Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
| structure of a pyrimidine |
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
| something epigenetic that can happen to cytosine when adde to nucleotide strand |
|
Definition
| the H atom where the arrow is pointing gets replaced by CH3; gets methylated
[image] |
|
|
Term
| where adenosine comes from |
|
Definition
adenine
Adenine becomes the nucleoside Adenosine when it becomes combined with a ribose |
|
|
Term
| when adenine becomes adenosine |
|
Definition
| when it becomes combined with a ribose |
|
|
Term
|
Definition
|
|
Term
| macromolecule ATP seems to be present in |
|
Definition
|
|
Term
| the phosphate you want to tag in ATP |
|
Definition
| the alpha phosphate, which is the closest to the ribose |
|
|
Term
| how a phosphate is tagged |
|
Definition
|
|
Term
|
Definition
|
|
Term
| what happens if you label the gamma phosphate? |
|
Definition
| it'll wind up in pyrophosphate |
|
|
Term
| the form of ATP that seems to be present in DNA |
|
Definition
|
|
Term
| in essence, our genetic material is basically... |
|
Definition
|
|
Term
|
Definition
|
|
Term
| structure of deoxyribose ATP |
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
| why RNA is less stable than DNA |
|
Definition
| because RNA contains that reactive OH group |
|
|
Term
| some questions the structure of DNA can answer |
|
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) |
|
|
Term
| why genetics is important to a cell |
|
Definition
| because cells have to keep their genetic constitution to stay alive |
|
|
Term
| how Rosalind Franklin contributed to discovering the structure of DNA |
|
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 |
|
|
Term
|
Definition
A = T
G = C
DNA obeys the rule, but RNA doesn't; it's a universal role of double-stranded DNA |
|
|
Term
| things to consider with DNA structure |
|
Definition
1: stabilizing forces
2: Double helix is directional/antiparallel
3: Major and minor grooves (asymmetrical threads of a screw) |
|
|
Term
| some stabilizing forces in DNA |
|
Definition
- Hydrophobic interactions
- H-bonding, W/C (Watson/Crick) pairing
- van der Waals forces act on adjacent stacked base pairs |
|
|
Term
|
Definition
|
|
Term
| distance between consecutive bases in DNA |
|
Definition
|
|
Term
|
Definition
| 1 100millionth of a centimeter
10-10 |
|
|
Term
| what the asymmetric threading of the "screw" does for the DNA molecule |
|
Definition
| presents different faces of the strands of the helix to the outside |
|
|
Term
| one reason the phosphate backbone is on the outside of the DNA molecule |
|
Definition
| because phosphates are more hydrophilic than bases |
|
|
Term
| side view of DNA molecule |
|
Definition
|
|
Term
|
Definition
|
|
Term
| depiction of the asymmetric "screw" of DNA |
|
Definition
|
|
Term
| depiction of the bonding between guanine and cytosine |
|
Definition
|
|
Term
| depiction of the bonding between adenine and thymine |
|
Definition
|
|
Term
| depiction of the van der Waals interactions in base stacking |
|
Definition
|
|
Term
| how DNA strands can be separated in the lab |
|
Definition
|
|
Term
|
Definition
The temperature at which half of the DNA
molecules are denatured |
|
|
Term
|
Definition
| separated DNA strands combining to form the double helix |
|
|
Term
| what alkali or chaotropic agents do to DNA |
|
Definition
| denature DNA by disrupting non-covalent interactions |
|
|
Term
| how chaotropic agents break down DNA |
|
Definition
|
|
Term
| which DNA absorbs more light? single stranded or double stranded? |
|
Definition
|
|
Term
| chart showing wavelength absorbance of single stranded and double stranded DNA |
|
Definition
|
|
Term
|
Definition
| the increase in light absorption that occurs when single strands flop around |
|
|
Term
| depiction of a hyperchromic shift |
|
Definition
|
|
Term
| dsDNA can be denatured by... |
|
Definition
| heat or chaotropic agents |
|
|
Term
| Extent of denaturation can be measured by... |
|
Definition
|
|
Term
|
Definition
| duplexes that are all A's and T's |
|
|
Term
|
Definition
| duplexes that are all G's and C's |
|
|
Term
| depiction of a Tm chart vs. UV absorbance by DNA |
|
Definition
[image]
Any DNA you put in there has to be between those 2 extremes |
|
|
Term
| the hallmarks of DNA structure |
|
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) |
|
|
Term
| this accounts for some of the compaction of the DNA |
|
Definition
|
|
Term
| Further compaction of DNA occurs by... |
|
Definition
| binding certain proteins to the DNA |
|
|
Term
| how much does an average chromosome have to be compacted? |
|
Definition
|
|
Term
|
Definition
| modifications of histones and effect of histones on DNA expression |
|
|
Term
| can epigenetic factors be inherited? |
|
Definition
|
|
Term
|
Definition
| protein octamers that have a strong affinity for DNA and bind to it in a certain way |
|
|
Term
| depiction of the histone octamer |
|
Definition
|
|
Term
| depiction of nucleosome core particle |
|
Definition
|
|
Term
| depiction of nucleosome core particle and linker DNA |
|
Definition
|
|
Term
| depiction of all the compaction that occurs with DNA |
|
Definition
|
|
Term
| the amount of DNA compaction we seem to have accounted for so far |
|
Definition
|
|
Term
| can characteristics of chromatin be inherited? |
|
Definition
|
|
Term
| A common structural motif seen in nucleic acids, most notably RNA |
|
Definition
|
|
Term
| the stem-loop occurs when... |
|
Definition
complementary
sequences in the same strand form a double helix |
|
|
Term
| do Non-Watson-Crick base pairs occur frequently in RNA? |
|
Definition
|
|
Term
| More elaborate structures of RNA are |
|
Definition
| often stabilized by Mg2+ ions |
|
|
Term
| depiction of stem loop structure |
|
Definition
|
|
Term
| depiction of Prokaryotic gene expression |
|
Definition
|
|
Term
| can RNA in prokaryotes have multiple protein coding sequences? |
|
Definition
|
|
Term
| depiction of Euokaryotic gene expression |
|
Definition
|
|
Term
| what occurs at each end of the mRNA molecule in eukaryotic gene expression? |
|
Definition
| covalent modifications to form a cap |
|
|
Term
| in eukaryotic gene expression, every step along the way has the potential to be... |
|
Definition
|
|
Term
| genetic mapping reveals... |
|
Definition
| order of genes on specific chromosomes |
|
|
Term
| composition of the human geneome |
|
Definition
|
|
Term
| how much of the human genome encodes proteins? |
|
Definition
|
|
Term
|
Definition
| gene that encodes RNA that never codes a protein product |
|
|
Term
| how much of the genome contains sequences linked to biological function? |
|
Definition
|
|
Term
| how much of the genome is transcribed at some point? |
|
Definition
|
|
Term
|
Definition
|
|
Term
| can transcripts be synthesized by both strands? |
|
Definition
|
|
Term
|
Definition
| Genome Wide ASsociation variants associated with diseases such as schizophrenia and type 2 diabetes |
|
|
Term
| GWAS studies try to understand... |
|
Definition
| pleiotropic things in the genome |
|
|
Term
| some challenges to defining a gene |
|
Definition
• Gene regulatory sequences
• Overlapping genes (introns and exons)
• Parasitic and mobile genes (transposons)
• “Junk” DNA is conserved
• Pseudogenes (duplicated genes)
• Pervasive transcription |
|
|
Term
|
Definition
| Parasitic and mobile genes |
|
|
Term
| what happens to “Junk” DNA? |
|
Definition
|
|
Term
| depiction of gene complexity |
|
Definition
|
|
Term
| why RNA is more unstable than DNA |
|
Definition
| because it has that reactive OH group |
|
|
Term
| depiction of the difference between DNA and RNA |
|
Definition
|
|
Term
| depiction of what happens to RNA when it is treated with NaOH |
|
Definition
|
|
Term
|
Definition
|
|
Term
| what CsCl does for separation of light and heavy DNA |
|
Definition
| forms density gradient along the centrifuge tube |
|
|
Term
| The reaction catalyzed by DNA polymerase |
|
Definition
| (DNA)n + dNTP <--> (DNA)n + 1 + PPi |
|
|
Term
| depiction of The reaction catalyzed by DNA polymerase |
|
Definition
|
|
Term
| depiction of RNA strand-elongation rxn |
|
Definition
|
|
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. |
|
|
Term
| what's required in the buffer for DNA synthesis? |
|
Definition
| Four deoxynucleoside triphosphates and Mg2+ |
|
|
Term
| ion required for DNA synthesis |
|
Definition
|
|
Term
| table of E. coli DNA polymerases |
|
Definition
|
|
Term
| where in the molecule does exonuclease start? |
|
Definition
|
|
Term
| where in the molecule does endonuclease start? |
|
Definition
|
|
Term
|
Definition
| nicks or 2bl stranded breaks |
|
|
Term
| general depiction of replication fork |
|
Definition
|
|
Term
| depiction of DNA polymerase holoenzyme |
|
Definition
| [image]
the β2 is basically a Sliding Clamp |
|
|
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 |
|
|
Term
| what the clamp loader in the DNA polymerase holoenzyme does |
|
Definition
| opens and closes the beta 2 donut ring |
|
|
Term
| depiction of the trombone model of the DNA polymerase holoenzyme |
|
Definition
|
|
Term
| single strand binding protein (SSB) |
|
Definition
| coats single stranded DNA to protect it from degradation |
|
|
Term
| what primase does for DNA synthesis in the lagging strand |
|
Definition
| adds RNA to the DNA to serve as a primer |
|
|
Term
| depiction of DNA synthesis from primer |
|
Definition
|
|
Term
| depiction of the type of nick sealed by ligase |
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
| relieves tension by introducing negative supercoils ahead of the fork |
|
|
Term
| depiction of Topoisomerase II in the replication fork |
|
Definition
|
|
Term
|
Definition
| the enzyme responsible for telomeres |
|
|
Term
| depiction of replication and telomeres |
|
Definition
|
|
Term
| depiction of telomeres in embryonic and adult stem cells |
|
Definition
|
|
Term
| depiction of extending the length of a telomere |
|
Definition
|
|
Term
| what happens with telomerases in aging? |
|
Definition
|
|
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 |
|
|
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 |
|
|
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. |
|
|
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 |
|
|
Term
|
Definition
|
|
Term
|
Definition
| enhances ability to recognize error |
|
|
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 |
|
|
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 |
|
|
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
|
Definition
| LacO operator is a region, O1 and O2 , of the promoter that binds LacI and blocks transcription of the Lac operon |
|
|
Term
| Defective LacO that can no longer bind LacI results in... |
|
Definition
| a Lac expression that is also independent of lactose |
|
|
Term
|
Definition
|
|
Term
| Loss of Lac promoter function (ie mutations in the -10 and -35 region) results in... |
|
Definition
| lower levels of expression under all conditions |
|
|
Term
| Lac merodiploid or partial diploid |
|
Definition
| Two copies of the Lac operon in one cell |
|
|
Term
| how the Lac operon is distributed when the cell is Lac merodiploid or partial diploid |
|
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. |
|
|
Term
| Combinatorial gene regulation controls... |
|
Definition
|
|
Term
| depiction of how proteins attached to DNA affect the results of a DNA gel shift assay (EMSA) |
|
Definition
|
|
Term
|
Definition
|
|
Term
| depiction of shift and supershift caused by proteins bound to DNA |
|
Definition
|
|
Term
| Why does a regulatory circuit like the Lac operon require basal level expression? |
|
Definition
| because you need a little permease gene |
|
|
Term
| what allolactose does to the repressor in the Lac operon |
|
Definition
| binds to it to decrease the binding affinity for the operator |
|
|
Term
| Transcription from the Lac promoter occurs when... |
|
Definition
|
|
Term
| Transcription from the Lac promoter is further activated by... |
|
Definition
|
|
Term
| the 2 components of the combinatorial control circuit of the Lac operon |
|
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 |
|
|
Term
| transcription is low when... |
|
Definition
| you can't bind to promoter |
|
|
Term
|
Definition
| artificial inducer of the Lac operon |
|
|
Term
|
Definition
-DNA bound to 2 proteins
-DNA-protein complex |
|
|
Term
| What are the three major classes of bacterial RNA? |
|
Definition
|
|
Term
| most abundant type of bacterial RNA |
|
Definition
|
|
Term
| least abundant type of bacterial RNA |
|
Definition
| mRNA; it's the least stable |
|
|
Term
| How does sigma help RNA polymerase transition from the closed to open promoter complex? |
|
Definition
| changes the binding constant for the promoter; lowers it almost 10,000 fold |
|
|
Term
| What would be the effect of a promoter mutation in the Lac operon? |
|
Definition
