Notes in DNA (Sollars)

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Published	08/06/2024	{{c1::Transposons}} are DNA sequences that can change their position within a genome
Published	08/06/2024	{{c1::euchromatin}} is loose and expressed and {{c2::heterochromatin}} is transcriptionally inactive
Published	08/06/2024	{{c1::histone code}} refers to all of the possible covalent modifications of histones (phosphorylation, acetylation, methylation, ADP-ribosylation, gl…
Published	08/06/2024	describe how histone acetyltransferases (HATs) work
Published	08/06/2024	describe how histone deacetylases (HDACs) work
Published	08/06/2024	each new DNA strand is initiated using {{c1::RNA primase}} to create an {{c2::RNA primer}} (prokaryotes)
Published	08/06/2024	{{c1::Primase}} creates RNA primer for DNA polymerase (prokaryotes)
Published	08/06/2024	what group of enzymes in DNA replication are targets for anticancer therapies
Published	08/06/2024	By modifying histone proteins, it changes the accessibility of chromatin to either be highly condensed ({{c1::heterochromatin}}) or easily expressed (…
Published	08/06/2024	the {{c1::direct repair system}} is responsible for fixing {{c2::pyrimidine dimers}} in {{c3::bacteria}}
Published	08/06/2024	the {{c1::direct repair system}} operates by using specific enzymes to target specific types of damage
Published	08/06/2024	mutations in the {{c1::BRCA1 & BRCA2}} of the {{c2::homologous recombination repair mechanism}} (double stranded break repair) increase the r…
Published	08/06/2024	mutations in the {{c1::BRCA1 gene}} of the homolgous recombination repair system increases the risk of a women developing ovarian cancer to 55%
Published	08/06/2024	can a chromosome without a centromere function
Published	08/06/2024	DNA:Primary structure – {{c1::covalent makeup and base pair sequence}}Secondary structure – {{c2::stable structure taken up by some or all of the nucl…
Published	08/06/2024	Chargaff's first rule is that {{c1::Adenosine = thymine and guanosine = cytidine}}
Published	08/06/2024	Chargaff's second rule is that {{c1::composition of DNA various from one species to another, but not within an organism}}
Published	08/06/2024	Nucleic acids are polymers of nucleotides joined by {{c1::3’,5’-phosphodiester bonds}}
Published	08/06/2024	DNA is usually double-stranded and contains {{c1::thymine}} and {{c1::deoxyribose}}.
Published	08/06/2024	RNA is usually single-stranded and contains {{c1::uracil}} and {{c1::ribose}}.
Published	08/06/2024	The sugar-phosphate backbone of each strand is linked by {{c1::3’,5’- phosphodiester bonds}}. That is, a {{c1::phosphate group}} links the {{c1…
Published	08/06/2024	Each strand has a distinct 5’ end and 3’ end, and thus has polarity. A {{c2::phosphate}} group is often found at the {{c1::5’}} end, and a {{c2::hydro…
Published	08/06/2024	In DNA, Hydrophilic backbone is on the {{c1::outside}}, hydrophobic bases are on the {{c1::inside}}
Published	08/06/2024	DNA has {{c1::major}} and {{c1::minor}} grooves
Published	08/06/2024	Most DNA occurs in nature as a right-handed double-helical molecule known as Watson- Crick DNA or {{c1::B-DNA.}}
Published	08/06/2024	There are about {{c1::10}} base pairs per complete turn of the helix
Published	08/06/2024	A rare left-handed double-helical form of DNA that occurs in {{c1::G-C}} rich sequences is known as {{c2::Z-DNA}}. The biological function of {{c2::Z-…
Published	08/06/2024	Another DNA form is the {{c1::A}} form, which is produced by {{c2::moderately dehydrating the B form}}. It is also a right-handed helix, but there are…
Published	08/06/2024	{{c1::Denaturation}} of DNA is the disruption of the {{c2::non-covalent}} interactions which hold the DNA duplex together. This can be caused by {{c3:…
Published	08/06/2024	Upon denaturation DNA solutions become {{c1::less}} viscous and they absorb {{c2::more}} ultraviolet light ({{c2::hyperchromic effect}})
Published	08/06/2024	Different regions of DNA will have different melting temperatures (Tm), based upon their relative amounts of {{c1::GC}} base pairs.
Published	08/06/2024	Viruses often consist of no more than {{c1::a genome surrounded by a protein coat}}. The genome of HIV is about {{c2::9,000}} nucleotides
Published	08/06/2024	Bacteria usually have a {{c1::single circular chromosome}} housed in their {{c2::nucleoid}} and {{c1::smaller circular DNAs}} called {{c3::plasmids}} …
Published	08/06/2024	The human genome is approximately {{c1::3 billion}} bp, with most cells having {{c1::2}} copies. Eukaryotic DNA is packaged into {{c2::chromatin}}
Published	08/06/2024	Chromatin – {{c1::the complex of nucleic acids (DNA and RNA) and proteins (histones and nonhistones) comprising eukaryotic chromosomes.}}
Published	08/06/2024	DNA wraps around {{c1::histone}} complexes to form the basic structure of {{c2::chromatin}} – the {{c3::nucleosome}} – that can form more complex and …
Published	08/06/2024	Histones are DNA-binding proteins that contain large amounts of {{c1::basic}} amino acids ({{c1::positively}} charged) such as lysine and arginine whi…
Published	08/06/2024	{{c1::Supercoiling}} – the twisting of a helical (coiled) molecule on itself, i.e. a colied coil.
