Foundations of Biology 2 - Gene Expression, Epigenetics, Phylogenies, and Translation

Vocabulary practice flashcards generated from the Foundations of Biology 2 study guide covering gene expression, epigenetics, phylogenies, and translation.

Heterochrony

A mechanism controlling morphology that regulates the time, duration, or timing of gene expression during development.

Heterotropy

A mechanism controlling morphology that regulates the spatial location where a gene is expressed.

Heterometry

A mechanism controlling morphology that regulates the amount of gene product expressed in a given area.

Pre-transcriptional Control

Gene expression regulation occurring prior to transcription, primarily through DNA modifications such as acetylation and methylation.

Transcriptional Control

Regulation of gene expression at the transcription level using promoters, transcription factors, enhancers, and silencers.

Post-transcriptional Control

Regulation of gene expression occurring after transcription, including alternative splicing and mRNA tags.

Pre-translational Control

Gene expression regulation mechanisms that delay or prevent the translation of mRNA into protein.

Post-translational Control

Gene expression regulation that modifies or degrades proteins after synthesis, such as applying protein tags for destruction.

Transcription Factors

Proteins that regulate gene expression (usually turning genes on) and are themselves regulated by other transcription factors, extracellular signals, or environmental stimuli.

Basal Transcription Apparatus

The core assembly of general transcription factors and RNA polymerase required to initiate eukaryotic transcription at the promoter.

TFIID

A general transcription factor that recognizes and binds directly to the promoter sequence (usually TATAAA).

TFIIB

A general transcription factor that binds to the promoter to line up and ensure correct binding of TFIID.

TFIIF

A general transcription factor similar to a sigma factor that binds RNA polymerase and links it to TFIID.

TFIIE

A general transcription factor that improves RNA polymerase function and assists in undoing DNA bonds.

TFIIH

A general transcription factor that helps unwind DNA bonds and enhances RNA polymerase function during transcription.

Specific Transcription Factors

Regulatory proteins that bind to enhancers or silencers located adjacent to or far from the promoter to modulate transcription rates.

Enhancers

Regulatory DNA sequences that act as switches to turn on or increase transcription, often functioning at a distance from the promoter via mediator proteins.

Silencers

Regulatory DNA sequences that act as switches to turn off or decrease transcription.

Mediator Protein

A protein that connects enhancers or silencers to the promoter by bending DNA, enabling distant regulatory elements to modulate transcription.

Weak Binding Affinity

A characteristic of specific transcription factors where single nucleotide mutations can significantly alter binding affinity, potentially resulting in developmental changes like extra limbs.

Structural Motifs

3D structural shapes within DNA-binding proteins that allow transcription factors to recognize and bind specific DNA sequences.

Helix-turn-helix

A structural motif in DNA-binding proteins designed to fit precisely into the major groove of DNA.

Major Groove

The larger of the two grooves in the DNA double helix where structural motifs like the helix-turn-helix insert to interact with bases.

Zinc Finger

A structural motif characterized by a finger-like shape consisting of a helix, a turn around a zinc molecule, and a beta-pleated sheet.

Alternative Splicing

A post-transcriptional process where exons are selectively retained or removed from pre-mRNA to generate distinct protein structures and functions.

miRNA (MicroRNA)

Small non-coding RNA molecules derived from DNA that mediate post-transcriptional gene inhibition.

siRNA (Small Interfering RNA)

Double-stranded RNA molecules that trigger mRNA degradation as a mechanism of post-transcriptional regulation.

Cross-Kingdom RNA Interference

A process utilizing siRNAs through which organisms, such as plants, regulate the microbiome of another kingdom.

Ubiquitin

A regulatory protein tag that attaches to target proteins to mark them for cellular destruction.

Lysine

The amino acid residue on target proteins to which ubiquitin binds during post-translational protein degradation.

Chromatin

The complex of DNA and histone proteins found in eukaryotic cells prior to full chromosome coiling.

Histones

Proteins with 8 tail regions around which DNA winds to form chromatin structures.

Histone Tails

N-terminal amino acid tails extending from histones that undergo modifications like acetylation to regulate DNA packing.

Acetylation

The addition of an acetyl group to histone tails, which neutralizes their positive charge, loosens DNA binding, and permits gene expression.

