Week 2 Notes
Week 2 Notes BISC 207025
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This 9 page Class Notes was uploaded by Lauren Buch on Sunday September 20, 2015. The Class Notes belongs to BISC 207025 at University of Delaware taught by Dr. Oyenike Olabisi in Spring 2015. Since its upload, it has received 33 views. For similar materials see Introductory Biology I in Nursing and Health Sciences at University of Delaware.
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Date Created: 09/20/15
Integrated Biology 207 Dr Olabisi Week 2 97911 23 Water The Medium of Life A All life depends on water a Single most abundant molecule in all cells b Good solvent capable of dissolving many substances c Leonardo da Vinci water is the driving force of all nature B Water is a polar molecule a Water molecules have polar covalent bonds uneven distribution of electrons b Polar having regions of positive and negative charge i Water soluble ii Can act in H bonding iii Unequal sharing of electrons c Molecules or portions of molecules fall into two classes i Hydrophilic water loving 1 Water itself 2 Polar 3 Dissolve readily in water ii Hydrophobic water fearing 1 Nonpolar 2 Arrange themselves to minimize their contact With water oil 3 Hydrophobic effect polar molecules exclude nonpolar molecules a Drives processes such as the formation of cellular membranes and the folding of proteins C pH a Measure of the concentration of protons in solution i Protons H and hydroxide ions OH ii pH log H b Ranges from 0 to 14 i 07 acidic ii 7 neutral iii 714 basic c Water is neutral pH of 7 i The pH of most cells are neutral except for certain cellular compartments blood is slightly basic at 74 ii Freshwater tends to be a bit acidic because of carbonic acid dissolved carbon dioxide D Hydrogen bonds a In uence the structure of liquid water and ice i When water freezes most water molecules become hydrogen bonded to four other water molecules to form a lattice ii As ice melts some hydrogen bonds are destabilized and the molecules can pack more closely together liquid water is denser than ice b Make water molecules cohesive i Tend to stick to one another ii Causes high surface tension iii Cohesion and surface tension contribute to the movement of water in plants able to be pulled upward c In uence how water responds to heating i When water is heated the increased motion of molecules first breaks the hydrogen bonds then leads to a temperature increase takes longer ii Water resists temperature change more than other substances maintains stability for biological functions oceans regulate the Earth s temperature 24 Carbon Life s Chemical Backbone Hydrogen and helium are the most abundant elements in the universe Earth solid earth is dominated by silicon oxygen aluminum iron and calcium not typical of the universe C Carbon oxygen hydrogen and nitrogen make up 94 of dry mass of human cells after water has been removed D Most abundant element is carbon all life is based on it E Carbon has the ability to combine with many other elements to form a wide variety of molecules each specialized for the functions it carries out in the cell F Carbon atoms form four covalent bonds a Behaves as it if had four unpaired electrons i Occurs because one of the electrons in the outermost sphere moves into the empty dumbbell shaped orbital single large spherical orbital and three dumbbellshaped orbitals change shape and become four equivalent hybrid orbitals each with one electron ii Allow the bonds to orient and rotate freely contributes to structural diversity of organic molecules G Carbonbased molecules are structurally and functionally diverse a Link with each other by covalent bonds to form long chains that can be branched two carbons at the end of the chain or within the chain can link to form a ring structure b Two adjacent carbon atoms can share two pairs of electrons two of the covalent bonds are shared between adjacent carbon atoms i Double bond is shorter and not free to rotate all carbons connected this way are in the same geometrical plane c Special arrangement of atoms in a molecule is very important formulas can be the same but structure dictates the substance i Isomers molecules that have the same chemical formula but different structures PU 25 Organic Molecules A Organic molecule carboncontaining molecule a Perform essential tasks of the cell establishment of a boundary storage and transmission of genetic information capture storage and usage of energy b Proteins nucleic acids carbohydrates lipids 0 Polymers complex molecules made up of repeated simpler units connected by covalent bonds d Polymers are like words reordering the molecules in the chain can change the entire structurefunction B Proteins a Provide structural support and act as catalysts that facilitate chemical reactions enzymes b Polymers of amino acids i Each amino acid contains a 1 central carbon atom alpha carbon covalently linked to 2 four groups a carboxyl group b amino group c a hydrogen atom d and an R group or side chain i changes chemical properties some polar some nonpolar ii carbon and hydrogen groups are typically nonpolar ii Every protein contains the carbon carboxyl COO amino H2N and hydrogen iii Identity of each amino acid is determined by the structure and composition of the side chain iv The carbon atom in the carboxyl group of one amino acid is joined to the nitrogen atom in the amino group of the next by a covalent bond peptide bond v Peptide bond formation involves the loss of hydrogen and oxygen which combine to form a