BIOL 302-Exam 1 Notes
BIOL 302-Exam 1 Notes BIOL 302
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Date Created: 02/01/16
Important Discoveries 1 Robert Hooke 1665 primitive microscope Corkfound it to be composed of quotcellsquot 2 VanLeeWeen Hook 1674 used magnifying glass Look at pond water saw 1st micro organisms Protozoa 3 Schleiden 1838 botanist examine tissue 4 Schwaan 1839 zoologist cells are building blocks of tissues LED TO 1839 cell theory proposed 5 Louis Pasteur 1860 proved cell theory showed cells only come from preexisting cells Cell Theory 0 All living things are made of cells 0 All cells come from other cells 0 Cells are the fundamental unit of life Unity and Diversity of Cells 0 Cells vary enormously in size appearance and function 0 All cells share the same basic chemistry 0 Composed of same set of molecules 0 Glycolysis set of chemical reactions cells use for energy 0 Genetic Codehow cells use info stored in DNA to make RNA and protein 2 Major Types of Cells 0 Prokaryoticsmall simpler primitive cells no nucleus no membrane bound organelles most are single celled 0 Ex bacteria EColi o Eukaryoticlarger more complex have nucleus cytoplasm various organelles amp cytoskeleton often found in multicellular assembles animals plants 0 Yeast single celled ex 8 Cereusae Microscopy Light Mircoscopy 17th cent uses beams of light resolution of light microscope is limited by the wavelength nature of light 0 Electron Microscopy 193039s uses beams of electrons greater magnification and resolution 0 TEM Transmission 0 SEM Scanning quot a 39 39 i Vii v quot351 55 quot 5 it if i w stead e E s I lt I 3 T Iiir h w NE W g 5 W x 39 a 7 gt a a h 1 lg i yf it tiai Mx a a i i an W a Emir we aft a a 2 1 if if Er3 mi KN 1 22 if 3 i iri f1 txi wttisifi km Mi was M summit page we 4 r gt a x c an 39 a fritw it it acmtget32q U a x mm um m w i A 395 V I if a A 1 amnyfxa quot iii ff t ia g f it i L u ikf fagl 393 EWUHXM 9 jhe wmmm wwwrww 39 ab 5 m M a v r y quot If I g I P g l i m 3w ain39k f rms 3 is x a a 1 x it x 4 t A a i wwmmm x w fgigi kki ibr1 EH aw w v WWW WW 2 5 I Wm E 3Lim3f m 9 f r f i a mwww wwmwm w at 3 5 5Q n at u c 1 42439s f H ii v K 2 V s w J Y g 2 my 4 l f 39 i i g gt H PVL W i 1 H A 2 quot n w V r q r t V t 7 39 atquot 2 539 739 t er 3 it gt 1 39 quot W a v in E f 3 tarP L 1 3v r i 39 If requot EM Fun 0 4 I i 13 1amp7 u Eukaryotic Cells and Basic Components Plasma membraneencloses the cell and separates inside from outside Cytoplasm surrounds the nucleus contents of cell contained in plasma membrane organelles amp cytoskeleton Cytoskeletoncontents of main compartments excluding organelles nucleus and cytoskeleton Nucleuslarge structure that contains DNA 0 Organized into chromosomesenclosed by double membrane nuclear envelope 0 Nuclear Pores Form openings in envelope Organellesdiscrete structures or subcompartments of eukaryotic specialized to carry out different functions enclosed by membranes Mitochondria present in almost all cells only eukaryotic several micrometers long enclosed by a double membrane inner membrane is highly folded contain DNA reproduce by dividing and generate chemical energy ATP for cells Chloroplastslarge green organelles chlorophyll perform photosynthesistraps energy from sunlight to use to generate sugar Surrounded by double membrane also has a thylakoid membrane DNA reproduce via dividing Endosymbiotic Theory Mitochondria amp chloroplasts likely arose because primitive eukaryotic cells engulfed bacterial cells DNA reproduce by dividing Outer and inner membrane characteristic of gram positive bacteria Endoplasmic Reticulum ER maze like membrane bound part of the cytoplasm rough ER ribosomes protein synthesis smooth ER membrane synthesis Golgi Apparatus stacks of flattened membrane bound compartments 1 Protein modification glycosylation addition of sugar groups to a protein 2 Protein Sorting receives molecules proteins amp lipids made in the ER modifies them sorts them amp sends them to a number of different final destinations ex Plasma membrane lysosomes outside cell endosome Lysosomes small organelle contain hydrolases for breakdown of materials Peroxisome small organelle contains H202 hydrogen peroxide oxidizes organic molecules Vesicles small found in cytoplasm move materials between various organelles and the outside of the cell 1 Inside to outside exocytosis 2 Outside to inside endocytosis 3 One compartment to another ex from ER to Golgi Vesicular Transport CHAPTER 2114 Chemical Components of