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BIO 111 Exam 4
| Question | Answer |
|---|---|
| Miescher | Swiss physician & biochemist; isolated nuclei from white blood cells in pus on soiled bandages; discovered an acidic substance containing nucleic substances, etc. |
| Griffith | English microbiologist; took the first step in identifying DNA as the genetic material; worked with S strain & R strain |
| Criteria of Identification of DNA | Information, Transmission, Replication, and Variation |
| Information (IDing DNA) | must contain the information necessary to make an entire organism |
| Transmission (IDing DNA) | must be passed from parent to offspring |
| Replication (IDing DNA) | must be copied in order to pass from parent to offspring |
| Variation (IDing DNA) | must be capable of changes to account for phenotypic variation in population |
| S strain | shiny & smooth looking; is virulent; capsule around which protects it from the host's immune system |
| R strain | rough and non-virulent; lacks the capsule and is recognized and destroyed more by the host's immune system |
| Griffith's research hypothesis | material in dead genetic cells could modify living cells |
| Who originally discovered transformation & how? | Griffith; through the R strain and S strain injections into mice. |
| Who tested & confirmed that DNA transformed the bacteria? | Avery, MacLeod, and McCarty |
| Avery, MacLeod, and McCarty experiment | Took heat killed S cell & removed lipids and carbs and put in 3 tubes; 1 tube for no protein; 1 tube for no RNA; 1 tube for no DNA; transformation occurred in all EXCEPT one with no DNA |
| Why wasn't Avery, MacLeod, and McCarty, etc. work accepted at first? | 1) they didn't think DNA was complex enough to be genetic material 2) Bacteria wasn't understood much back then & they didn't even know if bacteria had genes or not |
| Hershey & Chase | performed experiments using a virus that infects bacteria to confirm the DNA (with bacteriophages) |
| Bacteriophages | has a DNA core packed in a protein coat; DNA is in the head |
| What would understanding the structure of DNA answer? | How DNA is replicated between divisions and How DNA causes the synthesis of proteins |
| X-ray crystallography | provided clues to structure of DNA; Franklin used it to build on previous work |
| What did Franklin discover? | DNA was a spiral/helical molecule |
| Purines | Adenine and Guanine (two ring structures) |
| Pyrimidines | Cytosine and Thymine (one ring structures) |
| What is in RNA but not DNA? | Uracil (in place of Thymine in DNA) |
| Purines always pair with... | pyrimidines (and vice versa) |
| Adenine pairs with... | Thymine |
| Guanine pairs with... | Cytosine |
| In RNA, Uracil pairs with... | Adenine |
| What does constant pairing allow DNA to have? | a fixed width of it's helix |
| Nucleosides | have only a sugar and a base (no phosphate group) |
| Nucleotides | Sugar, base, and phosphate group |
| Phosphodiester backbone of DNA | made up of alternating sugar and phosphates |
| Rungs of ladder of DNA | made up of the paired bases |
| What type of reaction occurs when a second nucleotide comes in to form the backbone? | a condensation reaction that forms a phosphodiester bond (also forms water) |
| Watson and Crick | used the technique of model building to establish a general structure of DNA |
| Four key features that define DNA's structure | double helix with uniform diameter; right-handed twist; two strands run in diff. directions (antiparallel); outer edges of nitrogen bases are exposed to a major and minor groove |
| Minor groove | smaller width between two backbones in DNA |
| Major groove | bigger width between two backbones in DNA |
| How many hydrogen bonds are between Adenine and thymine? | two |
| How many hydrogen bonds are between Guanine and cytosine? | three |
| Anitparallel | phosphate group linked the 3-prime carbon to the 5 prime carbon of another so one end has an open 5 end and 3 end because OH free to bind is on the 3 carbon and the phosphate group is free to bind on carbon 5 on the 5 end |
| 5 prime end of DNA pairs with what end of another strand? | 3 prime end |
| Importance of major vs. minor groove? | more surface area for major groove which allows more interaction which is important during replication and expression of genetic info |
