Chapter 10 – Molecular Biology of the Gene
10.1 Experiments showed that DNA is the genetic material
Early in the 20th century, the identity of molecules of inheritance was not known. Both DNA and protein were
thought to be the molecules of heredity. Until the 1940s, protein was believed to be the molecule of heredity.
Biologists established the role of DNA through studies of bacteria and the viruses that infect them.
1928 – Frederick Griffith: He was studying two forms of bacteria: one harmless and a pathogenic one
known to cause pneumonia. Griffith heat killed the pathogenic bacteria and added it to the harmless one.
Eventually, some of the harmless bacteria became pathogenic. He realized that the harmless bacteria had
acquired the ability to cause disease and were able to pass this ability on to their offspring. He called the a
“transforming factor” that led to inheritable change.
1952- Alfred Hershey and Martha Chase: They were able to prove that DNA was the heritable molecule in a
virus known as T2, a bacteriophage that infects E. coli. Their experiments involving the bacteria, a blender,
and radioactive sulfur proved that DNA is the hereditary material.
10.2 DNA and RNA are polymers of nucleotides
 While scientists had identified all of the atoms in DNA, it was not clear how they were arranged. DNA has
unique properties: the capacity to store genetic information, copy it, and pass it on. Yet, the arrangement that
gives it these properties was not understood. Eventually, the 3D shape was determined, and with it, the strategy
of how it works was uncovered.
• DNA and RNA are nucleic acids consisting of nucleotides. Four types of nucleotide make up DNA, each one
having a different nitrogenous base: adenine, thymine, cytosine, or guanine. The sequence can vary in
length and arrangement, so the number of combinations is huge.
• Each nucleotide is made of three parts: a phosphate group, sugar, and one base. Nucleotides are joined
together by covalent bonds between the sugar of one and the phosphate of the next, making the sugar
phosphate backbone.
• The phosphate contains a phosphorous atom at its center, giving us the acid in DNacid.The sugar has five
carbons: four in the ring and one extending above it. The ring includes an oxygen but the sugar still has
one less oxygen than ribose, hence deOXYribose. Ribose is the sugar found in RNA.
• The nucleic comes from the fact that DNA is found in the nucleus. The four bases differ in structure. There
are only two types of bases: purines (double ringed like A and G) or pyrimidines (single ringed like T and
C). RNA does not have thymine; rather it has the base uracil.
10.3 DNA is a double-stranded helix
• American James Watson and Englishman Francis Crick determined the 3D structure of DNA. Studying the
X-ray crystallography image of Rosalind Franklin, Watson deduced the basic shape of DNA to be helical.
Watson and Crick began constructing a double helix that conformed to the data from Franklin and the
chemistry that was already known.
• Franklin concluded that the sugar-phosphate backbone had to be on the outside of the helix, forcing the
nucleotides to swivel in the interior. Yet the base pairing was unclear. It was initially believed that A
paired with A, C with C, etc... But that arrangement did not work due to molecular size of the bases.
• It was determined that a purine must pair with a pyrimidine to maintain the balance of sizes. They also
realized that individual bases made the pairing specific, and that hydrogen bonds formed between them.
• Adenine hydrogen bonds best with thymine, while cytosine bonds best with guanine. (A-T, C-G). This idea
fit with data discovered by Erwin Chargaff. He found that the amount of adenine corresponded with the
amount of thymine in the strand as the amount of cytosine corresponded with that of guanine.
• This would become Chargaff’s rule: A always pairs with T and C always pairs with G.
• While the Watson and Crick rules are very specific, they do not dictate the combinations of the order or
combinations of nitrogenous bases that exist. Sequences vary widely, and each gene has its own unique
sequence.
10.4 DNA replication depends on specific base pairing
• One of biology’s overarching themes is structure’s relationship to function. This is very evident in the
double helix of DNA. Watson and Crick noticed the importance of the base pairing methods, stating, “It
has not escaped our notice that the specific pairing we have postulated immediately suggests a possible
copying mechanism for the genetic material.”
