Module 1: DNA Flashcards
Linking of monomers to form polymers is done by a process known as _________.
Condensation/dehydration
The process of polymers being broken down into monomers is known as _________.
Hydrolysis
Be able to distinguish between purines and pyrimidines:
Purines: 2 rings (adenine, guanine)
Pyrimidines: 1 ring (Cytosine, Thymine, Uracil)
Which of the following purines contain a double bonded oxygen (carbonyl) on the top of the ring?
A. Adenine B. Guanine C. Cytosine D. Thymine E. Uracil
B. Guanine
Guanine = carbonyl
Adenine = NH2
What is the difference between a nucleotide and a nucleoside?
Nucleotide = sugar, base, phosphate
Nucleoside = sugar, base
What carbon does the base (purine/pyrimidine) attach to on the sugar?
Carbon 1 = base
Identify what attaches to the different carbons of a sugar:
Carbon 1 = base
Carbon 2 = ribose/deoxyribose
Carbon 3 = phosphodiester bond (phosphate)
Carbon 5 = phosphodiester bond (phosphate)
Which of the following pyrimidines contain a methyl group (CH3) bonded to the ring?
A. Adenine B. Guanine C. Cytosine D. Thymine E. Uracil
D. Thymine
Pyrimidines:
Cytosine = NH2 and carbonyl on the ring
Thymine = CH3 and 2 carbonyls
Uracil = 2 carbonyls (same as thymine w/o CH3)
Purines:
Adenine = NH2
Guanine = Carbonyl
What is the difference between ribose and deoxyribose?
Ribose = 2 OH’s
Deoxyribose = No OH on carbon #2
Where are phosphodiester bonds found in DNA?
Phosphodiester bonds link sugars
H-bonds link bases together (G-C has 3 H-bonds)
What 3 ways can you separate (denature) DNA strands?
- change pH
- increase heat
- DNA replication
Which of the following studies proved that genes were made of DNA and NOT protein?
A. Hershey and Chase experiment
B. Meselson and Stahl experiment
A. Hershey and Chase experiment
_______ revealed that DNA synthesis is semiconservative.
A. Hershey and Chase experiment
B. Meselson and Stahl experiment
B. Meselson and Stahl experiment
Hershey and Chase: genes are made of DNA
Meselson and Stahl: semiconservative
Which of the following is FALSE regarding DNA synthesis?
A. Occurs at the replication fork and is bidirectional B. Semiconservative C. Proceeds in the 3' to 5' direction D. Requires an RNA primer E. All of the above are true
C. Proceeds in the 3’ to 5’ direction
DNA synthesis proceeds in the 5’ to 3’ direction
Which of the following enzymes in DNA replication is a replication initiation factor that promotes denaturation of DNA at the origin of replication?
A. DnaA B. Helicase C. Single stranded DNA binding protein D. Topoisomerase E. Primase F. DNA polymerase G. Telomerase
A. DnaA
DNA replication steps:
- DnaA initiates partial denaturation of DNA (begins the unwinding of DNA)
- Helicase travels along DNA in the 5’ to 3’ direction and separates the DNA strands
- Single stranded binding proteins bind to the unzipped portion of DNA to prevent DNA from re-forming a double helix (keeps both strands of DNA from re-binding)
- Topoisomerase relieves the stress caused by unzipping DNA
- Primase synthesis RNA primers to prime DNA synthesis
- DNA polymerase replicate DNA
Which of the following DNA replication enzymes relieves the stress caused by helicase?
A. DnaA B. Helicase C. Single stranded DNA binding protein D. Topoisomerase E. Primase F. DNA polymerase G. Telomerase
D. Topoisomerase
You are studying DNA replication in your lab and decide to mutate DNA primase. What is the most likely scenario that you will observe?
A. SSBP will not attach to the DNA
B. No replication bubble will form
C. DNA polymerase III will not attach to the DNA
D. Semiconservative replication will occur without any problem
C. DNA polymerase III will not attach to the DNA
Which of the following has the highest processivity?
A. DNA pol I
B. DNA pol II
C. DNA pol III
D. All of the above
C. DNA pol III
Which of the following has the lowest processivity?
A. DNA pol I
B. DNA pol II
C. DNA pol III
D. All of the above
A. DNA pol I
Which of the following has 3’ to 5’ exonuclease activity (proofreading)?
A. DNA pol I
B. DNA pol II
C. DNA pol III
D. All of the above
D. All of the above
Which of the following has 5’ to 3’ exonuclease activity (proofreading)?
A. DNA pol I
B. DNA pol II
C. DNA pol III
D. All of the above
A. DNA pol I
Exonuclease activity hydrolyzes phosphodiester bonds:
- Base removal from 5’ terminus (5’ to 3’), removes RNA primers [DNA pol I]
- Base removal from the 3’ terminus (3’ to 5’), removes misincorporated bases (proofreading)
Which of the following DNA polymerases removes a base from the 5’ terminus, which removes RNA primers?
