Exam 3 Review: Nucleic Acids, Gene Expression, Protein Degradation, and Biophysical Methods

Comprehensive vocabulary flashcards covering Exam 3 review topics including nucleic acids, gene expression control, protein turnover, ChIP-seq, ATAC-seq, molecular dynamics, atomic force microscopy, and HDX mass spectrometry.

Deoxyribonucleic acid (DNA)

A nucleic acid that stores hereditary information, usually consisting of two complementary strands forming a double helix.

Ribonucleic acid (RNA)

A nucleic acid involved in gene expression and other cellular functions, usually single-stranded but capable of folding into complex structures.

Deoxyribose

The five-carbon sugar in DNA whose $2'$ carbon has a hydrogen atom instead of a hydroxyl (–OH) group.

Ribose

The five-carbon sugar in RNA whose $2'$ carbon contains a hydroxyl (–OH) group.

Nucleoside

A nitrogenous base attached to a sugar, without a phosphate group (for example, adenosine).

Nucleotide

A nucleoside with one or more phosphate groups attached, serving as the building blocks of DNA and RNA.

Pyrimidine

A nitrogenous base with one ring, including cytosine, thymine, and uracil.

Purine

A nitrogenous base with two fused rings, including adenine and guanine.

Central dogma

The general flow of genetic information: DNA → RNA → protein.

Phosphodiester bond

A covalent bond connecting nucleotides in the sugar-phosphate backbone, linking the $3'\text{-OH}$ of one sugar to a phosphate associated with the $5'$ position of the next sugar.

N-β-glycosidic bond

The bond connecting a nitrogenous base to the $1'$ carbon of its sugar, connecting to N-$9$ in purines and N-$1$ in pyrimidines.

Watson-Crick base pairing

Specific complementary pairing between bases where A pairs with T in DNA or U in RNA, and G pairs with C.

Stem-loop

A structure formed when complementary sequences within a single nucleic acid strand pair to create a double-stranded stem and an unpaired loop.

Semiconservative replication

DNA replication in which each daughter DNA molecule contains one original parental strand and one newly synthesized strand.

Melting temperature ($T_m$)

The temperature at which half of the DNA double-helical structure has separated into single strands under specified conditions.

Antiparallel strands

DNA strands that run in opposite directions: one $5' \rightarrow 3'$ and the other $3' \rightarrow 5'$.

Template strand

The DNA strand read by a polymerase to make a complementary DNA or RNA strand.

Primer

A short nucleic acid strand that provides a free $3'\text{-OH}$ group for DNA polymerase to extend.

Retrovirus

A virus that uses reverse transcriptase to make DNA from its RNA genome, which can then integrate into the host genome.

Messenger RNA (mRNA)

RNA that carries coding information from DNA to ribosomes for protein synthesis.

Transfer RNA (tRNA)

RNA that carries a specific amino acid to the ribosome and uses its anticodon to recognize an mRNA codon.

Ribosomal RNA (rRNA)

RNA that combines with proteins to form ribosomes and participates in protein synthesis.

Transcription

The synthesis of RNA using DNA as a template.

Promoter site

A DNA sequence where transcription machinery binds to initiate transcription.

Codon

A sequence of three nucleotides in mRNA that specifies an amino acid or a translation stop signal.

Anticodon

A three-nucleotide sequence in tRNA that pairs with a complementary mRNA codon.

Aminoacyl-tRNA

A tRNA attached to its correct amino acid; also called a charged tRNA.

Genetic code

The rules that relate mRNA codons to amino acids or stop signals.

Stop codon

A codon that signals the termination of translation rather than specifying an amino acid, specifically UAA, UAG, and UGA.

Codon bias

The tendency of an organism to use certain synonymous codons more frequently than others.

Ribosome

A molecular complex of rRNA and proteins that translates mRNA into a polypeptide.

Shine-Dalgarno sequence

A ribosome-binding sequence in many bacterial mRNAs that helps position the ribosome at the correct translation start site.

Operon

A group of bacterial genes controlled by a shared regulatory region and often transcribed together into one mRNA.

Operator site

A regulatory DNA sequence where a repressor can bind to control transcription.

Repressor

A protein that decreases gene transcription by interfering with transcription machinery or access to DNA.

Inducer

A molecule that increases gene expression, often by binding to a repressor and reducing its ability to bind DNA.

Corepressor

A molecule that binds to a repressor and helps it bind DNA or become active, thereby decreasing transcription.

β-galactosidase

An enzyme encoded by lacZ that breaks lactose into glucose and galactose, and can also produce allolactose from lactose.

Lac repressor

The protein encoded by lacI that binds the lac operator and represses transcription when lactose is absent.

DNA major groove

The wider groove of the DNA double helix whose exposed chemical patterns allow proteins to recognize specific DNA sequences.

DNA minor groove

The narrower groove of the DNA double helix that proteins can interact with, providing a different pattern of chemical information than the major groove.

Helix-turn-helix motif

A DNA-binding structure containing two α-helices separated by a tight turn, in which one helix often recognizes DNA bases in the major groove.

X-gal

A synthetic β-galactosidase substrate that produces a blue product when cleaved, used in reporter assays and blue-white screening.

Chromatin

DNA associated with histones and other proteins in eukaryotic cells, whose organization affects DNA accessibility and gene expression.

