BS1001 Summary BS1001
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This 29 page Study Guide was uploaded by Chong Yik Yan on Saturday September 12, 2015. The Study Guide belongs to BS1001 at Nanyang Technological University taught by Prof Alex Law in Summer 2015. Since its upload, it has received 655 views. For similar materials see Introduction to Biology in Biological Sciences at Nanyang Technological University.
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Date Created: 09/12/15
B51001 SUMMARY BASICS Amino Acids Nonpolar Glycine Alanine Valine Leucine Isoleucine Phenylalanine Tryptophan Polar Uncharged Serine Threonine Asparagine Glutamine Tyrosine Charged Aspartic Acid Glutamic Acid Histidine Cysteine Lysine Arginine Special Function Proline Methionine Cysteine Ionizable Tyrosine Serine Threonine Aromatic Phenylalanine Tyrosine Tryptophan Disulphide Cysteine Cystine Protein the final active product Poly peptide a series of amino acids linked together by peptide bonds also called amide bonds Primary structure the sequence of amino acids in the polypeptide from amino to carbonyl end Secondary ahelixes Bsheets turns and loops Tertiary arrangements of the secondary structures into modules or domains or motifs Quaternary more than one proteins combine to form a functional complex a Helix Formed by hydrogen bonds between atoms on the backbone Righthanded B Pleated Sheet Hydrogen bonds between backbone elements Parallel VS Antiparallel strands Proteins Poly morphic proteins same functions that lead to variations in phenotype eg in uenza virus H for Haemmagglutinin N for Neuraminidase 9change in one amino acid will not affect their function but will make than be able to evade immune system Rossmann fold consists a central 3 sheet anked by multiple helices Firstsolved 3D structure Myoglobin consisting of all a helices ONE polypeptide Myoglobin carries oxygen in the muscles Haemoglobin carries oxygen in the blood consists two a and two 3 subunits each a single polypeptide 9 makes up to the quaternary structure Forces that hold proteins together Covalent bonds peptide bonds between adjacent amino acids disulfide bonds between cysteine residues Ionic bonds between a carboxyl and an amino group Hydrogen bonds Hydrophobic interactions exclusion of water by nonpolar regions of the molecules Van der Waals forces weak noncovalent attractions at close range between nonpolar atoms Collagen Every third amino acid is a glycine Right handed triple helix structure with 3 left handed helices Most abundant protein in an animal 13 body s protein weight 75 of skin Type I 90 of body s collagen bone skin tendons ligaments cornea Type IV basal lamina lining blood vessels Type IX cartilage Carboydrates General formula CH20n Roles as sources of energy and as structural components in some cells and organisms Monosaccharides 3carbon sugar glyceraldehyde 5carbon sugars pentoses ribose deoxyribose 6carbon sugars hexoses fructose glucose galactose Disaccharides Sucrose 9 glucose fructose Lactose 9 galactose glucose Maltose 9 glucose glucose Note the linkages between the two subunits 9 specificity of enzymes Polysaccharides Chitin Consists many units of monosaccharides Can branch No absolute regulation of points of branching and length of branches polysaccharides have no define 3D structures Amylopectin amylose 9 starch granules in plant cells eg potato starch consists 20 amylose and 80 amylopectin Glycogen in animal starch is highly branched and insoluble 9 forms glycogen granules in animal cells Cellulose long unbranched polymer of Bglucose subunits linked by B 14 glycosidic bonds major component of plant cell walls can only be broken down by certain bacteria and protists 9 wood is a good long lasting structure in plants and manmade structures Starch chain of aglucose subunits linked by a 14glycosidic bonds can be broken down by enzymes in human and other animals 9 digestible 9 good energy source Polymer of Nacetylglucosamine 9 glucosamine is similar to Bglucose but amino group replaces hydrozyl group at carbon2 amino group of glucosamine is bonded to acetyl group in Nacetylglucosamine When crosslinked with proteins and calcium carbonate forms tough exoskeleton of insects and crustaceans Nucleic Acids Linear polymer of nucleotides DeoxyriboNucleic Acid and RiboNucleic Acid Nitrogenous bases with phospodiester bond Purines two rings Adenine Guanine Pyrimidines one ring Thymine Uracil Cytosine DNA and RNA are written in the 5 to 3 direction complementing strand will be 3 to 5 antiparallel RNA Messenger RNA copy of DNA for use as template for protein synthesis Transfer RNA recognition of codon on mRNA to put correct amino acid in the polypeptide chain Ribosomal RNA four different RNA pieces in the gigantic RNAprotein complex ribosome where protein synthesis takes place structurally supports and catalyzes protein synthesis snRNA in nucleus of eukaryotic cells to facilitate splicing of mRNA Regulatory RNA or MicroRNA play regulatory roles in controlling the protein contents of a cell Genetic material of some viruses eg HIV SARS Lipids Insoluble in water High levels of hydrophobic atoms like carbon and hydrogen and low level of polar atoms like oxygen and nitrogen Contained in butter oil egg yolk nuts detergents hand creams etc Some amphipathic in nature polar end and hydrophobic tail similar to detergents 9 forms emulsions with water Includes chlorophyll a major molecule responsible for absorption of sunlight in plants Bcarotene orange photosynthetic pigment vitamin A1 vitamin D2 prostaglandin D2 etc Triglycerides