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| structure of a pyrimidine |
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| something epigenetic that can happen to cytosine when adde to nucleotide strand |
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| the H atom where the arrow is pointing gets replaced by CH3; gets methylated
[image] |
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Term
| where adenosine comes from |
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Definition
adenine
Adenine becomes the nucleoside Adenosine when it becomes combined with a ribose |
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| when adenine becomes adenosine |
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Definition
| when it becomes combined with a ribose |
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| macromolecule ATP seems to be present in |
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| the phosphate you want to tag in ATP |
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| the alpha phosphate, which is the closest to the ribose |
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| how a phosphate is tagged |
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Definition
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| what happens if you label the gamma phosphate? |
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| it'll wind up in pyrophosphate |
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| the form of ATP that seems to be present in DNA |
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| in essence, our genetic material is basically... |
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| structure of deoxyribose ATP |
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| why RNA is less stable than DNA |
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| because RNA contains that reactive OH group |
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| some questions the structure of DNA can answer |
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Definition
1: replication
2: nature/function of a gene
3: genetic basis of heredity
4: molecular basis of evolution (this is a more modern matter because it requires ability to sequence DNA; the technology for that wasn't developed until 1970's) |
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| why genetics is important to a cell |
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Definition
| because cells have to keep their genetic constitution to stay alive |
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| how Rosalind Franklin contributed to discovering the structure of DNA |
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Definition
Franklin was a great crystallographer; got hired to determine structure of D-form DNA
Wilkins released Franklin's data and Franklin was oblivious to this |
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Definition
A = T
G = C
DNA obeys the rule, but RNA doesn't; it's a universal role of double-stranded DNA |
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| things to consider with DNA structure |
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Definition
1: stabilizing forces
2: Double helix is directional/antiparallel
3: Major and minor grooves (asymmetrical threads of a screw) |
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| some stabilizing forces in DNA |
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Definition
- Hydrophobic interactions
- H-bonding, W/C (Watson/Crick) pairing
- van der Waals forces act on adjacent stacked base pairs |
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| distance between consecutive bases in DNA |
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Definition
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Definition
| 1 100millionth of a centimeter
10-10 |
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| what the asymmetric threading of the "screw" does for the DNA molecule |
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Definition
| presents different faces of the strands of the helix to the outside |
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| one reason the phosphate backbone is on the outside of the DNA molecule |
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Definition
| because phosphates are more hydrophilic than bases |
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| side view of DNA molecule |
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Definition
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| depiction of the asymmetric "screw" of DNA |
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Definition
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| depiction of the bonding between guanine and cytosine |
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| depiction of the bonding between adenine and thymine |
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Definition
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| depiction of the van der Waals interactions in base stacking |
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| how DNA strands can be separated in the lab |
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Definition
The temperature at which half of the DNA
molecules are denatured |
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Definition
| separated DNA strands combining to form the double helix |
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| what alkali or chaotropic agents do to DNA |
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Definition
| denature DNA by disrupting non-covalent interactions |
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| how chaotropic agents break down DNA |
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Definition
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| which DNA absorbs more light? single stranded or double stranded? |
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Definition
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Term
| chart showing wavelength absorbance of single stranded and double stranded DNA |
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Definition
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Definition
| the increase in light absorption that occurs when single strands flop around |
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Term
| depiction of a hyperchromic shift |
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Definition
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Term
| dsDNA can be denatured by... |
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Definition
| heat or chaotropic agents |
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Term
| Extent of denaturation can be measured by... |
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Definition
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Definition
| duplexes that are all A's and T's |
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Definition
| duplexes that are all G's and C's |
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| depiction of a Tm chart vs. UV absorbance by DNA |
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Definition
[image]
Any DNA you put in there has to be between those 2 extremes |
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Term
| the hallmarks of DNA structure |
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Definition
-DNA consists of two chains of polynucleotides
-Paired via hydrogen bonds
-Running in opposite directions
