MCAT Biology & Biochemistry - Molecular Genetics & Gene Regulation Flashcards

Question 1

Helicase

Accepted Answer

An enzyme that unwinds the DNA double helix at the origin of replication by breaking hydrogen bonds between complementary base pairs, creating two single-stranded DNA templates.

Question 2

Topoisomerase (DNA Gyrase)

Accepted Answer

An enzyme that alleviates supercoiling and torsional strain ahead of the replication fork by introducing transient single- or double-strand breaks in the DNA backbone.

Question 3

Primase

Accepted Answer

An RNA polymerase that synthesizes short RNA primers (~10–12 nucleotides) to provide a free $3'-	ext{OH}$ group necessary for DNA polymerase to initiate synthesis.

Question 4

DNA Polymerase III vs. DNA Polymerase I (Prokaryotes)

Accepted Answer

• **DNA Pol III**: Main replicative enzyme; synthesizes DNA in the $5' \rightarrow 3'$ direction and proofreads in the $3' \rightarrow 5'$ direction.
• **DNA Pol I**: Removes RNA primers via $5' \rightarrow 3'$ exonuclease activity and replaces them with DNA.

Question 5

Leading Strand vs. Lagging Strand

Accepted Answer

• **Leading Strand**: Synthesized continuously in the $5' \rightarrow 3'$ direction toward the replication fork.
• **Lagging Strand**: Synthesized discontinuously away from the replication fork in short segments called **Okazaki fragments**.

Question 6

DNA Ligase

Accepted Answer

An enzyme that joins Okazaki fragments on the lagging strand by catalyzing the formation of phosphodiester bonds between adjacent $3'-	ext{OH}$ and $5'-	ext{phosphate}$ groups.

Question 7

Telomeres & Telomerase

Accepted Answer

• **Telomeres**: Repetitive non-coding DNA sequences (e.g., $5'-	ext{TTAGGG}-3'$) at eukaryotic chromosome ends that prevent loss of vital genes.
• **Telomerase**: A reverse transcriptase enzyme carrying its own RNA template to extend telomeres in germ cells, stem cells, and cancer cells.

Question 8

RNA Polymerase II & Promoters

Accepted Answer

RNA Polymerase II transcribes pre-mRNA in eukaryotes. It binds to the promoter region (specifically the **TATA box**, located around $-25$ to $-30$ base pairs upstream) with the help of general transcription factors.

Question 9

$5'$ Cap (7-Methylguanosine Cap)

Accepted Answer

A modified guanine nucleotide added to the $5'$ end of pre-mRNA during transcription. It protects the transcript from exonuclease degradation and serves as a recognition site for ribosomal binding during translation initiation.

Question 10

Poly-A Tail

Accepted Answer

A string of 100–250 adenine nucleotides added to the $3'$ end of pre-mRNA by polyadenylate polymerase. It protects against $3' \rightarrow 5'$ degradation and aids in nuclear export.

Question 11

Spliceosome & Pre-mRNA Splicing

Accepted Answer

A complex composed of **snRNAs** and **snRNPs** that removes non-coding **introns** as lariat structures and ligates coding **exons** together to form mature mRNA.

Question 12

Alternative Splicing

Accepted Answer

A post-transcriptional mechanism where different combinations of exons are joined together, allowing a single gene to encode multiple distinct protein isoforms.

Question 13

Wobble Hypothesis

Accepted Answer

Non-standard base pairing allowed at the 3rd position of an mRNA codon ($5'$ position of tRNA anticodon), explaining why 61 codons only require ~30–45 distinct tRNAs (degeneracy of the genetic code).

Question 14

Ribosomal Sites (A, P, E Sites)

Accepted Answer

• **A (Aminoacyl) site**: Holds incoming aminoacyl-tRNA.
• **P (Peptidyl) site**: Holds tRNA carrying the growing peptide chain; forms peptide bond via peptidyl transferase.
• **E (Exit) site**: Briefly holds uncharged tRNA before it exits the ribosome.

Question 15

Lac Operon Mechanics (Inducible System)

Accepted Answer

• **No Lactose**: Repressor binds operator $\rightarrow$ transcription blocked.
• **Lactose Present**: Allolactose binds repressor $\rightarrow$ repressor unbinds operator $\rightarrow$ transcription occurs.
• **Low Glucose**: High cAMP $\rightarrow$ cAMP-CAP complex binds upstream promoter $\rightarrow$ maximally enhances transcription.

Question 16

Trp Operon Mechanics (Repressible System)

Accepted Answer

• **Low Tryptophan**: Repressor is inactive $\rightarrow$ operon expressed to synthesize tryptophan.
• **High Tryptophan**: Tryptophan acts as a **corepressor**, binding the repressor to activate it $\rightarrow$ repressor binds operator and stops transcription.

Question 17

Histone Acetylation vs. Deacetylation

Accepted Answer

• **Acetylation (HATs)**: Adds acetyl groups to lysine residues on histones, reducing positive charge $\rightarrow$ loosens DNA interaction $\rightarrow$ forms **euchromatin** (transcriptionally active).
• **Deacetylation (HDACs)**: Removes acetyl groups $\rightarrow$ tightens DNA interaction $\rightarrow$ forms **heterochromatin** (transcriptionally silent).

Question 18

DNA Methylation

Accepted Answer

Addition of methyl groups to cytosine residues (often in CpG islands) by DNA methyltransferases. It silences gene expression by physically blocking transcription factors or recruiting histone deacetylases.

Question 19

Enhancers & Silencers

Accepted Answer

DNA control elements located thousands of base pairs away from the promoter. **Enhancers** bind activator proteins to upregulate transcription via DNA looping; **Silencers** bind repressor proteins to downregulate transcription.

Question 20

Mismatch Repair (MMR) System

Accepted Answer

A post-replication repair mechanism active during the $G_2$ phase of the cell cycle that detects, excises, and corrects base pairing errors missed by DNA polymerase proofreading.

MCAT Biology & Biochemistry - Molecular Genetics & Gene Regulation

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