Notes in NYUGSOM Preclinical Collaborative Deck

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Status	Last Update	Fields
Published	07/16/2024	{{c1::Phosphate groups}} give DNA a negative charge.
Published	07/16/2024	The two purines in nucleic acid are  {{c1::adenine }}and {{c1::guanine}}.
Published	07/16/2024	The three pyrimidines in nucleic acid are{{c1::Cytosine, Uracil, and Thymine}}
Published	07/16/2024	Deamination of cytosine yields {{c1::uracil}}
Published	07/16/2024	Deamination of adenine yields {{c1::hypoxanthine}}
Published	07/16/2024	Deamination of guanine yields {{c1::xanthine}}
Published	07/16/2024	Deamination of 5-methylcytosine yields {{c1::thymine}}
Published	07/16/2024	Of uracil and thymine, {{c1::uracil}} is found in RNA, while {{c1::thymine}} is found in DNA.
Published	07/16/2024	Methylation of {{c1::uracil}} makes thymine.
Published	07/16/2024	The {{c1::5’::5’ or 3’}} end of the incoming nucleotide bears the triphosphate (energy source for the bond)
Published	07/16/2024	What is the difference in bond strength between C-G and A-T?{{c1::C-G}} bonds are stronger than {{c1::A-T}} bonds
Published	07/16/2024	What are the amino acids necessary for purine synthesis?{{c1::Glycine, Aspartate, and Glutamine}}
Published	07/16/2024	The disease {{c1::adenosine deaminase deficiency}} results in increased dATP, decreased ribonucleotide reductase activity, and lymphotoxicity.
Published	07/16/2024	{{c1::Lesch-Nyhan}} syndrome is a disease of purine salvage that results in intellectual disability, self-mutilation, aggression, hyperuricemia (orang…
Published	07/16/2024	The base pairing rules in DNA dictate that {{c1::adenine}} pairs with thymine and {{c1::guanine}} pairs with cytosine.
Published	07/16/2024	{{c1::DNA polymerase}} is the enzyme responsible for DNA replication in eukaryotes.
Published	07/16/2024	In DNA replication, {{c1::DNA ligase::what enzyme}} joins Okazaki fragments together
Published	07/16/2024	In DNA replication, DNA ligase joins {{c1::Okazaki fragments}} together.
Published	07/16/2024	In DNA replication {{c1::DNA helicase::what enzyme}} unwinds the DNA double helix, producing the single strand template.
Published	07/16/2024	In DNA replication, {{c1::topoisomerase}} relieves strain in the DNA structure by causing breaks and rejoining the DNA.
Published	07/16/2024	In DNA replication, ________________ adds telomere repeats to chromosome ends to avoid loss of genetic information during replication.
Published	07/16/2024	_____________carries the appropriate amino acid to the ribosome for incorporation into the growing peptide chain.
Published	07/16/2024	What happens to DNA during mitosis?
Published	07/16/2024	The phosphate groups in DNA carry a _______________ charge.
Published	07/16/2024	What are the components of a nucleotide?
Published	07/16/2024	RNA Polymerase (I, II, III) synthesizes rRNA.
Published	07/16/2024	RNA Polymerase (I, II, III) synthesizes mRNA, miRNA, and snRNA.
Published	07/16/2024	RNA Polymerase (I, II, III) synthesizes 5S rRNA and tRNA.
Published	07/16/2024	“______ " genes are genes that are found mutated at higher frequencies in cancer cells compared to other genes, often leading to faster cell growth an…
Published	07/16/2024	___________________ mutations result in a change in an amino acid, changing protein sequence and can change protein function.
Published	07/16/2024	Non-synonymous mutations, which change the amino acid of a protein are also called _____________ mutations.
Published	07/16/2024	___________________ mutations do not result in a change in an amino acid, changing protein sequence and therefore do not result in cancer development.
Published	07/16/2024	Most cancers arise after (few/multiple) _________________ mutations.
