Term
| What are the biological roles of nucleotides? |
|
Definition
Carrying genetic information
Chemical links in signal transduction
Precursors for other molecules (structural components of a variety of enzyme cofoactors and metabolic intermediates)
Energy currency |
|
|
Term
| What are the differences between DNA and RNA? |
|
Definition
DNA - contains thymine instead of uracil; one less hydroxyl group (lost from 2' Carbon) on pentose than RNA (deoxy)
RNA - contains uracil instead of thymine |
|
|
Term
| What is the central dogma of genetics? |
|
Definition
|
|
Term
| What is involved in DNA transcription? |
|
Definition
| RNA polymerase copies transcribed strand from 5' to 3'. |
|
|
Term
| What are the main post-transcriptional modifications of RNA? |
|
Definition
| A 5' methyl cap and 3' poly A tail are added. |
|
|
Term
| What happens in RNA processing and splicing? |
|
Definition
| Introns are excised. There are codes that indicate what should be removed. |
|
|
Term
|
Definition
| The modified RNA molecule that is transported outside the nucleus. |
|
|
Term
|
Definition
| The production of polypeptides in the cytoplasm by ribosomes. |
|
|
Term
| What is involved in protein assembly? |
|
Definition
| The completely translated polypeptide is fully folded into its full secondary and tertiary structure. |
|
|
Term
| What are the five levels of regulation of gene expression? |
|
Definition
Epigenetics
Transcriptional control
RNA processing control
Translation control
Protein activity control |
|
|
Term
| What is the most efficient of the levels of gene expression regulation? |
|
Definition
|
|
Term
| What is a mechanism of gene expression control that is present at both the mRNA and protein levels? |
|
Definition
|
|
Term
| What types of phosphate bonds are considered high energy? |
|
Definition
| Bonds existing when more than one phosphate is present |
|
|
Term
| What is the main structural difference between purines and pyrimidines? |
|
Definition
Pyrimidines have one ring
Purines have two. |
|
|
Term
| How do the purines differ from each other in structure? |
|
Definition
Adenine - only has NH2 attached to top carbon on larger ring.
Guanine has two groups - a carboxyl on top C of main ring and NH2 on lower left carbon. |
|
|
Term
| Which two pyrimidines are most similar? |
|
Definition
| Cytosine (one amino and one carboxyl) and uracil (two carboxyl groups). One carboxyl is at same position (bottom left C) and different group is at top. |
|
|
Term
| How is thymine different from the other pyrimidines? |
|
Definition
| It has three functional groups; two carboxyls like uracil with one methyl group added to top right C. |
|
|
Term
| What is the most important methylated nucleoside in human biology? What is its role? |
|
Definition
5-methylcytidine (looks like thymine, but with NH2 on top)
Used in epigenetic gene regulation. The bulky side group prevents access to DNA. |
|
|
Term
| What methylated nucleosides are found in organisms other than humans? |
|
Definition
N6 methyl adenosine
N2 Methylguanosine
5-Hydroxymethylcytidine |
|
|
Term
| What minor tRNA nucleosides are important in the wobble effect of tRNA recognition of amino acids? |
|
Definition
Inosine
Pseudouridine
7-Methylguanosine
4-Thiouridine |
|
|
Term
| What ribonucleoside is problematic due to tautomerization? |
|
Definition
Uracil (can be Lactam, Lactim, or double lactin)
This happens enough times in a uracil molecule that it contributes to DNA instability. |
|
|
Term
| Which bases can form two hydrogen bonds? |
|
Definition
|
|
Term
| Which bases can form three hydrogen bonds? |
|
Definition
|
|
Term
| What tautomerization of adenine can cause mutations? |
|
Definition
| The rare imino form can pair with C |
|
|
Term
| What tautomerization of guanine can cause mutations? |
|
Definition
| The rare enol form of guanine can pair with T |
|
|
Term
| Which is more stable: DNA or RNA? |
|
Definition
|
|
Term
| Why is it likely that T is in DNA instead of U? |
|
Definition
| Tautomerization of U can form cyclic monophosphate derivative and shorten RNA. |
|
|
Term
| Why is energy exchanged by the PO4 bond of ATP? |
|
Definition
|
|
Term
| What three molecules are higher in E than ATP? |
|
Definition
1,3-bisphosphoglycerate (1,3-BPG)
Phosphoenolpyruvate (PEP)
Phosphocreatine (P-creatine) |
|
|
Term
| What two molecules are lower in E than ATP? |
|
Definition
|
|
Term
