ZOL2602 Exam Prep
SECTION 1
Unit 1: DNA
Briefly list the contributions made by Watson, Crick and Chargaff regarding the three
dimensional structure of the DNA double helix.
To solve the structure of DNA, Watson and Crick used model building—they built a scale
model of what they thought a DNA molecule must look like. The model had to obey the laws
of chemistry, which meant that if a polynucleotide was coiled in any way then its atoms must
not be placed too close together. It was equally vital that the model take account of the
results of other investigations into DNA structure. One of these studies was carried out by
Erwin Chargaff at Columbia University in New York, the other, by Rosalind Franklin at King’s
College, London.
Erwin Chargaff became interested in DNA in the 1940s, when scientists first realized that
DNA might be the genetic material. He decided to use a new technique, called paper
chromatography, to measure the amounts of each of the four nucleotides in DNA from
different tissues and organisms. They revealed a simple relationship between the
proportions of the nucleotides in any one sample of DNA. The relationship is that the number
of adenines equals the number of thymines, and the number of guanines equals the number
of cytosines. In other words, A = T and G = C.But once they became aware of the A = T and
G = C relationship, they knew this had to be accounted for in their model of DNA.
If the nucleotide sequence of one polynucleotide of a DNA double helix is 5'-
ATAGCAATGCAA-3', what is the sequence of the complementary polynucleotide?
3’- TATCGTTACGTT-5’
Unit 2: Genes
Explain in detail why not all the nucleotides of a DNA molecule contribute to a gene.
The genes are separated from one another within the DNA molecule by intergenic DNA. The
lengths of many genes are inflated by the presence within them of long tracts of DNA that do
not contain any biological information. . In a discontinuous gene (also called a split or mosaic
gene) the sections containing biological information are called exons and the intervening
sequences are referred to as introns. Discontinuous genes are common in higher organisms.
More than 95% of all human genes contain at least one intron, and the average number is
nine.
What is the function of the template strand of the double helix of a gene?
,In a DNA double helix, only one of the two strands carries the biological information;
therefore, it is known as the template. This strand therefore acts as a template for synthesis
of an RNA molecule whose nucleotide sequence is determined, by the base-pairing rules, by
the DNA sequence. For some genes the RNA transcript is itself the end product of gene
expression. For others the transcript is a short-lived message that directs a second stage of
gene expression, called translation. During translation the RNA molecule (called a
messenger RNA or an mRNA) directs synthesis of a protein. In a protein the monomers are
called amino acids, and there are 20 different ones, each with its own specific chemical
properties. When a protein is made by translation, its amino acid sequence is determined by
the nucleotide sequence of the mRNA. Each triplet of adjacent ribonucleotides specifies a
single amino acid of the protein, the identity of the amino acid corresponding to each triplet
being set by the genetic code.
Explain what gene expression is and how protein synthesis is related to it.
Gene expression is the process where biological information in genes is converted into
instructions to make functional products such as proteins. Gene expression is conventionally
looked on as a two-stage process. All genes undergo the first stage of gene expression,
which is called transcription and which results in synthesis of an RNA molecule. For some
genes the RNA transcript is itself the end product of gene expression. For others the
transcript is a short-lived message that directs a second stage of gene expression, called
translation. During translation the RNA molecule (called a messenger RNA or an mRNA)
directs synthesis of a protein.
Explain what is meant by the central dogma and indicate how the original concept was
adapted to accommodate recent discoveries.
The Central Dogma of genetics is: DNA is transcribed to RNA which is translated to protein.
Protein is never back-translated to RNA or DNA; and except for retroviruses, DNA is never
created from RNA. Furthermore, DNA is never directly translated to protein. DNA to RNA to
protein.
In other words, DNA can be built from the RNA plan. That this was possible, was established
later when the mechanism of viral infections was explained. The ''normal'' procedure is that
RNA is built according to the DNA plan.