-right-handed helix around a central axis
-Bases found on the inside of the helix
-Phosphates and sugars on the outside
-bases perpendicular to the axis (Bform) |
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| this accounts for some of the compaction of the DNA |
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Definition
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| Further compaction of DNA occurs by... |
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Definition
| binding certain proteins to the DNA |
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| how much does an average chromosome have to be compacted? |
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Definition
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Definition
| modifications of histones and effect of histones on DNA expression |
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| can epigenetic factors be inherited? |
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Definition
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Definition
| protein octamers that have a strong affinity for DNA and bind to it in a certain way |
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| depiction of the histone octamer |
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Definition
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| depiction of nucleosome core particle |
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Definition
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| depiction of nucleosome core particle and linker DNA |
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Definition
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| depiction of all the compaction that occurs with DNA |
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Definition
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| the amount of DNA compaction we seem to have accounted for so far |
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Definition
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Term
| can characteristics of chromatin be inherited? |
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Definition
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| A common structural motif seen in nucleic acids, most notably RNA |
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Definition
|
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Term
| the stem-loop occurs when... |
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Definition
complementary
sequences in the same strand form a double helix |
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Term
| do Non-Watson-Crick base pairs occur frequently in RNA? |
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Definition
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Term
| More elaborate structures of RNA are |
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Definition
| often stabilized by Mg2+ ions |
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Term
| depiction of stem loop structure |
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Definition
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Term
| depiction of Prokaryotic gene expression |
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Definition
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Term
| can RNA in prokaryotes have multiple protein coding sequences? |
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Definition
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Term
| depiction of Euokaryotic gene expression |
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Definition
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| what occurs at each end of the mRNA molecule in eukaryotic gene expression? |
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Definition
| covalent modifications to form a cap |
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Term
| in eukaryotic gene expression, every step along the way has the potential to be... |
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Definition
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Term
| genetic mapping reveals... |
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Definition
| order of genes on specific chromosomes |
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Term
| composition of the human geneome |
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Definition
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Term
| how much of the human genome encodes proteins? |
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Definition
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Definition
| gene that encodes RNA that never codes a protein product |
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| how much of the genome contains sequences linked to biological function? |
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Definition
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| how much of the genome is transcribed at some point? |
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Definition
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Term
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Definition
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Term
| can transcripts be synthesized by both strands? |
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Definition
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Term
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Definition
| Genome Wide ASsociation variants associated with diseases such as schizophrenia and type 2 diabetes |
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Term
| GWAS studies try to understand... |
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Definition
| pleiotropic things in the genome |
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Term
| some challenges to defining a gene |
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Definition
• Gene regulatory sequences
• Overlapping genes (introns and exons)
• Parasitic and mobile genes (transposons)
• “Junk” DNA is conserved
• Pseudogenes (duplicated genes)
• Pervasive transcription |
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Definition
| Parasitic and mobile genes |
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Term
| what happens to “Junk” DNA? |
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Definition
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Term
| depiction of gene complexity |
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Definition
|
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Term
| why RNA is more unstable than DNA |
|
Definition
| because it has that reactive OH group |
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Term
| depiction of the difference between DNA and RNA |
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Definition
|
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Term
| depiction of what happens to RNA when it is treated with NaOH |
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Definition
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Term
|
Definition
|
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Term
| what CsCl does for separation of light and heavy DNA |
|
Definition
| forms density gradient along the centrifuge tube |
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Term
| The reaction catalyzed by DNA polymerase |
|
Definition
| (DNA)n + dNTP <--> (DNA)n + 1 + PPi |
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Term
