LIFE 120 Midterm 1 Study Guide
LIFE 120 Midterm 1 Study Guide Life 120
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This 21 page Study Guide was uploaded by Skylar Hoscheit on Thursday September 15, 2016. The Study Guide belongs to Life 120 at University of Nebraska Lincoln taught by Dr. Peter Angeletti in Fall 2016. Since its upload, it has received 168 views. For similar materials see Fundamentals of Biology I in fundamental biology at University of Nebraska Lincoln.
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Date Created: 09/15/16
Chapter 1 Hierarchy of life (Biggest to Smallest) o Biosphere o Ecosystem o Community o Population o Organism o Organ System o Organ o Tissue o Cell o Organelle o Molecule o Atom Eukaryotic cells have a DNA-containing nucleus and other membrane- enclosed organelles Prokaryotic cells lack such organisms DNA contains genetic information that is encoded in the nucleotide sequences Domain Bacteria and domain Archaea consist of Prokaryotes Domain Eukarya consists of Eukaryotes Organisms interact with their environments, exchanging matter and energy o Two major processes Cycling of nutrients which return to the soil Flow of energy from sunlight to producers to consumers o Energy enters as light and exits as heat Chapter 2 • Atoms/elements ◦ Atomic Structure ▪ Protons (+) ▪ Electrons (-) ▪ Neutrons (0) ▪ (# protons = # electrons) • Subatomic Particles ◦ Quarks, Muon, Tau, Gluon, Photons, Neutrinos, Higgs boson strings • Isotopes - stable/unstable variants of elements with extra neutrons ◦ Isotopes of hydrogen ▪ Hydrogen 1 proton ▪ Deuterium 1 proton 1 neutron ▪ Tritium 1 proton 3 neutron ◦ Isotopes of carbon ▪ Carbon-12 6 protons 6 neutrons ▪ Carbon-14 6 protons 8 neutrons Hydrogen Bonds o Involve hydrogen and an electronegative atom Oxygen, Nitrogen, Phosphorous o Weak polar (hydrophilic) interactions o 10% the strength of a covalent bond The hydrogen bonding of water gives it special properties o Cohesion surface tension o Adhesion “wetting” o high Specific heat 1cal/gram/ C o Solid water (ice) is less dense than liquid water o Water ionizes Polarity of water allows it to solvate ions and charged molecules Ionic Bonds o Electropositive atoms Cations (+) More protons than electrons o Electronegative atoms Anions (-) More electrons than protons Chapter 3 • Aside from water, living organisms consist mostly of carbon-based compounds, organic compounds • Carbon is unparalleled in its ability to form large, complex, and diverse molecules • Importance of carbon — Variation in Carbon Skeletons ◦ Carbon it the most versatile atom on earth ◦ Produce a vast array of chemical structures — Diverse molecules • Isomers are molecules that have the same molecular formula and molecular weight, but a different arrangement of atoms • Structural isomers differ in the order which their atoms are attached • Chemical groups ◦ Carbon covalent bonds can connect with many different chemical groups ◦ the valences of carbon and its most frequent partners are the “building code” that governs the architecture of living molecules ◦ The properties of an organic molecule also depend on the chemical group • Critically important molecules of all living things fall into four main classes ◦ Carbohydrates ◦ Lipids (NOT macromolecules, associate by hydrophobic interactions) ◦ Proteins ◦ Nucleic acids • Carbohydrates, Proteins, and Nucleic acids can form huge molecules called macromolecules • Diversity of Polymers: Each cell has thousands of different macromolecules; Macromolecules vary among cells, within a species, between species • Critically important molecules of all living things fall into four main classes ◦ Carbohydrates ◦ Lipids ◦ Proteins ◦ Nucleic acids • Carbohydrates ◦ contain carbon, hydrogen and oxygen in the proportion CH O.2 • Monosaccharides ◦ The simplest carbohydrates are monosaccharides, or simple sugars, such as Glucose (C6H12 6 • Disaccharides • Polysaccharides ◦ Carbohydrate macromolecules ▪ Polymers of many sugar building blocks • Carbohydrates serve as fuel and building material. ◦ Cells store and release energy using a variety of carbohydrates, both simple and complex. ◦ Carbohydrates are used to build the molecules needed for cell structure and function. • Monosaccharides are the simplest form of sugar ◦ Monosaccharides serve as a major fuel for cells and as raw material for building molecules ◦ Monosaccharides are classified by the number ofcarbons in the carbon skeleton and the placement of the carbonyl group (C=O) • Polysaccharides, the polymers of sugars, have storage and structural roles. ◦ The structure and function of a polysaccharide are determined by its sugar monomers and the positions of glyosidic linkages. ◦ Polysaccharides: Starch, Glycogen, Cellulose, and Chitin • Critically important molecules of all living things fall into four main classes ◦ Carbohydrates ◦ Lipids ◦ Proteins ◦ Nucleic acids ◦ Lipids are large molecules that do not form true polymers • Lipids are a diverse group of hydrophobic molecules ◦ Hydrophobic ▪ The unifying feature of lipids is having little or no affinity for water (not soluble in water) ◦Lipids are hydrophobic because they consist mostly of hydrocarbons, which form nonpolar covalent bonds ◦Lipids are an efficient way to store energy. (fats) ◦Saturated Fats are the principal molecules in butter ◦Structural role: Lipids in membranes partition the cell into compartments. (phospholipids) ◦Functional role: Some lipids are signaling molecules. (steroids) ◦Lipids include: Fats, Phospholipids, and Steroids ◦Phospholipids oTwo FAs + phosphate group attached glycerol oPhosphate and glycerol group (hydrophilic head) oFatty acid tails (hydrophobic) ◦Steroids olipids of carbon skeleton consisting of four fused rings olipids that regulate many aspects of growth osmall modifications of a steroid molecule can make a big difference in its effects on physiology, growth, and development • Proteins ◦ Nearly every dynamic ◦ Nearly every dynamic function of a living being depends on proteins. ◦ Proteins account for more than 50% of the dry mass of most cells ◦ Proteins are structurally and functionally complex: a diversity of structures, resulting in a wide range of functions ◦ Proteins perform a vast array of functions within living organisms. ◦ A protein is a biologically functional molecule that consists of one or more polypeptides. ▪ Polypeptides are unbranched polymers built from the same set of 20 amino acids. ▪ Amino acids are organic molecules with carboxyl and amino groups. ▪ The two functional groups (amino and carboxyl) are involved in condensation reactions that create peptide bonds between amino acids. ▪ Hydrogen bonds stabilize the secondary structure of the protein keratins’ amino acids ◦ Polypeptides ◦ Polypeptides range in length from a few to more than a thousand monomers ◦ Each polypeptide has a unique linear sequence of amino acids, from the amino end to the carboxyl end. ◦ The sequence of amino acids leads to a unique 3D structure. ▪ The structure of a protein is described at 4 levels of complexity. ◦ Sickle Cell Disease ▪ Primary structure is the sequence of amino acids on the polypeptide chain ▪ A slight change in primary structure can affect a protein’s structure and ability to function ▪ Sickle-cell disease, an inherited blood disorder, results from a single amino acid substitution in the protein hemoglobin • Nucleic Acids ◦ Nucleic acids store, transmit, and help express hereditary information. ◦ There are two types of nucleic acids ▪ Deoxyribonucleic acid (DNA) ▪ Ribonucleic acid (RNA) ◦ Nucleic acids are polymers called polynucleotides ◦ Each polynucleotide is made of monomers called nucleotides ◦ Each nucleotide consists of a nitrogenous base, a pentose sugar, and one or more phosphate groups ◦ The portion of a nucleotide without the phosphate group is called a nucleoside ◦ Nucleic acids are polymers called polynucleotides ◦ Nucleotide consists of a phosphate group, a pentose sugar, and a nitrogenous base ◦ Formation of Polymer Nucleotides ▪ Adjacent nucleotides are joined by covalent bonds that form between the hydroxyl (-OH) group on the 3’ carbon of one nucleotide and the phosphate on the 5’ carbon of the next ▪ These links create a backbone of sugar-phosphate units with nitrogenous bases as appendages ◦ DNA Double Helix ▪ Two polynucleotides spiraling around an axis — double helix ▪ Antiparallel — backbones in opposite 5’ —> 3’ directions ▪ N Bases pair by hydrogen bonds ▪ Adenine and Thyme ▪ Guanine and Cytosine Chapter 4 All organisms are made of cells o Definition - cell is the simplest collection of matter that can live o Viruses are not cells Cell structure is correlated to cellular function o Structural order produces emergent properties o Structural variety is enormous o Basic continuity in cellular structure Microscopes o Most cells are between 1 and 100 m in diameter, too small to be seen by the unaided eye Cell Fractionation Microscopy o Light microscopy (LM), visible light; glass lens o Electron