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Select All matter any substance in the universe that has mass and occupies space atoms small particles that make up all matter electrons negatively charged subatomic particles that are transferred and shared between atoms ion a charged particle acid any substance that dissociates in water to increase the concentration of H+ ions; pH values of acids are from 1-7 base any substance that combines with H+ ions when dissolved in water; pH values from 7-14 oxidation the loss of an electron reduction the gain of an electron molecules groups of atoms held together by energy in a stable association chemical bond joins atoms in a molecule ionic bond attraction between ions of opposite charge in an ionic compound covalent bond a stable chemical bond formed when two atoms share one or more pairs of electrons pH indicates concentration of hydrogen ions in a solution (the more H+ ions a solution produces, the lower its pH; pH scale- less than 7 is acidic, 7 is neutral, above 7 is basic) chemical reactions formation and breaking of chemical bonds hydrogen bonds the weak bond bridging hydrogen atoms and atoms of the opposite charge adhesion attraction of water molecules to other molecules cohesion attraction of water molecules to water molecules reactants original molecules before the reaction starts products molecules resulting from the chemical reaction hydrophobic when nonpolar molecules do not form hydrogen bonds with water ("fearing water") hydrophilic when polar molecules readily form hydrogen bonds with water ("water-loving") hydrocarbons biological molecules consisting only of carbon and hydrogen functional groups specific groups of atoms with definite chemical properties that they retain no matter where they occur dehydration synthesis condensation reaction in which the -OH and H groups are removed during the synthesis of a new molecule- water is removed hydrolysis process in which a hydrogen atom is attached to one subunit and a hydroxyl group to the other- water is added denaturation process in which a protein's shape is changed due to a change in its environment- pH change, temperature, or ionic concentration of surrounding solution affect it Enzyme Biological catalyst made of amino acids. Substrate Reactant an enzyme catalyzes Active Site structure on the enzyme Reactants The molecules needed for a chemical reaction to occur Products Molecules that are made when a chemical reaction is over Activation Energy The amount of energy needed for a reaction to occur. Heat of Reaction The difference in energy between the reactants and products of a chemical reaction Exothermic a reaction that has a "-" heat of reaction b/c it releases more energy that it stores Endothermic a reaction that has a "+" heat of reaction and stores more energy than it releases. Catalyst Speeds up a chemical reaction Variables that effect enzyme reaction rate Temperature, pH, enzyme concentration, substrate concentration denature enzyme becomes "inactive" due to changes in the active site structure enzyme specificity enzyme only bonds to one substrate due to shape of active site cell membrane regulates movement of materials in and out of cells, maintains cell shape and allows cells to communicate with each other smooth endoplasmic reticulum makes or synthesizes lipids, detoxification of drugs/medicines rough endoplasmic reticulum has ribosomes associated with it and transports proteins ribosomes makes proteins Golgi modifies, sorts and packages substances made by the cell and sends them to vacuoles, other organelles or out of the cell lysosomes cell organelle filled with enzymes needed to break down certain materials in the cell vacuoles store food and water mitochondria Powerhouse of the cell, organelle that is the site of ATP (energy) production chloroplast organelle in plant cells that converts the energy in sunlight into sugars centrioles Located near the nucleus and help to organize cell division nucleus the control center of the cell nucleolus makes ribosomes chromosomes threadlike structures made of DNA molecules that contain the genes cytoplasm a jellylike fluid inside the cell in which the organelles are suspended nuclear membrane double membrane surrounding the nucleus that controls what enters and leaves the nucleus Organelle a tiny cell structure that carries out a specific function within the cell Cell theory idea that all living things are composed of cells, cells are the basic units of structure and function in living things, and new cells are produced from existing cells phospholipid A type of lipid that makes up the cell membrane. cytoskeleton network of protein filaments within some cells that helps the cell maintain its shape and is involved in many forms of cell movement Prokaryote A unicellular organism that lacks a nucleus and membrane bound organelles Eukaryote A cell that contains a nucleus and membrane bound organelles Cell Wall strong layer around the cell membrane in plants, algae, and some bacteria phospholipid a lipid made of a phosphate head and two fatty acid tails lipid bilayer cell membranes composed of two layers of phospholipids, with the tails pointed inwards towards each other, and the heads facing outward