| Chargaff | note that in DNA from all specific tested, the total abundance of purines equals the pyrimidines |
| Two rules from Chargaff | 1) A+G=C+T 2) content of A always= content of T and content of G always= content of C |
| Where does hydrogen bonding occur in DNA? | between the bases |
| Kornburg | American biochemist that discovered that DNA contained the info to replicate itself with DNA template and DNA polymerase and DNTPs |
| What three things does DNA need to replicate itself? | DNA template, DNA polymerase, and dNTPs |
| What are the dNTPs? | dATP, aCTP, dGTP, & dTTP |
| Three ways that DNA could serve as its own template | Semiconservative replication, conservative replication, and dispersive replication |
| Semiconservative replication | using strands as parents; part of original in both |
| Conservative replication | an entirely new helix would be made from the old one |
| Dispersive replication | when fragments of original DNA are templates for two molecules (the resulting strands would both be mixtures) |
| Meselson and Stahl | carried out experiments to prove Watson & Crick's theory to be correct (so semiconservative replication is the right one) |
| How does DNA actually serve as its own template? | Semiconservative replication |
| Two basic steps of DNA replication | DNA is unwound to separate two template strands and new nucleotides are joined by phosphodiester bonds in a sequence that is determined by complimentary base pairing |
| What end of the DNA chain are nucleotides added to? | 3 prime end |
| DNA polymerase | large complex with a groove that the DNA attaches to and slides through; shaped like an open right hand with palm; recognizes four base shapes of DNA |
| Primase | the enzyme that lays down the primer for the DNA polymerase to then bind and do its thing |
| What direction does DNA polymerase read from? | 3 prime end to the 5 prime end of template strand (which is 5 prime to 3 prime on the new strand) |
| Similarities of DNA & RNA polymerase | Incorporates nucleotide triphosphates; reads templates 3 prime to 5 prime; synthesizes new strand 5 prime to 3 prime |
| Differences between DNA & RNA polymerase | DNA: uses deoxyribonucleotides; template dependent (all); requires primer to add on to; proofreading RNA: uses ribonucleotides; most are template dependent (1 exception); can add 2 nucleotides to start chain (no primer required); no proofreading |
| Proteins involved in DNA replication | DNA helicase, ss binding proteins, primase, DNA polymerase, and DNA ligase |
| DNA helicase | unwinds helix of original DNA and takes place at origin of replication |
| ss binding proteins | hold open the replication fork |
| Leading strand | continuous replication |
| Lagging strand | discontinuous replication (fragments) |
| Okazaki fragments | fragments in the lagging strand |
| DNA ligase | an enzyme that mends the gaps between Okazaki fragments so there's one single continuous strand |
| Human chromosomes | linear chromosomes |
| Bacterial chromosomes | circular chromosomes |
| Topoisomerase | used to separate two interlocking circular chromosomes (is not needed for linear chromosomes) |
| What are chromosomes made up of? | DNA, proteins, and a bit of RNA |
| How are chromosomes distinguished? | by size and shape |
| Three essential parts of a chromosome | Telomeres, origin of replication sites, and centromere |
| Telomeres | repetitive sequences at the end and thru replication, those shorten and eventually are told to stop |
| Origin of replication | where replication starts on a chromosome |
| Centromere | portion of the chromosome that holds the two sister chromatids together |
| PCR | Polymerase Chain Reaction; lab method that revolutionized the ability to analyze genes and genomes by synthesizing multiple short copies of DNA |
| What does a PCR reaction mixture contain? | DNA polymerase, DNA template, dNTPs, & primase (and a type of helicase--such as heat for the lab usually) |
| Mullins | earned nobel prize by adding to technique of PCR |
| Four main aspects of cell division | 1) must be a reproductive signal 2) replication of DNA must occur so each of the two new cells have identical genes and cell function 3) cell must distribute replicated DNA to each cell 4) cytokinesis |