Consists 3 fatty acids hydrocarbon chain with a carboxylic acid group either same or different and one glycerol backbone linked by ester bonds Insoluble 9 aggregate into fat droplets within aqueous environment of a cell CH bonds serve as efficient form of energy storage in cells Phospolipids Consists a phosphate linked by phosphodiester bond two fatty acids linked by ester linkages and a glycerol backbone Amphipathic 9 commonly forms micelles and lipid bilayers in water A scaffold of phospholipid bilayer embedded with proteins forms the biological membrane 9 allows inside and outside of the cell to be defined Most common phospholipids phosphatidylcholine phosphatidylserine and phosphatidylinositol Sphingomyelin found in myelin sheath of nerve cells in animals 9 sphingosine component with phosphocholine head group and fatty acid linked to sphingosine Via amide bond Cardiolipin in inner membrane of mitochondria in animals and plants 9 two phospholipid units linked Via phosphate head groups Cholesterol Lipid with no glycerol backbone Found in all animal cell membranes Polar head group hydroxyl which can interact with polar head group of other lipids and a hydrophobic tail which consists a series of rings embedded in the hydrophobic region of bilayer Association with membrane lipid bilayer allows it to play an important role in the regulation of membrane uidity Precursor for synthesis of a series of steroid hormones including testosterone and estrogens CELLS Living organisms Unicellular organisms Prokaryotes unicellular organisms that have no specialized organelles Includes Bacteria and Archaebacteria O Uses decomposition fixation photosynthesis reducing N2 to NH3 symbiosis cellulose degrading bacteria in cattle bacteria producing vitamin K and B12 in human colon genetic engineering molecular biology techniques biofactories in the production of enzymes ProtistsEukaryotes cells with compartmentalization Grampositive Gramnegative Protein Protein Lipoteichoic acid Lipopolysaccharide Teichoic acid Porin Plasma membrane Plasma membrane Cell wall peptidoglycan Cell wall peptidoglycan and outer membrane Alcohol dehydrates thick peptidoglycan Alcohol has minimal e ect on thin layer traps dye complex peptidoglycan layer Red dye has no e ect Red dye stains colourless cell Multicellular organisms All eukaryotes Cells developed into specialized types Work together to sustain quotlifequot of the organism Bacteria 110 pm Cell wall of peptidoglycan No introns present Membrane of fatty acids No membranebound organelles 4subunit RNA polymerase Archaebacteria 110 pm Cell wall of various molecules NO peptidoglycan pseudopeptidoglycan protein Some introns present Membrane based on nonfatty acid lipids isoprenes 9 unusual lipid No membranebound organelles Manysubunit RNA polymerase Live in extreme conditions dead sea unusual salt composition deep sea vents gt100 C gt200 atmosphere Eukarya 10100 mm Cell wall of cellulose or chitin in many Introns present Membranes based on fatty acids Membranebound organelles Manysubunit RNA polymerase Parts of a typical prokaryote Pili O Made of pilin O For adhesion Cytoplasm Ribosomes O Reads the code in the mRNA and puts the proper amino acid according to the code Nucleoid DNA Plasma membrane Cell wall Capsule O Generally polysaccharides Q Have protective effect from the immune system Flagellum O Made of agellin for motility O Flagella of bacteria rotate O Flagella of eukaryotic cells beat microtubules Parts of a typical animal cell Plasma membrane O Similar to that of bacteria different from archaebacteria O Lipid bilayer formed of various lipids different membranes have different lipid composition outer and inner leaves of membrane can have different compositions O Impermeable to polar molecules including water O Proteins to serve as channels specific for certain ions and molecules to serve the specific needs of the cell or the intracellular compartments I Usually the smaller the molecule the less strongly it associates with water the more permeable it is I Eg aquaporin Cytoplasm O Cytoplasmic Extracellular mM mM Na 15 150 K 150 5 Cl39 7 110 Nucleus O Only in eukaryotes O Delimited by double membrane nuclear envelope decorated with nuclear pores for movement of molecules in and out of the nucleus selectively O Consists denser region of nucleolus where ribosomes are produced 9 rRNA and partly assembled ribosomes can be found O free ribosomes are involved in synthesis of cytoplasmic proteins ribosomes on ER involved in synthesis of secreted proteins and membrane proteins Rough endoplasmic reticulum RAP O quotroughnessquot from bound ribosomes O Cells for secreting proteins eg plasma cell B lymphocyte and antibodies have a lot of rough ER Smooth endoplasmic reticulum SERCL O No ribosomes O For synthesis of lipids and carbohydrates O Cells require extensive lipid biosynthesis eg testes brain intestine mammary glands have a lot of smooth ER O Enzymes of smooth ER in liver are involved in the detoxification of drugs O membranes of ERs are continuous possibly linked to nuclear membrane and golgi apparatus as well Golgi apparatus O Packaging and distribution of molecules in a cell and for secretion O Major protein modification 9 addition of short carbohydrate chains to make glycoproteins generally only proteins outside cell are glycosylated Actin filament 7nm Made of actin monomers Found in all eukaryotic cells Responsible for cell shape and whole cell locomotion pinching during cell division cellular extensions phagocytosis O Polar directional 9 two entwining strands are pointing the