,Do you agree with the following statement? Give reasons for your answer. "The development
and functioning of a living organism is nothing more than the coordinated activity of a wide
variety of protein molecules"
It would appear that by far the majority of the activities in the cell are the result of the kind of
proteins that are manufactured as the end product of gene expression. Although this only
arises later in the module, the process as contained in the central dogma could also
terminate in RNA. Therefore, the result of gene expression is RNA, which is not a protein
and performs vital functions in the cell.
Unit 3 TRANSCRIPTION OF DNA TO RNA AND TYPES OF RNA MOLECULE:
MESSENGER RNA (mRNA)
Make a brief but thorough summary of the process of transcription as it occurs in E. coli.
Transcription is divided into three phases, initiation, elongation and termination. initiation is
looked on as the most important phase because it is a key control point in the gene
expression pathway. Regulation of transcript initiation often determines whether or not a
gene is active in a particular cell at a particular time.
In E. coli, a direct contact is formed between the promoter and the RNA polymerase. The
sequence specificity of the polymerase resides in its σ subunit. The “core enzyme,” which
lacks this component, can make only loose and nonspecific attachments to DNA.
recognition of the promoter occurs through an interaction between the σ subunit and the –35
box.
The closed promoter complex is converted to the open form by the combined action of the b’
and s subunits, which break the base pairs within the –10 box, because –10 boxes of
different promoters are comprised mainly or entirely of A–T base pairs, which are linked by
just two hydrogen bonds and are therefore weaker than G–C pairs, which have three
hydrogen bonds.
Opening up of the helix requires that contacts be made between the polymerase and the
nontranscribed strand of the gene, again with the σ subunit playing a central role.
Dissociates of σ soon after initiation are complete, converting the holoenzyme to the core
enzyme.
During the elongation stage of transcription, the bacterial RNA polymerase is in its core
enzyme form, denoted as a2bb’.
Transcription bubble is where the growing transcript is held to the transcribed strand of the
DNA by approximately eight RNA– DNA base pairs
actively transcribing RNA polymerase enzymes have shown that the DNA molecule lies
between the b and b’ subunits, within a trough on the enclosed surface of b’, and the
nontranscribed strand of DNA looping away at this point
, The RNA transcript extrudes from the polymerase via a channel formed partly by the b and
partly by the b’ subunit.
The polymerase does not synthesize its transcript at a constant rate, pauses are present
during which the active site of the polymerase undergoes a slight structural rearrangement.
Bacteria use two distinct strategies for transcription .
An inverted repeat is a segment of DNA or RNA in which a sequence is followed by its
reverse complement. If the two halves of the inverted repeat are separated by a few
intervening nucleotides, as is the case at a termination site, then intrastrand base pairing
between the two sequence components can form a hairpin loop in a single-stranded
polynucleotide, in this case the RNA transcript.
the inverted repeat is followed by a run of deoxyadenosine nucleotides in the nontranscribed
strand, called intrinsic terminators. This causes the hairpin loop is favored, reducing the
number of contacts between the template DNA and transcript, and weakening the overall
DNA–RNA interaction. The interaction is further weakened when the run of As in the DNA is
transcribed, because the resulting A–U base pairs have only two hydrogen bonds each,
compared with three for each G–C pair. The net result is that detachment of the transcript is
favored over continued elongation.
The second type of bacterial termination signal is Rho-dependent. Signals of this type
usually include an inverted repeat as seen at intrinsic terminators, although the hairpin that is
formed is less stable and there is no run of. Termination requires the activity of a protein
called Rho, which attaches to the transcript and moves along the RNA toward the
polymerase
Which of the three types of RNA is not a final product of gene expression?
mRNA is one of the steps of gene expression, not the final result of gene expression.
How do prokaryotic ribosomes differ from eukaryotic ribosomes in terms of size?
tRNA fetches amino acids from the cytoplasm of the cell according to the sequence of
nitrogen bases in the mRNA and takes it to the bonding sites on the ribosome, where it is
bonded to other amino acids to form a polypeptide.
Eukaryotic ribosomes are slightly larger than prokaryotic ribosomes.
Draw a labelled diagram of the cloverleaf structure of the tRNA and indicate the various
regions
