Recitation 1 Terms! Brian Hua R08/R09 Chromosomes and Genes (P.

249-251) DNA: The biomolecule that contains all the genetic and hereditary information needed to create and maintain a functional organism. Gene: A short region of DNA that encodes for an mRNA and eventual protein that has a specific cellular function. Allele: A version of a gene. Two alleles of a gene may differ in just a single DNA base, or from large scale differences including deletions and insertions Chromosome: The packaged from of a single strand of DNA containing around a few thousand genes Each human cell (non-germ cell) has 46 chromosomes Diploid: Having two copies of each chromosome A human cell actually has 23 distinct chromosomes, but two copies of each making 46 total o 23 chromosomes from mom, 23 from dad Homologous chromosomes: The two copies of a particular They contain the same genes, but they may contain different alleles Haploid: Only one copy of each chromosome Sperm and egg are haploid cells containing 23 chromosomes each. They fuse to form the zygote which is a diploid cell Mitosis (P. 256, Figure 13.9) Mitosis: The process of cell division to create two identical cells for growth E.g. A human diploid cell duplicates its DNA and then divides, such that each daughter cell is also diploid and identical Consist of four phases in which DNA is ultimately partitioned off faithfully into each of the two daughter cells DNA replication: Copying/duplication of all of the chromosomes of the cell so that mitosis can occur. Metaphase: The first phase of mitosis where the duplicated DNA line up at the center of the cell and get ready for separation into the two daughter cells Mother cell: The cell undergoing mitosis

Daughter cells: The two products of mitosis, genetically identical to the mother cell. Meiosis (P. 256, Figure 13.9) Meiosis: The process of cell division of a diploid cell to create 4 germ cells that are now haploid DNA replication occurs in a diploid cell followed by TWO cellular divisions, resulting in FOUR haploid gametes Gametes: The products of meiosis, ultimately sperm or egg Mendelian Genetics (P. 265-269) Phenotype: The observable characteristic or trait associated with a certain gene E.g. The phenotype of the pea is green color Genotype: The specific allele makeup associated with a certain gene E.g. The genotype of the green-colored P is Gg at the gene responsible for pea color. Homozygous: A gene in which both alleles are the same E.g. The green pea is homozygous for the big G allele: GG E.g. The yellow pea is homozygous for the little g allele: gg Heterozygous: A gene in which the two alleles of a particular gene are different E.g. Gg Dominant: The phenotype that shows when you cross one organism that is homozygous for one allele and an organism that is homozygous for the other allele E.g. GG (green) x gg (yellow) Gg (Green) Green is the dominant phenotype Recessive: The phenotype that is not shown when you cross one organism that is homozygous for one allele and an organism that is homozygous for the other allele E.g. GG (green) x gg (yellow) Gg (Green) Yellow is the recessive phenotype Monohybrid cross: When you cross one organism that is homozygous for one allele and an organism that is homozygous for the other allele for one gene E.g. GG x gg Dihybrid cross: When you cross one organism that is homozygous for one allele of two genes and an organism that is homozygous for the other alleles of two genes E.g. GGRR x ggrr Independent assortment: The property that when looking at two genes, the inheritance of one trait is independent of the inheritance of the other

This assumes that the two genes of interest are far apart from each other on the chromosome or on different chromosomes entirely

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Recitation 2 Terms! Brian Hua R08/R09 Sex-linkage (P. 289-291) Sex-linked gene: Any gene that resides on the X or Y chromosomes (sex chromosomes) Hemizygous: While the terms homozygous and heterozygous apply to a female because she has two X chromosomes (XX), they dont apply to males because males only have one X chromosome (XY). Males are then hemizygous for the X chromosome Recombination/Crossing Over (P. 294-297) Recombination: The production of offspring with genotypes of neighboring genes that differ from those found in either parent. Crossing over: The physical event that takes place in meiosis where arms of homologous chromosomes swap, thus resulting in recombination Test cross: A cross that is used to determine the rate of recombination between two genes AB x ab ab ab Parental genotype: The genotypes that match the genotypes of one of the parents AB and a b would be the parental genotypes of the above test cross ab ab Recombinant genotype: The genotypes that do not match the genotypes of either parent, created by crossing over and recombination A b and A b would be the recombinant genotypes of the above test cross ab ab Recombination frequency: The total number of progeny with recombinant genotypes divided by the total number of progeny from the cross Linkage: A description of how closely two genes are physically located Two closely linked genes are very close together on the chromosome and thus a cross over event between them is rare o Physical distance between two genes is directly proportional to recombination frequency, up to a limit of 50% Linkage mapping: The use of recombination frequencies to determine the physical distance between two genes and place genes on a chromosome

Complementation Test (P. 326 for some definitions) Prototrophy: The ability of an organism to synthesize all of the normal organic compounds necessary for growth Prototrophs can grow on minimal media Auxotrophy: The inability of an organism to synthesize one or more organic compounds due to a loss of function mutation Auxotrophs can only grow on minimal media that has been supplemented with the organic compound that the organism can no longer synthesize on its own Minimal medium: A supply of all of the nutrients and organic compounds that a normal organism cant synthesize on its own. Biochemical synthetic pathway: A step-wise pathway in which an organic compound is synthesized through multiple intermediates Complementation test: You cross/fuse two mutant strains that show similar mutant phenotypes (Arg auxotrophy), and see if the WT phenotype results (Arg prototrophy), meaning that the mutations in the strains are in different genes of the Arg synthesis pathway and the two can provide WT copies of the mutant genes for each other Complementation group: The group of mutants that dont complement in a series of complementation tests. The simplest interpretation of a complement group is that all the mutants in the group suffer a mutation in the same gene. Epistasis Test (P. 327, Figure 17.2) Epistasis: The effect where the individual phenotype of one mutation is masked by the phenotype of another Epistasis test: You create a series of doubly mutant organisms and see which of the two mutant phenotypes is manifested. This allows you to determine the order in which these two genes act in the biochemical pathway.

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Recitation 3 Terms! Brian Hua R08/R09 Pedigree Analysis (P. 275-278) Pedigree: A family tree of the phenotypes of the parents and children of a particular disease over two or more generations Affected: An individual in the pedigree that shows a disease phenotype, typically shaded in Carrier: In the case of a disease showing a recessive mode of inheritance, an individual carrying one disease allele and not showing the disease phenotype. Sometimes this is depicted as a halfshaded box if the genotype is known Autosomal recessive: A disease caused by a mutation on a gene on an autosomal chromosome (not X or Y chromosome) such that two mutant alleles are required to show the disease phenotype Autosomal dominant: A disease caused by a mutation on a gene on an autosomal chromosome (not X or Y chromosome) such that only one mutant alleles is required to show the disease phenotype X-linked recessive: A disease caused by a mutation on a gene on the X chromosome such that two mutant alleles are required to show the disease phenotype for females, and only one mutant allele is required to show the disease phenotype in males (males only have one X chromosome) X-linked dominant: A disease caused by a mutation on a gene on the X chromosome such that only one mutant allele is required to show the disease phenotype Chemical Bonds (P. 38-41) Covalent bond: A strong bond where the electrons between two atoms are shared E.g. The hydrogens and the oxygen of water are covalently bonded Ionic bond: An electrostatic interaction where two permanently charged atoms of opposite charge interact E.g. The Na+ and Cl- ions of table salt form an ionic bond Hydrogen bond: An interaction caused by the partial positive charge on a hydrogen atom when it is covalently bond E.g. The hydrogens of water are partially positive due to the electronegative oxygen it is covalently bonded to, making the whole water molecule polar. Distinct water molecules can now interact with each other through hydrogen bonding van der Waals interactions: A very weak interaction between nonpolar atoms caused by minute and transient fluctuations in polarity when the two atoms are at very close proximity

Hydrophobic interaction: A weak interaction between hydrophobic domains in aqueous environments as a result of decreased entropy of the solvent molecules (water)