microscopy (EM), Electrons; magnetic lens o Image quality depends on Magnification LM – 1000x EM – 100,000 + Resolution LM – 200 nm EM - .002 nm Contrast Light Microscopy techniques to enhance contrast o Fluorescence – structures tagged with fluorescent dyes or antibodies o (artery cell) o Confocal – special aperture reduces stray light; focus in 3 dimensions o (nerve cells green; support cells red; yellow overlap) Electron Microscopy Techniques o Scanning electron microscopes (SEMs) Focus beam on specimen surface Images look 3-D o Transmission electron microscopes (TEMs) Focus beam through a specimen Examine internal structure Cell fractionation breaks up cells and separates the major organelles from one another Centrifuges fractionate cells into their component parts, and cell components separate based on their relative size. Basic features of all cells o Plasma membrane o Semifluid substance called cytosol o Chromosomes (carry genes) o Ribosomes (make proteins) Prokaryotic cell o No nucleus or organelles o Bacteria and Archaea Archaea utilize DNA as their genetic material but do not have their DNA enclosed within a nuclear envelope Eukaryotic cell o Membrane-enclosed organelles o Well defined Nucleus o Plants, animals & fungi No nucleus - DNA called the nucleoid No membrane-bound organelles The plasma membrane is a selective barrier that allows sufficient passage of oxygen, nutrients, and waste to service the volume of every cell. The general structure of a biological membrane is a double layer of phospholipids. A eukaryotic cell has internal membranes that divide the cell into compartments—organelles The plasma membrane and organelle membranes participate directly in the cell’s metabolism DNA in nucleus – bounded by nuclear envelope Complex endomembrane system Plant and animal cells have most of the same organelles. The nucleus contains most of the DNA in a eukaryotic cell Nucleus is usually the most conspicuous organelle In the nucleus, DNA is organized into discrete units called chromosomes Each chromosome is one long DNA molecule associated with proteins o The DNA and proteins of chromosomes are together called chromatin o Chromatin condenses to form discrete chromosomes as a cell prepares to divide The nucleolus is located within the nucleus and is the site of ribosomal RNA synthesis Ribosomes are complexes of ribosomal RNA and protein The nucleolus is located within the nucleus and is the site of ribosomal RNA (rRNA) synthesis Ribosomes carry out protein synthesis in two locations o In the cytosol (free ribosomes) o On the outside of the endoplasmic reticulum (rough ER) or the nuclear envelope (bound ribosomes) The endomembrane system regulates protein traffic and performs metabolic functions in the cell. Components of the endomembrane system o Nuclear envelope o Endoplasmic reticulum (ER) o Golgi apparatus o Lysosomes o Vacuoles o Plasma membrane These components are either continuous or connected through transfer by vesicles The endoplasmic reticulum (ER) accounts for more than half of the total membrane in many eukaryotic cells. The rough ER membrane is continuous with the nuclear envelope. There are two distinct regions of ER o Smooth ER: lacks ribosomes o Rough ER: surface is studded with ribosomes The smooth ER o Synthesizes lipids, such as oils, phospholipids, and steroids o Metabolizes carbohydrates o Detoxifies drugs and poisons o Stores calcium ions The rough ER o Has bound ribosomes o Distributes transport vesicles, proteins surrounded by membranes o Is a membrane factory for the cell A lysosome is a membranous sac of hydrolytic enzymes that can digest macromolecules o Lysosomal enzymes can hydrolyze proteins, fats, polysaccharides, and nucleic acids o Lysosomal enzymes work best in the acidic environment inside the lysosome Vacuoles are large vesicles derived from the endoplasmic reticulum and Golgi apparatus Food vacuoles are formed by phagocytosis o Phagocytosis is the process in which bacteria is engulfed in white blood cells Contractile vacuoles, found in many freshwater protists, pump excess water out of cells Central vacuoles, found in many mature plant cells, hold organic compounds and water Certain vacuoles in plants and fungi carry out enzymatic hydrolysis like lysosomes Mitochondria are the sites of cellular respiration, a metabolic process that uses oxygen to generate ATP. Chloroplasts, found in plants and algae, are the sites of photosynthesis. Peroxisomes are oxidative organelles. Chloroplasts contain the green pigment