Published	08/06/2024	Cells actively maintain {{c1::negative}} supercoiled state necessary to {{c2::facilitate access to DNA}}. This {{c1::“underwinding”}} of the DNA doubl…
Published	08/06/2024	The centromere of metaphase chromosomes is {{c1::narrower}} than the regions distal to it, and therefore it is called the {{c1::primary chromosomal co…
Published	08/06/2024	DNA {{c4::methylation}} acts by either {{c1::1) inhibiting the binding of transacting factors, typically repressing transcription if at promoter seque…
Published	08/06/2024	{{c1::DNA methyltransferases (DNMTs)}} – enzymes that catalyze DNA methylation using {{c2::S-adenosyl methionine (SAMe)}} as the donor. Removal of DNA…
Published	08/06/2024	{{c1::Thymine-DNA glycosylase (TDG)}} removes {{c2::thymine}} moieties from {{c3::G/T}} mismatches by hydrolyzing the carbon-nitrogen bond between {{c…
Published	08/06/2024	Most extensively studied modification is {{c1::acetylation}}, which occurs by {{c2::transfer of an acetyl group from acetyl coenzyme A to the ε-amino …
Published	08/06/2024	{{c1::Histone acetyltransferases (HATs)}} and {{c1::histone deacetylases (HDACs)}} control acetylation of histones
Published	08/06/2024	Acyclovir is phosphorylated by {{c1::a viral encoded thymidine kinase}} ensuring {{c2::phosphorylation mainly occurs in virally infected cells}}
Published	08/06/2024	The chemical structure of Acyclovir is {{c1::guanine attached to an incomplete ribose ring lacking a 3’ OH group necessary for polymerization, thus ac…
Published	08/06/2024	DNA is {{c1::semiconservative}}, meaning that {{c2:: the two complementary strands of parental DNA are pulled apart. Each of these parental …
Published	08/06/2024	prokaryotic DNA replication begins at {{c1::an origin}} and proceeds {{c1::bidirectionally}}{{c2::Origins of replication}} are unique sites …
Published	08/06/2024	DNA synthesis proceeds in a {{c1::5’ -> 3’}} direction and is {{c2::semidiscontinous}}Deoxynucleotides are added one at a time to the {{c1::3’}} en…
Published	08/06/2024	{{c1::AAA+ (ATPases associated with diverse cellular activities) ATPase}} – DnaA binds to the origin of replication and disassociates the helical stra…
Published	08/06/2024	{{c1::DNA Ligase}} – creates phosphodiester bonds by using the energy of ATP cleavage, this seals “nicks” in the DNA strand
Published	08/06/2024	Type I topoisomerases cleave {{c1::one of the strands of the double helix}}, Type II Topoisomerases cleave {{c1::both strands to perform their functio…
Published	08/06/2024	DNA replication steps: {{c1::initation, elongation, termination}}
Published	08/06/2024	Initiation: The base sequence at the origin of replication is recognized and bound by the DnaA protein. The two parental strands of DNA are pulle…
Published	08/06/2024	{{c1::Primase}} synthesizes a short (about 10 nucleotides) RNA {{c1::primer}} in the 5’ -> 3’ direction, beginning at the origin on each parental s…
Published	08/06/2024	The {{c1::leading strand}} can be made continously in one long piece. It is {{c2::complementary}} and {{c2::antiparallel}} to the paren…
Published	08/06/2024	The “lagging strand” is synthesized discontinuously as a series of small fragments (about 1000 nucleotides long) known as {{c1::Okazaki fragments}}.&n…
Published	08/06/2024	Each Okazaki fragment is initiated by the synthesis of an {{c1::RNA primer}} by {{c1::primase}}, and then completed by the synthesis of DNA by {{c1:: …
Published	08/06/2024	Each fragment is made in the 5’ -> 3’ direction DNA {{c1::gyrase}} (a type II DNA topoisomerase) provides a “swivel” in front of each replication f…
Published	08/06/2024	RNA primers are removed by {{c1::DNA polymerase I}}. This enzyme removes the ribonucleotides one at a time from the 5’ end of the primer (5’3’ exonuc…
Published	08/06/2024	Important mechanisms during elongation Alleviation of DNA supercoiling by topoisomerases and are important drug targets. All topoisomerase II-directed…
Published	08/06/2024	{{c1::DNA polymerase I and III}} have the ability to “proofread” their work by means of a {{c3::3’ -> 5’}} {{c2::exonuclease}} activity. If {{c1::D…
Published	08/06/2024	DNA {{c1::ligase}} seals the “nicks” between Okazaki fragments, converting them to a continuous strand of DNA
Published	08/06/2024	Replication is completed when {{c1::the two replication forks meet each other on the side of the circle opposite the origin}}