water molecule dehydration synthesis vi Polypeptide chain protein chain of amino acids 0 Cellular proteins are composed of 20 amino acids i Can be as short as 8 long as hundreds ii The amino group in only the first amino acid is intact and the carboxyl group in only the last is intact Nterminus or Cterminus iii Counting the amino acids in a polypeptide count the r group number of peptide bonds CN central carbons hydrogen and side chain attached d Body contains thousands of proteins 6 Levels of structure i Primary structure amino acid sequence determined by gene sequence C Nucleic acids a Information storage b Polymers of nucleotides i Nucleotides are composed of 1 a 5carbon sugar pentose sugar a look for the pentagon shape 2 a nitrogencontaining compound nitrogenous base AT CG 3 phosphate group ii Sugar in RNA is ribose and for DNA is deoxyribose 1 Ribose has an OH group on the second carbon iii Bases are built from nitrogencontaining rings and are of two types 1 Pyrimidine bases single ring thymine T cytosine C Uracil U 2 Purine bases doublering structure adenine A guanine G 3 DNA contains ATGC and RNA contains AUGC iv Phosphodiester bond links nucleic acids 1 forms when a phosphate group in one nucleotide is covalently joined to the sugar unit in another nucleotide loss of a water molecule c Deoxyribonucleic acid DNA genetic material in all organisms i Transmitted from parents to offspring ii Contains the information needed to specify the amino acid sequence of all the proteins synthesized in an organism iii Double helix two strands of nucleotides twisted around each other 1 Bases form specific complementary pairs AT and CG iv Sequence of nucleotides is vital to function d Ribonucleic acid RNA protein synthesis and gene expression D Complex carbohydrates a Monosaccharides one sugar b Disaccharides two sugars i Maltose sucrose lactose ii Linked by glycocidic bond dehydration synthesis c Polysaccharides Many sugars linked together i Energy storage Starch plants and glycogen animals 1 Starch some branches 2 Glycogen highly branched highly soluble short term storage ii Structure Cellulose and chitin 1 Cellulose linear unbranched chain strong fiber indigestible by most animals termites and ruminant animals have micro organisms in their digestive tract to digest the fiber d Complex carbohydrates long branched chains of monosaccharides e Distinctive molecules composed of CHO in 121 ratio f Provide a source of energy and make up the cell wall in bacteria plants and algae i Principal source of energy for metabolism g Polymers of simple sugars E Lipids i Monosaccharides simplest carbohydrates sugars 1 Dehydration synthesis one sugar becoming many sugars a Forming a bond while losing water glycocidic bond b Glycocidic bond forms polysaccharides polymers ii Linear or cyclic molecules containing five or six carbon atoms iii All 6carbon sugars have the same chemical formula C6 H12 06 and differ only in configuration 1 Glucose product of photosynthesis a Linear or ring form aldose b Energy source by breaking chemical bonds excess goes to energy storage converted into glycogen short term or fat longterm c Most carbs ultimately converted into glucose d Blood sugar how much glucose you have suspended in your blood 2 Galactose found in dairy products 3 Fructose commercial sweetener iv Monosaccharide simple sugar one sugar 1 Unbranched carbon chains with either an aldehyde HC O or a ketone C 0 group a Aldoses or ketoses aldose shaped like a y a top b Glucose and galactose aldose c Fructose ketose 2 Other carbons each carry one hydroxyl group and one H atom 3 Linear structure is written with the aldehyde or ketone group at the top and the carbons numbered from top to bottom 4 Virtually all monosaccharides in cells are in ring form with the group forming a covalent bond with the oxygen in the hydroxyl group carried by another carbon in the same molecule v Disaccharide two simple sugars linked together by a covalent bond sucrose glucose fructose vi Polymers are polysaccharides 1 Longterm energy storage starch and glycogen or structural support cellulose 2 Complex carbohydrates long branches of monosaccharides 3 Glycosidic bonds covalent bonds that attach monosaccharides a Large and diverse group of naturally occurring compounds i Fats 1 Longterm energy storage and insulation 2 head and three lines triglycerides ii Sterols 1 Regulate growth and development 2 Flat hexagonal structure iii Phospholipids 1 Form the membranes that enclose cells 2 Hydrophilic head and hydrophobic tail Make up cell membranes store energy signaling molecules Hydrophobic molecules Nonpolar not soluble in water but in other substances Share a property not a structure i Makes them a chemically diverse group of molecules f Fatty acids bonded to other organic molecules make up cell boundaries i Fatty acid long chain of carbons attached to a carboxyl group COOH at one end ii Differ in the length of their hydrocarbon chain iii Most fatty acids in cells contain an even number of carbons iv Some fatty acids have one or more carboncarbon double bonds Which can differ in number and location v Saturated fatty acids that do not contain double bonds maximum number of hydrogen atoms is attached to each carbon atom so all carbons are saturated With hydrogen atoms vi Unsaturated double carboncarbon bonds appear to be kinked While saturated appear straight g Triacylglycerol lipid used for energy storage animal fat and vegetable oil i Three fatty acids joined to glycerol three carbon molecule With OH groups attached to each carbon