| less or no transcription, depending on strength of mutation |
|
|
Term
| Does the Rho transcription termination factor act on DNA or RNA? |
|
Definition
|
|
Term
| In E. coli, the inability of the Lac repressor to bind an inducer would result in... |
|
Definition
no substantial synthesis of b–galactosidase
the repressor would be bound to the operator and you can't get it off |
|
|
Term
| What is the reason for basal level expression of the Lac operon? |
|
Definition
| permease to get a little bit of lactose into the cell |
|
|
Term
| depiction of the difference between prokaryote and eukaryote gene expression |
|
Definition
|
|
Term
| transcription and translation in prokaryotes |
|
Definition
|
|
Term
| transcription and translation in eukaryotes |
|
Definition
| transcribed in nucleus and translated outside of nucleus |
|
|
Term
| One scheme used for activation of transcription by estrogen |
|
Definition
|
|
Term
|
Definition
| nucleosomes wrapped around histone proteins |
|
|
Term
| how estrogen initiates activation of transcription |
|
Definition
| recognizes transcription factor and recruits coactivator |
|
|
Term
| coactivator is activated by... |
|
Definition
|
|
Term
| how activation of transcription by estrogen leads to loosening of DNA |
|
Definition
| acetylation of lysine in the histones |
|
|
Term
| all the steps in activation of transcription by estrogen |
|
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 |
|
|
Term
| depiction of Nuclear hormone receptor activation |
|
Definition
|
|
Term
| depiction of Recruitment of a coactivator triggered by estrogen |
|
Definition
|
|
Term
| what estrogen does to receptor protein |
|
Definition
| causes it to go under allosteric change, making it a good binding site for coactivator |
|
|
Term
|
Definition
| binds to the receptor but “antagonizes” its activation. |
|
|
Term
| estrogen tamoxifen can... |
|
Definition
| activate estrogen ligand in other tissues, such as uterus |
|
|
Term
| depiction of H3 lysine acetylation |
|
Definition
|
|
Term
| Recruitment of chromatin remodelers to acetylated histones |
|
Definition
|
|
Term
| what dictates the next steps after histone acetylation? |
|
Definition
|
|
Term
| some bromodomain proteins |
|
Definition
- Chromatin remodelers, some ATP dependent
- TAFs [TATA-box binding protein associated (TBP), factors], in particular TAF1 |
|
|
Term
| depiction of Assembly of Pol II |
|
Definition
|
|
Term
| depiction of Action of Mediator |
|
Definition
|
|
Term
| when transcription can occur |
|
Definition
| when mediator connects with both transcription factor and RNA polymerase II |
|
|
Term
| how the transcription factor gets activated |
|
Definition
|
|
Term
| how mediator contributes to transcription |
|
Definition
-stabilizes Pol II
-bridges activator
-stimulates transcription |
|
|
Term
|
Definition
| genes required for the function of all cells |
|
|
Term
| what acetylation does to lysine residues in histones |
|
Definition
| causes a charge change; changes it to something that's more acidic |
|
|
Term
|
Definition
| they are very basic proteins |
|
|
Term
| depiction of acetylation of lysine |
|
Definition
|
|
Term
| common method for studying DNA-protein interactions |
|
Definition
| DNA gel shift assay (EMSA) |
|
|
Term
| you can get a supershift if... |
|
Definition
| you have an antibody that's specific to the protein bound to the DNA |
|
|
Term
| depiction of prokaryotic gene expression |
|
Definition
|
|
Term
| depiction of eukaryotic gene expression |
|
Definition
|
|
Term
| some primary transcripts that must be further processed to be active |
|
Definition
|
|
Term
|
Definition
1. Removal of nucleotides
2. Addition of nucleotides
3. Covalent modification of nucleotides
4. Substituting nucleotides |
|
|
Term
| some things that happen in mRNA processing |
|
Definition
- Capping the 5’ end of the mRNA
- pA addition to the 3’ end of the mRNA
- RNA splicing
- RNA editing |
|
|
Term
| in mRNA processing, what goes on the 5' end? |
|
Definition
|
|
Term
| in mRNA processing, what goes on the 3' end? |
|
Definition
|
|
Term
| some reasons mRNA is processed |
|
Definition
- Protect mRNAs from premature degradation (some transcripts are huge)
- Additional levels of gene regulation possible (posttranscriptional)
- Assists in engaging the ribosome |
|
|
Term
| depiction of Capping the 5’ end of mRNA |
|
Definition
|
|
Term
| the nucleotide that's always in the 5' cap |
|
Definition
|
|
Term
| depiction of 3’ polyadenylation of a primary transcript |
|
Definition
|
|
Term
| what 3’ polyadenylation of a primary transcript does for mRNA |
|
Definition
-Stabilizes RNA
-Enhances translation
-Regulated turnover |
|
|
Term
| depiction of the torpedo model for transcription termination (human beta globulin gene) |
|
Definition
|
|
Term
| what disengages mRNA from the DNA strands in eukaryotes? |
|
Definition
| seems to be the torpedo model for transcription termination |
|
|
Term
| Pre-mRNA splicing takes place on... |
|
Definition
|
|
Term
|
Definition
| complexes of 45 proteins & 5 RNAs called small nuclear RNA (snRNA): U1, U2, U4, U5, U6 |
|
|
Term
| depiction of alternate splicing |
|
Definition
|
|
Term
| Advantages of alternative splicing |
|
Definition
| expands the amount of proteins you can make, because you can mix and match exons |
|
|
Term
| molecular basis of thalassemia and muscular dystrophies |
|
Definition
| problems with RNA splicing |
|
|
Term
|
Definition
| often as the mRNA is getting created |
|
|
Term
| depiction of Consensus sequences at splice sites in vertebrates |
|
Definition
|
|
Term
| the object of alternate splicing |
|
Definition
| to remove the intron and join the exons |
|
|
Term
| depiction of Spliceosome assembly and action |
|
Definition
|
|
Term
| what degrades this lariat? |
|
Definition
|
|
Term
| depiction of Intron removal in mRNA precursors |
|
Definition
|
|
Term
| depiction of First transesterifcation in splicing |
|
Definition
|
|
Term
| depiction of formation of a lariat |
|
Definition
|
|
Term
| depiction of separation of lariat from rest of mRNA precursor |
|
Definition
|
|
Term
| what happens to the lariat after it gets separated from the rest of the mRNA precursor? |
|
Definition
| gets degraded; the lariat is the intron |
|
|
Term
| depiction of 2’- 5’ circular lariat |
|
Definition
|
|
Term
| depiction of possible results of splicing mutations |
|
Definition
|
|
Term
| one reason a stop codon ignored in wild type |
|
Definition
| because it's in the intron |
|
|
Term
| when are mutations more severe? when the problem is with the exons or when the problem is with splicing? |
|
Definition
|
|
Term
| depiction of RNA transcription error that has good effect |
|
Definition
|
|
Term
| depiction of Coupling transcription to pre-mRNA processing: CTD |
|
Definition
|
|
Term
| can splicing occur at the same time as transcription? |
|
Definition
|
|
Term
| Genetic code Should explain... |
|
Definition
-how you get from DNA to protein
-heridity
-mutation
-molecular evolution |
|
|
Term
|
Definition
| defects in specific enzymes |
|
|
Term
| some ways the genetic code was deciphered |
|
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 |
|
|
Term
| depiction of the genetic code |
|
Definition
|
|
Term
| some amino acids that are not in the standard 20 |
|
Definition
-Selenocysteine (Archaea, Eubacteria, animals)
-Pyrrolysine (Archaea, bacteria) |
|
|
Term
| depiction of multiple open reading frames in the code |
|
Definition
[image]
the stars are the stop codons |
|
|
Term
| where degeneracy is in the codons |
|
Definition
|
|
Term
| is there any repair or proofreading of proteins? |
|
Definition
|
|
Term
| are there any tRNA's associated with stop codons? |
|
Definition
|
|
Term
| how DNA gets translated depends on... |
|
Definition
| what frame you're translating |
|
|
Term
| depiction of tRNA anatomy |
|
Definition
|
|
Term
| how tRNA links codons with amino acids |
|
Definition
| serves as the adaptor molecule |
|
|
Term
| amino acids are added to tRNA by... |
|
Definition
|
|
Term
| inosine (I) is derived from... |
|
Definition
|
|
Term
| where amino acid is added to the tRNA |
|
Definition
| the A residue at the 3’ end |
|
|
Term
| general depiction of tRNA, anticodon, codon, and amino acid |
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
| depiction of deamination of adenosine to form inosine |
|
Definition
|
|
Term
| depiction of how inosine binds with C, U, and A |
|
Definition
|
|
Term
| the smart enzymes in protein synthesis |
|
Definition
| Aminoacyl-tRNA synthetases |
|
|
Term
| Aminoacyl-tRNA synthetases |
|
Definition
| synthesize Aminoacyl-tRNAs (specific amino acid covalently attached to 3’ end of specific tRNAs (ie alanyl-tRNAAla) |
|
|
Term
| how many aminoacyl-tRNA synthetases are there? |
|
Definition
| At least 20 (1 per amino acid) |
|
|
Term
|
Definition
| high-energy molecules in which the amino acid has been “activated or charged” |
|
|
Term
| rxn by which aminoacyl-tRNA synthetase activates amino acids |
|
Definition
| Amino acid + tRNA + ATP --> Aminoacyl-tRNA + AMP + PPi |
|
|
Term
| steps of the Activation of amino acid by aminoacyl-tRNA synthetase |
|
Definition
Step 1: ATP + amino acid → aminoacyladenylate intermediate + PP
Step 2: aminoacyl-adenylate + tRNA → aminoacyl-tRNA + AMP |
|
|
Term
| depiction of the entire Activation of amino acid by aminoacyl-tRNA synthetase |
|
Definition
|
|
Term
| what part of the aminoacyl tRNA is used in protein synthesis? |
|
Definition
| the charged or activated tRNA |
|
|
Term
| Determinants of tRNA synthetase specificity |
|
Definition
1. Recognize the correct amino acid
2. Recognize the structure of the tRNA and the anticodon |
|
|
Term
| depiction of Determinants of tRNA synthetase specificity |
|
Definition
|
|
Term
| depiction of Threonyl tRNA synthetase |
|
Definition
|
|
Term
| comparison of Prokaryotic and eukaryotic ribosomes |
|
Definition
|
|
Term
| depiction of Sites for tRNA binding in ribosomes |
|
Definition
|
|
Term
| simple depiction of Position of tRNAs |
|
Definition
|
|
Term
| where prokaryotes and eukaryotes differ in translation |
|
Definition
|
|
Term
|
Definition
1: initiation
2: elongation
3: termination |
|
|
Term
| depiction of Shine-Dalgarno sequence |
|
Definition
|
|
Term
| depiction of Initiation of fMet-tRNA |
|
Definition
|
|
Term
| depiction of The initiation complex |
|
Definition
|
|
Term
| depiction of the Elongation cycle |
|
Definition
|
|
Term
| depiction of Peptide bond formation |
|
Definition
|
|
Term
| depiction of translocation step of translation |
|
Definition
|
|
Term
| what basically happens in translocation |
|
Definition
| polypeptide chain grows from N to C as ribosome moves 5’-3’ |
|
|
Term
| depiction of elongation of polypeptide |
|
Definition
|
|
Term
| direction of protein synthesis |
|
Definition
|
|
Term
| depiction of termination of translation |
|
Definition
|
|
Term
| how initiation occurs in prokaryotes |
|
Definition
| Scans for the first AUG (recognizes Cap, ATP dependent scan) |
|
|
Term
| depiction of how initiation occurs in prokaryotes |
|
Definition
|
|
Term
|
Definition
|
|
Term
| depiction of circular eukaryotic mRNA |
|
Definition
|
|
Term
| table of antibiotic inhibitors of protein synthesis |
|
Definition
|
|
Term
| what step is inhibited when mRNA freezes in position? |
|
Definition
|
|
Term
| how a ricin molecule kills a cell |
|
Definition
| causes elongation factors to be unable to bind |
|
|
Term
| an aspect of translation does not require GTP |
|
Definition
| charging tRNAs because it requires ATP |
|
|
Term
| things that could lead to an increase in the synthesis of a particular protein |
|
Definition
-Shine-Dalgarno sequence because you could make the sequence better
-3’ untranslated region because degradation occurs on the 3' end |
|
|
Term
| where does degradation occur within a gene? |
|
Definition
|
|
Term
| Why aren’t eukaryotic mRNAs polycistronic? |
|
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. |
|
|
Term
| composition of each monomer in the nucleic acid sequence |
|
Definition
|
|
Term
| this uniquely characterizes a nucleic acid |
|
Definition
| the sequence of bases that forms linear information |
|
|
Term
| depiction of DNA replication |
|
Definition
|
|
Term
| depiction of the polymeric structure of nucleic acids |
|
Definition
|
|
Term
| difference between ribose and deoxyribose |
|
Definition
| deoxyribose lacks the O at the 2' C |
|
|
Term
| depiction of the structure of ribose |
|
Definition
|
|
Term
| depiction of the structure of deoxyribose |
|
Definition
|
|
Term
| how monomers are linked in nucleic acids |
|
Definition
the 3' OH group of the sugar component of one nucleotide binds to the phosphate attached to the 5' C on the adjacent sugar
3' --> 5' phosphodiester linkages |
|
|
Term
| 2 ways RNA differs from DNA |
|
Definition
1: RNA uses riboses instead of deoxyriboses
2: RNA uses U instead of T |
|
|
Term
