DNA Profiles

DNA profiling involves the (partial) sequencing of genomes.

Profiles tend to focus on areas of satellite (junk) DNA which vary significantly between individuals.

Why use junk DNA for profiling: by sequencing a number of sections a unique ‘genetic fingerprint’ can be created for an individual.

Two uses of DNA profiling are paternity cases and forensic investigations.

Gel Electrophoresis

This laboratory technique is used to separate fragments of DNA in an effort to identify its origin.

Enzymes are used to chop up the long filaments of DNA in varying sized fragments. The DNA fragments are place into small wells (holes) in the gel which are aligned along one end. The gel is exposed to an electric current – positive on one side and negative on the other.

The effect is the biggest, heavies and least charged particles don’t move easily through the gel so they get stuck very close to the wells they were in at the origin. The smallest, least massive and most charged particles pass through the gel to the other side with little difficulty. Intermediate particles are distributed in between.

In the end, the fragments leave a banded pattern of DNA.

Outline the process of DNA profiling (genetic fingerprinting), including ways in which it can be used. (6)

·       Sample of DNA is obtained from hair

·       Satellite DNA (repetitive sequences) are used for profiling

·       Amplification of DNA by polymerase chain reaction

·       Cutting DNA into fragments of DNA by electrophoresis

·       Separation according to the length of the fragments

·       Pattern of bands obtained with DNA from different individuals

·       Used for criminal investigations

·       Used to check paternity

·       Used to check whether two organisms are clones

Cloning

A clone is a group of genetically identical organisms or a group of cells derived from a single parent cell.

Separated into reproductive cloning and therapeutic cloning.

Therapeutic cloning involves the isolation of stem cells (can be adult e.g. bone marrow or foetal – i.e. from an embryo/foetus)

Foetal stem cells are often harvested from unused IVF embryos.

These have the potential to be of great medical benefit. E.g. healing burns, heart tissue post cardiac arrest, kidney damage.

1.     Discuss the ethical arguments for and against the cloning of humans (4)

Arguments against cloning:

·      Reduces the value or dignity of an individual and may cause psychological problems

·      High miscarriage rates

·      Cloned individual are likely to have development disorders or health problems

·      Cloned individuals may show premature aging

·      Costly process and money could be better spent on other forms of healthcare

·      Cloning may be carried out for inappropriate motives e.g. to replace lost loved ones or achieve a perfect race

Arguments for cloning:

·      Identical twins are formed by cloning so it could be argued that it’s a natural process

·      Cloned embryos can be tested for genetic diseases (genetic screening)

·      Increased change of children for infertile couples

·      Cloning research may lead to spin-offs for other research areas such as cancer (transplant research or regeneration research)

2.     Outline a basic technique for gene transfer involving plasmids (5)

a.     Messenger RNA coded for insulin is extracted from human pancreas cells

b.     DNA copies of the messenger RNA coding for insulin are made using the enzyme reverse transcriptase

c.     Plasmids are small loops od DNA found in bacteria. They are cut open using the restriction enzyme endonucleouse

d.     The insulin gene and plasmid are mixed

e.     DNA ligase seals up the plasmid

f.      The plasmid with the human insulin gene is inserted into a recombinant plasmid

g.     The recombinant plasmid are mixed with a strain of E. Coli bacteria

h.     The E. Coli bacteria starts to make insulin which is then extracted, purified and used by patients suffering from diabetes

3.     Outline a technique for transferring genes between species (5)

a.    The gene of interesting is cut out with a restriction enzyme

b.    RNA is used to produce DNA using reverse transcriptase

c.     The plasmid is cut open with the same restriction enzyme

d.    The gene is inserted into the plasmid by the blunt/sticky ends

e.    They are spliced together by DNA ligase

f.      The recombinant plasmids are cloned and many copies are produced

g.     Recombinant plasmids are inserted into new host cells, could be a virus, bacteriophage or yeast. This insert is done by shooting/spraying/microencapsulating by heat treatment

4.4.1              Outline the use of polymerase chain reaction (PCR) to copy and amplify minute quantities of DNA.

Polymerase Chain Reaction (PCR)

PCR is a laboratory technique which takes a very small quantity of DNA and copies all the nucleic acids in it to make millions of copies of the DNA. PCR is used to solve a very simple problem: how to get enough DNA to be able to analyze it.

