Pennsylvania State University: Biology 110 study Guide 2 Latest,100% CORRECT

Pennsylvania State University: Biology 110 study Guide 2 Latest • Cells o Make up all living things o Smallest unit of life o At least one cell to be a living organism • Prokaryote cell o Small, has no nucleus, has no organelles • Eukaryote cell o Has a nucleus, larger, contains organelles o Many shapes and sizes • All cells have plasma membrane that surround the cells • Chromosomes, that are structures that have DNA • Cytosol, that is a jelly-like substance within a cell • Eukaryotic cell o Plasma Membrane (PM) ▪ Surrounds and encloses the cell ▪ Two layers of phospholipids, which is called the phospholipid bilayer ▪ It is a selective bilayer between the inside and outside of a cell ▪ There are specialized structures on the plasma membrane • Cilia move substances through hollow organs o Found in respiratory tract and in uterine tubes o Made of microtubules (hollow rods) ▪ Are of globular proteins called tubulins, which form into dimers o flagellum ▪ A single tail-like structure that propels a cell forward • It has the same pattern as cilia • It provides motility • The only human cells with flagellum are sperm • Microvilli o Folds in the PM to increase its surface area o This allows for rapid diffusions ▪ Large amounts of substance can be moved across them o Cytoplasm ▪ Material within cell • Cytosol: jelly-like fluid • Cytoskeleton: protein fiber • Organelles: structures with specific functions o Organelles ▪ Nucleus • Contains DNA in chromosomes o Human DNA in 46 chromosomes ▪ Discrete structures contain DNA ▪ 23 from the father, 23 from the mother ▪ DNA is wrapped around proteins called histones to form long stands of chromatin • Chromatin condenses, and becomes tightly packed to form chromosomes • Most cells have only one nucleus • Enclosed in a nuclear envelope o Two membranes that enclose and surround it ▪ Nuclear pore complexes for small molecules moving in or out of the nucleus ▪ Nucleolus • Mass of densely packed fibers: RNA and rRNA are made here, and ribosomes are produced here ▪ Endoplasmic Reticulum (ER) • Usually found near nucleus • Network of membranes form a channel o Molecules move through the channel ▪ Rough ER • Ribosomes on its surface o Made of proteins and rRNA o Large unit and small unit joined together o Make secretory proteins ▪ Exit the cell ▪ They enter the rough ER through holes in the membranes ▪ Inside, they become tertiary and add molecules ▪ Smooth ER • No ribosomes • Lipid and steroid synthesis • Stores calcium in muscle cells • Helps detoxify drug and poisons o Makes them more water soluble and easier to flush out of the body ▪ Golgi apparatus • Stacks of flattened membrane, which forms sacs called cisternae • Located near the rough ER • Refine proteins to final form o Modified into final form and packaged for secretion o Packaged into vesicles and bud off to fuse with plasma membrane for exocytosis ▪ Mitochondria • Only in animal cells • Produces energy • Energy (ATP) fuels all the reactions in the cell • Outer membrane and inner membrane o Inner membrane folded into cristae o The inner space is a matrix ▪ Chloroplasts • Plant and algae cells contain these • Energy (ATP) for plant cells • Contains green pigment, or chlorophyll, that absorbs sunlight, and through photosynthesis produces energy (ATP) ▪ Lysosomes • Membrane vesicles filled with digestive enzymes o Digest and break down foreign, and worn-out material, and debris o Brought into the cell through phagocytosis ▪ Cell engulfs and ingests particles ▪ Aptosis • Programmed cell death o Lysosome spills contents, killing cell ▪ The cell digests itself ▪ Peroxisomes • Contain enzymes that trigger breaking-down reactions • They remove the hydrogen atom from molecules, add them to oxygen (oxidation), and convert them to water by another enzyme o In most cells, but found most in the liver o They break down fatty acids, and toxic or harmful molecules o Lysosomes and Peroxisomes ▪ Waste and recycling center ▪ Foreign cells, dead broken-down cells, waste products, and toxic materials o Centrosomes ▪ Made of centrioles • Made of microtubules o Vacuoles ▪ Follow membranous sacs ▪ Secretory: carry to PM ▪ Storage: store reserves of materials ▪ Contractile: pump out excess air o Cytoskeleton ▪ Network that extends throughout either the cell or the cytoplasm ▪ microtubules • Hollow tublike structures • Made of globular proteins ▪ Microfilaments • Made of two intertwined strands • Each strand is made of actin proteins ▪ Intermediate fibers • Small keratin fibers coiled together to form rope structures ▪ Cytoskeleton provides support ▪ Cytoskeleton provides movement for the cell ▪ Cytoskeleton serves as a railway system for