Cells Chemistry of Living Organisms 1 Organic carbon compounds 2 Reactions take place in an aqueous environment Cells 70 water 3 Reactions take place in a very narrow temperature range 4 Complex 5 Dominated by large polymers ex Proteins DNA RNA Sugar amp Lipids NEED TO KNOW 1 Covalent Bonds 2 lonic Bonds 3 Hydrogen Bonds 4 HydrophilicHydrophobic Importance of Weak Bonds in Living Systems weak bonds often hold molecules together in cells If have lots of weak bonds bonds can have very tight bonding CHAPTER 3114 Energy Catalysis and Biosynthesis ch13 amp ch14 Metabolism All the chemical reactions that occur within a cell thousands of reactions organized into pathways pathways are interconnected and very complex 2 kinds of pathways catabolic break down and anabolic build up In a chemical reaction a reactants is converted to a products In a pathway reactions are connected The product of the first reaction is the reactant for the second reaction In cells chemical reactions are catalyzed by enzymes ch4 Catabolic Pathway quotbreak downquot release energy produce building blocks Anabolic Pathway quotbuild upquot use energy building blocks to make new molecules Ex Synthesis of DNA and proteins Thermodynamics 1st law Energy can be transferred or transformed from one form to another but it can39t be created or destroyed 2nd law In the universe or in any isolated system the degree of disorder can only increase the tendency toward disorder is spontaneous entropy refers to the amount of disorder in a system all energy transfers cause an increase in disorder cells are highly ordered and complex cells have to quotwork aroundquot the 2nd law of thermodynamics to maintain complex and organized structure cells maintain order at the expense of their environment cells take energy from environment and use it to create order some of the energy is released as heat which causes more disorder in the environment Cells obtain energy through the oxidation of organic molecules stable chemical energ in food is converted into easily useable forms of energy ex ATP Plants sugars produced by photosynthesis Animalsmixture of molecules that are eaten Respiration production of ATP occurs in a series of oxidation steps gt overall result sugar is completely broken down to 002 Photosynthesis amp Respiration are complementary processes quotCircle of Lifequot Photosynthesis COZH20 gtSugar02 using light energy Respiration Sugar02gt COZH20 generating energy ex ATP heat Photosynthesis occurs in plants and some photosynthetic bacteria 2 stages Light and Dark Reactions Lightenergy from the sun is captured production of high energy carrier molecules ATPNADHNADPH H20 is split gt 02 Dark carbon fixation C02 from air is used to make sugar using high energy carrier molecules from the light reactions ATP NADH Free Energy and Chemical Reactions All molecules have an energy associated with them called free energy G can be used to do work or drive reactions Each chemical reaction occurs with a change in G deltaG deltaGfree energy of productsfree energy of reactants 2 kinds of reactions with respect to energy spontaneous if energy is released reaction can occur spontaneously have more energy than products disorder increases negative deltaG energetically favorable nonspontaneous reactants have less energy than the products energy is absorbed by reaction input of energy disorder decreases against 2nd law of thermodynamics positive deltaG energetically unfavorable How do cells make energetically unfavorable reactions proceed by coupling unfavorable reactions to favorable reactions overall deltaG for combined reactions is negative And so the set of reactions with proceed spontaneously Chemical reactions are coupled using high energy intermediates coupling reactions use activated carrier molecules primary ex ATP NADH NADPHPAD ATP carries high energy phosphate group NADH amp NADPH carry high energy electrons EX Energy stored in ATP harnessed to join two molecules together Condensation reaction is unfavorable AHB OHgtABH20 Cells use an induced pathway that uses ATP 1 B OH ATP gt B O P03ADP Favorable BOPO3 is the high energy intermediate 2 AHBOPO3 gtABPi Favorable Net result B OHATPAHgtABADPPiH2O DNA amp Protein synthesis RNA Synthesis How cells get their energy Cells make ATP in 2 ways Glycolysis Does not require molecular oxygen TCA Cycle aka Krebs Cycle or Citric Acid Cycle and Electron Transport Chain Require Oxygen can only be carried out b aerobic organisms Food molecules are broken down