Homeodomain

A DNA-binding domain of about $60$ amino acids commonly found in developmental transcription factors, containing a helix-turn-helix-like structure.

Basic-leucine zipper (bZIP) proteins

Transcription factors with a basic region that binds DNA and a leucine zipper that helps two protein subunits join together.

Cys₂His₂ zinc-finger domains

DNA-binding domains in which cysteine and histidine residues coordinate a zinc ion, stabilizing a finger-like structure that can recognize DNA.

Transcription factor

A protein that binds DNA or interacts with transcription machinery to activate or repress transcription.

DNA-binding domain

The portion of a protein responsible for recognizing or binding DNA.

Activation domain

A protein region that stimulates transcription by interacting with coactivators, Mediator, or transcription machinery.

Mediator

A multiprotein complex that helps transmit regulatory signals from transcription factors to RNA polymerase II and the transcription machinery.

Pre-initiation complex

The group of proteins assembled at a eukaryotic promoter before transcription begins, including RNA polymerase II and general transcription factors.

Nuclear hormone receptor

A receptor that binds a hormone or other ligand and regulates gene transcription, often by interacting with DNA and regulatory proteins.

Coactivator

A protein or protein complex that increases transcription but generally does not recognize the target DNA sequence by itself.

Histone acetyltransferase (HAT)

An enzyme that adds acetyl groups to histone proteins, commonly weakening histone–DNA attraction and promoting transcriptional accessibility.

IPTG

A synthetic β-galactoside that induces the lac system by binding the lac repressor and reducing its ability to bind the operator.

Ubiquitin

A small protein that can be covalently attached to other proteins, often marking them in polyubiquitin chains for degradation by the proteasome.

Degron

A sequence or structural feature in a protein recognized by the degradation machinery that helps determine whether and when the protein is degraded.

Proteasome

A large protein complex (including the $26\text{S}$ proteasome) that recognizes many polyubiquitinated proteins, unfolds them using ATP, and feeds them into a catalytic core to degrade them into smaller peptides.

E1 (ubiquitin-activating enzyme)

An enzyme that uses ATP to activate ubiquitin in the protein degradation pathway.

E2 (ubiquitin-conjugating enzyme)

An enzyme that receives activated ubiquitin from E1 and carries it to the next step of ubiquitination.

E3 (ubiquitin ligase)

An enzyme that recognizes the target protein and facilitates ubiquitin transfer, providing much of the system's target specificity.

ChIP-seq

Chromatin immunoprecipitation followed by sequencing; a method that identifies genomic regions associated with a particular DNA-binding protein or histone modification.

ATAC-seq

Assay for Transposase-Accessible Chromatin using sequencing; a method that identifies regions of chromatin that are accessible to the transposase enzyme.

Tn5 transposase

An enzyme that inserts sequencing adapters into accessible DNA while cutting it into fragments during tagmentation.

Tagmentation

The combined process of cutting accessible DNA into fragments and tagging them with sequencing adapters using Tn5 transposase.

Molecular dynamics (MD)

A computational method that simulates the movement of atoms over time by calculating the forces acting on them and applying the laws of motion.

Force field

A mathematical model used to calculate a molecule's potential energy and the forces acting on its atoms.

Potential energy

Energy associated with the positions and interactions of atoms in a molecular system.

Lennard-Jones potential

A mathematical function describing short-range repulsion and longer-range attraction between nonbonded atoms, commonly used to model van der Waals interactions.

Electrostatic interactions

Interactions between charged or partially charged atoms calculated via Coulomb's law ($U(r) = \frac{1}{4\times\tau\times\text{vacuum permittivity}}\frac{q_i q_j}{r}$ or $U(r) = \frac{1}{4\times\text{constants}}\frac{q_i q_j}{r}$), where opposite charges attract and like charges repel.

Van der Waals interactions

Weak, short-range interactions between atoms arising from their electron distributions, including dispersion attractions and repulsion at very short distances.

Bond stretching

Changes in the distance between two covalently bonded atoms.

Bond bending

Changes in the angle formed by three bonded atoms.

Bond torsion

Rotation around a bond described by the dihedral angle formed by four atoms, where torsional energy helps determine preferred conformations.

Atomic force microscopy (AFM)

A microscopy technique that scans a sharp probe over a sample surface and detects interactions between the probe and sample to map surface properties.

Cantilever

A small flexible beam that holds the AFM tip, bending or moving in response to forces acting on the tip.

Topographic image

A map representing the surface's height or shape as the AFM probe scans across it.

Mass spectrometry

An analytical technique that measures the mass-to-charge ratio ($m/z$) of ions to help determine molecular masses and characterize molecules.

Deuterium

A stable isotope of hydrogen that contains one proton and one neutron, represented by D or $^{2}\text{H}$.

Hydrogen-deuterium exchange (HDX)

The replacement of exchangeable hydrogen atoms in a molecule with deuterium from the surrounding solvent, usually heavy water ($\text{D}_2\text{O}$).

Solvent accessibility

The degree to which parts of a molecule are exposed to surrounding solvent rather than buried within the structure or protected by interactions.

Backbone amide hydrogens

Hydrogens attached to backbone nitrogen atoms in peptide bonds, serving as the main structural readout in conventional protein HDX-MS.