Published	07/16/2024	Most changes in DNA causing cancer are due to (single base mutations/insertions or deletions) _________________.
Published	07/16/2024	Mutations in the human genome are (rare/common).
Published	07/16/2024	Telomeres are at (the end/center) ______________ of the chromosome.
Published	07/16/2024	The chromosome has (a single/many) ___________ origins of replication.
Published	07/16/2024	The enzyme that catalyzes the synthesis of nascent strands of DNA are called _________________.
Published	07/16/2024	These two DNA polymerases function on the lagging strand of DNA synthesis are ___________.
Published	07/16/2024	The primary DNA polymerase that functions on the leading strand of DNA synthesis is ___________.
Published	07/16/2024	The _____________ strand of DNA is synthesized by adding nucleotides to the 3’ end.
Published	07/16/2024	The leading strand of DNA is synthesized by adding nucleotides to the ____________ end.
Published	07/16/2024	The __________ strand of DNA is synthesized by adding nucleotides to the 3’ end.
Published	07/16/2024	The enzyme ______________ prevents formation of secondary structures on the lagging strand.
Published	07/16/2024	Even if DNA synthesis occurs with high fidelity, mutations can occur by incorporation of rare forms of a base (rather than the favored form), which ca…
Published	07/16/2024	The process by which DNA polymerase can identify and remove incorrect bases in DNA is referred to as __________________.
Published	07/16/2024	The two DNA polymerases with proofreading capability are ______________. These improve DNA polymerase fidelity by 100X.
Published	07/16/2024	The lagging strand of DNA is synthesized by adding nucleotides to the _____________ end.
Published	07/16/2024	The lagging strand of DNA is synthesized discontinuously through the production of ___________ fragments.
Published	07/16/2024	_______________ activity of DNA polymerase delta and epsilon allow them to remove aberrantly matched base pairs (proofreading).
Published	07/16/2024	An example of a nucleoside analog, used to treat cancer (leukemia and lymphoma) by mimicking cytosine and blocking DNA replication in rapidly-dividing…
Published	07/16/2024	An example of a nucleoside analog, used to treat HIV by mimicking thymidine and blocking HIV DNA replication is ___________________. While there are m…
Published	07/16/2024	Werner syndrome (Progeria) is a disease of premature aging that is due to a mutation in this type of enzyme, involved in DNA replication.
Published	07/16/2024	______________ cuts DNA on one strand, downstream from the replication fork to relieve torsional stress caused by replication, allowing unimpeded move…
Published	07/16/2024	___________________cuts both strands of DNA during mitosis to disentangle DNA.
Published	07/16/2024	_____________ repairs non-bulky lesions in the DNA, caused by deamination, alkylation or oxidation of nucleotide bases.
Published	07/16/2024	_____________ repairs DNA damage, caused ultraviolet light, as well as due to bulky lesions in the DNA.
Published	07/16/2024	Xeroderma pigmentosum is a cancer syndrome due to a defect in this DNA repair system.
Published	07/16/2024	_____________ repairs misincorporated nucleotides during DNA replication (not corrected by proofreading system of DNA polymerases).
Published	07/16/2024	Lynch syndrome is a cancer syndrome (colon, uterine, ovarian, among others) due to a defect in this DNA repair system.
Published	07/16/2024	The process of converting DNA into RNA is referred to as ______________.
Published	07/16/2024	In a gene, the protein-coding segment is referred to as an (intron/exon) ______________.
Published	07/16/2024	In a gene, the non-coding segment is referred to as an (intron/exon) ______________.
Published	07/16/2024	A ______________ is a region of DNA where RNA polymerase begins to transcribe a gene. It is typically located directly upstream or at the 5′ end …
Published	07/16/2024	_________________ are proteins that control the rate of transcription of genetic information from DNA to messenger RNA. They are essential f…
Published	07/16/2024	A ______________ is a DNA sequence that's found in the core promoter region of genes. It's a type of promoter sequence that tells other mole…
Published	07/16/2024	A ________________ is a protein that controls the expression of multiple genes. These genes often work together to drive a complex process.
