Notes in Biochemistry

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Status	Last Update	Fields
Published	07/28/2024	Hereditary Spherocytosis is an autosomal dominant hematological disorder that involves spheroid erythrocytes due to a {{c2::spectrin}} or {{c2…
Published	07/28/2024	{{c1::Patau Syndrome (Trisomy 13)}} is an autosomal trisomy that is associated with rocker-bottom feet and {{c2::microphthalmia}}
Published	07/28/2024	{{c1::Patau Syndrome (Trisomy 13)}} is an autosomal trisomy that is associated with {{c2::cleft lip::face}} and {{c2::cleft palate::face}}
Published	07/28/2024	{{c1::DiGeorge Syndrome}} is a 22q11 deletion syndrome that presents with {{c2::thymic}} aplasia, {{c2::parathyroid}} aplasia and {{c2::cardiac}} de…
Published	07/28/2024	A(n) {{c1::nucleosome (10 nm chromatin)}} is negatively charged DNA wrapped around the outside of positively charged proteins called {{c2::histon…
Published	07/28/2024	Histones are rich in the amino acids {{c1::lysine}} and {{c1::arginine}}
Published	07/28/2024	What class of histone is not found as a pair in a nucleosome? {{c1::H1}}
Published	07/28/2024	What class of histone is found outside the nucleosome and functions to condense the nucleosome together?{{c1::H1}}
Published	07/28/2024	What classes of histones are found as a pair in the nucleosome?{{c1::H2A, H2B, H3, H4::4}}
Published	07/28/2024	What is the function of the H1 class of histones?{{c1::Condense/link the nucleosomes together}}
Published	07/28/2024	A(n) {{c1::nucleosome}} is made up of a strand of DNA wrapped nearly twice around two copies of H2A, H2B, H3, and H4
Published	07/28/2024	In {{c1::mitosis::cell cycle phase}}, DNA condenses to form chromosomes
Published	07/28/2024	What cell cycle phase do DNA and histone synthesis occur?{{c1::S phase}}
Published	07/28/2024	What form of chromatin is highly condensed? {{c1::Heterochromatin}}
Published	07/28/2024	What form of chromatin is less condensed? {{c1::Euchromatin}}
Published	07/28/2024	What form of chromatin appears darker on EM? {{c1::Heterochromatin}}
Published	07/28/2024	What form of chromatin appears lighter on EM? {{c1::Euchromatin}}
Published	07/28/2024	What form of chromatin is transcriptionally inactive and sterically inaccessible? {{c1::Heterochromatin}}
Published	07/28/2024	What form of chromatin is transcriptionally active and sterically accessible? {{c1::Euchromatin}}
Published	07/28/2024	What form of chromatin do Barr bodies exist as? {{c1::Heterochromatin}}
Published	07/28/2024	{{c1::Heterochromatin}} is the highest order of packaging of the chromosome
Published	07/28/2024	Without H1, the nucleosome exists as {{c1::10}} nm chromatin
Published	07/28/2024	With H1, the nucleosome exists as {{c1::30}} nm chromatin
Published	07/28/2024	What process is used by mismatch repair enzymes to distinguish between old and new DNA strands in prokaryotes?{{c1::DNA methylation}}
Published	07/28/2024	DNA {{c1::methylation}} at {{c2::CpG}} islands {{c3::represses}} transcription
Published	07/28/2024	What process is used to genomically "imprint" DNA during embryogenesis?{{c1::DNA Methylation}}
Published	07/28/2024	Histone {{c1::methylation}} usually reversibly {{c2::represses}} DNA transcription
Published	07/28/2024	Histone {{c1::acetylation}} usually {{c2::activates}} DNA transcription
Published	07/28/2024	What process takes DNA and makes more DNA? {{c1::Replication}}
Published	07/28/2024	What process takes DNA and makes RNA? {{c1::transcription}}
Published	07/28/2024	What process takes RNA and makes protein? {{c1::translation}}
Published	07/28/2024	What process takes RNA and makes DNA? {{c1::reverse transcription}}
Published	07/28/2024	DNA is much {{c1::larger::size}} than RNA
Published	07/28/2024	Are RNA and protein typically fragmented before analysis? {{c1::No}}
Published	07/28/2024	Is DNA typically fragmented before analysis?{{c1::Yes}}
Published	07/28/2024	How many ring(s) do purines have?{{c1::Two}}
