Study Guide for Bio 190 Exam 2
Study Guide for Bio 190 Exam 2 Bio 190
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This 12 page Study Guide was uploaded by Danielle Francy on Saturday March 5, 2016. The Study Guide belongs to Bio 190 at Towson University taught by Joseph Velenovsky in Fall 2015. Since its upload, it has received 206 views. For similar materials see Intro Biology for Health Professions in Biology at Towson University.
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Date Created: 03/05/16
Exam 2 Study Guide What are the four levels of protein structure? Describe each. 1. Primary ○ Linear chain of amino acids held together in a specific sequence by covalent(“peptide”) bonds(polypeptide) ○ Folding occurs spontaneously ○ Changes in primary structure may affect the ability of the protein to fold ○ ***Upon denaturation, this level of structure is still intact. 2. Secondary ○ Distribution of alpha helices and beta pleated strands along a protein chain ○ Spatial arrangement of amino acid residues that are nearby in the sequence/local regions of the polypeptide chains ○ Regular coils(helices) and folds(pleated sheets) with connecting segments; Hbond ○ Alpha helix and beta pleated sheet are backbones ○ Both held together by hydrogen bonding ○ ***Amino acids are not involved ○ Most globular proteins are made of beta pleated sheets ○ Most fibrous proteins are made of alpha helix 3. Tertiary ○ Secondary structure folded into 3D shape ○ ***3D structure determines function ○ Globular ○ Interactions between R groups ○ Hydrogen bonding polar side chains; ionic bonding with charged ○ Refers to the spatial arrangement of amino acid residues that are a far apart in the sequence and to the pattern of disulfide bonds i. Hydrophobic side chains are buried in the interior and it’s polar, charged chains are on the surface. 4. Quaternary ○ Refers to the spatial arrangement of subunits and the nature of their interactions ○ Functional protein consisting of two or more individual polypeptide chains to assemble into multisubunit structures. ○ Two or more polypeptide chains makes one macromolecule ○ 4 subunits make up a protein What is denaturation? ● No enzyme required ● loss of quaternary, tertiary, and secondary structures ● Polar amino acids dissolve very well in water; aqueous ● Nonpolar amino acids dissolve very well in membranes ● in response to change from heat, pH, or salt How do proteins denature when exposed to salt, pH, and heat? Salt: ● There are more positive or negative ions available for interactions which are involved in keeping the protein’s shape and keeping it together pH: ● Proteins can change their shape when exposed to temp or pH ● Change in H+ atoms ● Hydrogen atoms attract the negative side of the polar amino acids ● So, if you change the pH, you change the stability of the protein structure Heat: ● Can be used to disrupt hydrogen bonds and nonpolar hydrophobic interactions. ● Heat increases the kinetic energy and causes the molecules to vibrate so rapidly that the bonds are disrupted ● Heat must be absorbed to break hydrogen bonds ● Heat is released when hydrogen bonds form ***None of these processes break peptide bonds, so the primary structure of the protein stays intact. Osmosis: ● Selectively permeable membrane ● Permeable to water, not solute(salt) ● Low water, high solute ● High water, low solute ● Water molecules cluster around solute molecules ● Fewer water molecules on the right side ● Movement of water molecules from high concentration to low concentration through a membrane Diffusion: ● Concentration gradient ● Movement of atoms/ions/molecules down their concentration gradient ○ From area of high concentration to area of low concentration ○ No external energy input needed ○ Energy for net movement comes from potential energy of concentration gradient ○ If 2 or more components are present, each moves down its own concentration gradient(generally in opposite directions) Passive Transport: ● O2 ● Ions and polar molecules Hypotonic vs. Hypertonic: Hypotonic: ● If one solution contains less solute than another solution, it is hypotonic to the other solution ● Less=burst Hypertonic: ● If one solution contains more solute than another solution, it is hypertonic to the other solution ● More=shriveled Endocytosis(Endo= inside/into): ● ex: amoeba engulfing a food particle ● Into cell ● Cell energy needed ● Plasma membrane indents ● Forms pocket around material to be transported ● Vesicle sides fuse ● Closed vesicle drops into cytoplasm inside cell Polar vs. Nonpolar The greater the electronegativity difference, the more ionic the bond is. Polar: ● Bonds that are partly ionic ● A bond between two nonmetal atoms that have different electronegativities=have unequal sharing of the bonding electron pair ● Hydrophobic Nonpolar: ● Equal sharing of the bond electrons, arise when the electronegativities of the two atoms are equal ● A bond between two nonmetal atoms that have the same electronegativity=have equal sharing of the bonding electron pair ● Hydrophilic Water molecules: ● Polar ● Two hydrogen atoms covalently bonded to an oxygen atom. ● Attract or are attracted to other polar molecules creating hydrogen bonds ● Difference in electronegativity between water’s hydrogen and oxygen atoms creates partial negative and partial positive charges Hydrocarbons: ● Organic compound consisting only of hydrogen and carbon. ● One hydrogen atoms has been removed ● Functional group called hydrocarbyls ● Can range from single bonds to triple bonds Chitin: ● The exoskeleton of insects and crustaceans ● Structural polysaccharide ● Cell wall of fungi Prokaryotic vs. Eukaryotic Cells: Prokaryotic Cells: ● Bacteria and archaea ● No membrane enclosed nucleus ● Nucleoid ● Cell walls ● Membrane enclosing the cytoplasm= plasma membrane ● Protects and maintains shape=cell wall ● No lysosomes ● ex. Penicillin ● Much smaller than eukaryotic cells ● DNA is circular; no limiting membrane; nucleoid ● Very few organelles ● Ribosomes are smaller than ribosomes in eukaryotes Eukaryotic Cells: ● Organelles ● Membrane bound ● Animal or human cells ● Not in animal cells: ○ Central vacuole ○ Chloroplast ○ Cell wall ○ Plasmodesma ● Larger in size than prokaryotic cells ● DNA is linear and paired; within membrane; true nucleus ● Many organelles; most enclosed in 12 membranes ● Ribosomes are larger than those of prokaryotes Cytoskeleton: 1. Microfilament 2. Intermediate filament 3. Microtubule Microfilament: ● Structure holding the cell together ● How the cell moves ● Thinnest fiber ● ***Composed of Actin ● Solid rods ● Mainly globular proteins (Actin); twisted double chain ● ***3D network just inside the plasma membrane ● Supports cell’s shape ● Muscle Cells (Actin and Myosin) Intermediate Filament: ● ***Fibrous subunits ● Various fibrous proteins ● Supercoil into thicker cables ● ***Reinforce cell shape and anchor organelles ● Nucleus is held in this way ● Generally permanent (microfilaments can be disassembled and reassembled elsewhere) Microtubule: ● Tubulin subunits ● Globular proteins called tubulin proteins ● Elongate by the addition of tubulin proteins(2 subunits) ● Can be disassembled and reused elsewhere ● Microtubule organizing center near the nucleus ● ***Centrioles (cellular division)= where microtubules come from ● Support and shape for cells ● Train tracks for organelles ● Guide chromosomes during cellular division ● Main component of cilia and flagella Extracellular Matrix(ECM) ● Tissues and protection ● Main component= glycoproteins long polysaccharide and complex ● Strong and abundant=collagen fibers ● ECM attaches to cell ● Influence each other ● Integrin directly affects/influences cellular behavior Tight Junctions: ● Neighboring cells and digestive tract. ● Water tight seal ● Looks like the adjacent membranes are sewn together ● Forms a watertight seal between two membranes ● Prevent passage of material between the cells ● Seen in intestinal epithelium where they prevent the passage of gut contents between gut lining cells Anchoring Junctions(aka desmosomes): ● Plasma membrane pressed and knit ● Screws fasten cells together into sheets ● Composed of Intermediate filaments ● Common in skin and heart muscle ● Stretching or mechanical stress ● Connect the intermediate filaments of the cytoskeletons of adjacent cells(desmosomes) ● May also anchor a cell’s intermediate filaments to the ECM ● Provide mechanical strength to the tissue by connecting many cells firmly together ● Seen between keratinocytes in the skin epidermis, where the multiple layers of dead, but firmly connected keratinocytes form the barrier that separates you from the environment Gap Junctions: ● Communicating junctions ● Allow small molecule ions in the cell ● Form pores that provide direct connection between the cytoplasm of adjacent cells ● Allow flow of molecules and ions from one cell to the next ● Permit communication between adjacent cells that coordinate the tissue’s reaction to stimuli Plasmodesmata: ● Keeps plants upright ● Cellulose and other polysaccharides and proteins ● Primary cell wall is thin and flexible ● Some cells add secondary cell wall ● Lignin ● Pectin glues cells together(polysaccharide) ● Plasmodesmata prevents isolation ● Water, nutrients, and