BIOCHEM LAB FINALS – CASE STUDIES
1. Chosen case study in DNA (Autism)
A genetic disorder - is a disease caused in whole or in part by a change
in the DNA sequence away from the normal sequence. It can be caused
by a mutation in one by mutations in multiple genes, by a combination
of gene mutations and environmental factors, or by damage to
chromosomes.
Autism or more precisely the autism spectrum disorders (ASDs) -
represent a broad group of developmental disorders characterized by
impaired social interactions, problems with verbal and nonverbal
communication, and repetitive behaviors or severely limited activities
and interests.
Causes of Autism
The causes of autism may be divided into 'idiopathic', (of unknown
cause) which is the majority of cases, and 'secondary,' in which a
chromosome abnormality, single-gene disorder or environmental agent
can be identified. Approximately 15 percent of individuals with autism
can be diagnosed with secondary autism; the remaining 85 percent have
idiopathic autism.
Symptoms of Autism
The hallmark symptom of autism is impaired social interaction. Children
with autism may fail to respond to their name and often avoid eye
contact with other people. They have difficulty interpreting what others
are thinking or feeling because they don't understand social cues
provided by tone of voice or facial expressions and they don't watch
other people's faces to pick up on these cues. Many children with
autism engage in repetitive movements such as rocking, spinning,
twirling or jumping, or in self-abusive behavior such as hand biting or
head-banging.
Treatment for autism
There is currently no cure for autism. However, autism can be managed
and shaped at a young age, even as early as pre-school. Early intensive
therapy can have a positive effect on development later in life.
Treatment of autism involves medical and behavioral therapies to help
children with conversational language and social interactions.
Treatment also involves helping children decrease their repetitive, self-
stimulatory behaviors, tantrums and self-injurious behavior.
Chosen case study of RNA ( HIV )
HIV stands for Human Immunodeficiency Virus - a pathogen that works
by attacking the human immune system.
- It belongs to a class of viruses called retroviruses and more
specifically, a subgroup called lentiviruses, or viruses that cause disease
slowly.
HIV cannot replicate on its own, so in order to make new copies of itself,
it must infect cells of the human immune system, called CD4 cells. CD4
cells are white blood cells that play a central role in responding to
infections in the body.
Over time, CD4 cells are killed by HIV and the body’s ability to recognize
and fight some types of infection begins to decline. If HIV is not
controlled by treatment, the loss of CD4 cells leads to the development
of serious illnesses, or ‘opportunistic infections. In people with normal
CD4 cell levels, these infections would be recognized and cleared by the
immune system.
The structure of HIV
HIV is called a retrovirus because it works in a back-to-front way. Unlike
other viruses, retroviruses store their genetic information using RNA
instead of DNA, meaning they need to ‘make’ DNA when they enter a
human cell in order to make new copies of themselves.
HIV is a spherical virus. The outer shell of the virus is called the envelope
and this is covered in spikes of the ‘glycoproteins’ gp120 and gp41,
which allow HIV to lock onto the CD4 receptor on CD4 T cells and enter
the cell.
Inside the virus envelope is a layer called the matrix. The core of the
virus, or nucleus, is held in the capsid, a cone-shaped structure in the
centre of the virion. The capsid contains two enzymes essential for HIV
replication, the reverse transcriptase and integrase molecules. It also
contains two strands of RNA – which hold HIV’s genetic material.
HIV’s RNA is made up of nine genes which contain all the instructions to
make new viruses. gag, pol and env – provide the instructions to make
proteins that will form new virus particles. tat, rev, nef, vif, vpr and vpu -
provide code to make proteins that control the ability of HIV to infect a
cell, produce new copies of virus or release viruses from infected cells.
The life-cycle of HIV
1. Attachment and entry
The process of producing new viruses begins when HIV gains entry to a
cell. This process happens in two stages, attachment and fusion.
HIV infects immune system cells which have a CD4 receptor on the
surface. These cells include T-lymphocytes (also known as t cells),
monocytes, macrophages and dendritic cells. The CD4 receptor is used
by the cell to signal to other parts of the immune system the presence
of antigens.
When HIV makes contact with a CD4 cell, the gp120 spikes on the
surface of HIV lock onto the CD4 receptor and another co-receptor,
either CCR5 or CXCR4.The gp41 protein is used to fuse the HIV envelope
with the cell wall. This process of fusion allows the HIV capsid to enter
the CD4 cell.
2. Reverse transcription
When HIV RNA enters the cell, it must be `reverse transcribed` into
proviral DNA before it can be integrated into the DNA of the host cell.
HIV uses its reverse transcriptase enzyme to convert RNA into proviral
DNA inside the cell.
