Gene Expression and Regulation

Nucleotide

the monomer of nucleic acids; made of a phosphate, a five-carbon sugar, and a nitrogenous base.

Five-carbon sugar

the pentose sugar in a nucleotide (deoxyribose in DNA, ribose in RNA).

Phosphate

the phosphate group of a nucleotide; forms the backbone and gives nucleic acids a negative charge.

Nitrogenous base

the part of a nucleotide that carries the genetic code (A, T/U, C, G).

Deoxyribose

the five-carbon sugar in DNA; lacks one oxygen compared to ribose.

Ribose

the five-carbon sugar in RNA.

Adenine

a purine base; pairs with thymine (DNA) or uracil (RNA).

Guanine

a purine base; pairs with cytosine.

Cytosine

a pyrimidine base; pairs with guanine.

Thymine

a pyrimidine base found in DNA; pairs with adenine.

Uracil

a pyrimidine base found in RNA (replaces thymine); pairs with adenine.

Phosphodiester bonds

the covalent bonds linking the sugar of one nucleotide to the phosphate of the next, forming the backbone.

Double helix

the twisted-ladder shape of DNA, with two strands wound around each other.

Watson, Crick, and Franklin

scientists who determined DNA's double-helix structure; Rosalind Franklin's X-ray diffraction images were key evidence.

Base pairing

the rule that specific bases bond together: A–T (or A–U) and G–C.

Complementary

describing two strands whose bases pair up along their length (one strand's sequence dictates the other's).

Antiparallel

the two DNA strands run in opposite directions (one 5′→3′, the other 3′→5′).

Hydrogen bonds

weak bonds holding the base pairs together (2 between A–T, 3 between G–C); easily separated for replication.

Gene

a segment of DNA that codes for a functional product (protein or RNA).

Genome

the complete set of an organism's DNA.

Chromosome

a long DNA molecule wound with proteins; carries many genes.

Histone

a protein that DNA wraps around to help package it.

Nucleosome

the basic packing unit: DNA wrapped around a cluster of histones ("beads on a string").

Euchromatin

loosely packed, accessible chromatin; genes here are generally active/expressed.

Heterochromatin

tightly packed chromatin; genes here are generally inactive/silenced.

DNA replication

the semiconservative copying of DNA before cell division.

Semiconservative

each new DNA molecule keeps one original strand and one new strand.

Origins of replication

specific sites where replication begins (many in eukaryotes).

Replication fork

the Y-shaped region where DNA is unwound and copied.

Helicase

the enzyme that unwinds and separates the two DNA strands.

Topoisomerase

the enzyme that relieves tension/supercoiling ahead of the replication fork.

RNA primase

the enzyme that lays down the RNA primer to start synthesis.

RNA primer

a short RNA sequence that provides a 3′ end for DNA polymerase to build on.

DNA polymerase

the enzyme that adds new nucleotides 5′→3′ and proofreads the new strand.

Leading strand

the strand synthesized continuously toward the replication fork.

Lagging strand

the strand synthesized discontinuously, away from the fork, in fragments.

Okazaki fragments

the short DNA pieces of the lagging strand, later joined together.

DNA ligase

the enzyme that seals gaps between fragments, joining them into one strand.

Telomeres

repetitive protective caps at chromosome ends that shorten with each division.

Central Dogma of Biology

the flow of genetic information: DNA → RNA → protein.

Transcription

making an RNA copy of a gene from a DNA template (in the nucleus).

Translation

building a protein from an mRNA sequence at the ribosome.

Messenger RNA (mRNA)

RNA that carries the genetic code from DNA to the ribosome.

Ribosomal RNA (rRNA)

RNA that (with proteins) makes up the ribosome.

Transfer RNA (tRNA)

RNA that carries amino acids to the ribosome and matches them to codons.

RNA polymerase

the enzyme that builds RNA from a DNA template during transcription.

Promoter

the DNA region upstream of a gene where RNA polymerase binds to begin transcription.

Start site

the specific spot where transcription actually begins.

Antisense / non-coding / minus / template strand

the DNA strand that RNA polymerase reads to build the RNA.

Sense / coding strand

the DNA strand with the same sequence as the mRNA (except T→U); not read directly.

Polycistronic transcript

one mRNA that codes for multiple proteins (common in prokaryotes/operons).

