Biochem - Molecular (DNA Basics)

Question 1

What is the purpose of chromatin?

Answer 1

DNA exists in the condensed, chromatin form in order to fit into the nucleus

Question 2

What forms the nucleosome “bead” in chromatin structure? What are the electric charges of these components?

Answer 2

Negatively charged DNA loops twice around positively charged histone octamer to form nucleosome “bead”; Think: “beads on a string”

Question 3

In what 2 amino acids are histones rich?

Answer 3

Histones are rich in the amino acids lysine and arginine

Question 4

What stabilizes the chromatin fiber, and how?

Answer 4

H1 binds to the nucleosome and to “linker DNA”, thereby stabilizing the chromatin fiber

Question 5

What happens to DNA in mitosis?

Answer 5

In mitosis, DNA condenses to form chromosomes

Question 6

What occurs during S phase?

Answer 6

DNA and histone synthesis occur during S phase

Question 7

Which histone(s) is (are) inside the nucleosome core of chromatin?

Answer 7

H1 is the only histone that is not in the nucleosome core; Nucleosome core histones H2A, H2B, H3, H4 (each x2)

Question 8

Describe heterochromatin in terms of condensation, transcription, and sterics. How does it appear on EM?

Answer 8

Condensed, appears darker on EM. Transcriptionally inactive, sterically inaccessible; Think: “HeteroChromatin = Highly Condensed”

Question 9

Describe euchromatin in terms of condensation, transcription, and sterics. How does it appear on EM?

Answer 9

Less condensed, appears lighter on EM. Transcriptionally active, sterically accessible; Think: “Eu = true, ‘truly transcribed’”, “Euchromatin is Expressed”

Question 10

What is the mechanism of DNA methylation, and when does it occur? What does this allow?

Answer 10

Template strand cytosine and adenosine are methylated in DNA replication, which allows mismatch repair enzymes to distinguish between old and new strands in prokaryotes

Question 11

What type of DNA methylation represses transcription?

Answer 11

DNA methylation at CpG islands represses transcription; Think: “CpG Methylation Makes DNA Mute”

Question 12

What effect(s) does histone methylation have?

Answer 12

Usually reversible represses DNA transcription, but can activate it in some cases; Think: “histone Methylation Mostly Makes DNA Mute”

Question 13

What effect(s) does histone acetylation have?

Answer 13

Relaxes DNA coiling, allowing from transcription; Think: “histone Acetylation makes DNA Active”

Question 14

Which nucleotides are the purines versus pyrimidines? How many rings does each have?

Answer 14

PURines (A,G) - 2 rings; PYrimidines (C, T, U) - 1 ring; Think: “PURe As Gold & CUT the PY (pie)”

Question 15

What functional group distinguishes thymine?

Answer 15

Thymine has a methyl; Think: “THYmine has a meTHYl”

Question 16

From what other nucleotide is uracil made, and how?

Answer 16

Deamination of cytosine makes uracil

Question 17

In which nucleic acid is uracil versus thymine found?

Answer 17

Uracil found in RNA; Thymine in DNA

Question 18

Which nucleotide bonds in DNA are stronger, and why?

Answer 18

G-C bond (3 H bonds) stronger than A-T bond (2 H bonds)

Question 19

What is a consequence of high G-C content in DNA?

Answer 19

High G-C content –> High melting temperature of DNA; Think: “C-G bonds are like Crazy Glue”

Question 20

What 3 amino acids are necessary for purine synthesis?

Answer 20

Amino acids necessary for purine synthesis: Glycine, Aspartate, Glutamine; Think: “GAG”

Question 21

What is a nucleoside versus nucleotide?

Answer 21

NucleoSide = base + (deoxy)ribose (Sugar); NucleoTides = base + (deoxy)ribose + phosphaTe

Question 22

What links nucleotides?

Answer 22

Linked by 3’-5’ phosphodiester bond

Question 23

Draw the structure of Purines (A, G) & associate aspects of this structure with the following 5 requirements for purine synthesis: (1) Aspartate (2) CO2 (3) Glutamine (4) Glycine (5) N10-Formyl tetrahydrofolate.

Answer 23

See p. 33 in First Aid 2017 for visual at top

Question 24

Draw the structure of Pyrimidines & associate aspects of this structure with the following 2 requirements for pyrimidine synthesis: (1) Carbamoyl phosphate (2) Aspartate.

Answer 24

See p. 33 in First Aid 2017 for visual at top

Question 25

Draw the chromatin structure.

Answer 25

See p. 32 in First Aid 2017 for visual at top left

Question 26

What are Barr bodies, and of what type of chromatin are they composed?

Answer 26

Barr bodies (inactive X chromosomes) are heterochromatin

Question 27

What is located at the 5’ versus 3’ end of a 3’-5’ phosphodiester bond, and what purpose does each serve?

Answer 27

5’ end of incoming nucleotide bears the triphosphate (energy source for the bond). Triphosphate bond is target of 3’ hydroxyl attack.