material in a cell to move along ▪ Motor proteins can move along fibers • Animal cells versus plant cells o Plants have an outside cell wall o Cellulose is the main component of the cell wall o Cell walls are thicker and more rigid compared to the plasma membrane o Cellulose protects plant cell, maintains the cell’s shape, and hold plants upright against gravity • Cells are organized into tissue in living organisms o Tissues are multiple cells grouped together to form a similar structure or function ▪ Sometimes joined together with no open spaces ▪ Sometimes loosely organized • Space between is the extracellular matrix (ECM) o Consists usually of glycogen fibers, and other carbohydrate molecules ▪ One main fiber, collagen • Tight cells are held together by complexes of proteins called cell junctions o Three types ▪ Tight junctions have a tight seal between two cells • This causes a barrier that prevents leakage between two cells ▪ Gap junctions • Proteins from a channel or pore between two cells o Connects cytoplasm o Allows small molecules to pass from cell to cell • Plasma Membrane (PM) ▪ Desmosomes • Attached at spots between two cells o Anchors the cells, but also allows them to move o Surrounds and encloses o Separates intracellular environment from extracellular environment ▪ Intracellular is inside the cell • Cytoplasm, organelles ▪ Extracellular is outside the cell o Hydrophobic portions go inward to stay away from water o Hydrophilic portions go outwards ▪ Not rigid o Phospholipid contains membrane proteins o Fluid mosaic model means that proteins can move across the surface ▪ Movement is temperature dependent • Cooling slows it down • When temperature is low enough, the molecules is locked into place, and the substance becomes solid o PM contains cholesterol ▪ Restrains the movements of phospholipids and causes them to be more rigid o Protein type based on location ▪ Integral protein penetrates into phospholipid bilayer and is permanent. ▪ Peripheral proteins are loosely attached to the surface and can move • Membrane proteins and functions o Structural support ▪ Attach cells together or to ECM o Cell signaling ▪ Receptors for hormones and other molecules ▪ Allow cells to bind together and recognize one another o Enzymatic activity ▪ Trigger chemical reaction within cell o Transport ▪ Move material from one side of a membrane to another • PM is a selective barrier o d permeability ▪ Some substances pass more easily than others ▪ Nutrients, oxygen, water, and waste products must cross in and out of the cell • There are two ways for this to happen o Nonpolar hydrophobic molecules directly cross membrane o Charged ions, polar, and hydrophilic cannot directly cross the PM ▪ Channel proteins in the PM transport material through the PM • Contain a hollow core or channel • Selective transport: only specific molecules and ions can cross • There are different mechanisms to move molecules through the PM o Net Diffusion o Passive transport: no energy ▪ Osmosis: movement of water: involves molecules movement in a solution ▪ Diffusion: molecules in a solution are in a constant state of motion ▪ Net movement of solute across the membrane • Many molecules are moving from side to side • No energy required • Requirements o Membrane is permeable ▪ The solute must be able to cross the membrane o Concentration gradient: concentration is different on each side of the membrane. o Nature wants to be in equilibrium: solute concentration should be the same on both sides ▪ Moves from high to concentration until there is an equal amount on both sides ▪ Diffusion can occur in living cells • Lipid-soluble molecules pass easily o Oxygen, carbon dioxide, and steroid hormones o Passive diffusion o Molecules flow down their concentration gradient ▪ No energy ▪ Passive net diffusion: direct ▪ Facilitated diffusion: cross by proteins • Channel or carrier proteins o Gated channels: can be open or closed o Carrier proteins change shape o Osmosis requirements ▪ Concentration gradient ▪ Membrane must be semi-permeable • Water can cross, solute cannot ▪ Osmosis rule • Water moves from low to high solute concentration • Water continues moving until equilibrium occurs o Tonicity ▪ Compares concentration of solute on one side to the other ▪ Tells us if and which direction osmosis will occur • Isotonic ▪ Affects blood cells o Equal ▪ Equal solute concentration (equilibrium) ▪ No osmosis • Hypotonic o Solution with lower concentration o Relative • Hypertonic o Solution with higher concentration o Water always moves here o Relative ▪ Osmosis occurs in living cells • Cell bursting is lysis • Cell shrinking is crenation • Active transport o Requires energy o Two types: pumps, bulk transport ▪ Pumps • Molecules