Unit 4: Molecular Genetics - DNA, RNA, and Protein Synthesis

Comprehensive flashcards covering DNA structure, replication, transcription, RNA processing, and translation based on molecular genetics lecture notes.

What are the three components of a DNA nucleotide?

A $5c$ deoxyribose sugar, a phosphate group, and an organic nitrogenous base.

Differentiate between the two types of nitrogenous bases.

Purines (Guanine and Adenine) have a double-ring structure, while pyrimidines (Thymine and Cytosine) have a single-ring structure.

What defines the sides and the bonds holding the DNA strands together?

The sides are a sugar-phosphate backbone held by phosphodiester bonds, and the two strands are joined by hydrogen bonds between nitrogenous bases.

What is Chargaff's Rule?

The amount of Adenine is equal to the amount of Thymine ($A=T$), and the amount of Cytosine is equal to the amount of Guanine ($C=G$).

What does it mean that DNA strands are antiparallel?

They run in opposite directions, which allows base pairing to occur between a purine and a pyrimidine.

How does the structure of RNA differ from DNA?

RNA has a ribose sugar (instead of deoxyribose), uses Uracil ($U$) instead of Thymine ($A=U$), and is typically single-stranded and shorter.

What experiment confirmed that DNA replication is semi-conservative?

The Meselson-Stahl experiment, which grew $E. coli$ in a heavy isotope of nitrogen ($^{15}N$) and then transferred it to a light isotope ($^{14}N$) to observe replication patterns.

What is the function of Helicase in DNA replication?

It unwinds and separates the DNA strands by breaking hydrogen bonds, forming a replication bubble.

What roles do Single Stranded Binding Proteins (SSBs) and Topoisomerase play?

SSBs prevent hydrogen bonds from reforming, while Topoisomerase relieves tension by cutting, swiveling, and releasing DNA strands.

In which direction is DNA synthesized?

DNA is synthesized in the $5' \rightarrow 3'$ direction.

Distinguish between the leading and lagging strands.

The leading strand is built continuously toward the replication fork, while the lagging strand is built discontinuously away from the fork in segments called Okazaki fragments.

What are the functions of RNA Primase and DNA Polymerase III?

RNA Primase attaches an RNA primer to the parent strand, and DNA Polymerase III adds new deoxyribonucleoside triphosphates to the $3'$ end.

What is the role of DNA Polymerase I during replication?

It cuts out RNA primers and replaces them with the appropriate DNA nucleotides.

What is the function of DNA Ligase?

It forms phosphodiester bonds to join Okazaki fragments together.

Define 'codon' and identify the start and stop signals.

A codon is a sequence of three nucleotides coding for an amino acid. The start codon is mainly $AUG$; stop codons include $UAA$, $UAG$, and $UGA$.

What enzymes are involved in proofreading during replication?

DNA Polymerase I and II proofread base pairing and replace incorrect nucleotides.

What are the three stages of DNA transcription?

Initiation, elongation, and termination.

What is the role of the TATA box in transcription?

It serves as the promoter region where RNA polymerase binds to the DNA to begin transcription.

What happens during RNA splicing?

Introns (non-coding regions) are removed, and exons are spliced together to produce the final mRNA transcript.

What are the two modifications made to the ends of pre-mRNA in eukaryotes?

A $5'$ cap (of 7 Gs) is added to the start for ribosome recognition, and a Poly-A Tail (approx. $200 \text{ Adenines}$) is added to the $3'$ end for protection from digestion.

Explain 'alternative splicing' and its significance.

It allows multiple different proteins to be made from a single gene, explaining why the human genome can produce more proteins than there are genes.

What are the requirements for translation to occur?

mRNA, a ribosome (made of protein and rRNA), tRNA molecules, and GTP for energy.

What is the function of tRNA?

It carries specific amino acids to the ribosome and uses its anticodon loop to bind to complementary mRNA codons.

Describe the three sites (A, P, and E) within a ribosome during translation.

tRNA first enters the A-site (aminoacyl), move to the P-site (peptidyl) where the peptide bond forms, and exits via the E-site.

What is a 'polysome'?

A complex where multiple ribosomes travel along a single mRNA molecule simultaneously to synthesize many polypeptides at once.

Define the four levels of protein structure.

Primary ($1^{\text{o}}$) is the polypeptide chain sequence; Secondary ($2^{\text{o}}$) is \text{̑-helices}; Tertiary ($3^{\text{o}}$) is the 3D shape; Quaternary ($4^{\text{o}}$) is the interaction of multiple subunits.