General chemistry chapter 17 &18

Gene Expression

The process by which DNA directs the synthesis of proteins (or, in some cases, just functional RNAs), serving as the link between genotype and phenotype.

One-Gene, One-Enzyme Hypothesis

The idea proposed by Beadle and Tatum that each gene contains the information needed to make a specific enzyme; later updated to the one-gene, one-polypeptide hypothesis.

Neurospora crassa

The haploid bread mold used by Beadle and Tatum to study biochemical pathways because mutating a single copy of a gene immediately reveals its phenotype.

Minimal Medium (MM)

A basic growth solution containing only essential inorganic salts, glucose, and biotin, used to identify nutritional mutants that cannot synthesize their own nutrients.

Complete Medium

A nutrient-rich growth medium supplemented with all 20 amino acids and other essential compounds, allowing nutritional mutants to survive.

Nutritional Mutants (Auxotrophs)

Cells mutated by X-rays that lack the ability to synthesize an essential nutrient and therefore cannot grow on a minimal medium without supplements.

Arginine Pathway Order

The biosynthetic sequence of molecules in Neurospora: Precursor -> Ornithine -> Citrulline -> Arginine, where each step is catalyzed by a distinct enzyme.

Class I Mutants

Neurospora mutants lacking Enzyme A; they cannot convert the precursor to ornithine, so they can grow if supplied with ornithine, citrulline, or arginine.

Class II Mutants

Neurospora mutants lacking Enzyme B; they cannot convert ornithine to citrulline, so they can grow only if supplied with citrulline or arginine.

Class III Mutants

Neurospora mutants lacking Enzyme C; they cannot convert citrulline to arginine, meaning they require arginine to grow.

Central Dogma

The molecular chain of command named by Francis Crick stating that genetic information flows unidirectionally from DNA to RNA to Protein.

Transcription

The DNA-directed synthesis of a complementary RNA molecule using information encoded in a DNA template strand.

Translation

The synthesis of a polypeptide chain using the genetic instructions carried by an mRNA molecule, converting nucleotide sequence into amino acid sequence.

Ribosome

The complex molecular machinery made of proteins and rRNAs that acts as the site of translation, facilitating the linking of amino acids.

Bacterial Compartmentalization

Lacks a nucleus, allowing translation of an mRNA molecule to begin simultaneously while transcription is still in progress.

Eukaryotic Compartmentalization

Has a nuclear envelope that separates transcription (nucleus) from translation (cytoplasm) in both space and time, requiring extensive RNA processing.

Pre-mRNA

The initial primary transcript synthesized from a protein-coding eukaryotic gene before undergoing modifications in the nucleus.

Triplet Code

The genetic instructions for a polypeptide chain written in DNA/RNA as a continuous series of nonoverlapping, three-nucleotide words.

Template Strand

The specific strand of the DNA double helix that provides the complementary pattern for assembling an RNA transcript during transcription.

Coding Strand (Nontemplate Strand)

The DNA strand that is identical in sequence to the mRNA transcript, except it contains thymine (T) instead of uracil (U).

Codon

A three-nucleotide sequence in mRNA (or along the DNA coding strand) that specifies a single amino acid or a termination signal; read 5' to 3'.

Redundancy without Ambiguity

Feature of the genetic code where multiple codons can specify the same amino acid, but no single codon ever specifies more than one amino acid.

AUG

The dual-function initiation codon that signals the start of translation and also codes for the initial amino acid methionine (Met).

Stop Codons

The three mRNA triplets (UAA, UAG, UGA) that do not code for amino acids but instead signal the termination of translation.

Reading Frame

The correct linear grouping of nucleotides in triplets that allows the cell's protein-synthesizing machinery to extract the intended genetic message.

RNA Polymerase

The enzyme that pries DNA strands apart and joins complementary RNA nucleotides together in the 5' to 3' direction to elongate an RNA transcript.

Promoter

The specific DNA nucleotide sequence where RNA polymerase attaches and initiates the first stage of transcription.

Transcription Unit

The entire stretch of downstream DNA that is transcribed into a single continuous RNA molecule.

Start Point

The exact nucleotide within the promoter region where RNA polymerase begins synthesizing the complementary mRNA transcript.

Transcription Initiation (Bacteria)

Process where a portion of the bacterial RNA polymerase directly recognizes and binds to the promoter sequence without external proteins.

Transcription Initiation (Eukaryotes)

Mediated by transcription factors binding to the promoter (such as a TATA box) to recruit and position RNA polymerase II.

Transcription Factors

A collection of proteins in eukaryotes that mediate the binding of RNA polymerase and the initiation of transcription.

TATA Box

A conserved eukaryotic DNA promoter sequence located roughly 25 nucleotides upstream of the start point, crucial for forming the transcription initiation complex.

Transcription Initiation Complex

The completed assembly of general transcription factors and RNA polymerase II firmly bound to a eukaryotic promoter.