Published	08/06/2024	Given the importance of genetic information to the stability and feasibility of life, it is extremely important that the fidelity of the information b…
Published	08/06/2024	DNA polymerase I – {{c1::involved in DNA repair and removes RNA primers during replication with its unique 5' -> 3’ exonuclease activity}}DNA polym…
Published	08/06/2024	Many of the proteins required for mitochondrial function are actually nuclear encoded, such as the enzyme responsible for mitochrondrial DNA replicati…
Published	08/06/2024	{{c1::Heteroplasmy}} – one cell contains multiple types of mitochondrial DNA, with varying levels of each from one cell to the next. Thus, unlike nucl…
Published	08/06/2024	Mutations in mitochondrial DNA can cause human diseaseThere is a link between {{c1::mutations with strong dysfunction}} and {{c1::heteroplasmy}}. Exam…
Published	08/06/2024	Mutations that cause {{c1::weak}} (Parkinson disease) or {{c1::moderate}} (Leber hereditary optic neuropathy (LHON)) dysfunction tend to occur in a {{…
Published	08/06/2024	A major difference between prokaryotic and eukaryotic DNA replication is that {{c1::synthesis occurs from numerous origins of replication in eukaryote…
Published	08/06/2024	Eukaryotic polymerases are denoted with Greek letters rather than Roman numerals. The enzymes that perform the bulk of DNA replication have proofreadi…
Published	08/06/2024	Nuclear DNA replication in eukaryotes is linked to {{c1::cellular division by the cell cycle}}
Published	08/06/2024	The linearity of eukaryotic nuclear chromosomes produces several problems associated with the ends of the DNA molecule that must be addressed. It is t…
Published	08/06/2024	Telomere structure contains a buffer region of {{c1::100-300 kb}} telomere associated repeats, followed by a {{c2::3-20 kb}} region of tandem {{c2::TT…
Published	08/06/2024	Telomerase is a special DNA polymerase containing an RNA molecule that functions as the template for the telomeric repeat. Telomerase is a {{c1::rever…
Published	08/06/2024	Telomerase mechanism {{c1::Telomerase extends the 3’ end of the ssDNA by the reverse transcriptase activity of telomerase}} {{c2::Primase synethe…
Published	08/06/2024	Acyclovir targets {{c1::viral DNA polymerase, such as chicken pox, shingles, and herpes simple virus}}.
Published	08/06/2024	3 main differences between eukaryotic and prokaryotic DNA replication{{c1::eukaryotic}} has multiple origins of replication{{c2::eukaryotes'}}&nb…
Published	08/06/2024	2 methods of epigenetic modifications{{c1::DNA methylation}}{{c1::Histone modification}}
Published	08/06/2024	Mechanism of DNA mismatch repair: The newly generated strand lacks {{c3::methylation marks present in the template strand, allowing determination…
Published	08/06/2024	Mechanism of Nucleotide-excision repair: {{c1::Excinuclease}} – a nuclease capable of making two specific endonucleolytic cleavages, compare to t…
Published	08/06/2024	Depurination is when {{c1::guanine spontaneously removes itself from ribose and forms apurinic site (AP)}}
Published	08/06/2024	Base- Excision Repair Mechanism A {{c1::uracil glycosylase}} recognizes and removes the {{c1::uracil}} base, leaving an {{c2::apyrimidinic (AP) site}}…
Published	08/06/2024	Direct Repair MechanismResponsible for repairing pyrimidine dimers in bacteria in a process known as {{c1::photoreactivation}}Mechanism varies dependi…
Published	08/06/2024	Double stranded break repair mechanisms {{c1::Nonhomologous end-joining}} is the more error prone of the mechanisms because it is associated with…
Published	08/06/2024	Double stranded breaks are caused by {{c1::high-energy radiation}} or {{c1::oxidative free radicals}}
Published	08/06/2024	{{c1::Recombination}} refers to the rearrangement or exchange of genetic information between two DNA molecules or between two different parts of the s…
Published	08/06/2024	Legitimate DNA recombination – {{c1::the recombination event occurs at aligned points on the genetic map, so that no information is lost.}} This occur…
Published	08/06/2024	Illegitimate DNA recombination – {{c1::recombination occurs between DNA segments not aligned on the genetic map}} Sequences that are similar in differ…
Published	08/06/2024	transposons are {{c1::mobile genetic elements}}{{c2::Alu sequences}} cause: breast cancer, ewing sarcome, familial HC, hemophilia, neurofibromato…
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