Published	07/28/2024	How many ring(s) do pyrimidines have?{{c1::One}}
Published	07/28/2024	Which bases are purines? {{c1::Adenine and guanine}}
Published	07/28/2024	Which bases are pyrimidines?{{c1::Cytosine, uracil, and thymine}}
Published	07/28/2024	Which purine is characterized by an amino group at the 12 o'clock position?{{c1::Adenine}}
Published	07/28/2024	Which purine is characterized by no amino group at the 12 o'clock position?{{c1::Guanine}}
Published	07/28/2024	Which pyrimidine is characterized by an amino group at the 12 o'clock position?{{c1::Cytosine}}
Published	07/28/2024	Which pyrimidine is characterized by no amino group at the 12 o'clock position AND no methyl group(s)?{{c1::Uracil}}
Published	07/28/2024	Which pyrimidine is characterized by the presence of methyl groups, but no amino group at the 12 o'clock position?{{c1::Thymine}}
Published	07/28/2024	{{c1::Deamination}} of cytosine makes {{c2::uracil}}
Published	07/28/2024	What is the difference (structurally) between thymine and uracil?{{c1::Thymine has a methyl group, uracil does not}}
Published	07/28/2024	Which pyrimidine is found in DNA only?{{c1::Thymine}}
Published	07/28/2024	Which pyrimidine is found in RNA only?{{c1::Uracil}}
Published	07/28/2024	A(n) {{c1::nucleoSide}} is a base plus a sugar (ribose or deoxyribose)
Published	07/28/2024	A(n) {{c1::nucleoTide}} is a base plus a sugar (ribose or deoxyribose) plus phosphate
Published	07/28/2024	What is the nucleoSide that is made with adenine? {{c1::Adenosine}}
Published	07/28/2024	What is the nucleoSide that is made with guanine? {{c1::Guanosine}}
Published	07/28/2024	What is the nucleoSide that is made with cytosine? {{c1::Cytidine}}
Published	07/28/2024	What is the nucleoSide that is made with uracil? {{c1::Uridine}}
Published	07/28/2024	What is the nucleoSide that is made with thymine? {{c1::Thymidine}}
Published	07/28/2024	Which carbon lacks a hydroxyl group in DNA strands?{{c1::2' carbon}}
Published	07/28/2024	DNA & RNA are made of {{c1::nucleotide monophosphates}} connected via a(n) {{c2::phosphodiester}} bond
Published	07/28/2024	Generally, the 5' end of DNA or RNA is a(n) {{c1::phosphate}} group
Published	07/28/2024	Generally, the 3' end of DNA or RNA is a(n) {{c1::hydroxyl}} group
Published	07/28/2024	Bases of a DNA strand are complementary and held together by {{c1::hydrogen}} bonds
Published	07/28/2024	How many hydrogen bonds exist between a G-C base pairing?{{c1::Three}}
Published	07/28/2024	How many hydrogen bonds exist between an A-T base pairing?{{c1::Two}}
Published	07/28/2024	What is the effect of increased G-C content on the melting temperature of a DNA strand?{{c1::Increased melting temperature}}
Published	07/28/2024	What amino acids are necessary for purine synthesis? {{c1::Glycine, Aspartate, Glutamine::3}}
Published	07/28/2024	One feature of the genetic code is that it is {{c1::unambiguous}}: each codon specifies only 1 amino acid
Published	07/28/2024	One feature of the genetic code is that it is {{c1::degenerate/redundant}}: most amino acids are coded by multiple codons
Published	07/28/2024	One feature of the genetic code is that it is {{c1::commaless, nonoverlapping}}: it is read from a fixed starting point as a continuous sequence of ba…
Published	07/28/2024	One feature of the genetic code is that it is {{c1::universal}}: genetic code is conserved throughout evolution
Published	07/28/2024	How many possible combinations of 3 base codons are there?{{c1::64}}
Published	07/28/2024	Of the 64 possible codons, how many encode amino acids?{{c1::61 (3 are stop codons)}}
Published	07/28/2024	How many amino acids are made from the 64 possible codons? {{c1::20}}
Published	07/28/2024	Which sequence of bases is a start codon (methionine) in mRNA? {{c1::AUG}}
Published	07/28/2024	What does AUG encode for in eukaryotes?{{c1::Methionine (start codon)}}