Published	07/16/2024	An ________________ is a mutated gene that can cause cancer.
Published	07/16/2024	Before it mutates, an oncogene is called a _______________, which helps regulate cell division.
Published	07/16/2024	mRNAs have a _______________ at their 5’ end, which plays a role in translation, splicing and RNA stabilization.
Published	07/16/2024	The process of removing the non-coding introns of mRNA and keeping the coding (exons) is termed ______________.
Published	07/16/2024	The 3’ end of a mature mRNA contains a repeat of ___________________, which stabilizes the mRNA.
Published	07/16/2024	The UI small nuclear ribonucleoprotein (UI snRNP) is involved in the process of ______________.
Published	07/16/2024	A means to increase the diversity of mRNAs developed from the same gene is _________________. This is quite common. Therefore most genes can produce m…
Published	07/16/2024	______________ is the area where heritable traits (phenotypes) can be acquired without alteration in DNA sequences.
Published	07/16/2024	_______________ changes, including alter chromatin structure, can result in modification of gene transcription without altering DNA structure.
Published	07/16/2024	______________ changes the expression of a DNA segment without changing the sequence.
Published	07/16/2024	Histone __________________ is a means of reversible transcriptional suppression. It can also cause activation.
Published	07/16/2024	Histone ____________ causes removal of histone’s positive charge leading to relaxed DNA coiling and increased transcription.
Published	07/16/2024	Histone _____________ leads to tightened DNA coiling and decreased transcription.
Published	07/16/2024	Histone modifications that impact transcription, typically occur on this area of the histone.
Published	07/16/2024	DNA methylation on _____________ residues turns off transcription.
Published	07/16/2024	DNA __________________ plays a key role in X-chromosome inactivation.
Published	07/16/2024	In order for DNA to fit into the nucleus, it takes this form:
Published	07/16/2024	_________________ binds to the nucleosome and to "linker DNA," stabilizing the chromatin fiber.
Published	07/16/2024	DNA and histone synthesis occur during the _________________ phase.
Published	07/16/2024	What form of DNA is circular and does not utilize histones?
Published	07/16/2024	________________ is a condensed form of DNA that appears darker on electron microscopy. It's sterically inaccessible, thus transcriptionally inactive.
Published	07/16/2024	________________ is a less condensed form of DNA that appears lighter on electron microscopy. It's transcriptionally active, sterically accessible.
Published	07/16/2024	Histone modification occurs when the chromatin is in this form:
Published	07/16/2024	Given their role in modifying gene expression, mutations in histone modifying genes are often seen in __________.
Published	07/16/2024	__________________ in the promoter of a tumor suppressor gene, causing reduced expression, may result in development of cancer.
Published	07/16/2024	These two amino acids give histones a positive charge:
Published	07/16/2024	____________ carries the genetic code from DNA to the ribosome for protein synthesis.
Published	07/16/2024	DNA looping twice around a histone octamer describes the structure of a __________________.
Published	07/16/2024	________________ is highly condensed and transcriptionally inactive, while ____________ is less condensed and transcriptionally active.
Published	07/16/2024	DNA methylation typically typically _________________ gene transcription.
Published	07/16/2024	_____________ removes the positive charge of the histone, causing relaxed DNA coiling and increased transcription.
Published	07/16/2024	______________ causes tightened DNA coiling and decreased transcription.
Published	07/16/2024	An ______________ is a DNA locus where regulatory proteins ("activators") bind, increasing expression of a gene on the same chromosome.
Published	07/16/2024	__________ is an enzyme that synthesizes RNA from a DNA template.
Published	07/16/2024	mRNAs have a _______________ at their 5’ end, which plays a role in translation, splicing and RNA stabilization
Published	07/16/2024	What are the three stop codons in mRNA?
