DNA Structure & Stability
DNA Replication Enzymes
Restriction Enzymes & Cloning
Transcription and Translation
Protein Binding & Function
100

What type of bond links nucleotides together in a DNA strand?

What are phosphodiester bonds between 3' and 5' carbons of neighboring sugars

100

Which enzyme unwinds the DNA double helix at the replication fork?

What is Helicase

100

What distinguishes sticky ends from blunt ends after restriction digestion?

Sticky ends have overhangs that can base pair, blunt ends are even cuts with no overhangs

100

What is the base-pairing rule used during transcription from the template strand?

A pairs with U, T with A, G with C and C with G

100

What does the term p50 represent in oxygen binding curves?

The partial pressure of O2 when half of the protein's binding sites are occupied

200

What base pair has three hydrogen bonds and increases DNA stability?

What is G-C base pairs

200

What is the function of primase in replication?

Synthesizes short RNA primers to act as starting point for DNA synthesis

200

How many different restriction enzymes should you use for directional cloning?
(don't overthink it)

2 enzymes that can generate sticky ends

200

What sequence on mRNA signals the start of translation? 

Start codon AUG (codes for methionine)

200

Which protein has a lower p50 and higher affinity for oxygen?

What is Myoglobin

300

What happens to DNA melting temperature (Tm) when salt concentration increases?

Tm increases because cations stabilize negatively charged backbone

300

Which enzyme seals nicks on lagging strand?

Bonus question: What are the segments between these gaps called?

What is DNA ligase

(Okazaki fragments)

300

What is the purpose of the multiple cloning site (MCS) in a plasmid?

It contains several unique restriction sites for inserting genes of interest

300

A point mutation that changes one base but doesn't alter the amino acid sequence. 

What is a silent mutation

300

What structural feature of hemoglobin allows for cooperative binding?

Its quaternary structure with four subunits that influence each other's O2 binding

400

How would very high or very low pH affect double stranded DNA?

Extreme pH disrupts hydrogen bonding and causes denaturation 

400

How does topoisomerase prevent DNA ahead of the fork from becoming overwound?

By cutting and rejoining DNA strands to relieve supercoiling tension

400

What are the two requirements for enzymes to be compatible in a double digest?

Same temperature, same buffer

400

When using CRISPR to add 100 aspartic acid residues, which DNA repair mechanism should be used and why?

HDR because it allows for precise sequence insertion using a template

CRISPR creates a double-strand break in DNA.

  • NHEJ (non-homologous end joining) quickly rejoins ends but introduces random insertions/deletions — good for knocking out genes.

  • HDR (homology-directed repair) uses a provided DNA template to copy in a new sequence exactly — good for adding a specific insert, like those aspartic acids.

400

Why is hemoglobin better suited than myoglobin for transporting O2 from lungs to tissues? 

Hemoglobin's cooperative binding allows it to release O2 where pO2 is low while myoglobin holds O2 tightly. 

500

Both GC content and salt concentration affect DNA stability. Explain how each influences Tm and why DNA melts at a higher temp that AT-rich DNA

GC base pairs have 3 H bonds (AT has 2) which creates stronger interaction requiring more heat to separate the strands. 

Higher salt concentration shields the negative phosphate backbone, reducing repulsion and stabilizing the helix, further increasing Tm. 

500

DNA polymerase has proofreading ability through which enzymatic activity and what error does it correct?

3'-->5' exonuclease activity; it removes mispaired nucleotides during replication

500

If a plasmid is cut with two different restriction enzymes and produces two fragments, what does this tell you about the cut sites and digestion success?

Both enzymes each successfully cut once on the plasmid so the double digest worked and the insert region was released/opened 

500

What would happen to the resulting protein if translation started in a different reading frame than the start codon?

(bonus question: how many reading frames are there?)

The amino acid sequence would be completely different, likely resulting in a nonfunctional protein

500

At high altitudes, how does the fractional saturation of hemoglobin in the lungs change, and what physiological response compensates? 

Fractional saturation decreases due to lower pO2, body compensates by increasing RBC production and 2,3-BPG levels


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