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Recitation 4 Terms! Brian Hua R08/R09 Lipids (P. 74-77) Lipid: A class of biomolecules that mix poorly with water due to their highly nonpolar and hydrophobic characteristics Fatty acid: A long hydrocarbon chain and a carboxyl group at the end of the molecule Hydrocarbon chain: A long nonpolar chain of hydrogen and carbon atoms, with carbons highly saturated with hydrogen bonds Hydrophobic: The property of not being able to mix well with water. This is due to the fact that water is a very polar substance with uneven distribution of charge, and hydrophobic substances are nonpolar with complete distribution of charge Phospholipid: An important cellular lipid that forms the membranes of cells Made up of two fatty acid chains, a three-carbon glycerol backbone, and a polar headgroup Head group: The polar (and charged) domain of a phospholipid that includes the phosphate atom often includes nitrogen atoms Ester bond: The polar bond that connects the fatty acid tails to the glycerol backbone in a phospholipid Condensation reaction: A chemical reaction in which hydrogen and oxygen atoms are released as water The joining of the fatty acid tails to the glycerol backbone to form the ester bond is an example of a condensation reaction Amphipathic: The characteristic of exhibiting both polar and nonpolar domains on the same molecule A phospholipid is amphipathic because it contains a polar, hydrophilic headgroup and a nonpolar, hydrophobic tail Lipid bilayer: The assembly of phospholipids into a structure in which there are two rows of phospholipids, the fatty acid tails of each row are oriented toward each other, and the headgroups facing away from each other out into the aqueous environment Cell membranes are composed of this lipid bilayer Cell membrane: The physical barrier of a cell that separates the cellular content from the environment Made of a lipid bilayer but includes proteins and other molecules important for transport of material into and out of the cell

Saturated: A characteristic of a fatty acid in which all of the bonds of the carbon atoms are single bonds Unsaturated: A characteristic of a fatty acid in which there is at least one pair of carbon atoms that are connected through a double bond Membrane fluidity: The ability of a the phospholipids in a lipid bilayer to move around Longer fatty acid length decreases membrane fluidity Higher fatty acid saturation decrease membrane fluidity Carbohydrates (P. 69-71) Carbohydrate: A biomolecule that encompasses all of the sugars Monosaccharide: The monomers and building blocks of all sugars Glucose is a monosaccharide that can be used to make disaccharides like fructose and polysaccharides like glycogen and cellulose Glycosidic linkage: The covalent linkage between monosaccharides in a polysaccharide The formation of a glycosidic linkage is condensation reaction Proteins (P.77-83) Protein: The biomolecule that play a wide variety of roles in the cell including catalysis of chemical reactions, signaling between cells, construction of other biomolecules, signaling between and into cells, etc. Amino acid: The monomers and building block of proteins There are 20 common amino acids that are classified into different chemical property groups including polar, nonpolar, charged, etc. Each of the 20 common amino acids shares a common three atom backbone but differ by whats known as the side chain Peptide bond: The covalent bond that links two amino acids together to form a polypeptide (string of two or more amino acids) N-terminus/C-terminus: An amino acid backbone consists of an amino group, a carbon off which the side group comes, and a carboxyl group. The N-terminus refers to the end of a polypeptide in which the terminal amino acid has a free amino group and the C-terminus refers to the end of a polypeptide in which the terminal amino acid has a free carboxyl group Primary structure: The linear chain of amino acids of a protein Secondary structure: Stabilized structures of a polypeptide chain formed by interactions of the polypeptide backbone Alpha helices, beta sheets

Tertiary structure: The overall three-dimensional shape of the protein, stabilized by interactions of the side chains of the amino acids Quaternary structure: The interaction of two or more separate polypeptide chains, forming a functional protein

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Recitation 5 Terms! Brian Hua R08/R09 Nucleic Acids (P. 86-89) Nucleotide base: The building blocks of RNA/DNA consisting of a sugar (ribose), phosphate groups, and a nitrogenous base In DNA, the four different nitrogenous bases are A, T, C, and G In RNA, the four different nitrogenous bases are A, U, C, and G Ribonucleic acid (RNA): A nucleic acid in which the 2-OH group is present on the ribose RNA is an intermediate genetic information carrier in the process of gene expression Deoxyribonucleic acid (DNA): A nucleic acid in which the 2-OH group is absent (hence the deoxy) on the ribose DNA is the stable carrier of all the genetic information needed to create an entire organism Phosphodiester bond: The covalent bond that links two nucleotide bases together in nucleic acids Forms between the 3-OH group of one nucleotide and the 5-phosphate of the other nucleotide The formation of the phosphodiester bond is a condensation reaction Base pairing: Complementary interaction of certain nucleotide bases: In DNA, A pairs with T, and C pairs with G C-G base pairs are stronger than A-T base pairs because C-G base pairs are mediate by three hydrogen bonds while an A-T base pair is mediated by two Double stranded: A property of nucleic acids in which two antiparallel strands of nucleic acids can interact through complementary base pairing Chargaffs rule: An arithmetic property of double stranded DNA that exhibits base paring in which the (% A = % T), (% C = % G), and (% A+ % T + % C + % G = 100%) Therefore, knowing the percentage of any one nucleotide base allows one to determine the percentages of all the other bases Enzymes (P. 152-153, and Figure 8.13 for an exergonic reaction) Enzymes: A protein that acts to speed up a chemical reaction by lowering the activation energy Catalysis: The speeding up of a reaction Thermodynamics Change in free energy (G): The total energy consumed or released in a chemical reaction

Activation energy: The energy that needs to be overcome in order to perform a chemical reaction Enzymes work by lowering the activation energy, and not affecting the change in free energy o Therefore, enzymes drive the chemical reaction MORE QUICKLY to equilibrium, but dont affect the final equilibrium! Exergonic reaction: A chemical reaction in which energy is released The free energy of the products is now lower than that of the reactants Endergonic reaction: A chemical reaction in which energy is required and consumed The free energy of the products is now higher than that of the reactants Equilibrium: The final concentrations of the reactants and products over time of the chemical reaction Enzymes do not affect the actually equilibrium, but rather how fast equilibrium is reached Respiration (Chapter 9, dont memorize the cycles, just the outcomes) Respiration: The breakdown of organic molecules (namely glucose) to create energy that can be used by the cell ATP: The molecule used by the cell to store chemical energy. This is the same molecule that can be incorporated into RNA!! Glucose: The monosaccharide that is broken down to for energy that is stored in ATP for cellular functions Glycolysis: The biochemical process by which glucose is broken down into two pyruvate molecules, thus generating a net of 2 ATPs NAD+ regeneration: NAD+ is an electron and energy carrier throughout respiration and must be regenerated in order for subsequent rounds of glycolysis to occur Anaerobic respiration (fermentation): In the absence of oxygen, NAD+ is regenerated upon the conversion of pyruvate to lactate (in humans) and ethanol/carbon dioxide in yeast Subsequent to glycolysis, no additional ATP is generated Aerobic respiration: In the presence of oxygen, NAD+ is regenerated by the electron transport chain, in which a lot more ATP is generated Electron transport chain: The process in aerobic respiration where the electrons and energy of NAD is converted to a proton gradient which is then used to generate ATP Terminal electron acceptor: The final acceptor of the electrons passed through the electron transport chain for ATP production Oxygen is the terminal electron acceptor!!!

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Recitation 6 Terms! Brian Hua R08/R09 Griffiths Experiment (P. 306, Figure 16.2) Smooth/virulent: The strain of S. pneumoniae bacterium that Griffith injected into mice that showed a smooth morphology This strain was virulent because it killed the mouse Rough/non-virulent: The strain of S. pneumoniae bacterium that Griffith injected into mice that showed a rough morphology This strain was non-virulent because it did not affect the mouse Heat-killed: Inactivated virus by cooking them so that they are no longer virulent Heat-killed smooth strains were not virulent when injected into mice Transformation: The passing on of virulence from one strain to another: When the virulent strain was heat-killed and mixed with the non-virulent strain, the nonvirulent strain transformed into a virulent strain Transforming principle: What the heat-killed passed onto the non-virulent strain, making the non-virulent strain now virulent DNA is the transforming principle! Hershey Chase Experiment (P. 307, Figure 16.4) Bacteriophage (virus): A virus that infects bacteria that injecting a viral substance (viral DNA)
35

S: A radioactive isotope that can be used to label protein P: A radioactive isotope that can be used to label DNA

