ○ set of chemical reactions that convert molecules into other molecules and transfer energy into living organisms, needed to sustain life ○ The building and breaking down of molecules and the harnessing and release of energy driven by chemical reactions in the cell ○ Chemical reactions often linked forming pathways and intersecting networks Two types of Metabolism: Catabolism: “catastrophe” breaks down molecules into smaller units and produces net ATP gain Anabolism: set of reactions build molecules from smaller units and requires input of ATP (uses up ATP) Enzymes: proteins that are biological catalysts (speeding up chemical reactions in a cell) Can either break down substrates into a product or combine substrates into a product Help chemical reactions occur to overcome two hurdles: ○ Reactants colliding in a precise orientation ○ Reactants having enough kinetic energy to overcome repulsion between electrons that come in contact as the bond forms ○ Bring substrate molecules together to the active site (substrate binding site) ○ Help substrates collide in a precise orientation so electrons can react ○ Active site is a cleft/cavity within globular shape of enzyme Induced Fit: when the enzyme wraps around substrates in order to direct them into the exact orientation they need to fit the active site and facilitate bond formation Downloaded by Kara Richie ([email protected])  lOMoARcPSD|46808047 Enzymes: (break things down or put things together) Enzymes typically catalyze a single reaction/substrate, they are highly specific The transition state is the inbetween state that is very temporary and unstable going from substrates of a product to a product ○ Old bonds breaking and new bonds forming ○ Enzymes help facilitate stabilizing that state A certain amount of kinetic energy (activation energy) is needed to strain chemical bonds in the substrates to achieve transition state The more unstable the transition state the higher the activation energy and the less likely a reaction is to proceed quickly Enzymes speeds up the activation state to facilitate reaching transition state that requires less activation energy ○ Enzymes lower activation energy because it helps stabilize transition state Three Step Process of Catalysis ○ Initiation: reactants bind to active site (in a specific orientation) forming an enzyme-substrate complex ○ Transition State: interactions between enzyme and substrate To facilitate stability and change of bonds ○ Termination: products have lower bond affinity for active site (highly specific for substrate) Molecules affinity change enough to not fit in enzyme and be released Know Catalyzed vs Uncatalyzed Reaction Curves ΔG: the overall change in free energy of a reaction in enzyme curve (5) (doesn't change) Enzyme Saturation: they reach a certain saturation to where all active sites are bound up by a substrate ○ Can only be overcome if more enzyme is added An enzyme's activity is sensitive to conditions that alter protein shape ○ If it’s too hot/too cold an enzyme can get misfolded to where it won’t work because of a now non functioning active site 3D structure is compromised ○ Range of pH the enzymes can work at Curves can shift through evolution in species based on the conditions they live in Enzyme Regulation ○ Noncovalent modifications (molecules that bind enzyme somewhere) Competitive inhibition: inhibitor molecule shaped like substrate can enter the active site and inhibit catalysis (ex: cancer drugs) Allosteric regulation: molecule binds on enzyme away from the active site, when it binds it changes the shape Inhibition:change enzyme for active site to not be available Downloaded by Kara Richie ([email protected])  lOMoARcPSD|46808047 Activation: changes for enzymes active site to be available for reaction Negative feedback pathway:product ○ Covalent Modification Phosphorylation: adds phosphate group to structure of enzyme Reversible Kinase:add phosphates Phosphatase: removes phosphates Cell Membranes: Selective barrier, helps maintain homeostasis Animal cells have only cell membrane, plants have cell membrane and cell wall Three major components: ○ Phospholipids are major component of cell membrane ○ Proteins ○ Carbohydrates Cell membrane is amphipathic: molecule has hydrophobic and hydrophilic components They spontaneously form structures in water Miciles: the heads, hydrophilic (water loving) Bilayer: 2 hydrocarbon tails, hydrophobic (water fearing) ○ Helps study permeability and how molecules move across membrane Molecules from highest to lowest permeability (move across bilayer by simple diffusion) ○ Small nonpolar molecules: carbon dioxide ○ Small uncharged polar molecules: water and glycerol ○ Large uncharged polar molecules: glucose, amino acids ○ Ions: sodium ions, anything with a charge has lowest permeability Nonpolar: hydrophobic Downloaded by Kara Richie ([email protected])  lOMoARcPSD|46808047 Polar: hydrophilic Cell membranes are dynamic: ○ Phospholipids move constantly around membrane making them dynamic ○ Fluidity: ability of phospholipids to move around membrane ○ Increased fluidity= increased permeability (tightly linked) Can be influenced by: Bond saturation Tail length Cholesterol Temperature Unsaturated hydrocarbon tails have double bonds present while saturated do not ○ saturated= no double bonds ○ unsaturated= 1+ double bonds ○ Kinks created by unsaturated causing spaces in cell membranes which leads to an increase in permeability and fluidity because not forming Vanderwaal interactions that hold hydrophobic tails together The longer the fatty hydrocarbon tails, the more Vanderwaal reactions occur, and the less fluid and permeable Cholesterol overall reduces membrane permeability because it fills the gaps in cell membrane ○ Cholesterol (amphipathic) can act as a buffer in different temperatures Prevents cell membrane from too much movement Prevents packing of phospholipids to freeze, cold temp needs more ○ Warmer temperatures produce more fluid membrane and colder temperatures lead to less fluidity/permeability Movement Across Cell Membranes: Simple diffusion: move across the bilayer by itself, all solutes in random motion Concentration Gradient: molecules move from areas with high to low concentration ○ In equal concentration on both sides of the cell membrane and equal movement across both sides of the membrane Osmosis: movement of water across cell membrane holding solutes back Movement of water is spontaneous to equalize solute concentrations Water moves to where there is more solute Total Osmolarity: ratio of total # of solutes to water present ○ More solutes= less water ○ Can predict movement between cells and how they move in an environment ○ High osmolarity= more solutes= more water moving toward that area Hypertonic: when the solution outside vesicle contains more solute than inside vesicle Hypotonic: solution outside vesicle contains more solute than inside, making inside hypotonic (less solute), water leaves the interior of the cell and cell shrinks/shrivels When more solution inside cell, water moves in and swells/bursts Isotonic: equal # of solutes outside and inside cell and water flows equally, equal concentrations, exterior and interior of cell are both isotonic in this case Downloaded by Kara Richie ([email protected])  lOMoARcPSD|46808047 Turgor pressure: water exerting pressure against cell wall (helps maintain shape) Membrane Proteins: Associate in different ways and have different functions Some molecules need proteins to move across membrane Transporters: move things across cell membrane ○ Moving ions (charged) and other large molecules ○ Passive (diffusion) and using ATP Receptors: get signal from outside and relay inside of the cell Enzymes: cell signaling pathways, catalyze chemical reactions Anchor: maintain cell shape and structure Integral Membrane Proteins: (running through bilayer) span bilayer, run through the core but have pieces on extracellular and intracellular surfaces (transmembrane) ○ Amphipathic: core is hydrophobic and hydrophilic ends are exposed to outside and inside of the cell Membrane Proteins and Movement: Membrane proteins form channels (paths across membrane) across lipid bilayer Facilitated diffusion: (relies on concentration gradient): assisting protein so molecule can move through membrane, passive, no ATP required ○ Molecules still move down concentration gradient Cystic Fibrosis and Mutated Ion Channels ○ Ions are charged and use proteins the most via channels ○ Cystic Fibrosis is a genetic mutation that causes issues with tissues that secrete (stomach, lungs, sweat glands) ○ Specialized membrane proteins- ion channels ○ In lungs secretions are thin and slippery but the mutation causes a mucus buildup because it causes a malformed chloride channel that it can’t flow through, chloride can’t move because water can’t move, usually water can flow through because it follows the chloride that thins mucus Channels are highly specific and allow only one specific type of molecule through ○ water moves 10x faster in aquaporin channels Channels can control whether its open or closed, some stay open ○ Gated channels: open/close depending on charge of cell and signals Shape and structure of channel does not change as molecules pass through, just highly selective Carrier proteins are different because they change their confirmation during transport as the molecule passes through which helps finish the molecule get through the membrane ○ Does not require energy, moves down concentration gradient ○ Glucose is important for carrier proteins, but lipid membranes have low permeability of glucose Active transport: requires ATP to move against the concentration gradient ○ ATP transfers a phosphate group to a pump protein Ex: sodium exchange pump Downloaded by Kara Richie ([email protected])  lOMoARcPSD|46808047 First: there is a high affinity for sodium, so it opens to the inside of cell with 3 binding sites Then, a phosphate group is added to pump after the sodium is added, changes the confirmation to be open to outside of cell and sodium ions leave because binding sites are different Then, confirmation is now suitable for potassium binding Lastly: phosphate is removed from protein that changes confirmation and now is back to favoring sodium pump and returns to its original shape Eukaryotic Cells: The nucleus is the defining feature of the eukaryotic cell, it contains genetic material Prokaryotic genetic material is in a singular circular chromosome and genome is streamlined for what’s absolutely necessary for survival and eukaryotic have multiple linear chromosomes with replication at multiple sites Organelles compartmentalize the cell, specialization of function Extensive cytoskeleton allows eukaryotic cells for a quick remodelling and shape change ○ “Highway” in the cell Endomembrane System: interconnected network of membranes, some directly connected and some require vesicles to move material between them Exocytosis: trafficking material out of the cell, vesicles fuse with plasma membrane Endocytosis: material moving into the cell, vesicles bud off from plasma membrane that encloses material from outside and bringing it in The nucleus is not closed off from rest of cell, transcription regulators, mRNA and pores control what enters and exits ○ Nucleus is continuous with endoplasmic reticulum ○ Endoplasmic reticulum: highly folded, interconnected sacs, important for the synthesis of lipids and transmembrane proteins Rough ER: studded with ribosomes to help synthesis of proteins like transmembrane proteins, organelle interiors and secreted proteins Smooth ER: fatty acid and phospholipid synthesis, sent off the cell membrane Materials move through vesicles that bud off and move from ER to golgi apparatus to modify Golgi Apparatus: ○ Modifies proteins and lipids produced by the ER ○ A traffic director, makes sure