| Reproductive signal | signal inities cell division and may originate from either inside or outside the cell |
| How do prokaryotes divide? | binary fission |
| Binary fission | The cell grows in size, replicates its DNA, and then separates the cytoplasm and DNA into two new cells |
| How many chromosomes do most prokaryotes usually have? | one chromosome--single long DNA molecule with proteins bound to it |
| How does DNA fit into the cell? | must be compacted by folding in on itself and the positively charged proteins bound to the negatively charged DNA contribute to this folding |
| Ori | the site where replication of the circular chromosomes starts (the origin of replication) |
| Ter | the site where replication ends (the terminus of replication) |
| Steps of prokaryotic cell division | Binary fission: Reproductive signals, replication of DNA; segregation of DNA; cytokinesis |
| How do eukaryotic cells divide? | Mitosis or meiosis (followed by cytokinesis) |
| cell cycle | the period between cell division |
| Interphase | the cell nucleus is visible and typical cell functions occur, including DNA replication |
| When does the cell cycle start and end? | starts with cytokinesis finishing and ends when mitosis begins |
| Interphase's three subphases | G1, S, and G2 (in that order) |
| S phase of mitosis | DNA replication occurs; each chromosome is duplicated and then consists of two sister chromatids joined together and awaiting segregation into two new cells |
| G1 phase of mitosis | each chromosome is a single, unreplicated structure; G1 is quite variable in length in diff. cell types; some go thru G1 super quick and others take years |
| G2 phase of mitosis | cell makes preparations for mitosis; by synthesizing components of the microtubules that will move the chromatids to opposite ends of the dividing cell |
| Cyclin-dependent kinases | CDKs; kinase is an enzyme that transfers phosphate; CDK plays role in initiating steps in the cell cycle; Cyclin alters the shape & exposes active site on CDK |
| Cyclin + CDK= | cyclin-CDK complex |
| cyclin-CDK complexes | Cyclin D CDK 4, Cyclin E CDK 2, Cyclin A CDK 2, and Cyclin B CDK 1 |
| Cyclin D CDK 4 | acts during the middle of G1, moving cell past the restriction point |
| Cyclin E CDK 2 | acts in middles of G1, works with previous complex to move cells past restriction point |
| Cyclin A CDK 2 | acts during S phase, helps to stimulate DNA replication |
| Cyclin B CDK 1 | acts at G2 to M phase boundary, initiating mitosis |
| internal controls | Cyclin CDK |
| external controls | growth factors |
| How are cyclin-dependent kinases activated? | by binding to a protein called cyclin |
| retinoblastoma protein | RB; acts as an inhibitor of the cell cycle at the R point in late G1; to being S phase, cell must get by the RB block; |
| Cell cycle checkpoints | points at which a cell cycle's progress is regulated |
| P21 | protein made if DNA is damaged by radiation during G1; p21 can bind to G1-K CDK preventing its activation by cyclin |
| Growth factors | external chemicals signals; these proteins activate a signal transduction pathway that often ends up with the activation of Cdk’s |
| Chromatin | complex of DNA & proteins; stringy |
| Sister chromatids | After it replicates during S phase, however, there are two double-stranded DNA molecules |
| Cohesion | sister chromatids are held together along most of their length by a protein complex called cohesion |
| How long is cohesion involved? | thru interphase G2 until mitosis |
| Centromere | at which the chromatids remain held together; made up of leftover cohesion |
| How long would human DNA be if put end to end? | nearly 2 meters long |
| Histones | proteins that are closely associated with DNA and help to achieved tight packing |
| Charge of histones and why? | positively charged because of high content of basic amino acids lysine and arginine |
| Nucleosomes | beadlike units formed from DNA histone interactions and histone-histone interactions |
| Chromatid | tightly coiled chromatin that is condensed as the nucleosomes pack together to form a chromatid |
| Mitosis | a single nucleus gives rise to two nuclei that are genetically identical to each other and to the parents nucleus |