| What serves as a charge stabilizer for ATP, stabilizing its phosphate bonds and overcoming EA for formation of them? |
|
Definition
|
|
Term
| What three instabilities are associated with nucleotides? |
|
Definition
Deamination of exocyclic amino groups
Depurination (hydrolysis of N-B-glycosyl bond between base and pentose) - looks like hole in helix
Tautomerization - migration of H atom or proton |
|
|
Term
| What does deamination of cytosine create? |
|
Definition
|
|
Term
| What type of nucleotide instability is rapidly repaired? |
|
Definition
|
|
Term
| Can the complementary strand of DNA which is depurinated at one or more locations still be read? |
|
Definition
|
|
Term
| Is depurination higher in purines or pyrimidines? |
|
Definition
|
|
Term
| What are the three metabolic pathways involving nucleotides? |
|
Definition
De Novo biosynthesis
Salvage biosynthesis
Degradation |
|
|
Term
| What does de novo purine synthesis begin with? |
|
Definition
|
|
Term
| What are the metabolic precursors of nucleotides? |
|
Definition
CO2
amino acids
ribose-5-P
NH3 |
|
|
Term
| What is the pyrimidine ring synthesized as? |
|
Definition
| Orotidylate (before conversion to UMP, UTP, or CTP) |
|
|
Term
| What provides the backbone in purine synthesis? |
|
Definition
|
|
Term
| What provides two N's in purine rings/ |
|
Definition
|
|
Term
| What provides two C's in purine synthesis? |
|
Definition
|
|
Term
| What provides just one N in purine synthesis? |
|
Definition
|
|
Term
| What provides just one C in purine synthesis? |
|
Definition
|
|
Term
| Where does purine synthesis take place? |
|
Definition
|
|
Term
| What is PRPP produced from? |
|
Definition
|
|
Term
| What is the important precursor for both purines and pyrimidines? |
|
Definition
|
|
Term
| How are reactive intermediates handled in de novo purine synthesis? |
|
Definition
| Shuttled to control reactivity with large molecules (proteins) |
|
|
Term
| In de novo synthesis of purines, is PRPP formed, then added to ring, or the other way around? |
|
Definition
| PRPP formed then added to ring |
|
|
Term
| What types of enzymes catalyze de novo purine synthesis? |
|
Definition
| large, multimeric protein complexes |
|
|
Term
| Do enzymes for de novo purine synthesis catalyze more than one step each? |
|
Definition
|
|
Term
| What molecule activates various groups as they are added to the ring in de novo purine synthesis? |
|
Definition
|
|
Term
|
Definition
| IMP; the first product of de novo synthesis of purines that has a complete ringWh |
|
|
Term
| What is the commited step in de novo purine synthesis? |
|
Definition
| The transfer of an amino group to PRPP from glutamine. |
|
|
Term
| What is the predominate N donor when rings are formed in purines and purimidines? |
|
Definition
|
|
Term
| How many ATP's are used in de novo purine synthesis of one molecule? |
|
Definition
|
|
Term
|
Definition
| The base associated with IMP |
|
|
Term
| What regulates purine biosynthesis? |
|
Definition
|
|
Term
| In what step of de novo purine synthesis is GTP used? |
|
Definition
| Conversion of inosinate to adenylosuccinate (before converting to adenylate) |
|
|
Term
| Why is it important that different cofactors (GTP and ATP) are used in AMP vs. GMP synthesis? |
|
Definition
| It allows for feedback tegulation |
|
|
Term
| What are a few analogs of glutamine, and why are they important as drugs? |
|
Definition
Azaserine
Acivicin
They are inhibitors of glutamine synthesis and therefore DNA replication. You would want to do this to halt cell division in cancer cells. |
|
|
Term
| What regulates the committed step of de novo purine synthesis? |
|
Definition
| The end products: AMP, GMP, IMP |
|
|
Term
| What inhibits IMP to GMP? IMP to AMP? |
|
Definition
|
|
Term
| What allosterically regulates ribose phosphate pyrophosphokinase (PRPP synthetase)? |
|
Definition
|
|
Term
| What is the order of ring formation versus addition to PRPP in pyrimidines? |
|
Definition
| Ring formed, then added to PRPP (opposite of purine synthesis) |
|
|
Term
| Where does most of the larger ring in pyrimidines come from? |
|
Definition
|
|
Term
| Where does the smaller portion of the ring (left) come from in pyrimidine synthesis? |
|
Definition
|
|
Term
| Are multienzyme complexes involved in pyrimidine biosynthesis? |
|
Definition
|
|
Term
| What is the first step in de novo pyrimidine synthesis? |
|
Definition
