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73 Cards in this Set
- Front
- Back
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What is the location of replication? |
Prokaryotes- cytoplasm; Eukaryotes- Nucleus |
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Where is the location of transcription? |
Prokaryotes- cytoplasm; Eukaryotes- Nucleus |
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Where is the location of translation? |
Prokaryotes- cytoplasm; Eukaryotes- cytoplasm |
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What are the nucleic acids involved in replication? |
DNA (deoxyribonucleic acid) two identical copies formed,occurs during interphase of the cell cycle |
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What are the nucleic acids involved in transcription? |
DNA forms RNA (ribonucleic acid) (mRNA) |
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What are the nucleic acids involved in translation? |
RNA makes proteins (tRNA) |
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What are the three types of macromolecules present in DNA? |
*a five-carbon sugar, deoxyribose (DNA) missinghydroxyl group at the 2’ carbon *a nitrogen base (A,C,T,G) *phosphate group (eachhaving -1 charge unless on an end) |
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How would you determine an RNA strand from a DNA strand? |
Look at the 2’ carbon for identification; ribose is in RNA has 2’ –OH |
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Where are the phosphodiester bonds on the molecules? |
Nucleotides are joined by 3’- to5’-phosphodiester bonds- meaning the 3’ carbon hydroxyl on the sugar has aphosphate from another sugar (which is attached to the second sugars 5’ carbon) |
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What are important factors about the double helical structure? |
* Stability -protects bases from attack by H2Osoluble compounds and H2O itself; base pairs are in the center ofthe DNA strand * Negatively charged backbone, which can attract positivelycharged proteins and other molecules for stabilization *Hydrogen bonding and hydrophobic stacking between base pairs within DNA • Provides easy mechanism for replicationH- bonding allows for easy breakage |
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What type of bonding is found between the strands of DNA? |
Anti-parallel |
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In DNA the major groove is the larger/smaller one? |
Larger |
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In DNA the minor groove is the larger or smaller one? |
Smaller
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In RNA the major groove is the larger/smaller one? |
Smaller
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In RNA the minor groove is the larger/smaller one?
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Larger
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At what position does a purine bond to a sugar molecule?
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N9 position
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At what position does a pyrimidine bone to a sugar molecule?
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N1 position |
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At what carbon position can you identify RNA sugar vs DNA sugar? |
Sugars of DNA bases have two hydrogen's in the 2' position Sugars of RNA bases have one hydrogen in the 2' position |
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What is a nucleoside? |
Nitrogen base, sugar, NO PHOSPHATE |
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What are the different types of nucleotides? |
NMP, NDP, NTP (monophosphate, diphosphate, triphosphate)
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What are the names of the purine nucleosides? |
RNA: Guanosine, Adenosine DNA: Deoxyadenosine, Deoxyguanosine |
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What are the names of the pyirmidine nucleosides? |
RNA: Cytidine, Uridine DNA:Deoxycytidine, thymidine or deoxythymidine |
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What is the most common form of DNA? |
B-DNA |
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What are the three forms of DNA? |
Z, B, A |
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What is/are the right handed forms of DNA? |
A & B |
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What is/are the left handed forms of DNA? |
Z
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List the forms of DNA from largest to smallest. |
A>B>Z |
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How many base pairs are there per helical turn in A form DNA? |
11
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How many base pairs are there per helical turn in B form DNA? |
10.5
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How many base pairs are there per helical turn in Z form DNA? |
12
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What is the most common form of RNA and RNA-DNA duplexes? |
A-form
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What grooves are more accessible to proteins? |
Larger grooves which is the minor groove in RNA and the major grove in DNA |
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What is the sugar pucker in RNA? |
• Sugarpucker C3'-endo (in RNA 2'-OH inhibits C2'-endo conformation) |
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What is the sugar pucker in DNA? |
• Sugarpucker C2'-endo |
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When does the favored conformation for DNA and RNA occur? |
DNA: high water conformation
RNA: low water conformation |
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What is the difference between U and T? |
U found in RNA and T found in DNA also T is methylated on C5
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What is the structure and numbering of A. |
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What is the structure and numbering of G. |
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What is the structure and numbering of T. |
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What is the structure and numbering of C. |
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What is the structure and numbering of U? |
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What are the effects of alkali on DNA and RNA? |
-OH is a great nucleophile DNA strands stay intact but they separate. RNA strands are degraded to nucleotides. |
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What are the hydrogen bonding pattern in the nucleic acids? |