A. DNA pol I
B. DNA pol II
C. DNA pol III
A. DNA pol I
Which of the following is FALSE regarding the leading strand in DNA replication?
A. DNA is synthesized as one long molecule
B. DNA primase makes a single RNA primer
C. DNA polymerase adds nucleotides in a 5’ to 3’ direction as it slides forward
D. DNA is synthesized from 5’ to 3’ as Okazaki fragments
D. DNA is synthesized from 5’ to 3’ as Okazaki fragments
Leading strand = one long molecule
Lagging strand = Okazaki fragments
Note: the lagging strand is synthesized as okazaki fragments by DNA polymerase that moves AWAY from the fork
List out the steps of the synthesis of the lagging strand:
- Primer added. Primase synthesized RNA primer
- 1st fragment synthesized. DNA pol III works in 5’ to 3’ direction, synthesizing first okazaki fragment of lagging strand
- 2nd fragment synthesized. Primase and DNA polymerase III synthesize another okazaki fragment
- Primer replaced. DNA pol I removes ribonucleotides of primer, replaces them with deoxyribonucleotides in 5’ to 3’ direction
- Gap closed, DNA ligase closes gap in sugar-phosphate backbone
Which of the following repairs UV-induced thymine-thymine dimers that prevent DNA polymerases from replication?
A. Nucleotide excision repair
B. Mismatch repair
C. Base-excision repair
A. Nucleotide excision repair
Which of the following repairs replication errors by using mut proteins to recognize the newly synthesized strand and excising out a single nucleotide?
A. Nucleotide excision repair
B. Mismatch repair
C. Base-excision repair
B. Mismatch repair
Which of the following repairs deamination of cytosine or misincorporation of uracil?
A. Nucleotide excision repair
B. Mismatch repair
C. Base-excision repair
C. Base-excision repair
What are the general steps of DNA repair?
- recognition of DNA error
- excision of error
- DNA pol fills in the gaps
- ligase joins the newly synthesized DNA piece to the original DNA
Give a quick definition for each of the following:
- Helicase
- SSBP
- Topoisomerase
- Primase
- DNA ligase
- DNA Pol I
- DNA pol III
- Exonuclease
- Telomerase
Helicase: unwinds DNA by breaking hydrogen bonds
SSBP: keeps bases from rebinding (reformation of double helix)
Topoisomerase: relieves strain during unwinding DNA
Primase: attaches RNA primers on DNA for DNA Pol to recognize
- 1 primer needed for leading strand
- multiple primers needed for lagging strand (Okazaki)
DNA Pol I: less proceessitivity, proofreading, removes RNA primer and replaces w/ DNA
*** contains exonuclease activity in 5’ to 3’
DNA Pol III: main polymerase, high processivity, high fidelity, proof reading
Exonuclease:
- 3’ to 5’ is proofreading
- 5’ to 3’ is removal of RNA primer
Telomerase: add copies of DNA repeats to ends of chromosomes. Uses RNA as template and makes the repeats leaving an overhang for next time!
Which of the following could be a daughter strand of the parental dsDNA after replication? Make sure to present the sequence in the accepted manner.
5’-ACGT-3’
3’-TGCA-5’
A. 3'-TGCA-5' B. 3'-TCCT-5' C. 5'-ACGT-3' D. 5'-TGCA-3' E. 3'-TGTC-5'
C. 5’-ACGT-3’
step one: when looking for a daughter strand you can automatically take out any answer choice the starts w/ the 3’ end
(A, B, E are crossed out)
step 2: take both strands and separate them
step 3: use complimentary base pair rules
step 4: pick answer that starts w/ 5’ end
Which of the following could be a daughter strand of the parental dsDNA after replication? Make sure to present the sequence in the accepted manner.
5’-ACCGGTCGAGT-3’
3’-TGGCCAGCTCA-5’
A. 5'-ACTCGACCGGT-3' B. 3'-ACTCGCAAGGT-5' C. 5'-ACCCGTGGAGT-3' D. 5'-TGAGCTGGCCC-3' E. 3'-TGGAACGCTCA-5'
A. 5’-ACTCGACCGGT-3’
step 1: separate two strands and draw the complimentary strand under each
step 2: look at the complementary strand in the 5’ to 3’ direction to find your answer
Which of the following is NOT related to DNA?
A. Deoxyribonucleotide B. Antiparallel C. Phosphodiester bonds D. Single stranded E. Complimentary F. Hydrogen bonding G. Hydrophobic and hydrophilic H. In ribosomes I. Nucleosomes
H. In ribosomes
note: DNA is located in the nucleus NOT in ribosomes
NOTE: DNA can be a single strand during replication
Which of the following is NOT related to RNA?
A. Deoxyribonucleotide B. Antiparallel C. Phosphodiester bonds D. Single stranded E. Complimentary F. Hydrogen bonding G. Hydrophobic and hydrophilic H. In ribosomes I. Nucleosomes
A. Deoxyribonucleotide
B. Antiparallel
I. Nucleosomes
