Gene Expression: Transcription, Translation, Mutations, and Genomics

Comprehensive vocabulary flashcards covering the Central Dogma, eukaryotic and prokaryotic transcription, the rules of the genetic code, translation mechanics, post-translational processing, genomics datasets, and classifications of DNA mutations.

Central Dogma of Biology

The core framework describing the flow of genetic information: DNA storage is transcribed into mRNA carriers, which are then translated into active proteins.

Genome

The complete set of DNA within an organism that stores the complete genetic instructions and defines what proteins can potentially be made.

Transcriptome

The entire collection of RNA molecules (including mRNA, small RNA, and long non-coding RNA) produced in a cell, indicating which genes are actively being expressed.

Proteome

The entire complement of proteins expressed, modified by post-translational modifications, and functioning in a given cell or organism at a specific time.

Metabolome

The complete collection of small-molecule metabolites present in a biological sample (such as serum, plasma, or urine) that reflects ongoing cellular function.

Terabase

A unit of genetic sequence measurement representing $1$ trillion base pairs ($10^{12}$ or $1{,}000{,}000{,}000{,}000$ bases).

Euchromatin

An open, loosely packed chromatin state where DNA is actively accessible to transcription machinery.

Heterochromatin

A tightly condensed chromatin state where DNA is packaged with histones and is not actively transcribed.

Histones

Basic protein complexes around which DNA winds to form nucleosomes, regulating whether chromatin is in an open or closed state.

Transcription Factors (TFs)

Proteins that recognize and bind specific DNA regulatory sequences via intermolecular hydrogen bonds to promote (activators) or repress (repressors) gene expression.

General Transcription Factors (GTFs)

Proteins that bind upstream of every eukaryotic gene at the TATA box to signal and recruit RNA polymerase to the promoter.

Promoter

A specific regulatory region of DNA located upstream of a gene that serves as the binding site for transcription factors and determines the initiation site of transcription.

RNA Polymerase

The enzyme that reads a DNA template strand in the $3' \rightarrow 5'$ direction to synthesize a complementary, antiparallel RNA transcript in the $5' \rightarrow 3'$ direction without requiring a primer.

Sigma Factor

A bacterial protein that binds the $-35$ and $-10$ boxes of the promoter region to guide prokaryotic RNA polymerase to the proper transcription start site.

Hairpin Structure

A secondary structure formed by self-complementary hydrogen bonding in bacterial mRNA, followed by a run of uracil bases, which triggers transcription termination.

Introns

Non-coding sequences within a eukaryotic pre-mRNA transcript that are excised during RNA splicing and remain in the nucleus.

Exons

Protein-coding sequences of eukaryotic genes that are spliced together during RNA processing to form mature mRNA and exit the nucleus.

Alternative Splicing

A eukaryotic post-transcriptional mechanism where exons are joined in varying combinations, allowing a single gene to encode multiple distinct protein variants.

5' Methyl-G Cap

A modified 7-methylguanosine added in a $5'\text{-to-}5'$ orientation to the $5'$ end of eukaryotic pre-mRNA to stabilize the transcript and aid in ribosome recognition.

3' Poly(A) Tail

A sequence of adenine nucleotides added to the $3'$ end of eukaryotic pre-mRNA following a poly(A) signal to enhance mRNA stability and translation efficiency.

Triplet Code

A property of the genetic code specifying that all nucleic acid 'words' (codons) are precisely three nucleotides in length.

Non-overlapping Code

A property of the genetic code where successive three-nucleotide codons are read consecutively in a single reading frame without sharing bases between adjacent codons.

Punctuated Code

A feature of the genetic code characterized by a universal start codon ($\text{AUG}$) that initiates translation and three stop codons ($\text{UAA}$, $\text{UAG}$, and $\text{UGA}$) that designate termination.

Redundant (Degenerate) Code

The property of the genetic code wherein most amino acids are specified by more than one codon.

Unambiguous Code

The property of the genetic code stating that each individual codon specifies one, and only one, amino acid.

Universal Code

A property of the genetic code establishing that the exact same codons specify the identical amino acids and stop signals across almost all living organisms.

Transfer RNA (tRNA)

An adaptor RNA molecule with a folded stem-and-loop structure that links an mRNA codon via an antiparallel anticodon to its corresponding amino acid at the $3'$ CCA attachment site.

Aminoacyl-tRNA Synthetase

An enzyme responsible for 'charging' a tRNA molecule by specifically catalyzing the covalent attachment of an amino acid to the tRNA carrying the corresponding anticodon.

Ribosome (rRNA)

A macromolecular machine consisting of large and small ribonucleoprotein subunits that mediates mRNA-tRNA base pairing and catalyzes condensation reactions to form peptide bonds.

A (Aminoacyl) Site

The binding site in the large ribosomal subunit where the anticodon of an incoming charged aminoacyl-tRNA matches and binds to its complementary mRNA codon.

P (Peptidyl) Site

The site on the large ribosomal subunit where the tRNA carrying the growing polypeptide chain is held as peptide bonds are formed.

E (Exit) Site

The site on the large ribosomal subunit where an uncharged tRNA resides briefly before dissociating from the ribosome.

Release Factor

A protein that recognizes and binds directly to a stop codon in the ribosomal A site, triggering the termination of translation and the disassembly of the ribosomal complex.

Polyribosome (Polysome)

A complex consisting of an mRNA molecule being translated simultaneously by multiple ribosomes to amplify protein synthesis.

Phosphorylation

A post-translational modification involving the addition of negative phosphate groups that alters the three-dimensional shape and function of a protein.

Glycosylation

A post-translational modification involving the covalent attachment of carbohydrate sugars to a protein, critical for molecular targeting and cellular recognition.

Proteolysis

A post-translational cleavage of the polypeptide backbone that allows the resulting protein fragments to fold into distinct, functional shapes.

Somatic Mutation

A mutation that occurs in non-germline body cells, potentially altering the individual's phenotype but incapable of being inherited by offspring.

Germ Line Mutation

A mutation occurring in reproductive gametes (egg or sperm) that is transmitted to offspring and affects all cells of future generations.

Loss-of-Function Mutation

A DNA mutation that causes the production of a nonfunctional protein or complete absence of the gene product.

Gain-of-Function Mutation

A DNA mutation that confers a novel biological function or altered catalytic activity upon the resulting protein.

Point Mutation

A gene mutation caused by the alteration, addition, or removal of a single nucleotide base pair in DNA.

Silent Mutation

A point mutation in DNA that changes the nucleotide sequence but codes for the identical amino acid due to degeneracy in the genetic code, leaving protein function unchanged.

Conservative Missense Mutation

A base substitution that replaces an amino acid with a chemically similar one (e.g., basic Lysine to basic Arginine), typically minimizing disruptions to tertiary structure.

Non-conservative Missense Mutation

A base substitution that replaces an amino acid with one possessing fundamentally different chemical properties (e.g., basic Lysine to polar Threonine), frequently changing protein folding and function.

Nonsense Mutation

A point mutation that converts an amino acid-specifying codon into a premature stop codon, terminating translation early and generating a truncated protein.

Frameshift Mutation

An insertion or deletion of nucleotides not in multiples of three within a protein-coding region, shifting the triplet reading frame and altering all subsequent downstream amino acids.

Splice Site Mutation

A DNA mutation altering consensus sequences ($5'$ donor $\text{GU}$, branch point $\text{A}$, or $3'$ acceptor $\text{AG}$) needed for snRNP binding, resulting in improper intron retention or exon skipping.