in 3 steps 1 Break down of large molecules into simple subunits Mostly outside of cells 2 break down of simple subunits into acetyl CoA Production of ATP amp NADH occurs mainly in cytosol glycolysis pyruvate gt acetyl CoA Occurs in mitochondria 3 Complete oxidation of acetyl CoA to C02 H2O get production of lots of ATP amp NADH occurs in mitochondria requires oxygen 02 TCA Cycle amp Electron Transport Chain Stage 2 Glycolysis pyruvate gt acetyl CoA Glycolysis Glucose 6 carbon gt 2 Pyruvate 3 Carbon requires an input of ATP net result 2 ATP 2 pyruvate 2 NADH glucose does not require oxygen Occurs in the cytosol pyruvate 3 carbonmove from cytosol to mitochondrial matrix Transport occurs 2 membranes pyruvate is converted to acetyl CoA Mitochondrial Matrx Acetyl CoAactivated carrier molecule Stage 3 acetyl CoA enters TCA cycle One form of cycle 3 NADH 1 GTP 1 FADH2 2 002 high energy electrons 2 turns for each glucose in Mitochondria requires 02 Final Step Electon Transport Chain Respiratory protein complexes embedded in inner membrane of mitochondria High energy electrons from NADH are passed along the chain Respiratory complexes use the energy from equot transfer to pump Hquot protons across the membrane matriXgtinner membrane space Creates a proton HA gradient Hquot gradient to needed to make ATP By ATP synthesis ATP from ADP amp Pi 30 32 ATPglucose CHAPTER 4 Protein Structure and Protein Function proteins consitute most of the dry mass of a cell different types of proteins enzymes DNA polymerase structural proteins keratins transport proteins hemoglobin ion channels storage proteins farritin motor proteins dyneine kinesine signaling insulin receptors rhodopsin gene regulatory proteins Amino Acid sequence of a protein determines 3D structure of a protein shape gt 3D Structure decreeing protein function Sting of amino acids aa polypeptide chain structure determined by the string of amino acids and the structure determines the function Proteins polypeptide chains long chains of amino acids Peptide Bonds Strong covalent bonds that link the amino acids together in polypeptide chains CHAPTER 4 cont Amino acid aa building blocks of proteins 20 aa Found in proteins in living organisms each have a distinct side group R group e W Di 9 Q N w wah Left side amino N Right side carboxyl C Amino acids are bonded via a condensation reaction connecting the OH of one amino acid to the H of the following Everything but the R groups are called quotpeptide backbonequot peptide bond strong covalent bond rigid planar unit no rotation around peptide bond Do see rotation around other bonds in polypeptide chain polypeptide chains can adopt a number of different shapes or conformations in theory Classification Scheme for 20 amino acids based on the chemistry of the R group 1 acidic aspartic acid amp glutamic acid 2 3 4 non polar many ex alanine amp glycine basic arginine lysine and histidine uncharged polar many ex serine and threonine 13 hydrophilic 4 hydrophobic Protein Shape Confirmation shape is determined by amino acid sequence long polypeptide chains are flexible rigid around the peptide bond each polypeptide chain will fold up in a characteristic manor due to interactions between atoms in polypeptide chains folding is controlled by LOTS of weak bonds H bonds ionic interactions hydrophobic interactions ATOM 1 ATOM 2 backbone Backbone R R backbone R many possible shapes that a polypeptide chain could ad0pt fold into But for proteins that are found in cells usually adopt a single stable shape usually fold up in the same way proteins always fold up into a shape with the lowest energy fold in a way that minimizes free energy EX polypeptide chain 300 amino acids long 1 2 3 4 20 20 20 20 203 possible amino acids sequences most of these possible proteins will not adopt a single stable shape for proteins that are found in cells the polypeptide chains DO adopt a singlestable shape can study purified proteins and watch how they fold Denature Denaturation loss of confirmation cause proteinsto unfold ex urea amp heat denatures proteins Renature Renaturation refold proteins proteins can fold up properly without any help NOTE In cells special proteins called chaperones may help with folding efficiency stress Protein Organization Primary structure 1quotosequence of amino acids in a polypeptide chain Secondary structure 2quoto alpha helix amp beta sheet Tertiary structure 3quoto 3D structure of single polypeptide chain Quaternary Structure 4quoto proteins are formed by