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55 Cards in this Set
- Front
- Back
Reverse transcription
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Forming DNA from RNA using reverse transciptase, HIV does this.
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Exons
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Part of the mRNA that are translated into proteins
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Introns
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Parts of the mRNA in eukaryotes that must be excised before translation takes place.
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DNA base pairs, stabilization and structure
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A to T and G to C.
These bonds are hydrogen bonds that occur when the bases are inverted with respect to eachother. Remember pyrimidines have a y in their names. DNA is stabilized by keto-enol isomerization in the keto form because of H-bonding. Purines have are a pyrimidine ring fused to an imadazole. |
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Other DNA bases
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5-methylcytosine will shutdown transcription after a polymerase hits it.
Uracil is a thymine without a methyl group. |
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Phosphodiester bonds
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Link base pairs together and are always polymerized in a 3-5 linkage.
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Energy for phosphodiester linkages
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Comes from the hydrolyis of phospates during poymerization.
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Direction of DNA synthesis
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Always 5-3 prime
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Oligonucleotide
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around 30 nucleotides long
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Polynucleotide
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longer than 30 nucleotides
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Difference between DNA and RNA structure
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RNA has a 2 prime hydroxyl group that makes it more susceptible to alkaline denaturation
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When writing a sequence
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It's always assumed to be RNA unless otherwise indicated, and 5-3 prime
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Endonuclease
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Severs a P-type linkage. Cleaves a phosphodiester bond within a nucleotide chain.
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Exonuclease
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Severs a D-type linkage
Hydrolyzes phosphodiester bonds from either the 3 or 5 prime terminus of a polynucleotide |
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Chargaff's rule
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A-T and G-C always in a 1:1 ratio
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X-ray diffraction and DNA
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Shows that DNA is double stranded.
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Opposite polarity
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Means that DNA strands pairs bases upside down and different directions
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Forms of DNA
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A,B,Z
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A-form DNA
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Dehydrated
Wider, shorter, right-handed Seen mostly in DNA/RNA hybrids like miRNA and siRNA |
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B-form DNA
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Normal right handed helix with 10bp per turn
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Z-form DNA
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Zig-zag DNA is a left handed helix.
It is formed by dinucleotide repeats of purines and pyrimidines. Only has one helical groove Stabilized by methylation and hydrophobic interactions but is inherently unstable. |
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DNA Grooves
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A and B have a major and minor groove.
Z form has one |
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B-Z DNA
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Z forms are ustable and must be connected to B form on either end.
These are theorized to be points of x-somal breakage. |
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Stabilizing DNA forces
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Hydrophobic interactions between bases
Electrostatic interactions of negative phosphate groups H-bonds Conterions that will counteract the negative groups to split and replicate DNA(Mg and basic proteins) |
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Breathing of DNA
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The ability of DNA to open and close, denature and renature of the same complementary strands. Easy breathing occurs at A-T rich sites like the origin of replication and different promoters.
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DNA absorbance
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260-280nm
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What is the significance of the melting temperature of DNA(Tm)?
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Tm is where half of the DNA is denatured at about 80 degrees Celsius
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What is hyperchromicity?
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An increase in the absorbance of a certain material as you unwind it. DNA strands do this when they denature and unwind, will not do this with single strands.
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Hyperchromicity and Tm?
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At the Tm there is 50% absorbance of light because half of the DNA is unwound. 100% absorbance would be totally denatured.
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Melting temperature and base pairs
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Tm is proportional to the GC content because 3 H bonds are harder to break than the 2 between AT.
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Single copy DNA
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Code for proteins and spaces. They are DNA that are only present in 1 copy.
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Moderately repetitive DNA
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Sequences that are repeated 100-1000 times, usually non-coding.
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Highly repetitive DNA
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Short sequences repeated a million times. This is the make up of satellite DNA, and is located in the centromeres and are non coding.
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Satellite DNA
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Have a different density from bulk DNA and form a second band of DNA when separated because of a different bp ratio.
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Types of DNA symmetry
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Inverted repeat
Mirror repeat Direct repeat |
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Palindrome
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Sequences that be read the same forwards and backwards. Can be mirror repeats or inverted.
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Cruciform structure
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The hairpin structure that can be created by endonuclease activity on inverted repeats.
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Histones
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Proteins that have evolved to compact and supercoil DNA. They have a high Lys-Arg content.
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Nucleosomes
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DNA wrapped around histone proteins in left handed superhelical turns.
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Histone charcteristics
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Highly conserved across species
Expressed during S-phase Have no introns and occur in tandem repeats Not in mitochondrial or bacterial DNA No poly A tail on their mRNA |
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Function of a poly A tail
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They protect the protein from degradation by exonucleases in the cytoplasm.
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Topoisomerases
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Facilitate the unwinding of DNA for transcription
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Nucleofilaments
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The regular spacing of histone/DNA associations into a fiber. Beads on a string
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DNA Replication, steps
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1. Begins at origins, one only in prokaryotes
2. Each 5-3 initiated by an RNA primer made by RNA primase. That means that leading strand has one, and lagging strand has multiple. 3. Nucleotides added 5-3 prime 4. Phosphodiester linkages happen 3-5 prime 5. Okazaki fragments are used to add to the lagging strand |
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3 modes of DNA replication
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Conservative, dispersive, semiconservative
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Semiconservative replication
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Strand spilts in two and each parent strand has a new daughter strand.
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Why do eukaryotes have multiple origins?
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Because their DNA is so large if they didn't they would never finish replication.
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Telomerase
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A reverse transcriptase that carries it's own RNA.
It's function is to add the telomere to DNA that prevents shortening. The sequence is TTACGGG |
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Prokaryotic Polymerases
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Pol 1 = primer removal
Pol 2 = DNA repair Pol 3 = DNA synthesis |
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Eukaryotic Polymerases
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Pol alpha = Initiator and primer
Pol beta = DNA repair Pol sigma = synthesis |
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Why does alkaline denature RNA and not DNA?
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The 2 prime hydroxyl of RNA will form a keto-enol structure that can break the strands under alkaline conditions.
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Acceptor stem of tRNA
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Region of tRNA that will carry the AA necessary for protein synthesis
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Ribozyme
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A modified RNA with enzymatic activity. RNase P, and D cut the ends of the 5 and 3 prime respectively.
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Nucleotidal transferase
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Puts the CCA onto the 3' end of all tRNAs, the 5' has GG
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45s RNA transcript in eukaryotes
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Made from the 28s, 5.8s, and 18s rRNAs. Makes mature rRNA. The s= sedimentation coefficient.
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