Genomics, Proteomics, Systems Biology, and Protein Synthesis

Vocabulary practice flashcards covering key genomics, proteomics, systems biology, translation, and protein regulation concepts.

Open Reading Frame (ORF)

A long stretch of nucleotide sequence that lacks all three stop codons ($\text{TAA}$, $\text{TAG}$, and $\text{TGA}$) and can potentially encode a polypeptide.

Human Genome Project

An international effort that published the preliminary sequence of the human genome in 2001, costing approximately $3\text{ billion USD}$ and taking about $11\text{ years}$ to complete.

Noncoding RNA Correlation to Complexity

The principle that while the number of protein-coding genes remains relatively constant among multicellular organisms, the number of miRNA-coding and lncRNA-coding genes increases significantly with organismal complexity.

Next-Generation Sequencing (NGS)

A high-throughput DNA sequencing technology where fragmented DNA with attached adapters is bound to a flow cell, amplified, and sequenced simultaneously using fluorophore-conjugated nucleotides.

Genome-Wide Association Studies (GWAS)

An approach that compares the genomes of thousands of individuals in a population with and without a specific phenotype or disease to identify genetic differences associated with that trait.

DNA Microarray

A hybridisation-based tool used to analyze gene expression by hybridising fluorescently labeled cDNAs to known DNA sequences immobilized on a glass slide or chip.

RNA-seq

A technique that uses next-generation sequencing to quantify total RNA transcript accumulation and frequency in a sample, enabling analysis of both known and unpredicted genes.

Proteomics

The large-scale systematic study of the complete set of proteins expressed in a given cell, tissue, or organism, which is called the proteome.

Mass Spectrometry

An analytical method used in proteomics to identify proteins by digesting them into peptides, ionizing them, and measuring their mass-to-charge ratios.

Tandem Mass Spectrometry

An advanced mass spectrometry technique where individual peptides are partially degraded by random breakage, allowing their specific amino acid sequences to be determined.

Yeast Two-Hybrid (Y2H) System

A molecular assay that detects protein-protein interactions by fusing a protein of interest to a Gal4 DNA-binding domain (DBD) and a candidate protein library to a Gal4 activation domain (AD) to drive reporter gene transcription.

CLIP-seq

Cross-linking and immunoprecipitation followed by sequencing, a method that uses UV light to cross-link proteins to associated RNA molecules to identify target RNAs bound by specific proteins.

Bioinformatics

An interdisciplinary field combining biology and computer science to perform computational analyses of large genomic, proteomic, and transcriptomic datasets.

Conserved Regulatory Pathways

Short regulatory DNA sequences that are conserved across distinct species, linking them to a common evolutionary ancestor.

Feedforward Relay

A network motif in signaling pathways where an upstream element stimulates a downstream target directly while also activating an intermediate component that stimulates the same target.

Crosstalk

The interaction between components of two distinct signaling pathways, which can result in either stimulatory or inhibitory regulation.

Synthetic Biology

A biological discipline focused on designing and constructing new biological parts, devices, and systems, or redesigning existing natural biological systems.

Codon

A sequence of three nucleotides in mRNA that specifies a particular amino acid or signals translation termination.

tRNA (Transfer RNA)

An adaptor RNA molecule approximately $70\text{ to }80$ nucleotides long that carries a specific amino acid to the ribosome during translation by base pairing with an mRNA codon.

Anticodon

A three-nucleotide sequence on the anticodon loop of a tRNA that forms complementary base pairs with a corresponding codon on an mRNA strand.

Aminoacyl tRNA Synthetases

A family of enzymes that covalently attach specific amino acids to their corresponding tRNA molecules in a reaction requiring ATP.

Ribosomes

Large complexes of rRNAs and proteins responsible for carrying out translation, designated as $70S$ in prokaryotes ($50S$ and $30S$ subunits) and $80S$ in eukaryotes ($60S$ and $40S$ subunits).

5' Untranslated Region (5' UTR)

The region of an mRNA molecule upstream of the initiation codon ($\text{AUG}$) that is not translated into a polypeptide.

3' Untranslated Region (3' UTR)

The noncoding sequence of an mRNA molecule located downstream of the translation stop codon.

