Lec3.Structure and Replication of DNA and RNA

Vocabulary flashcards covering the structure, replication, transcription, translation, and regulation of DNA and RNA, along with protein structures and gene expression mechanisms from the lecture notes.

Genotype

The specific genetic makeup or genes an individual possesses, determined by DNA base sequences.

Phenotype

The physical appearance or observable characteristics of an individual, determined by proteins produced via gene expression.

Codon

A sequence of $3$ bases or nucleotides on DNA or mRNA that specifies a particular amino acid in a protein sequence.

Stop Codons

The $3$ specific codons ($\text{UUA}$, $\text{UGA}$, $\text{UAG}$) in the genetic code that terminate translation.

Start Codon

The specific codon ($\text{AUG}$) used to signal the beginning of protein translation.

Degenerate Code

A feature of the genetic code where a single amino acid can be specified by more than one codon.

Template Strand

The strand of the DNA double helix used by RNA polymerase to synthesize RNA during transcription.

Coding Strand

The strand of DNA that is complementary to the template strand.

Phosphodiester Bond

The linkage between adjacent nucleotides in a nucleic acid, formed between the phosphate group of one nucleotide and the $3'$ $-\text{OH}$ group of another.

Chargaff's Rules

The rule discovered by Erwin Chargaff stating that in DNA, the amount of adenine equals the amount of thymine ($\text{A} = \text{T}$) and the amount of cytosine equals the amount of guanine ($\text{C} = \text{G}$).

B DNA

The classic right-handed double-helical structure of DNA identified by Rosalind Franklin, Maurice Wilkins, Watson, and Crick, having a diameter of $2\text{ nm}$ and a complete turn every $3.4\text{ nm}$.

DNA Ligase

An enzyme that seals gaps in the DNA backbone by joining Okazaki fragments on the lagging strand using energy supplied by ATP.

Replicons

Individual sections of DNA replicated from each distinct origin of replication on eukaryotic chromosomes.

Telomeres

Repeated DNA sequences located at the ends of eukaryotic chromosomes that protect genomic integrity and are synthesized by telomerase.

Photorepair

A specific DNA repair mechanism where the enzyme photolyase binds to damaged DNA and uses visible light energy to cleave thymine dimers.

Excision Repair

A non-specific repair mechanism where damaged or mismatched nitrogenous bases are recognized, removed by excision enzymes, and resynthesized by DNA polymerase.

Structural Genes

Genes that encode the amino acid sequence of polypeptides fulfilling metabolic, biosynthetic, or structural roles in the cell.

Regulatory Genes

Genes whose protein or RNA products function to control or alter the expression of other genes.

Regulatory Elements

Non-transcribed DNA sequences that bind regulatory proteins to control the transcription of adjacent genes.

RNA Structure

A polymer consisting of nucleotides containing a ribose sugar, a phosphate group, and one of four nitrogenous bases.

Messenger RNA (mRNA)

RNA that carries a complementary copy of a gene's DNA code from the nucleus to the ribosome, structured in triplet codons.

Transfer RNA (tRNA)

RNA that carries specific amino acids to the ribosome; contains an amino acid attachment site at one end and a triplet anticodon at the other.

Ribosomal RNA (rRNA)

RNA molecules that combine with cellular proteins to construct the structural subunits of ribosomes.

Introns

Non-coding sequence segments within a primary mRNA transcript that are removed during RNA splicing.

Exons

Coding sequence segments within a primary mRNA transcript that are spliced together to form the final mature mRNA transcript.

Alternative RNA Splicing

A regulatory process where a single primary mRNA transcript produces different mature mRNA transcripts by selective inclusion or exclusion of exons.

RNA Interference

A post-transcriptional regulation method where double-stranded RNA is processed by the enzyme Dicer into micro-RNAs or small interfering RNAs to block translation or degrade target mRNAs.

Levels of Gene Control

The six regulatory checkpoints in gene expression: DNA packing, transcription regulation, mRNA breakdown, translation inhibition, regulation after translation, and protein degradation.

Mutations

Random alterations in the genetic nucleotide sequence that result in missing or modified protein synthesis.

Substitution Mutation

A single gene mutation where one nucleotide is replaced by another, causing either a single amino acid change (missense) or the creation/loss of a stop codon (nonsense).

Frameshift Mutation

A mutation caused by the insertion or deletion of nucleotides, shifting the reading frame and changing all downstream amino acids.

Splice Site Mutation

A gene mutation at an intron-exon boundary that can cause an intron to be improperly retained in mature mRNA, disrupting protein structure.

Peptide Bond

The covalent bond ($\text{C-N}$) joining two amino acids, formed when the carboxyl group ($\text{-COOH}$) of one links with the amine group ($\text{-NH}_2$) of another in a condensation reaction.

Primary Structure

The linear sequence of amino acids in a polypeptide chain linked by peptide bonds.

Secondary Structure

Localized repetitive folding patterns within a polypeptide chain, such as $\text{α}$ helices and $\text{β}$ pleated sheets, stabilized by backbone hydrogen bonds.

Tertiary Structure

The overall three-dimensional shape of a single polypeptide, stabilized by side-chain (R group) interactions such as hydrophobic forces, ionic bonds, hydrogen bonds, and disulfide bridges.

Quaternary Structure

The spatial arrangement and combination of multiple individual polypeptide subunits forming a functional protein complex, such as hemoglobin.

Denaturation

The loss of a protein's three-dimensional higher-order structure caused by heat, pH extremes, or chemicals, leaving the primary amino acid sequence intact while abolishing function.

Ubiquitin

A small regulatory protein attached to target proteins to mark them for destruction at the proteasome.