Rozaini Othman (Guru Cemerlang Biologi): September 2010

Sep 28, 2010

The Greenhhouse Effect

Many people regard global warming or the greenhouse effect as the most serious environmental threat to our present way of life on earth. Put simply, the greenhouse effect is the natural "trapping in" of heat by some of the gases in the atmosphere. Figure 1 shows the key points of the greenhouse effect.

EXAM HINT - Candidates often confuse the greenhouse effect with ozone depletion. Although they have some common causes, their mechanisms and effects are very different.

Some of the greenhouse gases, for example, carbon dioxide, occur naturally in the atmosphere, whilst others such as the chlorofluorocarbons (CFCs) are entirely man-made. Regardless of their origin, such gases warm the lower atmosphere by trapping outgoing longwave radiation in a manner similar to that of glass in a greenhouse, hence the term greenhouse effect. It is important to realise that the greenhouse effect is a natural, essential process. Without it, the average temperature on earth would be about -170C and life would be impossible.

However, over the last hundred years human activities have resulted in rising concentrations of all the greenhouse gases. This has led to an increased or "enhanced" greenhouse effect and this in turn seems to have led to an increase in average global temperature.

It is the possible implications of this extra heating effect that are causing so much concern. We simply do not know how much the temperature will continue to rise and what effect any changes will have on local, regional and world climate. Which areas will benefit and which will suffer, and how, is still largely unknown. The temperature will not rise everywhere equally; in fact some areas will probably become cooler (because of this, most of the scientific literature now uses the term "global climate change" rather than global warming). The effects of possible changes will be discussed shortly, but first we need to look at the greenhouse gases in a little more detail.

Why is carbon dioxide so important?

In discussions of the greenhouse effect, attention is almost invariably focused on rising CO2 levels. This is not because it is an unusually powerful greenhouse gas - indeed, gases such as methane are thirty times more powerful weight for weight - but because of its sheer abundance. As a consequence, its effects outweigh those of all the other greenhouse gases combined. Historically, high carbon dioxide concentrations have always coincided with inter-glacial periods and low concentrations with ice ages.

What Can Be Done?

Strategies to reduce the emissions or levels of the greenhouse gases have mainly targeted carbon dioxide. These include:

1. Reducing the consumption of fossil fuels by increasing the fuel efficiency of buildings and vehicles. Improvements to the latter would also reduce N2O emissions.

2. Switching fuel from coal to oil and gas which release less carbon dioxide upon consumption.

3. Switching from fossil fuels to renewable energy sources such as solar, geothermal, wind, wave, tidal and hydro-electric.

4. Preventing destruction of the tropical rainforests, simultaneously removing a problem and providing a solution.

However, as mentioned earlier, because the other greenhouse gases absorb different infrared wavelengths to carbon dioxide, reductions in this gas alone are unlikely to be sufficient. CFC emissions have already been reduced as a result of the Montreal Protocol in 1989 and subsequent amendments. Alternatives to CFCs are now widely available. Any measures which reduced vehicle use or pollution would simultaneously help to

reduce emissions of carbon dioxide, nitrous oxide and levels of tropospheric ozone. Worldwide however, the trend is in the wrong direction, with one new car joining the roads every second. In Britain fo example, road transport is responsible for 18% of carbon dioxide emissions,45% of nitrous oxide emissions and 30% of all hydrocarbon emissions.

Sep 27, 2010

Trial Bio SPM 2010

Sep 17, 2010

Water Pollution

What is water pollution?

Water pollution is any chemical, physical or biological change in the quality of water that has a harmful effect on any living thing that drinks or uses or lives (in) it. When humans drink polluted water it often has serious effects on their health. Water pollution can also make water unsuited for the desired use.

What are the major water pollutants?

There are several classes of water pollutants. The first are disease-causing agents. These are bacteria, viruses, protozoa and parasitic worms that enter sewage systems and untreated waste.

A second category of water pollutants is oxygen-demanding wastes; wastes that can be decomposed by oxygen-requiring bacteria. When large populations of decomposing bacteria are converting these wastes it can deplete oxygen levels in the water. This causes other organisms in the water, such as fish, to die.

A third class of water pollutants is water-soluble inorganic pollutants, such as acids, salts and toxic metals. Large quantities of these compounds will make water unfit to drink and will cause the death of aquatic life.

Another class of water pollutants are nutrients; they are water-soluble nitrates and phosphates that cause excessive growth of algae and other water plants, which deplete the water's oxygen supply. This kills fish and, when found in drinking water, can kill young children.

