Week 1 Lecture Notes
Week 1 Lecture Notes Life Sciences 2
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This 7 page Class Notes was uploaded by Jenna Kovsky on Thursday October 15, 2015. The Class Notes belongs to Life Sciences 2 at University of California - Los Angeles taught by Dr. Cooper/Dr. Esdin in Fall 2015. Since its upload, it has received 36 views. For similar materials see Cells, Tissues, and Organs in Biology at University of California - Los Angeles.
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Date Created: 10/15/15
92815 Lecture 1 Bioloqical Molecules Covalent Bonds strongest type of bond sharing electrons between atoms notation HH or HH electrons may not be shared equally between the two atoms Nonpolar covalent bond O 0000 when electrons are equally shared eg HH CC CH Polar covalent bond when electrons are NOT equally shared eg H20 has to do with the difference in electronegativities of the atoms sharing the electrons WeakerNoncovalent Bonds lonic Bonds 0 O O 0 Water 0 eg NaCl sodium chloride One atom eg sodium donates an electron to another atom eg chlorine the one donating becomes positively charged and the one receiving becomes negatively charged lons important in the human body for certain functions eg communication of the nervous system Hydrogen Bonds very weak very important in biological system eg protein structure holding together the double helix of DNA since the bond between oxygen and hydrogen in water is polar it causes a slight difference in charges between the oxygen and the hydrogen the oxygen in H20 is slightly negative while the hydrogens are each slightly positive the hydrogen atom in water can form a hydrogen bond with the oxygen of an adjacent water molecule because of this any polar molecule is soluble in water cohesionsticking together of water molecules influenced by hydrogen bonds Hydrophobic Interactions eg oil and water oils in biological context are fatty acids oil when put in water sits on top does not dissolve because it is nonpolar the nonpolar substance when put in water is forced to the surface so it s not in the way of the water molecules forming hydrogen bonds with each other excludes fatty acid from aqueous solution Van Der Waal s Forces electrons are continuously oscillating between different parts of the molecule this movement creates dipole charges lead to transienttemporary very weak interactions between opposite dipoles only occur when atoms are in very close proximity help nonpolar molecules clump together when placed in water allow geckos to walk up vertical surfaces polar molecule polar covalent bonds 0 93015 pH hydrogen ion concentration in a solution pure distilled water has pH 70 10fold change in ion concentration is one pH unit unsaturated have carboncarbon double bonds saturated do not giving free rotation around the axis insoluble in water but dissolve in other solvents such as chloroform contain carbon hydrogen and oxygens fats triglycerides I glycerol 3 carbons with 3 carboxyl groups and fatty acids I stored in specialized adipose cells adipocytes I storage form of fat in the body I can be broken down to release ATP energy I provide thermal insulation phospholipids I glycerol backbone 2 fatty acids and a polar headgroup phosphate group polar hydrophilic head can interact with water nonpolar hydrophobic tails cannot amphipathic Describes a molecule with a polar end and a nonpolar end important in cell structure cell membraneplasma membrane is a phospholipid bilayer two layers of phospholipids interior of membrane is hydrophobic nonpolar fatty acid chains exterior on either side is hydrophilic polar phosphate head I individual phospholipids can rotate about an axis diffuse in the plane of the bilayer and flex fatty acid tails I diffusion is random molecular motion chaperone proteins Flippase can help phospholipids quotflipflop from one side of the membrane to the other very rare cholesterol I has a steroid ring structure I antipathic I important in cell membrane I can intercalate into the phospholipid bilayer because it is so thin I when it interacts with fatty acid tails of phospholipids it can slow down movement of phospholipids due to Van Der Waal s interactions I stabilizes the plasma membrane Lecture 2 Biological Molecules Continued 0 Cholesterol 0 O in all plasma membranes of animals not plants required by the human body but too much can build up in arteries leading to atherosclerosis which can lead to heart attacks and strokes made in liver required for stabilizing plasma membrane and for digestion makes bile salts as well as important for the endocrine system LDL Lowdensity lipoproteins carry cholesterol from liver to the tissues for use by cells but tend to leave some behind in arteries causing issues bad cholesterol 000 O