Chromatin Remodeling

Structural alterations to chromatin, such as histone acetylation, that modulate physical access to DNA for transcription.

DNA Methylation

The covalent addition of methyl groups ($\text{CH}_3$) to cytosine residues adjacent to guanines, typically repressing gene expression.

5-methyl Cytosine (5mC)

The modified cytosine base produced when a methyl group is added to cytosine by DNA methyltransferase.

DNA Methyltransferase (DNMT)

An enzyme responsible for adding methyl groups to cytosine bases in DNA.

Demethylase

An enzyme that removes methyl groups from methylated DNA bases.

Royal Jelly Epigenetic Effect

Dietary regulation in bees where feeding royal jelly to a female larva alters DNA methylation patterns, rendering her fertile as a queen.

Vertical Heritability of Methylation

The transmission of specific DNA methylation patterns directly from parent organisms to offspring.

Embryonic Demethylation

The process during early embryonic development where most parental methyl groups are stripped off, though some persist to be inherited.

Överkalix Study

A study showing that a grandfather experiencing famine as a teenager lowers the risk of cancer, cardiovascular disease, and diabetes in his grandson.

Grandparental Smoking Asthma Effect

An epigenetic trend where exposure to cigarette smoke as a tween increases asthma risk in grandchildren from $40\%$ up to $70\%$ if the father also smoked.

Grandparental Education Effect on Biological Age

An epigenetic phenomenon where lower educational status in grandparents correlates with faster biological aging (methylation changes) in descendants.

Seminal Fluid Methylation Effect

An experimental outcome in mice showing that nocturnal feeding alters seminal fluid methylation patterns, transmitting an altered enzyme phenotype to offspring.

Phylogenetic Tree

A diagram representing evolutionary relationships among various organisms based on common ancestry.

Node

A divergence point on a phylogenetic tree representing a common ancestor where lineages split.

Taxon (Tips)

The entity or organism group located at the tip of a phylogenetic branch.

Most Recent Common Ancestor (MRCA)

The most recent ancestral lineage from which two or more species directly evolved on a phylogenetic tree.

Clade

A monophyletic group consisting of a single common ancestor and ALL of its descendants.

Derived Traits

Traits present in a lineage that arose after splitting off from a common ancestor.

Ancestral Traits

Traits inherited from an older common ancestor present in both ancestral and descendant lineages.

Monophyletic Group

A phylogenetic grouping that includes an ancestor and all of its descendants, synonymous with a clade.

Paraphyletic Group

A phylogenetic grouping that includes a common ancestor and some, but not all, of its descendants.

Polyphyletic Group

A phylogenetic grouping of organisms that lacks a recent common ancestor, often assembled based on shared convergent traits.

Convergent Evolution

The independent evolution of similar features in distinct lineages due to similar environmental pressures rather than shared ancestry.

Analogous Traits

Structures or traits that perform similar functions and appear similar but evolved independently through convergent evolution.

Homologous Traits

Traits shared by different species because they were inherited directly from a common ancestor.

Polyphyletic Grouping of Eyes

The classification formed by grouping all species with eyes, reflecting that eyes evolved independently at least $40\text{--}65$ times.

Mature mRNA

The processed mRNA strand ready for translation after pre-transcriptional splicing and modification.

Initiation (Translation Stage 1)

The step where the small ribosomal subunit binds mRNA, locates the start codon, recruits methionine tRNA, and assembles with the large subunit.

5' Cap (Eukaryotic Translation)

The eukaryotic mRNA modification recognized and bound by the small ribosomal subunit during translation initiation.

Shine-Dalgarno Sequence

The prokaryotic mRNA sequence recognized and bound by the small ribosomal subunit to initiate translation.

Methionine (Met)

The initiator amino acid brought by tRNA that binds the start codon during translation initiation.

Start Codon ($5'\text{ AUG}$)

The specific mRNA codon sequence located by the small subunit to specify the beginning of translation.

Small Ribosomal Subunit

The ribosomal component that first binds the mRNA strand at the $5'$ cap or Shine-Dalgarno sequence to locate the start codon.

Large Ribosomal Subunit

The ribosomal component recruited by methionine and the small subunit complex to complete functional ribosome assembly.