| depiction of The reaction catalyzed by DNA polymerase |
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Definition
|
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Term
| depiction of RNA strand-elongation rxn |
|
Definition
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Term
| Key characteristics of DNA synthesis in vitro |
|
Definition
| 1. Four deoxynucleoside triphosphates and Mg2+ are required in the buffer.
2. A template strand is used to direct DNA synthesis.
3. A primer from which the new strand grows must be present. |
|
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Term
| what's required in the buffer for DNA synthesis? |
|
Definition
| Four deoxynucleoside triphosphates and Mg2+ |
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Term
| ion required for DNA synthesis |
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Definition
|
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Term
| table of E. coli DNA polymerases |
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Definition
|
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Term
| where in the molecule does exonuclease start? |
|
Definition
|
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Term
| where in the molecule does endonuclease start? |
|
Definition
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Term
|
Definition
| nicks or 2bl stranded breaks |
|
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Term
| general depiction of replication fork |
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Definition
|
|
Term
| depiction of DNA polymerase holoenzyme |
|
Definition
| [image]
the β2 is basically a Sliding Clamp |
|
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Term
| how the DNA polymerase holoenzyme is processive |
|
Definition
| it doesn't let go of the substrate; it can replicate many bases before it falls off the substrate |
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Term
| what the clamp loader in the DNA polymerase holoenzyme does |
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Definition
| opens and closes the beta 2 donut ring |
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Term
| depiction of the trombone model of the DNA polymerase holoenzyme |
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Definition
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Term
| single strand binding protein (SSB) |
|
Definition
| coats single stranded DNA to protect it from degradation |
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Term
| what primase does for DNA synthesis in the lagging strand |
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Definition
| adds RNA to the DNA to serve as a primer |
|
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Term
| depiction of DNA synthesis from primer |
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Definition
|
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Term
| depiction of the type of nick sealed by ligase |
|
Definition
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Term
|
Definition
|
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Term
|
Definition
| relieves tension by introducing negative supercoils ahead of the fork |
|
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Term
| depiction of Topoisomerase II in the replication fork |
|
Definition
|
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Term
|
Definition
| the enzyme responsible for telomeres |
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Term
| depiction of replication and telomeres |
|
Definition
|
|
Term
| depiction of telomeres in embryonic and adult stem cells |
|
Definition
|
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Term
| depiction of extending the length of a telomere |
|
Definition
|
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Term
| what happens with telomerases in aging? |
|
Definition
|
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Term
| what happens with telomerases in cancer? |
|
Definition
|
|
Term
| the type of enzyme telomerase is |
|
Definition
|
|
Term
| something telomerase conains |
|
Definition
| RNA molecule; this makes it a reverse transcriptase |
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Term
| The simplest source of DNA damage |
|
Definition
| the incorporation of an incorrect base during replication that escapes the proofreading capabilities of the DNA polymerases |
|
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Term
| some types of errors that can halt DNA synthesis |
|
Definition
| insertion, deletions or breaks in one or both strands |
|
|
Term
| depiction of Proofreading by replicative DNA polymerase |
|
Definition
|
|
Term
| how replicative DNA polymerase proofreads DNA |
|
Definition
-removes incorrect base
-repeats synthesis rxn |
|
|
Term
| depiction of triplet repeat expansion |
|
Definition
|
|
Term
| what triplet repeat expansion can do to mRNA |
|
Definition
|
|
Term
| how DNA is replicated when intrinsic repair mediated by replicative DNA polymerase fails |
|
Definition
1. Recognize the inappropriate base(s).
2. Remove the inappropriate base(s).
3. Fill in the resulting gap with repair DNA polymerase.
4. DNA ligase removes SS breaks, restores DS DNA. |
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Term
| Last resort to remove inappropriatebase(s) |
|
Definition
|
|
Term
| depiction of DNA mismatch repair |
|
Definition
|
|
Term
| what distinguishes old from newly replicated strands in E. coli? |
|
Definition
| adenine-methylation; new strands are unmethylated |
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Term
|
Definition
|
|
Term
|
Definition
| enhances ability to recognize error |
|
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Term
|
Definition
| makes single stranded break |
|
|
Term
| Damage to bases can occur by... |
|
Definition
|
|
Term
| types of mutagenic agents that can damage bases |
|
Definition
|
|
Term
| Hydroxyl radicals aka Reactive Oxygen Species |
|
Definition
| oxidize guanine to 8-oxoguanine |
|
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Term
|
Definition
| deaminates adenine, forming hypoxanthine |
|
|
Term
| types of chemical addition of DNA adducts |
|
Definition
-alkylation
-addition of bulky side groups |
|
|
Term
| how chemical addition of DNA adducts inhibits DNA replication |
|
Definition
|
|
Term
| what UV irradiation does to DNA |
|
Definition
forms covalent bonds between adjacent thymidines to form thymidine dimers
enzyme system can't fix the damage; this causes skin cancer |
|
|
Term
| depiction of how Hydroxyl radicals aka reactive oxygen species affect duanine |
|
Definition
|
|
Term
| depiction of Base Excision Repair (BER) |
|
Definition
|
|
Term
|
Definition
|
|
Term
| depiction of Adenine deamination: A to C transversion |
|
Definition
|
|
Term
| how Adenine deamination helps create immunity |
|
Definition
| mutates DNA at specific points in immunoglobulin genes in response to specific diseases; helps create immunity |
|
|
Term
| some things that can cause bulky adducts to be added to DNA bases |
|
Definition
-Tobacco smoke
-Aflatoxin
-Nitrated polycyclic hydrocarbons (Eat →Die)
-Some require oxidation by liver cytochrome P450 to react with DNA
-Nucleotide Excision Repair |
|
|
Term
| depiction of bulky adduct being added to DNA base |
|
Definition
|
|
Term
| If BER fails to recognize the damaged base, the mutation may be corrected by... |
|
Definition
| NER (bulky adducts, alkylated bases) |
|
|
Term
| how is a mutation corrected when all else fails? |
|
Definition