Monocistronic transcript

one mRNA that codes for a single protein (typical in eukaryotes).

Introns

non-coding sequences ("intervening") removed from pre-mRNA.

Exons

coding sequences ("expressed") that are kept and joined together.

Splicing

removing introns and joining exons to make mature mRNA.

Spliceosome

the complex of RNA and protein that carries out splicing.

5′ GTP cap

a modified guanine cap added to the 5′ end of mRNA; protects it and aids ribosome binding.

Poly(A) tail

a string of adenines added to the 3′ end of mRNA; protects it and helps export.

Codon

a three-nucleotide sequence in mRNA that codes for one amino acid (or a stop signal).

Anticodon

the three-nucleotide sequence on tRNA that pairs with a codon.

Start codon

AUG; signals the start of translation and codes for methionine.

Stop codons

UAA, UAG, UGA; signal the end of translation (code for no amino acid).

Wobble pairing

flexibility in the third base of a codon–anticodon match, letting one tRNA read several codons.

Initiation

the start of translation: ribosome, mRNA, and initiator tRNA assemble at the start codon.

Elongation

adding amino acids one by one as the ribosome moves along the mRNA.

Termination

ending translation when a stop codon is reached and the polypeptide is released.

A site, P site, E site

the three ribosome sites: A (accepts incoming tRNA), P (holds the growing chain/peptide bond forms), E (exit for empty tRNA).

Pre-transcriptional regulation

control of gene expression before transcription, e.g., by chromatin structure.

Transcription factors

proteins that bind DNA to turn transcription up or down.

Epigenetic changes

heritable changes in gene expression (e.g., DNA methylation, histone modification) that don't alter the DNA sequence.

Operon

a cluster of genes controlled together by one promoter and operator (in prokaryotes).

Structural genes

the genes in an operon that code for the actual proteins/enzymes.

Promoter (promoter genes)

the DNA sequence where RNA polymerase binds to start transcription of the operon.

Operator

the DNA site where a repressor can bind to block transcription.

Regulatory gene

a gene coding for a protein (like a repressor) that controls other genes.

Inducer

a molecule that turns on an operon (e.g., lactose activating the lac operon by inactivating its repressor).

Post-transcriptional regulation

control after transcription but before translation (e.g., alternative splicing, mRNA stability).

Post-translational regulation

control after the protein is made (e.g., folding, chemical modification, degradation).

RNA interference (RNAi) / silencing RNA (siRNA)

small RNA molecules that bind mRNA to block its translation or trigger its destruction, silencing genes.

Morphogenesis

the development of an organism's body shape and structure.

Fertilization

the fusion of a sperm and egg.

Zygote

the single diploid cell formed at fertilization.

Homeotic genes

master genes that regulate development of body structures.

Hox genes

a set of homeotic genes that control the body plan along the head-to-tail axis; mutations can put structures in the wrong place.

Mutation

any change in the DNA sequence.

Base substitution

a point mutation where one base is swapped for another.

Silent mutation

a substitution that doesn't change the amino acid (thanks to the redundant code); no effect.

Missense mutation

a substitution that changes one amino acid (may or may not affect function; e.g., sickle-cell).

Nonsense mutation

a substitution that creates an early stop codon, shortening the protein.

Insertions

adding one or more nucleotides to the DNA sequence.

Deletions

removing one or more nucleotides from the sequence.

Frameshift mutation

an insertion or deletion (not a multiple of 3) that shifts the reading frame, altering every codon downstream; usually severe.

Gene rearrangements

larger-scale changes that move or reorganize segments of DNA within or between chromosomes (includes duplications, inversions, translocations, and transposon movement). They can create new gene combinations, change gene dosage, or disrupt genes.

Duplications

a segment of DNA is copied, producing extra copies of genes.

Inversions

a DNA segment is flipped and reinserted in reverse orientation.

Translocations

a segment of DNA moves to a different (non-homologous) chromosome.

Transposons

"jumping genes"; DNA segments that can move to new locations in the genome, sometimes disrupting genes.

Bacteria

single-celled prokaryotes; reproduce asexually but can exchange DNA.

Plasmids

small, circular DNA molecules in bacteria, separate from the main chromosome; often used as vectors in genetic engineering.

Conjugation

transfer of DNA between bacteria through direct contact (via a pilus).