same way Intermediate filament 8 10 nm quotintermediatequot between actin filaments and microtubules Not found in cytoplasm of all cells Predominantly found in cells that are subject to mechanical stress 9 eg skin contains a layer of dead cells with keratin network still intact O Lamins made of intermediate filaments line the inner surface of nuclear envelope O Different types expressed in different cell types largest family keratins 50 genes I Family of keratin molecules over 20 types in human epithelial cells cells that are in sheet form in contact with an external surface I 10 more types of keratins specific to hair and nails I A single cell can express multiple types of keratin copolymerizing into a single network I Not microtubules 9 no MTOC not actin 9 not at periphery of cells 000 0000 Microtubule 9 25 nm O Serves as tracks for highspeed transport 9 vesicle connected to microtubule via dynein dynactin complex through other associated proteins O Flagella and cilia each are made of 92 sets of microtubule triplets 9 outside two at core 9 beating of agella in sperms Centrosome O MicroTubule Organizing Centre MTOC O Most animal cells have one Q Consists two centrioles O Each centriole contains 90 sets of microtubule triplets Lysosome O Contains digestive enzymes that work at pH levels 4 5 O Removes old or damaged organelles O Fusion of a vesicle with lysosome will result in vesicle being digested Peroxisome O Contains digestive and detoxifying enzymes that produce hydrogen peroxide which is harmful to cell as a byproduct O Contains calatase to break down hydrogen peroxide Mitochondrion O Thought to be remnant of ancient bacteria that makes use of oxygen to generate energy by oxidative phosphorylation bacterialike ribosome Parts of a typical plant cell Cell wall O Made of polysaccharide cellulose Vacuole O Contains water and soluble small molecules sugars ions etc O Affects turgidity of plants Tonoplast O Membrane surrounding the vacuole Nucleus Chloroplast O Photosynthesis O Contains I DNA I Ribosome I Thylakoid membrane I Thylakoid disk I Granum I Stroma I Outer membrane I Inner membrane The Plasma Membrane Parts 9 Extracellular matrix protein O Glycoprotein O Glycolipid Cholesterol Peripheral protein Integral proteins Actin filament of cytoskeleton Intermediate filaments of cytoskeleton Proteins present O Transmembrane proteins I Markers for self recognition major histocompatibility complex I Receptors to transmit info to cells hormone receptors and adhesion molecules I Transporters in the form of carriers and channels aquaporins and chloride channels 9 Interior protein network I Spectrin forms scaffold under membrane red blood cells I Clathrins forms vesicles for internalization of membrane bound proteins and membrane turnover coated pits Hormonal receptors eg insulin receptor Rhodopsin with the retinol Adhesion molecules for cells to crawl on Receptors for chemotactic factors to point the way Proton pump ATP synthase Membrane transport O Diffusion I Direct random molecular motion produces net migration of nonpolar molecules towards region of lower concentration movement of 02 I Protein channel polar molecules move through protein channel net movement towards region of lower concentration movement of ions O Facilitated diffusion I Protein carrier molecule binds to carrier protein in membrane and is transported across movement towards region of lower concentration glucose O Osmosis I Aquaporins diffusion of water across membrane via osmosis requires osmotic gradient water into cells in hypotonic solution O Active transport I Eg sodiumpotassium pump conformational changes in pump due to addition of ATP 9 phosphorylation of protein which changes the affinity to Na and K 3 Na out 2 K in I Eg coupled transport of Na and glucose driven by Na gradient generated by NaK pump sodium gradient when Na automatically diffuses in allows glucose to be carried into cell O Bulk transport endocytosis absorption I Phagocytosis receptors and actin filaments 0 Identification of bacteria to ingest o Actin filament changes shape of cell to ingest 00000 000000 I Pinocytosis no receptors 0 Caveolaecaveolin 0 Also clathrin system I Receptormediated endocytosis o Receptors for targets 0 Clathrincoated pits o Clathrincoated vesicles O Exocytosis I Secretory vesicle fuses to membrane 9 releases excretory products Cell Movement Crawling O Rapid polymerization of actin at leading edge O Protrusion of cell stabilized by microtubules O Receptors sensing outside environment direct crawling O Eg white blood cells migration from blood to tissues to form pus Swimming O Beating of agella in sperm Cilia O Sensory input for hearing clearing of debris and bacteria from the respiratory track Division of a prokaryotic cell 1 DNA replication prokaryotic chromosome consists double strand DNA 2 Elongation of cell 3 Growth in cellular contents growth of new membrane and cell wall 4 thZ ring grows between the two segments of cell 9 DNA attaches to cell membrane and is pulled apart to different sides of the dividing cell when membrane is stretched for elongation Septation inward growth of septum along thZ ring 6 Cell separation S Cell cycle of eukaryotes G1 cell growth G1 S checkpoint start or restriction point 9 non dividing cells remain at the end of the G1 phase referred to as G0 phase 46 chromosomes S DNA synthesis G2 replication of mitochondria and other organelles preparation for genomic separation 92 sister chromatids G2 M checkpoint M mitotic phase spindle checkpoint 9 prophase prometaphase metaphase anaphase telophase C cytokinetic