Water can also be polluted by a number of organic compounds such as oil, plastics and pesticides, which are harmful to humans and all plants and animals in the water.

A very dangerous category is suspended sediment, because it causes depletion in the water's light absorption and the particles spread dangerous compounds such as pesticides through the water.

Finally, water-soluble radioactive compounds can cause cancer, birth defects and genetic damage and are thus very dangerous water pollutants.

Where does water pollution come from?

Water pollution is usually caused by human activities. Different human sources add to the pollution of water. There are two sorts of sources, point and nonpoint sources. Point sources discharge pollutants at specific locations through pipelines or sewers into the surface water. Nonpoint sources are sources that cannot be traced to a single site of discharge.

Examples of point sources are: factories, sewage treatment plants, underground mines, oil wells, oil tankers and agriculture.

Examples of nonpoint sources are: acid deposition from the air, traffic, pollutants that are spread through rivers and pollutants that enter the water through groundwater.

Nonpoint pollution is hard to control because the perpetrators cannot be traced.

How do we detect water pollution?

Water pollution is detected in laboratories, where small samples of water are analysed for different contaminants. Living organisms such as fish can also be used for the detection of water pollution. Changes in their behaviour or growth show us, that the water they live in is polluted. Specific properties of these organisms can give information on the sort of pollution in their environment. Laboratories also use computer models to determine what dangers there can be in certain waters. They import the data they own on the water into the computer, and the computer then determines if the water has any impurities.

What is heat pollution, what causes it and what are the dangers?

In most manufacturing processes a lot of heat originates that must be released into the environment, because it is waste heat. The cheapest way to do this is to withdraw nearby surface water, pass it through the plant, and return the heated water to the body of surface water. The heat that is released in the water has negative effects on all life in the receiving surface water. This is the kind of pollution that is commonly known as heat pollution or thermal pollution.

The warmer water decreases the solubility of oxygen in the water and it also causes water organisms to breathe faster. Many water organisms will then die from oxygen shortages, or they become more susceptible to diseases.

What is eutrophication, what causes it and what are the dangers?

Eutrophication means natural nutrient enrichment of streams and lakes. The enrichment is often increased by human activities, such as agriculture (manure addition). Over time, lakes then become eutrophic due to an increase in nutrients.

Eutrophication is mainly caused by an increase in nitrate and phosphate levels and has a negative influence on water life. This is because, due to the enrichment, water plants such as algae will grow extensively. As a result the water will absorb less light and certain aerobic bacteria will become more active. These bacteria deplete oxygen levels even further, so that only anaerobic bacteria can be active. This makes life in the water impossible for fish and other organisms.

What is acid rain and how does it develop?

Typical rainwater has a pH of about 5 to 6. This means that it is naturally a neutral, slightly acidic liquid. During precipitation rainwater dissolves gasses such as carbon dioxide and oxygen. The industry now emits great amounts of acidifying gasses, such as sulphuric oxides and carbon monoxide. These gasses also dissolve in rainwater. This causes a change in pH of the precipitation – the pH of rain will fall to a value of or below 4. When a substance has a pH of below 6.5, it is acid. The lower the pH, the more acid the substance is. That is why rain with a lower pH, due to dissolved industrial emissions, is called acid rain.

Why does water sometimes smell like rotten eggs?

When water is enriched with nutrients, eventually anaerobic bacteria, which do not need oxygen to practice their functions, will become highly active. These bacteria produce certain gasses during their activities. One of these gases is hydrogen sulphide. This compounds smells like rotten eggs. When water smells like rotten eggs we can conclude that there is hydrogen present, due to a shortage of oxygen in the specific water.

What causes white deposit on showers and bathroom walls?

Water contains many compounds. A few of these compounds are calcium and carbonate. Carbonate works as a buffer in water and is thus a very important component.

When calcium reacts with carbonate a solid substance is formed, that is called lime. This lime is what causes the white deposit on showers and bathroom walls and is commonly known as lime deposit. It can be removed by using a specially suited cleaning agent.

Sep 15, 2010

Feedback control mechanisms

The role and nature of feedback control in homeostasis
It is essential that the physical and chemical processes of the body are controlled. Homeostasis is the maintenance of a stable internal environment by the regulation of these processes within acceptable limits. Organisms receive oxygen, food, water, salts and warmth from the environment and return carbon dioxide and other wastes to it. Due to homeostasis, mammals and birds have a measure of independence from the external environment, whilst still existing in equilibrium with it.

