DNA – Types, Structure, Functions

DNA, or deoxyribonucleic acid, is the hereditary material in humans and almost all other organisms. Nearly every cell in a person’s body has the same DNA. Most DNA is located in the cell nucleus (where it is called nuclear DNA), but a small amount of DNA can also be found in the mitochondria (where it is called mitochondrial DNA or mtDNA). Mitochondria are structures within cells that convert the energy from food into a form that cells can use.

Deoxyribonucleic acid is a molecule composed of two polynucleotide chains that coil around each other to form a double helix carrying genetic instructions for the development, functioning, growth and reproduction of all known organisms and many viruses. DNA and ribonucleic acid (RNA) are nucleic acids. Alongside proteins, lipids and complex carbohydrates (polysaccharides), nucleic acids are one of the four major types of macromolecules that are essential for all known forms of life.

The two DNA strands are known as polynucleotides as they are composed of simpler monomeric units called nucleotides.[2][3] Each nucleotide is composed of one of four nitrogen-containing nucleobases (cytosine [C], guanine [G], adenine [A] or thymine [T]), a sugar called deoxyribose, and a phosphate group. The nucleotides are joined to one another in a chain by covalent bonds (known as the phospho-diester linkage) between the sugar of one nucleotide and the phosphate of the next, resulting in an alternating sugar-phosphate backbone. The nitrogenous bases of the two separate polynucleotide strands are bound together, according to base pairing rules (A with T and C with G), with hydrogen bonds to make double-stranded DNA. The complementary nitrogenous bases are divided into two groups, pyrimidines and purines. In DNA, the pyrimidines are thymine and cytosine; the purines are adenine and guanine.

Both strands of double-stranded DNA store the same biological information. This information is replicated as and when the two strands separate. A large part of DNA (more than 98% for humans) is non-coding, meaning that these sections do not serve as patterns for protein sequences. The two strands of DNA run in opposite directions to each other and are thus antiparallel. Attached to each sugar is one of four types of nucleobases (or bases). It is the sequence of these four nucleobases along the backbone that encodes genetic information. RNA strands are created using DNA strands as a template in a process called transcription, where DNA bases are exchanged for their corresponding bases except in the case of thymine (T), for which RNA substitutes uracil (U).[4] Under the genetic code, these RNA strands specify the sequence of amino acids within proteins in a process called translation.

Within eukaryotic cells, DNA is organized into long structures called chromosomes. Before typical cell division, these chromosomes are duplicated in the process of DNA replication, providing a complete set of chromosomes for each daughter cell. Eukaryotic organisms (animals, plants, fungi and protists) store most of their DNA inside the cell nucleus as nuclear DNA, and some in the mitochondria as mitochondrial DNA or in chloroplasts as chloroplast DNA.[5] In contrast, prokaryotes (bacteria and archaea) store their DNA only in the cytoplasm, in circular chromosomes. Within eukaryotic chromosomes, chromatin proteins, such as histones, compact and organize DNA. These compacting structures guide the interactions between DNA and other proteins, helping control which parts of the DNA are transcribed.

DNA and RNA

DNA and RNA are nucleic acids that carry out cellular processes, especially the regulation and expression of genes.

Key Points

The two main types of nucleic acids are DNA and RNA.

Both DNA and RNA are made from nucleotides, each containing a five-carbon sugar backbone, a phosphate group, and a nitrogen base.

DNA provides the code for the cell ‘s activities, while RNA converts that code into proteins to carry out cellular functions.

The sequence of nitrogen bases (A, T, C, G) in DNA is what forms an organism’s traits.

The nitrogen bases A and T (or U in RNA) always go together and C and G always go together, forming the 5′-3′ phosphodiester linkage found in the nucleic acid molecules.

Key Terms

  • nucleotide: the monomer comprising DNA or RNA molecules; consists of a nitrogenous heterocyclic base that can be a purine or pyrimidine, a five-carbon pentose sugar, and a phosphate group
  • genome: the cell’s complete genetic information packaged as a double-stranded DNA molecule
  • monomer: A relatively small molecule which can be covalently bonded to other monomers to form a polymer.

Types of Nucleic Acids

The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material found in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is found in the nucleus of eukaryotes and in the chloroplasts and mitochondria. In prokaryotes, the DNA is not enclosed in a membranous envelope, but rather free-floating within the cytoplasm.