| one way DNA and RNA maintain stability |
|
Definition
| they have a negative charge, which repels nucleophilic species that would otherwise hydrolyze tham |
|
|
Term
| why DNA is more resistant to hydrolysis than RNA |
|
Definition
| because DNA lacks the 2' OH croup |
|
|
Term
| the backbone of nucleic acids |
|
Definition
|
|
Term
| depiction of the backbones of DNA and RNA |
|
Definition
|
|
Term
|
Definition
|
|
Term
| depiction of the pyrimidines |
|
Definition
|
|
Term
|
Definition
| a unit consisting of a base bonded to a sugar |
|
|
Term
| the 4 nucleoside units in DNA |
|
Definition
-deoxyadenosine
-deoxyguanosine
-deoxycytidine
-thymidine (no, that's not a misprint) |
|
|
Term
| why the prefix deoxy- is not added to thymidine |
|
Definition
| because thymine-containing nucleotides are found only rarely in RNA |
|
|
Term
| the 4 nucleoside units in RNA |
|
Definition
-adenosine
-guanosine
-cytidine
-uridine |
|
|
Term
| the C in the ribose/deoxyribose the nucleotide base is always attached to |
|
Definition
|
|
Term
| the type of linkage in a purine nucleoside |
|
Definition
|
|
Term
| depiction of the β-glycosidic linkage in a purine nucleoside |
|
Definition
|
|
Term
|
Definition
| nucleoside joined to 1 or more phosphoryl groups by an ester linkage |
|
|
Term
| the monomers that link to form DNA and RNA |
|
Definition
| nucleoside triphosphates (this includes ATP!) |
|
|
Term
| 5'nucleotide or nucleoside 5'-phosphate |
|
Definition
| compound formed by the attachment of a phosphoryl group to C-5' of a nucleoside sugar |
|
|
Term
| the most common site of phosphate esterfication |
|
Definition
|
|
Term
|
Definition
adenosine 5'-triphosphate
[image] |
|
|
Term
| the direction a sequence of DNA is written in |
|
Definition
|
|
Term
| depiction of the structure of a DNA strand |
|
Definition
|
|
Term
| replication of DNA is the basis for these cellular processes |
|
Definition
-duplication
-growth
-ultimately, reproduction |
|
|
Term
| distance between adjacent bases in nucleic acids |
|
Definition
|
|
Term
| how many bases does it take for the double helix to go 360⁰? |
|
Definition
|
|
Term
| side view of a DNA double helix |
|
Definition
|
|
Term
| end view of a DNA double helix |
|
Definition
|
|
Term
| some features of the Watson-Crick model |
|
Definition
1: right-handed helix with antiparallel strands
2: the sugar-phosphate backbone is on the outside and the purine and pyrimidine bases are on the inside
3: bases nearly perpendicular to axis, 3.4 angstroms between adjacent bases, and 10.4 bases per turn of helix
4: diameter of the helix is about 20 angstroms |
|
|
Term
| handednes of DNA 2bl helix |
|
Definition
|
|
Term
| diameter of DNA 2bl helix |
|
Definition
|
|
Term
| depiction of the structures of the base pairs proposed by Watson and Crick |
|
Definition
|
|
Term
| 2 forces that stabilize the DNA double helix |
|
Definition
1: hydrophobic effect between bases on opposite strands
2: van der Waals forces between stacked bases, known as base stacking |
|
|
Term
| depiction of semiconservative replication |
|
Definition
|
|
Term
| depiction of the detection of semiconservative replication of E. coli DNA by density-gradient centrifugation |
|
Definition
|
|
Term
| 2 ways to break the DNA double helix |
|
Definition
-heating it to break the H bonds between the bases on opposite strands
-adding acid or alkali to ionize bases and disrupt base pairing |
|
|
Term
|
Definition
| the temperature at which half the helical structure is lost |
|
|
Term
|
Definition
| renaturation of the double helix below the melting temperature (Tm) |
|
|
Term
|
Definition
-B-DNA (this is the form you're already familiar with)
-A-form
-Z-form |
|
|
Term
| depiction of B-form and A-form DNA |
|
Definition
|
|
Term
|
Definition
|
|
Term
| some things that can resemble A-DNA |
|
Definition
-double-stranded regions of RNA
-at least some RNA-DNA hybrids |
|
|
Term
|
Definition
|
|
Term
| why Z-DNA contains the letter Z |
|
Definition
| because the phosphate backbone zig-zags |
|
|
Term
|
Definition
|
|
Term
| comparison of A-, B-, and Z-DNA |
|
Definition
|
|
Term
| 2 types of grooves in B-DNA |
|
Definition
-major groove
-minor groove |
|
|
Term
| why B-DNA has major and minor grooves |
|
Definition
| because the glycosidic bonds of a base pair are not diametrically opposite to each other |
|
|
Term
| depiction of the major- and minor- groove sides of nucleotide pairs |
|
Definition
|
|
Term
| depiction of the major and minor grooves in B-DNA |
|
Definition
|
|
Term
| the importance of grooves in B-DNA |
|
Definition
| exposing potential H-bond donors and acceptors to enable interactions with proteins |
|
|
Term
|
Definition
| the axis of a double helix being twisted into a superhelix |
|
|
Term
| depiction of a negative superhelix |
|
Definition
|
|
Term
| the coiling of most naturally occurring DNA molecules |
|
Definition
|
|
Term
| negative supercoiling arises from... |
|
Definition
| the unwinding or underwinding of DNA |
|
|
Term
| what negative supercoiling does for DNA |
|
Definition
| prepares it for processes requiring separation of the DNA strands, such as replication and transcription |
|
|
Term
| why negative supercoiling is better for DNA than positive supercoiling |
|
Definition
| condenses DNA as effectively, but makes strand separation more difficult |
|
|
Term
| this has to happen to coiled DNA for it to be replicated |
|
Definition
| local unwinding to allow separation of the 2 strands |
|
|
Term
| what local unwinding of DNA causes to happen to the other DNA in the strand |
|
Definition
| overwinding or supercoiling |
|
|
Term
| what prevents the strain induced by overwinding? |
|
Definition
| specialized set of enzymes introduces supercoils that favor strand separation |
|
|
Term
|
Definition
| the final DNA-protein complex |
|
|
Term
|
Definition
| small basic proteins that DNA tightly binds to |
|
|
Term
|
Definition
| the entire complex of a cell's DNA and its associated protein |
|
|
Term
| the 5 major histones present in chromatin |
|
Definition
-H1
-H2A
-H2B
-H3
-H4
H2A, H2B, H3, and H4 associate with one another |
|
|
Term
| histones have strikingly basic properties because... |
|
Definition
| a quarter of the residues in each histone are either arginine or lysine |
|
|
Term
|
Definition
| repeating units, each containing 200 bp of DNA and 2 copies each of H2A, H2B, H3, and H4, called the histone octamer |
|
|
Term
|
Definition
| comtains 2 copies each of H2A, H2B, H3, and H4 |
|
|
Term
|
Definition
the repeating units of chromatin
repeating units, each containing 200 bp of DNA and 2 copies each of H2A, H2B, H3, and H4, called the histone octamer |
|
|
Term
|
Definition
| smaller complex of the histone octamer and the 145-bp DNA fragment |
|
|
Term
|
Definition
| the DNA connecting core particles in undigested chromatin |
|
|
Term
| what binds to linker DNA? |
|
Definition
| histone H1 binds, in part, to the linker DNA |
|
|
Term
| depiction of chromatin structure |
|
Definition
|
|
Term
| depiction of linked core particles |
|
Definition
|
|
Term
| depiction of a nucleosome core |
|
Definition
|
|
Term
| something that is done to histones to affect DNA transcription |
|
Definition
| covalent modifications of their tails play an essential role in modulating the accessibility of DNA for transcription |
|
|
Term
| the handedness of the superhelix that forms around the histone octamer |
|
Definition
|
|
Term
| how the protein core interacts with the superhelix that wraps around it |
|
Definition
| forms contacts with the inner surface of it, particularly along the phosphodiester backbone and the minor groove of the DNA |
|
|
Term
| how histone H1 interacts with the DNA wrapped around the core protein |
|
Definition
| seals off the nucleosome at the location at which the linker DNA enters and leaves the nucleosome |
|
|
Term
| how wrapping around histones contributes to the packing of DNA |
|
Definition
| by decreasing its linear extent |
|
|
Term
| wrapping around histones is just the 1st step in DNA packing. what's the next step? |
|
Definition
it's thought to be nucleosomes being packed into 2 interwound helical stacks; folding of nucleosomes into loops
this is higher order chromatin structure |
|
|
Term
| depiction of higher-order chromatin structure |
|
Definition
|
|
Term
| depiction of the compaction of DNA into a eukaryotic chromosome |
|
Definition
|
|
Term
| depiction of how cispaltin alters the structure of DNA |
|
Definition
|
|
Term
| why RNA can perform a host of functions that DNA can not |
|
Definition
because RNA is single stranded, enabling it to adopt a variety of elaborate structures
this includes some functions that were once thought to be exclusively done by proteins |
|
|
Term
| the simplest and most common structural motif in nucleic acids |
|
Definition
|
|
Term
| depiction of stem-loop structures |
|
Definition
|
|
Term
| some things that can happen to stem-loop structures |
|
Definition
-many have paired bases
-some have mismatched or unpaired bases that can bulge out and destabilize local structure, but introduce deviations from the standard 2bl helix that can be important for higher order folding and for function |
|
|
Term
| how some more complex structures in nucleic acids can form |
|
Definition
| by way of interactions between more distant bases |
|
|
Term
| depiction of the complex structure of an RNA molecule |
|
Definition
|
|
Term
|
Definition
catalyze the copying of DNA sequences
promote the formation of the phosphodiester linkages joining the units of the ADNA backbone |
|
|
Term
| the types of DNA polymerases |
|
Definition
-polymerase I
-polymerase II
-polymerase III
-polymerase IV
-polymerase V |
|
|
Term
| the better understood DNA polymerases |
|
Definition
-polymerase I
-polymerase II |
|
|
Term
| function of DNA polymerase I |
|
Definition
| primer removal and DNA repair |
|
|
Term
| function of DNA polymerase II |
|
Definition
| repairs attachment of bulky hydrocarbons to bases |
|
|
Term
| function of DNA polymerase III |
|
Definition
|
|
Term
| function of DNA polymerase IV |
|
Definition
| repairs attachment of bulky hydrocarbons to bases |
|
|
Term
| function of DNA polymerase V |
|
Definition
| repairs attachment of bulky hydrocarbons to bases |
|
|
Term
| additional enzyme activities of DNA polymerase I |
|
Definition
|
|
Term
| additional enzyme activities of DNA polymerase II |
|
Definition
|
|
Term
| additional enzyme activities of DNA polymerase III |
|
Definition
|
|
Term
| additional enzyme activities of DNA polymerase IV |
|
Definition
|
|
Term
| table of E. coli DNA polymerases |
|
Definition
|
|
Term
| DNA polymerases catalyze... |
|
Definition
| the step-by-step addition of deoxyribonucleotides to a DNA strand |
|
|
Term
| rxn of the addition of DNA strands, in its simplest form |
|
Definition
| (DNA)n + dNTP <--> (DNA)n + 1 PPi |
|
|
Term
|
Definition
|
|
Term
|
Definition
| sequence of nucleic acids that determines the sequence of a complementary nucleic acid |
|
|
Term
| depiction of a polymerization rxn catalyzed by DNA polymerases |
|
Definition
|
|
Term
| some characteristics of DNA synthesis |
|
Definition
| 1: requires all 4 aqctivated precursors -- that is, the deoxynucleoside 5'-triphosphates dATP, dGTP, dCTP, and TTP -- as well as the Mg2+ ion
2: the new DNA strand is assembled directly onto a preexisting DNA template; the DNA polymerase is a template-directed enzyme that synthesizes a complementary product
3: DNA polymerases require a primer to begin synthesis. Elongation proceeds from 5' to 3' direction
4: many DNA polymerases are able to correct mistakes by removing mismatched nucleotides |
|
|
Term
| what is required for DNA synthesis to occur? |
|
Definition
| -deoxynucleoside 5'-triphosphates
-Mg+2 ion |
|
|
Term
| the deoxynucleoside 5'-triphosphates |
|
Definition
|
|
Term
| how the phosphodiester bond between adjacent nucleotides is formed |
|
Definition
| nucleophilic attack by the 3' end of the growing strand on the innermost P atom of the dinucleoside triphosphate (dNTP) |
|
|
Term
|
Definition
| initial segment of of a polymer that is to be extended on which elongation depends |
|
|
Term
| the 3 distinct active sites of DNA polymerase I |
|
Definition
-polymerase site
-3' --> 5' exonuclease site
-5' --> 3' exonuclease site |
|
|
Term
| what the 3' --> 5' nuclease activity of DNA polymerase I does |
|
Definition
| contributes to the remarkable high fidelity of DNA replication; error rate is less than 10-8 base pair |
|
|
Term
| error rate of DNA replication |
|
Definition
|
|
Term
| depiction of the strand-elongation rxn |
|
Definition
|
|
Term
| depiction of DNA polymerase structure (Klenow fragment) |
|
Definition
|
|
Term
| depiction of shape complementarity of bases (in this case, adenosine) |
|
Definition
|
|
Term
| one reason DNA polymerase has such a low error rate |
|
Definition