When collecting DNA from the scene of a crime or from a cheek smear, often only a very limited number of cells are available. By using PCR, forensics experts or research technicians can obtain millions of copies of the DNA in just a few hours. Such quantities are large enough to get results from, notably using gel electrophoresis. 

Bioengineering

Bioengineering is the transfer of genes between species.

The genetic code is universal – this means that in any species so far identified, the same codons code for the same amino acids.

4.4.10            Discuss the potential benefits and possible harmful effects of on example of genetic modification.

Benefits

• ·       GM crops help farmers by improving food production
• ·       GM crops which produce their own pest-control substances are beneficial to the environment because fewer chemical pesticides will be needed
• ·       Using GMOs to produce rare proteins for medication or vaccines could be less costly and produce less pollution than synthesizing these proteins in laboratories
• ·       Farmers can be in more control of what crops or livestock they produce
• ·       The multinational companies who make GM plants claim they’ll enable farmers in developing nations to help reduce hunger by using pest-resistant crops or GM plants which require less water

Harmful Effects

• ·       The long term effects of GMOs in the wild are unknown. Efforts to keep GM plants under control in well-defined areas have failed and pollen from GM crops have escaped to neighbouring fields. Genes from GM plants could be integrated into wild species, giving them un unnatural advantage over other species and an ability to take over the habitat
• ·       There is a danger that the genes could cross species. It has been proven possible in laboratories, so it’s possible in nature too. Again, no one knows the consequences of genes crossing species
• ·       Crops which produce toxins to kill insects could be harmful to humans because, unlike chemical pesticides which are only applied to the outer surface, the toxins are found throughout the plant
• ·       There are risks for allergies. E.g. if someone is not allergic to natural tomatoes but is allergic to GM tomatoes, they will need to know which one they’re eating. But there is no difference in the outward appearance of the fruit and food labeling is not always clear
• ·       There are worries that large portions of the human food supply will be the property of a small number of corporations
• ·       High-tech solutions are not necessarily better than simpler solutions. Crop production could be increased by teaching farmers how to use water and natural pest-control systems more efficiently
• ·       A proliferation of genetically modified organisms may lead to a decrease in biodiversity

Explain how the sympathetic and parasympathetic nervous systems control the heart rate and flow of blood to the gut.

The autonomic section of the PNS consists of two systems, which are antagonists: the sympathetic and parasympathetic systems.

The sympathetic system is associated with ‘fight or flight’; when in an emergency, a quick supply of oxygen and glucose is needed. The sympathetic system increases both the heart rate and the stroke volume of the heart. The release of adrenaline in the body causes the heart to pump faster. The feedback stimulus for the increase of heart rate would be the increase of respiration, and therefore the increase of carbon dioxide in the blood. The carbon dioxide needs to be excreted quickly so the blood needs to be pumped around faster.
The sympathetic system is also responsible for dilating the bronchi to provide more oxygen.  Digestion in this state is not necessary, therefore, flow of blood to the gut is restricted by contraction of the smooth muscle of the blood vessels carrying blood to the digestive system – it causes the diameter of the blood vessels to narrow.

When not in an emergency situation and in a relaxed state, the parasympathetic system is in use. Parasympathetic nerves return the system to normal. The heart rate slows and stroke volume is released. Blood flow also returns to the digestive system as the smooth muscles of the blood vessels relax and the diameters of the blood vessels become wider. 

Source: Damon, A. McGonel R. Tosto P. and Ward W., 2007, Higher Level Biology, Essex: Pearson Education Limited

The Human Brain

Why is severing the spinal chord below the medulla instantly fatal?