Published	07/28/2024	What does AUG encode for in prokaryotes?{{c1::N-formylmethionine, or fMet (start codon)}}
Published	07/28/2024	Which three sequences of bases are mRNA stop codons? {{c1::UGA, UAA, UAG}}
Published	07/28/2024	The {{c1::origin of replication}} is a particular consensus sequence of base pairs in a genome where DNA replication begins
Published	07/28/2024	{{c1::AT}}-rich sequences are found in promoters and origins of replication
Published	07/28/2024	The {{c1::replication fork}} is a Y-shaped region along the DNA template where leading and lagging strands are synthesized
Published	07/28/2024	Which enzyme is responsible for unwinding the DNA template at the replication fork? {{c1::Helicase}}
Published	07/28/2024	{{c1::Single-stranded binding}} proteins prevent DNA strands from reannealing during replication
Published	07/28/2024	Which enzyme is responsible for relaxing the DNA strand by creating single- or double-stranded breaks in the DNA helix to add/remove supercoils? {{c1:…
Published	07/28/2024	What is another name for prokaryotic topoisomerase II? {{c1::DNA gyrase}}
Published	07/28/2024	What class of drugs inhibits prokaryotic topoisomerase II and topoisomerase IV? {{c1::Fluoroquinolones}}
Published	07/28/2024	What chemotherapeutic drugs (2) inhibit eukaryotic topoisomerase II? {{c1::etoposide/teniposide}}
Published	07/28/2024	Which enzyme is responsible for making an RNA primer on which DNA polymerase III can initiate replication (prokaryotes)? {{c1::Primase}}
Published	07/28/2024	Which enzyme is responsible for elongating the DNA strand? {{c1::DNA polymerase (specifically, DNA polymerase III in prokaryotes)}}
Published	07/28/2024	{{c2::DNA}} polymerase must see a(n) {{c1::RNA primer}} to bind, which is complementary and antiparallel to the polymerase
Published	07/28/2024	DNA/RNA polymerase always read in the {{c1::3' to 5'}} direction
Published	07/28/2024	DNA/RNA polymerase always build in the {{c1::5' to 3'}} direction
Published	07/28/2024	DNA polymerase pauses and checks ("proof-reads") via {{c1::3' -> 5' exonuclease}} activity
Published	07/28/2024	Is DNA synthesis high or low fidelity? {{c1::High}}
Published	07/28/2024	Which enzymes are responsible for removing the RNA primer in eukaryotes? {{c1::RNase H and FEN-1::2}}
Published	07/28/2024	Which enzyme catalyzes the formation of a phosphodiester bond between Okazaki fragments?{{c1::DNA ligase}}
Published	07/28/2024	The enzyme which adds {{c2::TTAGGG::sequence}} to 3' ends of chromosomes to avoid loss of genetic material with every duplication is known as {{c1::Te…
Published	07/28/2024	Which replication enzyme is a RNA-dependent DNA polymerase, and thus a major example of reverse transcriptase activity, in humans? {{c1::Telomerase}}
Published	07/28/2024	Telomerase is a rare example where {{c1::reverse transcriptase::enzyme}} activity occurs endogenously in humans
Published	07/28/2024	What pathology is associated with increased telomerase activity?{{c1::Cancer}}
Published	07/28/2024	What pathology is associated with decreased telomerase activity?{{c1::Progeria (premature aging)}}
Published	07/28/2024	{{c1::RNA}} polymerase doesn't have to see a RNA primer to bind
Published	07/28/2024	Does RNA polymerase have 3' exonuclease activity (proof-reading)? {{c1::No}}
Published	07/28/2024	Is RNA synthesis high or low fidelity? {{c1::Low (no proof-reading)}}
Published	07/28/2024	Which type of DNA mutation causes the least severe damage? {{c1::Silent mutations}}
Published	07/28/2024	Which type of DNA mutation causes the most severe damage? {{c1::frameshift mutations}}
Published	07/28/2024	A(n) {{c1::transition}} is type of DNA mutation in which a purine is mutated to another purine (or pyrimidine to pyrimidine)
Published	07/28/2024	A(n) {{c1::transversion}} is a type of DNA mutation in which a purine is mutated into a pyrimidine, and vice versa
Published	07/28/2024	What class of DNA mutations are characterized by a single nucleotide change? {{c1::Point mutations}}