The entire genetic content of a cell is known as its genome and the study of genomes is genomics. In eukaryotic cells, but not in prokaryotes, DNA forms a complex with histone proteins to form chromatin, the substance of eukaryotic chromosomes. A chromosome may contain tens of thousands of genes. Many genes contain the information to make protein products; other genes code for RNA products. DNA controls all of the cellular activities by turning the genes “on” or “off.”

The other type of nucleic acid, RNA, is mostly involved in protein synthesis. In eukaryotes, the DNA molecules never leave the nucleus but instead use an intermediary to communicate with the rest of the cell. This intermediary is the messenger RNA (mRNA). Other types of RNA—like rRNA, tRNA, and microRNA—are involved in protein synthesis and its regulation.

Nucleotides

DNA and RNA are made up of monomers known as nucleotides. The nucleotides combine with each other to form a polynucleotide: DNA or RNA. Each nucleotide is made up of three components:

  • a nitrogenous base
  • a pentose (five-carbon) sugar
  • a phosphate group

Each nitrogenous base in a nucleotide is attached to a sugar molecule, which is attached to one or more phosphate groups.

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DNA and RNA: A nucleotide is made up of three components: a nitrogenous base, a pentose sugar, and one or more phosphate groups. Carbon residues in the pentose are numbered 1′ through 5′ (the prime distinguishes these residues from those in the base, which are numbered without using a prime notation). The base is attached to the 1′ position of the ribose, and the phosphate is attached to the 5′ position. When a polynucleotide is formed, the 5′ phosphate of the incoming nucleotide attaches to the 3′ hydroxyl group at the end of the growing chain. Two types of pentose are found in nucleotides, deoxyribose (found in DNA) and ribose (found in RNA). Deoxyribose is similar in structure to ribose, but it has an H instead of an OH at the 2′ position. Bases can be divided into two categories: purines and pyrimidines. Purines have a double ring structure, and pyrimidines have a single ring.

Nitrogenous Base

The nitrogenous bases are organic molecules and are so named because they contain carbon and nitrogen. They are bases because they contain an amino group that has the potential of binding an extra hydrogen, and thus, decreasing the hydrogen ion concentration in its environment, making it more basic. Each nucleotide in DNA contains one of four possible nitrogenous bases: adenine (A), guanine (G) cytosine (C), and thymine (T).

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Adenine and guanine are classified as purines. The primary structure of a purine consists of two carbon-nitrogen rings. Cytosine, thymine, and uracil are classified as pyrimidines which have a single carbon-nitrogen ring as their primary structure. Each of these basic carbon-nitrogen rings has different functional groups attached to it. In molecular biology shorthand, the nitrogenous bases are simply known by their symbols A, T, G, C, and U. DNA contains A, T, G, and C whereas RNA contains A, U, G, and C.

Five-Carbon Sugar

The pentose sugar in DNA is deoxyribose and in RNA it is ribose. The difference between the sugars is the presence of the hydroxyl group on the second carbon of the ribose and hydrogen on the second carbon of the deoxyribose. The carbon atoms of the sugar molecule are numbered as 1′, 2′, 3′, 4′, and 5′ (1′ is read as “one prime”).

Phosphate Group

The phosphate residue is attached to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms a 5′3′ phosphodiester linkage. The phosphodiester linkage is not formed by simple dehydration reaction like the other linkages connecting monomers in macromolecules: its formation involves the removal of two phosphate groups. A polynucleotide may have thousands of such phosphodiester linkages.

The DNA Double Helix

The DNA double helix looks like a twisted staircase, with the sugar and phosphate backbone surrounding complementary nitrogen bases.

Key Points

The structure of DNA is called a double helix, which looks like a twisted staircase.

The sugar and phosphate make up the backbone, while the nitrogen bases are found in the center and hold the two strands together.

The nitrogen bases can only pair in a certain way: A pairing with T and C pairing with G. This is called base pairing.

Due to the base pairing, the DNA strands are complementary to each other, run in opposite directions, and are called antiparallel strands.