Homeostasis usually involves control by a combination of negative and positive feedback. In negative feedback control, if the physiological value deviates from the mean (norm) the deviation is sensed by receptors which initiate control mechanisms to return the value to the norm. The receptors are then no longer stimulated and the control mechanisms are either reduced (damped) or completely switched off. Control mechanisms may occur either via nerve impulses which are rapid or via hormones which (with the exception of adrenaline) are slow. In positive feedback control, the control mechanism acts to push the deviating value further away from the norm. Once a certain deviation has been reached, the controlling mechanism may be damped or switched off.

Many physiological values and processes vary in a regular fashion over a definite period of time. Most of these are daily (circadian) rhythms, such as temperature control, but some are on different time scales, such as the monthly menstrual cycle. Endogenous rhythms (those which originate from within), appear to follow a spontaneous internal cycle, e.g. core body temperature changes. Exogenous rhythms (those which are affected by external factors), appear to follow regular changes in environmental stimuli, e.g. heart rate and blood pressure changes.

Regulation of blood concentration

The counter current mechanism which operates in the loops of Henlé in the kidneys maintains a high salt concentration around the collecting ducts of the nephrons. This enables water to be reabsorbed osmotically from the collecting ducts, back into the blood, provided that the collecting duct walls are permeable to water. This permeability depends upon the presence or absence of Antidiuretic hormone (ADH) secreted by the posterior pituitary on the target receptors on the collecting duct walls. If ADH is absent, the walls are impermeable to water so no water can be absorbed back to the blood to dilute it, and the urine remains dilute (containing as little as 100 millimoles of NaCl per litre). If ADH is present, the walls become permeable to water and water is reabsorbed back to the blood, thus diluting it and raising the blood volume and pressure. Conversely the urine volume is reduced and its concentration is raised (to around 1200 mllimoles of NaCl per litre).

The presence or absence of ADH is controlled by negative feedback. Receptors in the hypothalamus of the midbrain sense an increase in the sodium concentration and osmotic pressure (osmolarity) of the blood plasma, and transmit nerve impulses down the pituitary stalk to the posterior pituitary body. These impulses cause the release of ADH from the posterior pituitary to the blood (neurosecretion). The ADH attaches to target receptors on the collecting duct walls and makes them permeable to water which can then be reabsorbed back into the blood. As a result, the blood sodium concentration and osmolarity fall, so the receptors in the hypothalamus are no longer stimulated. ADH release is thus damped or switched off and so the collecting duct walls revert to being water impermeable. Thus, the urine becomes more dilute whilst the blood osmolarity starts to rise once more, until the ADH release is switched on again. The control mechanism of ADH is illustrated in Fig 1.

Regulation of blood glucose concentration

Blood glucose concentration is regulated by the islets of Langerhans which are tiny patches of endocrine issue embedded in the pancreas. The islets contain two types of secretory cell, the beta cells, which secrete insulin and the alpha cells, which secrete glucagon. Insulin lowers blood glucose levels by:

1. accelerating the facilitated uptake of glucose into cells

2. accelerating the synthesis of the storage polymer glycogen from glucose in the liver and muscles

Glucagon raises blood glucose level by stimulating the conversion of unwanted amino acids and glycerol into lucose. The release of insulin and glucagon is regulated by negative feedback. When the blood glucose level falls below the norm, this is sensed by receptors on the alpha cells of the islets. This stimulates the alpha cells to release glucagon into the blood, which raises the blood glucose level back to the norm and the alpha receptors become switched off. When the blood glucagon level raises above the norm, it is sensed by receptors on the beta cells of the islets. Insulin is released into the blood, which lowers the blood glucose concentration back to the norm and so the beta receptors are switched off.

The insulin-glucagon control mechanism is illustrated in Fig 2.

Regulation of the menstrual cycle

The menstrual cycle depends initially on the secretion of the hormone gonadotrophin release factor (GnRF) by the hypothalamus. Increasing blood levels of GnRF stimulates the release of follicle stimulating hormone (FSH) from the anterior pituitary gland. Increasing blood levels of FSH stimulates the development of primary follicles in the ovary into ovarian (Graafian) follicles, and also stimulates the developing follicles to secrete oestrogens. Oestrogens stimulate the repair and rebuilding of the uterus lining after its shedding during menstruation.