| Carbamoyl phosphate added to aspartate |
|
|
Term
| What are the main steps in de novo pyrimidine synthesis after orotidylate is formed? |
|
Definition
| Orotidylate -> UMP -> UTP -> CTP |
|
|
Term
| How is de novo pyrimidine synthesis regulated? |
|
Definition
| CTP feedback inhibits to first step. Adding ATP can help nullify effect. |
|
|
Term
| What are pyrimidine nucleotides made from? |
|
Definition
| Aspartate, PRPP, carbamoyl phosphate |
|
|
Term
| What converts AMP to ADP in all cells? |
|
Definition
|
|
Term
| What are nucleoside monophosphate kinases? |
|
Definition
| Enzymes that donate phosphate from ATP to NMP's other than AMP. |
|
|
Term
| Can any NTP donate its third phosphate? |
|
Definition
| Yes, but usually ATP because it is most common |
|
|
Term
| Is nucleoside diphosphate kinase specific for base or sugar? |
|
Definition
|
|
Term
| What is responsible for conversion of ribonucleotides to deoxyribonucleotides? |
|
Definition
|
|
Term
| How is ribonucleotide reductase regulated? |
|
Definition
ATP binding activites
Substrate binding is specific - balance is produced in production of dNTP's (enzymes are specific for substrate in creating dNTP) |
|
|
Term
| Which comes first in synthesis: ribonucleotides or deoxyribonucleotides |
|
Definition
|
|
Term
| What is the immediate precursor of thymidylate? |
|
Definition
|
|
Term
| What two beginning molecules can dTMP be synthesized from? |
|
Definition
|
|
Term
| What step in dTMP synthesis must be efficient to avoid incorporation of dUTP into DNA? |
|
Definition
| The converstion of dUTP to UMP |
|
|
Term
| What deficiency can cause DNA strand breaks because of incorporation of uracil into DNA? |
|
Definition
|
|
Term
| What chemotherapeutic drugs target thymidylate synthesis? |
|
Definition
Fluorouracil
Trimethoprim
Methorexate |
|
|
Term
|
Definition
| Conversion of dUMP to dTMP |
|
|
Term
| What catalyzes dUMP to dTMP? |
|
Definition
|
|
Term
| What enzyme do Methotrexate, Aminopterin, and Trimethoprim inhibit? |
|
Definition
|
|
Term
| Deficiency in what enzymes causes "bubble boy" syndrome? |
|
Definition
| Adenosine deaminase, which converts adenosine to inosine in purine degradation. This increases dATP, which results in defects in development in T and B lymphocytes. |
|
|
Term
|
Definition
| Build up of Uric acid caused by under-excretion of urate; caused by a genetic deficiency in of one or more enzymes in purine metabolism |
|
|
Term
| What is the general pathway for purine degradation? |
|
Definition
| GMP or AMP are cleaved from ribose and turned into xanthine. This is converted to uric acid and excreted. |
|
|
Term
| What is produced by pyrimidine degradation? |
|
Definition
|
|
Term
| What catalyzes the linking of adenine and PRPP? |
|
Definition
| Adenosine phosphoribosyltransferase |
|
|
Term
| What do salvage pathways involve? |
|
Definition
| Linking of bases with PRPP |
|
|
Term
| What is lacking in Lesch-Nyhan Syndrome? |
|
Definition
| The conversion of hypoxanthine or guanine to IMP or GMP with HGPRT |
|
|
Term
| What are some problems associated with Lesch-Nyhan syndrome? |
|
Definition
Bizarre self-mutilation
Mental retardation
Neurological problems
Gout and kidney stones
Purine overproduction |
|
|
Term
| What makes the backbone in DNA? |
|
Definition
| Alternating phosphate and sugar of nucleic acids |
|
|
Term
| What part of DNA is hydrophobic? |
|
Definition
|
|
Term
| What part of DNA is hydrophilic? |
|
Definition
|
|
Term
| Is base stacking base specific? |
|
Definition
|
|
Term
| Which is stronger: H-bonding between bases or base stacking? |
|
Definition
|
|
Term
| What types of forces are involved in base stacking? |
|
Definition
| Van der walls, dipole interactions -> not base specific |
|
|
Term
| How much larger is major groove than minor grooove? |
|
Definition
| About 10 times (slightly larger than diameter) |
|
|
Term
| What is the most stable, reference form for DNA? |
|
Definition
|
|
Term
| What form is shorter and fatter than B form? |
|
Definition
|
|
Term
| What form is left-handed, longer, and skinnier than B form? |
|
Definition
|
|
Term
| What is formed by mirror repeats of DNA? |
|
Definition
|
|
Term
| What is formed by pallindromic DNA? |
|
Definition
|
|
Term
|
Definition
| Yes, by looping on itself because of sequence |
|
|
Term
| At what temperature does denaturing of DNA begin? |
|
Definition
|
|
Term
