Molec 1 Exam 3

Which types of protein domains are involved in nucleosome remodeling?

* Bromodomains* - recognizes acetylated lysines. * Chromodomains* - recognizes methylated lysines.

Unique intergenic DNA

- 25% of the genome. - contains pseudogenes (lack regulatory region), gene fragments, nonfunctional mutant genes. - has regulatory activity.

Repetitive intergenic DNA

- 50% of the genome. - genetic variation and regulation. - includes microsatellites, genome-wide repeats, and transposons.

Which of the following is a hexamer (or trimer of dimers or dimer of trimers)?

- Helicase. - Sliding clamp.

The palm domain of DNA polymerase

- PRIMARY CATALYTIC SITE. - binds two divalent cations. - makes extensive hydrogen bond interactions with the minor groove to monitor the bases. - consists of a β-sheet.

After replication, the RNA primer is removed by

- RNase H. - DNA polymerase.

SSBs (single stranded DNA binding proteins)

- binds cooperatively to ssDNA in order to protect it from degradation and keep them from re-biding to each other. - keeps DNA elongated for DNA/RNA primer synthesis. - directly contacted by helicase.

Fingers domain

- binds incoming dNTPs by moving them closer to the catalytic metal ions of the O-helix stimulating catalysis. - creates a 90 degree turn in template to prevent multiple template bases from entering the catalytic site.

Topo I

- creates ssDNA cuts. - does not need ATP.

B-DNA

- found in high humidity conditions. - found in physiological conditions of the cell. - Right handed. - associated with hgb in Watson experiment.

A-DNA

- found in low humidity conditions. - RNA-DNA, DNA-DNA helices. - Right handed

Z-DNA

- found in nucleosomes. - associated with transcription as a torsion strain reliever. - may regulate transcription initiation. - high G:C content. - Left handed.

Topo II

- is a dimer. - cleaves dsDNA. - passes an uncut segment of DNA through the gap then reseals the gap. - requires ATP.

Overlapping genes Which organism have them? Are they in introns, exons, intergenic DNA?

- many organisms have overlapping genes. - found in MITOCHONDRIA in humans. - overlapping genes may have one function in one gene, and another function in another meaning that even though they are composed of the same sequence, they do not necessarily have the same function.

Transposable elements (retroelements)

- moves to new positions often leaving the original copy behind (such as Alu). - can excise themselves and move to a different location in the genome without leaving a copy behind ("selfish jumping genes").

Thumb domain

- not involved with catalysis. - interacts with newly synthesized strand to maintain correct primer position and maintain strong association between DNA pol and substrate. - prevents DNA pol from falling off.

Helicase/ primase interaction

- primase greatly enhances DNA helicase activity. - necessary for primer synthesis at the lagging-strand priming site.

Chromosomes are beneficial to a cell because they allow for

- protection of the DNA. - a means of transfer to the daughter cells. - regulation of gene expression and recombination

Aurora

- senses the tension formed when the chromosomes line up on the metaphase plate during meiosis II and mitosis. - phosphorylation weakens microtubule binding. Low tension = aurora B phosphorylates kinetochores. High tension = aurora B separates from kinetochores.

DNA helicase

- unwinds the double helix ahead of the replication fork. - ATP can change the shape of the protein and each subunit moves in a different fashion. - helicase wraps around ssDNA. **as opposed to PCNA, which wraps around dsDNA. PCNA is a sliding clamp, and it needs to wrap around to both strands and bind to DNA pol to keep DNA pol from dissociating.

DNA is wrapped around the nucleosome _____ time(s).

1.65

Actively-transcribed regions of DNA would most likely be found in which conformation?

10-nm fiber.

There is/are ____ microtubule(s) attached per pair of sister chromatids during meiosis I, and there is/are ____ microtubule(s) attached per pair of sister chromatids during meiosis II.

1; 2

Which of the following are found as dimers or tetramers in the nucleosome?

2 sets of core histones: *H3 and H4 (tetramer).* - first structure formed during histone assembly. - bends DNA for H2A-H2B dimers. - binds middle and both ends of DNA. * H2A and H2B (dimer).* - joins H3 and H4 to form nucleosome. - provides stability.

How many different types of chromosomes do human males have per cell?

25 (22 autosomes, X + Y chromosome, mitochondria). Females 24 (22 autosomes, X chromosome, mitochondria).

A person that receives identical copies of a gene A on chromosome 10 from both their mother and father will have _____ gene As per cell in G1, and _____ gene As per cell in G2.

2; 4

During DNA synthesis, the template strand is read in the

3' → 5' direction.

Once a piece of DNA is melted by initiator proteins, a replication bubble forms. In eukaryotes, how many total polymerases are present in one entire bubble? Include any α, δ, and ε polymerases.

6

What percent of the human genome encodes proteins?

<5%

11% of the human genome is composed of

Alu elements.

