VyVy Truong

Take Home Exam

Genetics, Dr. Byrum
02/28/2016
1. Describe the three dimensional structure of DNA. For full credit,
address the following points:
a. nucleotides
b. base-pairing of purines/pyrimidines
c. hydrogen bonding
d. Chargaffs Rules
e. strand orientation
f. histones, nucleosome
g. DNA vs RNA
h. promoter region
i. TATA box
j. genes
1.

DNA is double helical in structure, that looks much like a ladder that is
twisted from the top to the bottom. And the strand orientation or
directionality of the structure is by convention 5 prime to 3 prime.
Which is determined by the naming of the carbon atoms within the
nucleotide sugar-ring. The DNA structure is made of sugar,
phosphate, and bases, held together by hydrogen bonding. Each of
the spiral strands, is composed of a sugar phosphate backbone and
attached bases. The twisted sides are made of sugars called
deoxyribose, in combination with a phosphate. It is all connected to a
complementary strand by hydrogen bonding between the paired
bases, adenine with thymine and guanine with cytosine. The larger
bases, adenine and guanine, are double-ringed structures called
purines. The single ringed, smaller ones, cytosine and thymine, are
the pyrimidines. The base-pairing in these are always A-T and G-C.
These pairs are held together by hydrogen bonds, A-T have two
hydrogen bonds, and G-C have three hydrogen bonds. Within this
structure, Erwin Chargaff discovered that the ration of adenine to
thymine is equal, and the same goes for the ration of cytosine and
guanine. Thus, became the rule that states that the DNA structure from
any cell should always be a 1:1 ratio in the pyrimidine and purine
bases in both strands of the DNA. The DNA as we discussed is the
double stranded helix that contains a pentose sugar Deoxyribose, the
single stranded RNA contains the pentose sugar ribose. The Histones
are the highly alkaline protein structures round in the cell nuclei that
package and order the DNA into structural units called nucleosomes.
The promoter is the region of the DNA that starts transcription. The

TATA box is known as the DNA sequence found to indicate specifically

where a genetic sequence can be read. Together these DNA make up
instructions for our molecules to form units of heredity known as our
genes.

2. Discuss the semiconservative mode of DNA replication. For full

credit, address the following points:
a. DNA polymerase
b. primase
c. helicase
d. single-stranded binding proteins
e. ligase
f. Okasaki fragments
g. origins of replication
h. leading strand
i. lagging strand
j. replication fork
2.

The three possible modes believed to have explain DNA replication

were conservative, dispersive, and semiconservative. Today we know
that DNA replicates in the semiconservative mode. In this mechanism,
the double-stranded DNA is half conserved following the replication
process. The newly made double-stranded DNA contains one parental
strand and one daughter strand. This replication would produce two
copies that each contain one of the original strands and one of the new
strand. Our origin of replication is the starting site where the
replication process begins. This begins with the Helicase enzymes
unwinding the parental double helix structure and proteins are used to
stabilize the strands, thus forming a replication fork. DNA
primase joins in by synthesizing the short RNA primer pieces to create
a 3 prime starting site. DNA polymerase continuously synthesizes
the leading strand by adding nucleotides in the 5 to 3 prime
direction. The lagging strand is synthesized discontinuously as RNA
polymerase synthesizes the short RNA primers. The short newly
synthesized DNA fragments on the lagging strand are the Okazaki
fragments. DNA polymerase digests the RNA primer and replaces it
with DNA. DNA ligase then joins the short lagging strand fragments
together.

3.Use the diagram below to comment on the following:

a. what is a karyotype and how is it organized

b. difference between the number of autosomes and sex
chromosomes
c. meaning of euploid, polyploid, aneuploidy
d. disjunction and nondisjunction
e. trisomy 21 details
f. Turner syndrome
g. Klinefelter syndrome
h. chromosome deletion
i. chromosome duplication
j. chromosomal inversions
3.

a. A karyotype is the complete set of chromosome in a species that

is organized based off of their appearance. This describes the
chromosome count and what they look like under a microscope.
They are observed and studied upon their length, position,
patterns, and other physical characteristics.
b. We also observe differences in their sex chromosomes, which
are chromosomes that determine the sex of the organism.
Autosomes appear in pairs that look alike, but differ from other
autosome pairs in the diploid cell. The autosomal chromosomes
are paired and ordered by their size and position of their
centromeres, from largest to smallest. Afterwards, the two sex
chromosomes are arranged at the end, thus determining the sex
of the organism.
c. Many problems come from a simple complication in our
chromosomes. A polyploid is an entire extra set of
chromosomes, giving a set of threes instead of twos. This is a

d.

e.
f.
g.
h.
i.
j.

result from fertilization of an oocyte by two sperms. These

organisms do not survive. Aneuploidy are cells missing or an
extra in a single chromosome. The survivors tend to have
intellectual disabilities due to a complication in protein synthesis
within the brain. Most cases have an extra chromosome called
trisomy. Euploidy refers to the state of which an organism
having the same number of each homologous chromosome, a
balanced set in any number.
Disjunction is used to describe the normal separation or moving
apart of the chromosomes to the opposite poles during cell
division. However, nondisjunction is when those homologous
chromosomes fail to separate properly. This results in aneuploidy,
the daughter cells with abnormal chromosome numbers.
Trisomy 21, otherwise known as Down syndrome results from
exactly the name itself. It is caused by the presence of all or part
of a third copy on chromosome number 21.
Turner Syndrome is the result of a female missing or partially
missing an X chromosome.
Klinefelter syndrome occurs in males what have a set of
symptoms due to two or more X chromosomes.
Chromosome deletion refers to the missing of or deletion of
DNA sequences.
Chromosome duplication is an extra in the DNA sequences.
Chromosomal inversions describe the portion of the
chromosome has been broken off, turned upside down, and then
reattached. Thus causing the genetic material to be inverted.