· A binds to T: 2-hydrogen bonds occur between thebases · A binds to U: 2-hydrogen bonds occur between thebases · G bind to C: 3-hydrogen bonds occur between thebases · The more G-C bond the more thermodynamicallystable the DNA molecule is because of the increased number of hydrogen bonds · The twoDNA strands are antiparallel |
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When do hair-pin turns occur? |
Palindromic DNA (orRNA) sequences can form alternative structures with intrastrand basepairing. When only a single DNA (or RNA) strand is involved, the structure iscalled a hairpin. |
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What is a cruciform? |
When both strands of a duplex DNA are involved with palindromic sequence This is a very stable form and caused by lack of histone orchaperon during DNA replication |
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What are the secondary structures in RNA? |
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What is the main absorption peak of nucleic acids? |
260nm |
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How can you determine the structure of a nucleic acid? |
NMR, 1H, or NOSEY |
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What are viruses containing double-stranded DNA? |
• adenovirus • smallpox virus • herpessimplex virus • humanpapilloma viruses * Epstein-Barr virus |
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What are the viruses the contain single-stranded DNA? |
• Torqueteno virus • ParvovirusB19 |
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What are the viruses that contain double-stranded RNA? |
rotavirus & reovirus. These genomes arealways segmented |
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What are the viruses that contain positive-sense single-stranded DNA? |
• Picornaviruses: • HepatitisA virus • enteroviruses, • rhinoviruses • poliovirus • foot-and-mouth virus * SARS virus * hepatitis Cvirus * yellow fevervirus * rubella virus * Chikungunyavirus |
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What does positive sense mean? |
("plus-strand"): 5' to 3‘ viral RNA that issimilar to host mRNA and thus can be immediately translated by the host cell |
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What does negative sense mean? |
("minus-strand"): 3' to 5‘ viral RNAthat is complementary to host mRNA and thus must be converted to positive-senseviral RNA by an RNA polymerase before translation |
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What is the difference between positive and negative sense single stranded RNA? |
Difference between positive and negative is how the virusenters the cell |
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What viruses contain negative-sense single-stranded RNA? |
* deadly Ebola * Marburg viruses * influenza virus * measles * mumps * rabies |
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What does lamivudine and adefovir dipivoxil treat? |
Approved for HBV (hepatitis B virus) -mimic purines and pyrmidines |
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What does acyclovir, valciclovir, famciclovir, and penciclovir treat? |
Approved for HSV (herpes simplex virus) infections - all mimic purinies |
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What does ganciclovir, valganciclovir, foscarnet, and cidofovir treat? |
Approved for HCMV (human cytomegalovirus) infections mimic phosphate backbone (foscarnet), pyrmidine, purines |
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What does brivudine treat?
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Used for VZV (varicella-zoster virus) infection mimics purine |
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Know the structure of C3' and C2' endo sugar puckers. |
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What is needed to make RNA? |
DNA |
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What is chromatins function? Do prokaryotes have chromatin? What does chromatin contain? |
o Eukaryotic DNA is bound to proteins, forming acomplex called chromatin. Chromatin contains DNA plus histonesand other proteins. During interphase (when cells are not dividing), some ofthe chromatin is diffuse (euchromatin) and some is dense (heterochromatin),but no distinct structures can be observed. The organization of eukaryotic DNAinto chromatin is essential for controlling transcription, as well asfor packaging. o No o Chromatin contains DNA plus histones and otherproteins |
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What is a polynucleosome? |
o DNA packed around many histones and chromatin. Histonesare highly alkaline proteins found in eukaryotic cell nuclei that package andorder the DNA into structural units called nucleosomes. |
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What chromosome determines sex? What dictates male? Female? |
o Chromosome 23, XY, XX |
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What causes down syndrome? |
o Chromosome 21 has a trisomy (three chromosomespresent instead of the normal 2) |
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What are homolog alleles |
o Homolog alleles (e.g., AA, Bb, CC, dD)may be identical (e.g., AA, CC) or may differ (e.g., Bb, dD) in DNA sequence.Therefore, the corresponding protein products may be identical or they maydiffer slightly in amino acid sequence. Come from homologous chromosomes |
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· What are ribosomes made of? What are the ribosomes and associatedsubunits for Prokaryotes? Eukaryotes? Which is larger? |
o rRNA o Prokaryotes: Subunits- 50s and 30s form to makethe 70s ribosome o Eukaryotes: Subunits- 60s and 40s form to makethe 80s ribosome o Subunits of the eukaryotes are larger then thoseof prokaryotes |
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· What are Hoogsteen pairs? When do they occur? |
o Hoogsteenpair (on sugar side), Watson Crick (magenta · black) |
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· What is the typical structure of tRNA? Where isthe attachment site of the amino acid? |
o Cloverleaf structureo Attachment site at the 3’ endo Be able to identify all associated structureswith the tRNA |
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· When does non-watson-crick base pairing occurand what is the pairing? |
o Occurs in E. coli RnaseP and our DNA I think o G-U pairing |
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Can DNA undergo reversible denaturation? |
Yes |
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· What can happen when heat is applied to DNA? |
o Depends on pH, ionic strength & on the sizeand base composition of the DNA. o DNA with more G/C base pairs has a highermelting temperature than A/T rich DNA, due to the three H-bonds between G/C |