| Stages of mitosis | prophase, metaphase, anaphase, and telophase (PMAT) |
| Centrosome | an organelle in the cytoplasm near the nucleus; determines orientation of spindle |
| Centrioles | in pair; each one a hollow tube formed by 9 triplets of microtubules |
| Prophase | beginning of mitosis; Individual chromatids are visible and still held by centromere |
| kineto-chores | specialized 3-layered structure that develops in the centromere region; one on each chromatid |
| Spindle | two types of microtubules; polar microtubules and kinetochore microtubules |
| Polar microtubules | form the frame work of the spindle and run from own pole to the other |
| Kinetochore microtubules | form later, and attach to the kinetochores on the chromosomes |
| Prometaphase | (1) The nuclear envelope breaks down and the compacted chromosome consisting of two chromatids attach to the kinetochore microtubules |
| Metaphase | (1) The chromosomes line up at the midline of the cell (equatorial position) (2) Spindle microtubules attach to shared centromeres if the chromosomes: each centromere binds only one spindle microtubule from each side. |
| Anaphase | The chromatids separate and move away from each other toward the poles; after they separate, chromatids are called daughter chromosomes |
| Daughter chromosomes | chromatids after separation of anaphase |
| cytoplasmic dynein | protein in kinetochores that acts as a molecular motor; hydrolyzes ATP to ADP |
| Telophase | (1) During this period, a nuclear envelope forms around each set of chromosomes, nucleoli appear, and the chromosomes become less compact. (2) The spindles also disappear at this time. (3) Results are two new nuclei in a single cell. |
| Cytokinesis | i) The division of the cell’s cytoplasm, which follows mitosis |
| Contractile ring (animal cells) | composed of microfilaments of actin and myosin which form a ring on the cytoplasmic surface of the plasma membrane |
| Cell plate (plant cells) | beginning of a new cell wall |
| Meiosis | produces just four daughter cells; b) Meiosis consists of two nuclear divisions that reduce the number of chromosomes to the haploid number, in preparation for sexual reproduction. Nucleus divides twice during meiosis, the DNA is replicated only once. |
| Asexual reproduction | sometimes-called vegetative reproduction is based on the mitotic division of the nucleus. |
| Clones | of a parent organism; the offspring are genetically identical to the parents; reproducing itself with each cell cycle, or it may be multicellular like the cholla cactus, that breaks off a piece to produce a new multicellular organism |
| Sexual reproduction | results in a organism that is not identical to its parents i) Sexual reproduction requires gametes created by meiosis; two parents each contribute one gamete to each of their off spring. |
| gametes | sex cells |
| Somatic cells | body cells that are not for reproduction |
| homologous pair | similar in size and appearance, except for the sex chromosomes found in some species. |
| Haploid | contain only single set of chromosomes (i.e. gametes) |
| Zygote | two haploid gametes fused by process called fertilization |
| Diplontic organism | the gametes are the only haploid cells in the life cycle, and the mature organism is diploid. |
| Hapontic organism | , the tiny zygote is the only diploid cell in the life cycle |
| Karyotype | a) Such a rearranged photomicrograph reveals the number, shape, and sizes of the chromosomes in a cell, which together constitute |
| Meiosis I | preceded by an interphase with an S phase, during which each chromosome is replicated. |
| Meiosis II | The sister chromatids are separated during meiosis II, which is not preceded by DNA replication ; similar to mitosis, in that it involves the separation of chromatids into daughter nuclei. |
| Are the four cells from meiosis genetically identical? | NO |
| Synapsis | in meiosis I; homologous chromosomes pair by adhering along their lengths in a process |
| Tetrad | or bivalent; Four chromatids of each pair of homologous chromosomes |
| chiasmata | regions having these attachments (with cohesion) take on an X-shaped appearance |
| Crossing over | A chiasma reflects an exchange of genetic material b/w non-sister chromatids on homologous chromosomes |
| Recombinant chromatids | contain genetic material from different homologs |
