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44 Cards in this Set
- Front
- Back
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How does DNA in prokaryotes compare with DNA in eukaryotes in terms of linearity? Where can it be found?
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Euks: linear, in nucleus
Proks: Circular, free |
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What organelles contain circular DNA?
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Mitochondria, chloroplasts
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What are the two categories of nitrogenous bases that comprise DNA? Name the bases.
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Purines: Adenine, Guanine (two rings)
Pyrimidines: Cytosil, Thymine, Uracil Pyrimidines are CUT from pyrines |
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What comprises a nucleoside in DNA? In RNA?
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DNA = nitrogenous base + deoxyribose
RNA = nitrogenous base + ribose |
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On which carbon do ribose and deoxyribose differ? Describe the nnumbring of the pentose sugar.
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Differ on 3' C
Start with C to right of O in ring, that is 1', then go clockwise |
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What comprises a nucleotide?
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Nucleoside + phosphate group on free floating oxygen (usually OH)
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Through what bonds are nucleotides joined? Which carbons join?
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Phosphodiester
3' to 5' |
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In a strand of DNA, what molecules are found on the 3' end? On the 5' end?
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5' end has free phosphate
3' end has 3' ribose or deoxyribose |
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In what direction is DNA synthesized?
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5'-->3'
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In what direction do we read the genetic code?
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5'-->3'
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What drugs are nucleoside analogs? Describe their mechanism of action.
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AZT (zidovudine), ddl (Didanosine)
Very similar to thymidine and deoxyadenosine (respectively), but lack 3'-OH Without 3'-OH, phosphodiester bond cannot be added and DNA cannot elonate; used to restrict replication of cancer and viruses |
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Which nitrogenous bases form stable H-bonds? How many?
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G≡C
T=A |
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What does Chagraff's rule state?
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1:1 ratio of C,T to A,G
i.e., A+G=C+T |
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Describe the alignment of two complimentary strands of DNA.
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antiparallel
5'-->3' 3'<--5' |
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What is the functional purpose of the major and minor groove of DNA?
How have these been used pharmacalogically? |
Regulatory proteins can bind these grooves.
Drugs can bind to grooves (e.g., anti-cancer drug dactinomyocin) intercalates into minor groove |
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What electrostatic forces stabilize DNA?
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H-bonds
Hpboic nature of nucleotides Base stacking (-) q on phosphates |
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Describe the three structural forms of DNA.
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A form: high salt, 11 nucleotides per turn
B: choromosmal form, 10 nucleotides per turn, RIGHT HANDED Z: high salt form, 12 nucleotides per turn, LEFT HANDED HELIX |
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What is the handedness of DNA?
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Right-handed
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How many times does DNA wrap around a nucleosome? What is a nucleosome?
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Twice
Nucleosome - Complex of histone proteins (DNA and linker DNA) |
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What is a telomere?
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Region of DNA near ends of chromosome
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What is a centromere?
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Region of DNA at center of chromosome
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Where does DNA replication begin on DNA?
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Origin of replication
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How are parental strands separated? How are they kept separated?
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DnaA protein binds TATA rich sequence and separates strands
ssDNA binding protein prevents sDNA from re-forming dsDNA |
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What does ssDNA nuclease do?
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Cleaves ssDNA--can be form of viral genome, doesn't affect ssDNA of the body because that's protected by SSB protein
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What occurs after DnaA protein separates DNA strands?
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DNA helicase binds near REPLICATION FORK and unzips dsDNA
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How to origins of replication differ in circular and linear DNA?
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Circular DNA only has one origin of replication where as linear DNA has multiple origins
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How do supercoils form? How are they dealt with?
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As ssDNA strands separate, dsDNA becomes super twisted (supercoiled) which can interfere with further separation
Topoisomerases remove supercoils |
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Describe the two kinds of topoisomerase.
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Type 1 DNA Topoisomerase cuts one strand of double helix to help remove supercoils
Type 2 DNA Topoisomerase cuts both of strands to remove supercoils |
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How does ciprofloxacin work?
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QUINOLONE; target = topoisomerase
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How is DNA formation semi-conservative?
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End product of DNA replication will contain one original strand and one synthesized strand
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Describe how DNA polymerase works. What are the consequences of this?
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Reads template in 3'->5' direction, adding nucleotides to match nucleotide present on template strand; thus synthesizes new DNA in 5'->3' direction
Get a leading strand synthesized continuously, but other parent strand must be transcribed in short (Okazaki) fragments |
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After SSB protein has bound DNA to be replicated, what occurs? How does this differ in leading and lagging strands?
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Primosome: protein complex including primase displaces SSB or any other proteins bound to template
PRIMASE then synthesizes RNA primer (about 10 nucleotides) Need primase every time you begin replication, so leading strand needs primase once whereas lagging strands require primase multiple times |
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How does DNA polymerase know where to begin?
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Recognizes RNA primer, uses 3'-OH of RNA primer as acceptor of first deoxyribonucleotide
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Which DNA polymerase is responsible to DNA synthesis? What is its other function?
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DNA polymerase III, also involved in mismatch repair
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What happens id DNA polymerase mispairs a nucleotide with the template?
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Uses 3'--5' exonuclease to excise mismatched nucleotide
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How do Okazaki fragments join together?
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RNA primer is excised by Dna polymerase I, one ribonucleotide at a time
Gap is then filled by DNA polymerase 1 Remaining nick filled by DNA ligase THIS IS ALL DONE READING 3'-->5', SYNTHESIZING 5'-->3' |
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Why do telomeres exist? How are they dealt with?
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DNA polymerase can't synthesize DNA at extreme 5' end of lagging strand following removal of last RNA primer
Ultimately primer is excised, leaving a gap Telomerase adds AGGGTT to one strand (3'), DNA polymerase completes other strand (Primase needed) TG strand loops back onto itself and complexes with TRF1 and TRF2 to protect telomere (area of ssDNA) from nucleases |
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How may telomerase play a role in aging? In cancer cells?
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In somatic cells, telomeres gradually shorten with every division
But lenth is maintained by telomerase in germ cells (stem cells) and in cancerous cells |
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Describe the function of each of the 5 DNA polymerases.
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I: primase
II: repair III: replicates mitoDNA IV: replicates leading and lagging V: repair |
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How does DNA polymerase 'know' which strand is parent strand when it's making a correction to a mismatched pair?
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Parent strand is METHYLATED
It cleaves unmethylated strand, removes, replaces, ligates |
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What is the effect of UV light on DNA? How is this dealt with?
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Dimerization of adjacent C, T
UV-specific endonuclease recognizes damaged DNA and nicks phosphodiester backbone Nucleotides several bases before and after dimer are removed DNA polymerase fills in gap DNA ligase seals |
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What occurs in Xeroderma Pigmentosum?
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Genetic deficiency in nucleotide excision repair (needed to correct UV damage); results in skin damage, skin cancers
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What nucleosides are affected by spontaneous deamination? How is this dealt with?
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C-->U
A-->hypozanthine Glycosylazes recognize U in DNA,a dn remove it, which results in apyrimidinic site (AP) AP-endonuclease removes phosphate backbone and DNA pol adds correct nuc Ligase seals |
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Briefly describe the steps involved in PCR. Describe length variation.
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Heat DNA to separate strands
Cool and add primers to flanking region just outside of target DNA Add nucleotides and heat-stable DNA polymerase Heat again to denature DNA and repeat process (newly created strand can act as template i next round of replication) Over first few cycles, length of DNA varies, but with each cycle more and more DNA copies become same length. |