3. Integration
After HIV RNA is converted into DNA, HIV’s integrase enzyme attaches
itself to the end of the proviral DNA strands and it is passed through the
wall of the cell nucleus. Once the proviral DNA enters the cell nucleus, it
binds to the host DNA and then the HIV DNA strand is inserted into the
host cell DNA.
HIV integrase inhibitors have been developed to block the transfer of
the HIV DNA strand into the host cell DNA.
After the proviral DNA is integrated into the DNA of the host cell, HIV
remains dormant within the cellular DNA. This stage is called latency
and the cell is described as ‘latently infected’. It can be difficult to detect
these latently infected cells even when using the most sensitive tests.
4. Transcription and Translation
The cell will produce HIV RNA if it receives a signal to become active.
CD4 cells become activated if they encounter an infectious agent.
When the cell becomes active, HIV uses the host enzyme RNA
polymerase to make messenger RNA. This messenger RNA provides the
instructions for making new viral proteins in long chains.
The long chains of HIV proteins are cut into smaller chains by HIV’s
protease enzyme.
5. Assembly and budding
These protein chains begin to assemble into new viruses at the cell wall.
• HIV protease inhibitors are designed to block the activity of
HIV’s protease enzyme.
As the virus buds from the cell wall, its genome becomes enclosed in a
capsid produced from HIV’s gag protein. After the new virus is
assembled, it must leave the cell by pushing through the cell wall. To
leave the cell completely and become infectious, the virus must take
lipids (fats) from the cell wall to make the surface glycoproteins.
• Maturation inhibitors are being developed to block the cutting
of the gag protein that is needed to produce a mature virus.
2. Gastroparesis
Gastroparesis is a condition in which your stomach cannot
empty itself of food in a normal fashion. It can be caused by damage to
the vagus nerve, which regulates the digestive system. A damaged vagus
nerve prevents the muscles in the stomach and intestine from
functioning, preventing food from moving through the digestive system
properly. Often, the cause of gastroparesis is unknown.
Causes of gastroparesis
 Uncontrolled diabetes
 Gastric surgery with injury to the vagus nerve
 Medications such as narcotics and some antidepressants
 Parkinson's disease
 Multiple sclerosis
 Rare conditions such as: amyloidosis (deposits of protein
fibers in tissues and organs) and scleroderma (a connective
tissue disorder that affects the skin, blood vessels, skeletal
muscles, and internal organs)
There are many symptoms of gastroparesis, including:
 Heartburn or GERD
 Nausea
 Vomiting undigested food
 Feeling full quickly when eating
 Abdominal bloating
 Poor appetite and weight loss
 Poor blood sugar control
Treatment
Gastroparesis is a chronic (long-lasting) condition. This means
that treatment usually doesn't cure the disease. But there are steps you
can take to manage and control the condition.
Some patients may benefit from medications, including:
 Reglan (metoclopramide): You take this drug 30 mins before
eating and it causes the stomach muscles to contract and
move food along. Reglan also decreases the incidence of
vomiting and nausea. Side effects include diarrhea,
drowsiness, anxiety, and, rarely, a serious neurological
disorder. Not allowed for children and when taking, it should
not exceed from 2-4 or 8-12 weeks.
 Erythromycin: This is an antibiotic that also causes stomach
contractions and helps move food out. Side effects include
diarrhea and development of resistant bacteria from
prolonged exposure to the antibiotic.
 Antiemetics: These are drugs that help control nausea.
People who have diabetes should try to control their blood sugar levels
to minimize the problems of gastroparesis.
In a severe case of gastroparesis, a feeding tube, or jejunostomy tube
(G-J gastro-jejunal tube), may be used. The tube is inserted through the
small intestine during surgery. To feed yourself, put nutrients into the
tube, which go directly into the small intestine; this way, they bypass
the stomach and get into the bloodstream more quickly.
3. Niemann-Pick disease
Niemann-Pick disease is an inherited disease that affects lipid
metabolism, or the way fats, lipids, and cholesterol are stored in or
removed from your body. People with Niemann-Pick disease have an
abnormal lipid metabolism that causes a buildup of harmful amounts of
lipids in various organs. Lipids (fatty materials such as waxes, fatty acids,
oils, and cholesterol) and proteins are usually broken down into smaller
components to provide energy for the body. In Niemann-Pick disease,
harmful quantities of lipids accumulate in the brain, spleen, liver, lungs,
and bone marrow.
THE DISEASE HAS THREE CATEGORIES
 Type A
the most severe form, begins in early infancy. Additional symptoms
include weakness, an enlarged liver and spleen, swollen lymph nodes,
and profound brain damage by six months of age. Children with this
type rarely live beyond 18 months.