cell surface markers a membrane protein that identifies the cell type receptor proteins a membrane protein that binds to signals outside the cell transport proteins transports substances unable to diffuse across a cell membrane active transport energy is required to move a substance across a cell membrane passive transport no energy is required to transport substances across cell membranes equilibrium when randomly moving molecules fill up a space evenly concentration the amount of a particular substance in a given volume concentration gradient a difference in the concentration of a substance across a distance diffusion substances moving down the concentration gradient (from high to low concentration) simple diffusion small, nonpolar molecules passing directly through the lipid bilayer facilitated diffusion transport proteins helping ions and polar molecules to diffuse through the bilayer channel proteins (pores) tunnels that open for ions and polar molecules to pass through the cell membrane carrier proteins a protein that transports substances across a cell membrane by changing shape osmosis the process of water diffusing across a selectively permeable membrane water channels channel proteins that aid in osmosis, and only allow water molecules to pass through hypertonic solution the solute has high concentration, the water has low, water moves out of the cell hypotonic solution the solute has low concentration, the water has high, water moves into the cell isotonic solution the solute and water have an equal concentration to the cell's cytoplasm, water moves into and out of the cell at equal rates contractile vacuoles colllect excess water in unicellular eukaryotes and force the water out of the cell sodium-potassium pump a carrier protein that uses ATP to actively transport 3 sodium ions out of a cell, and 2 potassium ions into a cell endocytosis the process of a large substance moving into a cell using a vesicle exocytosis the process of a large substance moving out of a cell by means of a vesicle signaling cell a cell that produces a signal that is detected by a target cell signal anything that serves to direct, guide or warn target cell a cell that responds to a signal sent by a signaling cell receptor proteins a protein that binds to specific signal molecules, causing the cell to respond binding site the outer folds of a receptor protein, where the signal binds permeability change transport proteins opening or closing in response to a signal second messenger a signal molecule inside a cell, generated when a substance attaches to the outside of the cell membrane, causes changes in the cytoplasm and nucleus Mitosis in eukaryotic cells, a process of cell division that forms two new nuclei, each of which has the same number of chromosomes Meiosis (genetics) cell division that produces reproductive cells in sexually reproducing organisms Cytokinesis organic process consisting of the division of the cytoplasm of a cell following karyokinesis bringing about the separation into two daughter cells Chromatin The complex of DNA and proteins that makes up a eukaryotic chromosome. When the cell is not dividing, it exists as a mass of very long, thin fibers that are not visible with a light microscope. Sister Chromatids Replicated forms of a chromosome joined together by the centromere and eventually separated during mitosis or meiosis II. Centromere a specialized condensed region of each chromosome that appears during mitosis where the chromatids are held together to form an X shape Cell Cycle series of events that cells go through as they grow and divide Interphase the period of the cell cycle during which the nucleus is not undergoing division, typically occurring between mitotic or meiotic divisions Centrioles Located near the nucleus and help to organize cell division Nucleoli dense masses of RNA and protein that manufacture ribosomes, several of these are located in the nucleus. Prophase first and longest phase of mitosis, during which the chromosomes become visible and the centrioles separate and take up positions on the opposite sides of the nucleus Metaphase second phase of mitosis, during which the chromosomes line up across the center of the cell Anaphase the third phase of mitosis, during which the chromosome pairs separate and move toward opposite poles Telophase the final stage of meiosis or mitosis, in which the separated chromosomes reach the opposite poles of the dividing cell and the nuclei of the daughter cells form around the two sets of chromosomes Cell Plate A double membrane across the midline of a dividing plant cell, between which the new cell wall forms during cytokinesis. Cleavage Furrow pinching of the cell ("drawstring"): develops in animal cells only Meiosis II the second phase of meiosis consisting of chromatids separating, along with the two diploid cells splitting in two Prophase I The first phase of meiosis I. the replicated chromosomes condense, homologous chromsomes pair up, crossing over occurs between homologous chromosomes, the spindle is formed, and the nuclear envelope breaks apart into vesicles. the longest phase of meiosis. Anaphase I The third phase of meiosis I. the replicated homologous chromosomes are separated (the