The medulla oblongata is the structure found in the brain responsible for a number of automatic and vital functions such as respiration, blood pressure, breathing and heart rate. This makes it a very critical part of the brain.

Severing the spinal chord below the medulla can instantly be fatal as it could damage the structure - the patient will be unable to breathe, swallow or perform basic motor functions.

Auditory Transduction

Sound is firstly picked up by the eardrum (tympanic membrane) as vibrations. These vibrations are then passed onto the bones of the middle ear, the oval window to the cochlea. The vibrations are then transmitted to the liquid within the cochlea, made possible by the round window. The hair cells of the cochlea then convert these vibrations to nerve impulses, which are sent to the brain and interpreted.

Eardrum -----> Bones of the middle ear -----> Oval window -----> Cochlea -----> Round window -----> Hairs of the cochlea

Excitatory & Inhibitory Drugs

Excitatory Drugs

Nicotine

Nicotine is a tobacco product that acts on the cholinergic synapses of the body and the brain to cause a calming effect. After it’s received by the receptors it’s broken down by acetylcholinesterase but the enzyme can’t break down the nicotine molecules, which bind to the same receptors. This excites the postsynaptic neuron and it begins to fire, release a molecule called dopamine.

Dopamine gives the feeling of pleasure, a molecule of the ‘reward pathway’ of our brains.

Cocaine

Dopamine transporters are responsible for removing dopamine molecules from the synaptic cleft after they’ve done their job. Cocaine blocks these transporters, leaving dopamine trapped in the synaptic cleft. This causes dopamine to bind again and again to the receptors over stimulating the cell.

Cocaine concentrates in the reward pathway. It also actives the part of the brain controlling voluntary movements – this is the reason cocaine abusers are unable to stay still.

Amphetamine

Ampetamine stimulates transmission at adrenergic synapses and gives increased energy and alertness. It acts by passing directly into the nerve cells which carry dopamine and noraderenaline. It moves directly into the cesicles of the presynaptic neurone and causes them to release into the synaptic cleft.

These neurotransmitters would normally be broken down by enzymes into the synapse, but amphetamines interfere with the breakdown. This causes a high concentration to build in the synapse which causes euphoria. High concentrations of noraderanline may be responsible for alertness and the high energy effect of amphetamines.

Inhibitory Drugs

Benzodiazepine

Benzodiazepine reduces anxiety and can also be used against epileptic seizures. Its effect is to modulate the activity of GABA, which is the main inhibitory transmitter. When GABA binds to the postsynaptic membrane, it causes chloride ions to enter the neuron. This hyperpolarizes the neuron and prevents action potential.

Benzadiazepine increases the binding of FABA to the receptor and causes the post synaptic neuron to become more hyperpolarized.

Alcohol

The inhibitory neurotransmitter GABA is active throughout the brain. These transmitters act to control neural activity along brain pathways. When GABA binds to its receptors, the cell is less likely to fire. However, in other areas of the brain, the neurotransmitter glutamate acts as the brain’s general-purpose excitatory neurotransmitter.

When alcohol enters the brain it delivers a double sedative punch. First, it interacts with GABA receptors to make them even more inhibitory. Second, it binds to glutamate receptors, preventing the glutamate from exciting the cell.

Alcohol particularly effects areas of the brain involved in memory formation, decision making and impulse control.

THC

THC is the main psychoactive chemical in marijuana. Before marijuana enters the system, inhibitory neurotransmitters are active in the synapse. These neurotransmitters inhibit dopamine from being released. When activated by the body’s own native cannabinoid (called anandamide) cannabinoid receptors turn off the release of inhibitory transmitters. Without inhibition, dopamine can be released.

THC mimics anandamide and binds to cannabinoid receptors; inhibition is turned off and dopamine is allowed to move into the synapse.

Anandamide is known to be involved in removing unnecessary short term memories. It’s also involved for slowing down movement, making the user feel relaxed and calm. Unlike THS, anandamide breaks down very quickly in the body. This explains why anandamide doesn’t produce a perpetual natural ‘high’. 