| translesion repair polymerases synthesize past the damage (error prone) |
|
|
Term
| depiction of Repair of thymine dimers by DNA photolyase |
|
Definition
|
|
Term
| what thymine dimers do to cells |
|
Definition
-causes replication to halt
-causes cells to die by apoptosis |
|
|
Term
| depiction of creation of a double stranded break |
|
Definition
[image]
X-rays can cause this type of DNA damage |
|
|
Term
| why Dideoxynucleotide triphosphates (ddNTPs) stop chain growth |
|
Definition
| because it is missing a 3' hydroxyl, which means there's nothing to be added to |
|
|
Term
| depiction of Dye terminator sequencing (pool rxns) |
|
Definition
|
|
Term
| Why is RNA synthesis essential for DNA replication? |
|
Definition
| because it can be used as a primer and DNA synthesis is activated by primers |
|
|
Term
| What are the functions of helicases and topoisomerases during replication? |
|
Definition
| helicase unwinds DNA and topoisomerase relieves tension by making nicks ahead of replication fork |
|
|
Term
|
Definition
|
|
Term
| function of topoisomerase |
|
Definition
| relieves tension by making nicks ahead of replication fork |
|
|
Term
| One simple way to avoid the end-replication problem |
|
Definition
circular genome
some viruses add more viral DNA at the end |
|
|
Term
| What are the steps required of most DNA repair systems? |
|
Definition
1: recognize error
2: remove error
3: resynthesize
4: reseal with ligase |
|
|
Term
| depiction of the Ames test |
|
Definition
|
|
Term
| sign of defective telomerase |
|
Definition
|
|
Term
| what you can do with PacBio SMRT sequencing |
|
Definition
| allows you to signal single molecules of DNA |
|
|
Term
|
Definition
| sequence of DNA that is transcribed and its RNA product |
|
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Term
|
Definition
| by new genes being created |
|
|
Term
| depiction of pseudogene formation |
|
Definition
|
|
Term
| how much of our genome is made of pseudogenes? |
|
Definition
|
|
Term
|
Definition
|
|
Term
| depiction of how retroviruses contribute to our genome |
|
Definition
|
|
Term
| depiction of the flow of genetic information |
|
Definition
|
|
Term
|
Definition
|
|
Term
| a lot of the specialization in the flow of genetic information comes from... |
|
Definition
|
|
Term
| what prions can do to proteins |
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
| has to be replicated into the + strand for transcription to occur |
|
|
Term
|
Definition
| just circular ssRNA, No coding potential! |
|
|
Term
|
Definition
| transcripts with a function |
|
|
Term
| Major classes of RNA synthesized in bacteria |
|
Definition
|
|
Term
|
Definition
| encodes the information to generate a protein |
|
|
Term
| Transfer RNA (tRNA) and ribosomal RNA (rRNA) |
|
Definition
| play key roles in translating mRNA information into protein |
|
|
Term
|
Definition
| something encoded in ribosomes to enhance expression |
|
|
Term
| the current frontier in terms of gene expression |
|
Definition
|
|
Term
| depiction of coding (sense) and template (antisense) strands of DNA and one strand of mRNA |
|
Definition
|
|
Term
| depiction of transcription bubble and synthesis of mRNA strand |
|
Definition
|
|
Term
| ______ specifies the coding and noncoding strands |
|
Definition
| Direction of transcription |
|
|
Term
| does RNA polymerase require a primer? |
|
Definition
|
|
Term
| why does RNA have more mistakes than DNA? |
|
Definition
| because RNA doesn't undergo any repair rxns |
|
|
Term
| table of subunits of E. coli RNA polymerase |
|
Definition
|
|
Term
| depiction of the Core + σ = holoenzyme |
|
Definition
|
|
Term
| depiction of the RNA polymerase rxn |
|
Definition
|
|
Term
| which polymerase is faster? RNA polymerase or DNA polymerase? |
|
Definition
|
|
Term
| depiction of how sigma factors act catalytically |
|
Definition
|
|
Term
| the steps of gene transcription |
|
Definition
1: Initiation: closed to open complex
2: Elongation |
|
|
Term
| how RNA polymerase generates mRNA |
|
Definition
1: polymerase and sigma factor bind to promoter
2: polymerase generates mRNA
3: sigma subunit breaks off to help another RNA polymerase transcribe another gene |
|
|
Term
| depiction of RNA–DNA hybrid separation |
|
Definition
|
|
Term
| how the RNA–DNA hybrid is separated |
|
Definition
| RNA polymerase extrudes the strand and DNA polymerase wants to keep the base pairing intact |
|
|
Term
| 2 types of termination of RNA synthesis |
|
Definition
-Rho independent
-Rho dependent |
|
|
Term
| Rho independent termination |
|
Definition
| has all the signals present for termination on the RNA |
|
|
Term
| depiction of Rho independent termination |
|
Definition
|
|
Term
| Rho dependent termination |
|
Definition
| uses Rho protein to dislodge polymerase from template |
|
|
Term
| depiction of Rho dependent termination |
|
Definition
|
|
Term
| what Rho independent and Rho dependent termination have in common |
|
Definition
| termination signals lie in newly synthesized RNA rather than DNA |
|
|
Term
| depiction of riboswitches with M ligand |
|
Definition
|
|
Term
| depiction of riboswitches without M ligand |
|
Definition
|
|
Term
|
Definition
| end product of a pathway, vitamin for example |
|
|
Term
| some similarities between DNA and RNA polymerase |
|
Definition
-need templates
-all 5'-->3'
-chemistry the same
-have replication bubbles; this means helicases are involved
-tend to be multiple subunit proteins |
|
|
Term
| some differences between DNA and RNA polymerase |
|
Definition
-speed (RNA pol slower)
-RNA pol doesn't need primer, but DNA pol does
-dNTP's vs. NTP's
-U/A differences
-error rate/proofreading
-DNA pol designed to maintain H bonding over replicated DNA; RNA pol doesn't |
|
|
Term
| transcription factors aka DNA binding proteins |
|
Definition
proteins that initiate or stop transcription of genes
they are upstream of the transcription start site |
|
|
Term
|
Definition
| where RNA polymerase transcribes mRNA from the DNA template |
|
|
Term
| The DNA components of an operon consist of... |
|
Definition
-a regulator gene
-an operator (binding site for a regulatory protein)
-a promoter
-structural genes |
|
|
Term
| gene specific behavior of the Lac operon |
|
Definition
| the regulatory gene encodes a protein called the lac repressor (lacI) that binds to the operator site (lacO) in the absence of lactose and prevents transcription of the structural genes |
|
|
Term
| global behavior of the Lac operon |
|
Definition
| In the absence of glucose, cAMP binds to the cAMP activator protein CRP. CRP-cAMP binds the promoter where contact is made with RNA Pol, which increases initiation of transcription. CRP-cAMP affects the expression of several hundred genes in addition to the Lac operon. |
|
|
Term
| Combinatorial gene regulation |
|
Definition
| Gene specific + global regulation |
|
|
Term
| depiction of the Lac operon and its repressor |
|
Definition
|
|
Term
| what has to happen for the Lac operon to be activated? |
|
Definition
| lactose has to be converted to allolactose, which binds to some receptor |
|
|
Term
| are regulatory circuits ever 100% induced or 100% off? |
|
Definition
|
|
Term
| depiction of Binding of Lac repressor to the Lac operator |
|
Definition
|
|
Term
| how allolactose activates the lac operon |
|
Definition
| Binding of the inducer allolactose to the repressor decreases binding affinity for the operator |
|
|
Term
| depiction of E. coli global control when glucose is present |
|
Definition
|
|
Term
| depiction of E. coli global control when glucose is absent |
|
Definition
|
|
Term