• Watson and Crick predicted that the cell applies the same complementary base pairing rules when
making a copy. The parental strands separate and become the template for assembly of a complementary
strand from a supply of free nucleotides. The nucleotides line up one at a time in complementary order to
the template strand. Enzymes link the nucleotides to form new DNA strands identical to the parent
molecule, and are termed daughter DNA.
• Watson and Crick’s method is termed semiconservative – one strand of the daughter DNA came from the
parent, while the other is new. Some complexity arises because the two sides are copying simultaneously,
but the process is extremely accurate, having possibly only one nucleotide per billion incorrectly paired.
It is also fast, human DNA can be copied in only a few hours.
10.5 DNA replication proceeds in two directions at many sites simultaneously
• Replication begins at specific places called origin of replication, which are sequences of nucleotides
where proteins attach to the DNA and separate the strands. Once open, replication can proceed in both
directions on the strand, creating replication bubbles. Running simultaneously shortens the amount of
time required to do replication.
• DNA polymerases are enzymes that link DNA nucleotides to the growing daughter strand. The
polymerase will work outward from the forking point and synthesize in short pieces as the fork opens.
Polymerase also carries out proof-reading steps that remove nucleotides that paired incorrectly. DNA
ligase links the pieces together in one strand. Both enzymes are responsible for repairs in DNA that can
result from environmental issues like UV light, x-rays, or chemicals such as those in smoke.
• Replication ensures that somatic (body) cells carry the same genetic information, and that they are
copied generation to generation.
10.6 The DNA genotype is expressed as proteins, which provide the molecular basis for phenotypic
traits
• An organism’s genotype is its genetic information, or inheritable traits contained in the DNA. The
phenotype is an organism’s specific traits. DNA inherited by an organism specifies traits by directing DNA
synthesis.A gene does not build a protein directly; it has to dispatch the instructions from the DNA in the
form of RNA to the ribosome. The two stages of protein synthesis are transcription and translation.
• Transcription transfers the information in DNA into RNA, while translation transfers the information of
RNA into proteins.
• The relationship between genes and proteins was proposed in 1909 by Archibald Garrod. He suggested
that genes dictate phenotypes through enzymes, the proteins that catalyze chemical processes in the cell.
To prove his ides, he studied inherited diseases. He hypothesized that an inherited disease resulted from
an “inborn error of metabolism” that did not allow the person to make a necessary enzyme. It was
decades later before his hypothesis was found true.
• George Beadle and Edward Tatum (1940s) studied the bread mold Neurospora crassa, particularly strains
that were unable to grow on a simple growth medium. They showed that a single defective gene caused
them to lack an enzyme needed by a particular metabolic pathway. This led to the one gene: one enzyme
hypothesis, which would be modified into the one gene: one polypeptide hypothesis.
10.7 Genetic information written in codons is translated into amino acid sequences
Genes provide the instructions for making proteins, but DNA does not do the work itself. It is transcribed into
mRNA and then translated into a protein. DNA is written in a linear sequence of nucleotide bases. Specific
sequences of bases with a beginning and end make up a gene. A typical gene is hundreds to thousands of
nucleotides long.
10.8 The genetic code dictates how codons are translated into amino Acids
The “genetic code” is a set of rules that relate codons of RNA to amino acids in proteins. Of the 64 triplet
codons, 61 code for amino acids. The codon AUG codes for the amino acid methionine as well as provides the
signal to start building a polypeptide. Three other codons, UAA, UAG, and UGA are stop codons that mark the
end of protein synthesis. This genetic vocabulary is shared by all living things from bacteria to the most
complex plants and animals.
10.9 Transcription produces genetic messages in the form of RNA
During transcription, the DNA strand opens and one of the strands serves as the template that the mRNA will
be written from. The RNA will follow the same base pairing rules that govern DNA pairing, but RNA does not
have thymine, so uracil will take its place.Nucleotides will be brought in one at a time, forming hydrogen
bonds with the DNA nucleotides. The RNA nucleotides are linked by the enzyme RNA polymerase.
