DNA Flashcards
What is the molecule that binds chromatids at the centromere?
Cohesin
Maternal and paternal pairs of chromosomes that contain similar but not identical genes are called what?
Homologous chromosomes.
What is the chromatin that is complexed with proteins, highly condensed, transcriptionally inactive, and concentrated at the periphery of the cell?
Heterochromatin
What is the translucent chromatin that is decondensed, is transcriptionally active, and is near the center of the cell?
Euchromatin
What is the highly condensed structure with in the nucleus that contains genes for rRNA?
Nucleolus
What is the meshwork of filaments that stabalize the nucelus?
Nuclear filaments
The perinuclear space is contiguous with what structure?
The ER
How do large molecules pass through the nuclear membrane?
Through specific channels
How do small molcules pass through the nuclear membrane?
Freely –through small, non-specific opening
What are the top three substances transported across the nuclear membrane?
mRNA, proteins, ribosomal subunits
What protein transports mRNA out of the nucleus so that ribosomes may act on it?
Ran
Where are ribosomal subunits synthesized? How does this aid in transcriptional regulation?
Cytoplasm
Prevents immediate translation
What are the two proteins that are involved in transport into the nucleus?
Ran and importin
True or false: the majority of mRNA is transported out of the nucleus by Ran-GTP
False–they go through a Ran-independent mechanism
What is the protein that is involved in Ran-independent transport, and is on the cytoplasmic side of the nucleus?
Dbp5
True or false: histones are recycled in the processing of new DNA
True
Where does DNA polymerase gamma fuction?
In the mitochondria
What do DNA polymerases need in order to begin synthesis of a new DNA strand?
An RNA primer
What is the direction of DNA synthesis?
5’ to 3’ direction
What is the driving factor of DNA replication?
Hydrolysis of pyrophosphate
What do DNA helicases do?
Unwind the DNA molecule
True or false: origins of replication can only be acted on once during DNA replication?
True–there are proteins that ensure this.
What is the action of topoisomerases?
Prevent supercoiling of the DNA strand by cutting and re-ligating strands
True or false: there are proteins that keep the DNA strands from re-associating once they are unwound
True
Which DNA polymerase synthesizes a new RNA primer?
DNA polymerase alpha
An RNA primer has what type of end to it?
3’ OH group
True or false: DNA polymerases can stay on DNA strands without the need for additional proteins
False
What is the DNA polymerase that usually transcribes DNA
Pol epsilon
What are the enzymes that remove the RNA primers?
ribonucleases
What are the enzymes that bind DNA fragments from okazaki fragments together?
DNA ligases
What is the action of telomerases?
They add additional DNA segments to the end of okazaki fragments so that it can be finished and not result in the shortening of the DNA strand.
What is the group that is at the 5’ end of a DNA molecule?
Phosphate group
What is the group at the 3’ end of a molecule?
Hydroxyl
What is the type of RNA that is most drastically changed from the original transcription?
tRNAs
What is the only modification of DNA
Methylation of Cytidine
Which bases have 3 hydrogen bonds? Which form 2?
A and T have 2
C and G have 3
Which form of DNA is the most common: B, A or Z
B
B form DNA helices are what “handed”? What about A? Z?
Right handed for B and A
Z is left handed
What are the class of molecules that fit exactly on the rungs of the DNA ladder, and cause a distortion of the DNA helix?
Intercalcating agents
What other structures can DNA be found in, besides the DNA helix?
Sequence dependent structures
What are the structures that arise from palindromic DNA sequences? RNA?
Cruciform structures
Hairpin loops
What are the structures that arise from long sequences of pyrimidines (and long purine sequences in the opposing strand)?
Triple helical structures
What is negative supercoiling?
When the DNA is twisted in the direction that unwinds the helix
What is positive supercoiling?
When the DNA helix is twisted in the direction that winds that helix further
What is the action of Type I topoisomerases?
Make a single cut in the phosphodiester backbone of a DNA molecule
What is the action of Type II topoisomerases?
Make a double stranded break
Doxorubicn acts on which topoisomerase? What is the consequence of this?
topoisomerase II–leads to double stranded breaks and cell death.
What are the four types of non-protein producing DNA sequences?
- Spacer DNA
- Introns
- Non-protein encoding DNA (for rRNA)
- Repetitous DNA sequences
What is the type of DNA that does not code for proteins, and is found BETWEEN genes?
Spacer sequences
What is the type of DNA that does not code for proteins, and is found WITHIN genes?
Introns
What are pseudogenes?
Duplicates of genes that are not transcribed, and are free to mutate.
What are the levels of chromatin?
11 nm (histone + DNA)
30 nm (nucleosomes together)
300 nm
700 nm
DNA and histone complexes are called what?
nucleosomes
How is the mitochondrial genome more closely related to prokaryotes than to humans (3)?
- It is circular
- Is present as multiple copies within a single mitochondria
3 .Has a very high gene density
What are the four components of a nuclear pore?
- Nuclear basket
- Protein ring in the double membrane
- Central transporter on the inside of the ring
- filaments on the cytoplasmic side of the ring
What is the action of Doxorubicin?
Acts on human topoisomerase II, causing double strand breaks in the DNA and cell death.
What is the action of Nalidixic acid and ciprofoxacin?
They act on topoisomerase II of bacteria, and caused cell death through the introduction of double stranded breaks. These are Abx.