THC & Cocaine

THC (Tetrahydrocannabinol) / Marijuana

Marijuana is usually smoked as a cigarette or in a pipe. When someone smokes marijuana, THC rapidly passes from the lungs into the bloodstream, which carries the chemical to the brain and other organs in the body.

THC acts on specific sites in the brain called cannabinoid receptor. They start off a series of cellular reactions that lead to the “high” that users experience when they use the drug. Some brain areas have many cannabinoid receptors while others have few or none. The highest density of cannabinoid receptors are found in parts of the brain that influence pleasure, memory, thinking, concentrating, sensory and time perception and coordinated movement. Marijuana intoxication can caused distorted perceptions impaired coordination, difficulty with thinking and problem solving and problems with learning and memory.

http://www.drugabuse.gov/infofacts/marijuana.html

Cocaine

Cocaine is a powerfully addictive central nervous system stimulant. This drug usually makes the user feel euphoric and energetic, but also increases body temperature, blood pressure and heart rate. Users risk heart attacks, respiratory failure, strokes, seizures, abdominal pain and nausea.

Cocaine also causes dopamine release. Cocaine blocks removal of dopamine from the synapse so that it builds up. This leads to over stimulation of the postsynaptic neurone. The synaptic effect of cocaine results from its ability to sustain the level of dopamine in the synapse. Since dopamine is the neurotransmitter in the ‘reward pathway’, the longer it stays in the synapse the better you feel.

http://www.nida.nih.gov/drugpages/cocaine.html

Synaptic Transmission

E1.

a)     Explain how pre-synaptic neurons can affect post-synaptic transmission of impulses (7)

Typically a presynaptic neurone excites a post synaptic neurone – the impulse is transmitted across the synapse. This is called an excitatory synapse. When the action potential reaches the area of the terminal buttons of the pre-synaptic neuron, it causes calcium ions to diffuse into the terminal buttons. Vesicles containing neurotransmitters fuse with the plasma membrane and release them into the synaptic cleft. The neurotransmitters bind with a receptor protein on the postsynaptic neurone membrane, this binding results in an ion channel opening and sodium ions diffusing through this channel. This initiates the action potential to begin moving down the post-synaptic neurone because it has been depolarized (made more positive).

However, some synapses are inhibitory synapses; the release of neurotransmitters into the cleft inhibits an action potential being generated in the post-synaptic neurone. At an inhibitory synapse the release of neurotransmitters into the synaptic cleft triggers the opening of ion channels, which allows Cl- ions to enter the neurone and K+ to leave. This makes the interior of the post-synpatic neurone more negative (hyperpolarised) and therefore less likely to initiate an action potential.


Mark Scheme: 
a. Pre-synaptic neurons can be excitatory or inhibitory
b. Chlorinegic  neurons released acetylcholine (standard wide use neurotransmitters)
c. Found in neuro-muscular junctions/ in autonomic nervous system/ most junction in voluntary nervous system
d. Adrengic nuerons release noradrenaline 
e. Found in sympathetic pathways 
f. Both types of neuron can be excitatory 
g. Neurotransmitters bind to receptors on post-synaptic membrane
h. Triggers opening of sodium channels / sodium moves across membrane
i. Causes depolarization 
j. Neurotransmitters are degraded/destroyed : acetyly choline esterase breaks down acetyl choline 
k. Other inhibitory neurotransmitters, e.g. GABA, dopamine 
l. Inhibitory neurotransmitters are less permeable to sodium / cause chloride ions to diffuse in
m. Causes hyperpolarisation
n. Potassium ions diffuse out 

b)     Explain the process of synaptic transmission (7)

At the far end of axons are swollen membranous areas called terminal buttons. Within these terminal buttons are many vesicles filled with neurotransmitters.

When an action potential reaches the area of the terminal buttons, it causes calcium ions to diffuse into the terminal buttons. Vesicles containing neurotransmitters fuse with the plasma membrane and releases the neurotransmitters into the synaptic cleft. Neurotransmitters diffuse across the synaptic cleft from the presynaptic neurone to the postsynaptic neurone.