Which of the following would you expect to occur during early anaphase?

Cohesin cleavage. * Cohesin keeps sister chromatids connected. * Present from S phase until anaphase (when sister chromatids are separated). * Cleaved by separase.

DNA Pol I DNA Pol III DNA Pol δ DNA Pol Epsilon DNA Pol Alpha

DNA Pol I = RNA primer removal, DNA repair DNA Pol III = Chromosomal replication (holoenzyme) DNA Pol δ = lagging strand synthesis. DNA Pol Epsilon = leading strand synthesis DNA Pol Alpha = primer synthesis during replication; works with primase.

DNA in the nucleosome has a 1.2 linking number, but it is predicted to be 1.65. What accounts for this discrepancy?

DNA in the nucleosome has less base pairs per turn.

What is the correct order with regards to replication of the lagging strand?

DNA is unwound, DNA is primed, sliding clamp loader adds a sliding clamp, DNA associates with DNA polymerase δ.

Which of the following does NOT act at the replication fork?

DNA ligase.

Higher order nucleosome structure (the 30 nm fiber) in eukaryotes is regulated by

H1. * linker histone.

Which of the following directly contacts the centromeric DNA (or associated histones)?

Kinetochore proteins.

Which checkpoint would you most likely find in late metaphase, which would signal to the cell that it is safe to continue mitosis?

Kinetochores signaling that proper attachment to the spindles has occurred.

In the presence of low levels of Cdk,

None of the above. Options: - preRCs cannot form. - preRCs are activated. - Both A and B.

In E. coli replication, which of the following happens LAST?

Primase primes the lagging strand.

E. coli prevents reinitiation of DNA synthesis by

SeqA binding to hemimethylated DNA.

Which higher order chromatin structure is mostly seen in eukaryotes?

Solenoid.

Nucleosomes are not sequence specific. What factors influence where they are placed?

The alternation of A/T and G/C rich sequences in the DNA.

Which of the following is TRUE regarding the human and mouse genomes?

The genes are nearly identical but usually found at different locations. Other options: - Both human and mouse genomes are contained in 23 pairs of chromosomes. - The overall architecture is nearly identical, with the major differences on the X and Y chromosomes. - The overall architecture is nearly identical, with the major differences only on the Y chromosome. - There is almost no sequence homology between humans and mice.

The majority of the time, _________ of the histone tails leads to transcription, and _________ leads to silencing.

acetylation; methylation acetylation = transcription methylation = silencing

Introns are beneficial because they

allow for diversification in the final protein product. - makes coding sequence discontinuous. - removed by splicing. - allow for diversification between species and organisms.

Human chromosomes, prior to S phase,

are composed of a single strand of dsDNA.

microRNAs (miRNA, NOT siRNA)

are tissue specific and play an important role in development. miRNAs - small, non-coding ssRNAs that regulate post-transcriptional gene expression by interfering with mRNA function via down-regulation (silence RNA). - tissue specific. - Not 100% complementary to the target gene. siRNA (dicer/ RISC) - originate from dsRNA. - response to foreign RNA (viruses). - 100% complementary to the target gene.

In the traditional view of DNA synthesis, a single holoenzyme replicates DNA on

both the leading and lagging strand.

A recent study of Drosophila suggests that histones are passed to the daughter cells

by being completely removed from DNA and added back from the local pool.

During meiosis II, the tension that holds sister chromatids at the metaphase plate results from

cohesin. * crossing over between sister chromatid and homologue creates tension in meiosis I.

The 90° bend in the template DNA

ensures only a single template base in DNA polymerase's active site, reducing mistakes.

Which of the following would you NOT find in the human genome?

functional GULO. Humans are unable to make Vit. C

As organism complexity increases, genome size tends to ______ and gene density tends to ______.

increase ; decrease * the large the genome size, the more complex the organism.

The nucleosome

interacts with the minor groove of DNA via nonspecific interactions. * the minor groove is useful to proteins because it can scan, detect, and repair.

DNA topology - linking number - twist - writhe

linking number = number of times one would have to pass one strand over the other to separate completely. twist = number of turns of one strand over the other. writhe = supercoiling Lk=Tw+Wr

The amino acids that project outward from histone proteins and interact with DNA are mostly

lysines and arginines.

DNA polymerase senses that the 'correct' nucleotide has been incorporated by

monitoring the geometry of the base pair.

Condensin

present from prophase to telophase.

In eukaryotes, DNA Pol α is involved in

primer addition and initiation.

In the cell, DNA polymerase

requires an RNA primer to initiate synthesis.

If a double-stranded break in DNA occurs during synthesis,

the cell cycle will halt at the S/G2 checkpoint.

Telomerase extends the ends of chromosomes by

using a built in template to extend the end of chromosomal DNA.

In DNA synthesis, the 3'OH attacks the

α-phosphate of the incoming nucleotide.