tetrad is split) and pulled to opposite sides of the cell. Metaphase I The second phase of meiosis I. the paired homologous chromsomes (tetrads) align at the center of the cell (the metaphase plate). Telophase I The fourth of meiosis I. the number of chromosoms is now reduced by half. After this phase the cell is considered to be haploid. Note however, that the chromosomes are still replicated, and the sister chromatids must still be separated during meiosis II. Prophase II The first phase of meiosis II. identical to the mitotic step, except that the number of chromosomes was reduced by half during meiosis I. Metaphase II The second phase of meiosis II. identical to the mitotic step, except that the number of chromosomes was reduced by half during meiosis I. Anaphase II The third phase of meiosis II. the sister chromatids are finally spearated at their centromeres and puled to opposite sides of teh cell. is identical to mitotic anaphase, excep the number of chromosmes was reduced by half during meiosis I. Telophase II The fourth and final phase of meiosis II. the number of chromosomes was reduced by half during meiosis. I. Haploid term used to refer to a cell that contains only a single set of chromosomes and therefore only a single set of genes Diploid (genetics) an organism or cell having two sets of chromosomes or twice the haploid number Synapsis the side by side pairing of homologous maternal and paternal chromosomes at the start of meiosis Tetrads the paired chromosomes consisting of four chromatids Crossing Over the interchange of sections between pairing homologous chromosomes during the prophase of meiosis Somatic Cells any cell other than a gamete, has 46 chromosomes, body cells Gametes sex cells Zygote a fertilized egg g1 Checkpoint checks to see if cell size is adequate; chromosomes replication is successfully completed and checks for DNA errors g0 Checkpoint if condidtions are not apporpiate for the cell to divide or if it is not programmed to divide they are in this phase g2 Checkpoint asses if DNA replication has occured, go ahead signal triggers mitosis Cyclin Dependent Kinases cdk enzymes activate proteins to regulate the cell Growth Factors factors that stimulate the cell to divide Density Dependent Inhibition The phenomenon observed in normal animal cells that causes them to stop dividing when they come into contact with one another. Anchorage Dependence the requirement that to divide, a cell must be attached to a solid surface. allele one of two alternate forms of a gene that can have the same locus on homologous chromosomes and are responsible for alternative traits Law of Segregation Mendel's law that states that the pairs of homologous chromosomes separate in meiosis so that only one chromosome from each pair is present in each gamete Law of Independent Assortment states that allele pairs separate independently during the formation of gametes Monohybrid Cross hybridization using a single trait with two alleles (as in Mendel's experiments with garden peas) Dihybrid Cross hybridization using two traits with two alleles each Incomplete Dominance creates a blended phenotype; one allele is not completely dominant over the other Codominance a condition in which both alleles for a gene are fully expressed Multiple Alleles three or more forms of a gene that code for a single trait (such as blood types) Epistasis A type of gene interaction in which one gene alters the phenotypic effects of another gene that is independently inherited., One gene masks the expression of a different gene for a different trait Pleiotropy A single gene having multiple effects on an individuals phenotype (more than one phenotypic expression) Linked Genes genes located on the same chromosome that tend to be inherited together in genetic crosses Sex Linked Inheritance Traits located on the sex cells. EX: Colorblindness, hemophilia. X Inactivation During development, females inactivate half of their X gene elles in order to prevent producing double the amount of the protein. Nondisjunction error in meiosis in which homologous chromosomes don't separate; gametes end up with wrong number of chromosomes Polyploidy condition in which an organism has extra sets of chromosomes Point Mutations changes in a DNA sequence caused by substitution of one nucleotide for another Aneuploidy an abnormality involving a chromosome number that is not an exact multiple of the haploid number (one chromosome set is incomplete)(causes down sydrome and turners syndrome) karyotype the appearance of the chromosomal makeup of a somatic cell in an individual or species (including the number and arrangement and size and structure of the chromosomes) homologous chromosomes chromosomes that have the same sequence of genes, that have the same structured, and that pair during meisosis Autosomes non-sex chromosomes Down Syndrome a congenital disorder caused by having an extra 21st chromosome 5' cap The end of a pre-mRNA molecule modified by the addition of a cap A site One of a ribosome's three binding sites for tRNA during translation. Holds the tRNA carrying the next amino acid to be added to the polypeptide chain. anticodon A specialized base triplet at one end of a tRNA molecule that recognizes a