Elongation (Translation Stage 2)

The process where the ribosome moves along mRNA, recruiting charged tRNAs to sequentially add amino acids to the growing polypeptide chain.

Charged tRNA

A transfer RNA molecule physically attached to its corresponding amino acid.

Uncharged tRNA

A transfer RNA molecule lacking an attached amino acid after its amino acid has been linked to the peptide chain.

A (aminoacyl) Site

The ribosomal entry/recruiter site that receives incoming charged aminoacyl-tRNAs.

P (peptidyl) Site

The ribosomal site that catalyzes peptide bond formation between amino acids and holds the growing peptidyl-tRNA in place.

E (exit) Site

The ribosomal site where uncharged tRNAs are released from the ribosome complex.

Termination (Translation Stage 3)

The final translation stage triggered when a stop codon reaches the A site, recruiting a release factor protein to disassemble the complex.

STOP Codon

An mRNA codon that lacks an associated tRNA, instead signaling for release factor protein binding.

Release Factor Protein

A protein that binds to the stop codon in the A site and knocks off the tRNA and polypeptide chain.

Polypeptide Chain Disassembly

The release of the completed amino acid chain and subsequent breakdown of the ribosomal subunits following release factor action.

TATA Box (TATAAA)

A conserved promoter consensus sequence recognized and bound by TFIID during basal transcription complex assembly.

Cortisol Gene Regulation Example

An example of an extracellular/environmental signal causing immediate stress responses that induce specific transcription factors and subsequent proteins.

Biological Age Epigenetics

Epigenetic methylation status influenced by ancestral socio-economic/educational factors, affecting individual aging speed.

TTN Gene

The human gene containing 364 exons that encodes the muscle contraction protein titin.

Titin Structural Diversity

Variations in muscle elasticity and stiffness created by alternative splicing of the 364 exons in TTN mRNA transcripts.

Giraffe Neck Heterochrony

The phenomenon where giraffe neck vertebrae spend a longer duration growing compared to human neck vertebrae, yielding longer necks.

Chick vs. Duck Hindlimb Example

A comparative evolutionary example used to illustrate morphological control through differential gene expression.

Bird Beak Morphology Control

A developmental example demonstrating how changes in regulatory processes (heterochrony, heterotropy, heterometry) dictate beak shape.

Mediator Denaturation in Heat

The loss of functional mediator protein structure at high temperatures, preventing enhancer-promoter looping and lowering transcription rates.

Polydactyly via Enhancer Mutation

A condition resulting from a single nucleotide mutation in a distant enhancer that alters TF binding affinity and leads to extra digits.

Sigma Factor Function Analogy

The structural role analogous to TFIIF in prokaryotes, helping target RNA polymerase to promoter regions.

Sharks and Whales Grouping

A polyphyletic taxon grouping because their shared aquatic morphology stems from convergent evolution rather than common ancestry.

Cytosine to Thymine Mutation via Methylation

A mutational path where cytosines are methylated to 5-methylcytosine ($5\text{mC}$), which can subsequently transition into thymine.

P-site Peptide Bond Catalysis

The biochemical reaction driven at the P site that links the carboxyl group of the current amino acid chain to the incoming amino acid.

Disassembly of Translation Players

The post-termination state where components are initially present separately and eventually degraded or recycled.

Phylogenetic Tip Accuracy Limitation

The principle that taxa tips alone do not reliably indicate detailed genetic relationships without analyzing nodes and MRCAs.

Introns

Non-coding pre-mRNA sequences that are spliced out prior to translation.

Exons

Coding mRNA sequences that remain after splicing to be translated into protein.

Translation Diagram: Meet the Players

The key molecular components involved in translation, including mRNA, tRNA, charged tRNA, ribosomes, single amino acids, amino acid chains, and release factors.

Translation Diagram: Initiation Stage

Diagram illustrating small subunit binding to mRNA, methionine recruitment, and subsequent large subunit attachment.

Translation Diagram: Elongation Stage

Diagram depicting codon reading across the E, P, and A sites to construct an amino acid chain.

Translation Diagram: Termination Stage

Diagram showing stop codon recognition, release factor recruitment, tRNA/polypeptide detachment, and subunit disassembly.