DNA Structure, Replication, and Technology Terms

Acetyl

A chemical group of one oxygen atom, two carbon atoms, and three hydrogen atoms that are added to another carbon, where the first carbon of the acetyl group has a double bond with oxygen and also binds to a methyl group. The acetyl group is commonly written as –COCH₃. Acetyl groups are added to histones to promote gene expression.

Adenine

One of four nucleic acids that compose DNA and RNA. Adenine is a purine derivative, like guanine. The name adenine refers to the fact that it was first isolated from the pancreatic gland (gland is adenas in Greek) by Albrecht Kossel. Go Albert.

Allele

A gene variant responsible for a specific inheritable trait. An allele is also the punch line for a bad joke about a guy named Al who owns an eel.

Amino

A chemical group that can be added to carbon composed of one nitrogen atom and two hydrogen atoms. It is commonly written as –NH2. Oh…amino.

Anaphase

The stage of mitosis or meiosis, where individual chromosomes are first pulled along microtubules toward either pole of centrosomes. Anaphase is also the punch line of a joke, where a girl grows up thinking her name is Ana.

Anticodon

The three-base sequence complementary to the codon sequence. Anticodon sequences are found on transcription RNA (tRNA) molecules, which are the links between codon sequences and a given amino acid.

Bacterial Artificial Chromosome (BAC)

A fragment of DNA used to clone or transform bacteria with inserted DNA sequences that range in size from 150 kilobases (kb) to more than 700 kb. BACs are commonly used to sequence large genomes of various organisms. One day, BACs hope to become real chromosomes.

Bacteriophage

A virus that infects bacteria, often shortened to "phage." That's all we got.

Base

A nucleotide or base is the basic unit or building block of DNA and RNA. Nucleotides include cytosine, thymine, and uracil, which are called pyrimidines, and also include guanine and adenine, which are called purines. Adenine (abbreviated A) pairs with thymine (T) or uracil (U), and guanine (G) pairs with cytosine (C). A goes with T, and G goes with C. Also, see Nucleic Acid. These guys are generally called "bases," so if you hear the phrase "DNA bases," it is referring to the nucleotides in DNA. Nucleotides strung together form nucleic acids.

Base-pairing Rule (Chargaff's Rule)

Named after Austrian chemist Erwin Chargaff, the rule that, for any amount of double-stranded DNA, there should be equivalent amounts of pyrimidines to purines. That is, for however many cytosines and thymines there are, called pyrimidines, there should be as many guanines and adenines, called purines. This rule was improved by Watson-Crick base pairing, which identifies the base pairings in DNA. Adenine (abbreviated A) pairs with thymine (T), and guanine (G) pairs with cytosine (C). A goes with T, and G goes with C.

Centrosome

An organelle responsible for organizing the microtubules. Centrosomes are also called the microtubule-organizing centers, particularly during mitosis. Centrosomes move to either end of the cell and pull chromosomes apart so that cell division can occur.

Chromatin Fiber

A coil of nucleosomes that is an intermediate level of packaging of DNA and can be condensed into chromosomes. These fibers are not the ones found in All-Bran cereal.

Chromosome

A single piece of DNA that contains many of the genes, regulatory elements, and nucleotide sequences of an organism. Chromosomes can either be circular, as in bacteria and archaea, or linear, as in eukaryotes.

Clone

A cell or organism that is genetically identical to the source from which it was derived. To clone is to produce an identical copy of something. Hey Dolly, what's up?

Codon

The three-letter sequence that encodes a specific amino acid. A transcription RNA (tRNA) with the amino acid attached binds specifically to this three letter sequence, and the specificity of the tRNA binding is determined by the codon, or, rather, the anticodon, sequence.

Complementary Base Pairs

See the previously defined base pairing rule (Chargaff's Rule). The complementary base pairs in DNA are adenine paired with thymine, and guanine paired with cytosine. In RNA, thymine is replaced with uracil.

Cosmid

A type of plasmid that contains cos sequences from lambda, ~, which is a type of phage, and can have 37-52 kb of DNA, compared to the 1-20 kb of normal plasmids. While normal plasmids are used to transform cells, cosmids transduce cells by using the phage cos sequences to integrate into the bacterial cell chromosome. The advantage of transduction when compared to transformation is that cosmids can hold larger DNA inserts due to decreased recombination compared to plasmids. Cosmids are used as cloning vectors and can help build genomic libraries.