Neurotransmitters bind with a receptor protein on the postsynaptic neurone membrane. This binding results in an ion channel opening and sodium ions diffusing in through this channel. This initiates the action potential to begin moving down the postsynaptic neurone because it’s been depolarized.

The neurotransmitter is degraded and broken into two or more fragments by specific enzymes. They’re then released from the receptor protein. The ion channel closes the sodium ions. The neurotransmitter fragments diffuse back across the synaptic gap to be reassembled into the terminal buttons of the presynaptic neurone. 


Mark Scheme: 
a. Presynaptic neurons pass the stimulus to post-synaptic neurons 
b. Presynaptic releases neurotransmitters into the synaptic cleft 
c. Process involves exocytosis
d. Exocytosis triggered by calcium ions entering into the bulb of the neuron
e. Neurotransmitter binds with the protein receptors on the post-synaptic cleft
f. Neurotransmitter binding causes ion channels to open
g. Ions diffuse into the cell
h. Causes depolarisation/hyperpolarisation of the pre-synaptic neuron
i. Outcome of the transmission depends on the type of receptor / channel opened
j. Specific example: sodium ions going into the post-synaptic neurone causes depolarisation
k. Specific example: chlorine ions going into the post-synaptic neurone causes hyperpolarisation
l. Neurotransmitters are destroyed by enzymes

Database Questions: Garter Snakes

DBQ Pg. 303-304

1.     (a) For each of the three populations calculate the percetages that were in the <5 and >5 groups. (3)

Lassen County Total = 567 + 114 = 681

Lassen County <5 % = (567 / 681) x 100 = 83.3%

Lassen County >5 % = (114 / 681) x 100 = 16.7%

Humboldt County Total = 149 + 314 = 463

Humboldt County <5 % = (149 / 463) x 100 = 32.2%

Humboldt County >5 % = (314 / 463) x 100 = 67.8%

Santa Cruz Total = 30 + 165 = 195

Santa Cruz <5% = (30 / 195) x 100 = 15.4%

Santa Cruz >5% = (165 / 195) x 100 = 84.6%

                 

(b)  Explain the differences in the behaviour of inland and coastal populations, in terms of natural selection. (4)

Coastal populations show a greater percentage of the population eating slugs more than five days while the inland population shows a greater number of the population eating slugs less than five days.

In coastal environments in California slugs are abundant so that coastal populations become more adapted to eating slugs through natural selection. Coastal snakes are adapted to eat slugs have an advantage and produce more healthy offspring. 


Slugs within inland areas are scarce so the inland populations of the garter snake are more adapted through natural selection to not eat slugs. Natural selection happens as inland snakes reliant on eating slugs struggle living within inland areas and their numbers begin to diminish, leaving the population of inland snakes not reliant on eating slugs to grow in the area. Inland snakes have a selection pressure to feed on other prey and these individuals are more successful. 

2.     Predict, with reasons, the result if garter snakes were moved from Lassen County to Santa Cruz. (3)

Garter snakes moved from Lassen County to Santa Cruz will face a greater abundance of slugs than they're used to. The Lassen County snakes will be less likely to survive in this new environment because they're more adapted to feed on other prey whereas in Santa Cruz there are more slugs. 

3.    Discuss the evidence from the bar charts for:

a.     The slug-eating response being inherited (2)

There’s a greater frequency of F1 hybrids accepted slugs during the first couple of days of the experiment. This is a similar characteristic of the Lassen County garter snakes that have the slug-eating response. The Lassen County and F1 hybrids have the same feeding pattern. 

b.     The alleles for slug eating being recessive (2)

In the F1 hybrid the behavioral pattern to not eat slugs seems to be prominent. This suggests that the gene to not eat slugs is dominant and the gene for eating slugs is recessive.

4. Suggest a type of receptor for the slug-eating snakes to detect slugs (1)

Chemoreceptors - they smell the slugs. They find the trail of the slug and follow it.