| What is the hyperchromic effect of DNA? |
|
Definition
| Afer it is melted and single stranged, it absorbs more light. Absorbance is usually at 260nm. |
|
|
Term
| How does DNA composition effect melting temp? |
|
Definition
| More G/C/ means higher melting temp |
|
|
Term
| Do eukaryotes have enzymes to promote unwinding? |
|
Definition
| No; nucleosomes introduce unwinding stress |
|
|
Term
| What alleviates positive supercoiling? |
|
Definition
|
|
Term
| what is the diameter of associated nucleosomes? |
|
Definition
|
|
Term
| How many coils in a chromatid? |
|
Definition
|
|
Term
| How many rosettes in a coil? |
|
Definition
|
|
Term
|
Definition
|
|
Term
| How do topoisomerases work? |
|
Definition
| Cutting phosphate backbone |
|
|
Term
| How are separated strands stabilized in replication? |
|
Definition
|
|
Term
| What is the chemical reaction in DNA polymerase? |
|
Definition
| The 3' hydroxyl group is the nucleophile attacking the alpha phosphorus of the deoxynucloside |
|
|
Term
| What enforces the accuracy of DNA polymerase? |
|
Definition
| The geometry of the active site; another site performs 3'->5' exonuclease (in which DNA pol stalls) |
|
|
Term
| What are the three activities of DNA polymerase? |
|
Definition
5' -> 3' polymerase
5' -> 3' exonuclease
3' -> 5' exonuclease |
|
|
Term
| What are the three prokaryotic DNA polymerases and their functions |
|
Definition
Pol I - Repair
Pol II - Repair
Pol III - Replication |
|
|
Term
| How many helicases per replication fork in prokaryotes? |
|
Definition
|
|
Term
| Which prokaryotic DNA polymerase is the workhorse of elongation? |
|
Definition
|
|
Term
| Which prokaryotic DNA polymerase I fills in the synthesis gaps and removes RNA primers? |
|
Definition
|
|
Term
| What directs primase activity on the on first the leading, then lagging strand? |
|
Definition
|
|
Term
| What is the key step in prokaryotic initiation? |
|
Definition
| The loading of helicase (DnaB) |
|
|
Term
| What is the only regulated step in prokaryotic DNA replication? |
|
Definition
|
|
Term
| How does prokaryotic DNA replication initiation work? |
|
Definition
DnaA-ATP's bind at DNA unwinding element
(DUE)
Strands open because of DnaA-ATP binding
DnaB (helicase) and DnaC (helicase loader) bind to each strand |
|
|
Term
| What resolves concatenation of prokaryotic chromosomes? |
|
Definition
|
|
Term
| How often do eukaryotes have origins of replication? |
|
Definition
|
|
Term
| In eukaryotes, which DNA polymerase does the majority of processivity of leading strand? |
|
Definition
|
|
Term
| In eukoaryotes, what causes processivity on lagging strand? |
|
Definition
|
|
Term
| What is responsible for mitochondrial replication and repair in eukaryotes? |
|
Definition
|
|
Term
| Which pol in euk starts synth on both strands? |
|
Definition
|
|
Term
| Which pol in euk is resp for repair? |
|
Definition
|
|
Term
| What marks correct sequence in mismatch repair? |
|
Definition
| methylation on adenines in e. coli (unsure for euk) |
|
|
Term
| What recognzies mismatches and cuts non-methylated strand in prok? |
|
Definition
|
|
Term
| What is Lynch syndrome or HNPCC? |
|
Definition
| A syndrome caused by problems with mismatch repair. There are defects in at least five mismatch repair genes. Cancers - esp of colon - dev. at early age |
|
|
Term
| What repairs abasic site in base-excission repair |
|
Definition
|
|
Term
| How many uracil DNA glycosylases do bacteria have? Humans? |
|
Definition
|
|
Term
| What does DNA glycosylase do? |
|
Definition
| Remove damaged base in base-excision repair |
|
|
Term
| Can AP endonuclease distinguish thymine from deaminated cytosine? |
|
Definition
|
|
Term
| What DNA repair removes lesions that cause large distrotions in helical structure? |
|
Definition
| Nucleotide-excision repair |
|
|
Term
| What type of smoke damage is repaired by nucleotide excision repair? |
|
Definition
| benso[alpha]pyrene-guanine damage |
|
|
Term
|
Definition
| Unique endonucleases that cut in two different pattens in nucleotide excision repair |
|
|
Term
| What causes xeroderma pigmentosum? |
|
Definition
| Inability of body to repair damage due to UV light. There are seven different groups due to seven different enzymes in NER |
|
|
Term
| Which enzyme is degraded after accepting methyl to repair O6methylguanine to guanine> |
|
Definition
| O6methylguanine-DNA methyltransferase |
|
|