32

Centrifugation: The separation of components in a mixture by differences in density and solubility 1) Virus DNA was labeled with 32P and Viral protein was labeled with 35S 2) Labeled viruses were allowed to infect bacteria 3) After centrifugation, bacteria were associated with the 32P label, suggesting that the virus injected its DNA and not its protein! Meselson Stahl Experiment (P. 312, Figure 16.11) DNA replication: The event of copying a double stranded DNA Conservative replication: The model in which the new DNA strands form their own new doublestranded DNA

Semi-conservative replication: The model where the old dsDNA split up, and each one is used as template for the new DNA, such that the product of copying is one old and one new strand in each dsDNA Dispersive replication: The model where whole segments of the old dsDNA are incorporated into the new DNA and vice versa.
14

N: The naturally occurring isotope of nitrogen N: The heavier, denser isotope of nitrogen 1) Label all DNA with 15N by culturing bacteria in 15N medium 2) Switch bacteria to 14N medium and allow DNA replication, such that all the newly synthesized DNA has 14N 3) Centrifuge the bacteria to separate DNA by density 4) After one replication cycle, only one band was seen, ruling out the conservative model 5) After two replication cycles, two bands were seen, ruling out the dispersive model

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Recitation 7 Terms! Brian Hua R08/R09 DNA Replication (P. 313-318) Origin of replication: The point on the DNA where the two strands of DNA are initially separated and where DNA replication begins Replication fork: The site of DNA replication The replication fork consists of separating the upcoming DNA and adding the new bases to the new DNA strand There are two replication forks generated from one origin, going in opposite directions DNA helicase: The enzyme that separates the strands of DNA for replication Primase: The enzyme that lays down the first bases (primes) of the new DNA strands DNA polymerase: The enzyme that actually synthesizes the new DNA strands by elongating the primers laid down by primase Synthesis of the new DNA strand is in the 5 3 direction!!! Leading strand: The new DNA strand that is constructed continuously and in the same direction of the movement of the replication fork Lagging strand: The new DNA strand that is constructed discontinuously as it is constructed in the opposite direction of the movement of the replication fork Okazaki fragments: The result of lagging strand synthesis, since replication there is discontinuous. These discontinuous fragments are called Okazaki fragments Ligase: The enzyme that ultimately joins the Okazaki fragments together as well as any two separate DNA fragments Topoisomerase: An enzyme that relieves the topological (twist, coils) stress of the DNA so that DNA replication can proceed. Proofreading: A function of DNA polymerase in which DNA polymerase can edit out a wrong base it has added Also called the 3 5 exonuclease activity as DNA polymerase backtracks to correct errors Transcription (P. 331-334) Transcription: The conversion of DNA information to RNA information

Messenger RNA (mRNA): The RNA corresponds to the DNA of a single gene that will eventually be translated to a final protein product Transfer (tRNA): RNA that serves as an adaptor to recruit the amino acids corresponding to the information given by an mRNA molecule to create a polypeptide in translation Ribosomal RNA (rRNA): The component of the ribosome, the site where the process of translation and protein synthesis occurs RNA polymerase: The enzyme responsible for synthesizing the RNA strand from the DNA template Synthesis of the RNA strand is in the 5 3 direction!!! Promoter: The initial binding site for RNA polymerase located on the DNA upstream of the gene to be transcribed Non-coding strand (transcribed strand): The strand of DNA that is used as a template for transcription Coding strand (non-coding strand): The strand of DNA that is not used as a template for transcription, but exhibits the base sequences that are representative of the base sequences of the synthesized RNA (except U vs. T)

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Recitation 8 Terms! Brian Hua R08/R09 Post-transcriptional Modifications (P. 334-335) Immature mRNA: The freshly synthesized RNA directly after transcription that needs to undergo modification before it can be translated to protein 5 cap: A nucleotide derivative that is added to the 5 end of the immature mRNA for stability and labeling purposes Poly-A tail: A series of 50-250 A bases added to the end of the immature mRNA important in the stability of the mRNA as well as export out of the nucleus and ribosome binding Exon: The ultimately expressed (translated) sequences of the immature mRNA. Intron: The non-expressed sequences of the immature mRNA that are cut out by a process called splicing Splicing: The cutting out of the introns of an immature mRNA and the pasting together of the resulting exons Alternative splicing: The cutting out of the introns of an immature mRNA and the pasting together of different combinations of exons Generates multiple distinct protein products from the same initial mRNA transcript Mature mRNA: The mRNA after it has undergone all the necessary post-transcriptional modifications Ready to be translated Translation (P. 337-341, dont get caught up in the details) Translation: The conversion of the information contained within the mature mRNA to protein Ribosome: The physical machinery that provides the site at which translation occurs The ribosome is made up of rRNA and an wide array of proteins tRNA: The adaptor molecule that reads the mRNA information and converts it to an amino acid message Codon: A group of three bases in the mRNA that is read as a group in translation by tRNA and converted to amino acid information Anticodon: The complementary group of three bases to the mRNA codon that is found on the corresponding tRNA

Genetic code: A table of all of the translations of all of the mRNA codons to the corresponding amino acid recruited by the tRNA Ribosome binding site: An RNA sequence at the 5 end of the mRNA where the ribosome binds The ribosome then scans in the 5 3 direction on the mRNA and looks for the first start codon Start codon: The AUG codon on the mRNA that specifies the start site of translation All proteins then start initially with the amino acid corresponding to the AUG codon Methionine! Stop codon: The codon on the mRNA that specifies the end of translation There are three stop codons These stop codons are read by release factors (RF) and do NOT have corresponding tRNAs Reading frame: The delineation of the three base codons in sequence. If you shifted the reading frame over by one base pair, a new delineation of the three-base groups is now created and a whole new set of information is presented Mutations (P. 345, Figure 17.24) Mutation: A change in the DNA sequence that deviates from what is normal. Mutations can be caused by DNA polymerase mistakes that were not caught, radiation, etc. Silent mutation: A mutation (in the DNA and subsequently in the mRNA) that ultimately does not change the ultimate amino acid sequence of the protein product May occur in an untranslated region May occur in a translated region but changes the normal codon to a codon that still corresponds to the correct amino acid Missense mutation: A mutation (in the DNA and subsequently in the mRNA) that ultimately changes the amino acid that corresponded initially to that codon Nonsense mutation: A mutation (in the DNA and subsequently in the mRNA) that introduces a premature stop codon in the mRNA, thus truncating the ultimate protein product Frameshift mutation: Typically the insertion or deletion of DNA, which ultimately results in the shifting of the reading frame of the codons, which affects all of the downstream codons. Gene Regulation (P. 352-355) lac operon: A form of gene regulation in the bacterium E. coli in which it can express the genes necessary to metabolize the sugar lactose depending on whether lactose metabolism is necessary

lactose: A disaccharide consisting of glucose and galactose. E. coli must digest lactose to free glucose for energy lacZ: The gene encoding the enzyme -galactosidase, the enzyme responsible for digesting lactose and freeing glucose lacY: The gene encoding the permease that is required to all lactose from the environment into the bacterium for metabolism lacA: The gene encoding a transacetylase enzyme of unknown function lac I: The gene encoding the lac repressor/inhibitor, which regulates the expression of the lacZ/lacY/lacA genes Operator: The DNA sequence where the lac repressor/inhibitor binds to inhibit the movement of RNA polymerase and transcription across the lacZ/lacY/lacA genes Induction: The removal of the lac inhibitor/repressor from the operator to allow of the transcription of lacZ/lacY/lacA Induction is promoted in the presence of lactose Lactose binds to the lac inhibitor, causing a conformational change in the lac inhibitor and releasing the lac inhibitor from the operator Constitutive: A condition in which the lac inhibitor cannot bind to the operator (or a lac inhibitor is not produced), such that the expression of lacZ/lacY/lacA occurs all of the time and under no regulation or lactose input Partial diploid: A genetic system in which two copies of the lac operon is present in a bacterium so that the functions of the individual elements of the lac operon can be studied cAMP: A signaling molecule whose levels are decreased in the presence of glucose CAP: A protein that is activated by high cAMP levels (low glucose levels) and promotes RNA polymerase binding to the lac operon and transcript of lacZ/lacY/lacA CAP binding site: The DNA sequence in the lac operon to which CAP binds in the absence of glucose to promote lacZ/lacY/lacA transcription x-gal: A lactose analogue that cannot induce the lac operon but can be cleaved by galactosidase Upon cleavage, the products give a blue color IPTG: A lactose analogue that can induce the lac operon, but can NOT be cleaved by galactosidase

