Bio chap 4: DNA & Genomics

Nucleotides

The monomers of nucleic acids, consisting of a pentose sugar, a nitrogenous base, and one or more phosphate groups joined by condensation reactions.

Phosphodiester bond

A strong covalent bond formed by a condensation reaction between the $3'OH$ group of one nucleotide and the $5'$ phosphate group of the next nucleotide.

Double helix

The molecular model of DNA consisting of two polynucleotide chains spiraled around an imaginary axis, characterized by a uniform width of $2\,nm$.

Antiparallel

The arrangement of the two polynucleotide chains in DNA where one strand runs in the $5'$ to $3'$ direction and the other runs in the $3'$ to $5'$ direction.

Complementary base pairing

The specific hydrogen bonding between nitrogenous bases where Adenine pairs with Thymine (or Uracil) via two hydrogen bonds, and Guanine pairs with Cytosine via three hydrogen bonds.

Chargaff’s rules

The principle stating that the amount of $A = T$ and $G = C$, and that the total amount of pyrimidine nucleotides ($T + C$) equals the total amount of purine nucleotides ($A + G$).

messenger RNA (mRNA)

A single-stranded RNA molecule synthesized by transcription in the nucleus that serves as a template for protein synthesis in the cytoplasm.

ribosomal RNA (rRNA)

RNA molecules synthesized in the nucleolus that, together with ribosomal proteins, are assembled into the small and large subunits of ribosomes.

transfer RNA (tRNA)

A single-stranded RNA molecule with an anticodon and an acceptor stem that transfers specific amino acids to the ribosome during translation.

Semi-conservative replication

The model of DNA replication where each daughter molecule consists of one conserved parental strand and one newly synthesized strand.

Meselson and Stahl experiment

An experiment using $^{15}N$ and $^{14}N$ isotopes in Escherichia coli that provided evidence for the semi-conservative model of DNA replication.

DNA helicase

An enzyme that unwinds and unzips the DNA double helix at the origin of replication by breaking hydrogen bonds between nitrogenous bases using energy from $ATP$.

DNA topoisomerase

An enzyme that prevents tighter twisting and strain in front of the replication fork by introducing a break in a single strand, rotating it, and resealing it.

Primase

A specialized RNA polymerase that synthesizes short segments of RNA (primers) to provide the free $3'OH$ end required for DNA polymerase to initiate elongation.

DNA polymerase III

The primary enzyme responsible for synthesizing new strands of DNA by adding deoxyribonucleoside triphosphates to the $3'OH$ end of a growing chain.

Okazaki fragments

Short, discontinuously synthesized segments of DNA produced on the lagging strand during replication.

DNA ligase

An enzyme that joins adjacent Okazaki fragments on the lagging strand by catalyzing the formation of phosphodiester bonds.

End-replication problem

The inability of DNA polymerase to completely replicate the $5'$ ends of linear eukaryotic chromosomes, resulting in a single-stranded $3'$ overhang and progressively shorter DNA molecules.

Transcription

The synthesis of an RNA molecule (mRNA, tRNA, or rRNA) using one of the DNA strands as a template.

Promoter

A specific sequence of DNA, such as the TATA box in eukaryotes, where transcription factors and RNA polymerase bind to initiate transcription.

5’ methylguanosine cap

A modification added to the $5'$ end of eukaryotic pre-mRNA that facilitates nuclear export, protects against exonucleases, and assists in ribosome binding.

3’ Poly-A tail

A sequence of approximately $200$ adenine residues added to the $3'$ end of pre-mRNA to increase stability and facilitate nuclear export.

RNA splicing

The post-transcriptional modification process of removing non-coding introns and joining coding exons together via a spliceosome.

Alternative splicing

A process where exons are joined in different combinations to produce different mature mRNAs from the same pre-mRNA, allowing one gene to code for multiple polypeptides.

Codon

A triplet of consecutive nucleotide bases in mRNA that specifies a particular amino acid or signals the start or termination of translation.

Wobble effect

The relaxation of base-pairing rules between the third nucleotide of an mRNA codon and the corresponding base of a tRNA anticodon, allowing some tRNAs to bind to multiple codons.

Aminoacyl-tRNA synthetase

One of $20$ different enzymes that catalyzes the covalent attachment of a specific amino acid to the $3'$ acceptor stem of its corresponding tRNA.

Polyribosomes (Polysomes)

Strings of multiple ribosomes that translate a single mRNA molecule simultaneously to produce many copies of a polypeptide rapidly.