| what happens in E. coli in the absence of glucose? |
|
Definition
| enzyme III (EIII) transfers a phosphate group to adenylate cyclase, activating the cyclase, cAMP increases |
|
|
Term
| what CRP /CAP-cAMP binding does |
|
Definition
| activates transcription of other genes |
|
|
Term
| depiction of Positive activation by CRP-cAMP; global combinatorial control in E. coli |
|
Definition
|
|
Term
| other than allolactose, what else further activates transcription of the lac operon? |
|
Definition
|
|
Term
|
Definition
| encodes the Lac repressor, which binds to the Lac Operator |
|
|
Term
| Defective Lac repressor results in... |
|
Definition
| Lac expression regardless if lactose is present |
|
|
Term
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Definition
| LacO operator is a region, O1 and O2 , of the promoter that binds LacI and blocks transcription of the Lac operon |
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Term
| Defective LacO that can no longer bind LacI results in... |
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Definition
| a Lac expression that is also independent of lactose |
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Term
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Definition
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Term
| Loss of Lac promoter function (ie mutations in the -10 and -35 region) results in... |
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Definition
| lower levels of expression under all conditions |
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Term
| Lac merodiploid or partial diploid |
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Definition
| Two copies of the Lac operon in one cell |
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Term
| how the Lac operon is distributed when the cell is Lac merodiploid or partial diploid |
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Definition
| Usually one copy is the Lac operon on the E. coli chromosome, and the second Lac operon is carried on a plasmid integrated into the chromosome at another location. Important controls are cells containing individual copies of Lac. |
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Term
| Combinatorial gene regulation controls... |
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Definition
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Term
| depiction of how proteins attached to DNA affect the results of a DNA gel shift assay (EMSA) |
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Definition
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Term
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Definition
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Term
| depiction of shift and supershift caused by proteins bound to DNA |
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Definition
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Term
| Why does a regulatory circuit like the Lac operon require basal level expression? |
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Definition
| because you need a little permease gene |
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Term
| what allolactose does to the repressor in the Lac operon |
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Definition
| binds to it to decrease the binding affinity for the operator |
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Term
| Transcription from the Lac promoter occurs when... |
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Definition
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Term
| Transcription from the Lac promoter is further activated by... |
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Definition
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Term
| the 2 components of the combinatorial control circuit of the Lac operon |
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Definition
1: Transcription from the Lac promoter occurs when allolactose is present
2: further activation of the Lac promoter by binding of cAMP to CRP |
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Term
| transcription is low when... |
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Definition
| you can't bind to promoter |
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Term
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Definition
| artificial inducer of the Lac operon |
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Term
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Definition
-DNA bound to 2 proteins
-DNA-protein complex |
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Term
| What are the three major classes of bacterial RNA? |
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Definition
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Term
| most abundant type of bacterial RNA |
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Definition
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Term
| least abundant type of bacterial RNA |
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Definition
| mRNA; it's the least stable |
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Term
| How does sigma help RNA polymerase transition from the closed to open promoter complex? |
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Definition
| changes the binding constant for the promoter; lowers it almost 10,000 fold |
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Term
| What would be the effect of a promoter mutation in the Lac operon? |
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Definition
| less or no transcription, depending on strength of mutation |
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Term
| Does the Rho transcription termination factor act on DNA or RNA? |
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Definition
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Term
| In E. coli, the inability of the Lac repressor to bind an inducer would result in... |
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Definition
no substantial synthesis of b–galactosidase
the repressor would be bound to the operator and you can't get it off |
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Term
| What is the reason for basal level expression of the Lac operon? |
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Definition
| permease to get a little bit of lactose into the cell |
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Term
| depiction of the difference between prokaryote and eukaryote gene expression |
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Definition
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Term
| transcription and translation in prokaryotes |
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Definition
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Term
| transcription and translation in eukaryotes |
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Definition
| transcribed in nucleus and translated outside of nucleus |
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Term
| One scheme used for activation of transcription by estrogen |
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Definition
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Term
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Definition
| nucleosomes wrapped around histone proteins |
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Term
| how estrogen initiates activation of transcription |
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Definition
| recognizes transcription factor and recruits coactivator |