Cytokinesis

The process by which the cytoplasm of a cell is partitioned into two daughter cells. Cytokinesis is similar to when they put a divider into your classroom, if your classroom has dividers.

Cytosine

One of four nucleic acids that comprise DNA and RNA. Cytosine is a pyrimidine derivative, like thymine and uracil. Mammalian cells can remove an amino group from cytosine to produce uracil, which prevents infection from retroviruses. Cytosine was first isolated from calf thymus by Albrecht Kossel. Yay, Albert!

Demethylation

The removal of a methyl group from a molecule.

Deoxyribose

A derivative of the pentose (five-membered ringed) sugar ribose with the formula C₅H₁₀O₄. Deoxyribose is the sugar that serves as the backbone for DNA, and lacks the 2'-hydroxyl group present in ribose.

DNA

Deoxyribonucleic acid. DNA is a macromolecule ("macro" = big) also known as a nucleic acid that is composed of phosphate groups, deoxyribose sugar groups, and the nucleotides adenine, guanine, cytosine, and thymine. DNA contains the genetic code needed by all cells to produce proteins and other molecules necessary to sustain life. He seems to make into every one of Shmoop's Biology glossaries.

DNA Polymerase

The enzyme that adds deoxyribonucleotides to a strand of DNA. The newly added deoxyribonucleotides are complementary to a template strand of DNA.

Double Helix

The common structure of double-stranded molecules of DNA or RNA, though it is mostly referred to in DNA because RNA is rarely found double-stranded. James Watson and Sir Francis Crick first reported the double helix structure of DNA in 1953 in the journal Nature.

DsDNA

Double-stranded DNA.

Epigenetics

The study of the changes that affect gene expression. Gene expression is controlled by factors beyond the DNA sequence, such as DNA methylation and histone modifications, like methylation and acetylation.

Euchromatin

The part of chromosomes that is actively transcribing DNA to produce messenger RNA (mRNA) and proteins. Euchromatin is typically characterized by demethylated DNA and acetylated histones that allow access to more transcription factors and RNA polymerase.

Gene

The basic unit of heredity in an organism, associated with the production of one type of RNA or protein that serves some function. In monogenic, or single gene, traits, one gene is responsible for determining a certain phenotype, while polygenic, or multiple gene, traits require multiple genes to determine the phenotype. Gene is also a great name for a boy who wants to be a movie critic.

Gene Expression

The way in which genes are used to synthesize a product that has a specific function or purpose. Gene expression often produces proteins. Gene expression is controlled by factors beyond the DNA sequence, such as DNA methylation and histone modifications, like methylation and acetylation.

Gene Open Reading Frame

A section of DNA that does not contain a stop codon within the reading frame. Also abbreviated ORF.

Genetic Code

The information present in a DNA sequence that is translated into a protein. The genetic code is broken into 3 nucleotide codons, where each codon encodes a single amino acid. As there are only 21 natural amino acids, many codons encode the same amino acid. Three codons encode a "stop codon," signaling the ribosome to stop synthesizing the protein.

Genome

All the genes and gene-related sequences that define an organism. Eukaryotes have much larger genomes than bacteria, archaea, and viruses. Genome size is likely a function of increased cell size, cell division rate, metabolic rate, developmental rate, and complexity of an organism.

Guanine

One of four nucleic acids that compose DNA and RNA. Guanine is a purine derivative, like adenine. The name guanine originates from the fact that it was first isolated from sea bird guano. It is a little classier than poopine.

Helicase

An enzyme (-ase gave that one away) that is responsible for unwinding DNA's double helix so that DNA replication as well as RNA synthesis can occur. Good on ya, Helicase.

Helix

The curved shape that many biological molecules adopt to perform their functions. A DNA molecule is formed from two intertwined helices.

Heredity

Heterochromatin

The opposite of euchromatin, in that it is DNA with little gene expression due to either DNA or histone methylation. Heterochromatin regions represent have packed DNA, which is why little transcription occurs here.

Histone

A positively charged protein that interacts with negatively charged DNA to help in the packing of DNA into chromosomes. Histones play an important role in gene expression; modifying histones by adding or removing methyl, acetyl, or other groups affects how tightly histones bind DNA, which controls gene expression.

Hydroxyl

A chemical group of oxygen and hydrogen that is added to a carbon. It is commonly written as –OH. Oh, snap.

