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218: Ch. 9
DNA and the Molecular Structure of Chromosomes
| Question | Answer |
|---|---|
| Replication | genotypic function the genetic material must store genetic information and accurately transit that information from parents to offspring. a duplication process that is accomplished by copying from a template |
| Gene Expression | phenotypic function control the development of the phenotype -dictate the growth of the organism from the single celled to adult The process by which genes produce RNAs and proteins and exert their effects on the phenotype of an organism |
| Mutation | evolutionary function the changes genetic material undergoes to produce variations that allow organisms to adapt to modifications in the environments; a chance in the DNA at a particular locus; can be a single gene change or a chromosome change |
| DNA | the information carrying genetic material that comprises the genes. |
| RNA | the info-carrying material in some viruses; more generally a molecule derived from DNA bu transcription that may carry info, provide subcellular structure, transports amino acids or facilitate in biochemical modification of itself or other molecules |
| Transformation | genetic alteration of an organism brought about by the incorporation of foreign DNA into cells |
| DNase | enzyme that degrades DNA |
| RNase | enzyme that degrades RNA |
| Protease | enzyme that degrades proteins |
| Transfection | the uptake of DNA by a eukaryotic cell, followed by the incorporation of genetic markers present in the DNA into the cell's genome. |
| Nucleotide | phosphate group, pentose, cyclic nitrogen compound (base; AGTCU) |
| Adenine | purine; -NH2 |
| Guanine | purine; =O -NH2 |
| Thymine | pyrimidine; =O =O -CH3 |
| Cytosine | pyrimidine; =O |
| Purine | double ring; AG |
| Pyrimidines | single ring; CTU |
| Complimentary | result of specific base pairing. makes DNA uniquely suited to store and transmit genetic information from generation to generation |
| Antiparallel | directions of the complimentary strands: 5' to 3' and 3' to 5'; "opposite polarity" |
| B-DNA | Watson-Crick conformation; right handed helix with 10.4bp per turn; present in aqueous solutions w low [salt] (majority of the time) |
| A-DNA | present in high concentrations of salt or in partially dehydrated states; right handed helix with 11bp per turn; shorts and thicker with 2.3 nm; almost never in vivo; important for DNA-RNA heteroduplexes and RNA-RNA duplexes exist very similar structure |
| Z-DNA | left handed; zig zagged sugar phosphate back bones; G:C rich with alternating purine and pyrimidine residues; 12bp per turn 1.8nm diameter, single deep groove. function unclear |
| Negative Supercoiling | underwound DNA (left; the formation of coiled tertiary structures in double-stranded DNA molecules with fixed ens when the molecules are underwound |
| Folded genome | the condensed intracellular state of the DNA in the nucleoid of a bacterium. The DNA is segregated into domains and each domain is independently (-) supercoiled |
| Domains | loops of independently (-) supercoiled DNA. These allow for single strand "nicks" that relaxes a domain |
| Chromatin | the complex of the DNA, chromosomal proteins, and other chromosome constituents isolated from nuclei H2-H4 protect the segments of DNA in the nucleosome core from cleavage by endonuclease |
| Histones | group of proteins rich in basic amino acids. they function in the coiling of DNA in chromosomes and in the regulation of gene activity. positively charged at neutral pH They are basic because they contain 20-30% arginine and lysine |
| Nonhistone chromosomal protein | all of the proteins in chromosomes except for histones. likely candidates for roles in regulating the expression of specific genes or sets of genes. acidic (negatively charged at neutral pH) |
| Nucleosomes | the nuclease-resistant subunit of chrimatin that consists of about 146 nucleotides of DNA wrapped as 1.65 turns of negative superhelix around an octamere of histones- two molecules of each H2a H2b H3 H4 |
| Multineme | "multistrand" model (multiple DNA strands/helices) |
| Unineme | "single strand" model (1 double helix); this theory is more supported |
| Linkers | interbead threads of DNA; unprotected DNA helix that is susceptible to nuclease attack |