Key Terms

  • mutation: any error in base pairing during the replication of DNA
  • sugar-phosphate backbone: The outer support of the ladder, forming strong covalent bonds between monomers of DNA.
  • base pairing: The specific way in which bases of DNA line up and bond to one another; A always with T and G always with C.
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DNA is a Double Helix: Native DNA is an antiparallel double helix. The phosphate backbone (indicated by the curvy lines) is on the outside, and the bases are on the inside. Each base from one strand interacts via hydrogen bonding with a base from the opposing strand.

A Double-Helix Structure

DNA has a double-helix structure, with sugar and phosphate on the outside of the helix, forming the sugar-phosphate backbone of the DNA. The nitrogenous bases are stacked in the interior in pairs, like the steps of a staircase; the pairs are bound to each other by hydrogen bonds. The two strands of the helix run in opposite directions. This antiparallel orientation is important to DNA replication and in many nucleic acid interactions.

Base Pairs

Only certain types of base pairing are allowed. This means Adenine pairs with Thymine, and Guanine pairs with Cytosine. This is known as the base complementary rule because the DNA strands are complementary to each other.

If the sequence of one strand is AATTGGCC, the complementary strand would have the sequence TTAACCGG.

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Antiparallel Strands: In a double stranded DNA molecule, the two strands run antiparallel to one another so one is upside down compared to the other. The phosphate backbone is located on the outside, and the bases are in the middle. Adenine forms hydrogen bonds (or base pairs) with thymine, and guanine base pairs with cytosine.

DNA Replication

During DNA replication, each strand is copied, resulting in a daughter DNA double helix containing one parental DNA strand and a newly synthesized strand. At this time it is possible a mutation may occur. A mutation is a change in the sequence of the nitrogen bases. For example, in the sequence AATTGGCC, a mutation may cause the second T to change to a G. Most of the time when this happens the DNA is able to fix itself and return the original base to the sequence. However, sometimes the repair is unsuccessful, resulting in different proteins being created.

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DNA Packaging

DNA packaging is an important process in living cells. Without it, a cell is not able to accommodate the large amount of DNA that is stored inside.

Key Points

In eukaryotic cells, DNA and RNA synthesis occur in a different location than protein synthesis; in prokaryotic cells, both these processes occur together.

DNA is “supercoiled” in prokaryotic cells, meaning that the DNA is either under-wound or over-wound from its normal relaxed state.

In eukaryotic cells, DNA is wrapped around proteins known as histones to form structures called nucleosomes.

Key Terms

  • nucleosomes: The fundamental subunit of chromatin, composed of a little less than two turns of DNA wrapped around a set of eight proteins called histones.
  • histones: The chief protein components of chromatin, which act as spools around which DNA winds.

A eukaryote contains a well-defined nucleus, whereas in prokaryotes the chromosome lies in the cytoplasm in an area called the nucleoid. In eukaryotic cells, DNA and RNA synthesis occur in a separate compartment from protein synthesis. In prokaryotic cells, both processes occur together. What advantages might there be to separating the processes? What advantages might there be to having them occur together?

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Eukaryotic and prokaryotic cells: A eukaryote contains a well-defined nucleus, whereas in prokaryotes, the chromosome lies in the cytoplasm in an area called the nucleoid.

The size of the genome in one of the most well-studied prokaryotes, E.coli, is 4.6 million base pairs (approximately 1.1 mm, if cut and stretched out). So how does this fit inside a small bacterial cell? The DNA is twisted by what is known as supercoiling. Supercoiling means that DNA is either under-wound (less than one turn of the helix per 10 base pairs) or over-wound (more than 1 turn per 10 base pairs) from its normal relaxed state. Some proteins are known to be involved in the supercoiling; other proteins and enzymes such as DNA gyrase help in maintaining the supercoiled structure.

Eukaryotes, whose chromosomes each consist of a linear DNA molecule, employ a different type of packing strategy to fit their DNA inside the nucleus. At the most basic level, DNA is wrapped around proteins known as histones to form structures called nucleosomes. The histones are evolutionarily conserved proteins that are rich in basic amino acids and form an octamer. The DNA (which is negatively charged because of the phosphate groups) is wrapped tightly around the histone core. This nucleosome is linked to the next one with the help of a linker DNA. This is also known as the “beads on a string” structure. This is further compacted into a 30 nm fiber, which is the diameter of the structure. At the metaphase stage the chromosomes are at their most compact, approximately 700 nm in width, and are found in association with scaffold proteins.

