In molecular biology, two nucleotides on opposite complementary DNA or RNA strands that are connected via hydrogen bonds are called a base pair (often abbreviated bp). Molecular biology is the study of Biology at a molecular level Nucleotides are Organic compounds that consist of three joined structures a nitrogenous base a Sugar, and a Phosphate group In Molecular biology, complementarity is a property of double-stranded Nucleic acids such as DNA and RNA as well as DNARNA duplexes Deoxyribonucleic acid ( DNA) is a Nucleic acid that contains the genetic instructions used in the development and functioning of all known Ribonucleic acid ( RNA) is a Nucleic acid that consists of a long chain of Nucleotide units A hydrogen bond results from a Dipole-dipole force between an Electronegative atom and a Hydrogen atom bonded to Nitrogen, Oxygen In the canonical Watson-Crick base pairing, adenine (A) forms a base pair with thymine (T), as does guanine (G) with cytosine (C) in DNA. Adenine is a Purine with a variety of roles in Biochemistry including Cellular respiration, in the form of both the energy-rich Adenosine Thymine is one of the four bases in the Nucleic acid of DNA that make up the letters ATGC Guanine is one of the five main Nucleobases found in the Nucleic acids DNA and RNA, the others being Adenine, Cytosine, Cytosine is one of the five main bases found in DNA and RNA. It is a Pyrimidine derivative with a Heterocyclic Aromatic ring In RNA, thymine is replaced by uracil (U). Thymine is one of the four bases in the Nucleic acid of DNA that make up the letters ATGC Uracil is a common and naturally occurring Pyrimidine derivative Non-Watson-Crick base pairing with alternate hydrogen bonding patterns also occur, especially in RNA; common such patterns are Hoogsteen base pairs. A Hoogsteen base pair is a minor variation of base-pairing in Nucleic acids such as the A•T pair Pairing is also the mechanism by which codons on messenger RNA molecules are recognized by anticodons on transfer RNA during protein translation. The genetic code is the set of rules by which information encoded in genetic material ( DNA or RNA sequences is translated into Proteins Messenger ribonucleic acid ( mRNA) is a molecule of RNA encoding a chemical "blueprint" for a Protein product Transfer RNA (abbreviated tRNA) is a small RNA (usually about 74-95 nucleotides that transfers a specific Amino acid to a growing polypeptide chain at Transfer RNA (abbreviated tRNA) is a small RNA (usually about 74-95 nucleotides that transfers a specific Amino acid to a growing polypeptide chain at Translation is the first stage of Protein biosynthesis (part of the overall process of Gene expression) Some DNA- or RNA-binding enzymes can recognize specific base pairing patterns that identify particular regulatory regions of genes.
The size of an individual gene or an organism's entire genome is often measured in base pairs because DNA is usually double-stranded. History See also History of genetics The existence of genes was first suggested by Gregor Mendel (1822-1884 who in the 1860s studied inheritance In classical genetics the genome of a Diploid Organism including Eukarya refers to a full set of chromosomes or genes in a Gamete, thereby Hence, the number of total base pairs is equal to the number of nucleotides in one of the strands (with the exception of non-coding single-stranded regions of telomeres). Nucleotides are Organic compounds that consist of three joined structures a nitrogenous base a Sugar, and a Phosphate group A telomere is a region of repetitive DNA at the end of Chromosomes which protects the end of the chromosome from destruction The haploid human genome (23 chromosomes) is estimated to be about 3 billion base pairs long and to contain 20,000-25,000 distinct genes. "Haplo" redirects here For the fictional character see The Death Gate Cycle. The human genome is the Genome of Homo sapiens, which is stored on 23 chromosome pairs A chromosome is an organized structure of DNA and Protein that is found in cells. [1]
A Kilobase is a unit of measurement in molecular biology denoting 1000 base pairs of DNA or RNA. Molecular biology is the study of Biology at a molecular level Deoxyribonucleic acid ( DNA) is a Nucleic acid that contains the genetic instructions used in the development and functioning of all known Ribonucleic acid ( RNA) is a Nucleic acid that consists of a long chain of Nucleotide units
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Examples
The following DNA sequences illustrate pair double-stranded patterns. By convention, the top strand is written from the 5' end to the 3' end; thus the bottom strand is written 3' to 5'. Directionality, in Molecular biology, refers to the end-to-end chemical orientation of a single strand of Nucleic acid. Directionality, in Molecular biology, refers to the end-to-end chemical orientation of a single strand of Nucleic acid.
