Biochem Answers:

1. A. The monomeric unit of DNA is a nucleotide which is composed of a

deoxyribose, a phosphate group, and a nitrogenous base which is adenine,
guanine, cytosine or thymine. An example of a monomeric unit that
differentiates a DNA from RNA is deoxythymidine monophosphate.
B. The monomeric unit of RNA is a nucleotide which is composed of a ribose, a
phosphate group, and a nitrogenous base which is adenine, guanine, cytosine or
uracil. An example of a monomeric unit that differentiates RNA from DNA is
uridine monophosphate.
C. Nucleotides
D. DNA is found in the nucleus, mitochondria, and chloroplasts (for plants) of the
cell
E. RNA can be found in the cytoplasm of the cell
2. DNA structure from Watson and Cricks model is a double-stranded helix, with
the two strands connected by hydrogen bonds. A bases are always paired with
Ts, and Cs are always paired with Gs, which is consistent and accounts for
Chargaff's rule. Most DNA double helices are in their B-form or right-handed; that
is, if you were to hold your right hand out, with your thumb pointed up and your
fingers curled around your thumb, your thumb would represent the axis of the
helix and your fingers would represent the sugar-phosphate backbone. DNA
double helix is anti-parallel, which means that the 5' end of one strand is paired
with the 3' end of its complementary strand and vice versa. Major and minor
grooves are the empty spaces in an imaginary cylinder that encloses the DNA
helix, which also serves as the binding sites of polypeptides.
3. Complementary strands refer to the relation between the two nucleotide strands
of DNA in which each purine on one strand pairs with a specific pyrimidine on the
opposite strand (A pairs with T, bonded by 3H bonds, and G pairs with C, by 2H
bonds).
4. Tm, or the melting temperature, is the temperature at which 50% of the DNA is
denatured. GC base pairs are held together with three hydrogen bonds, while A
T base pairs have only two. Therefore, the higher the percentage of GC base
pairs, the higher the Tm required to melt the DNA.
5.

6. *Refer to the picture you took in your phone*

7. A. During DNA replication, both strands of the double helix act as templates for
the formation of new DNA molecules. Copying occurs at a localized region called
the replication fork, which is a Y shaped structure where new DNA strands are
synthesised by a multi-enzyme complex. Here the DNA to be copied enters the
complex from the left. One new strand is leaving at the top of frame and the
other new strand is leaving at bottom. The first step in DNA replication is the
separation of the two strands by an enzyme called helicase. This spins the
incoming DNA to unravel it: at ten thousand RPM in the case of bacterial
systems. The separated strands are called three prime and five prime,
distinguished by the direction in which their component nucleotides join up. .
The 3' DNA strand, also known as the leading strand, is diverted to a DNA
polymerase and is used as a continuous template for the synthesis of the first
daughter DNA helix. The other half of the DNA double helix, known as the
lagging strand, has the opposite 3' to 5' orientation and consequently requires a
more complicated copying mechanism. As it emerges from the helicase, the
lagging strand is organised into sections called Okazaki fragments. These are
then presented to a second DNA polymerase enzyme in the preferred 5' to 3'
orientation. These sections are then effectively synthesised backwards. When
the copying is complete, the finished section is released and the next loop is
drawn back for replication. Intricate as this mechanism appears, numerous
components have been deliberately left out to avoid complete confusion. The
exposed strands of single DNA are covered by protective binding proteins. And in
some systems, multiple Okazaki fragments may be present. The molecular
reality is very different from the iconic image of the double helix neatly
separating into two DNA copies as so often depicted.
B. The Central Dogma of Molecular Biology: "DNA makes RNA makes protein"
Here the process begins. Transcription factors assemble at a specific promoter
region along the DNA. The length of DNA following the promoter is a gene and it
contains the recipe for a protein. A mediator protein complex arrives carrying the
enzyme RNA polymerase. It manoeuvres the RNA polymerase into place...
inserting it with the help of other factors between the strands of the DNA double
helix. The assembled collection of all these factors is referred to as the
transcription initiation complex... and now it is ready to be activated. The
initiation complex requires contact with activator proteins, which bind to specific
sequences of DNA known as enhancer regions. These regions may be thousands
of base pairs distant from the start of the gene. Contact between the activator

proteins and the initiation-complex releases the copying mechanism. The RNA
polymerase unzips a small portion of the DNA helix exposing the bases on each
strand. Only one of the strands is copied. It acts as a template for the synthesis
of an RNA molecule which is assembled one sub-unit at a time by matching the
DNA letter code on the template strand. The sub-units can be seen here entering
the enzyme through its intake hole and they are joined together to form the long
messenger RNA chain snaking out of the top.
C. The job of this mRNA is to carry the genes message from the DNA out of the
nuceus to a ribosome for production of the particular protein that this gene
codes for. There can be several million ribosomes in a typical eukaryotic cell
these complex catalytic machines use the mrna copy of the genetic information
to assemble amino acid building blokes into the three dimensional proteins that
are essential for life. Lets see how it works. The ribosome is composed of one
large and one small sub-unit that assemble around the messenger RNA, which
then passes through the ribosome like a computer tape. The amino acid building
blocks (that's the small glowing red molecules) are carried into the ribosome
attached to specific transfer RNAs. That's the larger green molecules also
referred to as tRNA. The small sub-unit of the ribosome positions the mRNA so
that it can be read in groups of three letters known as a codon. Each codon on
the mRNA matches a corresponding anti-codon on the base of a transfer RNA
molecule.The larger sub-unit of the ribosome removes each amino acid and join
it onto the growing protein chain. As the mRNA is ratcheted through the
ribosome, the mRNA sequence is translated into an amino acid sequence. There
are three locations inside the ribosome, designated the A-site, the P-site and the
E-site. The addition of each amino acid is a three step cycle: First, the tRNA
enters the ribosome at the A-site and is tested for a codon/anti-codon match
with the mRNA. Next, provided there is a correct match, the tRNA is shifted to
the P-site and the amino acid it carries is added to the end of the amino acid
chain. The mRNA is also ratcheted on three nucleotides or one codon. Thirdly,
the spent tRNA is moved to the E-site and then ejected from the ribosome to be
recycled. As the protein synthesis proceeds, the finished chain emerges from the
ribosome. It folds up into a precise shape, determined by the exact order of
amino acids. Thus the Central Dogma explains how the four letter DNA code is quite literally - turned into flesh and blood.