| Benign tumors | Tumors resemble the tissue they come from, grow slowly, and remain localized where they developed. |
| Malignant tumors | Tumors do not look like their parents tissue at all; (1) A flat, specialized epithelial cell in the lung wall may turn into a relatively featureless, round, malignant lung cancer cell. |
| What are the two reasons that Mendel used garden peas? | 1) easily grown 2) pollination is controlled easily |
| self-pollination | plant impregnates itself |
| cross-pollinating | manually moving pollen from one plant to another |
| Stigma | female reproductive part (receives the pollen) |
| Anthers | male reproductive parts (produce the pollen) |
| True-breeding trait | when it is the only trait that occurs throughout many generations of breeding generations |
| Parental generation | true-breeding plants when crossed with another true-breeding plant (P1) |
| Filial 1 | F1; progeny from P1 generation cross |
| Filial 2 | F2; progeny from F1 generation cross |
| Seven traits Mendel observed | shape (round vs. wrinkled); color (yellow vs. green); pod shape (inflated vs. constricted); pod color (green vs. yellow); flower color (purple vs. white); flower position (axial vs. terminal); stem length (tall vs. dwarf) |
| Monohybrid cross | involves one trait and its different phenotypes |
| Homozygous | true-breeding |
| Alleles | different forms o f a gene (i.e. R & r) |
| True-breeding individuals | two copies of the same allele and are homozygous |
| Phenotype | physical appearance |
| Genotype | arrangement of alleles for a particular gene |
| Mendel's conclusions | 1) Genes do not blend together 2) Peas have two versions, or alleles, of each gene 3) Each gamete contains one allele of each gene 4) Males & Females contribute equally to the genotype of their offspring 5) Some alleles are dominant to others |
| Genome | all the genes of an organism |
| Genes | Mendel's unit of inheritance |
| Law of segregation | each gamete receives one member of a pair of alleles (can view this via a punnett square which shows expected outcomes/frequencies of genetic crosses) |
| Locus | particular site on a gene that codes for a particular function |
| What helps to explain Mendel's law of segregation? | Meiosis I |
| What ratio did Mendel observe for monohybrid crosses? | 3:1 (dominant to recessive) |
| Test cross | dominant trait crossed with recessive trait will show whether the dominant trait individual was homozygous or heterozygous |
| Law of Independent Assortment | alleles of different genes assort into gametes independently of one another -this law is not universal—accurate for genes on separate chromosomes, but not necessarily for genes on the same chromosome -Meiosis accounts for independent assortment of allel |
| Dihybrid cross | involves the outcomes of two traits |
| Pedigrees | show phenotype segregation in several generations of humans |
| On average, what percentage of individuals will be affected by a recessive gene? | 25% (1/4) |
| Mutations may cause... | a new allele |
| Wild type allele | most common allele in population (i.e. human eye color wild type allele=brown) |
| If more than two alleles exist in a population... | an individual can still only have a maximum of two alleles (one from each parent) |
| Incomplete dominance | intermediate phenotype; dominant trait is not completely dominant over the recessive; example: red flowers crossed with white flowers could produce pink flowers; disproves blending theory |
| Codominance | two different alleles for a single gene produces two different phenotypes in heterozygous individuals; ex: blood typing |
| Who discovered that blood types are different & cannot be mixed? | Karl Landsteiner |
| Pleiotropic alleles | single alleles that have more than one distinguishable phenotypic effect; ex: siamese cats and their color pattern & eyes come from one allele |
| Genes on the same chromosome are... | linked; although linkage is not absolute |
| Genes can be exchanged... | among chromosomes (on same one usually) |
| Genes that are closer together... | tend to stay together and tend to be transferred together |
| Genes that are farther apart... | are more likely to cross-over |
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amay322