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Term
| coactivator is activated by... |
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Definition
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Term
| how activation of transcription by estrogen leads to loosening of DNA |
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Definition
| acetylation of lysine in the histones |
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Term
| all the steps in activation of transcription by estrogen |
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Definition
0: Activate transcription factor
1: Recruitment of a coactivator
2: Coactivator recruits HAT, acetylation of lysine residues in the histone tails,
3: Binding of a chromatin remodeling complex to the acetylated lysine residues
4: ATP-dependent remodeling of the chromatin structure to expose DNA
5: Recruitment of RNA polymerase II, starting with TFIID/TBP
6: Mediator stabilizes Pol II, bridges activator, stimulates transcription |
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Term
| depiction of Nuclear hormone receptor activation |
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Definition
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Term
| depiction of Recruitment of a coactivator triggered by estrogen |
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Definition
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Term
| what estrogen does to receptor protein |
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Definition
| causes it to go under allosteric change, making it a good binding site for coactivator |
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Term
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Definition
| binds to the receptor but “antagonizes” its activation. |
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Term
| estrogen tamoxifen can... |
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Definition
| activate estrogen ligand in other tissues, such as uterus |
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Term
| depiction of H3 lysine acetylation |
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Definition
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Term
| Recruitment of chromatin remodelers to acetylated histones |
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Definition
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Term
| what dictates the next steps after histone acetylation? |
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Definition
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Term
| some bromodomain proteins |
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Definition
- Chromatin remodelers, some ATP dependent
- TAFs [TATA-box binding protein associated (TBP), factors], in particular TAF1 |
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Term
| depiction of Assembly of Pol II |
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Definition
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Term
| depiction of Action of Mediator |
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Definition
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Term
| when transcription can occur |
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Definition
| when mediator connects with both transcription factor and RNA polymerase II |
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Term
| how the transcription factor gets activated |
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Definition
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Term
| how mediator contributes to transcription |
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Definition
-stabilizes Pol II
-bridges activator
-stimulates transcription |
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Term
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Definition
| genes required for the function of all cells |
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Term
| what acetylation does to lysine residues in histones |
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Definition
| causes a charge change; changes it to something that's more acidic |
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Term
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Definition
| they are very basic proteins |
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Term
| depiction of acetylation of lysine |
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Definition
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Term
| common method for studying DNA-protein interactions |
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Definition
| DNA gel shift assay (EMSA) |
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Term
| you can get a supershift if... |
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Definition
| you have an antibody that's specific to the protein bound to the DNA |
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Term
| depiction of prokaryotic gene expression |
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Definition
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Term
| depiction of eukaryotic gene expression |
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Definition
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Term
| some primary transcripts that must be further processed to be active |
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Definition
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Term
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Definition
1. Removal of nucleotides
2. Addition of nucleotides
3. Covalent modification of nucleotides
4. Substituting nucleotides |
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Term
| some things that happen in mRNA processing |
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Definition
- Capping the 5’ end of the mRNA
- pA addition to the 3’ end of the mRNA
- RNA splicing
- RNA editing |
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Term
| in mRNA processing, what goes on the 5' end? |
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Definition
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Term
| in mRNA processing, what goes on the 3' end? |
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Definition
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Term
| some reasons mRNA is processed |
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Definition
- Protect mRNAs from premature degradation (some transcripts are huge)
- Additional levels of gene regulation possible (posttranscriptional)
- Assists in engaging the ribosome |
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Term
| depiction of Capping the 5’ end of mRNA |
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Definition
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Term
| the nucleotide that's always in the 5' cap |
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Definition
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Term
| depiction of 3’ polyadenylation of a primary transcript |
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Definition
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Term
| what 3’ polyadenylation of a primary transcript does for mRNA |
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Definition
-Stabilizes RNA
-Enhances translation
-Regulated turnover |
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Term
| depiction of the torpedo model for transcription termination (human beta globulin gene) |