• Initiation – The attachment of RNA polymerase to the promoter and the start of RNA synthesis.
• Elongation – RNA synthesis continues, and the RNA peels away from the DNA template, allowing the two
strands of DNA to come back together.
• Termination – RNA polymerase reaches a sequence of bases in the template that signals the end of the
gene.
10.10 Eukaryotic RNA is processed before leaving the nucleus
• In eukaryotic cells, which have a nucleus, mRNA must exit the nucleus through nuclear pores and enter
the cytoplasm, where the machinery for protein synthesis is located. Before leaving, the mRNA is
modified. A cap is added to one end (it is a single “G” nucleotide), and a tail of 50-250 adenine nucleotides
is added to the other end. The cap and tail serve to protect the mRNA from cellular enzymes and assist in
the binding of the mRNA to the ribosome.
• Not all of the regions of a gene are coding regions. The noncoding regions are referred to as introns, while
the coding regions are called exons, these regions will be the ones expressed as amino acids. Before
leaving the nucleus, the introns will be removed and the exons join together to produce an mRNA
sequence with a continuous coding sequence. The cap and tail will remain and serve as the only exons on
the chain. RNA splicing is the procedure used to remove noncoding sections.
10.11 Transfer RNA molecules serve as interpreters during translation
• To convert the three letter codons of mRNA, a cell uses transfer, tRNA. The amino acids cannot recognize
information on the codons, so the tRNA is required to pick up the appropriate amino acids and recognize
the appropriate codons in the mRNA.
• tRNA has a shape that is specialized to its function. It is made of one strand of DNA about 80 nucleotides
in length. This strand folds on itself, making several double stranded regions where the RNA base pairs
with other stretches. A single stranded loop is at one end of the folded molecule, and it serves as the
anticodon loop. At the other end is an area where an amino acid can attach. tRNA is similar, but has slight
differences that allow for specificity in bonding to the amino acid that is coded on the mRNA.
10.12 Ribosomes build polypeptides
• Ribosomes are organelles found in the cytoplasm that coordinate the functioning of the mRNA and tRNA
and actually make the proteins. Ribosomes are made of two subunits, the large and small; each of those
are made of proteins and rRNA (ribosomal).
• tRNA anticodons and mRNA codons fit together on the ribosomes. Each ribosome has a binding site for
mRNA, and two binding sites for tRNA. The ribosomal subunits hold the tRNA and mRNA close together,
allowing the amino acids that are carried in to be connected into a polypeptide chain.
10.13 An initiation codon marks the start of an mRNA message
A sequence of nucleotides at an end of the molecule is not part of the message, but it helps mRNA bind to the
ribosome. Initiation ensures where translation will begin, ensuring that mRNA codons are translated into the
correct sequence of amino acids.
It occurs in two steps:
1. mRNA molecule binds to the small ribosomal subunit. A special initiator tRNA binds to the specific
“start” codon. The initiator carries the amino acid methionine. Its anticodon UAC binds to the start
codon AUG.
2.
The large ribosomal subunit binds to the small one, creating a functional ribosome. The initiator
tRNA fits into one of the two tRNA binding sites, called the P site. This will hold the growing protein.
The next site is termed the A site, and it waits for the next amino acid to enter.
10.14 Elongation adds amino acids to the polypeptide chain until a stop codon terminates translation
Once initiation is complete, amino acids are added one by one. Each addition occurs in a 3 step process:
1. Codon recognition – the tRNA anticodon carrying its amino acid pairs with the mRNA codon in the A
binding site.
2. Peptide bond formation – the polypeptide separates from the tRNA to which it was bound (P site)
and attaches by a peptide bond to the amino acid of the tRNA in the A site. A ribosome catalyzes the
formation of a bond.
3. Translocation – The P site tRNA leaves the ribosome, and the tRNA that had been in the A site moves
into the P site. The mRNA and tRNA remain bonded and move as a unit. This movement opens the A
site and allows for the addition of the next tRNA.