everything is sent to the right place of the cell, sorting station ○ Carbohydrate synthesis Lysosomes: “garbage trucks of the cell” breaking down extra/unneeded macromolecules by maintaining an acidic environment that allows enzyme to act optimally ○ Shows the importance of compartmentalization, most proteins can’t function in acidic environment but those enzymes within lysosomes can ○ Whole cell can’t have same pH, some work and some don’t Downloaded by Kara Richie ([email protected])  lOMoARcPSD|46808047 Mitochondria: generation and harvesting of energy, “powerhouse of cell” ○ Double membrane organelle ○ Making ATP, converting energy from chemical compounds (sugars) to ATP oxygen is consumed and carbon dioxide is released Chloroplasts: generation and harvesting of energy ○ Making sugar molecules from carbon dioxide, can be broken down and utilized by mitochondria ○ Photosynthesis uses carbon dioxide, released oxygen ○ Sexual reproduction is unique to eukaryotes using meiosis, genetic diversity is created, prokaryotes only get genetic variation through mutations Evolution of Multicellularity Unicellular eukaryotes belong to protist and fungi lineages Properties of simple multicellular eukaryotes: ○ Cells stick together, all look the same, no specialization, little communication ○ Retain full range of functions, cell deaths irrelevant because no specialization and all have a full range ○ Every cell is in direct contact with the environment , can communicate with environment but not each other, not very thick- more flat Selection pressures that favored evolution of multicellularity ○ Help organisms not be eaten, predation ○ Optimal positioning for nutrients and light ○ Feeding, working together to obtain food more easily Three features of complex multicellular organisms ○ Cell adhesion, once fertilization occurs cells divide and must stick together using cell adhesion molecules ○ Cell communication (cell to cell) ○ Complex patterns of cellular and tissue differentiation Simple and complex multicellular organisms both share cell adhesion characteristics Cadherins: proteins that stick out of cell membrane on outside of cell (extracellular), will interact between cells to stick together (cell to cell) Integrins: cells secrete extracellular matrices and attach themselves to this matrix by transmembrane proteins (cell to matrix) to form tissues Pectin: plans use polysaccharides as cell adhesion molecules Choanoflagellates (protists) most closely related to animals, live together in colonies, sponges derives from their genome and contain cadherins and integrins, sticking together to substrates, coming together to capture prey Complex multicellular organisms use molecular signals to communicate with each other ○ Can be small: hormones ○ Receptors bound by signalling molecules, flip molecular switch and activate gene expression Transmembrane proteins (all cells have) respond to signals in the environment ○ Single celled can also communicate with other cells in same species or neighboring cells further away Downloaded by Kara Richie ([email protected])  lOMoARcPSD|46808047 Cell communication in animals ○ (all except sponges) ○ Special cellular ○ Gap junctions: protein channels ○ Proteins line up to form a channel between cells and allow ions and signaling molecules from one cell to another Cell communication in plants ○ (also multicellular algae) ○ Plasmodesmata: intercellular channels, part of plasma membrane in direct communication, flow of ions and water continuously Cell differentiation in unicellular organisms ○ Different life cycles/shapes/types during different times ○ Different cell types alternate in time Cell differentiation in complex multicellular organisms ○ Simple DONT show differentiation ○ Complex have cell differentiation in space, leads to different cell functions ○ Differences in gene expression (diff proteins produced, diff types result) during development ○ Undifferentiated cells become different cell types based on molecular cell messages they receive Genes dictating different cell types in unicellular, those same genes re-deployed and used in multicellular algae as gene differentiation Disadvantages of cell differentiation in complex multicellular organisms ○ Cell death can be detrimental to an entire organism ○ Cancer- de-differentiated cells, self sustain themselves, blood vessel growth for nutrients, few cells devotes to reproduction Complex multicellular organisms are 3D so cells on the interior dont have direct access to nutrients and cells are exposed to different environments ○ In simple they are exposed to every same part of the environment ○ Consuming food that then disperse to get nutrients ○ Also light, outside of body exposed while inside is not ○ skin cells in constant contact with oxygen and light ○ Led to evolutionary solutions Diffusion in Organisms (complex multi) ○ Diffusion helps get CO2 and oxygen in and out of cells dependent on concentration differences, diffusion only works over small distances, placing limitations on size and cell thickness- larger gradient slows to become ineffective Sea invertebrate: put metabolically active cells on the outside surface that are in contact contact with the environment Land plants and animals: use combo of bulk flow and diffusion to get gases and nutrients into the cell Bulk flow: moving something faster than the rate of diffusion ○ Ex: blood flow, plants use to move sugars ○ Respiration: bulk flow when we breath in , generates pressure differences to Downloaded by Kara Richie ([email protected])  lOMoARcPSD|46808047 allow oxygen to flow in, air enters in lung tissues: thin sacs (abioli) go through diffusion and moves oxygen into cells and CO2 out, blood vessels use bulk flow for pumping red blood cells through the body, closely associated with body tissue to allow oxygen to diffuse from blood and tissues Downloaded by Kara Richie 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