Published	07/16/2024	Codons are formed by (number) __________ of bases.
Published	07/16/2024	The genetic code is _______________, meaning that every amino acid is coded for by multiple codons.
Published	07/16/2024	The genetic code is ____________________, meaning that every codon specifies an amino acid.
Published	07/16/2024	All proteins are coded, beginning with this codon sequence ___________.
Published	07/16/2024	Bacterial ribosomes are composed of these two subunits:
Published	07/16/2024	Human ribosomes are composed of these two subunits:
Published	07/16/2024	The _______________ subunit is responsible for binding mRNA, interpreting the genetic code and binding tRNA.
Published	07/16/2024	The small (40S) ribosome subunit is responsible for ____________________.
Published	07/16/2024	The _______________ subunit is responsible for forming the peptide bonds and the exit channel.
Published	07/16/2024	The large (60S) ribosome subunit is responsible for ____________________.
Published	07/16/2024	In bacterial mRNA, the __________________ sequence is located near the AUG start sequence, allowing recognition by the 30S ribosome.
Published	07/16/2024	In eukaryotes, the methyl cap at the 5’ end of mRNA is recognized by  ___________________, facilitating binding of the small 40S ribosomal subuni…
Published	07/16/2024	In order to start translation, the ________________ complex scans the mRNA until it encounters the AUG start sequence.
Published	07/16/2024	The first tRNA that initiates translation is loaded with this amino acid:
Published	07/16/2024	The tRNA, loaded with an amino acid enters the ribosome at the ________________ site.
Published	07/16/2024	The amino acid peptide bonds are formed within the ________________ site of the ribosome.
Published	07/16/2024	As the polypeptide is formed within the ribosomes, the leading amino acids leave the ribosome through the ___________________ site.
Published	07/16/2024	In order to stop translation and release the peptide, _________________ factors trigger hydrolysis of the polypeptide-tRNA.
Published	07/16/2024	An important translation factor, ________________________, helps load the MET-tRNA onto the mRNA within the ribosome.
Published	07/16/2024	In order to inhibit bacterial synthesis of proteins (translation) in human cells, antibiotics often target the bacterial _________ subunits.
Published	07/16/2024	A _________________ is a mutation that changes an amino acid in a protein to a stop codon which ends synthesis of the protein at that location.
Published	07/16/2024	mRNAs containing premature termination codons are destroyed by this process ____________.
Published	07/16/2024	_________ are small non-coding RNAs processed from the primary transcript, which may, in turn, regulate translation and decay.
Published	07/16/2024	The characteristics of an amino acid are determined by its __________________ group.
Published	07/16/2024	The ____________________ structure of a protein is defined by the amino acid sequence.
Published	07/16/2024	The primary structure of a protein is defined by _______________.
Published	07/16/2024	The ____________________ structure of a protein is defined by folding into alpha helices and beta sheets.
Published	07/16/2024	The secondary structure of a protein is defined by _______________.
Published	07/16/2024	The ____________________ structure of a protein is defined by how the secondary structure of a protein is arranged in 3D (How it is folded).
Published	07/16/2024	The tertiary structure of a protein is defined by _______________.
Published	07/16/2024	The ____________________ structure of a protein is defined by how more than 1 protein chain interacts with one or more protein chains.
Published	07/16/2024	The quaternary structure of a protein is defined by _______________.
Published	07/16/2024	The simplest amino acid, which contains a H+ as a side group is ________________.
Published	07/16/2024	The diversity of amino acids can be increased by modification of the amino acid ______________.
Published	07/16/2024	Proper folding of proteins requires the function of __________________.
Published	07/16/2024	Alzheimer, Parkinson, Huntington and Amyotrophic lateral sclerosis (conformational diseases) are all diseases due to aberrant ________________.