phase 9 division of cytoplasm Parts 1 2 and 3 are considered interphase Mitosis Interphase G2 O DNA replicated O Centrioles replicated O Cell prepared for replication Prophase O Chromosomes condense and become visible double helix condenses and coils around histone cores O Chromosomes appear as two sister chromatids held together at the cen tromere O Cytoskeleton is disassembled spindle begins to form O Golgi and ER are dispersed O Nuclear envelope breaks down Prometaphase O Chromosomes attach to microtubules at the kinetochores O Each chromosome is oriented such that kinetochores of sister chromatids are attached to microtubules from opposite poles O Chromosomes move to the equator of the cell Metaphase O All chromosomes are aligned at equator of the cell called metaphase plate O Chromosomes are attached to opposite poles and are under tension Anaphase O Proteins holding centromeres of sister chromatids are degraded freeing individual chromosomes O Chromosomes are pulled to opposite poles anaphase A O Spindle poles move apart anaphase B Telophase O Chromosomes are clustered at opposite poles and decondense O Nuclear envelopes reform around chromosomes O Golgi complex and ER reform Meiosis One DNA synthesis 2 cell divisions Meiosis I 9 pairing of homologous chromosomes formation of synaptonemal complex between two different chromosome types fusion of kinetochore of sister chromatids sister chromosomes are together after meiosis I O Prophase I metaphase I anaphase I telophase I Meiosis II 9 sister chromatids are pulled apart resulting in haploid gametes O Prophase II metaphase II anaphase II telophase II Crossing over of homologous chromosome segments creates more diversity O Same region 9 may be linked genetically but not physically O Same chromosome 9 linked physically but may not be genetically linked due to crossover Cytokinesis In animal cells cleavage furrow forms to divide the cell In plant cells cell plate forms to divide the cell Signal transduction Start a signal in the form of a molecule such as a growth hormone outside the cell End cell proliferation one component DNA replication in the nucleus Upon binding of receptor with growth hormone receptor performs conformational change Molecule gets into nucleus via nuclear pore and interacts with nuclear proteins to initiate DNA replication Cell Death Programmed cell death Apoptosis Delivery of rececptormediated signal Cancer cells do not undergo apoptosis Cells in humans O Skin replaced 1000 times in life time Q Gut lining renewed every week O Erythrocytes red blood cells 120 days 2 million new cells per second O Sperms 100 200 million per day Q Immune system I Clonal deletion cells bearing receptors that recognize self have to be eliminated I Clonal expansion upon encountering antigen clones with the proper epitope will expand to 1000 fold eg production of antibody I Expansion accompanies terminal differentiation cells survive and remain active only in continual presence of the antigen 9 undergo apoptosis when the antigen is eliminated some differentiated into memory cells MENDEL GENETICS Genetics Dominant Recessive phenotypic exhibited traits ratio 3 1 Selfcrossing phenotypes gives genotypes inherited traits 1 2 1 TT Tt tt Dihybrid cross ratio 9 3 3 1 DNA DNA replication DNA grows from the 5 end to the 3 end Protein Role Size kDa Molecules cell Helicase Unwinds double helix 300 20 Primase RNA polymerase 9 synthesizes 6O 50 RNA primers to extend strand with DNA nucleotides Singlestrand Stabilizes singlestranded regions 74 300 binding protein DNA gyrase Relieves torque 9 uncoils DNA 400 250 strands during replication to prevent supercoiling DNA Synthesizes DNA polymerase 111 DNA Erases primer and fills gaps 103 300 polymerase I DNA ligase Ioins ends of DNA segments 74 300 okazaki fragments and primers DNA repair In replication DNA duplex unravels to create two separate strands to be used as template for new strand 9 antiparallel strands since DNA polymerase reads DNA only from 3 end to 5 end replicates from 5 to 3 O Original strand with 3 to 5 sequence is bound to leading strand O Original DNA strand with 5 to 3 sequence creates okazaki fragments lagging strand 9 primers start from random parts of the template Telomere replication required where removal of primer results in shortening of DNA chain 9 telomerase with bound RNA template strand extends the parental DNA template strand with noncoding RNA 9 DNA polymerase forms complementary strand 9 DNA chain is not shortened Transcription Transcription of mRNA from parental DNA strand forms RNADNA hybrid helix mRNA breaks off after transcription and DNA rewinds 9 at end point of transcription mRNA strand forms mRNA hairpin loop 9 mRNA strand falls off when complementary base pairs appear to form the hairpin The Genetic Code Watson and Crick s 20 amino acids Glutamic acid Aspartic acid Leucine Serine Lysine Glycine Valine Proline Arginine Alanine Threonine Isoleucine Tyrosine Phenylalanine Histidine Methionine Tryptophan Cysteine Asparagine Glutamine I Exclusion inclusion from Gamow s list due to limited numbers in the body secondary structures can be broken down into simpler structures and conversion to acid inclusion Start codon AUG Met 9 all proteins will start with methionine may or may not be removed Stop codons UAA UAG UGA trp Stop codons in mitochondria AGA AGG 000000000000000000 Translation To make a protein O Amino acids O AminoacyltRNA transferases binds amino acids to tRNA O Transfer RNAs binds to mRNA Via anticodons I Charged tRNA and AMP produced after binding with amino acid 9 