4. Review the video on epigenetics to address the following:

a. what is epigenetics
b. how does epigenetics relate to histones
c. epigenetic marks
d. environmental influences on marks
e. impact of maternal behavior on epigenetics
f. reversible nature of marks
g. what is a tumor suppressor gene (hint: p53 is a good example to
review)
h. impact of mutations on suppressor genes
i. role of suppressor genes and cancer therapy
j. challenges of medicine for the future (think epigenetics)
4.

a. Epigenetics is an influence in the changes of the regulation of

gene activity and expression, found outside of the gene. These
external changes cause the DNA to turn certain genes on or off.
But there is not change to the DNA sequence itself. These

b.

c.
d.

e.

f.

g.

h.

i.

j.

changes are not a mutation, but simply how genes are read or
not read.
The histones are found to interact with the chemical groups in
DNA. They related to the exposure of the DNA to transcription
factors and block the expressions due to shielding. Group
interactions allow these genes to adapted to the changing
conditions. Acetyl, methyl, and phosphate groups are the
molecule types that bind to these histones.
Epigenetic marks are like chemical tags that can tell theses
genes to switch on or off, or compact or de-compact. Making
these genes either accessible or inaccessible.
Our environment has a great influence on these genetic marks,
as early as embryonic development. They can be based off of all
our surroundings and what choices we make in our exposure and
consumption. Such as proper diet, poor social habits, or even
mental stability. These influence chemical signals through the
bloodstream that influence the marks in our embryo.
With these influences impacting as early as embryonic
development, maternal behavior is critical. All of the mothers
choices on consumption and activity is constantly absorbed into
the childs bloodstream. Woman who choose poor diets, poor
habits, have a very high chance of developing problems for the
child when born, such as asthma and obesity.
Though these marks can be set early, there are possible ways to
reverse them. Current development goes into pharmaceutical
drugs that can directly target these silencing marks. Thus,
naturally allowing the gene to turn on and function properly
again.
A tumor suppressor gene is a gene that is meant to protect
cells from leading towards cancer. However, if these genes were
to mutate or be silenced, this can cause loss or reduction of its
function. Causing the cells to become cancerous.
The impact of these suppressor genes could be a huge
underlying cause to cancer. After understanding the mutations in
these suppressor genes we can find a way to stop them. Thus
giving us a different approach to not only curing, but reversing
the disease, and eventually prevent it altogether.
With our understanding of these suppressor genes, we can work
towards not killing our cells, but to be able to target theses
genes to get these cells working again. If a drug or therapy that
can target these suppressor genes to work properly, this can
reverse our entire approach on cancer treatment. Being able to
naturally have a body and cells function the way that they
should, without killing or poisoning other cells in our body.
With this we have can an entirely different approach towards
illnesses and diseases. Instead of constantly attacking diseases

and discovering ways to cure and treat them, we can now find
ways to prevent them. Because with the understanding of
epigenetics, we know that we can positively influence our
epigenomes. Overall, that DNA is not set in stone, and that we
can make a positive chance to help us a live a healthy lifestyle
and pass onto our future offspring.

5.
a.
b.
c.
d.

The Hardy Weinberg Equation is p2 + 2pq + q2 = 1

what does the p represent
what does the q represent
what does 2pq represent
why the equation must equal 1
5.

a. P represents the variable for the frequency of the Dominant

allele
b. q represents the variable for the frequency of the recessive allele
c. 2pq represents the frequency of the heterozygous genotype Aa
d. Mathematician Hardy and physician Weinburg reasoned that the
combined frequencies in the variables p and q must equal 1,
because together they represent all the alleles for that trait
found in the population.
Sickle-cell anemia is an interesting genetic disease. Normal
homozygous individuals (SS) have normal blood cells that are easily
infected with the malarial parasite. Thus, many of these individuals
become very ill from the parasite and many die. Individuals
homozygous for the sickle-cell trait (ss) have red blood cells that
readily collapse when deoxygenated. Although malaria cannot grow
in these red blood cells, individuals often die because of the genetic
defect. However, individuals with the heterozygous condition (Ss)
have some sickling of red blood cells, but generally not enough to
cause mortality. In addition, malaria cannot survive well within
these "partially defective" red blood cells. Thus, heterozygotes tend

to survive better than either of the homozygous conditions. If 9% of

an African population is born with a severe form of sickle-cell
anemia (ss), what percentage of the population will be more
resistant to malaria because they are heterozygous (Ss) for the
sickle-cell gene? Show all work