| conformational change by induced fit triggered by the binding of a dNTP into the active site such that it forms a tight pocket in which only a properly shaped base will fit |
|
|
Term
| depiction of shape selectivity of DNA polymerase |
|
Definition
|
|
Term
| depiction of the helicase mechanism |
|
Definition
|
|
Term
|
Definition
|
|
Term
| negative supercoiling arises from... |
|
Definition
| the unwinding or underwinding of DNA |
|
|
Term
| negative supercoiling prepares DNA for... |
|
Definition
| processes requiring separation of the DNA strands, such as replication |
|
|
Term
| what unwinding of part of a strand does to adjacent DNA |
|
Definition
|
|
Term
| why DNA must be locally unwound |
|
Definition
| to expose single-stranded templates for replication |
|
|
Term
| depiction of the consequences of strand separation |
|
Definition
|
|
Term
|
Definition
| to move in a circle or spiral or to revolve, usually about a fixed point or on an axis |
|
|
Term
|
Definition
| introduce or eliminate supercoils by temporarily cleaving DNA |
|
|
Term
|
Definition
| catalyze the relaxation of supercoiled DNA, which is thermodynamically favorable |
|
|
Term
|
Definition
| utilize free energy from hydrolysis to add negative supercoils to DNA |
|
|
Term
|
Definition
| type II topoisomerases in bacteria |
|
|
Term
| function of the exonuclease on DNA polymerase I |
|
Definition
| removes mismatched nucleotides from the 3' end of DNA by hydrolysis |
|
|
Term
| why it's easy for mismatched nucleotides to be removed |
|
Definition
weaker H bonding due to mismatch of nucleotides makes the malformed product flop around and be hot held as tightly in the polymerase active site
it finds itself in the exonuclease active site, where the trespassing nucleotide is removed |
|
|
Term
| depiction of proofreading of DNA |
|
Definition
|
|
Term
| what happens if an incorrect base is incorporated into the DNA strand? |
|
Definition
enzyme stalls due to structural disruption caused by the mismatch
the pause gives it time to wander into te exonuclease active site |
|
|
Term
| cost of exonuclease activity |
|
Definition
| DNA polymerase I removes about 1 correct nucleotide in 20; slight wasteful energetically |
|
|
Term
| origin of replication (oriC locus) |
|
Definition
| unique site within the genome where replication begins |
|
|
Term
|
Definition
|
|
Term
| what the origin of replication is in E. coli |
|
Definition
| a 245-bp region that has several unusual features |
|
|
Term
| composition of the oriC locus in E. coli |
|
Definition
-binding sites for DnaA protein
-tandem array of 13-bp sequences (AT rich) |
|
|
Term
|
Definition
| structure in the E. coli chromosome where replication begins |
|
|
Term
| how the prepriming complex is formed |
|
Definition
1: oriC locus wraps around DnaA protein
2: DnaB (a helicase) unwinds strand, including AT rich regions
3: single-strand-binding proteins (SSB) bind to newly generated single strands, preventing re-forming of 2bl helix |
|
|
Term
| depiction of the origin of replication in E. coli and formation of the prepriming complex |
|
Definition
|
|
Term
| depiction of the oriC locus in E. coli |
|
Definition
| refer to p. 634 (figure 34.11 A) |
|
|
Term
| DNA polymerases can add nucleotides only to... |
|
Definition
|
|
Term
| why a primer is required for DNA synthesis |
|
Definition
| because DNA polymerases can't start a strand de novo |
|
|
Term
| what primes the synthesis of DNA? |
|
Definition
|
|
Term
|
Definition
| specialized RNA polymerase that joins the prepriming complex in a multisubunit assembly called the primosome |
|
|
Term
|
Definition
| multisubunit assembly that primase joins the prepriming complex in |
|
|
Term
|
Definition
| synthesizes a stretch of about 10 RNA nucleotides that is complementary to one of the template DNA strands |
|
|
Term
| what removes the RNA primer? |
|
Definition
|
|
Term
|
Definition
|
|
Term
| depiction of DNA replication at low resolution |
|
Definition
|
|
Term
| how Okazaki fragments are joined |
|
Definition
| covalently by way of DNA ligase, which uses ATP hydrolysis to power the joining of DNA fragments |
|
|
Term
|
Definition
| strand formed from Okazaki fragments |
|
|
Term
|
Definition
| strand synthesized continuously 5' --> 3' |
|
|
Term
| depiction of Okazaki fragments |
|
Definition
|
|
Term
| the enzyme responsible for the rapid and accurate synthesis of DNA in E. coli |
|
Definition
| the holoenzyme DNA polymerase III |
|
|
Term
| hallmarks of the holoenzyme DNA polymerase III |
|
Definition
-its fidelity
-its very high catalytic potency
-its processitivity |
|
|
Term
|
Definition
| the ability of an enzyme to catalyze many consecutive rxns without releasing its substrate |
|
|
Term
| the amount of phosphodiester linkages formed by the holoenzyme DNA polymerase III before releasing its template |
|
Definition
| many thousands, compared with only 20 for DNA polymerase I |
|
|
Term
| catalytic potency of the holoenzyme DNA polymerase III |
|
Definition
| adds 1000 nucleotides per second compared to only 10 per second by DNA polymerase I |
|
|
Term
| why the holoenzyme DNA polymerase III is able to add 1000 nucleotides per second |
|
Definition
| largely because of its processitivity |
|
|
Term
| the source of the holoenzyme DNA polymerase III's processitivity |
|
Definition
| the β2 subunit, which has the form of a star shaped ring that can readily accommodate the DNA strand, encircle it, and spin around it to add nucleotides |
|
|
Term
| function of the β2 subunit in the holoenzyme DNA polymerase III |
|
Definition
| functions as a sliding clamp that spins around the molecule and adds nucleotides as it spins |
|
|
Term
| depiction of the structure of a sliding DNA clamp (the β2 subunit in the holoenzyme DNA polymerase III) |
|
Definition
|
|
Term
| how DNA gets into the β2 subunit in the holoenzyme DNA polymerase III |
|
Definition
| by way of sliding clamp loaders |
|
|
Term
|
Definition
| unwinds the DNA duplex ahead of the DNA polymerase |
|
|
Term
| single-strand-binding proteins |
|
Definition
| they bind to unwound strands to keep the strands separated so that both strands can serve as templates |
|
|
Term
|
Definition
| introduces negative supercoils ahead of the replication fork to avoid a topological crisis |
|
|
Term
| depiction of the replication fork |
|
Definition
|
|
Term
| depiction of the DNA polymerase holoenzyme |
|
Definition
|
|
Term
| the DNA polymerase holoenzyme consists of... |
|
Definition
-2 copies of the polymerase core enzyme linked to a central structure
-the central structure includes the clamp-loader complex, which binds to the hexameric helicase Dnab |
|
|
Term
| what fills the gaps between fragments of the nascent lagging strand in the trombone model? |
|
Definition
|
|
Term
| what removes the RNA primers in the lagging strand? |
|
Definition
| the 5' --> 3' exonuclease activity in DNA polymerase I |
|
|
Term
| why DNA polymerase III can't erase the RNA primers |
|
Definition
| because it doesn't have 5' --> 3' editing capacity |
|
|
Term
| how DNA ligase joins fragments of DNA |
|
Definition
| catalyzes the formation of a phosphodiester linkage between the 3'-hydroxyl group at the end of one DNA chain and the 5'-phosphate group at the end of the other |
|
|
Term
| depiction of the trombone model |
|
Definition
|
|
Term
| depiction of the DNA ligase rxn |
|
Definition
refer to p. 638
this is how it occurs in archaea and eukaryotes |
|
|
Term
| why DNA synthesis is more complex in eukaryotes than in bacteria |
|
Definition
-size of genome
-eukaryotes have pairs of chromosomes that must be replicated
-eukaryotes have linear instead of circular chromosomes
-the nature of DNA synthesis on the lagging strand; linear chromosomes subject to shporteninbg on each round of replication unless countermeasures are taken |
|
|
Term
| how the challenges of size of genome and number of chromosomes are dealt with |
|
Definition
| multiple origins of replication |
|
|
Term
| how far apart are the different origins of replication? |
|
Definition
| 30-300 kilobase pairs (kbp) apart |
|
|
Term
| how many origins of replication are in humans? |
|
Definition
| about 30,000, with each chromosome having several hundred |
|
|
Term
|
Definition
|
|
Term
|
Definition
proteins that bind to the origin of replication and permit (license) the DNA synthesis initiation complex
they ensure that each each replicon is replicated only once in each round of DNA synthesis |
|
|
Term
| how replicons are controlled such that each replicon is replicated only once in each cell division |
|
Definition
licensing factors bind to the origin of replication and get destroyed after the initiation of the initiation complex
license expires after 1 use |
|
|
Term
| the 2 distinct polymerases needed to copy a eukaryotic replicon |
|
Definition
-DNA polymerase α
-DNA polymerase δ |
|
|
Term
|
Definition
begins the copying of a replicon
includes primase subunit to synthesize RNA primer as well as an active DNA polymerase
adds about 20 deoxynucleotides to the primer |
|
|
Term
|
Definition
replaces DNA polymerase α
more processive than DNA polymerase α and is the principal replicative polymerase in eukaryotes |
|
|
Term
|
Definition
| DNA polymerase α being replaced by DNA polymerase δ |
|
|
Term
| complications introduced by having linear chromosomes |
|
Definition
-unprotected termini at the ends of chromosomes more vulnerable to digestion by exonuclease if left to dangle at the end of the chromosome during replication
-complete replication of DNA ends is difficult because polymerases act in 5' --> 3' direction and the lagging strand would have an incomplete 5' end after the removal of the RNA primer; each round of replication would shorten the chromosome |
|
|
Term
| depiction of telomere shortening |
|
Definition
|
|
Term
|
Definition
| the DNA at the end of a chromosome; consists of hundreds of repeats of a hexanucleotide sequence characteristic of the organism |
|
|
Term
| the most notable feature of telomeric DNA |
|
Definition
| it contains hundreds of tandem repeats of a hexanucleotide sequence |
|
|
Term
| how the telomere is structured in humans |
|
Definition
one of the strands is G rich at the 3' end and is slightly longer than the other
it is proporsed to loop back to form a DNA duplex with another part of the repeating sequence, displacing part of the original telomeric duplex |
|
|
Term
| the G rich repeating strand in human telomeres |
|
Definition
|
|
Term
| depiction of a proposed model for telomeres |
|
Definition
|
|
Term
| the simplest source of damage in the DNA double helix |
|
Definition
| errors introduced in the replication process |
|
|
Term
| how mismatching DNA bases causes damage |
|
Definition
| distorts double helix, which can become mutagenic |
|
|
Term
| how a mismatch of bases is mutagenic |
|
Definition
| results in daughter helices with different sequences |
|
|
Term
| some types of errors in DNA |
|
Definition
-mismatches
-insertions
-deletions
-breaks in one or both strands |
|
|
Term
| how errors in DNA can inhibit replication |
|
Definition
| replicative polymerases can stall or fall off the damaged template entirely, making replication of the genome halt before it's complete |
|
|
Term
| one way to repair damage in DNA |
|
Definition
| translesion or error-prone polymerases |
|
|
Term
| function of translesion or error-prone polymerases |
|
Definition
| allow for the completion of a draft sequence of the damaged area of the genome that can be at least partly repaired by DNA-repair processes |
|
|
Term
| drawback to the use of translesion or error-prone polymerases |
|
Definition
| substantially more error prone than other polymerases when replicating DNA |
|
|
Term
| depiction of triplet-repeat expansion |
|
Definition
|
|
Term
| bases in DNA can be damaged by... |
|
Definition
-oxidizing agents
-alkylating agents
-light |
|
|
Term
|
Definition
| chemical agents that alter specific bases within DNA after replication is complete |
|
|
Term
| how hydroxyl radical (a reactive oxygen species) is mutagenic |
|
Definition
| converts guanine to 8-oxoguanine, which is mutagenic because it pairs with adenine instead of cytosine |
|
|
Term
| depiction of guanine oxidation |
|
Definition
refer to p. 645
this is mutagenic |
|
|
Term
| how deamination causes mutations |
|
Definition
| example: deaminates adenine to form hypoxanthine, which pairs with cytosine instead of thymine |
|
|
Term
| depiction of adenine deamination |
|
Definition
refer to p. 645
this causes mutations |
|
|
Term
|
Definition
| aflatoxin B1, which is produced by molds that grow on peanuts and other foods |
|
|
Term
| how aflatoxin B1 causes mutations |
|
Definition
| cytochrome P450 enzyme converts it into a highly reactive epoxide, which reacts with the N-7 atom of guanine to form a mutagenic adduct that binds with adenine instead of cystine |
|
|
Term
| depiction of aflatoxin B1 activation |
|
Definition
