Figure 8.6
The DNA double helix. The two sides are the sugar-phosphate backbones, composed of alternating phosphate groups and deoxyribose sugars. The nitrogenous bases face the center of the double helix.
The double helical nature of DNA, together with the findings of Chargaff, demonstrated the base-pairing nature of the bases. Adenine always pairs with thymine, and guanine always pairs with cytosine (Figure below). Because of this complementary nature of DNA, the bases on one strand determine the bases on the other strand. These complementary base pairs explain why the amounts of guanine and cytosine are present in equal amounts, as are the amounts of adenine and thymine. Adenine and guanine are known as purines. These bases consist of two ring structures. Purines make up one of the two groups of nitrogenous bases. Thymine and cytosine are pyrimidines, which have just one ring structure. By having a purine always combine with a pyrimidine in the DNA double helix, the distance between the two sugar-phosphate backbones is constant, maintaining the uniform shape of the DNA molecule.
Figure 8.7
The base-pairing nature of DNA. Adenine always pairs with thymine, and they are held together with two hydrogen bonds. The guanine-cytosine base pair is held together with three hydrogen bonds. Note that one sugar-phosphate backbone is in the 5 3 direction, with the other strand in the opposite 3 5 orientation.
The two strands in the DNA backbone run in anti-parallel directions to each other. That is, one of the DNA strands is built in the 5' → 3' direction, while the complementary strand is built in the 3' → 5' direction. In the DNA backbone, the sugars are joined together by phosphate groups that form bonds between the third and fifth carbon atoms of adjacent sugars. In a double helix, the direction of the nucleotides in one strand is opposite to their direction in the other strand. 5' and 3' each mark one end of a strand. A strand running in the 5'→ 3' direction that has adenine will pair with base thymine on the complementary strand running in 3'→ 5' direction.
So it is this four letter code, made of just A, C, G, and T, that determines what the organism will become and what it will look like. How can these four bases carry so much information? This information results from the order of these four bases in the chromosomes. This sequence carries the unique genetic information for each species and each individual. Humans have about 3,000,000,000 bits of this information in each cell. A gorilla may also have close to that amount of information, but a slightly different sequence. For example, the sequence AGGTTTACCA will have different information than CAAGGGATTA. The closer the evolutionary relationship is between two species, the more similar their DNA sequences will be. For example, the DNA sequences between two species of reptiles will be more similar than between a reptile and an elm tree.
DNA sequences can be used for scientific, medical, and forensic purposes. DNA sequences can be used to establish evolutionary relationships between species, to determine a person’s susceptibility to inherit or develop a certain disease, or to identify crime suspects or victims. Of course, DNA analysis can be used for other purposes as well. So why is DNA so useful for these purposes? It is useful because every cell in an organism has the same DNA sequence. For this to occur, each cell must have a mechanism to copy its entire DNA. How can so much information be exactly copied in such a small amount of time?
DNA Replication
DNA replication is the process in which a cell’s entire DNA is copied, or replicated. This process occurs during the Synthesis (S) phase of the eukaryotic cell cycle. As each DNA strand has the same genetic information, both strands of the double helix can serve as templates for the reproduction of a new strand. The two resulting double helices are identical to the initial double helix. For an animation of DNA replication, see http://www.hhmi.org/biointeractive/media/DNAi_replication_vo1-sm.mov.
Helicase and Polymerase
DNA replication begins as an enzyme, DNA helicase, breaks the hydrogen bonds holding the two strands together and forms a replication fork. The resulting structure has two branching strands of DNA backbone with exposed bases. These exposed bases allow the DNA to be “read” by another enzyme, DNA polymerase, which then builds the complementary DNA strand. As DNA helicase continues to open the double helix, the replication fork grows.
5' → 3'
The two new strands of DNA are “built” in opposite directions, through either a leading strand or a lagging strand. The leading strand is the DNA strand that DNA polymerase constructs in the 5' → 3' direction. This strand of DNA is made in a continuous manner, moving as the replication fork grows. The lagging strand is the DNA strand at the opposite side of the replication fork from the leading strand. It goes in the opposite direction, from 3' to 5'. DNA polymerase cannot build a strand in the 3' → 5' direction. Thus, this “lagging” strand is synthesized in short segments known as Okazaki fragments. On the lagging strand, an enzyme known as primase builds a short RNA primer. DNA polymerase is then able to use the free 3' OH group on the RNA primer to make DNA in the 5' → 3' direction. The RNA fragments are then degraded and new DNA nucleotides are added to fill the gaps where the RNA was present. Another enzyme, DNA ligase, is then able to attach (ligate) the DNA nucleotides together, completing the synthesis of the lagging strand (Figure below).
Figure 8.8
DNA replication. The two DNA strands are opened by helicase. The strands are held open by a single strand of binding proteins, preventing premature reannealing. Topoisomerase solves the problem caused by tension generated by winding/unwinding of DNA. This enzyme wraps around DNA and makes a cut permitting the helix to spin and relax. Once DNA is relaxed, topoisomerase reconnects broken strands. DNA primase synthesizes a short RNA primer which initiates the Okazaki fragment. Okazaki fragments are attached by DNA ligase.
