Term
| How are nucleotides joined together? |
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Definition
| 3'C to 5'C by phosphodiester bridges |
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Term
| What are the biological functions of nucleotides? |
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Definition
| substrates for nucleic acids, recognition units, energy metabolites, protein synthesis, lipid synthesis, carb metabolism, signal molecules, energy carriers, Cellular Metabolism, Found in all Cells |
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Term
| What are the biological functions of nucleic acids? |
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Definition
| serve as distinctive side chains and give polymer unique identity |
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Term
| What is the Structure & Chemistry of Nitrogenous Bases? |
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Definition
| Relatively insoluble in water due to aromatic character |
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Term
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Definition
| a nitrogenous base linked to a pentose sugar via a β-glycosidic bond, sugar makes nucleoside more water-soluble than free bases |
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Term
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Definition
| linear polymers of nucleotides; sequence is always read 5' to 3' |
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Term
| What are the different classes of Nucleic Acids? |
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Definition
Deoxyribonucleic Acid (DNA)
Ribonucleic Acid (RNA): ribosomal RNA, messenger RNA, transfer RNA, small nuclear RNA, & small non-coding RNA |
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Term
| What types of Secondary Structures do double-stranded DNA molecules adopt? |
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Definition
| Double helix stabilized by interchain hydrogen bonds; helix = two antiparallel polynucleotide strands wound together |
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Term
| Can DNA secondary structure be denatured and renatured? |
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Definition
| Yes; it's denatured at 80+ deg C, as Temp is lowered absorbance drops - renatures |
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Term
| What is the Tertiary Structure of DNA? |
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Definition
| 10bp/turn helix that is supercoiled around protein spools; interacts with enzymes (topoisomerase & gyrase) which introduce & remove supercoils |
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Term
| What is the structure of Eukaryotic Chromosomes? |
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Definition
2 meters of DNA packed into 5 micrometer nucleus
2nm DNA wrapped around histone - 10nm Nucleosome wound into solenoid - 30nm Filament forms long DNA loops (18 loops) - a miniband unit1 |
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Term
| What are the Pyrimidines? Is each one in DNA or RNA? |
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Definition
Cytosine (DNA, RNA)
Uracil (RNA)
Thymine (DNA) |
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Term
| What are the Purines? Are the found in DNA or RNA? |
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Definition
Adenine (DNA, RNA)
Guanine (DNA, RNA) |
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Term
| What is the difference between the primary structure of RNA and DNA? |
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Definition
RNA has D-ribose (2'-OH)
DNA has 2-deoxy-D-ribose (2'-H)
Difference affects secondary structure & stability of nucleic acids (DNA is more stable) |
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Term
| What is the structure of Nucleotides? |
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Definition
| phophoric acid is esterified to sugar OH group of nucleoside; have acidic properties |
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Term
| What is the major biochemical reaction of nucleotides? |
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Definition
| phosphoryl & pryophosphoryl group transfer (phosphoric bonds are prime source of chemical energy) |
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Term
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Definition
| The number of purine residues equals the numbe of pyrimidine residues in all organisms |
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Term
| Describe the A helix of DNA. |
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Definition
| right-handed, short & broad, 2.3 A, 11bp/turn (probably doesn't exist in vivo) |
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Term
| Descrive the B helix of DNA. |
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Definition
| right-handed, longer, thinner, 3.32 A, 10bp/turn (most common) |
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Term
| Describe the Z helix of DNA. |
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Definition
| left-handed, longest, thinnest, 3.8 A, 12 bp/turn (G-C rich regions) |
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Term
| What method and what molecules are used to determine the primary structure of DNA? |
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Definition
| Chain Termination; dideoxynucleotides (ddATP, ddGTP, ddCTP, or ddTTP) |
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Term
| What are the four major characteristics of DNA Replication? |
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Definition
| It is semi-conservative, bi-directional, semi-discontinuous, & requires unwinding of the DNA helix |
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Term
| What does DNA Polymerase I need to form a short double-stranded region? |
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Definition
| all 4 deoxynucleotides, a template, and a primer |
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Term
| In what direction does replication occur? In what direction is Pol I's exonuclease activity? |
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Definition
5' to 3'; nucleotides are added to the 3' end of the strand
5' to 3' and 3' to 5' |
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Term
| How many cycles does Pol I catalyze before the new strand dissociates from the template? |
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Definition
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Term
| Which DNA Polymerase is considered the "real" polymerase in E. coli? How effective is it's processivity? |
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Definition
| DNA Pol III; 5mil bases = enormous processivity |
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Term
| How many subunits does DNA Pol III have? What are the "Core" subunits & what do they do? |
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Definition
at least 10
Alpha: polymerase
Epsilon: 3'-exonuclease
Theta: holoenzyme assembly |
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Term
| What enzyme unwinds the DNA double helix? |
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Definition
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Term
| What enzyme periodically primes synthesis of lagging strand (RNA primers)? |
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Definition
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Term
| Each half of what dimeric enzyme is a "core" polymerase bound to its template strand? |
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Definition
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Term
| What enzyme removes RNA primers & replaces them with DNA? |
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Definition
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Term
| What enzyme connects the Okazaki fragments? |
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Definition
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Term
| What enzyme compensates for DNA supercoiling? |
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Definition
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Term
| What are the functions of the four proteins that initiate DNA replication in bacteria? |
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Definition