Recitation 9 Terms! Brian Hua R08/R09 Recombinant DNA (P. 396-398) Recombinant DNA: Any molecular biology engineering where the DNA comes from two different organisms Restriction enzyme: An enzyme that can cut double stranded DNA at specific sites Restriction site: Usually a 4-6bp sequence in DNA that is specifically recognized by a particular restriction enzyme and is cut by this enzyme DNA ligase: The enzyme that joins to DNA fragments together Same ligase as used in joining together Okazaki fragments in DNA replication Vector: A piece of DNA that can be taken up by an organism and get replicated by that organism Plasmid: A common type of vector derived from bacteria that normally contain origins of replication as well as antibiotic resistance genes Reporter gene: A gene found on the vector that allows you to select for organisms that took up/have the vector Origin of replication: A sequence of DNA found on the vector that allows the vector to be replicated by the organism that took it up Origins of replication are species specific!! o An E. coli origin is recognized only by E. coli Transformation: The act of introducing a vector into an organism Cloning: The use of organisms, typically bacteria and yeast, to replicate a vector with a DNA fragment of interest, therefore replicating your fragment of interest. Gel Electrophoresis (P. 405-406) DNA gel electrophoresis: A molecular biology tool that can be used to separate different species of DNA fragments within a pool of DNA by size Larger DNA fragments migrates slower through the gel matrix, smaller DNA fragments migrate faster DNA ladder: A mixture of DNA fragments of known size, such that on a gel you have a scale of the DNA fragments sizes for comparison when running samples of unknown DNA fragment sizes

Recitation 10 Terms! Brian Hua R08/R09 Cloning by Complementation (P. 400-401 for making libraries) Cloning by complementation: The use of cloning of an entire genomic library and screening these clones by complementation to identify the gene responsible for a particular auxotrophy (inability to synthesize an organic compound required for life) Genomic library: A collection of vectors with inserted DNA in which the collection of inserted DNA represents the entire genome of the organism that you wish to clone cDNA library: A collection of vectors with inserted cDNA in which the collection of inserted cDNA represents all of the expressed genes of the organism that you wish to clone Complementary DNA (cDNA): DNA made from mRNA by reverse transcription This DNA does not contain any introns or untranslated regions Reverse transcription: The creation of DNA from mRNA. This DNA is called cDNA. Dependent upon the non-human enzyme reverse transcriptase Recombinant plasmid: A plasmid in which a DNA fragment of interest has been successfully inserted by restriction digest and ligation PCR (P. 403-404) Polymerase chain reaction (PCR): A molecular biology tool that can copy DNA fragments of interests at an exponential rate Template: The DNA that harbors the fragment that is to be copied Primers: Short nucleotide polymers that are specific to the end regions of the DNA that is being amplified and serve as starting points for elongation by DNA polymerase Primers are typically 18-22 nucleotides in length to promote specificity and ease of annealing to the template Annealing: The complementary and specific binding of primers to the template Taq polymerase: A heat stable DNA polymerase that is used in PCR since it can withstand the temperatures required to melt DNA stands from each other DNA Sequencing (P. 408) Dideoxyribonucleotide: A ribonucleotide in which both the 2-OH AND the 3-OH groups have been removed, such that no further nucleotides can be added to the end of this nucleotide Also referred to as a chain terminator

Sanger sequencing: A sequencing method in which radiolabeled dideoxynucleotides are used to terminate chain elongation at all the spots of the DNA fragment being sequenced The positions of the radiolabeled dideoxynucleotides can be d determined by gel d electrophoresis, thus giving information as to the sequence of the fragment Primer walk: A strategy used because of the limit of DNA sequencing, in which sequencing is done in overlapping patches and these patches are then compiled together Shotgun sequencing: A strategy used to sequence large stretches of DNA by fragmenting the DNA and cloning them into vectors, sequencing these vectors, and the compiling all of these nd sequences to reconstruct the sequence of the large DNA fragment of interest Modern day (next generation) sequencing: A quick and efficient method of sequencing in which a reversible chain terminator is used, such that the chain can be halted, read for the base, reverse ble the blocker to add the next reversible blocker, read the base, and repeat Can sequence 300 billion bp on a single sequencin chip sequencing

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Recitation 11 Terms! Brian Hua R08/R09 Mapping with SNPs Single nucleotide polymorphism (SNP): A single base-pair difference in a particular sequence when comparing two corresponding sequences of DNA (can compare between two different individuals or the two homologous chromosomes of a single individual) SNPs can be used as markers in the genome, namely markers for unknown genes corresponding to diseases Completely linked: In the case of SNP mapping, the SNP marker and the disease-corresponding gene are completely linked, meaning that the two are essentially adjacent on the DNA. This means that the SNP marker and the disease gene are always inherited together, thus allowing the SNP to serve as a marker or label for the disease gene. SNP allele: When looking at a pedigree, each individual in the pedigree has two particular SNP alleles, (particular SNPs associated with that person). The goal of disease mapping with SNPs is to identify which SNP allele is associated with the gene that is associated with the disease in question. Protein Localization Cell Components: Organelle: A component of the cell that carries out a specialized function. Typically, organelles have their own lipid bilayer membrane inside of the cell (which already has a lipid bilayer membrane) Nucleus: The cellular organelle that holds all of the genomic DNA. This is the site of DNA replication and transcription. Endoplasmic reticulum (ER): The cellular organelle that processes secretory proteins and membrane proteins, namely folding these proteins and modifying these proteins (e.g. adding sugars) ER lumen: The inner space of the ER organelle. Golgi apparatus: The cellular organelle that sorts similar secretory/membrane proteins coming from the ER and prepares them for transport to the cell membrane. Cytosol: The space in the cell not contained by any organelle in particular (basically the space between organelles). This is the initial site of translation for all proteins

Types of Proteins: Cytosolic protein: A protein that remains and functions in the cytosol Glycolysis enzymes, often nutrient biosynthesis pathway enzymes, etc. Nuclear protein: A protein that is found and functions normally in the nucleus DNA polymerase, RNA polymerase, DNA ligase, topoisomerase, etc. Secretory (secreted) protein: A protein that is secreted from the cell and functions somewhere outside of the cell where it was synthesized Hormones, antibodies, structural proteins, etc. Membrane protein: A protein that functions at and is embedded in the cell membrane Insulin receptor, adrenaline receptor, ion channels, etc. Transmembrane protein: A membrane protein that completely passes through the cell membrane, such that there is an intracellular domain, a transmembrane domain, and an extracellular domain. Transmembrane domain: The section of a transmembrane protein that is actually embedded in the cell membrane and interacting with the fatty acid tails of the phospholipids of the membrane Transmembrane domains of transmembrane proteins often consist of many hydrophobic amino acids (to interact with the hydrophobic cell membrane fatty acid components Types of Localization Signals: Nuclear localization signal: The amino acid signal on nuclear proteins that is required for localization to the nucleus Signal peptide (or signal sequence): The amino acid signal on secretory and membrane proteins that is required for localization to the ER. Stop transfer sequence: The amino acid signal on membrane proteins that is required for embedding into the membrane of the ER and eventually the cell membrane. Protein Translocation (moving certain proteins from the cytosol to the ER): Signal recognition particle (SRP): A cytoplasmic protein that recognizes and binds to the signal peptide of nascent secretory and membrane proteins and is required for localization of the protein to the ER. SRP receptor: A membrane protein located on the ER membrane that binds SRP and physically links the nascent secretory or membrane to the ER surface. Translocon: The channel by which nascent secretory and membrane proteins are pushed through the ER membrane from the cytosol to the ER lumen.

Dr. G. Weaver, Colorado University at Denver

Molecular Biology of the Cell. 4th edition. Alberts B, Johnson A, Lewis J, et al. New York: Garland Science; 2002.