refer to p. 646
causes mutations |
|
|
Term
| the most pertvasive DNA-damaging agent |
|
Definition
| the UV light from sunlight |
|
|
Term
|
Definition
| by covalently linking adjacent pyrimidine residues along the DNA strand |
|
|
Term
| depiction of a cross-linked dimer of 2 thymine bases |
|
Definition
|
|
Term
| how high energy em radiation, such as X-rays, damages DNA |
|
Definition
by producing high concentrations of reactive chemicals
also causes sinbgle- and double-stranded breaks |
|
|
Term
| many systems repair DNA by... |
|
Definition
| using sequence information from the uncompromised strand |
|
|
Term
| mechanistic outline followed by many single-strand replication systems |
|
Definition
1: recognize the offending base(s)
2: remove the offending base(s)
3: repair the resulting gap with a DNA polymerase ad a DNA ligase |
|
|
Term
| a mechanism in essentially all cells that corrects errors not corrected by proofreading |
|
Definition
|
|
Term
| how mismatch repair works in E. coli |
|
Definition
1: detecting mismatch
2: removing part of the strand containing the mismatch
3: replace it with correct sequence |
|
|
Term
| the mismatch repair proteins in E. coli |
|
Definition
|
|
Term
| the endonuclease in E. coli |
|
Definition
|
|
Term
| depiction of mismatch repair |
|
Definition
|
|
Term
| how mismatch repair machinery determines incorrect base in E. coli |
|
Definition
| some adenine bases in the parent strand are methylated, whereas the newly synthesized daughter strand is not yet methylated. thus, the machinery recognizes that the methylated base is correct and the unmethylated mismatch is incorrect |
|
|
Term
|
Definition
| repairing damage to DNA without having to remove any fragments of the DNA |
|
|
Term
|
Definition
| a photoreactivating enzyme that direct repairs DNA by photochemical cleavage of pyrimidine dimers |
|
|
Term
| how photochemical cleavage works |
|
Definition
| photolytic enzyme binds to distorted region and absorbs photon to form an excited state that cleaves the dimer into its component bases |
|
|
Term
| what happens to damaged bases in E. coli? |
|
Definition
|
|
Term
|
Definition
| replacing damaged bases with undamaged bases |
|
|
Term
| depiction of base-excision repair |
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
| site in DNA strand devoid of base |
|
|
Term
|
Definition
| knicks the backbone adjacent to the missing base |
|
|
Term
| deoxyribose phosphodiesterase |
|
Definition
| excites residual phosphate unit |
|
|
Term
| role of DNA polymerase I in base-excision repair |
|
Definition
| inserts undamaged nucleotide |
|
|
Term
| how the base-excision-repair system know to remove T in the T-G pair |
|
Definition
| because the C-->T mutation is so common |
|
|
Term
| depiction of the deamination of 5-methylcytosine forms thymine. |
|
Definition
|
|
Term
| what mechanism recognizes improper nucleotide pairs that escape the base-excision-repair system? |
|
Definition
| nucleotide-excision repair |
|
|
Term
| what the nucleotide-excision repair system does |
|
Definition
| recognizes distortions in the DNA double-helix caused by the presence of a damaged base |
|
|
Term
| depiction of nucleotide-excision repair |
|
Definition
|
|
Term
|
Definition
| in nucleotide-excision repair, this cuts out DNA sequence that contains the defective base |
|
|
Term
| why DNA uses thymine instead of uracil |
|
Definition
-cytosine spontaneously deaminates to form uracil
-thymine contains methyl group, but uravil instead contains an H in that place
-thus, the methyl group is a tag that distinguishes thymine from deaminated cytosine, which is uracil; this mechanism enhances the fidelity of the genetic message |
|
|
Term
| depiction of uracil repair |
|
Definition
|
|
Term
|
Definition
| hydrolyzes the glycosidic bond between the uracil and deoxyribose moieties, but does not attack thymine-containing nucleotides |
|
|
Term
| double-strand breaks arise when... |
|
Definition
|
|
Term
| one thing that can cause replication to stall |
|
Definition
| when the polymerase encounters an unrepaired nick in one of the template strands at the replication fork |
|
|
Term
| depiction of generation of a double-strand break |
|
Definition
|
|
Term
| things that can cause double-strand breaks |
|
Definition
-unrepaired nicks
-ionizing radiation, such as gamma rays and X-rays |
|
|
Term
| what happens when the replication machinery encounters a nick in the DNA? |
|
Definition
| the replication fork collapses, leaving a double-stranded break on one of the daughter helices |
|
|
Term
| types of ionizing radiation that can cause double-stranded breaks |
|
Definition
-x-rays
-gamma rays
they are powerful enough to break the DNA backbone |
|
|
Term
| where recombination is most efficient |
|
Definition
| between stretches of DNA that are similar in sequence |
|
|
Term
|
Definition
| parent DNA duplexes align at regions of sequence similarity, and new DNA molecules are formed by the breaking and joining of homologous segments |
|
|
Term
| one key protein in recombination in humans |
|
Definition
| RAD 51, which is an ATPase that binds single-stranded DNA |
|
|
Term
| depiction of repair of double-strand break by using recombination |
|
Definition
|
|
Term
| something recombination between alleles can be used for |
|
Definition
| generation of new DNA sequences and molecular diversity |
|
|
Term
| a biochemical tool recombination is the foundation for |
|
Definition
-gene knock-out
-gene knock-in |
|
|
Term
|
Definition
|
|
Term
|
Definition
| specific gene is inserted |
|
|
Term
| depiction of RNA polymerase |
|
Definition
|
|
Term
| the role of Mg2+ in RNA polymerase |
|
Definition
| part of the active site at the center of the structure |
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
| the 2 substrates required by RNA polymerase |
|
Definition
-DNA template strand
-nucleoside triphosphates |
|
|
Term
| the ribonucleoside triphosphates that are usen to synthesize RNA |
|
Definition
|
|
Term
| 2 divalent metal cations that can work in RNA polymerase |
|
Definition
|
|
Term
| depiction of complementarity between mRNA and DNA |
|
Definition
|
|
Term
|
Definition
| (RNA)n residues + ribonucleoside triphosphate <--> (RNA)n+1 residues + PPi |
|
|
Term
| difference between RNA polymerase and DNA polymerase |
|
Definition
| RNA polymerase doesn't require a primer |
|
|
Term
| depiction of the RNA strand-elongation rxn |
|
Definition
|
|
Term
|
Definition
| the segments of DNA that encode the various species of RNA |
|
|
Term
| 3 types of RNA in all cells |
|
Definition
|
|
Term
| composition of the RNA polymerase holoenzyme |
|
Definition
|
|
Term
| role of the σ subunit in the RNA polymerase holoenzyme |
|
Definition
-helps to find a site where transcription begins
-participates in the initiation of RNA synthesis
-it then dissociates from the rest of the enzyme |
|
|
Term
| composition of the RNA polymerase core enzyme |
|
Definition
|
|
Term
| table of the subunits of E. coli RNA polymerase |
|
Definition
|
|
Term
| the 3 stages of RNA synthesis |
|
Definition
1: initiation
2: elongation
3: termination |
|
|
Term
| how RNA polymerase knows where to begin transcription |
|
Definition
| promoters direct it to the proper site |
|
|
Term
| where the promoters are in DNA |
|
Definition
| about 10 and 35 nucleotides upstream of the start site |
|
|
Term
| depiction of bacterial promoter sequences |
|
Definition
|
|
Term
| depiction of consensus (average) sequences deduced from the analysis of many promoters |
|
Definition
|
|
Term
| how strength of promoter affects transcription |
|
Definition
| genes with stronger promoters get transcribed more frequently |
|
|
Term
|
Definition
| regulatory proteins that bind to specific sequences near promoter sites and interact with RNA polymerase |
|
|
Term
| how the upstream element (UP element) increases efficiency of transcription |
|
Definition
| by binding to the α subunit of RNA polymerase, creating an additional binding site for the polymerase |
|
|
Term
| the role of the σ subunit in RNA polymerase |
|
Definition
| helps to recognize promoter sites |
|
|
Term
| how the σ subunit helps RNA polymerase recognize promoter sites |
|
Definition
| 1: decreases affinity of RNA polymerase for general regions of DNA by a factor of 104, allowing t to slide rapidly in search of the promoter
2: enables RNA polymerase to recognize promoter sites |
|
|
Term
| depiction of the RNA polymerase holoenzyme complex |
|
Definition
|
|
Term
| depiction of how sigma factors act catalytically |
|
Definition
|
|
Term
| depiction of DNA unwinding |
|
Definition
|
|
Term
| depiction of RNA strand growth |
|
Definition
|
|
Term
|
Definition
region containing RNA polymerase, DNA, and nascent RNA
contains "bubble" of about 17 separated base pairs |
|
|
Term
| depiction of transcription bubble |
|
Definition
|
|
Term
| depiction of RNA-DNA hybrid separation |
|
Definition
|
|
Term
| why the higher error rate of RNA polymerase can be tolerated |
|
Definition
| because mistakes in RNA are not transmitted to progeny |
|
|
Term
|
Definition
| RNA polymerase can backtrack and remove the incorrect nucleotide using its inherent nuclease activity |
|
|
Term
|
Definition
termination of DNA transcription onto RNA within or just after a GC rich stem-and-loop structure followed by 4 U residues
terminates within or just after the termination signal |
|
|
Term
| depiction of termination signal |
|
Definition
|
|
Term
| how the combination hairpin-oligo(U) strucvture terminates transcription |
|
Definition
1: RNA polymerase appears to pause immediately after synthesising sequence that folds into a hairpin
2: RNA-DNA hybrid helix in the oligo(U) tail is unstable because rU-dA base pairs are the weakest of the Watson-Crick base pairs, thus allowing the pause caused by the hairpin to dissociate from the DNA template and the enzyme |
|
|
Term
| protein-dependent termination |
|
Definition
| termination that requires the participation of with ATPase activity caller the rho (p) protein |
|
|
Term
| how the rho (p) protein terminates RNA transcription |
|
Definition
1: hexameric p gets brought into action by sequences rich in C and poor in G
2: p then races down the strand searching for the RNA polymerase
3: p collides with RNA polymerase at the transcription bubble, breaking the RNA-DNA hybrid helix, unwinding the hybrid helix and stopping transcription |
|
|
Term
| common feature of protein-independent and protein-dependent termination |
|
Definition
| the functioning signals lie in the RNA rather than the DNA |
|
|
Term
| depiction of the mechanism for the termination of transcription by p protein |
|
Definition
|
|
Term
| tRNA and rRNA are generated by... |
|
Definition
| cleavage and other modifications of the transcription product |
|
|
Term
|
Definition
| noncoding regions of RNA product |
|
|
Term
| depiction of primary transcript of RNA |
|
Definition
|
|
Term
| S value vs. how fast RNA molecules move in a centrifugal field |
|
Definition
| the larger the S value, the larger the molecule moves |
|
|
Term
| some ways rRNA's and tRNA's are processed |
|
Definition
-excision from precursor
-addition of nucleotides to the termini of some strands (common for tRNA)
-modification of bases and ribose units |
|
|
Term
| type of RNA processing common for tRNA |
|
Definition
| addition of nucleotides to termini of molecules |
|
|
Term
| how bases and ribose units are modified in mRNA and tRNA |
|
Definition
-some bases being methylated (bacteria)
-unusual bases formed in all tRNA molecules by the enzymatic modification of a standard ribonucleotide in a tRNA precursor |
|
|
Term
| depiction of base pair modifications in RNA |
|
Definition
|
|
Term
| depiction of antibiotic action |
|
Definition
|
|
Term
| an essential enzyme in the metabolism of lactose |
|
Definition
|
|
Term
|
Definition
| hydrolyzes lactose into galactose and glucose |
|
|
Term
| depiction of β-galactosidase induction |
|
Definition
|
|
Term
| the 2 other proteins that are synthesized when β-galactosidase is synthesized |
|
Definition
-galactoside permease
-thiogalactoside transacetylase |
|
|
Term
| function of galactoside permease |
|
Definition
| it is required for the transport of lactose across the bacterial cell membrane |
|
|
Term
| function of thiogalactoside transacetylase |
|
Definition
| not essential for lactose metabolism, but may play a role in the detoxification of compounds that also may be transported by the permease |
|
|
Term
|
Definition
| coordinated unit of genes that cnahge expression in response to environmental changes |
|
|
Term
| the DNA components of the regulatory system of the lac operon |
|
Definition
-regulator gene
-operator site
-set of structural genes |
|
|
Term
| depiction of the general structure of an operon |
|
Definition
|
|
Term
| depiction of the lac operon |
|
Definition
|
|
Term
which part of the lac operon is i?