Published	07/16/2024	Enzymes function by lowering the __________________ energy, by stabilizing the transition state that favors a reaction.
Published	07/16/2024	Since their mechanisms are all the same, the specificity of serine proteases is determined by the conformation of their ________________.
Published	07/16/2024	The _________________ equation describes the rate of enzymatic reaction.
Published	07/16/2024	The substrate concentration at which 50% Vmax (reaction velocity) is obtained is called the _____________.
Published	07/16/2024	A _______________ inhibitor of an enzyme requires far more substrate to reach the Vmax.
Published	07/16/2024	A __________________ inhibitor of an enzyme binds within the active site.
Published	07/16/2024	A __________________ inhibitor of an enzyme binds outside the active site.
Published	07/16/2024	On the graph below, what type of inhibitor is responsible for the blue line (same Km, different Vmax)?
Published	07/16/2024	On the graph below, what type of inhibitor is responsible for the red line (same Vmax, different Km)?
Published	07/16/2024	On the Lineweaver-Burk plot below, what type of inhibitor is indicated by the red line?
Published	07/16/2024	On the Lineweaver-Burk plot below, what type of inhibitor is indicated by the red line?
Published	07/16/2024	In the T (tense) state, hemoglobin has a (high/low) _______________ affinity for oxygen.
Published	07/16/2024	In the R (relaxed) state, hemoglobin has a (high/low) _______________ affinity for oxygen.
Published	07/16/2024	When a hemoglobin molecule binds a molecule of oxygen, it undergoes a conformational change that makes it (easier/harder) ________________ to bind ano…
Published	07/16/2024	What term is used to describe the condition by which hemoglobin binding one molecule of oxygen makes it easier to bind the next molecule.
Published	07/16/2024	Hemoglobin can bind __________ molecules of oxygen, while myoglobin can bind ______________.
Published	07/16/2024	H+ and CO2 stabilize the ______________ state of hemoglobin, making it (easier/more difficult) ______________to hold onto oxygen.
Published	07/16/2024	2,3 BPG stabilize the ______________ state of hemoglobin, making it (easier/more difficult) ______________to hold onto oxygen.
Published	07/16/2024	Fetal hemoglobin has a {{c1::higher::higher or lower}} affinity for oxygen.
Published	07/16/2024	What are the assumptions of the Hardy-Weinberg law?1. {{c1:: No mutation occurring at the locus}}2. {{c1:: Natural selection is not occurring}}3. {{c1…
Published	07/16/2024	{{c1::Hardy-Weinberg}} equilibrium postulates that genetic variation in a population will remain constant across generations in the absence of disturb…
Published	07/16/2024	What is the Hardy-Weinberg equation?{{c1::p2+2pq+q2=1}}where p2 is the {{c2::frequency of homozygous normal genotype}}2pq is the {{c2::frequency …
Published	07/16/2024	In the hardy-Weinberg equation, for an autosomal recessive disease, which factor represents the disease frequency?{{c1::q2}}
Published	07/16/2024	When trying to calculate the risk a person is a carrier of an autosomal recessive disease, you would use the {{c1::Hardy-Weinberg equation}}.
Published	07/16/2024	Sickle cell anemia is the most common monogenetic (autosomal recessive) disease, possible because it offers a protective advantage against malaria. Th…
Published	07/16/2024	While most mendelian diseases are rare, some are more common due to population {{c1::bottlenecks}} and/or cultural {{c1::isolation}}.
Published	07/16/2024	{{c1::Genome-wide association studies (GWAS)}} studies are used to identify genomic variants that are statistically associated with risk for a common …
Published	07/16/2024	The results of Genome-wide association studies are often expressed as a {{c1::Manhattan plot}}, which looks at the genes on chromosomes and seeing whi…
Published	07/16/2024	Complex disorders arise from joint contributions of many {{c1::genetic}} and {{c1::environmental}} factors.