- A base-paired DNA sequence:
ATCGAT TAGCTA
- The corresponding base-paired RNA sequence, in which uracil is substituted for thymine:
ATCGAT UAGCUA
Length measurements
The following abbreviations are commonly used to describe the length of a DNA/RNA molecule:
- bp = base pair(s)—one bp corresponds to ca 3. Uracil is a common and naturally occurring Pyrimidine derivative 4 Å of length along the strand
- kb (= kbp) = kilo base pairs = 1,000 bp
- Mb = mega base pairs = 1,000,000 bp
- Gb = giga base pairs = 1,000,000,000 bp
In case of single stranded DNA/RNA we talk about nucleotides, abbreviated nt (or knt, Mnt, Gnt), rather than base pairs, as they are not paired. An ångström or angstrom (symbol Å) (ˈɔːŋstrəm Swedish: ˈɔ̀ŋstrœm is an internationally recognized non- SI unit of length equal Nucleotides are Organic compounds that consist of three joined structures a nitrogenous base a Sugar, and a Phosphate group For distinction between units of computer storage and bases kbp, Mbp, Gbp etc may be used for disambiguation. Computer data storage, often called storage or memory, refers to Computer components devices and recording media that retain digital
The Centimorgan is also often used to imply distance along a chromosome, but the number of base-pairs it corresponds to varies widely. In Genetics, a centimorgan (abbreviated cM) or map unit (mu is a unit of Recombinant frequency for measuring Genetic linkage. In the Human genome, it is about 1 million base pairs[2] [3]. .
Hydrogen bonding and stability
Hydrogen bonding is the chemical mechanism that underlies the base-pairing rules described above. A hydrogen bond results from a Dipole-dipole force between an Electronegative atom and a Hydrogen atom bonded to Nitrogen, Oxygen A hydrogen bond results from a Dipole-dipole force between an Electronegative atom and a Hydrogen atom bonded to Nitrogen, Oxygen A hydrogen bond results from a Dipole-dipole force between an Electronegative atom and a Hydrogen atom bonded to Nitrogen, Oxygen Appropriate geometrical correspondence of hydrogen bond donors and acceptors allows only the "right" pairs to form stably. The GC base pair has three hydrogen bonds, whereas the AT base pair has only two; as a consequence, the GC pair is more stable.
The larger nucleic acids, adenine and guanine, are members of a class of doubly-ringed chemical structures called purines; the smaller nucleic acids, cytosine and thymine (and uracil), are members of a class of singly-ringed chemical structures called pyrimidines. Purine ( 1) is a heterocyclic Aromatic Organic compound, consisting of a Pyrimidine ring fused to an Imidazole ring Pyrimidine is a Heterocyclic Aromatic Organic compound similar to Benzene and Pyridine, containing two Nitrogen Atoms Purines are only complementary with pyrimidines: pyrimidine-pyrimidine pairings are energetically unfavorable because the molecules are too far apart for hydrogen bonding to be established; purine-purine pairings are energetically unfavorable because the molecules are too close, leading to electrostatic repulsion. The only other possible pairings are GT and AC; these pairings are mismatches because the pattern of hydrogen donors and acceptors do not correspond. (It should be noted that the GU pairing, with two hydrogen bonds, does occur fairly often in RNA but rarely in DNA. Ribonucleic acid ( RNA) is a Nucleic acid that consists of a long chain of Nucleotide units Deoxyribonucleic acid ( DNA) is a Nucleic acid that contains the genetic instructions used in the development and functioning of all known )
Paired DNA and RNA molecules are comparatively stable at room temperature but the two nucleotide strands will separate above a melting point that is determined by the length of the molecules, the extent of mispairing (if any), and the GC content. The melting point of a solid is the temperature range at which it changes state from solid to Liquid. Higher GC content results in higher melting temperatures; it is therefore unsurprising that the genomes of extremophile organisms such as Thermus thermophilus are particularly GC-rich. Thermus thermophilus is a gram negative Eubacterium used in a range of biotechnological applications including as a Model organism for Conversely, regions of a genome that need to separate frequently - for example, the promoter regions for often-transcribed genes - are comparatively GC-poor (for example, see TATA box). Transcription is the synthesis of RNA under the direction of DNA The TATA box (also called Goldberg-Hogness box) is a DNA sequence ( Cis-regulatory element) found in the Promoter region of most genes in GC content and melting temperature must also be taken into account when designing primers for PCR reactions. A primer is a strand of Nucleic acid that serves as a starting point for DNA replication.