| Nucleosome Core | 146-nucleotide-pair-long segment of DNA that remains present in each nucleosome. It is nuclease resistant. Also contains 2 molecules of Histones H2-H4 |
| Chromatin fibers | a basic organizational unit of eukaryotic chromosomes that consist of DNA and associated proteins assembled into a strand of average diameter 30nm (tightly coiled or folded lumpy fibers) |
| Scaffold | the central core structure of condensed chromosomes. This is composed of nonhistone chromosomal proteins |
| Telomeres | the unique structure found at the end of eukaryotic chromosomes introduced by Muller McClintock showed that sticky ends fuse together |
| TRF-2 (telomere repeat binding factor) | protein in shelterin that binds to double stranded sequences. Helps hold POT1 to DNA. Associated with Rap! that helps regulate telomere length |
| Denaturation | when bonds are broken and the complementary strands of DNA separate (performed by adding heat) |
| DNA Composition | long chain of deoxyribonucleotides joined by phosphodiester linkages. |
| Deoxyribonucleotides | phosphate group, 5-carbon sugar 2-deoxyribose, nitrogen containing base |
| Replication bubble | the localized region of complementary strand separation that occurs at the origin of replication during the initiation of DNA replication |
| Replication fork | the Y-shaped structure where the two parental strands of a DNA double helix are unwound and are being used as template for the synthesis of new complimentary strands |
| mRNA | messenger; carry's genetic information |
| rRNA | ribosomal; provides subcellular structure |
| tRNA | transfer; transports amino acids |
| Frederick Griffith | transformation in S. pneumoniae heat killed 3S with live 2R led to finding the "transforming principle" and recovering 3S cells |
| Sia and Dawson | performed the Griffith experiment in vitro to show that mice had no role in the transformation principle |
| Avery, McLeod, McCarty | showed that DNA was the only component needed to carry out the 2R/3S experiment. Used RNase, Protease and DNase. |
| Hershey-Chase experiment | Bacteriophage T2 and E.coli;tagged 35S and 32P, but only the 32P was in the progeny viruses. DNA actually infects while protein coat remains outside. |
| Uricil | pyrimidine; =O =O |
| Watson - Crick | determined that DNA was a double helix. Based on Chargoff's rules and Xray diffraction patters |
| Chargoff's rules | [A]=[T] [C]=[G] [A+G]=[C+T] |
| Xray Diffraction | x rays focused through fibers of purified molecules; used to determine the structure of molecules. |
| dTMP | deoxythymidine monophosphate |
| dCMP | deoxycytidine monophosphate |
| dAMP | deoxyadenosine monophosphate |
| dGMP | deoxyguanosine monophosphate |
| Helical structure | major groove, minor groove; repeating substructures every .34nm (GtoC,etc) requires phosphodiester bonds and Hbonds 3.4nm for full twist |
| Watson and Franklin | provided the xray diffraction image of DNA |
| phosphodiester bonds | link the nucleotides in the DNA; join at adjacent deoxyribose moieties |
| hydrogen bonding | holds the two polynucleotide strands together to make the helical configuration |
| DNA configuration | 10bp per 360 degrees. base pairs are .34nm apart, so each full turn is 3.4 nm |
| major histones | H1 H2a H2b H3 H4 1 : 2 : 2 : 2 : 2 H1 is the tape, the rest are specifically complexed with DNA to produce the basic structural subunits of chromatin important in chromatin structure (DNA packaging) |
| histone interaction with DNA | polyionic interaction because of negatively charged phosphate groups |
| solenoid model | type of substructure of chromatin fiber |
| zigzag model | type of substructure of chromatin fiber; fig. shows expanded and contracted forms |
| functions of telomeres | -prevent deoxyribonucleases from degrading the ends of the linear DNA molecules -prevent fusio of the ends with other DNA molecules -facilitate replication of the ends of the linear DNA molecules without loss of material |
| conserved telomeres | TTAGGG ~500-3000 repeats that shorten with age |
| upstream | towards 5' on the template strand |
| POT1 | binds specifically to single stranded TTAGGG |
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ktl34
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