Exam 1 Notes - Chemical Bonds, Ionic and Covalent Bonds | BIOL 1201, Study notes of Biology

Download Exam 1 Notes - Chemical Bonds, Ionic and Covalent Bonds | BIOL 1201 and more Study notes Biology in PDF only on Docsity! January 20, 2011 Moodle Quiz 1 after today’s lecture – before class on Tuesday CHEMICAL BONDS Strong  Covalent bonds involve sharing of electrons  Hydrogen (H2)  Oxygen (O2) o Water (H2O) o Methane (CH4) Weak  Non-covalent bonds o Ionic interactions – attraction of opposite charges. One atom donates an electron to another o Hydrogen bond between partially charged atoms VALENCE VS. VALENCE ELECTRONS  Valence is the number of electrons needed to fill the outermost shell of an atom o Hydrogen valence = 1 o Oxygen valence = 2  Valence electrons are the electrons contained in the outermost electron shell of an atom MOLES AND MOLAR CONCENTRATION  1 Mole = the mass of a substance equal to its gram molecular weight  1 Molar solution = a solution containing 1 mole of a substance per 1 liter of solution Can you have a 1 Molar solution of insulin? No  5.727 kg/liter or 5.727 g/cm3 IONIC BONDS  Weak bond  Transfer of an electron from one atom to another o NaCl = Na+ and Cl- COVALENT BONDS  Strong bond  Sharing of electrons to complete valence shell o Water (H20): polar covalent with 104.5° angle, so the Hydrogens have a partial positive charge and the oxygen has a partial negative charge (partial charges represented by lower case delta) POLAR BONDS  Unequal sharing of electrons  Partial + and partial – regions  No net charge HYDROGEN BONDS  Weak (non-covalent) bonds  Between partial positive and partial negative charges o Water (H20) and Ammonia (NH3); weak bond between the hydrogen and nitrogen WATER  70 to 90% of weight of most life forms  Sets the lower temperature limit for life  Sets the upper temperature limit? (Probably not) o How quickly biological molecules break down in high temperatures  Important role in structures and properties of biological molecules  Water is a biological molecule THE UNUSUAL PROPERTIES OF WATER  Result from hydrogen bonding  Water behaves as a much larger molecule BONDS  Covalent: H-O 110 kcal per mole  Angle 104.5°  Weak (hydrogen bond): 4.5 kcal/mol o H bonding effectively makes water a larger molecule o In ice a water molecule interacts with exactly 4 other water molecules o In liquid water, on average 3.6 or fewer other molecules (can be made and broken very quickly) SMALL MOLECULES – A COMPARISON OF PROPERTIES  Water – H20 o BP: 100°C o FP: 0°C  Ammnonia – NH3 o BP: 35°C o FP:-37°C  Ethanol – o BP: 78.5°C o FP: -117.3° UNUSUAL PROPERTIES OF WATER  High heat capacity o Amount of heat to raise temperature of 1 g of water by 1°C o 1 cal per g of water  High heat of vaporization o Amount of heat to vaporize 1 g of water o 540 cal per g at 100°C  High heat of fusion o Amount of heat removed to freeze 1 g of water o 80 cal per g CARBOHYDRATES  General formula (CH2o)n o E.g., n = 6 o C6H12O6  Also are sugars, monosaccharides  Ring structures & linear structures  Disaccharide – loses 2 H and 1 O (H2O)  Starch in plants; Glycogen in animals – polymers of glucose  Energy roles o Metabolic fuel  Glucose  Sucrose o Storage form  Starch (plants)  Glycogen (animals)  Structural roles o Cellulose (in plants)  Monomer of glucose o Chitin (animals)  Polymer of glucose  Exoskeleton of insects LIPIDS  Water-insoluble organic biomolecules made up of “non-polar” groups o Due to their nonpolar groups  Structural components of cell membrane  Storage and transport form of fuel  Protective surface coating o E.g. leaves  Cell component in cell recognition  Hormone  Hydrophobic FAT TYPES  Saturated o Saturated with H, no double bonds between adjacent carbons o Bad because they raise LDL cholesterol  Unsaturated o Double bonds, lower melting point o The “good” fat o “better” than