HDL highdensity lipoproteins remove cholesterol from cells transport to the liver for excretion as bile good cholesterol Lower ration plasma LDLHDL is associated with a decreased risk of atherosclerotic heart disease Blood cholesterol levels of 200 mgdL or less is desirable Less than 130mgdL of LDL is desirable 130159 mgdL of LDL is borderline high risk 160mgdL or over of LDL is high risk 0 Carbohydrates O O O 0 main function is to provide energy important in cell recognition ratio of Hydrogen to Oxygen is about 21 classified according to size I monosaccharides o simplest sugars 0 glucose is the major one found in blood 0 most have 5 pentose or 6 hexose carbon atoms 0 linked together to form larger sugars I disaccharides 0 made of 2 monosaccharides eg glucosefructosesucrose a dehydration reaction results in formation of a glycosidic bond galactoseglucoselactose glucoseglucosemaltose Lactose lntolerant lack the enzyme lactase that breaks the glycosidic bond of lactose I ngosacchandes 0 about 320 residues sugars 0 important on surface of cells I polysaccharides o greater than 20 residues sugars o starch polymer ofglucose present in plants 0 glycogen storage form of carbohydrate in animals 0 branched polymer of glucose 0 localized in the liver and skeletal muscle 0 glycosidic bonds can be broken to release glucose when energy is needed 0 cellulose long chains large part of plant cell wall chains lie parallel and form hydrogen bonds between them 0 Proteins O 0000 Know names of 20 amino acids and whether they are polar or nonpolar humans have about 30000 different proteins made up of amino acids there are 20 amino acids amino acid I amino group with a carboxyl group and a side chain which varies between each of the 20 amino acids I categories O O O 0 Polar side chains serine threonine glutamine asparagine etc o Nonpolar alkine valine leucine isoleucine methionine phenylalanine tryptophan glycine cysteine proline peptide bond I does not have free rotation I double bond characteristics give peptide bonds rigidity Structural organization primary structure 0 linear sequence of the amino acids 0 usually an amino group at one end of the sequence and a carboxylic acid group on the other 0 also depends on the number of amino acids that make up the chain I secondary structure 0 localized o polar acids tend to face outward to interact with water while nonpolar face inward 0 Alpha helix 0 O 0 hydrogen bonds link alpha helix together like a corkscrew hydrogen bonds form H linked to Nitrogen and the Oxygen in another peptide bond 0 Beta pleated sheet 0 0 like a folded fan or accordion type thing held together by hydrogen bonds formed between peptide bonds tertiary structure 0 overall 3d shape of a protein 0 the way it folds in 3 dimensions 0 factors that influence 0 O O 0 hydrogen bonds ionic bonds disulfide bonds which are covalent the amino acid cysteine has a sulfide group in its sidechain two cysteines can form a disulfide bond van der waal s forces I quaternary structure OOOOOOO Protein function biological catalysts enzymes 0 not ALL enzymes are proteins but most transporters not all proteins have it caused by association of more than one polypeptide chain the arrangement of individual chains that are called subunits Hemoglobin a protein localizes in Red Blood Cells RBCErythrocytes carries oxygen 02 made of 4 chains 2 alpha subunits and 2 beta subunits each subunit has iron Fe which can bind oxygen can carry 4 oxygen molecules at a time tetramer because it has 4 subunits o eg hemoglobin transports oxygen I facilitating movement 0 myosin attaches to actin both are proteins and together they allow sliding motion to occur in muscle fibers 0 myosin head group noncovalently bonds to the globular actin I structure and support 0 eg collagen is present in skin ligaments and bones I defense 0 Denaturation I when proteins get unfolded I can be caused by changes in pH temperature salinity etc of environment I sometimes proteins can be renatured o Sickle Cell Disease Sickle Cell Anemia o hereditary Polar glutamic acid gets changed to nonpolar valine change in primary structure causes change in secondary which causes change in tertiary worse under low oxygen levels chains of hemoglobin occur distorting the shape of the RBC becomes shaped like a sickle this awkward shape makes it hard for the RBC to flow through blood vessels more fragile than normal RBCs OOOOOO 10215 Lecture 3 Biological Molecules cont amp Cells BIOLOGICAL MOLECULES CONT 0 Nucleic acid long polymers made of nucleotides 0 5 carbon sugar with Hydrogen group in DNA and Hydroxyl group OH in RNA I Deoxyribose in DNA I Ribose in RNA I The carbon atoms making up each sugar are numbered followed by a prime mark 1 2 3 4 and 5 Phosphate group Nitrogencontaining base Types I Punnes o