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Definition
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Term
| what disengages mRNA from the DNA strands in eukaryotes? |
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Definition
| seems to be the torpedo model for transcription termination |
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Term
| Pre-mRNA splicing takes place on... |
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Definition
|
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Term
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Definition
| complexes of 45 proteins & 5 RNAs called small nuclear RNA (snRNA): U1, U2, U4, U5, U6 |
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Term
| depiction of alternate splicing |
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Definition
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Term
| Advantages of alternative splicing |
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Definition
| expands the amount of proteins you can make, because you can mix and match exons |
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Term
| molecular basis of thalassemia and muscular dystrophies |
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Definition
| problems with RNA splicing |
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Term
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Definition
| often as the mRNA is getting created |
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Term
| depiction of Consensus sequences at splice sites in vertebrates |
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Definition
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Term
| the object of alternate splicing |
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Definition
| to remove the intron and join the exons |
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Term
| depiction of Spliceosome assembly and action |
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Definition
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Term
| what degrades this lariat? |
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Definition
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Term
| depiction of Intron removal in mRNA precursors |
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Definition
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Term
| depiction of First transesterifcation in splicing |
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Definition
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Term
| depiction of formation of a lariat |
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Definition
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Term
| depiction of separation of lariat from rest of mRNA precursor |
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Definition
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Term
| what happens to the lariat after it gets separated from the rest of the mRNA precursor? |
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Definition
| gets degraded; the lariat is the intron |
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Term
| depiction of 2’- 5’ circular lariat |
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Definition
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Term
| depiction of possible results of splicing mutations |
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Definition
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Term
| one reason a stop codon ignored in wild type |
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Definition
| because it's in the intron |
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Term
| when are mutations more severe? when the problem is with the exons or when the problem is with splicing? |
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Definition
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Term
| depiction of RNA transcription error that has good effect |
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Definition
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Term
| depiction of Coupling transcription to pre-mRNA processing: CTD |
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Definition
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Term
| can splicing occur at the same time as transcription? |
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Definition
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Term
| Genetic code Should explain... |
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Definition
-how you get from DNA to protein
-heridity
-mutation
-molecular evolution |
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Term
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Definition
| defects in specific enzymes |
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Term
| some ways the genetic code was deciphered |
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Definition
-Synthesize or isolate short RNA sequences
-Develop a cell-free protein synthesis extract from E. coli
-Add RNA + individual radioactive amino acids
-Relate incorporation of labeled amino acids to RNA sequence |
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Term
| depiction of the genetic code |
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Definition
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Term
| some amino acids that are not in the standard 20 |
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Definition
-Selenocysteine (Archaea, Eubacteria, animals)
-Pyrrolysine (Archaea, bacteria) |
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Term
| depiction of multiple open reading frames in the code |
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Definition
[image]
the stars are the stop codons |
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Term
| where degeneracy is in the codons |
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Definition
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Term
| is there any repair or proofreading of proteins? |
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Definition
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Term
| are there any tRNA's associated with stop codons? |
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Definition
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Term
| how DNA gets translated depends on... |
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Definition
| what frame you're translating |
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Term
| depiction of tRNA anatomy |
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Definition
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Term
| how tRNA links codons with amino acids |
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Definition
| serves as the adaptor molecule |
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Term
| amino acids are added to tRNA by... |
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Definition
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Term
| inosine (I) is derived from... |
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Definition
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Term
| where amino acid is added to the tRNA |
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Definition
| the A residue at the 3’ end |
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Term
| general depiction of tRNA, anticodon, codon, and amino acid |
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Definition