Recitation 12 Terms! Brian Hua R08/R09 Cell Signaling Cell signaling: A series of cellular events in which a signal from the environment is relayed throughout the responsive cell that leads ultimately to some adaptive response. For example: the adrenaline cell signaling pathway: When you are frightened, adrenaline is released into the blood stream. The cells in the heart muscle sense the adrenaline, and through a series of cellular events, respond to the adrenaline by increasing heart rate Receptor: A cellular protein that physically interacts with the environmental (outside of the cell, or extracellular) signal and then relays the signal to within the cell. For example: the adrenaline receptor is a transmembrane protein in heart muscle cells that can bind adrenaline molecules and relay the signal to increase heart rate. Ligand: The environmental signal that interacts with the receptor. Adrenaline would be the ligand for the adrenaline receptor Autocrine signaling: A form of short distance signaling in which a cell produces the ligand which binds to a receptor on the same cell Paracrine signaling: A form of neighbor signaling in which a cell produces the ligand which binds to a receptor on a neighboring cell Endocrine signaling: A form of long distance signaling in which a cell produces the ligand which is secreted into the blood stream and binds to a receptor on a cell that may be in a totally different part of the body/organism G protein: The first signal relayer in G-protein linked receptor signaling. In the absence of adrenaline, there is no ligand bound to the adrenaline receptor and the adrenaline receptor cannot activate the G-protein so there is no transduction of the signal. If adrenaline is present, the adrenaline receptor binds adrenaline and then activates the G-protein, which then relays the signal. o Inactive G-protein=GDP bound form o Active G-protein=GTP bound form Signal cascade: The relay of an environmental signal down a cellular pathway that involves the subsequent activation of many proteins, such that the signal is amplified in the cell. Viruses Protein coat (capsid): A necessary structural component of all viruses that is made of protein and carries within it the viral genome

Envelope: A lipid bilayer that surrounds the viral capsid. Virus can be enveloped (lipid bilayer present) or naked (no lipid bilayer present) Enveloped viruses o Can fuse membranes with the host cell o When releasing newly synthesized viruses, can pinch off membrane of host cell to form new viral envelopes, leaving the host cell relatively unharmed Naked viruses o Must inject viral genome into host cell o When releasing newly synthesized viruses, must break open the host cell. Lysis: Rupturing or breaking open of a cell Naked viruses must lyse the host cell to release all the newly synthesized viruses Plus-stranded RNA: RNA that essentially serves as the viral mRNA Can be immediately translated by the host ribosome upon infection of the host cell Minus-stranded RNA: RNA that is complementary to the viral mRNA Must be converted to plus-stranded RNA before it can be translated by the host ribosome DNA-dependent RNA polymerase (DdRP): Our normal RNA polymerase in transcription. DNA-dependent means it uses DNA as a template and makes an RNA strand from it (normal transcription) RNA-dependent RNA polymerase (RdRP): A viral polymerase that uses RNA as a template (as opposed to DNA) to make a complementary RNA strand. RNA viruses must encode for or bring their own RdRP in order to replicate their genomes, with the exception of retroviruses Retroviruses: RNA viruses that convert their RNA genomes to double-stranded DNA (through reverse transcriptase) so that they can integrate their viral genomes into the host cell genome. For example: HIV is a plus-stranded RNA virus that upon infection of a particular human immune cell (T cells), converts its RNA genome into a double-stranded DNA genome and inserts its genome into the T cell genome. The viral genomic insertion can then undergo normal transcription and translation to create new virus. Reverse transcriptase: A viral enzyme found mainly in retroviruses that can use RNA as a template to make DNA (converts single-stranded RNA to double stranded DNA).

Recitation 13 Terms! Brian Hua R08/R09 Cancer Genes Pp. 373-374 Cancer: A disease characterized by uncontrolled cell growth. Cells grow and divide without regulation, often causing tumors. Tumor: A mass of cells, usually derived from a single transformed cancerous cell that has undergone numerous and uncontrolled divisions. Tumor suppressor gene: A gene in the cell that normally inhibits cell cycle progression/cell division when cell division is inappropriate A cell can turn cancerous if both copies of a particular tumor suppressor gene lose function (loss of function mutation). Cancers caused by mutant tumor suppressor genes exhibit genetically recessive phenotypes Proto-oncogene: A gene in the cell that normally promotes cell cycle progression/cell division when cell division is appropriate A cell can turn cancerous if just one copy of a particular proto-oncogene is mutated and given the new property of having constitutive activity (gain-of-function mutation) Oncogene: The mutated form of a proto-oncogene characterized by uncontrolled cell division/growth. Rous Sarcoma Virus (RSV) Rous Sarcoma Virus (RSV): A chicken virus that has the ability to transform normal chicken cells into cancerous and tumor-causing cells. RSV is a retrovirus. It harbors a positive-sense single-stranded RNA genome, that gets converted to dsDNA by reverse transcriptase, and the dsDNA viral genome is incorporated into the dsDNA chicken genome Sarcoma: A cancer that is found in these particular tissues - bone, cartilage, fat, muscle, and blood. c-src: Cellular-src. A normal cellular proto-oncogene that encodes a protein that normally promotes cell division when cell division is appropriate. v-src:Viral-src. The oncogenic form of c-src that is carried by RSV. v-src is a deletion mutant of c-src v-src is missing a portion of the c-terminus of c-src When RSV infects a chicken cell, the v-src copy is integrated into the chicken cellular DNA. The chicken cell now has two copies of c-src as usual, but now also a copy of v-src. Since v-src is oncogenic, src has now gained a new function (constitutive activity), and the infected cell is now cancerous.

Retinoblastoma Retinoblastoma: Cancer of the retina (the light-sensing tissue of the eye) Germline mutation: A mutation that is found in the sperm of a male or egg of a female and can be passed on to that individuals offspring Inherited genotype: Genotype of an individual in which mutations (if any) were already present on the chromosomes inherited from the parents (germline mutations) An inherited genotype of Rb+/Rb- means that one of the parents passed on the Rb- allele to the child. An inherited genotype of Rb-/Rb- is lethal (individual would be aborted before birth). Therefore, no living individual can have the inherited genotype of Rb-/RbSomatic mutation: A mutation that happens at the cellular level, in which a single autosomal and isolated cell (non-germline) suffers a mutation by chance (perhaps from DNA replication infidelity, UV irradiation, etc.) A somatic mutation is not in the germline cells, therefore a somatic mutation is NOT passed on to progeny (as opposed to a germline mutation) For an individual with inherited genotype Rb+/Rb-, a single cell in the retina may undergo a somatic mutation in the Rb+ allele at some point in life o This single cell is now Rb-/Rb- and would now be cancerous and form a tumor Sporadic Rb: Case of Rb where cancer emerges in an individual where no history of Rb in the family tree is present. This is rare. Typically, individuals in a pedigree exhibiting sporadic Rb have inherited genotypes of Rb+/Rb+. Therefore, in order to develop a tumor in the retina, a single retinal cell must undergo TWO somatic mutations in Rb, which is rare. Familial Rb: Case of Rb where multiple individuals in a family show the Rb cancer phenotype (have retinal cancer). Individuals in a family exhibiting familiar Rb typically have inherited genotypes of Rb+/Rb-. Therefore, in order to develop a tumor in the retina, a single retinal cell must undergo only ONE somatic mutation (in the only functional copy of Rb), which is much more likely than two somatic mutations in the same cell.

