Nucleic Acids Flashcards
What do the major and minor grooves do?
Provide access for binding of regulatory proteins along the DNA chain
What does it mean to be antiparallel?
5’ end of one strand is paired with 3’ end of other strand
The two strands are opposite in direction
Two key features of Z-DNA?
Left handed and high GC content (also rare)
Most common structural form of DNA?
B-DNA (Watson and crick form); right handed
Another word for renaturation
Reannealing
DNA with more ___ bonds will denature slowest
CG
What type of interaction between stacked bases?
Hydrophobic
Difference in structure between DNA and RNA?
RNA has -OH attached to carbon 2, DNA does not (just H)
Structural difference between Uracil and Thymine?
Thymine is exactly same as Uracil except with an added methyl group
What provides the energy necessary for nucleic acid synthesis?
What makes these compounds high energy?
Nucleotide triphosphates (NTPs) such as ADP and ATP
The energy associated with anhydride bonds
What is attached to carbon 3?
OH group (in both DNA and RNA) required for polymerization of nucleic acids, joined to the 5’ carbon through a phosphodiester bond
- Free ___ group at 3’ end
2. Free ___ group at 5’ end
- Hydroxyl
2. Phosphate
Complementary means?
By what kind of bonds?
A always pairs with T; G always pairs with C
Hydrogen bonds
5’-AGGTCCTTAGG-3’
What is complementary strand of above?
5’-CCTAAGGACCT-3’
What is the name of the rule that allows you to determine the % of each of the 4 nucleotides
Chargaff’s Rule
- Denaturation breaks____ but does not break _____
2. What does denaturation result in?
- Denaturation breaks hydrogen bonds between base pairs but does not break phosphodiester bonds linking the nucleotides
- Single stranded DNA (ssDNA)
What does Tm represent?
When will you have a higher Tm?
Temperature required to melt 50% of the DNA in a sample
When there are high GC content DNA
- DNA gyrase is a type of ____ that is inhibited by ____
2. DNA gyrase promotes ___
- DNA gyrase is a type of topoisomerase II that is inhibited by quinolones
- Supercoiling (quinolones inhibit supercoiling)
If DNA is relaxed, what cannot happen?
Division (needs to be condensed)
Quinolones function as ___ but?
Antibiotics but are toxic in high concentrations (because they inhibit supercoiling)
Histones are rich in __ and ___; so they bind strongly to ____
Lysine and arginine (+ charged, basic amino acids); so they bind strongly to negatively charged DNA
- Histones help DNA to ____
2. Answer from 1. Is good for?
- Condense
2. Condensation is good for division (beads on a string is good for gene expression; decondensed a bit)
What is “beads on a string”?
What is it sensitive to?
What is it necessary for?
A group of free nucleosomes (without H1)
Sensitive to nuclease degradation
Necessary for gene expression
Type of RNA that can base pair back on itself?
TRNA
2 features that eukaryotic mRNA have that prokaryotic mRNA do not have?
M7G-cap on 5’ terminus and a poly-a tail on 3’ terminus
- Function of rRNA?
- Sizes of eukaryotic and prokaryotic sub units of rRNA?
- Antibiotics usually target which sub unit?
- What does the S unit mean?
- Combine with proteins to form ribosomes
- Pro: 50S + 30S = 70S
Eu: 60S + 40S = 80S - 30S
- Means you’re talking about the ability of this component to pass through a gradient when being centrifuged
Where is the amino acid attachment site on tRNA?
CCA-3’ terminus
Why is tRNA considered to have unusual bases?
It’s the only RNA that contains a T
Differences in tRNA lie where?
In the anti codon region
What is the function of the anticodon loop?
Determines amino acid specifically by base pairing with mRNA during translation
- SnRNA (small nuclear RNA) is only located where?
2. Function?
- In the nucleus of eukaryotes
2. Combine with certain proteins to form snRNPs used for splicing hnRNA to form mRNA
What are ribozymes?
RNAs that act as enzymes