particular complementary codon on an mRNA molecule. base-pair substitution A type of point mutation; the replacement of one nucleotide and its partner in the complementary DNA strand by another pair of nucleotides. codon A three-nucleotide sequence of DNA or mRNA that specifies a particular amino acid or termination signal; the basic unit of the genetic code. deletion 1) A deficiency in a chromosome resulting from the loss of a fragment through breakage. (2) A mutational loss of one or more nucleotide pairs from a gene. E site One of a ribosome's three binding sites for tRNA during translation. The place where discharged tRNAs leave the ribosome. exon A coding region of a eukaryotic gene or expressed region frameshift mutation A mutation occurring when the number of nucleotides inserted or deleted is not a multiple of three, resulting in the improper grouping of the following nucleotides into codons. insertion A mutation involving the addition of one or more nucleotide pairs to a gene. intron A noncoding, intervening sequence within a eukaryotic gene. messenger RNA (mRNA) A type of RNA, synthesized from DNA, that attaches to ribosomes in the cytoplasm and specifies the primary structure of a protein. missense mutation The most common type of mutation, a base-pair substitution in which the new codon makes sense in that it still codes for an amino acid. mutagen A chemical or physical agent that interacts with DNA and causes a mutation. mutation A rare change in the DNA of a gene, ultimately creating genetic diversity. nonsense mutation A mutation that changes an amino acid codon to one of the three stop codons, resulting in a shorter and usually nonfunctional protein one gene-one polypeptide hypothesis The premise that a gene is a segment of DNA that codes for one polypeptide. P site One of a ribosome's three binding sites for tRNA during translation. Holds the tRNA carrying the growing polypeptide chain. (P stands for peptidyl tRNA point mutation A change in a gene at a single nucleotide pair poly-A tail The modified end of the 3' end of an mRNA molecule consisting of the addition of some 50 to 250 adenine nucleotides. primary transcript An initial RNA transcript; also called pre-mRNA when transcribed from a protein-coding gene promoter A specific nucleotide sequence in DNA that binds RNA polymerase and indicates where to start transcribing RNA ribosome A cell organelle constructed in the nucleolus and functioning as the site of protein synthesis in the cytoplasm; consists of rRNA and protein molecules, which make up two subunits. ribozyme An enzymatic RNA molecule that catalyzes reactions during RNA splicing. RNA polymerase An enzyme that links together the growing chain of ribonucleotides during transcription. RNA processing Modification of RNA before it leaves the nucleus, a process unique to eukaryotes. RNA splicing The removal of noncoding portions (introns) of the RNA molecule after initial synthesis. signal-recognition particle (SRP) A protein-RNA complex that recognizes a signal peptide as it emerges from the ribosome. spliceosome A complex assembly that interacts with the ends of an RNA intron in splicing RNA, releasing the intron and joining the two adjacent exons. TATA box A promoter DNA sequence crucial in forming the transcription initiation complex. template strand The DNA strand that provides the template for ordering the sequence of nucleotides in an RNA transcript. terminator In prokaryotes, a special sequence of nucleotides in DNA that marks the end of a gene. It signals RNA polymerase to release the newly made RNA molecule, which then departs from the gene. transcription The synthesis of RNA on a DNA template. transcription unit A region of a DNA molecule that is transcribed into an RNA molecule. transfer RNA (tRNA) An RNA molecule that functions as an interpreter between nucleic acid and protein language by picking up specific amino acids and recognizing the appropriate codons in the mRNA. translation The synthesis of a polypeptide using the genetic information encoded in an mRNA molecule. There is a change of languagefrom nucleotides to amino acids recombinant DNA DNA molecules formed when segments of DNA from two different sources are combined in vitro biotechnology manipulation of organisms or their components to make useful products genetic engineering direct manipulation of genes for practical purposes plasmids small circular DNA molecules that replicate separately from the bacterial chromosome gene cloning production of multiple copies of a single gene restriction enzymes enzymes naturally occurring in bacteria, cut DNA molecules at a limited number of specific locations restriction site sequence of DNA 4-8 nucleotides long, symmetrical where the restriction enzyme cuts restriction fragments created when a specific restriction enzymes cuts a piece of DNA many times sticky ends single-stranded ends formed when restriction enzyme cuts DNA DNA ligase enzyme that bonds sticky ends with other DNA molecules cut with the same enzyme cloning vector DNA molecules that can carry foreign DNA into a host cell and replicate there ampR gene on plasmid; if bacterium has this plasmid, will be able to grow on agar with ampicillin. If does not have