charged tRNA contains specific amino acid attached to 3 acceptor stem of its RNA O Messenger RNA O Ribosomes I 2 ribosome subunits I 3 tRNA binding sites 9 A aminoacyl P peptidyl E exit I A introduces amino acid P forms peptide bond between amino acid and existing chain E provides exit for spent tRNA Prokaryotic transciprtion of mRNA and translation into proteins can take place simultaneously 9 no compartmentalization Eukaryotic transcription occurs in nucleus with DNA translation in cytoplasm O Processing of mRNA into mature mRNA occurs before export into cytoplasm I 5 cap stabilizes primary transcript I 3 polyA tail 100200 As I Introns are spliced out using snRNA O introns have to exist BETWEEN exons O In the primary transcript EXONGU INTRON AGEXON quotGUquot and quotAGquot code mostly invariant Alternative splicing of mature mRNA produces more proteins O Some tissue specific depending on which cell the gene is expressed Terms Split genes Primary transcripts Mature mRNA Intravening sequences Introns Exons Splicing Alternative splicing 00000000 Genetic Disorders Linked to mutation of proteins enzymes Sickle Cell Anemia O 1945 Linus Pauling postulated that sickle cell anemia was a molecular disease O Transmission typical autosomal recessive O Carriers are not 100 healthy 9 show signs on discomfort under severe stress conditions O Sickle cell anemia sufferers have abnormal deoxygenated tetramers 9 sticky nonpolar sides exist 9 form long chains when deoxygenated which distorts the normal red blood cell shape into a sickle shape O People with sicklecell trait are more resistant to malaria 9 sickle cell allele confer genetic advantage over the normal allele Thalassaemia O Affects both a and 3 subunits of haemoglobin O Many different forms of mutation most leading to low level of either subunit resulting in abnormal haemoglobin O Not eliminated possibly due to their heterozygous advantage over malaria infection Point mutation one base substituted with another O Silent mutation still produces the same amino acid sequence 9 DNA polymorphism Frameshift mutations one or limited base deletion or insertion Types of mutation Type Analogy Wild Original DNA template THE ONE BIG FLY HAD ONE RED EYE Missense Change in one amino acid to another THQ ONE BIG FLY HAD ONE which may or may not affect the RED EYE protein structure and or function protein polymorphism if non deleterious Nonsense Truncation THE ONE BIG Frameshift Completely different amino acid THQ ONE QBI GFL YHA DON sequence results ERE DEY Deletion of Removes a single amino acid may THE ONE BIG HAD ONE RED 3 letters or may not be deleterious EYE Duplication THE ONE BIG FLY FLY HAD ONE RED EYE Insertion THE ONE BIG WET FLY HAD ONE RED EYE Expanding P1 THE ONE BIG FLY HAD mutation ONE RED EYE F2 THE ONE BIG FLY FLY FLY HAD ONE RED EYE F2 THE ONE BIG FLY FLY FLY FLY FLY FLY HAD ONE RED EYE Effects of mutation O Prevents a protein from forming O Lowers amount of a protein O Alters a protein O Adds a function to a protein Chromosomal Abnormalities Polyploidy extra full set of chromosomes Aneuploidy extra or missing chromosomes Deletion part of a chromosome missing Duplication part of a chromosome present twice Inversion piece of chromosome reversed Translocation piece of chromosome attached to another chromosome Human generally gain or less of an autosome do not develop properly Exception O Trisomy 13 15 or 18 causes severe developmental defects 9 infants usually die in a few months O Trisomy 21 or 22 allows survival to adulthood but mentally retarded 9 trisomy 21 is down syndrome VIRUSES Classification of viruses Viruses infect plant and animal cells Bacteriophages infect bacteria Early classification by shape and size of Viruses Current classification by mode of transmission DNA Viruses Class I DS Smallpox Hepatitis B Class Ila SS fX174 Class 11b 88 Parvoviruses RNA Viruses Class 111 DS Rotaviruses Class IV SS TMV Coromaviruses Poliovirus Class V SS Ebola In uenza A Mumps Class VI SSDNA HIV Viruses Minimal number of genes No genes for ribosomes 4 pieces or RNA 40 proteins Examples Polio HIV Hepatitis B Smallpox Ebola In uenza SARS Pandoraviruses Kuru Bovine spongiform encephalopathy mad cow disease 0000000000 Strategies of viral genome replication 1 Making the mRNA for viralspecific proteins Class Ila DNA ss Class llb DNA ss 39 Class I DNA ds Reverse transcriptase a Class VI RNA ssl l Eigt Class III RNA ds Class IV R A ss Class V RNA 55 lt3 50 2 Making the genome Class Ila DNA ss Class llb DNA ss Class I DNA clsO Class VI RNA rs739 I 1 l Class III RNA ds Claw 55quotquot Class V RNA ss 4 s quot3 lt3 V 9 nontemplate strand mRNA comes from the template strand Viroid Single strand RNA a few hundred nucleotides with highly complementary sequences Infect host and replicate No coding for any Viroidspecificquot proteins One million coconut palms are killed by cadangcadang Viroid each year BIOTECHNOLOGY Plasmids Key players O Ioshua Lederberg gene transfer by plasmid movement 1947 O Ed Tatum and George Beadle used mutants to study metabolic pathways O Lederberg Tatum experiment something was passing through the medium from one cell type to another transferring the hereditary material Small circular DNA found naturally in cells of some organisms primarily in bacteria Extrachromosomal and can replicate independent of the host genome Most important tool in recombinant DNA technology Common plasmids used in molecular biology laboratories are from 25 to 15 Kb 1 Kb 1000 bp Common methods to get the plasmid into cell is by O Electroporation O Treating the bacteria