Published	07/28/2024	A(n) {{c1::silent}} mutation occurs when a nucleotide substitution codes for the same amino acid
Published	07/28/2024	A(n) {{c1::missense}} mutation occurs when a nucleotide substitution codes for a different amino acid
Published	07/28/2024	A(n) {{c1::nonsense}} mutation occurs when a nucleotide substitution codes for a stop codon
Published	07/28/2024	A(n) {{c1::frameshift}} mutation occurs when there is a deletion or insertion of a number of nucleotides not divisible by {{c2::3}}, resulting in…
Published	07/28/2024	A mutation at a(n) {{c1::splice site}} results in a retained intron in the mRNA, leading to a protein with impaired or altered function
Published	07/28/2024	Lac Operon: In the presence of {{c1::low glucose}}, there is increased {{c2::adenylyl cyclase}} activity, leading to an increase in {{c2::cAMP}}
Published	07/28/2024	Lac Operon: Increased cAMP (low glucose) leads to activation of {{c1::catabolite activator protein (CAP)}}, which resides upstream from the promoter, …
Published	07/28/2024	Lac Operon: In the presence of {{c1::high lactose}}, the {{c2::repressor}} protein is unbound from the {{c3::operator}} site, leading to increased tra…
Published	07/28/2024	Lac Operon: What is the expression level of the Lac genes in the presence of low glucose and lactose available? {{c1::Strong expression}}
Published	07/28/2024	Lac Operon: What is the expression level of the Lac genes in the presence of high glucose and lactose unavailable? {{c1::No expression}}
Published	07/28/2024	Lac Operon: What is the expression level of the Lac genes in the presence of low glucose and lactose unavailable? {{c1::No expression}}
Published	07/28/2024	Lac Operon: What is the expression level of the Lac genes in the presence of high glucose and lactose available? {{c1::Low (basal) expression}}
Published	07/28/2024	What mutation is induced by UV radiation?{{c1::Pyrimidine dimers (e.g. thymine dimers)}}
Published	07/28/2024	What form of DNA repair fixes mutations induced by UV radiation?{{c1::Nucleotide excision repair}}
Published	07/28/2024	The enzyme that recognizes and excises pyrimidine dimer mutations is {{c1::excision endonuclease}}
Published	07/28/2024	The enzymes that repair pyrimidine dimer mutations are {{c1::DNA polymerase}} and {{c1::DNA ligase}}
Published	07/28/2024	What phase of the cell cycle do nucleotide excision repairs occur?{{c1::G1}}
Published	07/28/2024	Xeroderma Pigmentosum is an inherited pathology due to a defective {{c1::Nucleotide Excision Repair}} pathway
Published	07/28/2024	DNA replication errors lead to {{c1::mismatch base}} mutations
Published	07/28/2024	What form of DNA repair fixes mutations due to DNA replication errors?{{c1::Mismatch repair}}
Published	07/28/2024	Recognition and facilitation of excision of {{c2::mismatched nucleotides}} occur via enzymes found on two genes: {{c1::MSH2 (MutS)}} or {{c1::MLH1 (Mu…
Published	07/28/2024	The enzymes that repair mismatched base mutations are {{c1::DNA polymerase}} and {{c1::DNA ligase}}
Published	07/28/2024	What pathology is characterized by a deficiency of the enzymes used in mismatch base repair? {{c1::Lynch syndrome (hereditary nonpolyposis colorectal …
Published	07/28/2024	What phase of the cell cycle do mismatch base repairs predominantly occur?{{c1::S}}
Published	07/28/2024	{{c1::Deamination (e.g. cytosine to uracil)}} is a mutation that may occur spontaneously or due to heat or nitrates
Published	07/28/2024	What form of DNA repair fixes mutations due to spontaneous/toxic deamination?{{c1::Base excision repair}}
Published	07/28/2024	In base excision repair, base-specific {{c1::glycosylases}} remove the altered base and create a(n) {{c2::AP (apurinic/apyrimidinic)}} site
Published	07/28/2024	Which base excision repair enzyme is responsible for removing nucleotides at the 5' end?{{c1::AP-endonuclease}}
