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HY Cell Bio Day 9

Day 9

What is the difference in location between carbamoyl phosphate synthetase I and II? CPS I is found in the mItochondria. CPS II is found in the cytosol.
What is the difference in pathways between carbamoyl phosphate synthetase I and II? CPS I acts in the urea cycle pathway. CPS II acts in the pyrimidine synthesis pathway.
What is the difference in nitrogen source between carbamoyl phosphate synthetase I and II? CPS I gets its nitrogen from ammonia. CPS II gets its nitrogen from glutamine.
What is the RLS in purine synthesis? glutamine PRPP aminotransferase
What is the RLS in pyrimidine synthesis? CPS II (carbamoyl phosphate synthetase II)
What are the sources of carbons in the formation of purines? CO2, glycine, and tetrahydrofolate
What are the sources of carbons in the formation of pyrimidines? CO2 and aspartate
What accounts for the positive charge of histones? Lysine and arginine
What accounts for the negative charge of DNA? Phosphate groups
Which medication matches the following statement?: inhibits ribonucleotide reductase hydroxyurea
Which medication matches the following statement?: inhibits dihydrofolate reductase MTX (eukaryotes), TMP (bacteria)
Which medication matches the following statement?: inhibits thymidylate synthase 5-FU
Which medication matches the following statement?: inhibits inosine monophosphate dehydrogenase Mycophenylate
Which medication matches the following statement?: inhibits PRPP synthetase 6 mercaptopurine (metabolized by xanthine oxidase, so made more toxic by allopurinol)
Child presents with orotic acid in urine, megaloblastic anemia that is non-responsive to B12 or folic acid administration, and failure to thrive. No hyperammonemia is present. Orotic aciduria (AR)
What causes orotic aciduria? Inability to convert orotic acid to UMP (de novo pyrimidine synth path) due to defect in either orotic acid phosphoribosyltransferase or orotidine 5'-phosphate decarboxylase
How does UV light damage DNA? Creates thymine dimers (thymine paired to thymine) in the same strand of DNA
What eukaryotic DNA polymerase matches the following description?: replicates lagging strand, synthesizes RNA primer DNA polymerase alpha
What eukaryotic DNA polymerase matches the following description?: repairs DNA DNA polymerase beta and epsilon
What eukaryotic DNA polymerase matches the following description?: replicates mitochondrial DNA DNA polymerase gamma
What eukaryotic DNA polymerase matches the following description?: replicates leading strand DNA DNA polymerase delta
Hypersensitivity to UV light; 1000x increased risk of developing skin cancers due to DNA repair defect Xeroderma pigmentosum
Sensitivity to ionizing radiation, immunodeficiency, ataxia beginning at 1-2 years, increased AFP levels in an infant >8mos old. DNA repair defect. Ataxia-telangiectasia (telangiectasias develop later on)
Hypersensitivity to sunlight, leukemias, and lymphomas are common; average age of cancer onset is 25yo. DNA repair defect. Bloom's syndrome.
Regulation of transcription: structural genes that are transcribed + promoter region + all regulatory genes Operon
Regulation of transcription: Where must transcription factors bind in order for transcription to take place (be specific)? Must bind to promoter region= TATA box 25 upstream and CAAT box 75 upstream
Name 4 structural motifs which allow proteins to bind to DNA. 1. Helix-loop-helix 2. Helix-turn-helix 3. Zinc finger 4. Leucine zipper
Regulation of transcription: binds repressor (stops transcription), or inducer (starts transcription) located between the promoter region and the start site Operator region
Regulation of transcription: Increase or decrease the rate of transcription when bound by protein factors; location may be close to, far from, or within the promoter region Response elements (enhancer region and repressor region)
What are two methods for terminating prokaryotic RNA transcription? 1. GC rich DNA forms hairpin loop in RNA that pushes RNA polymerase off at a weak spot 2. Rho factor uses the energy from an ATPase to kick off the RNA polymerase
Transcription can be either activated or repressed by the ______ repressor. Lambda (activation vs repression depends on exact binding site on DNA)
What does the lac operon control expression of? B-galactosidase (breaks down lactose into useable monomers like glucose and galactose)
What is the only situation in the lac operon that will allow transcription to take place? Absent glucose, excess lactose, and present CAP (CAP will not show up in presence of glucose, the repressor will hang around in the absence of lactose, and the lac operon can only be turned on if the repressor is gone and cap is present)
Which antibiotic matches the following description?: inhibits 50S peptidyltransferase Streptogramins, chloramphenicol