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Term
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Definition
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Term
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Definition
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Term
| depiction of deamination of adenosine to form inosine |
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Definition
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Term
| depiction of how inosine binds with C, U, and A |
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Definition
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Term
| the smart enzymes in protein synthesis |
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Definition
| Aminoacyl-tRNA synthetases |
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Term
| Aminoacyl-tRNA synthetases |
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Definition
| synthesize Aminoacyl-tRNAs (specific amino acid covalently attached to 3’ end of specific tRNAs (ie alanyl-tRNAAla) |
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Term
| how many aminoacyl-tRNA synthetases are there? |
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Definition
| At least 20 (1 per amino acid) |
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Term
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Definition
| high-energy molecules in which the amino acid has been “activated or charged” |
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Term
| rxn by which aminoacyl-tRNA synthetase activates amino acids |
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Definition
| Amino acid + tRNA + ATP --> Aminoacyl-tRNA + AMP + PPi |
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Term
| steps of the Activation of amino acid by aminoacyl-tRNA synthetase |
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Definition
Step 1: ATP + amino acid → aminoacyladenylate intermediate + PP
Step 2: aminoacyl-adenylate + tRNA → aminoacyl-tRNA + AMP |
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Term
| depiction of the entire Activation of amino acid by aminoacyl-tRNA synthetase |
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Definition
|
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Term
| what part of the aminoacyl tRNA is used in protein synthesis? |
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Definition
| the charged or activated tRNA |
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Term
| Determinants of tRNA synthetase specificity |
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Definition
1. Recognize the correct amino acid
2. Recognize the structure of the tRNA and the anticodon |
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Term
| depiction of Determinants of tRNA synthetase specificity |
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Definition
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Term
| depiction of Threonyl tRNA synthetase |
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Definition
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|
Term
| comparison of Prokaryotic and eukaryotic ribosomes |
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Definition
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Term
| depiction of Sites for tRNA binding in ribosomes |
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Definition
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Term
| simple depiction of Position of tRNAs |
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Definition
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Term
| where prokaryotes and eukaryotes differ in translation |
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Definition
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Term
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Definition
1: initiation
2: elongation
3: termination |
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Term
| depiction of Shine-Dalgarno sequence |
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Definition
|
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Term
| depiction of Initiation of fMet-tRNA |
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Definition
|
|
Term
| depiction of The initiation complex |
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Definition
|
|
Term
| depiction of the Elongation cycle |
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Definition
|
|
Term
| depiction of Peptide bond formation |
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Definition
|
|
Term
| depiction of translocation step of translation |
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Definition
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Term
| what basically happens in translocation |
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Definition
| polypeptide chain grows from N to C as ribosome moves 5’-3’ |
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Term
| depiction of elongation of polypeptide |
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Definition
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Term
| direction of protein synthesis |
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Definition
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Term
| depiction of termination of translation |
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Definition
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Term
| how initiation occurs in prokaryotes |
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Definition
| Scans for the first AUG (recognizes Cap, ATP dependent scan) |
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Term
| depiction of how initiation occurs in prokaryotes |
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Definition
|
|
Term
|
Definition
|
|
Term
| depiction of circular eukaryotic mRNA |
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Definition
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|
Term
| table of antibiotic inhibitors of protein synthesis |
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Definition
|
|
Term
| what step is inhibited when mRNA freezes in position? |
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Definition
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Term
| how a ricin molecule kills a cell |
|
Definition
| causes elongation factors to be unable to bind |
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Term
| an aspect of translation does not require GTP |
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Definition
| charging tRNAs because it requires ATP |
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Term
| things that could lead to an increase in the synthesis of a particular protein |
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Definition
-Shine-Dalgarno sequence because you could make the sequence better
-3’ untranslated region because degradation occurs on the 3' end |
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Term
| where does degradation occur within a gene? |
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Definition
|
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Term
| Why aren’t eukaryotic mRNAs polycistronic? |
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Definition
| Since eukaryotic mRNAs don’t have sequences equivalent to the Shine-Dalgarno sequence, there is no way to identify which internal methionines might be used for initiation. |
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