Many replication forks develop along a chromosome. This process continues until the replication forks meet, and the all of the DNA in a chromosome has been copied. Each new strand that has formed is complementary to the strand used as the template. Each resulting DNA molecule is identical to the original DNA molecule. During prophase of mitosis or prophase I of meiosis, these molecules of DNA condense into a chromosome made of two identical chromatids. This process ensures that cells that result from cell division have identical sets of genetic material, and that the DNA is an exact copy of the parent cell’s DNA.
RNA
DNA → RNA → Protein
“DNA makes RNA makes protein.” So what exactly is RNA? Ribonucleic acid, or RNA, is the other important nucleic acid in the three player act. When we say that “DNA makes RNA makes protein,” what do we mean? We mean that the information in DNA is somehow transferred into RNA, and that the information in RNA is then used to make the protein.
To understand this, it helps to first understand RNA. If you remember from the chapter titled Cell Division and Reproduction, a gene is a segment of DNA that contains the information necessary to encode an RNA molecule or a protein. Keep in mind that even though you have many thousands of genes, not all are used in every cell type. In fact, probably only a few thousand are used in a particular type of cell, with different cell types using different genes. However, while these genes are embedded in the large chromosomes that never leave the nucleus, the RNA is relatively small and is able to carry information out of the nucleus.
RNA Structure
RNA structure differs from DNA in three specific ways. Both are nucleic acids and made out of nucleotides; however, RNA is single stranded while DNA is double stranded. RNA contains the 5-carbon sugar ribose, whereas in DNA, the sugar is deoxyribose. Though both RNA and DNA contain the nitrogenous bases adenine, guanine and cytosine, RNA contains the nitrogenous base uracil instead of thymine. Uracil pairs with adenine in RNA, just as thymine pairs with adenine in DNA. A comparison of RNA and DNA is shown in Table below and Figure below.
A Comparison of RNA and DNA RNA DNA
single stranded double stranded
Specific Base contains uracil contains thymine
Sugar rib
ose deoxyribose
Size relatively small big (chromosomes)
Location moves to cytoplasm stays in nucleus
Types 3 types: mRNA, tRNA, rRNA generally 1 type
Figure 8.9
A comparison of RNA and DNA. RNA is single stranded and contains the base uracil, which replaces thymine.
Three Types of RNAs
So what does RNA do? There are three types of RNA: messenger RNA (mRNA), transfer RNA (tRNA), and ribisomal RNA (rRNA). All three of these nucleic acids work together to produce a protein. The mRNA takes the instructions from the nucleus to the cytoplasm, where the ribosomes are located. Ribosomes are where the proteins are made. The ribosomes themselves are made out of rRNA and other proteins. The mRNA binds to the ribosome, bringing the instructions to order the amino acids to the site of protein synthesis. Finally, the tRNA brings the correct amino acid to the site of protein synthesis (Figure below and Figure below). In mRNA, the four nucleotides (A, C, G, and U) are arranged into codons of three bases each. Each codon encodes for a specific amino acid, except for the stop codons, which terminate protein synthesis. tRNA, which has a specific “3-leaf clover structure,” contains a three base region called the anticodon, which can base pair to the corresponding three-base codon region on mRNA. More will be discussed on these processes during the lesson on translation that follows.
Remember, proteins are made out of amino acids, so how does the information get converted from the language of nucleotides to the language of amino acids? The process is called translation.
Figure 8.10
2-Dimensional tRNA structure depicting the 3-leaf clover structure. The D arm (D) is one stem ending in a loop. The anticodon arm (A) is a second stem whose loop contains the anticodon on the bottom of the tRNA. The T arm (T) is the third stem opposite the D arm.
Figure 8.11
3-Dimensional representation of a tRNA. Coloring: CCA tail in orange, Acceptor stem in purple, D arm in red, Anticodon arm in blue with Anticodon in black, and T arm in green. The acceptor stem is made by the base pairing of the 5'-terminal nucleotide with the 3'-terminal nucleotide. The CCA tail is a CCA sequence at the 3' end of the tRNA molecule, used to attach the amino acid. This sequence is important for the recognition of tRNA by enzymes critical in translation.
Small interfering RNA (siRNA), microRNA (miRNA) and small nuclear RNA (snRNA): siRNA and miRNA are revolutionizing molecular biology, developmental biology, and even medicine. The 2006 Nobel prize in Physiology and Medicine was awarded to Dr. Andrew Fire and Dr. Craig Mello for their discovery of siRNA, which is a type of double-stranded RNA that inhibits gene expression at the mRNA level. Specifically, siRNA acts on homologous processed mRNA by targeting it for degradation. siRNA is responsible for RNA interference (RNAi). RNAi has a natural role in that it is used by plants in defense against plant viral RNAs. miRNAs are also involved in the regulation of gene expression. They are transcribed but not translated into proteins. snRNAs are found within the nucleus of eukaryotic cells. They are involved in a variety of important processes such as RNA splicing (removal of introns), and regulation of transcription factors (discussed in Lesson 8.2: Protein Synthesis).