with various salts to make their membrane leaky Restriction Enzymes Some Viruses were found to be able to infect certain strains of bacteria and not others 9 enzymes are responsible for host restrictionquot Also called restriction endonucleasesquot Indispensable in modern biotechnology industry Cutting of DNA 9 causes sticky endsquot Restriction enzymes must recognize the base pairs only exposed in the major and minor grooves of the DNA double helix 9 where bases are exposed and can be seen Own DNA is protected by methylation Recombinant DNA Technology 1972 by Herbert Boyer Stanley Cohen and Paul Berg O Cleaving of plasmid and genome using restriction enzymes at both strands to leave sticky ends that are compatible O Ligase introduced into mixture to result in a some larger plasmids with an insert Reverse Transcriptase From retroviruses 9 RNA viruses that need to copy their RNA into DNA first Addition of reverse transcriptase to mature mRNA creates cDNA Final product double stranded cDNA with no introns that can be used to code for proteins Polymerase Chain Reaction PCR Developed by Kary Mullis 1983 9 amplifying DNA without having to go through a biological system Chemically synthesize oligonucleotides according to the sequences at the ends of the region of interest one sequence from each strand at opposite sides eg from 5 to 3 synthesize oligonucleotides from the portion beyond the 5 end of the region of interest for both strands Oligonucleotides act as primers for reaction DNA nucleotides not RNA 15 to 20 nucleotides to ensure specificity Denaturation heating to 94 C small fragments 9 not necessary to have replication fork gyrase helicase etc 9 3 mins Annealing primers to anneal to their appropriate positions 50 60 C 9 1 min Synthesis 68 72 C where thermophilic archaebacterial enzymes are used 9 used because they will not be denatured at 94 C 9 5 mins May have longer sequences during first few rounds 9 synthesis has no reason to stop at the region of interest 9 will be truncated due to limitation by primer which can only extend in one direction Repeat of steps will result in exponentially amplified region of interest subsequent rounds only those with the same size as the region of interest will be amplified to produce dominant product Done in thermocycler 9 no need to add anything to reaction after initial setup Application of PCR in combination with other techniques such as DNA sequencing O Detection of genetic disorder O Detection of infectious diseases O Forensics to detect if the small amount of blood bodily uid or tissue left at the crime scene would match that of a suspect O To amplify a piece of DNA for cloning and expression of a protein for research and other purposes ENERGY Laws of Thermodynamics First Law Energy conservation Second Law Entropy of system increases spontaneously Terms Anabolic energy in Catabolic energy out Endergonic endothermic Exergonic exothermic Gibbs Free Energy AG AH TAS 9 In any reaction it is the CHANGE in energy that counts AG0 depends on the intrinsic character of the reaction under standardized conditions O T 37 C O Concentrations of reagents 1 M I Since concentrations of reactants are never 1 M AC AG0 RTlnproducts reactants AG lt O for reactions to be favourable O Coupling of an unfavourable reaction with one that is energetically favourable can result in overall AG lt O 9 coupled reaction is favourable Enzyme Activity Enzyme catalytic cycle O Substrate sucrose consists glucose and fructose bonded together O Substrate binds to enzyme forming enzymesubstrate complex O Binding of substrate and enzyme places stress on glucosefructose bond 9 bond breaks I Chemical steps conformational changes take place in order for bond to break O Products are released and enzyme is free to bind other substrates 9 Enzymes are not consumed when catalyzing a reaction Dependenton O Temperature 9 pH O Salt concentration O Divalent cations 9 presence of which allows enzyme activity Regulation O Competitive inhibitor interferes with active site of enzyme so that substrate cannot bind O Allosteric inhibitor changes shape of enzyme so it cannot bind to the substrate noncompetitive O Negative feedback final product from a chain of enzyme activity inhibits action of first enzyme Pyruvate dehydrogenase enzyme complex O 60 subunits 8 trimers of lipoamide reductase transacetylase 6 dimers of dihydrolipoly dehydrogenase 24 pyruvate decarboxylase O Advantages of enzyme complexes I Subunits often involve in sequential reactions 9 product of one reaction can be delivered to the next enzyme without releasing it to diffuse away contains entropy I Elimination of unwanted sidereactions 9 product may encounter other enzymes to be drained away from the reaction I Complex can be regulated as a single unit Obtaining Energy from Food Sugar O Stepwise oxidation of sugar in cells 39 Small EA I Carrier molecules I Storage of energy O Direct burning of sugar I Large EA I All energy released at one shot I No energy stored ATP O ATP 9 ADP Pi 9 AGO 73 kcalmol 0xidative reduction O Energy stored in chemical bonds O Chemical reaction electron transfer from bond to bond O Ultimately complex molecules release the stored energy back to H20 and C02 O Electrons in the central carbon is progressively pulled away by the oxygen Nicotinamide adenine dinucleotide NAD O Electron carrier 9 NAD reduction NADH Anabolism building organic molecules VS Catabolism breaking down organic molecules for energy How humans obtain energy from food O Extracellular breakdown of macromolecules into simple subunits I Polysaccharides to