[image] |
|
Definition
| the gene encoding the repressor |
|
|
Term
which part of the lac operon is o?
[image] |
|
Definition
|
|
Term
which part of the lac operon is z?
[image] |
|
Definition
| structural gene for β-galactosidase |
|
|
Term
which part of the lac operon is y?
[image] |
|
Definition
|
|
Term
which part of the lac operon is a?
[image] |
|
Definition
|
|
Term
which part of the lac operon is p?
[image] |
|
Definition
|
|
Term
| function of the promoter site in the lac operon |
|
Definition
| directs the RNA polymerase to the correct transcription-initiation site |
|
|
Term
| function of the z, y, and a proteins |
|
Definition
| they are transcribed to yield a single mRNA molecule that codes for all 3 proteins |
|
|
Term
| polygenic or polycistronic transcript |
|
Definition
| mRNA molecule encoding more than 1 protein |
|
|
Term
| how does the lac repressor inhibit the expression of the lac operon? |
|
Definition
| in the absence of lactose, the repressor binds very tightly to the operator to block the bound RNA polymerase from using the DNA as a template |
|
|
Term
| how the repressor is removed from the lac operon |
|
Definition
| inducer binds to repressor, causing a structural change that greatly reduces the affinity of the repressor for the operator DNA |
|
|
Term
| depiction of the induction of the lac operon |
|
Definition
|
|
Term
| a type of lac operon inducer |
|
Definition
|
|
Term
|
Definition
| combination of galactose and glucose with an α-1,6 rather than an α-1,4 linkage |
|
|
Term
| what generates allolactose? |
|
Definition
| it's a side product of the few molecules of β-galactosidase that are always present before induction |
|
|
Term
| structure of 1,6-allolactose |
|
Definition
|
|
Term
| one DNA-sequence specific protein that stimulates the transcription of the lac operon when glucose is in short supply |
|
Definition
| catabolite activator protein (CAP), aka cyclic AMP (cAMP) response protein (CRP) |
|
|
Term
|
Definition
| in this case, it's glucose inhibiting the expression of the lac operon |
|
|
Term
| cellular glucose concentration vs. concentration of cAMP |
|
Definition
|
|
Term
| depiction of the binding site forcatabolite activator protein (CAP) |
|
Definition
|
|
Term
| how the level of cAMP is controlled in bacteria |
|
Definition
-enzyme IIA (EIIA) is phosphorylated at the expense of the glycolytic intermediate phosphoenolpyruvate
-phosphorylated EIIA then transfers phosphate to glucose, generating G6P
-if glucose is absent, phosphorylated EIIA activates adenylate cyclase, leading to an increase in cAMP and enhanced transcription of the lac operon |
|
|
Term
|
Definition
| mRNA molecules that form secondary structures capable of binding small molecules, thus preventing further transcription of mRNA |
|
|
Term
| how multicellular eukaryotes differentiate cells, in general |
|
Definition
| they differentially use transcriptional regulation of DNA common to all cells to create different cell types |
|
|
Term
| 3 important characteristics unique to eukaryotes that influence gene expression |
|
Definition
1: more complex transcriptional regulation
2: RNA processing
3: nuclear membrane |
|
|
Term
| depiction of transcription and translation |
|
Definition
|
|
Term
| how many types of RNA polymerases are there in bacteria? |
|
Definition
|
|
Term
| how many types of RNA polymerases are there in eukaryotes? |
|
Definition
|
|
Term
| table of the different types of eukaryotic RNA polymerases |
|
Definition
|
|
Term
| location of RNA polymerase I |
|
Definition
|
|
Term
| location of RNA polymerase II |
|
Definition
|
|
Term
| location of RNA polymerase III |
|
Definition
|
|
Term
| what RNA polymerase I synthesizes |
|
Definition
-18S rRNA
-5.8S rRNA
-28S rRNA |
|
|
Term
| what RNA polymerase II synthesizes |
|
Definition
|
|
Term
| what RNA polymerase III synthesizes |
|
Definition
|
|
Term
| depiction of additional classes of RNA |
|
Definition
|
|
Term
| something unique about RNA polymerase II |
|
Definition
| contains carboxyl-terminal domain (CTD) |
|
|
Term
| how RNA polymerase II is regulated |
|
Definition
| by phosphorylation mainly on the serine residues of the carboxyl-terminal domain (CTD) |
|
|
Term
| what phosphorylation of the carboxyl-terminal domain (CTD) does to RNA polymerase II |
|
Definition
| enhances transcription and recruits other factors required to process the RNA polymerase II product |
|
|
Term
| some types of eukaryotic RNA polymerase promoters |
|
Definition
-RNA polymerase I promoters
-RNA polymerase II promoters
-RNA polymerase III promoters |
|
|
Term
| depiction of common eukaryotic promoter elements (RNA promoters) |
|
Definition
|
|
Term
| characteristics of promoters for RNA polymerase I |
|
Definition
| have one at the start site (ribosomal initiator element (rInr)) and one 125-150 bp upstream of the start site (upstream promoter element (UPE)) |
|
|
Term
| ribosomal initiator element (rInr) |
|
Definition
| a sequence at the transcription start site that helps recruit RNA polymerase I to start transcription |
|
|
Term
| upstream promoter element (UPE) |
|
Definition
| sequence 150-200 bp further upstream of ribosomal initiator element (rInr); helps recruit RNA polymerase I to initiate transcription |
|
|
Term
| how ribosomal initiator element (rInr) and upstream promoter element (UPE) aid transcription |
|
Definition
| by binding proteins that recruit RNA polymerase I |
|
|
Term
| how transcription gets started |
|
Definition
| ribosomal initiator element (rInr) and upstream promoter element (UPE) aid transcription by binding proteins that recruit RNA polymerase I |
|
|
Term
| characteristics of promoters for RNA polymerase II |
|
Definition
-have set of conserved-sequence elements that define the start site and include the polymerase
-can contain any combination of possible elements, such as enhancer elements, which are unique to eukaryotes |
|
|
Term
| characteristics of promoters for RNA polymerase III |
|
Definition
| they are within the transcribed sequence, downstream of the start site |
|
|
Term
|
Definition
| DNA sequences that regulate the expression of a gene located on the same molecule of DNA |
|
|
Term
| trans-acting elements aka transcription factors |
|
Definition
| proteins that recognize cis-acting elements and regulate RNA synthesis |
|
|
Term
| importance of the regulation of RNA polymerase II |
|
Definition
| accounts for cell differentiation and development in higher organisms |
|
|
Term
|
Definition
| the most common cis-acting element for our genes transcribed by RNA polymerase II |
|
|
Term
| depiction of the TATA box |
|
Definition
|
|
Term
| the TASTA box is often paired with... |
|
Definition
| an initiator element (Inr) |
|
|
Term
|
Definition
| sequence found at the transcriptional start site |
|
|
Term
| downstream core promoter element (DPE) |
|
Definition
| found downstream of the start site and is commonly found in conjunction with the Inr in transcripts that lack the TATA box |
|
|
Term
|
Definition
| genes that tend to be continuously expressed instead of regulated |
|
|
Term
| genes that tend to have GC boxes in their promoters |
|
Definition
|
|
Term
| strands GC and CAAT boxes can be effective on |
|
Definition
-template (antisense)
-coding (sense) |
|
|
Term
| depiction of the CAAT and GC boxes |
|
Definition
|
|
Term
| RNA polymerase II is guided to the start site by... |
|
Definition
a set of transcription factors known collectively as TFII
TF stands for transcription factor and II stands for RNA polymerase II |
|
|
Term
| how transcription initiation using TFII begins |
|
Definition
| TFIID binding to the TATA box |
|
|
Term
| depiction of transcription initiation |
|
Definition
|
|
Term
| the key initial event in TATA-box promoters |
|
Definition
| recognition of the TATA box by the TATA-box-binding protein (TBP); this widens the minor groove |
|
|
Term
| the part of TFIID that binds to the TATA-box |
|
Definition
| the TATA-box-binding protein (TBP) |
|
|
Term
| depiction of the complex formed by the TATA-box-binding protein and DNA |
|
Definition
|
|
Term
| essential catalytic activities of TFIIH |
|
Definition
-it is an ATP-deppendent helicase that unwinds the DNA as a prelude to transcription
-the protein is also a kinase that phosphorylates the CTD of the polymerase |
|
|
Term
| this marks the transition from initiation to elongation |
|
Definition
| phosphorylation of the CTD by TFIIH |
|
|
Term
|
Definition
a type of cis-acting element that greatly increases the activities of many promoters in higher eukaryotes
they have no promoter activity of their own, but can exert their stimulatory actions over the span of several thousand base pairs |
|
|
Term
|
Definition
| upstream, downstream, or even in the midst of a transcribed gene |
|
|
Term
| something enhancers have in common with promoter sequences |
|
Definition
| they are bound by transcription activators that participate in the regulation of transcription |
|
|
Term
| transcription factors in eukaryotes don't act on their own, but instead... |
|
Definition
| recruit other proteins to form a complex that interacts with the transcriptional machinery to activate or repress transcription |
|
|
Term
|
Definition
| huge complex of 25-30 subunits that joins the transcription machinery (transcription factor and RNA polymerase II) before transcription takes place |
|
|
Term
|
Definition
refer to p. 680
in this case, it's basically acting in combinatorial control |
|
|
Term
|
Definition
| means of controlling gene expression in eukaryotes in which each transcription factor, rather than acting on its own to effect transcription, recruits other proteins to build up large complexes that regulate the transcription machinery |
|
|
Term
| advantage of combinatorial control |
|
Definition
a given regulatory protein can have different effects, depending on the other proteins present in the cell
helps eukaryotes with different cell types |
|
|
Term
| one way steroid receptors are different from other receptors |
|
Definition
| they are soluble and found in the cytoplasm or nucleoplasm rather than being bound to the membranes |
|
|
Term
| the general mode of action for steroid hormone receptors |
|
Definition
| on binding with the signal molecule (geberic term ligand), the ligand-receptor complex modifies the expression of specific genes by binding to control elements in the DNA |
|
|
Term
| nuclear hormone receptors |
|
Definition
| large family of transcription factors that, on the binding of a signal molecule such as a steroid hormone, modify the expression of specific genes by binding to control elements in DNA |
|
|
Term
|
Definition
| specific DNA sites that nuclear hormone receptors bind to |
|
|
Term
| 2 highly conserved domains of the nuclear hormone-receptor family |
|
Definition
-DNA-binding domain
-ligand-binding domain |
|
|
Term
|
Definition
| DNA-binding domains in which eight of the cysteine residues bind zinc ions to form DNA-binding domains that are called zinc-binding domains |
|
|
Term
| depiction of the structure of 2 nuclear hormone-receptor domains |
|
Definition
|
|
Term
| how ligand binding leads to transcription |
|
Definition
| causes significant structural change in the receptor and allows the receptor to recruit other proteins that facilitate transcription |
|
|
Term
| depiction of ligand binding to nuclear hormone receptor |
|
Definition
|
|
Term
|
Definition
| proteins that bind to the receptor only after it has bound to the steroid |
|
|
Term
| when the site for the interaction between the nuclear hormone-receptor complex and the coactivators is fully formed |
|
Definition
| only when the ligand is bound |
|
|
Term
| depiction of coactivator recruitment |
|
Definition
|
|
Term
|
Definition