Lesson Summary
Griffith demonstrated the process of transformation, which is the change in genotype and phenotype due to the assimilation of the external DNA by a cell.
Avery and colleagues demonstrated that DNA was the transforming material.
The Hershey and Chase experiments conclusively demonstrated that DNA is the genetic material.
Watson and Crick demonstrated the double helix model of DNA.
The Base paring rules state that A always pairs with T and G always pairs with C.
DNA replication is the process by which a cell’s entire DNA is copied, or replicated.
During DNA replication, the two new strands of DNA are “built” in opposite directions, starting at replication forks.
RNA is a single-stranded nucleic acid.
RNA contains the nitrogenous base uracil.
There are three types of RNA: mRNA, tRNA, and rRNA.
mRNA is the intermediary between the nucleus, where the DNA lives, and the cytoplasm, where proteins are made.
Review Questions
Discuss how DNA was identified as the genetic material.
Define transformation.
In DNA, why does the amount of adenine approximately equal the amount of thymine?
What are the base pairing rules?
Explain Watson and Crick’s double helix model of DNA.
How is DNA replicated?
Discuss the importance of mRNA.
Explain the main differences between mRNA, rRNA,and tRNA.
Further Reading / Supplemental Links
Campbell, N.A. and Reece, J.B. Biology, Seventh Edition, Benjamin Cummings, San Francisco, CA, 2005.
Biggs, A., Hagins, W.C., Kapicka, C., Lundgren, L., Rillero, P., Tallman, K.G., and Zike, D., Biology: The Dynamics of Life, California Edition, Glencoe Science, Columbus, OH, 2005.
Nowicki S., Biology, McDougal Littell, Evanston, IL, 2008. The Dolan DNA Learning Center.
http://www.dnalc.org/home_alternate.html
DNA Interactive:
http://www.dnai.org/
A Science Odyssey:
http://www.pbs.org/wgbh/aso/tryit/dna/
National Human Genome Research Institute:
http://www.genome.gov
The RNA Modification Database:
http://library.med.utah.edu/RNAmods/
The RNA World:
http://nobelprize.org/nobel_prizes/chemistry/articles/altman/index.html
http://en.wikipedia.org
Vocabulary
amino acid
The monomers that combine to form a polypeptide (protein).
anticodon
A 3 base sequence on the tRNA that base pairs with the codon on the mRNA.
anti-parallel
Describes the orientation of the two DNA strands; one of the DNA strands is built in the 5' → 3' direction, while the complementary strand is built in the 3' → 5' direction.
bacteriophage
A virus that infects bacteria.
codon
A sequence of three nucleotides within mRNA; encodes for a specific amino acid or termination (stop) sequence.
deoxyribonuclease
An enzyme which degrades DNA.
DNA
Deoxyribonucleic acid, the genetic (heredity) material.
DNA polymerase
The enzyme that builds a new DNA strand during DNA replication.
DNA helicase
The enzyme that breaks the hydrogen bonds holding the two DNA strands together during DNA replication.
DNA ligase
An enzyme that joins broken nucleotides together by catalyzing the formation of a bond between the phosphate group and deoxyribose sugar of adjacent nucleotides in the DNA backbone.
DNA replication
The process in which a cell’s entire DNA is copied.
double helix
The shape of DNA, resembling a spiral staircase.
gene
A segment of DNA that contains the information necessary to encode an RNA molecule or a protein.
lagging strand
The DNA strand at the opposite side of the replication fork from the leading strand.
leading strand
The DNA strand that DNA polymerase constructs in the 5' → 3' direction.
mRNA
Messenger RNA; serves as a nucleic acid intermediate between the nucleus and the ribosomes.
nucleotide
Monomer of nucleic acids, composed of a nitrogen-containing base, a five-carbon sugar, and a phosphate group.
Okazaki fragments
Short fragments of DNA that comprise the lagging strand.
primase
An enzyme that builds a short RNA primer on the lagging strand during DNA replication.
purines
Nitrogenous b
ases consisting of two ring structures; adenine and guanine.
pyrimidines
Nitrogenous bases consisting of one ring structure; thymine and cytosine.
ribosome
Non-membrane bound organelle; site of protein synthesis.
RNA
Ribonucleic acid; single-stranded nucleic acid.
rRNA
Ribosomal RNA; together with proteins, forms ribosomes.
sugar-phosphate backbone
The sides of the DNA double helix; composed of alternating phosphate groups and deoxyribose sugars.
transcription
The process of making an mRNA from the information in the DNA sequence.
translation
The process of making a protein from the information in a mRNA sequence.
transformation
The change in genotype and phenotype due to the assimilation of external DNA (heredity material) by a cell.
tRNA
Transfer RNA; brings amino acids to the ribosome.
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