Week2: DNA Structure and Function Flashcards

Question

What happens during DNA replication?

Answer 1

Once the replication origins are established DNA helicases bind and unwind the double helix by disrupting hydrogen bonds between base pairs. Topoisomerases bind to the DNA helix ahead of the origin to reduce torsional strain caused by the unwinding. Once the strands are separated and a replication bubble is formed with two replication forks, DNA replication occurs bi-directionally which means both strands are replicated from a 5’end to 3’ end in different directions. The leading strand is continuously replicated moving towards the replication fork whereas the lagging strand is replicated discontinuously away from the replication fork. DNA polymerase is responsible for the addition of complimentary nucleotides along the template strand at only the 3’ end. The 3’ OH group of the last nucleotide creates a phosphodiester (covalent) bond to the 5’ phosphate group of the added nucleotide (Pray, 2008).

Answer 2

DNA polymerase can only add nucleotides to a 3’ end and DNA polymerase can only synthesize DNA going from 5’ to 3’ direction. In DNA replication topoisomerase first unwinds the tightly coiled DNA. Helicase divides the two strands of DNA. DNA primase adds an RNA primer to the lagging strand, so DNA polymerase can start adding nucleotides to the 3’ end. The leading strand can add in the 5’ to 3’ direction rather easily. The lagging strand replicates (also in 5’ to 3’) but in little fragments called Okazaki fragments with new primer for each of the short Okazaki fragments. RNAase removes the primers, DNA polymerase beta fills in the gaps left by the removal of primers. Then DNA ligase seals the gaps left DNA polymerase beta, linking the Okazaki fragments together. This ultimately ends in replication of the DNA strand. Here is a short video of this process from Khan Academy (2016): https://www.youtube.com/watch?v=eM7arWJJ3zk

Answer 3

DNA gyrase is a type II topoisomerase (Voet, Voet, Pratt, 2016). T Topoisomerase is an enzyme that relaxes DNA supercoiling to allow the replisome, composed of DNA polymerases’, and the initiation factor, DNA helicase, to continue replicating and splitting DNA respectively (Voet et al., 2016). Thus, bacterial DNA replication continues. If ciprofloxacin’s method of action is to inhibit bacterial DNA gyrase, then the antibiotic inhibits the bacteria’s ability to uncoil DNA (Voet et al., 2016). Ultimately, this prevents bacterial DNA gyrase from facilitating bacterial DNA replication and slows the growth of the bacteria (Voet et al., 2016). Ciprofloxacin inhibits bacteria from replicating therefore it is a bacteriostatic agent (Endmunds, 2016)

Answer 4

At each cell division, the telomeres shorten because of the incomplete replication of the linear DNA molecules by the conventional DNA polymerases (Maestroni, Matmati, & Coulon, 2017). Because of this replication problem, part of the end strand of DNA is not copied in each of the replication. After several rounds, the chromosome will ultimately get shorter. The gradual loss of sequence information at the extreme end of chromosomes owing to incomplete replication by DNA polymerases (which only synthesize DNA in the 5’ to 3’ direction and are unable to fill in the gap left behind by the 5’ most RNA primer) defines the chromosome end-replication problem.

Answer 5

Chromatin remodeling is essential for the access of replication proteins to DNA. Chromatin is formed when DNA is tightly condensed and wrapped around histones and makes up the nucleosome. Chromatin remodeling involves chromatin being changed from this condensed state to an accessible state. Without chromatin becoming “loose” it is very difficult for proteins to access the DNA (What Is Epigenetics, n.d.).

Answer 6

A cell spends most of its life in interphase that consist of three parts: G1, S, G2. G1 is the longest phase and it occurs between mitosis and DNA replication, synthesis of RNA and proteins occurs in this phase” (Jorde et al., 2020). Synthesis is the next phase where replication of DNA takes place (Jorde et al., 2020). G2 is the shortest phase. DNA repair may occur in G2 and the cell gets ready for division, known as mitosis (Jorde et al., 2020). Somatic cells do not spend most of their time diving and replicating, thus they most often reside in the longest phase, G1. G0 phase is a “resting” state for the cells, somatic cells can be in G1 and enter into this “resting” state.

Answer 7

The process of chiasmata formation does not occur during the process of mitosis. Chiasmata form during prophase I of the meiotic process. Chiasma are formed in the shape of a cross and mark attachments between homologous chromosomes specifying the point in which they exchange genetic material (Jorde, Carey, & Bamshad, 2020). This process is referred to as crossing over and serves as points of attachment between two non-sister chromatids of a homologous pair of chromosomes. This chromosomal shuffling produces chromosomes that have combinations of parts of the original chromosomes (Jorde, Carey, & Bamshad, 2020).

Answer 8

Interphase: - Cell develops and grows § Towards the end of phase DNA/chromosomes doubles - Prophase: - Chromosome are visible § Nuclear membrane and nucleolus disappears - Metaphase: - Chromosome line up across center § Spindle fibers attach to center of each chromosome - Anaphase: - Chromosome split § Each half is pulled to opposite side of cell - Telephase: - Chromosome clusters in center of each new cell § Nuclear membrane begin to form § Cells begin to separate - Cytokinesis: - Cytoplasm divides § 2 new daughter cells form § Same no. of chromosome as parent cell

Answer 9

G1 phase - Cell increases in size - Cellular contents are duplicated S phase - DNA replication - Each of the 46 chromosomes (23 pairs) is replicated by t he cell G2 phase - Cell grows more - Organelles and proteins develop in preparation for cell division M phase Mitosis followed by cytokinesis (cell separation) Formation of two identical daughter cells G0 phase While some cells are constantly dividing, some cell types are quiescent. These cells exit G1 and enter a resting state called G0. In G0, a cell is performing its function without actively preparing to divide. G0 is a permanent state for some cells, while others may restart division if they get the right signals.

Answer 10

5' to 3' direction

Answer 11

**Interphase**: - Cell develops and grows § Towards the end of phase DNA/chromosomes doubles - P**rophase:** - Chromosome are visible § Nuclear membrane and nucleolus disappears - **Metaphase:** - Chromosome line up across center § Spindle fibers attach to center of each chromosome - **Anaphase**: - Chromosome split § Each half is pulled to opposite side of cell - **Telephase**: - Chromosome clusters in center of each new cell § Nuclear membrane begin to form § Cells begin to separate - **Cytokinesis**: - Cytoplasm divides § 2 new daughter cells form § Same no. of chromosome as parent cell