saturated fats MELTING POINTS DIFFER  Saturated fats are solids at higher temperatures than unsaturated fats  Acyl chains of unsaturated fats are kinky and therefore require a lower temperature to become solid POLYMERS  Triglycerides o Components: glycerol and three fatty acids  Phospholipids o Phospholipid bilayer COMPARISON OF LIPIDS AND CARBOHYDRATES  Twice as much energy from fat  Stored without water  1 g of glycogen is store with 2 to 5 g of water  (Disadvantage – not as rapidly mobilized as carbohydrates)  lipids metabolized in the mitochondria in the presence of O2 The hump of camel is filled with lipid. CAMEL  Up to 20% of body mass is fat when food is plentiful  Subcutaneous fat would cause thermoregulatory problems BEAR  Hibernation 100 days without eating o Due to accumulated fat HUMAN  Normal weight – 40 day reserve of energy  Moderately obese – up to a year NUCLEIC ACIDS  Nitrogenous heterocyclic bases  Pentose sugar (5C)  Phosphoric acid  Examples: o Coenzymes (NAD, NADP, FAD) o Genetic material (DNA and RNA) o ATP PROTEINS  Excellent example of a polymer  Made of amino acids o 20 naturally occurring amino acids are L-isomers o Proteins vary in the number and sequence of the different kinds of amino acids ENZYMES  Protein catalyst  Every chemical reaction in a living cell is catalyzed by a specific enzyme STORAGE PROTEIN  Seed  Eggs CONTRACTILE PROTEINS  In muscle  Actin  Myosin DEFENSIVE BLOOD PROTEINS  Antibodies TOXINS  For example from bacteria  Pertussis toxin  Botulinum toxin HORMONES AND RECEPTORS  Hormones – chemical messengers o E.g. insulin  Receptors – specific recognition sites for chemical messengers STRUCTURAL PROTEIN o Hair o Silk AMINO ACIDS  The monomers  20 kinds AMINO ACID STRUCTURE  Central Carbon  Amino group (NH2)  Carboxyl group (acid) (COOH)  Hydrogen  R group (20 different R groups) NOTE THERE ARE DIFFERENT TYPES OF R GROUPS  Polar (hydrophilic) o Can be electrically charged R groups o Interact with the partial + and – charges of water  Non-polar (hydrophobic) o No partial charges on the R group  Charged ( + or - ) THE CHARACTERISTICS OF THE INDIVIDUAL AMINO ACIDS DETERMINE THE STRUCTURE OF THE PROTEIN Saturated fats have higher melting points. COVALENT BOND BETWEEN AMINO ACIDS  Peptide bond  Dehydration synthesis THE PEPTIDE BOND  Does not involve the R groups  The amino and carboxyl groups (common to all amino acids) are involved PRIMARY STRUCTURE  Sequence of amino acids in a protein or peptide  Determines what the protein will look like and how it functions 80,000 Americans have sickle cell disease 2.5 million express sickle trait SECONDARY STRUCTURE  4 suspected cases alive in the UK  6 of the other 48 cases worldwide resided in the UK for some time  In US  3 cases  all epidemiologically linked to cattle product contaminated with BSE CHRONOLOGY IN THE UK  1970s – mid 1980s spread from sheep to cattle o sheep meat and bones aadded to cattle feed o 1982 Prusiner discovers prions o 1986 Mad cow disease indentified o in 10 years 165,000 cattle affected o November 1989 British government banned use of animal- derived feed supplements o March 1996 EU bans British beef BANNED FEED  Sold in Europe and Asia  Sold for “use” in poultry  vCJD in Great Britain and France o All but one of vCJD patients younger than 40 years old UNUSUAL DISEASES  Not caused by “germs”  Not a virus, bacteria, or fungus  Not caused by organism with genetic material!  However – this is still controversial PRIONS  Proteinaceous Infectious Particles  Discover in 1982 by Stanley Prusiner o Nobel Prize in 1987 February 1, 2011 BSE IN US  December 2003  Discovered in “downer” dairy cow in the state of Washington NORMAL CELLULAR FORM OF THE PRION PROTEIN  Alpha helix o Present in all mammals o May protect neurons from toxic copper ions DISEASE FORM  Beta-pleated sheet o Resistant to most denaturation techniques SAME AMINO ACID SEQUENCE!  