Adenine o Guanine I Pyrimidines o Cytosine o Thymine DNA only 0 Uracil RNA only 0 Condensation reaction between nucleic acids eliminates water and forms a phosphoester bond between the phosphate group of one nucleic acid and the sugar of another 0 DNA I hereditary material I AT CG complementary bases I 5 gt3 I Hydrogen bonds between complementary bases I Van der Waal s forces between stacked bases I Replication o strands separate the hydrogen bonds connecting them are easily broken 0 Semiconservative replication I usually single stranded but can be double eg tRNA I mRNA messenger RNA I rRNA ribosomal RNA I tRNA transfer RNA 0 triplet genetic code3 bases code for each amino acid 0 Steps of protein synthesis I DNA transcribed into mRNA transcription I RNA translated into proteins translation 0 Small and large ribosomal subunits separately bind to either side of the RNA strand tRNA has 3 bases anticodon and amino acids covalently attached tRNA matches its anticodon to the codon on the mRNA strand at the ribosome which hydrogen bond you can only hydrogen bond the bases with their complementary bases the amino acids attached to each tRNA join up making peptide bonds between them 0 Ribozyme catalytic RNA CELLS o How and Where did the small molecules of life originate 0 1950s Miller and Urey experiment I Hypothesis organic chemical compounds can be generated under conditions similar to those that existed in the atmosphere of primitive earth I electrical sparks simulated lightning which they believed provided energy for the synthesis of organic molecules that are the building blocks of life successful I They used gases that they believed were in the atmosphere at the time actually we know now that there is more HZS than they believed I suggests that life could have originated on earth itself 0 The RNA World I researchers believe that RNA existed before DNA and proteinbased life I Then RNA was first made it could have acted as a catalyst for its own synthesis and then led ultimately to the synthesis of proteins 0 Cell Structure 1 Characteristics of Prokaryotes and Eukaryotes molecule cluster of atoms held together by chemical bonds organelle structure within a cell that performs a specific function cell simplest entity that has all the properties of life a membranebounded unit with DNA and cytoplasm 0 tissue a group of similar cells that carry out a particular function in an organism I epithelial tissue forms boundaries packed tightly together in sheets held together by proteins that form tight junctions provide permeability layer I connective tissue cells interspersed in a matrix range from where matrix is hard and calcified as in bone to a plasma matrix as in blood also adipocytes where triglycerides are localized O O nervous tissue neurons conduct and generate electrical signals action potentials I muscle tissue skeletal muscle bicep etc cardiac muscle heart smooth muscle digestive tract blood vessels organ structures composed of more than one tissue type eg skin epithelial cells over connective tissue organ system related organs performing a common function organism an individual independent living entity 0 Characteristics of Living systems 0 O 0 Cellular organization all organisms consist of one or more cells sensitivity organisms respond to various stimuli in different ways growth interconvert chemical molecules metabolism and energy released is used to grow I anabolism making a complex molecule from a simpler one eg forming glycogen from glucose to store energy I catabolism breaking a complex molecule down into a simpler one eg breaking down glycogen to get glucose reproduction reproduce passing on traits to new generations homeostasis maintain relatively constant internal conditions eg pH temperature etc different from their environment I homeo quotsamequot stasis stay stay the same I interstitial fluid fluid between cells I acidosis blood becoming more acidic bad thing I maintaining relatively constant environment 0 Viruses 0 00000 a virus is a piece of bad news wrapped in a protein made up of a core of nucleic acid surrounded by a protein sheath lack a membrane nucleus and organelles cannot reproduce on their own do not carry out metabolism not considered to be alive 0 The Cell Theory 0 O 0 All organisms are composed of cells the cell is the basic building block of lifegtchemical reactions of life take place within cells all cells arise by division of a preexisting cell 0 Size of Cells 0 O 0 most cannot be seen by the naked eye need microscope as an object gets larger its volume increases more rapidly than its surface area cells must maintain a large surface areatovolume ratio to function has to do with the efficient transfer of materials in and out of the cell therefore it is advantageous for cells to be small