Gene expression and regulation vocab

Histones

Proteins found in chromatin

Nucleosome

Cluster of DNA wrapped around histones

Purine

Nitrogenous base with two rings

Pyrimidine

Nitrogenous base with one ring

Antiparallel

Running in opposite directions

Semiconservative

Each replicated DNA helix consists of one old and one new strand

Origin of replication

Specific nucleotide sequence where DNA replication begins

Replication bubbles

Formation of “bubbles” in DNA due to replication occuring in both directions

Replication forks

Sites where separation and replication occur

Helicase

Enzyme that breaks the hydrogen bonds between base pairs, unwinding the DNA

Topoisomerase

Enzyme that prevents the DNA from winding too tightly ahead of the replication fork

DNA polymerase

Enzyme that adds nucleotides to the daughter DNA strand

RNA polymerase

Enzyme that adds the RNA primer

RNA primer

Short sequence of RNA nucleotides that DNA nucleotides are added to to form the daughter strand

Leading strand

Daughter DNA strand that is synthesized in one continuous piece

Lagging strand

Daughter DNA strand that is synthesized in small pieces

Okazaki fragments

DNA fragments in the lagging strand

DNA ligase

Enzyme that connects the Okazaki fragments

Plasmid

Small extrachromosomal, double-stranded, circular DNA molecules in prokaryotes that replicate on their own

Telomere

Non-replicated nucleotide sequence at the ends of eukaryotic chromosomes

Telomerase

Enzyme that creates space for a primer on telomere DNA

Gene expression

Turning on a gene to produce RNA and protein

Gene regulation

Mechanism that controls when a gene is expressed and how much protein is made

Differential gene expression

Differences in what genes are expressed in different cells, which creates different cell types

Operon

Group of related genes that are transcribed from one promoter

Inducible system

Gene or operon that is turned off by default until a certain condition is reached

Regulatory DNA sequence

Sections of DNA where regulatory proteins can bind to turn transcription on or off

Operator

Regulatory DNA sequence in the lac operon

Negative regulatory protein

Blocks transcription of an operon

Activator

Protein that allows transcription to occur in an inducible system

Positive regulatory protein

Induces transcription of an operon

Epigenetics

Regulation by controlling physical access to DNA

Methylation

Tight packing of nucleosomes, preventing transcription factors from binding to the DNA

Acetylation

Loosening of nucleosomes, allowing transcription factors to bind to DNA

Silenced genes

Genes that are not transcribed as usual and therefore not expressed

Repressor

Type of transcription factor that prevents transcription from occuring

Enhancers

Far-away clusters of binding sites for activators on a gene that each activate gene in a certain cell type

Tissue-specific enhancer

Enhancer that control a gene’s expression in a certain part of the body

Co-expressed genes

Genes on the same or different chromosomes that are controlled by the same transcription factors and are transcribed simultaneously

RNA stability

Rate of decay of RNA based on a defined lifespan

miRNA

microRNA; small RNA that bind to mRNA to degrade them or block translation

siRNA

Small interfering RNA; inhibit gene expression

Biotechnology

Use of biological agents for technological advancement

Agarose powder

Substance that forms a gel when added to a buffer

Casting tray

Device used for gel electrophoresis that holds the gel and DNA

Wells

Holes in the casting tray where DNA is loaded

Restriction enzyme

Protein that cuts DNA into fragments

Marker

First well, used as a size reference

Polymerase chain reaction

Technique to amplify a specific DNA region

Gel electrophoresis

Technique to separate DNA molecules by size

Denaturation (PCR)

Separating DNA strands using high heat

Annealing (PCR)

Cooling of the DNA so PCR primers can bond to the single-stranded DNA templates

Extension (PCR)

Extending the primer to synthesize new DNA

PCR primer

Single-stranded DNA used in PCR

Taq polymerase

DNA polymerase found in bacteria that synthesizes new DNA in PCR

Reverse transcriptase PCR

Enzyme that turns an organism’s mRNA into DNA for use in PCR

cDNA

Complementary DNA; DNA made during reverse transcription

DNA cloning

Technique that makes many identical copies of a piece of DNA

Target gene

DNA piece that is inserted into an existing organism

Transformation

Bacteria taking in DNA from its environment and making it a part of its genetic makeup

Recombinant plasmid

Plasmid with a specific target sequence added in

Heat shock

Exposing a cell to extreme heat in order to open its membrane

Antibiotic gene

DNA sequence that gives an organism that ability to survive in the presence of a specific antibiotic

Purification

Separation of target proteins from bacteria using beads with antibodies that they bind to and then washing away all other molecules from the column

Genetic engineering

Alteration of an organism’s genotype using recombinant DNA technology to modify an organism’s DNA to achieve desired traits

Genetically modified organism

Organism that receives the recombinant DNA

Transgenic organism

GMO whose recombinant DNA comes from a different species

Gene therapy

Genetic engineering technique used to cure diseases

Central dogma

DNA is transcribed into RNA which is translated into proteins that create phenotypic traits

Transcription

Copying DNA code into mRNA

Template strand

DNA strand that transcription occurs along

TATA box

Promoter sequence of the DNA here transcription begins, named for its pattern of thymines and adenines

Sigma subunit

Part of RNA polymerase in prokaryotes that recognizes and binds to the promoter sequence

Transcription factors

Proteins in eukaryotes that recognize and bind to the promoter sequence

Transcription initiation complex

Eukaryotic structure consisting of transcription factors and RNA polymerase II

Terminator sequence

Sequence of bases that code for the release of RNA polymerase

Pre-mRNA

Unmodified eukaryotic mRNA

Mature mRNA

Modified eukaryotic mRNA

Intron

Noncoding segment of mRNA

Exon

Coding segment of mRNA

RNA splicing

Cutting out introns from eukaryotic mRNA

Spliceosomes (snRNPs)

Protein complexes that do RNA splicing

snRNA

Proteins and RNA molecules that make up spliceosomes

Alternative splicing

1 pre-mRNA can be spliced in different ways, resulting in different proteins

Peptide bond

Bond formed between amino acids to form a polypeptide

Codon

Triplet of mRNA nucleotides that codes for a specific amino acid

Initiator tRNA

First tRNA to arrive at the ribosome and bind to the start codon

Translation initiation complex

Structure consisting of the small and large ribosomal subunits, initiator tRNA, and mRNA

Initiation factors

Proteins that bring the translation initiation complex together

Anticodon

Sequence of three bases at the bottom of tRNA that bind to complementary mRNA

Release factor

Protein that enters the A site after the stop codon is reached causes hydrolysis, freeing the polypeptide from the final tRNA

Chaperone

Molecule that helps with protein folding

Protein targeting

Addition of signal sequences to a polypeptide that guide it to specific parts of a cell

Retroviruses

Viruses that have RNA as their genetic material

Reverse transcription

Transcription of RNA into DNA

Reverse transcriptase

Enzyme that is required for reverse transcription

Mutation

When a genetic material is changed

Mutagen

Physical or chemical factor that causes a mutation

Gene mutation

Mutation in a single gene

Chromosomal mutation

Mutation that changes the whole chromosome