Recitation 14 Terms! Brian Hua R08/R09 Cancer Therapies Onco-protein: The cancer-promoting form of a protein Encoded by the oncogene, as opposed to the proto-oncogene Antibodies: Small proteins that normally play essential roles in the immune system by targeting pathogens and foreign materials Each antibody exhibits a high level of specificity for its particular target o This specificity can be used to target specific onco-proteins in the treatment of cancer. Gene therapy: A genetic strategy to treat disease by physically deleting a gene (for example, an oncogene), replacing a defective gene in the genome with a functional copy, etc. Gene therapy has proven extremely difficult for two reasons: 1) Hard to specifically target a single gene in the genome without affecting other genes 2) Hard to make stable changes to the genome that will propagate through all subsequent cell divisions Breast Cancer HER2/Neu: Human EGF Receptor 2. HER2 is a growth factor receptor found on the surface of cells, namely cells in the breast tissue. When growth factors bind HER2, HER2 initiates a cell signaling pathway that ultimately promotes cell division o This pathway is analogous to the EGF pathway from Question 1 on Recitation 12 Handout HER2 is overexpressed in breast cancer cells, thus rendering these cells ultrasensitive to growth factor signaling, and thus resulting in extremely heightened signals for cell division > Cancer Herceptin: An antibody that specifically targets and inhibits global HER2 Used to treat breast cancer by decreasing the ultrasensitivity of breast cancer cells to growth factor induced cell division Herceptin targets and inhibits HER2 on normal cells as well, which can actually harm the normal function of non-cancerous cells! Therapeutic window: A level of drug administration such that you maximize the inhibition of cancer cells while minimizing the harmful impact on normal, non-cancerous cells.

http://www.roche.com/pages/facets/9/herc.htm CML Chronic myelogenous leukemia (CML): Cancer of the white blood cells. Translocation: A swapping of portions of two different (non-homologous) chromosomes Philadelphia chromosome: The particular chromosome resulting from a translocation that is responsible for CML. The translocation occurs between chromosomes 9 and 22 The Philadelphia chromosome is the smaller of the two translocated chromosomes ABL: The gene that lies normally on chromosome 9 that after the translocation event with chromosome 22 encodes an onco-protein with constitutive activity Normal ABL encodes a tyrosine kinase protein, analogous to c-src o ABL is a proto-oncogene, and normally promotes cell division in a controlled manner BCR: The gene that lies normally on chromosome 22 and gets positioned adjacent to ABL on chromosome 9 after the translocation event. ABL-BCR fusion protein: After the translocation event, the chromosome 9 ABL gene and the chromosome 22 BCR gene are positioned next to and in frame with each other. This gene fusion encodes for the ABL-BCR fusion protein The ABL-BCL fusion protein exhibits constitutive ABL activity o Constitutive promotion of cell division Cancer!

Gleevec: The greatly effective cancer drug compound that specifically targets and inhibits the activity of the ABL-BCR fusion protein, thus treating CML.

http://www.carolynshope.com/About_CML.html

Recitation 15 Terms! (A lot this time, apologies!) Brian Hua R08/R09 Readings given for Reese Biology 8th Edition The Neuron (Pg. 1048 second column, Pg. 1049 first figure) Neuron (nerve cell): A specialized cell that processes electrical signals and relays them to different parts in the body. Neurons make up a signaling highway throughout the entire body, and can relay the messages needed for movement, touch, smell, sight, hearing, taste, etc. Dendrites: The highly branched section at the head of the neuron which serves as sensors/receptors for environmental or upstream signals. The receptor section of the neuron Cell body: The segment of the neuron that is most circular and cell looking Defined by the presence of the nucleus The cell body does NOT exhibit action potentials Axon: The slender region of the neuron in which action potentials (electrical signals) are propagated through the neuron. Axon hillock: The very beginning portion of the axon in which action potentials initiate in the neuron and then propagate down the axon. Nerve terminus: The tail end of the neuron in which the electrical signal is relayed to the next neuron or final signal receptor (effector). Synapse: The actual event of relaying the electrical signal (action potential) from one neuron to the next or from one neuron to the final signal receptor (effector). Effector: Usually a muscle cell, a hormone gland, or organ that serves as the final signal receptor and interprets this signal as an instruction to contract (muscle cell), release a hormone (gland), etc. Resting Potential (Pg. 1050-1051) Ion: An atom that carries a permanent charge. Common ions involved in the membrane potential are Na+, K+, Ca2+ Ion channel: A transmembrane protein that selectively allows ions to cross the plasma membrane (lipid bilayer) Ion pump: A transmembrane protein that uses ATP energy to move a specific ion across the plasma membrane Typically when moving ions AGAINST their concentration/electrochemical gradient

Concentration gradient: When an uneven distribution of a particular ion exists across the plasma membrane, this ion typically wants to equalize its concentrations on either side of the membrane If the ion moving against this tendency (building the concentration difference), it is going UP/AGAINST its concentration gradient If the ion moving along with this tendency (decreasing the concentration difference), it is going DOWN its concentration gradient Electrochemical gradient: When an uneven distribution of charge exists across the plasma membrane, ions typically want to equalize the overall charge on either side of the membrane If the ion moving against this tendency (building the charge difference), it is going UP/AGAINST the electrochemical gradient If the ion moving along with this tendency (decreasing the charge difference), it is going DOWN the electrochemical gradient Na+/K+ ATPase (pump): A transmembrane protein that uses ATP energy to pump 3 Na+ ions out of the neuron (against its concentration gradient) and 2 K+ ions into the neuron (also against its concentration gradient) Ca2+ ATPase (pump): A transmembrane protein that uses ATP energy to pump Ca2+ ions out of the neuron (against its concentration gradient) K+ channel: A transmembrane protein that allows K+ ions to flow freely into and out of the neuron. Membrane potential: The difference of the voltage inside of the neuron and the voltage outside of the neuron Resting Potential: The membrane potential of the neuron at rest. -70 mV o Inside of the neuron is negatively charged relative to the outside Established by the equilibrium between the electrochemical and concentration gradients of Na+, K+, and Ca2+ Action Potential (Pg. 1052-1054) Threshold potential: The membrane potential at which an action potential is activated Action potential: A large and drastic change in the membrane potential of the neuron that serves as a binary electrochemical signal. The action potential is relayed down the axon and ultimately to the next neuron or the effector Voltage-gated Na+ Channel: A transmembrane protein that normally is closed (does not allow passage of Na+ ions, but at -50mV will open and allow Na+ ions to flow down its concentration gradient (into the neuron) Causes depolarization of the neuron

Voltage-gated K+ Channel: A transmembrane protein that normally is closed (does not allow passage of K+ ions, but at around +30mV will open and allow K+ ions to flow down its concentration gradient (out of the neuron) Causes repolarization of the neuron Depolarization: Movement of the membrane potential from resting (-70mV) toward 0mV Caused by the activation of voltage-gated Na+ channels Repolarization: After depolarization, movement of the membrane potential back to the resting potential of -70mV. Dependent upon the activation of voltage-gated K+ channels Hyperpolarization: During repolarization, the overshooting of the membrane potential past the initial resting potential of -70mV Refractory Period: The length of time in which an action potential cannot be fired again from the same position on the axon This way action potentials are propagated only in a single direction and not backwards Propagation (Pg. 1055-1056) Myelin sheath: A fatty layer that surrounds segments of the axon Insulates the wrapped axon and does not allow action potentials to occur at these positions Action potentials must skip over the segments of myelin sheath insulation to propagate down the axon, which in fact speeds up signal propagation Node (of Ranvier): Openings in the myelin sheath in which the axon is exposed and can exhibit action potentials Action potentials skip from node to node, allowing for fast propagation of the signal down the axon

http://humanphisiology.wikispaces.com/file/view/neuron.png/216460814/neuron.png

http://faculty.washington.edu/chudler/ap.html

http://tle.westone.wa.gov.au/

Recitation 16 Terms! Brian Hua R08/R09 (Readings are for Reeses Biology 8th Edition) The Synapse (Pg. 1057-1058) Synapse: The signaling of one neuron to another (or one neuron to a cell, for example a muscle cell). An action potential in the upstream neuron is converted into a chemical signal, the downstream neuron senses the chemical signal and exhibits a change in membrane potential Pre-synaptic neuron: The upstream neuron that relays its signal to the next neuron Post-synaptic neuron: The downstream neuron that receives the signal from the pre-synaptic neuron Synaptic cleft: The space between the pre-synaptic and post-synaptic neuron in which the synapse occurs Neurotransmitter: A chemical molecule that upon the appropriate signal is released from the presynaptic neuron into the synaptic cleft, and binds to its receptor on the dendrites of the postsynaptic neuron, causing a change in the post-synaptic neurons membrane potential Synaptic vesicle: The small circular membrane vehicle in the pre-synaptic neuron that contains the neurotransmitter Synaptic vesicle fusion: The event where the vesicle in the pre-synaptic neuron that holds the neurotransmitter fuses with the membrane of the nerve terminus of the pre-synaptic neuron, thus releasing the neurotransmitter into the synaptic cleft Synapsin: A protein found in the nerve terminus of the pre-synaptic neuron that inhibits synaptic vesicle fusion in the relaxed state of the neuron Voltage-gated Ca2+ channel: An ion channel in the nerve terminus of the pre-synaptic neuron that is activated once the action potential coming down the pre-synaptic neuron reaches the end of the axon. The channel allows Ca2+ to flow down its concentration gradient Since Ca2+ levels are high outside the neuron, Ca2+ ions will rush into the pre-synaptic neuron when the channel is activated Ca2+-dependent protein kinase: A protein found in the nerve terminus of the pre-synaptic neuron that is activated upon Ca2+ influx into the nerve terminus. This tyrosine kinase phosphorylates (adds a phosphate group) to synapsin, which inactivates synapsin so that the synaptic vesicle can now fuse with the nerve terminus membrane, releasing the neurotransmitter in to the synaptic cleft