simple sugars I Proteins to amino acids I Fats into fatty acids and glycerol O Intracellular processing of subunits to acetylCoA with limited production of ATP and NADH O Complete oxidation of acetylCoA with consumption of oxygen to give H20 and C02 in mitochondria accompanied by production of large amounts of ATP and NADH O NADH is also converted to ATP 1 Glycolysis Glucose 2 ADP 2 Pi 2 NAD 9 2 pyruvate 2 ATP 2 NADH 2 H 2 H20 Not very high efficiency 35 9 glucose 686 kcalmol 2 ATP 12 kcalmol 6carbon sugar to 3carbon sugar pyruvate 9 much energy left in pyruvate 2 Krebs Cycle AcetylCoA 3 NAD GDP Pi FAD 9 2 C02 3 NADH 3 H GTP FADH2 Cycle with nine carboxylic acids Takes in acetylCoA and converts it to carbon dioxide Makes energyrich NADH FADH2 and GTP Glycolysis Krebs cycle Oxidative respiration Glucose 6C breaks down to pyruvate 2 x 3C gains 2 net ATP and 2 NADH Each pyruvate transfers the acetyl group to coenzyme A releasing one C02 and building up another NADH AcetylCoA enters the Krebs cycle by converting oxaloacetate 4C to citrate 6C By going through the cycle once 2 C02 are released generating one GTP converting to ATP 3 NADH and one FADH2 Thus far 6 C02 are produced Only 4 ATP has been generated but the energy is reserved in the 10 NADH and 2 FADHz Electrons stored will go through the electron transport chain each NADH pumps 3 protons H out to the periplasmic between inner and outer membrane space of the mitochondria each FADH2 pumps 2 protons Final acceptor of the electrons are oxygen which is reduced to water adding hydrogen electron carrier Proton gradient is built up to drive the ATP synthase to make ATP Photosynthesis In the light reaction of photosynthesis 4 photons are absorbed to photosystem II exciting two pairs of electrons 2 molecules of water are oxidized to give a molecule of exygen 4 protons are generated from water 2 protons are pumped into the thylakoid space when the electrons are transferred to photosystem I 4 photons are absorbed to photosystem I to excite the 4 electrons 2 NADP reacts with 4 electrons and 2 protons give 2 NADPH 2 protons are pumped into the thylakoid stroma to yield 2 ATP NADPH and ATP will be used for the fixation of C02 Dark reaction 9 carbon fixation Calvin Cycle 3 C02 9 ATP 6 NADPH H20 9 glyceraldehyde 3phosphate 8 Pi 9 ADP 6 NADP As long as you have ATP and NADPH from the light reaction and a supply of carbon dioxide you can make carbohydrate EVOLUTION Convergent evolution 9 many marsupial species in Australia resemble placental mammals occupying similar ecological niches elsewhere in the rest of the world Marsupials evolved in isolation after Australia separated from other continents Population genetics by Godfrey Harold Hardy and Wilhelm Weinberg Conditions under which HW equilibrium can be maintained O Population size is sufficiently large O Random mating is occurring O No mutation takes place O No genes are transferred to and from other sources no migration O No selection occurs 2 alleles B and b frequency p and q Q pq1 39 mqF1 O 9 BB genotype is p2 Bb is pq bb is q2 Conditions under which HW equilibrium cannot be maintained O Genetic drift I Founder effect 9 genetic drift of one specific genotype phenotype to one region I Bottleneck effect 9 drastic reduction in population 9 future diversity will be dependent on surviving individuals Nonrandom mating Mutation Gene ow Selection Sterile genotypes 0000 Selection types Disruptive O Forms two peaks O Seeds come in two categories large or small 9 selection against intermediates 9 african firebellied seedcracker finch with large or small beaks but very few intermediatesized beaks Directional O Peak shifts O Directional selection for phototropism in Drosophilia 9 ies that moved towards the light were discarded only ies that moved away from the light were allowed to breed Stabilizing selection O Peak narrows O Stabilizing selection for birth weight in humans 9 death rate among babies is lowest at intermediate birth weight 9 smaller and large babies have higher tendency to die than those around 7 to 8 pounds Species Definition reproductive isolation Reproductive isolation mechanisms Geographic isolation I Species occur in different areas I Often separated by a physical barrier such as a river or mountain range Ecological isolation I Species occur in the same area but occupy different habitats and rarely encounter each other Behavioural isolation I Species differ in their mating rituals Temporal isolation I Species reproduce in different seasons or at different times of the day Mechanical isolation I Structural differences between species prevent mating Prevention of gamete fusion I Gametes of one species function poorly with the gametes of another species or within the reproductive tract of another species Hybrid inviability or infertility I Hybrid embryos do not develop properly I Hybrid adults do not survive in nature I Hybrid adults are sterile or have reduced fertility Allopolyploid speciation I Hybrid offspring from parents with different numbers of chromosomes often cannot reproduce sexually I Number of chromosomes in such hybrid doubles to produce a tetraploid individual that can under go meiosis and reproduce with similar tetraploid individuals Death Mass extinction Asteroid impact Volcanic eruption Earthquakes Drastic temperature change Etc Sporulation of Bacillus subtilis Mother cell produces spores with genetic material undergoes autolysis Properties 00000000 Thick spore coat Unique peptidoglycan wall Calcium dipicolinic acid present in core Very low water content and water activity Absence