chemicals Plasma Membrane: ● Not the same as phospholipid bilayer ● When you add proteins, it will become a plasma membrane ● Regulates traffic in the cell ● Nonpolar O2 CO2 ● Ions and polar molecules ● Channel proteins ● Pumps ● Semipermeable ***Cell Theory: ● All things are composed of cells ● All cells come from other cells Atoms Unreactive atoms: He, Ne Reactive atoms: H, C, N **If outermost electron shell is filled, it will not form bonds. Covalent bonds: ● Strongest chemical bond, two atoms share one or more pairs of valence shell electrons ● Two or more atoms held together by covalent bonds form a molecule ● Atoms within a molecule are constantly trying to take the electrons they share ● ***An atom’s attraction for shared electrons is electronegativity ● The more electronegativity, the more strongly electrons are pulled Electronegativity and Electrons: ● **hen you give away an electron, you have aositive charge ● Molecules composed of atoms with very different electronegative values ● Oxygen and nitrogen are very electronegative ● In water, oxygen attracts the shared electrons much more than the lesser electronegative hydrogen ● Electrons spend more time near the oxygen atom than the hydrogen atoms ● Unequal sharing of electrons results polar covalent bond ● Hydrogen is partially positive and oxygen is partially negative due to the unequal sharing of electrons Electrons and Ionic Compounds: ● Atoms can strip an electron or electrons from other atoms ● Difference in electronegativity between sodium and chlorine is large ● Sodium donates electron to chlorine resulting in sodium and chloride formation ● ***Two ions with opposite charges attract and fo ionic bond ● Ionic compounds areneutral Hydrogen Bonds: ● Weak, but just as important as covalent bonds ● Most large molecules are held together by weak bonds. These bonds are generally eaily breakable and able to be formed ● Partial charges and water ● Hydrogen bonding in water ● Hydrogen bonds in protein shape and function Donations: ● An acid donates ● Carboxyl group acts as an acid which donates an ionized hydrogen ion ● Carboxylic acids, acetic acids ● Amino groups act as bases ● Aminesaccepts ● Phosphate groups, ATP ***Aldehyde, carbon is on the end….Ketone, carbon is in the middle Macromolecules: 1. Carbohydrates 2. Proteins 3. Nucleic Acids ***Lipids arNOT macromolecules ● Monomers and polymers ● Dehydration reaction lose a water molecule ● Hydrolysis add water Lipids: ● Hydrophobic because of fatty acids ● Nonpolar ● Glycerol alcohol found on top of lipid ● Polarhydroxyl groups ● Overall name for lipid with three tails= fat/triglyceride ○ Kinked fatty acid tail ○ Unsaturated ○ Kinks prevent tight molecular packing Trans Fat: ● All bonds are ‘cis’ in direction ● Can change the double bonds ● long term energy storage Mono vs Poly Unsaturated Fat: ● Single double bonds ● Multiple double bonds ● ***Top group is cholinetwo tails ● Choline, phosphate, and glycerol=very hydrophilic Cholesterol: ● Steroid four rings ● Animal cell membranes ● Cholesterol is the four rings plus the extra top pieces Dehydration Synthesis: ● Removal of OH from one amino acid and H from the other amino acid, releasing one H2O molecule ● Allows direct covalent linkage between two amino acids ● Water is taken out (dehydration) as a larger molecule is made (synthesis) ● ***Dehydration synthesis to make a polypeptide chain is translation ● The covalent bond between two amino acids(monomers) in a polypeptide (polymer)=peptide bond(amino bond) Protein Hydrolysis: ● Enzyme is required ● loss of primary structure Hydrophilic: Water loving Hydrophobic: Repels with water Enzymes speed up a chemical reaction. Carbohydrates: ● Glucose aldose (top)(C=O) ● Fructose ketose (middle)(C=O) ● complex sugarsdisaccharides ● Polysaccharides ● Six carbons, pentose, hexoses ● Linear to ring structure ● break glucose down ● carbon skeletons (points on ring structure) used to make amino acids, fatty acids ● disaccharides, polysaccharides ***Two glucose makes maltose ***Glucose and fructose make sucrose Starch: ● Polysaccharide ● Storage molecule ● Amylase breaks down starch ● Plant storage polysaccharide that can be eaten by humans and other animals Glycogen: ● How animals and humans store ● Granules in the liver and muscle cells ● Need to have access to glucose for a lot of functions ● Storage molecule ● Glucose monomers ● In liver and muscle cells because it is easily accessible ***Also know the functional groups and distinguish which are which. Should also be familiar with what each macromolecule looks like and be able to label it if just given the picture of