Different secondary structures  Disease form converts the normal cellular form to the beta pleated sheet protein  Secondary structure o Important in determining the role/function of the protein Mad cow disease was spread by contaminated feed – true! Eating beef from “mad cows” may result in vCJD. The normal protein and the disease causing prion differ in the secondary structure. CELLS: STRUCTURE AND FUNCTION PROBLEMS  Increase size means relatively less surface area for a unit of volume  This causes a problem with movement of materials into and out of the cell  A second problem is controlling and coordinating metabolic processes within the cell OVERVIEW – CELL STRUCTURE  Keeping cell distinct from the environment  Organizing and coordinating metabolic processes THREE DOMAINS  Bacteria  Archaea  Eukarya WE’LL USE TWO CATEGORIES BASED ON STRUCTURAL FEATURES  Prokaryotes o Archaea o Eubacteria  Eukaryotes o Eukarya PROKARYOTES  “Before” the nucleus  No internal membrane-bound organelles EUKARYOTES  “True” nucleus  Have organelles bounded by membranes PROKARYOTES (BACTERIA AND BLUE-GREEN ALGAE) 1. Cell wall of carbohydrates and peptides 2. Ribosomes differ from Eukaryotes in size and antibiotic sensitivity 3. No nucleus or linear (histone-complex) chromosomes 4. No internal membranes EUKARYOTES (ANIMALS, PLANTS, FUNGI, YEASTS)  Larger cell size o Need increased internal membranes o Problem of intake of nutrients o Problem of coordinating and control of metabolism o More opportunities as a heterotroph Prokaryote Animal Plant Plasma Membrane + + + Cell Wall + - + Nucleus - + + DNA Circular Linear Linear Ribosomes Smaller Larger Larger ER - + + Gogli - + + Lysosomes - + + Vacuoles - Small or absent Large, one Mitochondria - + + Chloroplasts - - + 9+2 Flagella - + Not higher plants Plants and animals are Eukaryotes. PLASMA MEMBRANE  Present in Prokaryotes and Eukaryotes  Semi-fluid mosaic  Phospholipids  Proteins  Semi-permeable barrier between contents of cell and environment A phospholipid consists of a hydrophobic tail and hydrophilic head NUCLEUS  Present in eukaryotes  Enclosed by nuclear envelope – a double membrane with pores  Contains linear chromosomes  Contains nucleolus – region of nucleus where ribosomal subunits are assembled GENETIC MATERIAL IN EUKARYOTES  Liner strands of DNA complexed with proteins (histones)  Linear chromosomes GENETIC MATERICAL IN PROKARYOTES  Circular strands of DNA  “Naked” – not complexed with histone proteins NUCLEOLUS  Region of the nucleus where ribosomal subunits are assembled RIBOSOMES  Present in eukaryotes and prokaryotes  Differ in size (prokaryotes have smaller ribosomes) and antibiotic susceptibility  Consist of two subunits  Subunits made of rRNA and protein  Site of protein synthesis  Occur free in cytoplasm of in association with the rough ER ENDOMEMBRANE SYSTEM  Endoplasmic Reticulum (ER) o Eukaryotes only o Internal membrane system  Initially cytoplasm (ground substance) was thought to be without structure o Improved techniques showed this to be wrong FLAGELLA AND CILIA  Organelles involved in movement  Bacteria have “flagella” but are constructed differently than in eukaryotes  Same structural design in flagella and cilia  9+2 structure – only in eukaryotes (absent in higher plants) o Different than the flagella of bacteria  Flagella larger and fewer in number than cilia Other elements involved in movement  Sliding filaments o Proteins involved in movement  E.g. actin and myosin  Molecular motors o Proteins o Use ATP  Centriole o In animals (but not higher plants) o Similar to the base of a flagellum of cilium o Involved in mitosis and meiosis THE PROBLEM  The interior of a cell is different than it’s environment  How to defend the internal environment but still communicate with the external environment