are moved up their concentration gradient • Used to help maintain concentration gradient • Living cells use them (Na+/K+ pumps) o Sodium is Na+ o Potassium is K+ • Pumps 3Na+ out for every 2K+ pumped in o Ion pumps help determine membrane plasma osmosis in cell o Membrane potential differ in charge on each side of the PM ▪ Caused by the difference in ion concentration in and out of the cell ▪ How ions are distributed in a typical cell • More anions inside • More cations outside • Not distributed evenly • Different in charge in membrane potential o 70 mv • Bulk transport o Moves material too large to fit through protein channels ▪ Move large numbers of molecules at once ▪ Requires energy o Endocytosis ▪ Brings material into a cell ▪ Two main types • Phagocytosis o Cells ingest material o Some cells, limb-like structures called pseudopods ▪ Engulf large things and bring them into a cell • Pinocytosis o Brings many molecules into the cell at once o PM furrows inward, molecules enter space o Membrane pinches off and molecules are brought into the cell • Exocytosis o Large cellular products (proteins) are brought out of the ell o Products are packaged into vesicles, fuse to membrane, and contents spill out of the cell • Chemical reactions must have a constant supply of energy and enzymes o Chemical reactions equal metabolism equals life o Chemical energy source or living cells is adenosine triphosphate or ATP ▪ Consists of a ribose sugar and an adenine nitrogen bases with three attached phosphates • Stores energy in bonds • Broken down to release energy o Third phosphate is removed from the molecule o Turns into a diphosphate, or ADR ▪ Animal cells make it by cellular respiration • Breakdown, or catabolism, of glucose ▪ Animals must have steady glucose in the bloodstream to make ATP • From food and from energy from lipids and glycogen o Aerobic respiration: inhaling oxygen o Anaerobic: no oxygen • Glucose is broken down into CO2 and H2O • As it is broken down, energy is released that is used to make ATP o Specifically, energy is released with electrons, or e’s, and is removed form molecules ▪ Oxidation/reduction • Electron gain: reduction • Electron loss: oxidation ▪ Often called redox electrons • Chapter 8: • Metabolism o Sum of all the biochemical reactions occurring in an organism ▪ Two categories • Anabolism, or anabolic reactions o Small molecules joining to from larger molecules o “Building-up” reactions • Catabolism, or catabolic reactions o Larger molecules broken down into smaller molecules ▪ “Breaking-down” reactions o Metabolic pathway ▪ Series of chemical reactions • Chemical reaction o Molecule is altered in series of chemical reaction o Final product doesn’t happen with a single reaction o Each step is triggered by specific enzymes ▪ Chemical reactions can release or require energy • Exergonic is releasing energy o Break-down causes energy release (usually catabolism) o Less free energy is in the product • Endergonic is requiring energy o Build up reactions (anabolic) o More free energy is in the product • Coupled reactions o Endergonic and exergonic together ▪ Energy released in the exergonic reaction fuel the endergonic reaction: free energy ▪ A system’s energy can be used to perform work ▪ In a cell, available energy is used to fuel reactions in the cell o Energy is the capacity to cause change ▪ Kinetic: motion of objects • Moving objects, perform work by making other things move ▪ Thermal energy: random movement of atoms and molecules • Transferred from object to object ▪ Potential energy • Net movement possessed by objects • Stored for later ▪ Chemical energy • Potential energy to be released during a reaction • Found in living cells • Bioenergetics o Flow of energy in living systems ▪ Obeys laws of thermodynamics • First Law of Thermodynamics o Energy cannot be destroyed or created, only transformed o Cells need energy to: ▪ Three different types of work • Chemical work equals anabolic reaction equals synthesis of large molecules • Transport work equals physical movement of cell equals cilia beating, muscle cells concentration, cell division ▪ All run off the energy created by adenosine triphosphate or ATP • Enzymes o Required for living cells, as well as energy o Usually proteins o Function as a catalyst ▪ Causes other molecules to change without changing itself o Speed up reactions o Don’t change reaction’s nature • Mechanism of Enzyme Action o Substrates ▪ Molecules that go into reactions and become altered ▪ Must physically bind to enzymes for reaction to occur o End products ▪ Produced by reactions o Active site ▪ Where substrate binds on enzymes o Lock and Key Model ▪ Substrate must perfectly fit into active site for reaction to occur o Enzymes work to