| binds to a site in the ligand-binding domain that overlaps the coactivator binding site |
|
|
Term
| the template for RNA synthesis in eukaryotes |
|
Definition
|
|
Term
|
Definition
| complex of DNA and histones |
|
|
Term
| one way DNA gets loosened around histones |
|
Definition
| enzymatic attachment of acetyl groups to histones |
|
|
Term
| depiction of acetylation of histones |
|
Definition
|
|
Term
| histone acetyltransferases |
|
Definition
| catalyzes the acetylation of histones |
|
|
Term
| depiction of the structure of histone acetyltransferase |
|
Definition
|
|
Term
| how histone acetylation loosens DNA |
|
Definition
| dramatically reduces the affinity of the histone for DNA by neutralizing the positive charge of the lysine residfue while adding a negative charge to it |
|
|
Term
|
Definition
an acetyl binding domain that is present in many proteins that regulate eukaryotic transcription
these proteins serve as docking sites to recruit proteins that play a variety of roles in transcription and chromatin remodeling |
|
|
Term
| how acetylation of histone tails provides a mechanism for recruiting other components of the transcriptional machinery |
|
Definition
| they serve as docking sites to recruit proteins that play a variety of roles in transcription and chromatin remodeling |
|
|
Term
| a large complex bromodomains are also present in |
|
Definition
| chromatin-remodeling engines |
|
|
Term
| chromatin-remodeling engines |
|
Definition
-large complexes that contain bromodomains and domains somilar to those of helicases
-utilize the free energy of ATP hydrolysis to shift the positions of nucleosomes along the DNA and induce other conformational changes in the DNA |
|
|
Term
| 3 mechanisms histone acetylation can activate transcription |
|
Definition
1: reducing the affinity of the histones for DNA
2: recruiting other components of the transcriptional machinery
3: initiating the remodeling of the chromatin structure |
|
|
Term
| some means by which histones can be modified |
|
Definition
-acetylation
-methylation
-phosphorylation |
|
|
Term
| depiction of chromatin remodeling |
|
Definition
|
|
Term
| table of selected histone modifications |
|
Definition
|
|
Term
| general effect of acetylation on histones |
|
Definition
|
|
Term
| general effect of methylation on histones |
|
Definition
|
|
Term
| general effect of phosphorylation on histones |
|
Definition
|
|
Term
| key reaction in repression |
|
Definition
| deacetylation of acetylated lysine |
|
|
Term
|
Definition
| catalyze deacetylation of lysine residues in histone tails |
|
|
Term
| the products of RNA polymerase II action |
|
Definition
| pre-mRNA molecules (the primary transcripts) |
|
|
Term
| what happens to nearly all mRNA precursors in higher eukaryotes? |
|
Definition
|
|
Term
|
Definition
| encoding regions of genes that are kept after splicing |
|
|
Term
|
Definition
| noncoding regions of genes that are removed by splicing |
|
|
Term
| depiction of the processing of eukaryotic pre-rRNA |
|
Definition
|
|
Term
| how eukaryotic pre-rRNA gets processed |
|
Definition
1: extensive modification of certain sequences on the pre-rRNA, on both ribose and base components, directed by many small nucleolar ribonucleoproteins (snoRNPs)
2: the pre-rRNA is assembled with ribosomal proteins in a large ribonucleoprotein
3: cleavage of modified pre-rRNA |
|
|
Term
| small nucleolar ribonucleoproteins (snoRNPs) |
|
Definition
direct the modification of certain sequences on the pre-rRNA, both on the ribose and base components
each of these proteins consists of 1 small nucleolar RNA (snoRNA) and several proteins |
|
|
Term
| where more of the modification of pre-rRNA takes place |
|
Definition
|
|
Term
|
Definition
| cleaves nucleotides from the 5' end of the tRNA precursor |
|
|
Term
|
Definition
| cleaves nucleotides from the 3' end of the tRNA precursor |
|
|
Term
| tRNA nucleotidyltransferase |
|
Definition
| adds CCA to the tRNA precursor |
|
|
Term
| depiction of transfer RNA precursor processing |
|
Definition
|
|
Term
| what endonuclease does to tRNA precursor |
|
Definition
|
|
Term
| the most extensively modified transcription product |
|
Definition
| that of RNA polymerase II |
|
|
Term
| what happens to most of the transcription product of RNA polymerase II? |
|
Definition
| most of it gets processed to mRNA |
|
|
Term
| how the 5' end of the nascent RNA strand is modified shortly after the initiation of RNA synthesis |
|
Definition
1: phosphoryl group removed by hydrolysis by RNA triphosphatase
2: the diphosphate 5' end of the RNA attacks the α-phosphorus atom of a molecule of GTP to form an unusual 5'-5' triphosphate linkage, catalyzed by guanylyltransferase; this forms the 5' cap
3: the N-7 N atom of the terminal guanine is then methylated by RNA N-7 guanine methyltransferase, which uses S-adenosylmethionine as the methyl donor; this forms cap 0 |
|
|
Term
| how the 5' cap is formed during RNA synthesis |
|
Definition
| the diphosphate 5' end of the RNA attacks the α-phosphorus atom of a molecule of GTP to form an unusual 5'-5' triphosphate linkage, catalyzed by guanylyltransferase |
|
|
Term
|
Definition
| the N-7 N atom of the terminal guanine is then methylated by RNA N-7 guanine methyltransferase, which uses S-adenosylmethionine as the methyl donor |
|
|
Term
| how 5' caps make mRNAs more stable |
|
Definition
| by protecting their 5' ends from nucleases and phosphatases |
|
|
Term
| how caps enhance translation |
|
Definition
| they enhance translation by eukaryotic protein-synthesizing systems |
|
|
Term
| depiction of capping the 5' end |
|
Definition
|
|
Term
| something most eukaryotic mRNAs have added to their 3' end after transcription |
|
Definition
| a polyadenylate (poly(A)) tail |
|
|
Term
| how is the final form of the 3' end of the pre-mRNA created? |
|
Definition
| the 3' end of the pre-mRNA is generated by a complex that contains a specific endonuclease (the cleavage and polyadenylation specifity factor, CPSF) that recognizes the sequence AAUAAA |
|
|
Term
| depiction of polyadenylation of a primary transcript |
|
Definition
|
|
Term
| possible roles of the poly (A) tail that is added to mRNA |
|
Definition
-might enhance translation efficiency
-might make the mRNA more stable
-more effective template for protein synthesis |
|
|
Term
|
Definition
| the removal of introns and combining of exons to form the final product |
|
|
Term
| this is required for accurate splicing of mRNA |
|
Definition
| clear marking of correct splice sites |
|
|
Term
| common structural motif of splice sites in eukaryotes |
|
Definition
| the intron begins with GU and ends with AG |
|
|
Term
| depiction of the transcription and translation of the β-globin gene |
|
Definition
|
|
Term
| depiction of splice sites |
|
Definition
|
|
Term
| what are the molecular machines that so precisely excise introns and join exons? |
|
Definition
|
|
Term
|
Definition
| large splicing complex formed by a group of special RNAs and more than 300 proteins that combine with pre-mRNA |
|
|
Term
| small nuclear RNAs (snRNAs) |
|
Definition
| class of RNAs that is essential in the spliceosome |
|
|
Term
| small nuclear ribonucleoprotein particles (snRNPs) (pronounced "snurps") |
|
Definition
| RNA-protein complexes that are composed of small nuclear RNAs (snRNAs) and their associated proteins |
|
|
Term
| depiction of spliceosome assembly and action |
|
Definition
|
|
Term
| what forms the catalytic center of the spliceosome? |
|
Definition
|
|
Term
| depiction of the splicing catalytic center |
|
Definition
|
|
Term
| 2 noteworthy features of the splicing process |
|
Definition
1: RNA molecules play key roles in directing the alignment of splice sites and in carrying out catalysis
2: ATP-powered helicases unwind RNA duplex intermediates that facilitate catalysis and induce the release of snRNPs from the mRNA |
|
|
Term
|
Definition
| rxn of an alcohol with an ester to form a different alcohol and a different ester |
|
|
Term
| mRNA transcription and processing seem to be coordinated by... |
|
Definition
| the carboxyl-terminal domain (CTD) of RNA polymerase II |
|
|
Term
| how the carboxyl-terminal domain (CTD) of RNA polymerase II contributes to efficient transcription |
|
Definition
| by recruiting proteins to the pre-mRNA |
|
|
Term
| depiction of the CTD: coupling transcription to pre-mRNA processing |
|
Definition
|
|
Term
| proteins recruited by the carboxyl-terminal domain (CTD) of RNA polymerase II |
|
Definition
-capping enzymes
-components of the splicing machinery
-an endonuclease that cleaves the transcript at the poly(A) addition site |
|
|
Term
|
Definition
| methylate the 5' guanine on the pre-mRNA immediately after transcription begins |
|
|
Term
| what endonuclease does to the pre-mRNA |
|
Definition
| cleaves it at the poly(A) addition site, creating a free 3'-OH group that is the target for 3' adenylation |
|
|
Term
| why protein synthesis is called translation |
|
Definition
| because the 4 letter alphabet of nucleic acids is translated into the 20 letter alphabet of proteins |
|
|
Term
| some characteristics of the genetic code |
|
Definition
1: 3 nucleotides encode an amino acid
2: the code is nonoverlapping
3: the code has no punctuation; it is read sequentially from a fixed starting point without punctuation
4: the genetic code has directionality (5'-->3')
5: the genetic code is degenerate |
|
|
Term
|
Definition
| group of 3 bases that encodes an amino acid |
|
|
Term
| is the genetic code overlapping or nonoverlapping? |
|
Definition
|
|
Term
|
Definition
| sequentially from a fixed starting point with no punctuation |
|
|
Term
| direction the genetic code is read |
|
Definition
|
|
Term
| how the genetic code is degenerate |
|
Definition
| this means that some amino acids are encoded by more than 1 codon |
|
|
Term
|
Definition
| codons that specify the same amino acid |
|
|
Term
| depiction of the genetic code |
|
Definition
|
|
Term
| why the degeneracy of the genetic code is advantageous |
|
Definition
| because it minimizes the deleterious effects of mutations |
|
|
Term
| why the genetic code is almost, but not entirely, universal |
|
Definition
| because some codons translate differently in different organisms |
|
|
Term
| why the genetic code of mitochondria differs from the rest of the cell |
|
Definition
| because mitochondrial DNA encodes a distinct set of transfer RNAs, adaptor molecules that recognize the alternative codons |
|
|
Term
| depiction of the distinctive codons of human mitochondria |
|
Definition
|
|
Term
|
Definition
| serves as the adaptor molecule between the codon and its specified amino acid |
|
|
Term
| how tRNA acts as an adaptor |
|
Definition
| by binding to a specific codon and brings with it an amino acid for incorporation into the polypeptide chain |
|
|
Term
| some features of all known transfer RNA molecules |
|
Definition
1: single strand containing 73-93 ribonucleotides
2: the 3D molecule is L-shaped
3: contain many unusual bases, typically 7-15 per tRNA, such as methylated derivatives of A, U, C, and G
4: can be arranged in a clover leaf pattern when depicted in 2D; it also has about half the nucleotides base-paired to form double-helices; also has 5 groups of bases that are not base paired
5: the 5' end is phosphorylated, with the 5' residue usually being pG
6: the activated amino acid is attached to a hydroxyl group of the adenosine residue located at the end of the 3' CCA component of the acceptor stem
7: the anticodon is present in a loop near the center of the sequence |
|
|
Term
| depiction of transfer RNA structure |
|
Definition
|
|
Term
| what methylation of certain bases does for tRNA |
|
Definition