Shine-Dalgarno Sequence

A sequence in bacterial mRNA upstream of the start codon that pairs with the $16S$ rRNA to align the ribosome at the correct initiation site.

Cap-Dependent Translation

The standard mechanism of eukaryotic translation initiation in which initiation factors recruit the $40S$ ribosomal subunit to the $5'$ $m^7G$ cap, followed by scanning for the start codon.

Eukaryotic Initiation Factors (eIFs)

A set of non-ribosomal proteins required for the assembly of the initiation complex and ribosomal scanning during eukaryotic translation.

Internal Ribosome Entry Site (IRES)

A structural region within certain mRNAs that allows the ribosome to initiate translation internally, independently of the $5'$ cap structure.

Eukaryotic Elongation Factors (eEFs)

Proteins such as eEF1$\alpha$ and eEF2 that assist in bringing aminoacyl-tRNAs to the ribosome and driving ribosome translocation along mRNA.

Aminoacyl (A) Site

The ribosomal binding site that accepts incoming charged aminoacyl-tRNA molecules during polypeptide elongation.

Peptidyl (P) Site

The ribosomal site containing the tRNA attached to the growing polypeptide chain.

Exit (E) Site

The ribosomal site that holds uncharged tRNAs before they are released from the ribosome.

Release Factors

Proteins that recognize translation stop codons ($\text{UAA}$, $\text{UAG}$, or $\text{UGA}$) in the A site, triggering hydrolysis and release of the completed polypeptide chain.

Polysome

A complex formed when multiple ribosomes simultaneously translate a single mRNA molecule.

RNA Interference (RNAi)

A cellular regulatory mechanism where short double-stranded RNA molecules inhibit gene expression by repressing translation or degrading target mRNAs.

microRNAs (miRNAs)

Endogenous small noncoding RNAs that bind to RISC complexes and pair with complementary sequences in target mRNAs to inhibit translation and promote mRNA cleavage or deadenylation.

Chaperones

Proteins that bind and stabilize unfolded or partially folded polypeptide chains during translation and transport, preventing nonproductive folding or aggregation without altering final native conformation.

Amyloids

Fibrous protein aggregates with characteristic secondary structure formed by misfolded proteins, associated with neurodegenerative diseases like Alzheimer's and Parkinson's.

Prions

Infectious misfolded proteins capable of converting normally folded cellular proteins ($PrP^C$) into the pathogenic misfolded amyloid state ($PrP^{Sc}$).

Proteolysis

The enzymatic cleavage of a polypeptide chain, required for removing N-terminal methionine residues or converting inactive precursor proteins (such as preproinsulin) into functional forms.

Glycosylation

The post-translational attachment of carbohydrate chains to proteins, yielding glycoproteins via N-linkages (to asparagine) or O-linkages (to serine or threonine).

GPI Anchor

A glycolipid attached to the C-terminus of a protein that anchors the protein to the extracellular face of the cell membrane.

Guanine Nucleotide Exchange Factors (GEFs)

Enzymes that activate regulatory G proteins by promoting the exchange of bound GDP for GTP.

GTPase-Activating Proteins (GAPs)

Proteins that stimulate the intrinsic GTPase activity of G proteins, hydrolyzing bound GTP to GDP to convert them back to their inactive state.

Serine/Threonine Kinases

Enzymes that regulate protein function by transferring a phosphate group from ATP to the hydroxyl side chains of serine or threonine residues.

Tyrosine Kinases

Enzymes that transfer a phosphate group from ATP specifically onto tyrosine residues of target proteins.

Protein Phosphatases

Enzymes that reverse the action of protein kinases by catalyzing the removal of phosphate groups from specific amino acid residues.

Ubiquitin-Proteasome Pathway

The primary eukaryotic pathway for targeted intracellular protein degradation, in which ubiquitin is sequentially activated and conjugated to target proteins by E1, E2, and E3 enzymes prior to degradation.

Proteasome

A large cylindrical protein complex in eukaryotic cells that recognizes polyubiquitinated proteins and degrades them into small peptides in an ATP-dependent manner.