decrease activation energy ▪ Activation energy is the energy required to drive a reaction and cause it to occur • Much less energy is needed when the enzyme is present ▪ Work by physically holding and aligning substrates together • Reaction requires less energy, occurs faster • Most reactions are reversible o Control of enzyme activity ▪ Activity measured by rate at which substrate is converted to product ▪ Influenced by different factors in the environment • Temperature o Increase of temperature will increase reaction until approximately 40 degrees C, at which point it will rapidly decline o High temperature causes the enzymes to denature and lose their three-dimensional shape o Enzymes lose active site, and the substrate cannot bind, so the reaction does not occur • pH o peak activity is within a narrow pH range o changes in the pH equals changes to the active site equals no bond o optimum pH reflects the environments the enzymes are found in • substrate concentration o increases of concentration makes increase in substrate activity until every substrate has an enzyme attached to it (saturation) • Law of Mass Action o Reaction is driven from high concentration to low concentration • Coenzymes and cofactors o Small molecules that help substrates fit into active sites o Coenzymes are molecules derived from water-soluble vitamins o Cofactors are metal ions • Enzyme inhibitors o Competitive inhibitor ▪ Competes with substrate for active site ▪ Prevents substrate from binding ▪ Competitive • Prevents substrate from binding ▪ Non-competitive • Binds to enzyme, though not on the active site, and the enzyme changes shape • Substrate and end products of respiration o Glucose + oxygen + ADP + P → CO2 + H2O + ATP o Energy is released when electrons are moved from the molecules • Oxidation/reduction o Electron gain is reduction o Electron loss is oxidation o These are both known as redox reactions • During cell respiration, glucose is oxidized, then electrons are removed, energy is released. Electrons are often with H+ ions. When H+ ions are removed, the electrons go with them. • Aerobic respiration o Metabolic pathway o Glucose is not converted to ATP all at once ▪ Glycolysis • Glucose is split into two molecules called pyruvate o This occurs in the cytoplasm o Two phases ▪ Energy investment phase • ATP is burned (2 molecules) ▪ Energy payoff phase • ATP is made (4 molecules o Net gain of 2 ATP molecules o Two places where the molecule is oxidized o NAD+ is reduced to NADH and that acts as an electron carrier molecule o For each glucose molecule, there are 2 molecules of NADH • End products o 2 molecules of pyruvic acid o 2 molecules of ATP o 2 molecules of NADH ▪ Pyruvic acid is the substrate for the next step ▪ Preparatory step • Pyruvate is oxidized and converted into acetyl CoA o Leaves cytoplasm and enter the inner matrix of the mitochondria • CO2 and H with electrons are removed to form acetic acid o Molecule is oxidized • H with electrons in tow combine with NAD for more NADH • The acetic acid combines with coenzyme A and acetyl CoA • End products o 2 acetyl CoA o 2 carbon dioxide o 2 NADH ▪ Krebs cycle (acetyl CoA), (cycle happens twice) • Acetyl CoA enters cycle and is converted into six different acids • Acetyl CoA combines with oxaloacetate to form citrate (6 carbons) • End products o 6 NACH o 2 FADH2 o 2 ATP o 4 CO2 ▪ Electron transport chain • Oxidation phosphorylation pathway • Each glucose molecule yields 12 electron carriers • These carriers and the new substrate • Occurs in the cristae, or folds, of the mitochondria • Electron transport molecules are embedded in the membrane o Transport molecules in the cristae membrane ▪ FMN ▪ Coenzyme ▪ ? o Takes from carrier molecules and pass the electrons along ▪ Each get reduced and oxidized ▪ Exergonic reaction, and energy released makes ATP ▪ Aerobic respiration • Oxygen is the final electron acceptor o Binds to and removes electrons at the end of the chain o Without oxygen, the electrons would get stuck and stop o Water is formed when reduced oxygen binds to hydrogen in the environment o Phosphate added to ADP, and you get ATP • Chemiosmotic Theory o ATP Production ▪ Proton pumps pump H+ ions from the matrix into the space between the inner and outer membrane • This causes a concentration gradient o The leads to diffusion, and it flows down the concentration gradient, movement of the H+ causes ATP synthase to make ATP o End products of and electron transport chain ▪ About 30 molecules of ATP ▪ 6 molecules of H2O o About 36 ATP molecules for glucose molecule • Anaerobic respiration (fermentation) o Just glycolysis ▪ End products • 2 ATP • 2 NADH • 2 pyruvic acid o Two last are converted into an end product ▪ Acid ▪ Gas ▪ alcohol