Published	07/28/2024	Which base excision repair enzyme is responsible for removing nucleotides at the 3' end?{{c1::Lyase}}
Published	07/28/2024	Which base excision repair enzymes are responsible for filling and sealing the gap from the excised bases?{{c1::DNA polymerase-β::specific}} (filling)…
Published	07/28/2024	What phase of the cell cycle do base excision repairs occur?{{c1::Throughout the cell cycle}}
Published	07/28/2024	Which forms of DNA repair repairs double-stranded breaks (due to ionizing radiation)?{{c1::Nonhomologous end joining}} and {{c2::homologous recombinat…
Published	07/28/2024	Mechanisms to repair {{c1::dsDNA}} breaks are defective in Ataxia telangiectasia, Fanconi anemia, and SCID
Published	07/28/2024	The direction of protein synthesis is {{c1::N}}-terminus to {{c1::C}}-terminus
Published	07/28/2024	The {{c2::triphosphate}} bond of DNA is the target of {{c1::3' hydroxyl}} attack (strand elongation)
Published	07/28/2024	Drugs that block DNA replication often have a modified {{c1::3' OH}}, preventing addition of the next nucleotide ("chain termination")
Published	07/28/2024	Does reverse transcriptase require a primer?{{c1::Yes! Because it is a DNA polymerase (RNA dependent DNA polymerase)}}
Published	07/28/2024	While DNA polymerase binds to a primer, RNA polymerase binds to a(n) {{c1::promoter}}
Published	07/28/2024	The {{c1::template}} strand is the dsDNA strand used for transcription; it is complementary and antiparallel to mRNA
Published	07/28/2024	The {{c1::coding}} strand is the strand of dsDNA that is NOT used during transcription, but is identical to mRNA (substitute T/U)
Published	07/28/2024	Where is most of rRNA synthesized?{{c1::Nucleolus}}
Published	07/28/2024	Where is most mRNA / tRNA synthesized?{{c1::Euchromatin (nucleus)::chromatin}}
Published	07/28/2024	The dsDNA sequence reported in databases is the {{c1::coding}} strand, unless specifically stated otherwise
Published	07/28/2024	Practice: If a DNA template sequence is TAGC, what is the mRNA sequence?{{c1::GCUA}}
Published	07/28/2024	The {{c1::untranslated region (UTR)}} of mRNA is the portion of mRNA which contains no protein information
Published	07/28/2024	Does prokaryotic mRNA have introns and exons?{{c1::No}}
Published	07/28/2024	Does prokaryotic mRNA have post-transcriptional processing?{{c1::No}}
Published	07/28/2024	Prokaryotic transcription terminates when there is a "{{c1::stem-loop}}" sequence, which is a(n) {{c2::GC}} rich region
Published	07/28/2024	Prokaryotic translation begins when a ribosome binds a(n) {{c1::Shine-Dalgarno}} sequence
Published	07/28/2024	In eukaryotes, each gene has it's own {{c1::promoter}}, to which RNA polymerase II may bind
Published	07/28/2024	The initial mRNA of eukaryotes contains {{c1::introns}} and {{c1::exons}}, which undergo splicing
Published	07/28/2024	Eukaryotic translation begins when a ribosome binds a(n) {{c1::7-methyl-G-cap}}
Published	07/28/2024	The {{c1::promoter}} is the site where {{c2::RNA polymerase II}} and general transcription factors bind to DNA upstream from a gene locus
Published	07/28/2024	The promoter is an AT-rich upstream sequence with {{c1::TATA}} and {{c1::CAAT}} boxes
Published	07/28/2024	A mutation in the promoter commonly results in a dramatic {{c1::decrease}} in the level of gene transcription
Published	07/28/2024	Promoters serve as binding sites for {{c1::general::general/specific}} transcription factors
Published	07/28/2024	{{c1::Enhancers}} are stretches of DNA that increase gene expression by binding specific transcription factors
Published	07/28/2024	{{c1::Silencers}} are sites where negative regulators (repressors) bind to DNA
Published	07/28/2024	Enhancers increase transcription via enhanced activity of the enzyme {{c1::RNA polymerase II}}
Published	07/28/2024	Enhancers serve as binding sites for {{c1::specific::specific/general}} transcription factors
Published	07/28/2024	Are enhancers/silencers close or far from the gene it regulates?{{c1::May be close to, far from, or within the gene (in an intron)}}
