Reading Guide
Chapter 7: The Blueprint of life, from DNA to protein
This chapter is about the characteristics and structure of DNA, the process of DNA replication,
the process of protein synthesis, and a look at ways to regulate gene expression. Let’s start with a quick
review of DNA. Think of some of the key ideas you already know about the structure and function of
DNA and make a list of them…..here are the keys ideas you should include.
All organisms (whether it be a bacterium or human) have a genome which consists of all the
genetic material of the cell. This genome is composed of DNA, and in all cells is in the form of doublestranded DNA. Bacterial cells have just one chromosome which is double-stranded and in a circular form.
So what exactly is the chemical composition of DNA? It is composed of a phosphate-sugar
backbone, the sugar and phosphate are covalently bonded in alternating subunits. The sugar found in the
structure of DNA is deoxyribose and it is here that the nitrogenous bases bind. In DNA, these nitrogenous
bases are adenine, guanine, cytosine, and thymine. Can you draw a model of DNA?
A few more characteristics of DNA…it has two strands that are antiparallel, meaning that one
strand has the orientation 5’-3’ and the other is in the opposite orientation running 3’5’. What do the
terms 5’ (5-prime) and 3’ (3-prime) refer to? These are references back to the structure of the sugar,
deoxyribose, specifically the number of the carbon in the sugar. At the 3’ position there is a hydroxyl
group in deoxyribose and at the 5’ position there is a phosphate group. What kinds of bonds are holding
the sugar and phosphate groups together in the backbone of DNA? What kinds of bonds are holding the
bases together? Which reminds me….we need to mention that there are also base pairing rules. If you
know the sequence of bases on one strand of DNA you can predict the sequence in the complementary
strand. The rules for base pairing are adenine and thymine pair together and cytosine and guanine pair
together.
The DNA is essential for two key processes in the cell, cell replication and protein synthesis.
Every time a new cell is made the genetic information needs to be replicated. Let’s look this process
briefly first. In DNA replication, the two strands of DNA open and an enzyme reads one of the strands
and synthesizes a complementary strand of DNA. In bacterial cells this process begins at a location in the
chromosome called the origin of replication, and replication proceeds bidirectionally with the enzyme
DNA Polymerase synthesizing the new strand of DNA. DNA polymerase is an amazing enzyme that can
build a complementary strand of DNA in the direction 5’3’ and proofread itself to make sure that the
correct base is inserted. This enzyme will only start the process of replication when a primer is placed on
the DNA strand, essentially the restriction with DNA polymerase is that it can only build a new strand
with a starting fragment….or primer in place. This primer is made by another enzyme called primase and
consists of a short sequence of RNA. So….if you are following me I just stated that DNA replication
involves the synthesis of a new strand of DNA from an RNA primer. This means that the DNA strand
will have sections which consist of RNA, which is only temporary as the DNA Polymerase enzyme will
remove these sections of RNA and replace them with DNA. A few other terms…the replication fork is
the place where replication is occurring. There are other enzymes involved in the process of DNA
replication, helicases and DNA gyrase are important in unwinding the strand so that replication can
proceed.
One more thing about DNA replication. Remember the enzyme DNA Polymerase can only
synthesize a new strand in the direction 5’3’, if the DNA is double stranded with the strands in
antiparallel orientation, how does this happen? What is meant by the terms leading and lagging strands of
DNA? Can you describe the process of replication of these two strands? (Use Fig 7.7 as a guide).
DNA is also essential for gene expression in cells. Gene expression is used to describe the
process of protein synthesis, which includes transcription and translation. Transcription is the first step
towards synthesis if a protein and requires the enzyme RNA polymerase and the DNA (as a template).
Since we are synthesizing only one strand of RNA in the direction 5’-3’, the enzyme will bind to the
appropriate strand of DNA to generate a single strand of RNA. This process begins at a sequence in the
DNA called the promoter region and continues until the terminator sequence in the DNA is reached. It is
the promoters that regulate the direction of transcription, or rather indicates which of the DNA strands is
to be read by RNA Polymerase. Once the process of transcription is complete…what do you have? A
strand of RNA!