interactions between more than one polypeptide chain Secondary structure due to interactions between aromas of the repeating backbone of a polypeptide chain R groups not involved backbone is invariant except the R group 2 common folding patterns beta sheet found in the core of many different proteins found in cells rigid structure with H bonds causing formation H bonds joining peptide bonds in neighboring chains R groups not involved Rgroups stick out from the two surfaces of the sheet paralle form when polypeptide chains run in the same direction anti parallel polypeptide chains run in opposite directions alpha helix single polypeptide chain that folds around itself to form a rigid cylinder distance from 1 turn of the helix to the next is 054nm 36 amino acids for each turn of the helix very common in membrane proteins Coiled coilform when two alpha helices wrap around each other nonpolar side chains lined up in a stripe along one face of a helix stripe along length of the helix non polar stripes interact with each other Ex keratin Youtube garland science short videos from textbook Another level of protein organization protein domain Protein domain any segment of a polypeptide chain that folds up independently into a compact stable structure often associated with a specific function Ex CAP Protein small domain can bind to DNA large domain can bind to a nucleotide CAMP Large protein molecules often contain more than one polypeptide chain gt quaternary structure each polypeptide chain is referred to as a subunit binding site any region of a protein surface that interacts with another molecule via sets of non covalent bonds like H bonds Ex homo dimer 2 polypeptide chains are the same Hetero dimer 2 polypeptide chains are different Homotetramer 4 polypeptide chains are the same Heterotetramer 4 polypeptide chains are different Quaternary Structure con39t very large assemblages of protein subunits that can interact with each other mircotubules ring heHces Proteins can be classified in families similar amino acid sequences similar 3D shapes similar function Ex DNA polymerases actin serine proteases Disulfide Bonds covalent bond that often stabilizes extra cellular proteins stronger than noncovalent bonds but are relatively weak in comparison to other covalent bonds C a 5l4 mugg r l 0 3 C 5 Qu N le l gkr cytoso is a reducing environment disulfide bonds are not important in cytosol proteins see disulfides in extra cellular proteins ER lumen Golgi lumen and vesicles lumen How Proteins Work protein structure determines function How by binding to other proteins or other molecules Binding is specific each protein can bind to one or a few out of the thousand of molecules it might encounter any molecule that binds to a protein is called a ligand But binding depends on weak noncovalent bonds between matching surfaces of a protein and ligands Binding site usually a cavity in surface of the protein some proteins have multiple binding sites binding between protein and ligand often induces a change in the protein39s shape quotconformational changequot highly selective quothandinglovequot Enzymes are powerful and highly selective catalysts are proteins mostly that catalyze chemical reactions in cells speed up reactions not used up in reactions Perform reactions over amp over bind to ligands one or more ligand is the substratereactant enzymes often work in teams can speed up reactions by a factor of 1 million names end in quotasequot Ex nuclease protease synthase polymerase EX lysozyme Lysozyme performed hydrolysis add a H20 to break a bond between 2 adjacent sugars and a polysaccharide reaction has deltaG spontaneously has high activation energy lysozyme holds its substrate in such a way that the reaction can proceed more readily bond is distorted gt activation energy is lowered How proteins are controlled can control how much is synthesizes and when rate at which a protein is turned over rate of degradation control how much of a protein is active v inactive Activeon inactive off gt protein activity can be controlled by many different mechanisms negative regulationactivity of the protein is inhibited positive regulation activity of the protein is increased Feedback Inhibition regulates flow of metabolites through a metabolic pathway AgtBgtCgtDgtE the final product of a pathway E inhibits the first enzyme that is unique to its synthesis o gt enzymes 2 amp 5 are allosteric enzyme 0 and product of pathway is a ligand for allosteric enzyme inhibiting their