 Type B (called juvenile onset)
Occurs in the pre-teen years, with symptoms that include ataxia and
peripheral neuropathy. The brain is generally not affected. Other
symptoms include enlarged liver and spleen, and pulmonary difficulties.
In types A and B, insufficient activity of an enzyme called
sphingomyelinase causes the build up of toxic amounts of Changes to the diet will not prevent disease progression, but limiting
sphingomyelin, a fatty substance present in every cell of the body. milk, sugar, and dairy products has helped some individuals
experiencing excessive mucus. 
 Type C

Appear early in life or develop in the teen or adult years. It is caused by 5. Phenylketonuria
a lack of the NPC1 or NPC2 proteins. Affected individuals may have  or simply PKU it's an autosomal recessive disease in which
extensive brain damage that can cause an inability to look up and down, there's a problem and one of the enzymes involved in the
difficulty in walking and swallowing, and progressive loss of vision and metabolism of phenylalanine.
hearing. There may be moderate enlargement of the spleen and liver.
Normal Phenylalanine Metabolism
4. Mucopolysaccharidoses
The proteins from the food that we ingested broken down into
individual amino acids and one of these amino acids is
The mucopolysaccharidoses are a group of inherited metabolic diseases
phenylalanine.25% of these phenylalanine is used to build new proteins
caused by the absence or malfunctioning of certain enzymes needed to
inside the body. 75% of Phenylalanine is used in the liver to generate
break down molecules called glycosaminoglycans - long chains of sugar
another amino acid known as Tyrosine.
carbohydrates in each of our cells that help build bone, cartilage,
Tyrosine
tendons, corneas, skin, and connective tissue. Glycosaminoglycans
(formerly called mucopolysaccharides) are also found in the fluid that  used to generate new protein because we need 20 amino acid
lubricates our joints. to generate protein.The remaining Tyrosine inside the liver is
metabolized to create acetate and fumarate.
People with a mucopolysaccharidosis either do not produce enough of
one of the 11 enzymes required to break down these sugar chains into Acetyl acetate - transformed into ketone bodies.
proteins and simpler molecules or they produce enzymes that do not
work properly. Over time, these glycosaminoglycans collect in the cells, Fumarate - transformed into glucose.
blood, and connective tissues. The result is permanent, progressive
(*The cells in our body can use the ketone bodies and glucise for
cellular damage that affects the individual's appearance, physical
energy)
abilities, organ and system functioning, and, in most cases, cognitive
development.  Phenylketonuria
Different Types  high levels of phenylketone also known as phenylpyruvate in
Mucopolysaccharidosis I or MPS I, is a rare genetic disorder that affects our urine.
many body systems and that leads to organ damage. It is caused by an Where do we get Phenylketone?
alteration in the gene that makes an enzyme called alpha-L-iduronidase.
Because of this alteration, cells either produce the enzyme in low  accumulation of phenylalanine inside our body that
amounts or cannot produce it at all. The enzyme is needed to break phenylalanine is transformed into phenylketone also called
down substances called “glycosaminoglycans” (GAGs) which are by- phenylpyruvate
products of chemical reactions in the body’s cells. If GAGs are not
broken down, they build up in the cell, eventually leading to cell, tissue, Problem in the patients of Phenylketonuria are? - elevated levels of
and organ damage. phenylalanine, due to the absence of Phenylalanine Hydroxylase when
transforming Phenylalanine into Tyrosine.
Mucopolysaccharidosis II or MPS II, also called Hunter syndrome , is a
rare disease that's passed on in families. It mainly affects boys. Their Phenyllalanine Hydroxylase
bodies can't break down a kind of sugar that builds bones, skin,
 is a mixed function oxygenase that uses a cofactor known as
tendons, and other tissue. Those sugars build up in their cells and
tetrahydrobiopterin.
damage many parts of the body, including the brain. Exactly what
happens is different for every person. (*If there is a problem within the enzyme Phenylalanine Hydroxylase or
there is a problem in building the co factor (Tetrahydrobiopterin) the
Diagnosis
reaction Phenylalanine Metabolism will not take place, and the result is
Clinical examination and urine tests (excess mucopolysaccharides are the person will develop Phenylketonuria.)
excreted in the urine) are the first steps in the diagnosis of an MPS
disease. Enzyme assays (testing a variety of cells or blood in culture for
enzyme deficiency) are also used to provide definitive diagnosis of one
of the mucopolysaccharidoses. Prenatal diagnosis using amniocentesis
and chorionic villus sampling can verify if a fetus is affected with the
disorder.

Treatment

Currently there is no cure for these disorders. Medical care is directed at

treating systemic conditions and improving the person's quality of life.
Physical therapy and daily exercise may delay joint problems and
improve the ability to move.