Hydrolysis

Hydrolysis is a reaction that splits a water molecule into its H⁺ and OH^- ions, and in the process, breaks a polymer by adding an ion to each fragment. This chemical reaction effectively makes two polymer fragments, an acid and a base. Hydrolysis can occur in a sequence-specific manner (see Restriction Enzymes) or nonspecifically.

Messenger RNA (mRNA)

The molecule of RNA that contains the "blueprint" of a protein that will be synthesized.

Metaphase

The stage of mitosis where all the chromosomes line up in the middle of the cell along microtubules to prepare to be separated during anaphase.

Methyl

A chemical group of one carbon and 3 hydrogen atoms that is added to another carbon. It is commonly written as –CH₃. Methyl groups are treated a lot like currency; they are often added or removed according to a molecule's needs. It's not clear whether everyone is fighting to have them or fighting to get rid of them. Poor little guys.

Methylation

The process of adding a methyl group to a carbon atom. Methylation commonly happens with silencing of gene expression by DNA methylation. Histone methylation also occurs, though it can either activate or silence gene expression, depending on where the histone is methylated.

Microtubule

One of three components of the cytoskeleton, including actin and intermediate filaments. Microtubules are polymers of molecules called tubulin. They are instrumental in organizing the process of mitosis and ensuring that each daughter cell has the right chromosomes. Microtubules primarily function by forming a path for each chromosome to go to the appropriate daughter cell.

Mitosis

The process of cell division where a cell copies all of its genetic information and divides into two identical daughter cells. All cellular contents are duplicated and shared among the two daughter cells. Thanks, Pops.

Mutation

A change in the genetic sequence, which may or may not be harmful to the organism. Mutations in most cases result in evolution, where mutants that are better suited for survival outcompete those that lack that particular mutation. However, some mutations may be lethal or deleterious, where mutants are weaker than the wild-type organism, aka the organism without a mutation. Typical mutations include missense, or replacing one nucleotide with another; deletions; and insertions.

Nuclease

An enzyme (there's that –ase aain) that is responsible for breaking down polymers of DNA or RNA. Nucleases break down DNA or RNA polymers by hydrolyzing 5´-3´ phosphodiester bonds (the unit described by two covalent ester bonds among a phosphate group and two pentose sugars) between nucleotides. Hydrolysis is a reaction that splits a water molecule into its H⁺ and OH^- ions, and in the process, breaks a polymer by adding an ion to each fragment. This chemical reaction effectively makes two polymer fragments, an acid and a base. Hydrolysis can occur in a sequence-specific manner (see Restriction Enzymes) or nonspecifically.

Nucleic Acid

A macromolecule (read: big) composed of a pentose (five-membered ringed) sugar, like ribose or deoxyribose, a phosphate group, and a base, either adenine, guanine, cytosine, thymine, or uracil. They are called "acids" due to the negatively charged phosphate groups. DNA replication is the process of polymerizing nucleic acids.

Nucleotide

A nucleotide is the basic unit or building block of DNA and RNA. Nucleotides include cytosine, thymine, and uracil, which are called pyrimidines, and also include guanine and adenine, which are called purines. Adenine (abbreviated A) pairs with thymine (T) or uracil (U), and guanine (G) pairs with cytosine (C). A goes with T, and G goes with C. Also, see Nucleic Acid. These guys are generally called "bases," so if you hear the phrase "DNA bases," it is referring to the nucleotides in DNA. Nucleotides strung together form nucleic acids.

Nucleus

Called the "brain" of the cell, it stores all DNA necessary to make RNA and protein, with the exception of mitochondrial DNA, which is in the…mitochondria. The nucleus is encased in two lipid bilayers, called the nuclear membrane, that serve to house the DNA in the nucleus and restrict the flow of cytoplasmic components into the nucleus. Basically, the nuclear membrane keeps everyone in their places. Nuclei also hate being pronounced "nuculei," so do not do that. At least not to their faces.

Nucleolus

A structure within the nucleus that is not membrane-bound but is instead a protein and nucleotide-dense region of the nucleus where transcription of ribosomal RNA (rRNA) occurs. The nucleus can be easily observed using light microscopy (light + microscopes).

Nucleosome

The basic unit of DNA packaging, where DNA loops twice around 8 histone proteins, forming a nucleosome core. Like a rollercoaster, except not at all.

Phylogenetics Or Phylogeny

The area of biology that studies the relationships of various organisms to each other, as described by either genetic information or morphological (shape) relationships.