one. Definitions: Amino Group: Carbon bonded to three hydrogens Aqueous Solutions: solution in which water is the solvent Buffers:Substances that minimize changes in pH Carbon Skeleton: The chain of carbon atoms in an organic molecule Carbonyl Group: Carbon atom is linked by a double bond to an oxygen atom Carboxyl Group: Carbon doublebonded to an oxygen atom Cellular Metabolism: Many of the chemical activities of cells occur in the cellular membrane Chemical Bonds: An attraction between two atoms resulting from a sharing of outershell electrons or the presence of opposite charges on the atoms Covalent Bonds: Strongest kind of chemical bondtwo atoms share one or more pairs of outershellelectrons Cytoskeleton: A network of protein fibers in the cytoplasm of a eukaryotic cell; includes microfilaments, intermediate filaments, and microtubules Dehydration Reaction: A reaction that removes a molecule of water Denaturation: Polypeptide chains unravel, losing their specific shape and lose their function Diffusion:The tendency for particles of any kind to spread out evenly in an available space Disaccharide: Cells construct a disaccharide from two monosaccharide monomers by a dehydration reaction ECM: Extracellular matrix. Helps hold cells together in tissues and protects and supports the plasma membrane Electronegativit An atom’s attraction for shared electrons Electron Shells:Electrons move around the nucleus only at certain levels Enzyme: Specialized macromolecules that speed up chemical reactions in cells Facilitated DiffusioPolar or charged substances can move across a membrane with the help of specific transport proteins Functional Groups: Affect a molecule’s function by participating in chemical reactions in characteristic ways Hydrocarbons: Compounds composed only of carbon and hydrogen Hydrogen Bond: Positively charged region in (water molecules) is always a hydrogen atom Hydrophilic:aterloving Hydrophobic: Waterfearing Hydrolysis:Break with water Hydroxyl Group: Hydrogen atom bonded to an oxygen atom which is bonded to the carbon skeleton IntegrinsSpan the membrane, attaching on the other side to proteins connected to microfilaments of the cytoskeleton Ionic Bond:Two ions with opposite charges attract each other and the attraction holds them together Ion:An atom or molecule with an electrical charge resulting from a gain or a loss of one or more electrons Isomer: Compounds with the same formula but different structural arrangements Kinetic Energy:The energy of motion Macromolecules: Carbohydrates, proteins, and nucleic acids Methyl Group: Carbon bonded to three hydrogens Monomer: The building blocks of polymers Monosaccharide: The carbohydrate monomers Molecule: Two or more atoms held together by covalent bonds form this Nonpolar Covalent Bond: Electrons are equally shared between the atoms Nucleoid: he DNA is coiled into a region Organelle: Perform specific functions in the cell Organic Compounds: Carbonbased molecules Osmoregulation: The control of water balance Osmosis: The diffusion of water across a selectively permeable membrane Passive Transport: A cell does not have to do work when molecules diffuse across its membrane Phosphate Group: Phosphorus atom bonded to four oxygen atoms Phospholipids: The major component of cell membranes Polar Covalent Bond: Unequal sharing of electrons Polar Molecule: Unequal distribution of charges Polymer: Cells make most of their macromolecules by joining smaller molecules into chains Receptor Mediated Endocytosis: Highly selective. Receptor proteins for specific molecules are embedded in regions of the membrane that are lined by a layer of coat proteins Saturated Fatty Acid: Fatty acids with no double bonds in their hydrocarbon chain have the max number of hydrogen atoms Solute: A substance that is dissolved in a solution Solution: A liquid that is a homogeneous mixture of two or more substances Solvent: The dissolving agent of a solution Steroids: A type of lipid whose carbon skeleton is in the form of four fused rings with various chemical groups attached Tonicity:The ability of a solution surrounding a cell to cause that cell to gain or lose water Trans Fat: An unsaturated fat, formed artificially during hydrogenation of vegetable oils Transmembrane Protein: Type of membrane protein spanning the entirety of the biological membrane to which it is permanently attached Unsaturated Fatty Acid: Kinked bend in third fatty acid. Has one fewer hydrogen atom on each carbon of the double bond Valence Electrons: E lectrons in the outer shell of an atom Valence Shells: Outermost shell of an atom
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