Chapter 4: Molecular Genetics - DNA, Replication, Protein Synthesis, and Gene Regulation

Flashcards testing core concepts of DNA structure, replication mechanism, transcription, translation, genetic code properties, and lac operon regulation from Chapter 4 lecture notes.

What is the concept of Central Dogma in molecular biology?

Central Dogma explains the flow of genetic information within a biological system, flowing from DNA to DNA during replication, and from DNA to protein during phenotypic expression.

Which process of genetic information transfer in the Central Dogma is considered irreversible?

The transfer of genetic information from RNA to protein is irreversible.

What mechanism of DNA replication was proposed by Watson and Crick and proven by Meselson and Stahl in 1957?

Semi-conservative replication.

In the Meselson and Stahl experiment shown in the diagram, what band pattern is observed in the third generation after incubating heavy cells in $^{14}\text{N}$?

A band pattern consisting of a $\frac{1}{4}$ hybrid density band and a $\frac{3}{4}$ light density band.

What is the primary function of DNA helicase during DNA replication?

To unwind the parental DNA double helix and separate the two strands by breaking hydrogen bonds between complementary bases.

How do single-strand binding proteins (SSB proteins) function during DNA replication?

They bind to separated DNA strands to prevent them from rejoining.

What is the role of topoisomerase during DNA replication?

It relieves the strain of unwound DNA caused by overwinding or supercoiling by breaking phosphodiester bonds (making a nick), swiveling, and rejoining the DNA strands.

What enzyme catalyzes the synthesis of the short RNA primer needed to initiate DNA replication?

Primase.

What are the distinct functions of DNA polymerase III and DNA polymerase I in DNA replication?

DNA polymerase III synthesizes new DNA strands by adding complementary DNA nucleotides to the free 3'-OH end of an RNA primer, whereas DNA polymerase I replaces RNA primers with DNA nucleotides.

What enzyme joins Okazaki fragments on the lagging strand, and what chemical bond does it create?

DNA ligase, which catalyzes the formation of phosphodiester bonds between Okazaki fragments.

What speed and accuracy are reported for human DNA replication in the lecture notes?

Human DNA is copied at about $50\,\text{base pairs per second}$ with an error rate of less than one mistake in a billion ($10^9$) nucleotides.

What three functions does the promoter region serve in a gene structure?

It marks the beginning of a gene, acts as the binding site for RNA polymerase, and determines which strand of DNA is used as the template.

In what direction does RNA polymerase synthesize mRNA during the elongation stage of transcription?

In the $5' \rightarrow 3'$ direction.

What process and nuclear complex are depicted in the diagram showing pre-mRNA modification in eukaryotes?

RNA splicing, where introns are removed and exons are joined together by a spliceosome.

What are the three stop codons in the genetic code, and what do they code for?

UAG, UAA, and UGA; they do not code for any amino acid and serve as signals to terminate translation.

What start codon initiates translation, and which amino acid does it encode?

AUG, which encodes methionine (met).

What does it mean that the genetic code is 'degenerate'?

It means that most amino acids are coded by more than one codon, as $61$ codons represent the $20$ standard amino acids.

Identify the three tRNA binding sites located on the 50S large ribosomal subunit shown in the diagram.

The E (exit) site, P (peptidyl-tRNA binding) site, and A (aminoacyl-tRNA binding) site.

What enzyme catalyzes amino acid activation, and what type of bond connects the amino acid to the tRNA?

Aminoacyl-tRNA synthetase, which links the amino acid to the 3' end of the tRNA via an ester bond.

Based on the provided tRNA diagram, what functional regions are located at the 3' end and the middle loop?

The protruding 3' end contains the acceptor stem (attachment site for a specific amino acid), and the middle loop contains the three-base anticodon.

What catalytic component forms peptide bonds during translation elongation, and where is it located?

Peptidyl transferase, an rRNA component of the large ribosomal subunit that functions as a ribozyme.

What sequence of movements occurs during the translocation step of translation?

The ribosome advances one codon ($5' \rightarrow 3'$), moving the tRNA in the A site to the P site, while the uncharged tRNA in the P site shifts to the E site and exits.

How does a release factor terminate translation when a stop codon reaches the A site?

It binds to the stop codon and causes the addition of a water molecule, hydrolyzing the bond between the completed polypeptide chain and the tRNA in the P site.

What is a polyribosome (polysome)?

A structure formed when multiple ribosomes attach to and translate a single mRNA strand simultaneously to produce many copies of a polypeptide.

Who proposed the operon model for gene regulation in 1961, and what organism did they study?

François Jacob and Jacques Monod, who studied Escherichia coli (E. coli).

What are the three structural genes of the lac operon and their respective enzyme products?

lacZ encodes $\beta$-galactosidase, lacY encodes lactose permease, and lacA encodes transacetylase.

What type of growth curve is depicted in the figure when E. coli is grown in a mixture of glucose and lactose?

A diauxic (or diphasic) growth curve, where glucose is metabolized first, followed by a short lag phase for enzyme synthesis, after which lactose is used.

How is the lac operon inactivated when lactose is absent from the cellular environment?

The regulatory gene lacI continuously produces an active repressor protein that binds to the operator site, physically blocking RNA polymerase from transcribing the structural genes.

Based on the diagram, what occurs in the lac operon mechanism when lactose is present?

Allolactose acts as an inducer that binds to the repressor protein, changing its shape so it becomes inactive and detaches from the operator, allowing RNA polymerase to transcribe lacZ, lacY, and lacA.