Base stacking
Base stacking interactions between the pi orbitals of the bases' aromatic rings also contribute to stability, and again GC stacking interactions with adjacent bases tend to be more favorable. Stacking in Supramolecular chemistry refers to a stacked arrangement of Aromatic Molecules which interact through aromatic interactions In Chemistry, pi bonds ( π bonds) are covalent Chemical bonds where two lobes of one involved electron orbital overlap two lobes (Note, though, that a GC stacking interaction with the next base pair is geometrically different from a CG interaction. ) Base stacking effects are especially important in the secondary structure of RNA; for example, RNA stem-loop structures are stabilized by base stacking in the loop region. Stem-loop intramolecular Base pairing is a pattern that can occur in single-stranded DNA or more commonly in RNA.
- Further information: pi stacking
Base analogs and intercalators
Chemical analogs of nucleotides can take the place of proper nucleotides and establish non-canonical base-pairing, leading to errors (mostly point mutations) in DNA replication and DNA transcription. Stacking in Supramolecular chemistry refers to a stacked arrangement of Aromatic Molecules which interact through aromatic interactions Nucleic acid analogues are compounds structurally similar ( analog) to naturally occurring RNA and DNA used in medicine and in molecular biology research A point mutation, or single base substitution, is a type of Mutation that causes the replacement of a single base nucleotide with another nucleotide of the genetic DNA replication is the process of copying a double-stranded DNA molecule to form two double-stranded molecules Transcription is the synthesis of RNA under the direction of DNA One common mutagenic base analog is 5-bromouracil, which resembles thymine but can base-pair to guanine in its enol form. 5-Bromouracil (or 5-bromo-24(1H3H-pyrimidinedione or 5-BrU or 5-BU) is a brominated derivative of Uracil that acts as an Antimetabolite Enols (also known as alkenols) are Alkenes with a Hydroxyl group affixed to one of the carbon atoms composing the Double bond.
Other chemicals, known as DNA intercalators, fit into the gap between adjacent bases on a single strand and induce frameshift mutations by "masquerading" as a base, causing the DNA replication machinery to skip or insert additional nucleotides at the intercalated site. In Chemistry, intercalation is the reversible inclusion of a Molecule (or group between two other molecules (or groups A frameshift mutation (also called a framing error) is a genetic Mutation caused by Indels ie Most intercalators are large polyaromatic compounds and are known or suspected carcinogens. The term carcinogen refers to any substance Radionuclide or radiation that is an agent directly involved in the promotion of Cancer or in the fatation of its propagation Examples include ethidium bromide and acridine. Ethidium bromide (sometimes abbreviated as "EtBr", the abbreviation also confusingly used for Bromoethane) is an intercalating agent Acridine, C13H9N is an Organic compound and a nitrogen heterocycle.
See also
- DNA
- Nucleobase
- Wobble base pair
- Hoogsteen base pair
- List of binary polymorphisms
External links
- DAN - webserver version of the EMBOSS tool for calculating melting temperatures
Cited references
- ^ International Human Genome Sequencing Consortium (2004). Deoxyribonucleic acid ( DNA) is a Nucleic acid that contains the genetic instructions used in the development and functioning of all known Structure The "skeleton" of adenine A Hoogsteen base pair is a minor variation of base-pairing in Nucleic acids such as the A•T pair "Finishing the euchromatic sequence of the human genome. ". Nature 431 (7011): 931-45. PMID 15496913. [1]
- ^ The Genetic and Rare Diseases Information Center - Office of Rare Diseases redirect
- ^ Matthew P Scott, Paul Matsudaira, Harvey Lodish, James Darnell, Lawrence Zipursky, Chris A Kaiser, Arnold Berk, Monty Krieger (2004). Molecular Cell Biology, Fifth Edition. San Francisco: W. H. Freeman, 396. ISBN 0-7167-4366-3. “". . . in humans 1 centimorgan on average represents a distance of about 7. 5x10E5 base pairs"”
General references
- Watson JD, Baker TA, Bell SP, Gann A, Levine M, Losick R. (2004). Molecular Biology of the Gene. 5th ed. Pearson Benjamin Cummings: CSHL Press. See esp. ch. 6 and 9.
Dictionary
base pair
-noun
- (biology) In molecular biology, two nucleotides on opposite complementary DNA or RNA strands that are connected via hydrogen bonds.
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