-prevents the formation of certain base pairs, rendering some of the bases accessible for for interactions with other components of the translation machinery
-gives some regions of tRNA hydrophobic character |
|
|
Term
| the 5 groups of bases that are not base paired in tRNAs |
|
Definition
-the 3' CCA terminal region, which is part of the acceptor system
-the TψC loop, which got its name from ribothymine-pseudouracil-cytosine
-the "extra arm," which contains a variable number of residues
-the DHU loop, which contains several dihydrouracil residues
-the anticodon loop |
|
|
Term
| depiction of the general structure of transfer RNA molecules |
|
Definition
|
|
Term
| why some tRNAs can recognize more than 1 codon |
|
Definition
|
|
Term
|
Definition
| states that some tRNAs can recognize more than 1 codon because of steric freedom in pairing of the 3rd base of the codon |
|
|
Term
| depiction of allowed pairings at the third base of the codon according to the wobble hypothesis |
|
Definition
|
|
Term
| 2 generalizations that can be made concerning the codon-anticodon interaction |
|
Definition
1: codons that differ in either of their first 2 bases must be recognized by different tRNAs
2: the first baser of an anticodon determines whether a particular tRNA molecule reads 1, 2, or 3 kinds of codons; thus, part of the degeneracy of the genetic code arises from imprecision in the pairing of the third base of the codon with the first base of the anticodon |
|
|
Term
| part of the degeneracy of the genetic code arises from... |
|
Definition
| imprecision in the pairing of the third base of the codon with the first base of the anticodon |
|
|
Term
| the observed error rate of protein synthesis |
|
Definition
|
|
Term
| table of the accuracy of protein synthesis |
|
Definition
|
|
Term
| aminoacyl-tRNA synthetases |
|
Definition
| catalyze the activation of amino acids |
|
|
Term
| 2 reasons the specific linkages between amino acids and specific tRNAs are crucial |
|
Definition
1: the attachment of a given amino acid to a particular tRNA establishes the genetic code
2: the formation of a peptide bond is not thermodynamically favorable, so the amino acid must first be activated |
|
|
Term
| what establishes the genetic code? |
|
Definition
| the attachment of a given amino acid to a particular tRNA |
|
|
Term
| why an amino acid must be activated before being added to the polypeptide chain |
|
Definition
| because the formation of that bond is thermodynamically unfavorable |
|
|
Term
| the activated intermediates in protein synthesis |
|
Definition
|
|
Term
|
Definition
|
|
Term
| aminoacyl-tRNA aka charged tRNA |
|
Definition
| an amino acid ester of tRNA |
|
|
Term
| amino acids are activated by... |
|
Definition
| attachment to transfer RNA |
|
|
Term
| depiction of aminoacyl-tRNA |
|
Definition
|
|
Term
| amino acids are first activated by... |
|
Definition
|
|
Term
| the first step in the activation of amino acids |
|
Definition
| the formation of an aminoacyl adenylate from the amino acid and the ATP |
|
|
Term
| depiction of aminoacyl adenylate aka aminoacyl-AMP |
|
Definition
|
|
Term
| the 2 steps of activation of an amino acid by adenylation |
|
Definition
1: formation of an aminoacyl adenylate from an amino acid and ATP
2: the transfer of the aminoacyl group to a particular tRNA molecule to form aminoacyl-tRNA |
|
|
Term
| the net rxn of the activation of amino acids |
|
Definition
| amino acid + ATP + tRNA + H2O --> aminoacyl-tRNA + AMP + 2 Pi |
|
|
Term
| the energy consumed in the synthesis of aminoacyl-tRNA |
|
Definition
| equivalent of 2 molecules of ATP consumed in the synthesis of each aminoacyl-tRNA |
|
|
Term
| how translation takes place |
|
Definition
| takes place with the formation of the ester linkage between an amino acid and a specific tRNA |
|
|
Term
| the actual translators of the genetic code |
|
Definition
| the aminoacyl-tRNA synthetases |
|
|
Term
| how aminoacyl-tRNA synthetases are specific in their binding |
|
Definition
| they have highly discriminating amino acid activation sites |
|
|
Term
| depiction of the active site of threonyl-tRNA synthetase |
|
Definition
|
|
Term
| one way the fidelity of protein synthesis is increased |
|
Definition
| proofreading by aminoacyl-tRNA syntyhetases |
|
|
Term
| how the aminoacyl-tRNA can be edited without dissociating from the synthetase |
|
Definition
| the CCA arm with the amino acid attached to it can swing out of the activation site and into the editing site, which hydrolyzes the bond between the amino acid and the tRNA, providing an opportunity for correction |
|
|
Term
| depiction of the editing of aminoacyl-tRNA |
|
Definition
|
|
Term
| the point at which translation takes place |
|
Definition
| synthetases choosing their tRNA partners |
|
|
Term
| depiction of the recognition sites on tRNA |
|
Definition
|
|
Term
| depiction of the ribosome at high resolution |
|
Definition
|
|
Term
|
Definition
| the molecular machines that coordinate the interplay of aminoacyl-tRNAs, mRNA, and proteins |
|
|
Term
|
Definition
-large subunit
-small subunit
-both subunits made of nearly 2/3 RNA and 1/3 protein |
|
|
Term
| depiction of ribosomal RNA folding pattern |
|
Definition
|
|
Term
| the catalytic sites in the ribosome are composed almost entirely of... |
|
Definition
|
|
Term
| one reason it's advatageous for mRNA to be translated in the 5' --> 3' direction |
|
Definition
| allows for translation to take place as it's being transcribed |
|
|
Term
| a key feature of bacterial gene expression |
|
Definition
| translation and transcription are closely coupled in space and time |
|
|
Term
|
Definition
| a group of ribosomes bound to an mRNA molecule |
|
|
Term
|
Definition
|
|
Term
| the 3 parts of protein synthesis |
|
Definition
1: initiation
2: elongation
3: termination |
|
|
Term
| protein-synthesis initiation requires the the cooperation of... |
|
Definition
-the ribosome
-tRNA
-mRNA
-various protein factors |
|
|
Term
| the 3 tRNA binding sites in ribosomes |
|
Definition
-A site (aminoacyl)
-P site (peptidyl)
-E site (exit) |
|
|
Term
| depiction of the binding sites of transfer RNA |
|
Definition
|
|
Term
| depiction of an active ribosome |
|
Definition
|
|
Term
| the start signal for translation is usually... |
|
Definition
|
|
Term
|
Definition
| when an mRNA encodes 2 or more polypeptide chains |
|
|
Term
| all known mRNA molecules contain... |
|
Definition
| the start and stop signals of the polypeptide chain(s) they encode |
|
|
Term
| other than the initiating codon, what else is involved in initiation in bacteria? |
|
Definition
| a purine-rich sequence called the Shine-Dalgarno sequence |
|
|
Term
|
Definition
| purine-rich sequence upstream of start codon that helps initiate translation |
|
|
Term
| depiction of initiation sites |
|
Definition
|
|
Term
| function of untranslated regions of mRNA |
|
Definition
| usually to regulate the usage of mRNA molecules |
|
|
Term
| the 2 kinds of interactions that determine where protein synthesis starts in bacteria |
|
Definition
1: pairing of mRNA bases with the 3' end of 16S rRNA
2: pairing of the initiator codon on mRNA with the anticodon of an initiator tRNA molecule |
|
|
Term
| bacterial protein synthesis is initiated by... |
|
Definition
|
|
Term
| protein synthesis in bacteria starts with... |
|
Definition
| the modified amino acid N-formylmethionine (fMet) |
|
|
Term
| depiction of N-formylmethionine (fMet) |
|
Definition
|
|
Term
| depiction of the formylation of methionyl-tRNA |
|
Definition
|
|
Term
| the rate-limiting step in protein synthesis |
|
Definition
| formation of the 70S complex |
|
|
Term
| depiction of translation initiation in bacteria |
|
Definition
|
|
Term
|
Definition
| basically where the ribosome reads the mRNA |
|
|
Term
|
Definition
| deliver aminoacyl-tRNA to the ribosome |
|
|
Term
|
Definition
rotation of the aminoacyl-tRNA in the A site so that the amino acid is brought into proximity with the aminoacyl-tRNA in the P site on the ribosome
this process aligns the amino acids for peptide bond formation |
|
|
Term
| are internal AUG codons read by the initiator tRNA? |
|
Definition
|
|
Term
| peptidyl transferase center |
|
Definition
| catalyzes the formation of a peptide bond |
|
|
Term
| the ribosome gets much of its catalytic power from... |
|
Definition
| catalysis by proximity and orientation |
|
|
Term
| depiction of peptide bond formation |
|
Definition
|
|
Term
| depiction of the mechanism of protein synthesis |
|
Definition
|
|
Term
| translocation in ribosomes is enhanced by... |
|
Definition
| elongation factor G (EF-G) aka translocase |
|
|
Term
| elongation factor G (EF-G) aka translocase |
|
Definition
| enhances elongation in ribosomes |
|
|
Term
| depiction of the translocation mechanism |
|
Definition
|
|
Term
| where the peptide chain stays during translation |
|
Definition
| in the P site of the ribosome; it leaves thru the exit tunnel |
|
|
Term
| how tRNA moves thru the ribosome |
|
Definition
| in the A site, thru the P site, and out the E site |
|
|
Term
| direction the polypeptide chain is synthesized in |
|
Definition
| amino-terminal-to-carboxyl-terminal |
|
|
Term
| depiction of polypeptide chain growth |
|
Definition
|
|
Term
| which terminus are new amino acids added to in protein synthesis? |
|
Definition
|
|
Term
| protein synthesis is terminated by... |
|
Definition
| release factors that read stop codons |
|
|
Term
| stop codons are recognized by... |
|
Definition
|
|
Term
| depiction of the termination of protein synthesis |
|
Definition
|
|
Term
| what a release factor does |
|
Definition
| recognizes a stop codon in the A site and stimulates the release of the completed protein from the tRNA in the P site |
|
|
Term
| where bacteria and eukaryotes differ in protein synthesis |
|
Definition
|
|
Term
| some areas where bacteria and eukaryotes differ in the initiation of protein synthesis |
|
Definition
1: ribosomes
2: initiator tRNA
3: initiation
4: the structure of mRNA
5: elongation and termination
6: organization |
|
|
Term
| difference between bacterial and eukaryotic ribosomes |
|
Definition
| eukaryotic ribosomes are larger |
|
|
Term
| difference in initiator tRNA between bacteria and eukaryotes |
|
Definition
-the initiator in bacteria is N-formylmethionine
-the initiator in eukaryotes is methionine |
|
|
Term
| the initiating amino acid in bacteria |
|
Definition
|
|
Term
| the initiating amino acid in eukaryotes |
|
Definition
|
|
Term
| the initiating codon in eukaryotes |
|
Definition
|
|
Term
| initiation in eukaryotes begins with... |
|
Definition
| the formation of the ternary complex consisting of the 40S ribosome and Met-tRNAi in association with eIF-2 |
|
|
Term
| why a bacterial mRNA can serve as the template for the synthesis of several proteins |
|
Definition
| because it can have multiple Shine-Dalgarno sequences, thus multiple start sites, making it able to serve as the template for multiple proteins |
|
|
Term
| part of the reason the initiation mechanisms between bacteria and eukaryotes are different |
|
Definition
| difference in RNA processing |
|
|
Term
| depiction of eukaryotic translation initiation |
|
Definition
|
|
Term
| the shape of eukaryotic mRNA |
|
Definition
|
|
Term
| depiction of how protein interactions circularize eukaryotic mRNA |
|
Definition
|
|
Term
| how the translation machinery is organized in higher eukaryotes |
|
Definition
| organized into large complexes associated with the cytoskeleton |
|
|
Term
| some antibiotic inhibitors of protein synthesis |
|
Definition
-streptomycin and other aminoglycosides
-tetracycline
-chloramphenicol
-cycloheximide
-erythromycin
-puromycin |
|
|
Term
| table of antibiotic inhibitors of protein synthesis |
|
Definition
|
|
Term
| depiction of the antibiotic action of puromycin |
|
Definition
|
|