Which antibiotic matches the following description?: Bind 30S, preventing attachment of aminoacyl-tRNA Tetracyclines
Which antibiotic matches the following description?: inhibits prokaryotic RNA polymerase Rifampin
Which antibiotic matches the following description?: inhibits prokaryotic topoisomerase Fluoroquinolones
Which antibiotic matches the following description?: inhibits prokaryotic dihydrofolate reductase TMP
What are the 3 different mechanisms cells employ to break down proteins? 1. Ubiquitin (ubiquitin protein ligase) 2. Lysosome 3. Ca-dependent enzyme
What enzyme catalyzes peptide bond formation during protein synthesis? Peptidyl transferase (ribozyme/ribosomal RNA)
What enzyme matches amino acids to tRNA? aminoacyl tRNA synthetase
What are the mRNA stop codons? UGA, UAA, UAG (U Go Away, U Are Away, U Are Gone)
What are the 3 different RNA polymerases in eukaryotes? RNA polymerase I makes rRNA. RNA polymerase II makes mRNA. RNA polymerase III makes tRNA. I, II, and III are numbered as their products are used in protein synthesis
What amino acid frequently has more coding sequences in the mRNA than are represented in the peptide that is created from that mRNA? Methionine (b/c AUG is a start codon and methionine may be removed b/f translation is complete)
How must hnRNA (heterogeneous nuclear RNA) be processed before it is allowed to leave the nucleus? 1. 5' cap, 2. poly A tail, 3. Splicing out of introns (INtrons are INtroverts who like to stay INside the nucleus. EXons are EXtroverts who like to EXit the nucleus so they can go EXpress themselves in the cytoplasm)
What is the characteristic sequence of the promoter region? What does a mutation in the sequence cause? -25 TATA box and -75 CAAT box; mutation causes a decrease in the amt of gene transcribed
What enzyme is deficient in Lesch-Nyhan syndrome? What is the treatment? HGPRT; allopurinol for gout symptoms
Which histone is the only one that is not part of the nucleosome core? H1 (helps package nucleosomes into more compact structures by binding and linking DNA between adjacent nucleosomes)
Condensed, transcriptionally inactive, sterically inaccessible chromatin Heterochromatin
Less condensed, transcriptionally active, sterically accessible Euchromatin
Where is ribosomal RNA synthesized? In the nucleus
What are the purine nucleotides? A and G (PURe As Gold)
What are the pyrimidine nucleotides? C, U, T (CUT the Py)
Which will have a higher melting point-- G-C rich DNA or A-T rich DNA? Why? G-C rich DNA will have a higher melting point because G-C has 3 H bonds (A-T only has 2), which makes it harder to break apart.
What is the general difference in the beginning of the pyrimidine and purine synthesis pathways? Pyrimidine synth starts with a base (orotic acid) and then adds a sugar. Purine synth starts with a sugar (ribose 5-P) and then adds a base.
Purines are made from ______ precursor. IMP (inosine monophosphate)
Pyrimidines are made from ______ precursor with _____ added later. Orotate; PRPP (phosphoribosyl pyrophosphate)
Ornithine transcarbamoylase deficiency (urea cycle) leads to an accumulation of carbamoyl phosphate which is then converted to _________. Orotic acid (will have hyperammonemia b/c body cannot get rid of ammonia without urea)
What are the symptoms of hyperammonemia? Tremor, slurred speech, somnolence, vomiting, cerebral edema, and blurring of vision.
What is the treatment for orotic aciduria? Oral uridine administration (b/c they can't make their own)
Excess ATP and dATP imbalances nucleotide pool via feedback inhibition of ribonucleotide reductase--> prevents DNA syntehsis and thus decreases lymphocyte count. What enzyme is deficient and what disease is assoc'd? Adenosine deaminase deficiency; SCID
Retardation, self-mutilation, aggression, hyperuricemia, gout, choreoathetosis (involuntary limb movements). What enzyme is deficient and what disease is assoc'd? HGPRT (He's Got Purine Recovery Trouble); Lesch-Nyhan syndrome
What is the 1 exception to the redundancy/degeneracy of the genetic code? Methionine is encoded by only 1 codon: AUG (start codon; inAUGurates)
Name that genetic code feature!: CAU can only make histidine. Unambiguous: each codon specifies only 1 AA
Name that genetic code feature!: Histidine can be made by both CAU and CAC Degenerate/redundant: more than 1 codon may code for the same AA
Name that DNA mutation!: Same AA, often base change in 3rd position of codon (tRNA wobble) Silent
Name that DNA mutation!: changed AA (ocservative; new AA is similar in chemical structure) Missense (just a little mishap!)
Name that DNA mutation!: Change resulting in an early STOP codon Nonsense (STOP this nonsense!)
Name that DNA mutation!: Change resulting in misreading of all nucleotides downstream, usually resulting in a truncated, non-functional protein Frame shift (Oh shift! You messed the whole thing up!)