dnaA: major initiator protein
dnaB: helicase, part of the primosome
dnaG: DNA primase, part of the primosome
dnaC: helicase inhibitor |
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Term
| Which complex is present at the replicators throughout the cell cycle in eukaryotes? |
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Definition
| Origin Recognition Complex (ORC) |
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Term
| What polymerase subunits serve the leading and lagging strands in mammals? |
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Definition
Leading: DNA pol Epsilon
Lagging: DNA pol Alpha and Delta |
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Term
| Where do the three replication checkpoints take place? |
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Definition
G2: before entering Mitosis
Metaphase: after Metaphase
G1: before DNA synthesis |
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Term
| What complex controls whether a cell replicates? What are the three major types of the complex? |
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Definition
| Cyclin-Cdk; G1/S, S, and M |
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Term
| What are the structures at the ends of eukaryotic chromosomes called? Describe their structure. |
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Definition
| Telomeres; 5-8bp tandem repeats of G-rich sequences, 1-12kb long |
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Term
| What enzyme replictes Telomeres? |
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Definition
| Telomerase; an RNA-dependent DNA polymerase |
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Term
| What is needed for Telomerase activity? |
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Definition
| internal RNA template & reverse transcriptase activity |
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Term
| What does RNA Reverse Transcriptase use as a primer? |
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Definition
| a tRNA molecule that the virus captures from the host |
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Term
| What are the three enzyme activities of reverse transcriptase? |
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Definition
1. RNA-directed DNA polymerase
2. RNase H activity (degrades RNA in DNA:RNA hybrids)
3. DNA-directed DNA polymerase (makes DNA duplex after RNase destroys viral genome) |
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Term
| What was the 1st approved drug for AIDS treatment? What is its target? |
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Definition
| AZT nucleoside; its substrate analog (AZTTP) binds HIV reverse transcriptase & blocks further elongation |
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Term
| What is defined as rearrangements in genetic info creating new associations and involves the breakage & reunion of DNA strands? |
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Definition
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Term
| What type of recombination involves similar DNA sequences? |
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Definition
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Term
| What proteins are responsible for genetic recombination? |
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Definition
| RecA, RecBCD, RuvA, RuvB, & RuvC |
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Term
| What type of genetic recombination uses very different nucleotide sequences & occurs at low frequency? |
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Definition
| Nonhomologous recombination |
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Term
| What is characterized by enzymatic insertion of mobile DNA segments? |
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Definition
| Transposition (transposons) |
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Term
| For what mechanism can any pair of homologous DNA segments be used as substrates? |
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Definition
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Term
| What do duplex unwinding, strand invasion & ligation create? |
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Definition
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Term
| What is the function of RecBCD? |
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Definition
| initiates recombination in E. coli; directs binding of RecA |
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Term
| What is the function of RecA? |
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Definition
| forms nucleoprotein (helical) filament for strand invasion & homologous pairing |
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Term
| What is the function of RuvA, RuvB, & RuvC? |
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Definition
drive branch migration & help resolve Holliday junction into recombination products
RuvA & RuvB act as helicase to dissociate RecA filament
RuvC is an endonuclease, binds & cuts DNA |
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Term
| What method is used to investigate the essentiality of a gene and is based on homologous recombination? |
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Definition
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Term
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Definition
| a gene transfer technique |
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Term
| What is a transposon and what are its characteristics? |
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Definition
| Genes that can move freely about the genome; inverted nucleotide-sequence repeats at its termini |
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Term
| What term is used for chemical reactions that reverse damage, returning DNA to proper state? |
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Definition
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Term
| What mechanism of DNA repair relies on the intact complementary strand to guid repair? |
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Definition
| Single-Strand Damage Repair |
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Term
| What are the three systems that repair single-strand breaks? |
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Definition
| Mismatch repair (MMR), Base Excision Repair (BER), and Nucleotide Excision Repair (NER) |
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Term
| In Double-strand breaks (DSBs), can lost information be recovered from the same DNA? By what method is it repaired? |
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Definition
| No - particular threat to genome stability; Nonhomologous DNA End Joining (NHEJ) |
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Term
| Can a stalled replication fork be restarted? |
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Definition
| Yes, through homologous DNA recombination |
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Term
| What mechanism corrects errors introduced in DNA replication? |
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Definition
| Mismatch Repair; repair proteins identify methylated strand as parent & remove mismatched bases on other strand |
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Term
| Describe Base Excision Repair. |
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Definition
| damaged base is excised creating an apurinic acid (AP) site, then DNA polymerase I and DNA ligase repair the gap |
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Term
| What types of mutation are Point Mutations? |
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Definition
| Transition (Pu-Pu, Py-Py), Transversion (Py-Pu, Pu-Py), Mis-sense (1 base for another), Framshift (insertion or deletion) |
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Term
| What type of mutation involves swapping chromosome segments? |
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Definition
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Term
| List the Diseases of DNA Repair. |
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Definition
| Ataxia-Telangiectasia, Bloom Syndrome, Cockayne Syndrome, Fanconi Anemia, Xeroderma Pigmentosum, Hereditary non-polyposis colorectal cancer |
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