Plasmid

A DNA molecule commonly found in bacteria that is independent from the chromosome. A plasmid can replicate independently from chromosomal DNA, and often encodes pathogenic factors (that cause disease) as well as antibiotic resistance genes (that resist antibiotics). Unlike chromosomal DNA, plasmid DNA can easily be transferred from one bacterium to another, which makes it super handy for DNA technology applications.

Ploidy

The number n of sets of chromosomes in a given cell. Hello, Algebra; nice to see you. A haploid cell has n chromosomes, and a diploid cell has 2n chromosomes. Ploidy, ploidy, ploidy.

Polyadenylation

The step in the process of RNA transcription where messenger RNA (mRNA) transcripts are tagged with a series of adenine nucleotides to aid in the export of the mRNA and maintain its stability during translation.

Polymer

A long-ish molecule made of repeating smaller molecules.

Primer

A short oligonucleotide sequence that serves as the starting point for DNA polymerization. For DNA replication, the primer is often an RNA sequence that is later degraded and replaced with a DNA sequence.

Promoter

A regulatory region that is often upstream of the start site of a gene open reading frame. Promoters activate gene expression by recruiting transcription factors, which in turn recruit RNA polymerase (an enzyme) to the site to be transcribed.

Prophase

The stage in which the chromatin fibers condense into distinct chromosomal bodies that are visible under microscope. The nucleus also begins to break down in this stage, though most of the nuclear breakdown occurs in late prophase/early metaphase, in a stage that some refer to as prometaphase.

Purine

A nitrogenous base that is composed of a pyrimidine and imidazole ring (double ring). Purines such as adenine and guanine serve as bases for DNA or RNA, though other purines such as caffeine, hypoxanthine, and theobromine also exist. Mmm, Starbucks.

Pyrimidine

A nitrogenous base similar to benzene (a six-membered ring), and includes cytosine, thymine, and uracil as bases used for DNA or RNA.

Recombination

The process of joining one molecule of DNA to another molecule. Recombination can either occur through the exchanging of similar sequences, called homologous recombination; the joining of ends of unrelated sequences together, called non-homologous end joining; or the falling off of polymerases from one template strand and onto another, creating a recombinant sequence. DNA that has been recombined is called recombinant DNA.

Replication

Specifically, the process of taking double-stranded DNA and making two identical copies of that double-stranded DNA. Each strand serves as a template for daughter strand synthesis.

Replication Fork

The structure that forms when DNA is replicating. When the DNA is unwound by helicases for DNA replication, one strand, called the leading strand, is synthesized while the DNA unwinds, while short sequences are filled in on the other strand, called the lagging strand, to make two daughter double helices. The junction where the DNA is split and the leading strand and lagging strands are being replicated is called the replication fork.

Repressor

A protein that binds to a DNA sequence upstream of a gene or somewhere at the beginning of a gene and stops gene expression. A repressor should not be confused with a depressor, or the person who kills all the fun at a party.

Restriction Enzyme

A specific nuclease that cuts double-stranded DNA at a specific sequence. Restriction enzymes were first discovered in bacteria, which use these enzymes as a defense mechanism against foreign DNA.

Retrovirus

A virus that has an RNA genome and uses the enzyme reverse transcriptase to generate a double-stranded DNA genome. Retroviruses are typically used for gene therapy or other biotechnology applications. They are not useful for 70s theme parties.

Reverse Transcriptase

A DNA polymerase (enzyme) that copies from RNA templates. Reverse transcriptase is sloppy and error prone, due to a lack of proofreading. It also does not tuck in its shirt.

Reverse Complement

A strand of DNA that is in the opposite orientation and is complementary to the first strand. It is not a compliment that is really an insult. In double-stranded DNA, one strand is in a 5´ to 3´ direction, while the other is in the 3´ to 5´ direction, as you look at it from left to right, or top to bottom. Therefore, with respect to any strand, the other strand is the reverse complement.

Ribonucleic Acid

A series of nucleotides with ribose (a five-membered ring) as the backbone sugar. Ribonucleic acid often codes for proteins like messenger RNA (mRNA), or may be functionally active like ribozymes, including ribosomal RNA (rRNA) molecules, or may function in translation, like in transfer RNA (tRNA) by serving as the link between codons and amino acids.

Ribose

A pentose (five-membered ring) sugar with the formula C₅H₁₀O₅. Ribose is the sugar that serves as the backbone for RNA.

Ribosomal RNA

The part of RNA that is in the ribosome and helps mRNA code into amino acids.