chlorophyll, as well as enzymes and other molecules that function in photosynthesis Chloroplasts are found in leaves and other green organs of plants and in algae The chloroplast is one of a group of plant organelles called plastids; double membrane plant organelles. Peroxisomes o specialized metabolic compartments o bounded by a single membrane Chemical factories o Make hydrogen peroxide, a strong oxidizer, bleaching agent and disinfectant. o Detoxify o Glyoxysomes, specialized peroxisomes, found in plants, convert fats to sugar Cytoskeleton is a network of fibers that organizes structures and activities in the cell. Cytoskeleton network extends throughout the cytoplasm o organizes the cell’s structures o anchors many organelles Functions: o Supports the cell & maintains shape o Regulates biochemical activities o Produces cell motility Three main types of fibers make up the cytoskeleton o Microtubules are the thickest of the three components of the cytoskeleton o Microfilaments, also called actin filaments, are the thinnest components o Intermediate filaments are fibers with diameters in a middle range Microtubules are hollow rods constructed from globular protein dimers called tubulin Functions of microtubules o Shape and support the cell o Guide movement of organelles o Separate chromosomes during cell division o useful to impart cell motility Microtubules grow from centrosome In animal cells o centrosome has pair centrioles o each with nine triplets of microtubules in a ring Flagella undulate to propel sperm cells. o Flagella are limited to one or a few per cell Cilia go back & forth to propel protozoan o cilia occur in large numbers on cell surfaces Share a common structure: o microtubules sheathed by membrane o A basal body that anchors the cilium or flagellum o Dynein, the motor protein, drives the bending movements Microfilaments are thin solid rods, built from molecules of globular actin subunits The structural role of microfilaments is to bear tension, resisting pulling forces within the cell. Bundles of microfilaments make up the core of microvilli of intestinal cells. Microvilli of intestinal cells o increase cell surface o Improves nutrient absorption Cellular extensions reinforced by microfilaments Connected to intermediate filaments at base Muscle Cells - microfilaments that function in cellular motility contain myosin plus actin o actin filaments arranged parallel to one another o Thicker myosin filaments interdigitate with thinner actin fibers o Myosin “walks”, contracting the muscle cell Pseudopodia o Actin filaments interact with myosin at cell’s trailing end to squeeze interior forward Cytoplasm streaming o Circular flow of the cytoplasm involves actin-myosin interaction Intermediate filaments are larger than microfilaments but smaller than microtubules They support cell shape and fix organelles in place Intermediate filaments are more permanent cytoskeleton elements than the other two classes Most cells synthesize and secrete materials that are external to the plasma membrane. These extracellular materials are involved in many cellular functions. Extracellular components and connections between cells help coordinate cellular activities The cell wall is an extracellular structure that distinguishes plant cells from animal cells. Prokaryotes, fungi, and some protists also have cell walls. The cell wall protects the plant cell, maintains its shape, and prevents excessive uptake of water. Plant cell walls are made of cellulose fibers embedded in other polysaccharides and protein. o Cellulose is a major structural component of plant cell walls. Plant cell walls may have multiple layers: o Primary cell wall: relatively thin & flexible o Middle lamella: thin layer – glue between adjacent cells o Secondary cell wall: Adds more strength Plasmodesmata - channels that perforate plant cell walls o Passage of water and small solute o Proteins and RNA o Viruses encode special proteins to pass Animal cells lack cell walls but are covered by an elaborate extracellular matrix (ECM). The ECM is made up of glycoproteins such as collagen, proteoglycans, and fibronectin. ECM proteins bind to receptor proteins in the plasma membrane called integrin’s. Neighboring cells in tissues, organs, or organ systems often adhere, interact, and communicate through direct physical contact Intercellular junctions facilitate this contact Types of intercellular junctions o Plasmodesmata (plant cell) o Tight junctions o Desmosomes o Gap junctions Tight junctions - sites where cells press together, prevent leakage of fluid Desmosomes - anchoring junctions, fasten cells together into strong sheets Gap junctions -communicating junctions; provide cytoplasmic channels between adjacent cells Chapter 5 The plasma membrane separates the living cell from its surroundings. Membranes constituents: lipids, proteins, carbohydrates. The plasma membrane exhibits selective permeability, allowing some substances to cross it more easily than others. Phospholipids are the Major Constituents of Membranes o Plasma membrane - 8nm thick exist as a stable boundary between two aqueous compartments, Selective permeability, controls passage o Phospholipid bilayer amphipathic molecules. The hydrophobic/hydrophilic interactions between water and phospholipids create a bi- layer of lipid molecules that separates inside from outside. Membranes are not static sheets of molecules. Most of the lipids and some proteins in a membrane can shift about laterally. The lateral movement of phospholipids is rapid; proteins move more slowly. How quickly molecules move within and across membranes is a function of temperature and the structure of the hydrocarbon tails in the bilayer. Short chain fatty acids and unsaturated fatty acids in phospholipids increase fluidity o Cholesterol reduces membrane fluidity at moderate temperatures, but at low temperatures hinders solidification. Integral membrane proteins, also amphipathic, often contain - helical regions with hydrophobic R-groups that interact with the fatty acids tails of phospholipids. (transmembrane proteins) Peripheral proteins are loosely bound to the surface of the membrane, and can attach to phospholipids, fatty acids, other hydrophobic hydrocarbons that insert into the membrane. Six major functions of membrane proteins o Transport hydrophilic channels selective passage uses ATP energy o Enzymatic enzymes expose active sites connected to organize pathways o Signaling receptors accept message on outside shape change relays message on inside o Cell Recognition glycoproteins are ID tags development & cell recognition Abs & blood types o Intercellular joining components of cell junctions gap junctions tight junctions plasmodesmata o Attachment microfilaments & cytoskeleton integrin’s attach ECM to cytoskeleton A cell must regulate transport of substances across cellular boundaries. Plasma membranes are selectively permeable, regulating the cell’s molecular traffic o Hydrophobic (nonpolar) molecules can dissolve in the lipid bilayer of the membrane and cross it easily. o Polar molecules, such as sugars, do not cross the membrane easily. How do molecules get in and out of membranes? o Passive transport: passive process depends on concentration gradient, Diffusion and Facilitated Diffusion. o Active transport: process requires energy o Endocytosis/Exocytosis: for bulk transport, and active processes requiring energy Diffusion is the tendency for molecules to spread out evenly into the available space. (random thermal motion) Although each molecule moves randomly, diffusion of a population of molecules may be directional -- a net movement of solutes. At dynamic equilibrium, molecules are still moving randomly, but no net movement. Osmosis is the diffusion of free water across a selectively permeable membrane. Water diffuses across a membrane from the region of lower solute concentration to the region of higher solute concentration until the solute concentration is equal on both sides o Osmosis – H 0 2iffuses across selective permeable membrane o H 02– moves from region of lower solute [concentration] to region of higher solute [concentration] Tonicity is the ability of a surrounding solution to cause a cell to gain or lose water o Isotonic: Solute concentration same as the cell o Hypertonic: a great solute concentration. Solute concentration higher than cell, water move out of cell o Hypotonic: a lesser solute concentration Solute concentration less than inside cell, water move into cell o Water Balance of Cells Without Walls Hypotonic – water goes in, cell swells, cell busts; Isotonic - no net movement of water; Hypertonic – water lost, cell shrivels; o Water Balance in Plant Cells with Walls Hypotonic – water goes in, cell swells, wall opposes uptake; cell is turgid (firm) Isotonic - no net movement of water; cell becomes flaccid (limp), plant wilts Hypertonic – water lost, the membrane pulls away from the wall, cell plasmolyzes & dies, plant wilts and dies In facilitated diffusion, transport