Excitatory Neurons (Pg. 1058) Excitatory neuron: A pre-synaptic neuron that relays a signal such that the post-synaptic neuron experiences a membrane potential shift toward the threshold potential (gets more positive), often resulting in the post-synaptic neuron action potential. Acetylcholine (ACh): A classic excitatory neurotransmitter used specifically in nerve-muscle cell synapses. Ligand-gated Na+ channel: A Na+ channel located on the dendrites of the post-synaptic neuron that is activated upon binding of the neurotransmitter For example: The pre-synaptic neuron experiences an action potential, causing it to ultimately release ACh into the synaptic cleft Ach binds to its receptor on the postsynaptic neuron (this receptor is a ligand-gated Na+ channel) Na+ flows down its concentration gradient and rushes into the post-synaptic neuron Na+ influx causes the inside of the post-synaptic neuron to become more positive the membrane potential of the post-synaptic neuron increases toward the threshold potential Acetylcholineesterase (AChE): When the synapse has occurred, AChE degrades ACh so that the neurotransmitter signal is stopped If ACh is not degraded, there will be constitutive excitation of the post-synaptic neuron, which could cause paralysis Inhibitory Neurons (Pg. 1058) Inhibitory neuron: A pre-synaptic neuron that relays a signal such that the post-synaptic neuron experiences a membrane potential shift away from the threshold potential (gets more negative), often resulting in the inhibition of a post-synaptic neuron action potential. Gamma-amino butyric acid (GABA): A classic inhibitory neurotransmitter used in the central nervous system (nerve-to-nerve signaling) Ligand-gated Cl- channel: A Cl- channel located on the dendrites of the post-synaptic neuron that is activated upon binding of the neurotransmitter For example: The pre-synaptic neuron experiences an action potential, causing it to ultimately release GABA into the synaptic cleft GABA binds to its receptor on the post-synaptic neuron (this receptor is a ligand-gated Cl- channel) Cl- flows down its concentration gradient and rushes into the post-synaptic neuron Cl- influx causes the inside of the post-synaptic neuron to become more negative the membrane potential of the post-synaptic neuron decrease, away from the threshold potential more difficult to have action potential in the post-synaptic neuron

Summation of Multiple Input Signals (Pg. 1058) Summation: The addition of the excitatory and inhibitory signals of multiple pre-synaptic neurons acting on the same post-synaptic neuron These signals can occur at different times, simultaneously, and in different combinations The signals are additive o Two excitatory signals results in a big excitatory signal o An excitatory signal and a inhibitory signal can cancel each other out Often for an action potential to be generated in the post-synaptic cell, two or more excitatory signals must be summed to reach the threshold potential.

http://click4biology.info/c4b/6/images/6.5/synapse.gif

Reese BIOLOGY 8th edition

Recitation 18(17) Terms! Brian Hua R08/R09 Stem Cells (P. 415) Stem cell: An unspecialized cell that can renew itself indefinitely and can give rise to one of more specialized cell types through differentiating Asymmetric division: The characteristic division of a stem cell in which after mitosis, the two daughter cells are not both identical to the mother cell. This Results in a daughter cell identical to the mother cell (self-renewal) and a daughter cell that has acquired more tissue specific characteristics (differentiation) Self-renewal: The ability of a stem cell to divide and reproduce itself without having lost any potency. Differentiation: The ability of a stem cell to acquire tissue-specific, specialized characteristics. This differentiation results in a change in gene expression Lineage: All the cells that are derived from a single stem cell Potency Potency: Degree in the ability of a stem cell to give rise to more differentiated cells Totipotent: Can give rise to all the cells needed in the organism as well as all of the cells of the placenta E.g. The zygotes (fused sperm and egg) is a totipotent cell Pluripotent: Can give rise to all of the cells needed in the organism E.g. The cells of the blastocyst/embryo Multipotent: Can give rise to all the cells of a certain (or a few) cell lineages E.g. Hematopoietic stem cells can give rise to all the different blood cell types Oligopotent: Can give rise to a few cell types Bipotent/Unipotent: Can give rise to two or one cell types, respectively Terminally differentiated: A cell type that is no longer able to differentiate any further, and exhibits no potency Typically also is no longer a dividing cell E.g. Neuron Progenitor: A cell that is more differentiated than a stem cell as it has committed to a certain level, for example it has committed to a single tissue lineage

Intestinal Stem Cells Intestinal stem cell (intestine/gut are synonymous): Stem cells that reside in the crypt of the intestinal wall that give rise to the specialized cells lining the intestinal wall Villus: Finger-like projections from the intestinal wall that increase the surface area of the intestine for more nutrient absorption Crypt: A chamber in the intestinal wall that houses the intestinal stem cells and is where all the specialized cells lining the intestinal wall originate Adenomatous polyposis coli: A cancer caused by the mutations in the APC tumor suppressor gene. APC is involved in the migration of the differentiating and differentiated intestinal cells out of the crypt APC-/- intestinal cells results in a clumping of these intestinal cells at the top of the crypt called a polyp Polyp: The clump of cells that result from impaired migration caused by APC mutation This polyp contains stagnant intestinal cells that are being exposed to harsh digestive materials that may cause mutations. Since these cells cannot migrate, these mutations accumulate and eventually lead to intestinal cancer. Identification of Stem Cells Pulse-chase labeling: A way to assess the loss of fluorescence over time For example, label all cells with a pulse of fluorescent DNA such that all cells incorporate the fluorescence (pulse). Now flush the cells with non-fluorescent DNA so that any new DNA incorporation is non-fluorescent Assess the rate of loss of fluorescence o Stem cells, which divide slower than more differentiated cells, will retain the fluorescent signal longer Stem cell markers: Typically, receptors that are expressed only on stem cells and are lost in more differentiated cells These receptors can serve as ID markers for stem cells Verifying Stem Cells (P. 414, figure 20.19) Chimera: An organism that is actually made up of two populations of different cells For example, mixing the embryonic stem cells of two separate embryos (1 and 2) will result in the development of a chimeric organism that has tissues made of distinct cells derived from embryo 1 and embryo 2.

Organismal cloning: The act of making entire animals from single cells of a particular identity E.g. If the nucleus of a differentiated cell from an adult organism is injected into an enucleated (nucleus removed) egg, the egg will develop into an organism with the same genetic makeup of the injected nucleus The nucleus of any cell (even terminally differentiated cells) carries all of the information needed to make an entire organism o Some nuclei undergo DNA information loss, in which case it may not be able to be used to clone an organism Stem Cell Therapy (P. 416) Embryonic stem (ES) cell: Stem cells that have the ability to give rise to all of the cells in the organism. This can prove useful in therapy in a case where a certain tissue may have degenerated, it can be reconstituted by ES cells This is highly controversial because it requires the use and destruction of embryos Induced pluripotent stem cell (iPSC): A differentiated cell that has been reprogrammed (or undifferentiated, if you will) back to pluripotency. This does not require the destruction of an embryo Tissue rejection is also not an issue because the cell that was induced back to pluripotency is from the patient!