Elongation continues until a stop codon is reached. Three stop codons do not represent amino acids, but act
as signals to stop translation. The three are UAA, UAG, and UGA.
10.15 Review: the flow of genetic information in the cell is DNA RNA  protein
In transcription, mRNA is written from the DNA template. In eukaryotes, this happens in the nucleus, so the
mRNA will have to travel to the ribosome. Translation occurs in 4 steps, but the end result is that the mRNA is
made into an amino acid.
10.16 Mutations can change the meaning of genes
• Any change in the sequence of DNA is called a mutation. They can involve large regions of a chromosome,
or just a single nucleotide pair. Mutations can be divided into two general categories: base pair
substitutions/insertions or deletions.
• A substitution is the replacement of one nucleotide with another. In some cases, this will have no effect.
In other cases, the one pair changes the codon that is read, resulting in the wrong amino acid being
brought in. This can lead to a protein that is prevented from functioning normally, but rarely, it leads to
an improved protein that enhances an organism’s performance.
• Insertions or deletions of one or more nucleotides are disastrous. mRNA is read as a triplet, therefore,
adding or subtracting nucleotides shifts the frame that is being read. This results in the codons further
down being read in the wrong order. The proteins made as a result are usually nonfunctional.
• Mutagenesis is the production of mutations. Spontaneous mutations result during errors in replication or
recombination. Mutagens like UV and X-rays can lead to mutations.
10.17 Viral DNA may become part of the host chromosome
A virus is an infectious particle consisting of genetic material wrapped in a protein coat called the capsid.
Viruses are parasites that can only reproduce (replicate) within a host cell; the host cell providing the
components necessary for transcribing and translating the viral nucleic acid. Viral replication can occur in
two ways: the lytic cycle where the virus destroys the cell after replication is complete –or- the lysogenic
cycle where the viral DNA is uptaken by the host cell and replicates with it .
10.18 Many viruses cause disease in animals and plants
A typical virus has a membranous outer envelope covered in glycoprotein spikes that helps the virus enter
and leave the host cell. The amount of damage a virus causes a body is dependent on how quickly the body
responds to fight it, and to a lesser degree, on the body’s ability to repair the tissue damaged by the virus.
10.19 Emerging viruses threaten human health
Emerging viruses are those that appear suddenly or are new to scientists. The question then becomes: from
where and how do such viruses come in to the human population?
Possible sources:
• Mutations from an existing virus
• Movement of a virus from one species to a new species
• Spread of a virus from an isolated population
10.20 The AIDS virus makes DNA on an RNA template
AIDS is caused by the HIV virus, an RNA virus. RNA viruses have a unique method of reproduction, and are
termed retroviruses. The RNA uses an enzyme, reverse transcriptase, to “write” its RNA into DNA.
10.21 Viroids and Prions are formidable pathogens in plants and animals
Viroids are small circular RNA molecules that infect plants by seemingly causing errors in regulatory systems
that control plant growth. Prions are infectious proteins known to cause degenerative nervous disorders such
as Mad Cow.
10.22 Bacteria can transfer DNA in three ways
1. Transformation – the uptake of DNA from the surrounding environment
2. Transduction – the transfer of bacterial genes by a phage as during the lytic cycle (if the host DNA is
packaged with the phage’s coat, then it can be passed to another cell)
3. Conjugation – the physical union of two bacterial cells to transfer DNA between them using a sex
pilus (this can be in same or different species)
10.23 Bacterial plasmids can serve as carriers for gene transfer
E. Coli can carry out conjugation due to a piece of DNA called the F factor, which allows for the production of a
sex pilus. The F factor can exist as a plasmid, which is a circular piece of DNA separate from the bacterial
chromosome. Many bacteria have several different plasmids, and some can carry gene codes that help the cell
survive. A specific plasmid, the R plasmid, is of concern in the medical community, as it contains the codes for
antibiotic resistance.