plasmid, will not grow on agar with amp. lacZ gene part of the lac operon. If gene is intact, produces a product that can break down lactose and Xgal, colony will be blue. If not intact, will not break down Xgal, colony will be white. Step 1 bacterial transformation isolate plasmid and DNA sample Step 2 bacterial transformation cut both plasmid and dna with same restriction enzyme Step 3 bacterial transformation plasmid may take up DNA Step 4 bacterial transformation seal DNA with DNA ligase Step 5 bacterial transformation put the plasmids into bacteria with no functioning lacZ gene. Use heat or high Ca2+ to stimulate transformation Step 6 bacterial transformation grow bacteria on agar with ampicillin and xgal genomic library complete set of plasmid-containing cell clones, each carrying copies of a particular segment from the original genome phage library clones in bacteriophages reverse transcriptase enzyme that makes single-stranded DNA transcripts from mRNA molecules Step 1 gel electrophoresis cut DNA with restriction enzyme, put sample in well of chamber, let fragments "run," add dye so you can see DNA, observe with UV light In gel electrophoresis, smaller fragments move faster towards the postive end DNA - function and structure contains hereditary information (genes) of the cell; double helix mRNA - function and structure provides the instructions for assembling amino acids into a polypeptide chain; linear; nucleotides are codons tRNA - function and structure short RNA molecule; transports amino acids to their proper place; "clover-leaf" shaped; nucleotides are anticodons rRNA -function and structure building blocks of ribosomes; DNA is transcribed into rRNA in the nucleolus; globular DNA Replication Process in which unzipped DNA strands serve as templates for complementary strands. Occurs during interphase of the cell cycle. semiconservative replication DNA replication; each double-stranded molecule of DNA consists of a single strand of old DNA and a single strand of new, replicated DNA. helicase enzyme that unwinds the DNA helix during DNA replication replication fork Y-shaped structure that arises when helicase unwinds a DNA helix single strand binding protein protein that attaches to each strand of uncoiled DNA during DNA replication to keep the strands separate DNA polymerase enzyme that assembles the new DNA strand in DNA replication. Moves in 3' to 5' direction. antiparallel 5' to 3'; direction in which complement strand grows Okasaki segments Short segments of complementary DNA formed when DNA polymerase assembles DNA on the 5' to 3' strand; caused b/c polymerase must return to replication fork after each segment. Connected by DNA ligase. DNA ligase Connects Okazaki segments formed during DNA replication on the 5' to 3' template strand. lagging strand The 5' to 3' template strand of DNA replication. Takes longer to assemble, and so "lags" behind the 3' to 5' strand. primase enzyme that initiates DNA replication with a short segment of RNA nucleotides (RNA primer) RNA primer A short segment of RNA nucleotides that begins, in DNA replication, the leading strand as well as every Okazaki segment on the lagging strand. Enables DNA polymerase to attach DNA nucleotides to the primer. telomerase enzyme which attaches itself to the end of the template strand in DNA replication to extend the strand by adding a short sequence of DNA nucleotides over and over again. Prevents loss of preceding coding DNA. one-gene-one-polypeptide hypothesis the gene is a DNA segment that codes for a particular polypeptide. one-gene-one-enzyme hypothesis the gene is a DNA segment that codes for a particular enzyme. Proven false and replaced with one-gene-one-polypeptide hypothesis. protein synthesis the process that describes how enzymes and other proteins are made from DNA 3 steps of protein synthesis transcription, RNA processing, translation transcription a step of protein synthesis in which RNA molecules are created by using DNA molecules as a template RNA processing RNA molecules are modified with deletions and additions translation processed RNA molecules are used to assemble amino acids into a polypeptide. codon three adjacent nucleotides on mRNA that code for a specific amino acid anticodon three adjacent nucleotides on tRNA which base pair with the codon of the mRNA during translation. wobble Allows anticodons of some tRNAs to base-pair with more than one type of codon, because exact base pairing between the third nucleotide of the anticodon and codon are usually not required. 3 phases of transcription initiation, elongation, termination initiation (transcription) RNA polymerase attaches to the promoter region on the DNA and begins to unzip the DNA into two strands. TATA box the nucleotide sequence T-A-T-A; often occurs in the promoter region during mRNA transcriptions. elongation (transcription) RNA polymerase unzips the DNA and assembles RNA nucleotides using one strand of DNA as a template. termination (transcription) RNA polymerase reaches a special sequence of nucleotides that serves as a termination point. In eukaryotes, the termination region contains the DNA sequence AAAAAA. promoter region region of DNA that RNA polymerase attaches to to begin transcription.