ligand 0 allosteric enzymes are inactivated by binding of end product 0 Protein phosphorylation regulate protein activity via addition or removal of a chemical phosphate group to a protein of interest 0 gt A phosphate from ATP is added to a protein kinases enzymes that take terminal phosphate from ATP and add the phosphate group to a protein phosphatases remove phosphate groups Practice exam posted on BB on Monday 21 answer key available Thursday 24 Exam 1 Tuesday 29 on chapters 12 31314 4 5 6 7 CHAPTER 5 DNA and Chromosomes DNA deoxyribonucleic acid material in cells that contains genetic information genes region of DNA that contains the instructions for making a particular proteinor RNA genome the complete set of information contained within an organism39s DNA chromosome long thread like structures that are composed of DNA and associated proteins that carry a part of the genetic information of an organism Central Dogma of Molecular Biology DNA gt RNA gtProtein gtdo work in cell Transcription Translation Genetic Information flows from DNA to RNA to Protein DNA Structure double helix determined by James Watson amp Francis Crick in 1953 Nobel Prize in 1962 Structure determined by Xray diffraction Rosalind Franklin 2 strands of DNA wound into a helix DNA Structure 1 two polynucleotide chains aka DNA strands DNA chains 2 each chain is composed of 4 types of nucleotides 3 a DNA nucleotide one phosphate group 5 carbon sugar deoxyribose one of 4 nitrogen containing bases ATCG Adenine A Thymine T Cytosine C Guanine G 4 the nucleotides are linked via covalent bonds via phosphates and sugars phosphodiester bond 5 the alternating sugars and phosphates form a backbone the bases come off from backbone 6 sugarphosphate backbone on outside of molecule 7 each of the DNA strands has polarity 2 ends are different Free 539 phosphate 539end Free 339 OH group 339 end 8 the 2 strands of DNA are antiparallel the 539 end of one of the strands is opposite the 339 end of the other strand 9 the 2 strands of DNA are held together via weak hydrogen bonds between the bases of nucleotides 10 hydrogen bonding occurs between complementary bases A bonds to T 2 hydrogen bonds weaker due to bonds C bonds to G 3 hydrogen bonds stronger due to bonds Purines A and G double ring Pyrimidines C and T single ring Base pair two nucleotides in a RNA or DNA molecule that are paired by hydrogen bonds AT or GC AU for RNA 11 2 strands of DNA are complementary to one another if you are given a sequence of one strand of DNA you can deduce the sequence of the 2nd strand of DNA EX539AAGATCT339 339 T T C T A G A 539 Always read from the 539 end EX If a molecule is 15 A calculate the of the other 3 nucleotides A 15 T 15 30 G 35 C 35 70 12 10 bases per helical turn of DNA 13 DNA has a major groovebigger DNA binding proteins usually interact in major groove minor groove EX 2 different double stranded DNA molecules use heat to separate the 2 strands gets rid of the hydrogen bond As you increase temperature which one falls apart 1st at lower temp a 539 TGC AAT GAT A 339 b 539 TGC AAG GCT A 339 SOLN A because there are fewer hydrogen bonds than B Information in DNA the information in DNA is encoded by order sequence of nucleotides along a DNA strand like the order of letters in a word or sentence DNA has a 4 letter alphabet ATCG protein 20 amino acids found in polypeptide chains 20 letter alphabet the correspondence between the 2 alphabets is called the quotgenetic codequot Gene Expression the process by which the linear sequence of nucleotides in a gene is converted into amino acid sequence transcription mRNA processing mRNA export and translation Eukaryotic Chromosomes total length of DNA in a human cell is 2meter nucleus is 56 micrometers in diameter DNA is packed in an organized manner into chromosomes so that they may easily fit inside the nucleus and can be easily replicated and split into daughter cells also transcribed Chromatin is a complex of DNA and proteins that makes up chromosomes chromosomes contain long strings of genes genes are functional units of heredity in general the more complex an organism the more genes in the genome bacteria 500 genes humans 30000 genes Genes along a chromosome are interspersed with linker DNA Prokaryotic Chromosomes bacteria have a single circular chromosome bacterial DNA is associated with proteins but different from eukaryotic chromosomes replication is also different due to circular shape
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