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Eukaryotic chromosomes: These figures illustrate the compaction of the eukaryotic chromosome.

In interphase, eukaryotic chromosomes have two distinct regions that can be distinguished by staining. The tightly packaged region is known as heterochromatin, and the less dense region is known as euchromatin.

Heterochromatin usually contains genes that are not expressed, and is found in the regions of the centromere and telomeres. The euchromatin usually contains genes that are transcribed, with DNA packaged around nucleosomes but not further compacted.

Types of RNA

RNA is the nucleic acid that makes proteins from the code provided by DNA through the processes of transcription and translation.

Key Points

The nitrogen bases in RNA include adenine (A), guanine (G), cytosine (C), and uracil (U).

Messenger RNA (mRNA) carries the code from the DNA to the ribosomes, while transfer RNA (tRNA) converts that code into a usable form.

Ribosomes are the sites where tRNA and rRNA assemble proteins.

RNA differs from DNA in that it is single stranded, has uracil instead of thymine, carries the code for making proteins instead of directing all of the cell ‘s functions, and has ribose as its five-carbon sugar instead of deoxyribose.

Key Terms

  • codon: a sequence of three adjacent nucleotides, which encode for a specific amino acid during protein synthesis or translation
  • transcription: the synthesis of RNA under the direction of DNA

RNA Structure and Function

The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material found in all living organisms and is found in the nucleus of eukaryotes and in the chloroplasts and mitochondria. In prokaryotes, the DNA is not enclosed in a membranous envelope.

The other type of nucleic acid, RNA, is mostly involved in protein synthesis. Just like in DNA, RNA is made of monomers called nucleotides. Each nucleotide is made up of three components: a nitrogenous base, a pentose (five-carbon) sugar called ribose, and a phosphate group. Each nitrogenous base in a nucleotide is attached to a sugar molecule, which is attached to one or more phosphate groups.

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RNA Structure: A nucleotide is made up of three components: a nitrogenous base, a pentose sugar, and one or more phosphate groups. Carbon residues in the pentose are numbered 1′ through 5′ (the prime distinguishes these residues from those in the base, which are numbered without using a prime notation). The base is attached to the 1′ position of the ribose, and the phosphate is attached to the 5′ position. When a polynucleotide is formed, the 5′ phosphate of the incoming nucleotide attaches to the 3′ hydroxyl group at the end of the growing chain. Two types of pentose are found in nucleotides, deoxyribose (found in DNA) and ribose (found in RNA). Deoxyribose is similar in structure to ribose, but it has an H instead of an OH at the 2′ position. Bases can be divided into two categories: purines and pyrimidines. Purines have a double ring structure, and pyrimidines have a single ring.

In RNA, the nitrogenous bases vary slightly from those of DNA. Adenine (A), guanine (G), and cytosine (C) are present, but instead of thymine (T), a pyrimidine called uracil (U) pairs with adenine. RNA is a single stranded molecule, compared to the double helix of DNA.

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The DNA molecules never leave the nucleus but instead use an intermediary to communicate with the rest of the cell. This intermediary is the messenger RNA (mRNA). When proteins need to be made, the mRNA enters the nucleus and attaches itself to one of the DNA strands. Being complementary, the sequence of nitrogen bases of the RNA is opposite that of the DNA. This is called transcription. For example, if the DNA strand reads TCCAAGTC, then the mRNA strand would read AGGUUCAG. The mRNA then carries the code out of the nucleus to organelles called ribosomes for the assembly of proteins.

Once the mRNA has reached the ribosomes, they do not read the instructions directly. Instead, another type of RNA called transfer RNA (tRNA) needs to translate the information from the mRNA into a usable form. The tRNA attaches to the mRNA, but with the opposite base pairings. It then reads the sequence in sets of three bases called codons. Each possible three letter arrangement of A,C,U,G (e.g., AAA, AAU, GGC, etc) is a specific instruction, and the correspondence of these instructions and the amino acids is known as the “genetic code.” Though exceptions to or variations on the code exist, the standard genetic code holds true in most organisms.