Ribosome

A complex of RNA and protein that converts an messenger RNA (mRNA) sequence into a series of amino acids. It serves as the protein factory of the cell.

Ribozyme

If you read this word, and thought to yourself "Sounds like enzyme!" you are pretty close. An RNA molecule that catalyzes chemical reactions. "Ribozyme" comes from ribonucleic acid enzyme.

RNA

Ribonucleic acid. RNA is a macromolecule ("macro" = big) composed of phosphate groups (aka –H₂PO₄R, where R is a functional group), ribose sugars, and the nucleotides adenine, guanine, cytosine, and uracil. It functions as a go-between for DNA and proteins as messenger RNA, or mRNA; as a key player in protein synthesis as ribosomal RNA, or rRNA; as a bridge as transfer RNA, or tRNA; as a gene regulator as small interfering RNA, or siRNA; and as microRNA, or miRNA. Why do there need to be so many different kinds of RNA? We were wondering the same thing. Don’t worry about all the different types for now.

SsDNA

Single-stranded DNA.

Supercoil

An overwound circular piece of DNA. It has no superpowers, beyond being really twisted.

Stop Codon

A three-base sequence that tells the ribosome to stop adding amino acids to the growing peptide chain. Stop already, please! The stop codon causes the ribosome to release mRNA and protein.

Telomerase

An enzyme that, during each round of DNA replication, replaces the lost DNA sequence with a repeat sequence. Loss of telomerase activity generally leads to cell death. Sad face.

Telomeres

The ends of DNA in vertebrates. Telomeres are highly repetitive sequences, partially due to the activity of telomerase, and enzyme (—ase). Shortening of telomere length is important for controlling the age of a cell. Cancer cells and other diseased cells have abnormal telomeres.

Telophase

The antithesis of prophase, where daughter chromatids begin to decondense as the nucleus reforms for each future daughter cell. These are not unique cells yet, as this phase is followed by cytokinesis, where the two cells are finally separated.

Termination

The completion of a metabolic process, such as DNA replication, RNA transcription, or translation. There are different cues for each: DNA replication terminates by replication forks running into each other or reaching the end of DNA, RNA transcription terminates with either the formation of a 3´ hairpin loop or the arrival at a polyadenylation signal, and translation terminates with the stop codon.

Thymine

One of four nucleic acids that compose DNA. Thymine is replaced with uracil, a variant of thymine without a methyl group, in RNA. Thymine is a pyrimidine derivative, like cytosine and uracil. Thymine was first isolated from calf thymus by Albrecht Kossel.

Topoisomerase

An enzyme responsible for unwinding DNA, generally by cutting one strand of DNA to relieve the torsional force that causes supercoiling. Topoisomerases relax the DNA structure so that helicases can enter and unwind the helix.

Transduction

The insertion of foreign DNA into a bacterial cell by means of a bacteriophage. The bacteriophage injects DNA into the cell, along with factors that help the integration of the DNA into the bacterial chromosome.

Transfer RNA (tRNA)

The molecule of RNA that helps messenger RNA (mRNA) transfer the three-letter genetic code into the twenty-letter code of amino acids.

Transformation

The process by which bacteria nonspecifically uptake (take up) genetic material. Transformation has been used by biotechnologists to amplify plasmids and to express various proteins. The usefulness of transformation can be seen in the "Spiderman and other examples of recombinant DNA" in the "In the Real World" section.

Transcription

The process of generating an RNA copy of a gene, which is initiated by transcription factors binding to double-stranded DNA at a promoter sequence, and then recruiting RNA polymerase to transcribe a gene.

Transcription Factor

A protein that binds DNA and activates transcription.

Translation

The synthesis of proteins from an mRNA template. Each codon sequence on the mRNA copy of the gene encodes a specific amino acid that is recognized by the anticodon sequence of the tRNA. It has a specific amino acid based upon the tRNA anticodon sequence. Translation is mediated by ribosomes and terminates when a stop codon is reached on the mRNA template.

Uracil

One of four nucleic acids that compose RNA. Uracil replaces thymine in RNA, and is also a pyrimidine derivative, like cytosine and thymine. Uracil was first isolated in 1900 from yeast hydrolysis.

Vector

A plasmid that is used specifically for genetic engineering and biotechnology purposes. Vectors are constructed for specific purposes and typically have an antibiotic resistance gene as well as a multiple cloning site, or a site with various restriction endonuclease recognition sequences.