o Transport materials across the barrier Biological membranes consist of phospholipids and proteins. INTEGRAL MEMBRANE PROTEINS  Amiphipathic o Hydrophobic (nonpolar) regions o Hydrophilic (polar) regions AN OPTIMAL INTERMEDIATE “FLUIDITY”  Not too solid  Not too fluid  Preserves membrane function  At the cell/body temperature o Similar fluidity in different species o Species with a body temperature of 10 ° C will have fluidity similar to a species with a body temperature of 20° C  (Do not take “fluidity” too literally) The fluidity of membranes of a 10°C species and a 20°C are compared to 15°C.The membranes adapted to 10° will be more fluid. HENRIQUE AND HANSEN 1901  Raised pigs wearing underwear in a hot room  Change the properties of subcutaneous fats o Had a higher melting point  Membrane fluidity can acclimate  Membrane fluidity adjusted by changing the ratio of unsaturated to saturated fatty acids To make a membrane more fluid you would increase unsaturated fats because they have a lower melting point and are more disorganized. INCREASE UNSATURATED FATS o Increases the fluidity of the membrane What kind of molecules would pass through a membrane, i.e. phospholipid bilayer? Nonpolar and small o Examples: o Gases o Steroid hormones o Water DIRECTION OF MOVEMENT o Expect – down from high concentration to low o What about against the gradient? o E.g. Sodium 5 – 15 MM in the cell; 145 mM outside the cell TRANSPORT PROCESSES o Active o Against the concentration gradient o Requires supplied energy (ATP) o Carrier molecule o Work must be done o Passive o Down concentration gradient o Does not require supplied energy o Diffusion (simple or facilitated) SIMPLE DIFFUSION o Down concentration gradient o Depends on molecular movement o Does not require supplied energy o Does not use a carrier molecule FACILITATED DIFFUSION o Down concentration gradient o Depends on molecular movement o Does not require supplied energy o Employs a carrier molecule When solute concentrations are equal on both sides of the diffusion barrier the molecules no longer move -- False o Molecules keep moving o There is no net change in solute concentration SEMI-PERMEABLE BARRIER o Only some types of molecules pass through February 7, 2011 Review session tonight 5:30 A101 Life Sciences building DIFFUSION  Movement of molecules down concentration gradient  From regions of high concentration to low concentration regions [Active transport requires energy and employs a carrier molecule Passive transport is movement down a concentration gradient and may employ a carrier molecule.] MOVEMENT OF WATER ACROSS MEMBRANES  From high to low water potential Create free energy gradients: these can be used to do work  How does the membrane allow the creation of a free energy gradient?  What is the relative free energy of molecules at different concentrations? The molecules on the left have greater free energy because they are in higher concentration. MEMBRANE PERMEABILITY  Size and shape of molecules  Solubility in lipids  Net electric charge  Other chemical properties  Water always freely permeable  Aquaporins – channel protein which facilitate water diffusion through the membrane DIFFUSION  Physical property of matter  Individual molecules move randomly, but the net effect is non-random  What forces causes the net movement? o Kinetic energy associated with the molecules OSMOSIS  The net movement of water across (through) a semi-permeable membrane.  Diffusion of water  From higher (fewer solutes) water potential to lower water potential o Fresh water has higher water potential Which way will water flow? To the right (the higher sugar concentration) PROBLEMS CONFRONTING ORGANISMS  What if the concentration of solutes differs between the intracellular compartment and the environment? HYPERTONIC  Lower water potential  More solutes dissolved