MCM_Final_DSA4

Question 1

DNA and RNA bonds are…

Answer 1

• phosphodiester linkages
  
  • sugar-phosphate backbone + nitrogenous bases
  • the sugar of one nucleotide to the phosphate group of the next nucleotide

Question 2

Two DNA strands in a helix are bonded by

Answer 2

• hydrogen bonds between the paired bases
• van der Waals interactions between the stacked bases

Question 3

Deoxyribonucleic Acid (DNA)

Answer 3

• found in the nucleus and mitochondria
• encodes the genetic makeup
• central molecule of life

Question 4

Replication

Answer 4

• part of the process of passing genetic information from parent to offspring
• DNA is faithfully replicated

Question 5

Transcription

Answer 5

• DNA → RNA

Question 6

Translation

Answer 6

• RNA → protein

Question 7

Retroviruses

Answer 7

• exception to central dogma
• RNA → DNA
• Replication of viral RNA occurs via a DNA intermediate in host cell.
• RNA-dependent DNA polymerase reverse transcribes viral RNA → DNA, which then integrates into the host genome.

Question 8

Nucleotides

Answer 8

Nucleotides ( = nitrogenous base [ATCG] + a five-carbon sugar + and phosphate) a

• the monomeric units of DNA and RNA.
• DNA contains the sugar 2’-deoxyribose and RNA contains ribose.

Question 9

Pyrimidies versus Purines

Answer 9

• Purines: double-ring structure
  
  • DNA + RNA contain Adenine (A) & Guanine (G)
  • “All Gold is Pure”
• Pyrimidines: single ring structure
  
  • DNA has Cytosine (C) & Thymine (T)
  • RNA C and Uracil (U)
  • “Methylation of Uracil produces Thymine.”

Hydrogen Bonding between Purine + Pyrimidine:

• A + T = TWO H-bonds
• G + C = THREE H-bonds

Question 10

Watson-Crick Model of DNA Structure

Answer 10

• In addition to the double helical (held together by noncovalent interactions) formation, each strand runs
• antiparallel (**one strand runs in the 5’→3’ direction versus the other runs in the 3’→5’direction*)

Question 11

Chromatin Formation

Answer 11

• Coiling of DNA is done by electrostatic interactions between the (+) charged histones and the (-) charged phosphate backbone of DNA.
  
  • DNA wraps around pairs of four histones (H2A, H2B, H3, and H4) to make nucleosome.

Question 12

Histones

Answer 12

• histones are nuclear proteins that are abundant, small, basic AA (lysine- and arginine-rich)
• assists with DNA supercoiling

Question 13

Heterochromatin vs Euchromatin

Answer 13

• During the nondividing phase of the cell cycle (i.e., interphase: G1, G0, S, G2),
  
  • DNA is loosely packed/ easily accessible (“euchromatin”), there it is transcriptionally active,
• versus heterochromatin = highly condensed chromatin = transcriptionally inactive.
  
  • In metaphase, heterochomatin = prefered state of DNA, to prevent physical damage to gene during cell divsion

Question 14

Methylation versus Acetylation of DNA

Answer 14

methylation and acetylation regulate chromatin condensation

• methylation = heterochromatin =↓ gene expression
• acetylation (of LYSINE) = euchromatin= opens chromatin for ↑ gene expression
  
  • ​how?
    
    • acetylation ​↓ the overall (+) charge of the histones, = DNA loosely coils

Question 15

DNA Replication is … (3)

Answer 15

1. semiconservative
   
   • one old strand (template) + one new strand (daughter)
2. bidirectional
   
   • because the two strands of DNA are antiparallel and DNA ALWAYS replicates from 5’→3, the replication fork is created and the DNA is replicated in two directions
3. semi- discontinuous
   
   • DNA synthesizes from 5’→3: new nucleotide is added to the free 3’-OH, therefore synthesis occurs in a semi discontinuous manner
     
     • Continuous = Leading strand = 5’→3’ (same direction of replication fork)
     • Discontinuous = Lagging strand = 5’→3’ (in short Okazaki fragments)

Question 16

DNA Replication

Step 1: Parental Strand Seperation (“Duplex Opening, Origin of Relipcation”)

Answer 16

1. HELICASE: unwinds DNA helix by breaking H-bond.
   
   • ​​favors A-T base pair regions b/c they are easier to break (only double bonds)
2. TOPOISOMERASE: ahead of the replication fork & relieves the overwound supercoils (The topoisomerase of bacteria is DNA gyrase.
3. Single-stranded DNA-binding proteins (SSBPs): proteins bind to the separated DNA strands to PREVENT them from REANNEALING.

Question 17

More on Topoisomerase

(Inhibitors & Types)

Answer 17

Types:

1. Topoisomerase I enzymes cleave only one strand of DNA to REDUCE** **TENSION from sueprcoiling
2. Topoisomerases II cleave both strands (“double strand break”) to UNTANGLE them

Inhibitors:

1. Anthracyclins + Etoposide = inhibitor of Topoisomerase II (Eukaryotic)
2. Fluoroquinolones (i.e Ciprofloxacin and Levofloxacin) = inhibitors of DNA gyrase (bacterial).

Question 18

Streptomyces

Answer 18

• Isolated from the fungus, Streptomyces, is anthracyclins, which INHIBITS Topoisomerase II

Question 19

DNA polymerases

Answer 19

• DNA Pol binds to RNA primers (put down my primase)
• prokaryotic DNA pols are numbered (I, II, III)
• eukaryotic DNA pols are labeled with Greek letters (α, δ, ε).
• have high fidelity ( very accurate )
• DNA pol I and III have proofreading capabilities

Question 20

DNA POL III

Answer 20

DNA Pol III assembles the majority of daughter strands

• DNA pol III on the leading strand will continue polymerization as long as the helicase continues to separate the two-parent strands.
• DNA pol III on the lagging strand will operate until it encounters the RNA primer of the previous Okazaki fragment.

Pocessivity is used to describe how likely** a **DNA** **pol is to remain bound to the template strand.

• DNA pol III has a very high processivity because it binds with a sliding clamp that anchors it to the template strand.

Question 21

DNA POL I

Answer 21

DNA pol-I replaces RNA primers with DNA nucleotides

• DNA pol-I possesses 5’ → 3’exonuclease activity… removes RNA nucleotides one-by-one from the primer’s 5’ end
• simultaneously, using its 5’ → 3’ polymerase activity to pair free DNA nucleotides, replacing the RNA primer.

DNA pol-I fills gap after removal of the RNA primers

Question 22

DNA Mispairing

Answer 22

​

• DNA pol has proofreading abilities
• If a mispairing is identified, both DNA pol I and III possess 3’ → 5’ exonuclease activity to correct the error.

Question 23

DNA Ligase

Answer 23

DNA ligase then seals the nick between adjacent Okazaki fragments.

Question 24

Telomerase

Answer 24

There is shortening of chromosomes that lack telomerase

• it is common for newly synthesized DNA strand that is shortened at one end.
• Telomerase is an enzyme with reverse transcriptase activity that adds repeat sequences (ATTATTATTA) at end of chromosomes beyond the coding region (“*telomeric regions*”)

Telomerase is expressed in germline cells and neoplastic cells.