This strand of RNA is then processed through translation, where we have synthesis of a protein as
the final product. The steps in this process are not as important as understanding what components are
necessary. For translation you need your mRNA strand, amino acids, ribosomes, and tRNAs. The mRNA
associates with the ribosomes (the 30S ribosome bind to the ribosome-binding site) and the first time the
codon AUG appears after that site translation starts. The ribosome assembles at the first AUG…meaning
that additional initiation factors bind and the 50S subunit of the ribosome binds creating a complete
ribosome….and translation begins. There are two “places” for the ribosome to hold a tRNA carrying an
amino acid. I like to think of the structure of the ribosome as a two-seated car, once both of the “seats” are
filled with tRNAs a peptide bind can be formed between the two amino acids. This process will continue
until a STOP codon (UAG, UGA, or UAA) is read by the ribosome. When the stop codon is reached
enzymes called release factors break the bond between the peptide and the tRNA, the ribosome falls off
the mRNA and dissociates. You now have a polypeptide strand that needs to be folded or modified before
it can function as a protein.
The last big key idea in this chapter has to do with gene regulation. It is important that bacteria
regulate genes, essentially “making” only the proteins that are needed at a given time. While many genes
are regulated (turned on or off) others are actually always made. For example, the genes to metabolize
glucose via glycolysis are always made or constitutive. Why do you think that these genes are always
made??
When looking at different types of gene regulation there are three main categories, constitutive
enzymes, inducible enzymes, and repressible enzymes. Remember that constitutive enzymes are always
made, as I mentioned in the above paragraph. Inducible enzymes are turned “on” when needed. Think of
“inducing” or turning the pathway “on” when it is needed. Repressible enzymes are always “on” and can
be repressed or turned “off” when the conditions are right.
Before we take a look at the model of the lactose operon as an example of gene regulation we
need to consider that there are mechanisms to control transcription….remember we are talking about
regulating the expression of genes which means controlling the protein product. Some proteins bind to the
DNA directly at a specific location called the operator and repress the ability for transcription to proceed.
Figure 7.21 identifies some good models for how repressor proteins play a role in inducible enzymes and
repressible enzymes. Activators are proteins that facilitate transcription….they promote the process of
transcription. Often these proteins (activators) work by binding to the DNA and enhance the ability of
RNA polymerase to bind. Figure 7.22 is a good visual for the mechanism of activators.
The lactose operon is a good model of enzyme induction. Before we talk anymore about it, let’s
define an operon as a collection of closely associated genes. The lactose operon consists of genes required
to metabolize (breakdown) lactose. Since these enzymes have a specific function (to facilitate the
metabolism of lactose) they are only needed when lactose is present. In the absence of lactose the
repressor protein binds to the operator region and no transcription occurs. In the presence of lactose the
repressor protein is bound to a form of lactose known as allolactose, with the operator region not blocked
RNA polymerase can bind to the promoter region and transcribe mRNA for these proteins. Of course
there are a few more details to consider in order to have the genes transcribed or the lactose operon turned
on. There also has to be an increase in the levels of cAMP in the cell which bind to the CAP protein, this
complex functions as an activator. So…inorder to get the lactose operon turned “on” you need to have
lactose present, glucose absent, and high levels of cAMP. Review the figures 7.23 and 7.25 for a
summary of lactose operon regulation.
Section 7.5 provides some nice examples of applications of how bacterial organisms can regulate
genes in response to their environment. Bacteria can respond to their environment and alter gene
expression using signal transduction mechanisms (such as quorum sensing and two-component regulatory
systems) or natural selection. As you read this section think of examples we have already mentioned in
class. What advantage is their to an organism to be able to regulate gene expression in response to their
environment?