Transcription Elongation

The moving of RNA polymerase downstream along the template strand, exposing 10-20 nucleotides at a time and adding matching RNA bases to the 3' end.

Transcription Termination (Bacteria)

Transcription runs through a terminator sequence in DNA, forming an RNA sequence that causes the polymerase to detach immediately.

Transcription Termination (Eukaryotes)

RNA polymerase II transcribes a polyadenylation signal sequence (AAUAAA), signaling nuclear proteins to cleave the pre-mRNA transcript free.

5' Cap

A modified guanine nucleotide added onto the 5' end of a eukaryotic pre-mRNA transcript to facilitate export, protect from degradation, and assist ribosome attachment.

Poly-A Tail

A sequence of 50-250 adenine nucleotides added to the 3' end of a processed eukaryotic mRNA transcript to protect it and aid in cellular export.

Untranslated Regions (UTRs)

Noncoding segments located at the 5' and 3' ends of a mature mRNA molecule that remain untranslated but function in ribosome binding and stability.

RNA Splicing

The post-transcriptional process in the eukaryotic nucleus where large noncoding regions are removed and the remaining coding regions are joined.

Introns

Intervening, noncoding segments of a primary RNA transcript that are excised and degraded during RNA splicing within the nucleus.

Exons

The coding segments of a primary transcript that remain in the processed mRNA molecule and exit the nucleus to be expressed as amino acid sequences.

Spliceosome

A massive complex of proteins and small RNAs that carries out pre-mRNA splicing by binding to intron ends, clipping them out, and joining exons together.

Ribozymes

Catalytic RNA molecules that function as enzymes; their single-stranded structure, functional groups, and hydrogen-bonding capabilities enable them to catalyze reactions.

Alternative RNA Splicing

A regulatory process where different segments of a single pre-mRNA are treated as exons, enabling a single gene to encode multiple distinct polypeptides.

Domains

Discrete structural and functional regions of a protein's modular architecture, with different exons frequently coding for different domains.

Transfer RNA (tRNA)

The translator molecule of translation that transfers a specific amino acid from the cytoplasmic pool to the growing end of a polypeptide at a ribosome.

Anticodon

A unique nucleotide triplet on a tRNA molecule that base-pairs antiparallelly with a complementary codon on an mRNA strand.

Amino Acid Attachment Site

The protruding single-stranded 3' end of a transfer RNA molecule where a specific amino acid is covalently bound.

Aminoacyl-tRNA Synthetase

A family of 20 distinct enzymes that utilizes ATP hydrolysis to catalyze the precise covalent attachment of a specific amino acid to its corresponding tRNA.

Wobble

Flexible, relaxed base-pairing rules at the third nucleotide position of an mRNA codon, explaining why some tRNAs can read more than one synonymous codon.

A Site (Aminoacyl-tRNA Binding Site)

The ribosomal binding pocket that holds the incoming tRNA carrying the next amino acid to be appended to the growing polypeptide.

P Site (Peptidyl-tRNA Binding Site)

The ribosomal pocket that holds the tRNA molecule currently attached to the growing polypeptide chain.

E Site (Exit Site)

The location on a ribosome where discharged, empty tRNAs lose their affinity and are released back into the cytoplasm.

Ribosome Assembly / Initiation

Step where a small subunit binds mRNA and an initiator tRNA at the AUG codon, followed by a large subunit attaching via GTP energy expenditure.

Translation Elongation Cycle

A rapid three-step mechanism: (1) Codon recognition requiring GTP, (2) Peptide bond formation catalyzed by rRNA, and (3) Translocation requiring GTP.

Peptide Bond Catalyst

Ribosomal RNA (rRNA) in the large subunit acts as a ribozyme to link the amino end of the new amino acid to the carboxyl end of the growing chain.

Translation Termination

A stop codon reaches the A site, recruiting a release factor protein that triggers a water molecule addition to hydrolyze and free the completed polypeptide.

Release Factor

A protein shaped like an aminoacyl tRNA that binds directly to a stop codon in the A site to terminate translation through hydrolysis.

Polyribosomes (Polysomes)

Clusters of multiple ribosomes simultaneously translating a single mRNA molecule, enabling a cell to quickly mass-produce polypeptides.

Point Mutation

A small-scale genetic change involving an alteration in just a single nucleotide pair of a gene.

Sickle-Cell Point Mutation

A point mutation in the beta-globin gene where a single nucleotide pair substitution changes a GAG codon to GUG, substituting Valine for Glutamic acid.

Silent Mutation

A single nucleotide-pair substitution that alters a codon but, due to genetic code redundancy, still translates into the exact same amino acid.

Missense Mutation

A nucleotide substitution that alters a codon, changing one amino acid to another, which can range from neutral to destructive to protein function.

Nonsense Mutation

A point mutation that prematurely converts an amino acid codon into a stop codon, terminating translation early and producing a truncated, nonfunctional protein.

Frameshift Mutation

An insertion or deletion of nucleotides that is not a multiple of three, altering the downstream reading frame and producing extensive missense and nonsense.