ii Can contain different types of fatty acids attached to the glycerol backbone iii All are extremely hydrophobic and form oil droplets inside the cell 1 Nonpolar all electrons are distributed evenly and the molecules remain uncharged 2 Movement of electrons can cause regions of slight positive and negative charge 3 Van der Waals forces temporarily polarized molecules bind to each other weaker than hydrogen bonds but many of them acting together help to stabilize molecules a Cause the melting points of fatty acids to vary higher number of bonds higher melting point iv Efficient form of energy storage because by excluding water molecules a large number can fit into a small volume v Animal fat butter are composed of triacylglycerol With saturated fatty acids solid at room temperature 9906 vi Plant fat and fish oil are composed of unsaturated fatty acids liquid at room temperature h Steroids sterols i Cholesterol component of animal cell membranes ii Steroid hormones estrogen testosterone iii Core composed of 20 carbon atoms bonded to form four fused rings iv Hydrophobic V Fused ringshaped molecules hydroxyl group on the end i Phospholipids i Major component of the cell membrane ii Amphipathic two behaviors nonpolar and polar iii Made up of glycerol attached to two fatty acids and a third molecule that contains a phosphate group phosphate head 1 Head is hydrophilic polar 2 Tail is hydrophobic fatty acid 3 Glycerol backbone iv Form a variety of structures all of which limit the exposure of the tails to water 1 Bilayer twolayered structure with the hydrophilic heads pointing outward toward the aqueous environment and the tails oriented inward 41 Molecular Structure of Proteins A Amino acids differ in their side chains a Proteins consist of central carbon atom alpha carbon connected by four covalent bonds to four groups i Amino group NH2 ii Carboxyl group COOH iii Hydrogen atom iv R group side chain b Tetrahedron shape c Hydrophobic amino acids i Alanine valine leucine isoleucine methionine phenylalanine trypotophan tyrosine ii Nonpolar iii Tend to be buried in the interior of folded proteins d Hydrophilic amino acids i Lysine arginine histidine aspartic acid glutamic acid glutamine asparagine serine threonine ii Polar iii Basic side chains are positively charged at intracellular pH and acidic negatively charged e Special amino acids i Glycine 1 R group is hydrogen 2 symmetrical ii Proline 1 R group is linked back to amino group kink in polypeptide chain iii Cysteine 1 When two cysteine chains in the same or different polypeptides they can react to form an 88 disulfide bond which covalently joins the side chains B Peptide bonds connect successive amino acids in proteins a 9906 g Carboxyl group of one amino acid reacts with the amino group of the next amino acid in line molecule of water is released R groups of each amino acid end up facing in different directions Carbonyl group CO group in the peptide bond Amide group NH group Arrangement results in the delocalization of electrons i Peptide bond is shorter than a single bond not free to rotate like a single bond Amino end and carboxyl end i One end has a free amino group and the other has a free carboxyl group Protein polypeptide especially once it has folded into a stable three dimensional conformation h Amino acid residues amino acids that are incorporated into a protein C The sequence of amino acids dictates protein folding which determines function a b C Primary structure sequence of amino acids Secondary structure interactions between stretches of amino acids i Result from hydrogen bonding in the polypeptide backbone ii Xray crystallography to discover this iii Alpha helix 1 Tightly twisted righthand coil stabilized by hydrogen bonds that form between each amino acid s carbonyl group and the amide group four residues ahead in the sequence iV Beta sheet 1 Folds back and forth on itself pleated stabilized by hydrogen bonds between the carbonyl groups in one chain and amide groups in the other chain across the way 2 Typically denoted by broad arrows Tertiary structure longer range interactions between secondary structures support the three dimensional shape i Results from interactions between side chains ii Determined by primary structure iii Determines function Quaternary structure results from the interactions of polypeptide subunits only some proteins i Many proteins function Without this ii Subunits can be similar or different slight change in structure 1 Hemoglobin has subunits that make it easier to pick up oxygen Function depends on the three dimensional shape positive or negative pockets rigid rods for structure hydrophobic side chains in membrane Amino acids are listed in order for left to right amino end to carboxyl end Structure determines function i Denature unfolding of proteins by chemical treatment or high temperature ii When the chemical is removed or the temperature is reduced the protein refolds and continues to function Folding process take place Within milliseconds for 75 of proteins as the molecule is synthesized Hydrophobic effect the longer the polypeptides remain denatured the longer their hydrophobic groups are exposed to other macromolecules in the cytoplasm can prevent proper folding When the groups bond to each other i Chaperones proteins in cells that help protect slowfolding or denatured proteins until they can attain tertiary structure ii Bind With hydrophobic groups and nonpolar side chains to shield them from inappropriate aggregation
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