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Genetics > Week2: DNA Structure and Function > Flashcards

Week2: DNA Structure and Function Flashcards

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1
Q

Complementary Base Pairing: DNA

A

Adanine pairs with Thymine (2 hydrogen bonds)

Cytosine with Guanine (3 hydrogen bonds)

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2
Q

What are the 4 bases in DNA?

A

Adenine and Thyanine

Cytasine and Guanine

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3
Q

How do you calculate percentage of bases in DNA?

A

DNA bases are complementary, so if Adenine is 40%, then so would Thynine.

This leaves 20% left, so the other two bases Cytosine and Guanine would split that at 10% each.

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4
Q

Where is DNA found?

A

In the nucleus of the cell

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5
Q

DNA can exist in many different forms. Explain what a chromosome is

A
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6
Q

What is a histone?

A

A nucleosome is formed as DNA tightly winds over histones. This is done to cram what would be 2 meters long into a tiny cell nucleus (Jorde et al., 2020).

Histones are proteins that are positively charged which helps them bind to the negatively charged phosphate backbone of DNA. There are five histone proteins. These can combine to form a disk-shaped histone core. About 150 bases wrap around each histone to make a nucleosome (Lee & Weaver, 2001).

Histones are also important structures that play a role in gene expression, which in terms of health can impact disease phenotypes.

Histones are the proteins closely associated with DNA molecules. They are responsible for the structure of chromatin and play important roles in the regulation of gene expression.

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7
Q

What are nucleosomes?

Whare are 3 functions of nucleosomes?

A

A nucleosome is formed as DNA tightly winds over histones. This is done to cram what would be 2 meters long into a tiny cell nucleus (Jorde et al., 2020).

Three functions of the nucleosome include

  • organizing DNA,
  • regulating recruitment of chromatin enzymes, which promotes stability,
  • and to further compact the genome through the ability to self-assemble
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8
Q

What are chromatin?

A

Combination of DNA and histone proteins

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9
Q

What are genes?

A

Regions on chromasomes that code for proteins

there are approximately 20,000 to 25,000 genes in the genome

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10
Q

DNA Replication

A
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11
Q

What is the role of DNA polymerase?

A

Travels along the single DNA strand, addind free nucleotides to the 3’ end of the new strand. Nucleotides can only be added to the 3’ strand, so replication always proceeds fro 5’ to 3’ end

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12
Q

What is the function of DNA helicase?

A

unwinds and separates double-stranded DNA as it moves along the DNA.

It forms the replication fork by breaking the hydrogen bond between nucleotide pairs in DNA

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13
Q

What is the function of DNA ligase?

A

Glue DNA fragments together

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14
Q

What is the role of DNA primase?

A

A type of RNA polymerase that generates RNA primers.

Primers are short RNA molecules that act as templates for the starting point of DNA replication

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15
Q

What is the role of DNA gyrase?

A
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16
Q

What is a telomere and what is its function?

A

Telomeres prevent the ends of chromosomes from being damaged.

Telomeres prevent the shortening of chromosomes during replication and the accidental fusion of two chromosomes at their ends.

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17
Q

What net charge does DNA have?

A

The DNA backbone carries negatively-charged oxygen molecules which result in an overall negative charge at the phosphate-sugar backbone of DNA.

This negative net charge is crucial for the transcription process. If DNA didn’t have a net negative charge, it would impair the process of transcription. It would affect the ability for histones (positively charged) to bond with DNA. Histones are integral for the regulation and compaction of DNA in the nucleus.

The negative charge comes from the phosphodiester backbone. Particularly, because of the phosphate group that is attached.

18
Q

What is the role of DNA topoisomerase?

A

unwinds and rewinds DNA strands to prevent the DNA from becoming tangled or supercoiled

19
Q

What are exonucleases?

A

a group of enzymes that remove nucleotide bases from the end of a DNA chain

20
Q

What is DNA ligase?

A

Joins DNA fragments together by forming phosphodiester bonds between nucleotides

21
Q

Is DNA replication Bi-Directional?

A

DNA replication is bi-directional and involves the formation of a bond between 3’ hydroxyl group of the sugar of one nucleotide and the 5’ phosphate of another nucleotide.

22
Q

What is DNA replication?

A

In order for the body to make new cells, DNA must be replicated in a very distinct way.

DNA replication is the process by which a double-stranded DNA molecule is copied to produce two identical DNA molecules.

Each time a cell divides, the two resulting daughter cells must contain exactly the same genetic information, or DNA, as the parent cell.

23
Q

What does the DNA molecule consist of?

(DNA molecule consists of…)

(DNA nucleotides are made up of…)

(____ bonds link ____)

(When referencing each strand, the ___’ end refers to …)

A

The DNA molecule consists of two long strands of nucleotides arranged in a helical structure.

DNA nucleotides are made up of a phosphate group, sugar group and one of four different types of nitrogen bases (adenine, thymine, cytosine and guanine).

Hydrogen bonds link the nitrogen bases of opposite strands together and the sugar group of one nucleotide is covalently bonded to the phosphate of another nucleotide creating the backbone of the helix.

When referencing each strand, the 3’ end refers to the number 3 carbon in the sugar group attached to the hydroxyl group and the 5’ end refers to the number 5 carbon in the sugar group attached to the phosphate group (Alberts et al., 2002).

24
Q

Where is DNA replication initiated?

A

DNA replication is the creation of identical copies of DNA by using the already existing DNA strands as templates.

This process is initiated at many replication origins along the chromosome resulting in concurrent copying of DNA (Jorde et al., 2020).

25
Q

What happens during DNA replication?

A

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).

26
Q

DNA replication fork

A

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

27
Q

How does fluoroquinolone work on DNA in relation to gyrase and topoisomerase?

A

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)

28
Q

Why do telemeres get shorter with each round of division?

A

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.

29
Q

Chromatin Remodeling

A

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.).

30
Q

At which stage of the cell cycle do somatic cells reside?

A

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.

31
Q

One key difference between Miosis and Mitosis is…

A

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).

32
Q

P & Q of a chromosome

A
33
Q

Gene Locus

A
34
Q

What is mitosis?

A
35
Q

What are the phases of the cell cycle?

A
36
Q

Name the phases of mitosis?

A
37
Q

DNA Replication fork slide

A
38
Q

What is Mitosis? What are the phases?

A

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

39
Q

What are the phases of the cell cycle?

A

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.

40
Q

What direction is DNA synthesized?

A

5’ to 3’ direction

41
Q

Phases of Mitosis

A

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

Genetics (7 decks)

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