Recitation 19 Terms! Brian Hua R08/R09 General Immune Responses (P. 929-930, Figure 43.2) Pathogen: Any foreign substance that causes disease in the body Can be a bacterium, virus, fungus, etc. Innate immunity: The first line of defense against pathogens in the environment and upon the identification of any foreign substance that has made it into the body All pathogens are targeted (non-specific) Skin and mucous are physical barriers in the innate immune system Phagocytosis of pathogens Fast response Acquired (adaptive) immunity: Specific targeting of a pathogen and creation of memory of this particular pathogen Consists of the humoral and cell-mediated responses Slow response upon first exposure, fast response upon second exposure to particular pathogen Humoral response: Specific targeting of a pathogen in which peptides called antibodies are secreted in the blood stream to neutralize pathogens directly Cell-mediated response: Specific targeting of body cells that have been infected by a particular pathogen Phagocytosis: Ingestion and digestion of a pathogen Macrophages, dendritic cells, etc are specialized immune cells (phagocytes) that ingest pathogens as part of the innate response, and also present them for specific recognition in the acquired response Antigen: Any substance that elicits an immune response in the acquired immune response Often, it is a protein fragment from the pathogen that resulted from phagocytosis Antigen presentation: Localization of the antigen to the surface of the antigen-presenting cell so that it can be recognized by B and T cells The antigen presenting cells are macrophages, dendritic cells, and B lymphocytes! MHC Class I: A cell surface receptor that is responsible for the presentation of the antigen on an infected cell MHC Class I is present on all nucleated cells MHC Class I is also crucial for recognition of self from non-self, as the MHC Class I receptor is specific to one individual.

MHC Class II: A cell surface receptor that is responsible for the presentation of the antigen after the pathogen has been phagocytosed and digested. Cell-mediated Response (P. 940-941) T-cell lymphocyte: The progenitor to both helper T-cells and cytotoxic T-cells, which expresses a specific T-cell receptor T-cell receptor: An antigen receptor that is present on T-cells that imparts T-cell specificity to a particular pathogen Helper T-cell (TH): A T-cell that first recognizes the antigen presented on the MHC Class II of a macrophage/dendritic cell and then activates the effector cells of that immune response In the cell-mediated response, TH sees the presented antigen on the macrophage/dendritic cell and then activates its corresponding cytotoxic T-cell In the humoral response, TH sees the presented antigen on the macrophage/dendritic cell and then activates its corresponding B-cell lymphocyte Cytotoxic T-cell (TC): A T-cell that is activated by its corresponding TH cell and then secretes factors to kill cells infected by that particular pathogen. Cytokine: An activating molecule that the TH secretes and uses to activate its complementary TC (as well as its complementary B-cell lymphocyte in the humoral response) Memory helper T-cell: A T-cell lymphocyte that is created after TH activation and set aside in case a secondary exposure to the particular pathogen arises, a fast response can be mounted Memory cytotoxic T-cell: A T-cell lymphocyte that is created after TH activation and set aside in case a secondary exposure to the particular pathogen arises, a fast response of killing infected cells can be mounted Humoral Response (P. 942-944) B-cell lymphocyte: The progenitor to the plasma cell, the cell that ultimately makes and secretes the antibodies Upon activation by its corresponding TH cell, the B-cell lymphocyte undergoes differentiation to give plasma cells as well as memory B-cells B-cell antigen receptor: An antigen receptor that is present of B-cell lymphocytes (mature Bcells) that imparts B-cell specificity to a specific antigen Plasma cell: A terminally differentiated B-cell that solely manufactures soluble antibodies and secretes them into the blood for circulation Antibody (immunoglobulin): A protein that is specific to a particular pathogen and helps to neutralize and contain the pathogen

Neutralization: Binding of antibodies to a pathogen such that the pathogen is inhibited from normal pathogenic functions Opsonization: Binding of antibodies to a pathogen to mark the pathogen for degradation by macrophages/dendritic cells Memory B-cell: A B-cell lymphocyte that is created after TH cell activation and set aside in case a secondary exposure to the particular pathogen arises, a fast response of plasma cell creation and antibody secretion can be mounted Antigen Recognition (P. 935-938) Antigen receptor: For example, the T-cell Receptor (TCR) and the B-cell antigen receptor. Imparts the specificity of a particular antigen to the B-cell and T-cell A B-cell antigen receptor is made up of two heavy chains and two light chains, and each of these chains have variable and constant regions Heavy chain: The large protein chain in the B-cell receptor/antibody Light chain: The small protein chain in the B-cell receptor/antibody Variable region: The domain of the heavy or light chain of the antigen receptor/antibody that varies greatly between lymphocytes, allowing the diversity of lymphocytes to recognize a wide array of pathogens Constant region: the domain of the heavy or light chain of the antigen receptor/antibody that is shared among 5 classes of antigen receptor/antibody across all lymphocytes Antigen binding site: The interface made by the heavy and light chains at which the antigen binds In the B-cell receptor/antibody, there are two antigen binding sites In the TCR, there is only one antigen binding site V(D)J recombination: DNA recombination of the immunoglobulin gene in which different segments of the DNA corresponding to the variable region of the immunoglobulin (light or heavy chains) are randomly deleted and the remaining segments pasted together to form the final immunoglobulin gene Allows for the generation of the diversity seen in the immunoglobulins seen across all lymphocytes Occurs at the DNA level, in which DNA information is cut out and lost! Class switching: Variation of the constant region of the immunoglobulin. E.g. In the mature B-cell lymphocyte, the B-cell antigen receptor immunoglobulin is of class type IgM, as it sits in the membrane of the lymphocyte. However, in the

corresponding plasma cell, this immunoglobulin is switched to class type IgG, which is a soluble class of the immunoglobulin and can be secreted in the blood Human Immunodeficiency Virus (HIV) (P. 949-950) Human Immunodeficiency virus (HIV): An RNA retrovirus that targets specifically the TH cells of humans by interacting with the TH cell CD4 adaptor protein Acquired Immunodeficiency Syndrome (AIDS): The disease caused by HIV in which the TH cells of infected individuals fall below a certain critical value and the infected individual has a very crippled immune response CD4: An adaptor protein found on TH cells that is specifically targeted by HIV and is required for HIV internalization CD4 normally serves to reinforce the interaction of the TCR on TH cells and the MHC Class II receptor on an antigen presenting cell Latency: A period after infection in which HIV lies dormant within the TH cell and does not replicate, waiting for an opportune time to begin proliferation such as the infection of the individual with another pathogen.

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Recitation 20 Terms! Brian Hua R08/R09 Familial Hypercholesterolemia Cholesterol: A large hydrophobic organic molecule that plays an important role in cell membrane integrity but can also form buildups in the blood vessels causing dangerous impediments to blood circulation Plaque: A buildup of cholesterol crystals and dead cells in the blood vessel wall, which can impede blood circulation Atherosclerosis: A thickening of the blood vessel wall in response to plaques, further restricting blood circulation A heart attack can result if a blood vessel leading to the heart is blocked A stroke can result if a blood vessel leading to the brain is blocked HMG CoA reductase: A metabolic enzyme required in the synthesis of cholesterol in cells Low density lipoprotein (LDL): A packaged particle of cholesterol esters surrounded by a lipid monolayer that is used to transport cholesterol in the blood LDL receptor: A transmembrane protein receptor found notably on the liver cells that allows for the uptake of LDLs and hence cholesterol out of the blood stream, lowering blood cholesterol Familial hypercholesterolemia: A disease resulting the inability to take cholesterol out of the blood stream into the liver Typically a mutation in the LDL receptor gene that shows an incompletely dominant phenotype Gene therapy: A genetic therapeutic strategy to introduce ectopic genes into a diseased individual In familial hypercholesterolemia, gene therapy aims to introduce a WT copy of the LDL receptor gene so that functional LDL receptor can be expressed and LDL can be taken up by the liver and out of the blood Typically done by viral introduction of the WT gene Molecular Evolution Phylogeny: How biological organism are related to each other in the context of evolution Divergence: The events of the drifting two similar species to become more differentiated and unique

Evolutionary tree: A diagram tracing the phylogeny of organism, depicting the most related organism, as well as the points in time when divergence occurred and the ancestors of each organism 16S/18S ribosomal sequence: Genes that are common in all organisms across life that can be used to track evolution and divergence among organisms Mitochondrial DNA (mDNA): DNA that is passed on only by mothers that serves as a medium to trace the evolution and divergence of humans within a population Y-chromosome: DNA that is passed on from father to son that serves as a medium to trace the migration of males with a human population Microarrays Microarray: A biological technique used to assess the gene expression profile of particular cell types, tissues, or individuals Can be used to characterize different forms of cancers, as well as different levels of severity within the same cancer Directly measures mRNA levels, which is a direct readout of gene expression

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