The ribosome acts like a giant clamp, holding all of the players in position, and facilitating both the pairing of bases between the messenger and transfer RNAs, and the chemical bonding between the amino acids. The ribosome has special subunits known as ribosomal RNAs (rRNA) because they function in the ribosome. These subunits do not carry instructions for making a specific proteins (i.e., they are not messenger RNAs) but instead are an integral part of the ribosome machinery that is used to make proteins from mRNAs. The making of proteins by reading instructions in mRNA is generally known as “translation.

The Cell

The cell is the basic structure of the body. The human body is built of billions and trillions of cells. Cells of various organs vary according to their function.

Each cell contains the hereditary material and can make copies of itself by reproducing and multiplying. After a specific life span, the old cells die off.

Parts of the cell are called organelles. Human cells contain the following major parts:

  • Nucleus – This is the central part of the cell that carries the blueprint for the cell functioning and tells the cell when to grow, reproduce and die. It also houses DNA (deoxyribonucleic acid).
  • Mitochondria – These are the cell’s powerhouses and produce energy for the various activities of the cell.
  • Cytoplasm – This is a jelly-like fluid within the cell in which the other organelles float.
  • Endoplasmic reticulum (ER) – This helps process the molecules (e.g., proteins) created by the cell.
  • Ribosomes – These lie over the ER and process the genetic instructions or the blueprints within the DNA and create new proteins. These can also float freely in the cytoplasm.
  • Lysosomes and peroxisomes – These help in digesting foreign bacteria that invade the cell, rid the cell of toxic substances
  • Cell membrane – This is the outer lining of the cell.

The Chromosomes

Within the nucleus, the DNA strands are tightly packed to form chromosomes. During the cell division, the chromosomes are visible.

Each chromosome has a constriction point called the centromere from where two arms are formed. The short arm of the chromosome is labeled the “p arm.” The long arm of the chromosome is labeled the “q arm.”

Each pair of chromosomes is shaped differently by the location of the centromere and the size of the p and q arms.

Humans typically have 23 pairs of chromosomes, for a total of 46. Twenty-two of these pairs, called autosomes, look the same in both males and females.

The 23rd pair is called the sex chromosomes and differs between males and females. Females have two copies of the X chromosome or XX, while males have one X and one Y chromosome.

The Genes

Genes are hereditary material that lies within the cell nucleus. Genes, which are made up of DNA, act as instructions to make molecules called proteins.

The Human Genome Project has estimated that humans have between 20,000 and 25,000 genes. Every person has two copies of each gene, one inherited from each parent. These are mostly similar in all people, but a small number of genes (less than 1 percent of the total) are slightly different between people, and this forms the basis of paternity tests and DNA analysis.

Where is DNA found?

DNA, or deoxyribonucleic acid, is the hereditary material that lies within the nucleus of all cells in humans and other living organisms. Most of the DNA is placed within the nucleus and is called nuclear DNA. However, a small portion of DNA can also be found in the mitochondria and is called mitochondrial DNA or mtDNA.

What is DNA made of?

DNA contains four chemical bases:

  • Adenine (A)
  • Guanine (G)
  • Cytosine (C)
  • Thymine (T).
DNA Structure

DNA base pairs

DNA bases pair up with each other, A with T and C with G, to form units called base pairs. Each base is also attached to a sugar molecule and a phosphate molecule.

DNA in humans contains around 3 billion bases, and these are similar in two persons for about 99% of the total bases. These bases are sequenced differently for various information that needs to be transmitted. This is similar to how different sequences of letters form words and sequences of words form sentences.

Nucleotides and the double helix

A base, sugar, and phosphate in combination are called a nucleotide. Nucleotides are arranged in two long strands that form a spiral called a double helix. This looks like a twisted ladder, and the base pairs form the ladder’s rungs, and the sugar and phosphate molecules form the sides of the ladder.

How does DNA replicate itself?

The DNA can make copies of itself. Both the DNA strands open up and make a copy of each and become two DNA strands. Thus each new DNA has one copy of the old DNA from where the copy is made.

Mitochondrial DNA

The mitochondria contain a small amount of DNA. This genetic material is known as mitochondrial DNA or mtDNA.

Each cell contains hundreds to thousands of mitochondria that lie within the cytoplasm. Mitochondrial DNA contains 37 genes that help it to function normally. Thirteen of these genes provide instructions for making enzymes involved in energy production by oxidative phosphorylation. The rest of the genes help make molecules called transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs) that help in protein synthesis.

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