proteins speed the passive movement of molecules across the plasma membrane Facilitated diffusion is passive, solute moves down its concentration gradient without energy consumption Transport proteins allow passage of hydrophilic substances across the membrane A transport protein is specific for the substance it moves Transport proteins: Channel proteins and Carrier Proteins Channel proteins have hydrophilic channels that allow a specific molecule or ion to cross the membrane. Channel proteins include o Aquaporin’s, o Ion channels Carrier proteins undergo a conformational change, which is triggered by binding and release of the transported molecule No net energy input is required How do molecules get in and out of membranes? o Passive transport: passive process depends on concentration gradient, Diffusion and Facilitated Diffusion. o Active transport: process requires energy o Endocytosis/Exocytosis: for bulk transport, and active processes requiring energy Facilitated diffusion speeds transport of a solute by providing efficient passage through the membrane but does not alter the direction of transport Some transport proteins, however, can move solutes against their concentration gradients Active transport moves substances against their concentration gradients Active transport requires energy, usually in the form of ATP Active transport allows cells to maintain concentration gradients that differ from their surroundings The sodium-potassium pump is one type of active transport system Electrogenic pump o transport protein that generates voltage across a membrane – e.g. Na/K pump in animal cells Proton pump o electrogenic pump of plants, fungi, & bacteria ATP drives H+ ions across membrane generates voltage useful for cell work Two combined forces, collectively called the electrochemical gradient, drive the diffusion of ions across a membrane. (acts like battery) o A chemical force (the ion’s concentration gradient) o An electrical force (the effect of the membrane potential on the ion’s movement) Cotransport is coupled transport by a membrane protein o occurs when active transport of a solute indirectly drives transport of other solutes For example, plant cells use the gradient of hydrogen ions generated by proton pumps to drive active transport of nutrients into the cell Moves sucrose into cells against concentration gradient (leaf to veins) H+ diffuses back to give energy to drive sucrose transporter How do molecules get in and out of membranes? o Passive transport: passive process depends on concentration gradient, Diffusion and Facilitated Diffusion. o Active transport: process requires energy o Endocytosis/Exocytosis: for bulk transport, active processes requiring energy Small solutes and water enter or leave the cell through the lipid bilayer or by means of transport proteins (passive or active transport). Large molecules, such as polysaccharides and proteins, cross the membrane in bulk by means of vesicles. Bulk transport requires energy. Bulk transport across the plasma membrane occurs by exocytosis and endocytosis. Exocytosis o Transport vesicles migrate, fuse and release contents o Secretory cells Insulin Neurotransmitters Cellulose Endocytosis o In endocytosis, the cell takes in molecules and particulate matter by forming new vesicles from the plasma membrane o Endocytosis is a reversal of exocytosis, involving different proteins o There are three types of endocytosis Phagocytosis (“cellular eating”) Particle engulfed into a vacuole vacuole fuses with lysosome to digest Pinocytosis (“cellular drinking”) molecules are taken up when extracellular fluid is “gulped” into tiny vesicles Receptor-mediated endocytosis Recognition leads to specific binding of ligands to receptors triggers vesicle formation and uptake Cholesterol uptake In multicellular organisms, cell-to-cell communication allows the cells of the body to coordinate their activities. Communication between cells is also essential for many unicellular organisms Cells respond to a variety of physical (e.g. touch, odor, light) and chemical (e.g. hormones) signals. The plasma membrane plays a key role in most cell signal two categories: Local and Long-Distance Signaling o In long-distance signaling, plants and animals use chemicals called hormones. o In hormonal signaling in animals (called endocrine signaling), specialized cells release hormone molecules that travel via the circulatory system. o Hormones vary widely in size and shape.
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