Published	07/16/2024	________________ is a technique where chromosomes are stained, ordered, and numbered according to morphology, size, arm-length ratio, and banding patt…
Published	07/16/2024	_____________ is a technique where a fluorescent DNA or RNA probe binds to a specific gene site of interest on chromosomes. It is used for specific lo…
Published	07/16/2024	_______________ is a technique that involves the production of a recombinant DNA molecule in a bacterial host.
Published	07/16/2024	The ____________ system is a technique that can inducibly manipulate genes at specific developmental points.
Published	07/16/2024	__________________ is a genetic test that is used to identify numerical (ex. monosomies, trisomies) and large structural changes to chromosomes.
Published	07/16/2024	Karyotyping requires _____________ cells and takes days to weeks to complete.
Published	07/16/2024	Genetic _________________ is a genetic test that allows you to look for single nucleotide mutations, insertions, deletions and other changes that cann…
Published	07/16/2024	To perform karyotyping, the cells are blocked in this phase of the cell cycle.
Published	07/16/2024	In karyotyping,______________ stains darkly and is rich in A-T.
Published	07/16/2024	In karyotyping, ______________ stains lightly and is rich in G-C.
Published	07/16/2024	To diagnose a fetus with a trisomy, such as with Down syndrome, you would identify the increased chromosome number using _________________.
Published	07/16/2024	______________ is a genetic technique that requires you to culture the cells.
Published	07/16/2024	___________________ is a genetic test that requires you to know the gene of interest because you need to use a probe that is complementary for that ge…
Published	07/16/2024	To detect smaller genetic changes that can be seen by karyotyping, but not at the nucleotide level, you can use _____________________.
Published	07/16/2024	Fluorescence in situ hybridization (FISH) (does/does not) __________________ require dividing cells.
Published	07/16/2024	__________________ sequencing examines the sequence of the coding region of the DNA.
Published	07/16/2024	__________________ sequencing allows for analysis of epigenetic DNA changes
Published	07/16/2024	__________________ sequencing allows for analysis of epigenetic DNA changes
Published	07/16/2024	_________________ will allow for tailored dosing and medication choice for a given patient, based on their genetic variants.
Published	07/16/2024	The vast majority of clinical variants (mutations) (are/are not) ________________ clinically important.
Published	07/16/2024	The term {{c1::single nucleotide variant (SNV)}} is synonymous with the term {{c2::mutation}}
Published	07/16/2024	{{c1::short tandem repeats (STRs)}} aka {{c1::microsatellites}}, are repeated units of 2-7 base pairs, duplicated on a chromosome.
Published	07/16/2024	{{c1::translocation}} refers to {{c2::when a segment of DNA is removed from one chromosome and added to another.}}
Published	07/16/2024	STRs are {{c1::unstable::stable/unstable}}
Published	07/16/2024	{{c1::Huntington's disease}} is a neurologic movement disorder caused by trinucleotide repeats of {{c2::CAG}} in the {{c3::HTT}} gene.
Published	07/16/2024	In {{c1::anticipation}}, such as is seen in Huntington disease, the onset of a disease appears earlier with each successive generation.
Published	07/16/2024	Genetics changes in which the phenotypic effect cannot be predicted to be either pathogenic or benign are referred to as {{c1::Variants of unknown sig…
Published	07/16/2024	In {{c1::frameshift mutations}}, insertions or deletions of DNA bases, leading to different codons, altering the structure of a protein.
Published	07/16/2024	{{c1::splicing}} variants impact intron/exon junctions.
Published	07/16/2024	A {{c1::pedigree}} is a visual representation of a family history of disease.
Published	07/16/2024	In {{c1::autosomal dominant}} transmission, the phenotype is seen in heterozygous individuals, there is disease in each generation and a 50% risk of t…
Published	07/16/2024	In {{c1::autosomal recessive}} transmission, the phenotype is seen in homozygous individuals, there is not disease in each generation and a 25% risk o…
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