3.5: Nucleic Acids

3.5.1: DNA and RNA

Learning Objective

Describe the structure of nucleic acids and the types of molecules that contain them

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

genome

the cell's complete genetic information packaged as a double-stranded DNA molecule

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

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:

1. a nitrogenous base
2. a pentose (five-carbon) sugar
3. a phosphate group

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

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).

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.

3.5.2: The DNA Double Helix

Learning Objective

Describe the structure of DNA

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

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.

sugar-phosphate backbone

The outer support of the ladder, forming strong covalent bonds between monomers of DNA.

mutation

any error in base pairing during the replication of DNA

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.

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.

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.

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.

3.5.3: DNA Packaging

Learning Objective

Describe how DNA is packaged differently in prokaryotes and eukaryotes

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

histones

The chief protein components of chromatin, which act as spools around which DNA winds.

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.

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?

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.

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.

3.5.4: Types of RNA

Learning Objective

Describe the structure and function of RNA

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

transcription

the synthesis of RNA under the direction of DNA

codon

a sequence of three adjacent nucleotides, which encode for a specific amino acid during protein synthesis or translation

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.

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.

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."

Attributions

• DNA and RNA
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  • "monomer." http://en.wiktionary.org/wiki/monomer. Wiktionary CC BY-SA 3.0.
  • "nucleotide." http://en.wiktionary.org/wiki/nucleotide. Wiktionary CC BY-SA 3.0.
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  • "genome." http://en.wiktionary.org/wiki/genome. Wiktionary CC BY-SA 3.0.
  • "OpenStax College, Nucleic Acids. October 16, 2013." http://cnx.org/content/m44403/latest/Figure_03_05_01.jpg. OpenStax CNX CC BY 3.0.
• The DNA Double Helix
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  • "mutation." http://en.wiktionary.org/wiki/mutation. Wiktionary CC BY-SA 3.0.
  • "OpenStax College, Biology. October 16, 2013." http://cnx.org/content/m44403/latest/?collection=col11448/latest. OpenStax CNX CC BY 3.0.
  • "OpenStax College, Nucleic Acids. October 16, 2013." http://cnx.org/content/m44403/latest/Figure_03_05_03.png. OpenStax CNX CC BY 3.0.
  • "OpenStax College, Nucleic Acids. October 16, 2013." http://cnx.org/content/m44403/latest/Figure_03_05_02.jpg. OpenStax CNX CC BY 3.0.
• DNA Packaging
  • "Histones." https://en.wikipedia.org/wiki/Histone. Wikipedia CC BY-SA 3.0.
  • "DNA structure." http://cnx.org/contents/GFy_h8cu@9.87:U7tPDRxK@7/DNA-Structure-and-Sequencing. OpenStax CNX CC BY-SA 3.0.
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  • "figure6.jpg." http://cnx.org/contents/185cbf87-c72e-48f5-b51e-f14f21b5eabd@9.87. OpenStax CNX CC BY-SA 3.0.
• Types of RNA
  • "Boundless." http://www.boundless.com/. Boundless Learning CC BY-SA 3.0.
  • "OpenStax College, Biology. October 16, 2013." http://cnx.org/content/m44403/latest/?collection=col11448/latest. OpenStax CNX CC BY 3.0.
  • "codon." http://en.wiktionary.org/wiki/codon. Wiktionary CC BY-SA 3.0.
  • "Fact Sheet: DNA-RNA-Protein." http://microbe.net/simple-guides/fact-sheet-dna-rna-protein/. microBEnet CC BY-SA 3.0.
  • "transcription." http://en.wiktionary.org/wiki/transcription. Wiktionary CC BY-SA 3.0.
  • "OpenStax College, Nucleic Acids. May 20, 2015." http://cnx.org/contents/cb178029-ce17-4c82-aa11-94a2acf4accf@8/Nucleic_Acids. OpenStax CNX CC BY-SA 3.0.