of enzymatic activities Absence of macromolecule synthesis High resistance to heat chemicals and radiation Resistane to lysozyme RANDOM KNOWLEDGE Origin of life Earliest evidence of life 35 x 109 years ago 9 fossils in rock in Australia and Africa Age of Earth and Solar System 45 x 109 years Age of Universe Big Bang 115 20 x 109 years Collision of Earth and a Marssized object lead to formation of a moon or two Collapse of hydrogen by gravity leads to formation of stars Galaxy 1011 galaxies in the observable universe The Milky Way 1012 solar masses 200400 x 109 stars Orion Sagittarius and Perseus Arm The Solar System Orion Arm Planets Mercury Venus Earth Mars Iupiter Saturn Uranus Neptune TheSun Second or third generation stars population I 1989 x 1030 kg 138 x 106 km diameter Contains 98 of matter of Solar System 9 remaining materialize into planets Proximity favours heat resistant silicates 9 farther out allows lighter molecules to condense including water Earth Contains heavier elements necessary for our life type Singapore Latitude 13 degrees North Longitude 1039 degrees East Equator 0 degrees latitude Greenwich Royal Observatory England 0 degrees longitude The Search for ET Evidence of water on Europa and Callisto Iupiter satellites 6th and 8th satellite 4th and 2rld largest respectively 9 possibility of life Curiosity landed on Mars 06082012 SETI Search of ExtraTerrestrial Intelligence 9 Allen Telescope Array to scan the sky and search for signals Wow Signal Ohio State University program 9 Big Ear Telescope received for 72 seconds 15081977 Pioneer Plaque Arecibo Broadcast 9 Arecibo Radio Telescope in Puerto Rico to M13 Star Cluster with 300 000 stars 25 000 light years away OUR Intelligence Wireless communication only theoretical before 1900 9 Michael Faraday s demonstration of induction Radio broadcasting after 1900 MillerUrey Experiment Stimulated conditions of early Earth Limitations enclosed atmosphere quotdilutequot reagents nonrepresentative elemental mixture Beginning of Life Current model Began in the deep sea hydrothermal vents protected from the continuous bombardments of meteors Extinctions caused by cosmic bombardments rise and fall of sea level elevation of carbon dioxide level severe volcanic eruption clashes of tectonic plates tsunamis and combinations First living organisms probably the Archaebacteria 9 extremophiles high temperatures pressure extreme pH range and salt concentrations 35 x 109 years ago Then Bacteria Oxygen in the atmosphere 20 x 109 years ago Eukaryotes 15 x 109 years ago Multicellular organisms 850 x 106 years ago First primates 20 x 106 years ago Homo sapiens 025 x 106 years ago Elemental abundance Earth crust Oxygen 466 Silicon 277 Earth Iron 321 Oxygen 301 Silicon 151 Human body Oxygen 650 Carbon 185 Hydrogen 95 Nitrogen 33 Elemental importance Iron for haemoglobin to bind oxygen and carbon dioxide iron deficiency will lead to anaemia Iodine found in thyroxine thyroid hormone lack of which leads to swelling of thyroid gland Zinc found in many enzymes zinc fingers in DNA binding domainsquot Ceruloplasmin major coppercarrying enzyme in blood Water properties High melting point High boiling point High specific heat 1 calg C Large temperature range in liquid state Excellent general solvent Cohesion to surface and to each other leads to surface tension Adhesion leads to capillary action Versatility of Carbon Able to form different types of bond and bond orders Graphite diamond organic molecules grapheme bucky ball buckminsterfullerene etc Salt concentrations Ocean 3 wv 9 mostly NaCl Dead Sea 315 Human body uid 1 The Genetic Material DNA 1928 Frederick Griffith experiment genetic material can be transformed between organisms 19305 Ioachim Hammerling use of green alga to prove that genetic material is in the nucleus 1944 Oswald Avery with Colin Macleod and Maclyn McCarty obtained DNA at purity of 9998 9 transforming quotprinciplequot remains 9 transforming activity is insensitive to protease and RNAse DNAse destroyed all transforming activity 9 DNA is the genetic material 1952 The Waring Blenderquot HersheyChasequot experiment to find out what bateriophages transfers to bacteria to cause phage growth 9 proteins have no phosphorus true for phage protein DNA have no sulfur 9 DNA and protein independently labeled with 32F and 355 respectively and blended together 9 T2 bacteriophage to infect E coli Genomics Function of the genome is to carry the information to sustain quotlifequot Smallest genome Mycoplasma genitalium Genome size 580 070 nucleotides 477 genes 37 for nonmessenger RNAs 440 for proteins Absolute minimum number of genes not less than 200300 for a viable cell in today s environment Human genome 32 x 109 nucleotides and 25 000 genes 50 are repeating elements E Coli genome 46 x 106 nucleotides 9 Humans have 1000 times DNA into 23 chromosomes each 40 times of E Coli chromosome Viruses 1892 Discovery Dmitri Ivanovsky 9 extracted infectious agents from leaves of tobacco plant Tobacco Mosaic Virus which cannot be removed by filtration 02 pm 1896 Martinnus Beijerinck 9 demonstrated that the agent can be used to infect healthy plants and the cycle can be repeated Tobacco Mosaic Virus Q 20 nm x 300 nm O Consists capsomers proteins surrounding an RNA helix O Protein subunits can assemble to rodlike structures without RNA O Proper RNA required for proper assembly into viruses O 6395 bases RNA not base pairs 9 RNA not DNA 4 genes T2 bacteriophages in Hershey and Chase experiment O Genome 168 903 bp 100 genes
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