Published	07/28/2024	Within an enhancer, there are domains known as {{c1::response elements (RE)}}, to which specific transcription factors bind
Published	07/28/2024	How can enhancers be far away from the gene it regulates?{{c1::DNA will bend to bring enhancer to promoter}}
Published	07/28/2024	Steroid receptors are specific transcription factors that bind to {{c1::steroid response elements}} to cause a steroid response
Published	07/28/2024	What class of protein receptor is common to all steroid hormones, thyroid hormones, and vitamins A/D? {{c1::Zinc finger}}
Published	07/28/2024	{{c1::cAMP response element binding (CREB)}} proteins are specific transcription factors that bind to cAMP response elements (CREs) to cause a respons…
Published	07/28/2024	What class of protein receptor is common to cAMP response element binding (CREB) proteins? {{c1::Leucine zipper}}
Published	07/28/2024	{{c1::Homeodomain}} proteins are specific transcription factors that regulate gene expression during development
Published	07/28/2024	The genes that are responsible for the generation of homeodomain proteins are the {{c1::homeobox (HOX)}} gene and {{c1::PAX}} gene
Published	07/28/2024	What pathology is associated with a defective PAX gene?{{c1::Klein Waardenburg Syndrome}}
Published	07/28/2024	What morning sickness drug (no longer used) inadvertently prevents binding of homeodomain proteins to enhancers, thus causing limb abnormali…
Published	07/28/2024	{{c1::Peroxisome proliferator-activated receptors (PPARs)}} are specific transcription factors that bind to peroxisome proliferator response elements …
Published	07/28/2024	What class of drugs acts via activation of PPAR-gamma? {{c1::Thiazolidinediones}}
Published	07/28/2024	What class of drugs acts via activation of PPAR-alpha?{{c1::Fibrates}}
Published	07/28/2024	What class of drugs acts via suppression of NF-kB signaling? {{c1::Glucocorticoids}}
Published	07/28/2024	RNA polymerase {{c1::I}} makes {{c2::r}}RNA
Published	07/28/2024	RNA polymerase {{c1::II}} makes {{c2::m}}RNA
Published	07/28/2024	RNA polymerase {{c1::III}} makes {{c2::t}}RNA and 5S rRNA
Published	07/28/2024	Which RNA polymerase binds to DNA at a promoter site?{{c1::RNA polymerase II}}
Published	07/28/2024	In eukaryotes, {{c2::RNA polymerase II}} may be inhibited by {{c1::α-amanitin}}
Published	07/28/2024	What drug is an inhibitor of prokaryotic RNA polymerase? {{c1::Rifampin}}
Published	07/28/2024	What drug is an inhibitor of both prokaryotic AND eukaryotic RNA polymerase? {{c1::Actinomycin D}}
Published	07/28/2024	How many different RNA polymerases do prokaryotes have? {{c1::One (makes all 3 kinds of RNA)}}
Published	07/28/2024	The initial (primary) transcript transcribed from eukaryotic DNA is {{c1::heterogenous nuclear RNA (hnRNA)}}
Published	07/28/2024	Capped, tailed, and spliced hnRNA is called {{c1::mRNA}}
Published	07/28/2024	In what part of the cell is mRNA formed?{{c1::Nucleus}}
Published	07/28/2024	In what part of the cell is mRNA translated?{{c1::Cytosol}}
Published	07/28/2024	One co-transcriptional modification is the addition of a(n) {{c1::7-methylguanosine cap}} at the {{c2::5}}' end
Published	07/28/2024	One post-transcriptional modification is the addition of a(n) {{c1::poly-A tail}} at the 3' end
Published	07/28/2024	One post-transcriptional modification is the {{c2::splicing out}} of {{c1::introns}}
Published	07/28/2024	Does Poly-A polymerase require a template (post-transcriptional processing)? {{c1::No}}
Published	07/28/2024	What sequence of bases represents a polyadenylation signal?{{c1::AAUAAA::6}}
Published	07/28/2024	mRNA quality control occurs at {{c1::cytoplasmic processing bodies (P-bodies)}}, which contain exonucleases, decapping enzymes, and microRNAs
Published	07/28/2024	mRNAs may be stored in {{c1::P-bodies}} for future translation
Status	Last Update	Fields