What is the severity of damage among the following 3 mutations: missense, nonsense, silent? Nonsense > missense > silence
What is the typical outcome of a splice site mutation? Larger protein with altered function but preserved immune reactivity
What enzyme converts ribose to PRPP in the purine synth path? PRPP synthetase (inhibited by 6 mercaptopurine)
What enzyme converts UDP to dUDP in the pyrimidine synthesis pathway? Ribonucleotide reductase (inhibited by hydroxyurea)
What enzyme converts dUMP to dTMP? Thymidylate synthetase (inhibited by 5-FU)
What enzyme converts dihydrofolate to tetrahydrofolate? Dihydrofolate reductase (inhibited by MTX and TMP)
Unwinds DNA template at replication fork (Y shaped region where leading and lagging strands are synthesized) Helicase
Prevent strands from reannealing Single-stranded binding proteins
Create a nick in the helix to relieve supercoils created during replication DNA topoisomerases
What drug inhibits DNA gyrase (specific prokaryotic topoisomerase)? What is its counterpart in eukaryotes? Fluoroquinolones; etoposide is the eukaryotic counterpart (used to eradicate ball cancer he he he)
What direction does DNA polymerase III synthesize? What direction does it proofread? Synthesize is 5'-->3'. Proofread is 3'-->5'.
What is the only DNA polymerase that has 5'-->3' exonuclease activity? DNA polymerase I (prokaryotic only)
Okazaki fragments: __________ cuts out all the individual RNA primers and ________ glues the fragments together to make one continuous strand. DNA polymerase I; DNA ligase
In what direction does DNA polymerase read the strand? 3'-->5' (synthesizes 5'-->3')
Adds a piece of RNA to act as RNA primer so DNA can begin polymerizing Primase
True or false? The poly A tail is separately transcribed from DNA before it can be added to mRNA. False. Poly-A tail is not transcribed from DNA.
Repeats of codons at the ends of DNA that act as a safety mechanism to protect against loss of DNA during replication; shorten with age. Telomeres
What action signals the removal and replacement of UV-damaged DNA? A specific endonuclease initiates the process by nicking the strand at the thymine dimer.
What occurs after endonucleases remove the damaged bases in nucleotide excision repair? DNA polymerase fills the gap and DNA ligase seals it
Which DNA repair mechanism is mutated in hereditary nonpolyposis colorectal cancer (HNPCC)? mismatch repair
How does radiation exposure induce DNA damage? DNA double strand fractures and formation of oxygen free radicals
mRNA is read in what direction? 5'-->3'
What toxin is found in death cap mushrooms? Which RNA polymerase does it inhibit? What organ failure does it cause? Alpha-amanitin inhibits RNA polymerase II and causes liver failure if ingested.
What is the most abundant type of RNA? rRNA (Rampant)
What is the longest type of RNA? mRNA (Massive)
What is the smallest type of RNA? tRNA (Tiny)
Splicing of pre-mRNA is accomplished by what cell machinery? Spliceosome
Patients with which disease make antibodies to spliceosomal snRNPs? Lupus
What factors are responsible for the accurate selection of AA? Aminoacyl-tRNA synthetase and binding of charged tRNA to the codon.
What class of drugs binds the 30S subunit preventing attachment of aminoacyl-tRNA? Tetracyclines (this makes it impossible for bacteria to select the appropriate AA)
What end of the tRNA molecule is the site of AA binding? 3' end
What is the tRNA wobble? Accurate base pairing is required only in the first 2 nucleotide positions of an mRNA codon, so codons differing in the 3rd wobble position may code for teh same tRNA/AA (due to degeneracy of code).
Which site on the ribosome carries the elongating strand during protein synthesis? P site
From which site does the empty tRNA exit? E site (E for Exit)
Which site accepts the incoming aminoacyl tRNA? A site
What are the steps of protein synthesis elongation? 1. Aminoacyl-tRNA binds to A site (except for initiator Methionine) 2. Ribosomal rRNA catalyzes peptide bond formation, transfers growing polypep to AA in A site. 3. Ribosome moves 3 nucleotides toward 3' end, moving peptidyl RNA to P site (translocatio
Which class of antibiotics inhibits formation of the initiation complex and cause misreading of mRNA during protein synthesis? Aminoglycosides (-mycin drugs like gentamycin, neomycin, amikacin, tobramycin, streptomycin)
Which antibiotics inhibit the 50S peptidyl transferase? Chloramphenicol and streptogramins
Which antibiotics bind 50S, blocking translocation? Macrolides, clindamycin, and linezolid
Where are ribosomes synthesized? In the nucleus (and then transported out into the cytoplasm)
Where does the post-translational modification of proteins take place? In the Golgi
Where does the aminoacyl-tRNA synthetase act on the tRNA molecule? At the 3'-OH end
Makes an RNA primer on which DNA polymerase III can initiate replication Primase
tRNA has what sequence at its 3' end which is used as a recognition site by proteins? CCA (prob lower yield)
Created by: sarah3148



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