High oestrogen levels in the blood around the time of ovulation have two effects. Firstly, they inhibit the further release of GnRF and hence of FSH by negative feedback. Secondly they cause the anterior pituitary to release increasing amounts of luteinising hormone (LH) - this is a good example of positive feedback.

LH stimulates ovulation, in which the ovarian follicle ruptures to release the secondary oocyte into the ovarian (fallopian) funnel. It also stimulates the remains of the follicle in the ovary to develop into the corpus luteum (yellow body) which then starts to secrete the hormone progesterone as well as oestrogen. Together, oestrogen and progesterone maintain and develop the uterine wall further.

If fertilisation does not occur, the increasing levels of these hormones eventually inhibit the further release of LH by negative feedback. Without the maintaining effect of LH, the corpus luteum degenerates and so the concentrations of oestrogen and progesterone fall and their maintaining action on the uterine wall is lost. Thus, the uterine wall breaks down, resulting in the menstrual flow of cells and blood out through the vagina.

Fig 3 illustrates the changes in hormonal concentrations which occur during the menstrual cycle.

Days 8-12

Increasing oestrogen concentrations stimulate LH release by positive feedback.

Days 16-22
Increasing oestrogen and progesterone concentrations inhibit any further release of LH by negative feedback.

Regulation of the birth process

1. Throughout pregnancy, high concentrations of progesterone secreted by the placenta inhibit contractions of uterine muscle and thus prevent birth and maintain the pregnancy. Towards the end of pregnancy, from about week 36 in humans, the placenta starts to age. This has two main effects which increase as time passes, resulting in birth at around 40 weeks (humans). The two effects are: 1. The development of foetal anoxia (insufficient oxygen) which causes foetal discomfort resulting in struggling and kicking. This increases the mechanical stimulation on the uterine wall sending nerve impulses to the hypothalamus. When these reach a certain intensity the hypothalamus sends nerve impulses to the posterior pituitary, causing the release of the hormone oxytocin into the blood. This hormone stimulates the contractions of uterine muscle. As the intensity of nervous stimulation increases, so does the output of oxytocin (positive feedback).

2. The ageing placenta produces progressively less progesterone until eventually it no longer inhibits uterine contractions which then commence, initiating the birth process. Secretion of oestrogen from the foetus also occurs at this time which also stimulates uterine contractions (positive feedback). The placenta also secretes substances known as prostaglandins which also stimulate uterine contractions and stimulate oxytocin release from the posterior pituitary (positive feedback). Eventually the amnion ruptures, releasing the ‘waters’ and the foetus is then in direct contact with the uterine wall. This greatly increases mechanical and thus nervous stimulation, resulting in further increases in oxytocin output by positive feedback. The oxytocin also causes dilation of the cervix, so that eventually the uterine contractions push the baby out.

Following the birth of the baby, the high concentration of oxytocin in the blood causes more powerful uterine contractions to expel the bleeding placenta from the damaged uterine wall. The release of oxytocin then falls
back into a lower level by negative feedback, since the mechanical stimulation of the uterine wall is no longer present.

Regulation of body temperature

Precision temperature control is only found in endothermic animals such as mammals and birds, which can maintain their body temperatures within narrow limits by balancing their heat production with their heat loss. The regulation of temperature is due to a thermostat in the hypothalamus which becomes activated if the temperature varies from a set point (370C in humans). The thermostat contains two centres, one promoting heat loss and one promoting heat gain. These centres receive information from temperature receptors (thermoreceptors) in the skin which sense the surface temperature of the body, and in the hypothalamus which senses the core blood temperature.

If the skin or blood temperatures fall below the set point, the heat promoting centre of the hypothalamus is stimulated. This sends impulses through the sympathetic nerves, which stimulate responses leading to an increase in temperature. These responses include:

· Vasoconstriction of arterioles in the skin so that less heat is lost from the blood by radiation and conduction through the skin.

· Contraction of the erector pili muscles to raise the hairs. This traps a thicker layer of air which is a good insulator thus preventing heat loss.

· Release of adrenaline and noradrenaline from the adrenal medulla which stimulates an increase in cell metabolism, thus increasing heat production.

· An increase in striated muscle tone which causes shivering, generating heat.

As the body temperature rises back to the set point, the heat promoting centre is no longer activated. Thus no further impulses are generated and the adjusting mechanisms are damped or switched off by negative feedback. If the skin or blood temperature rises above the set point, the heat losing centre of the hypothalamus is stimulated. This sends impulses, mainly through parasympathetic nerves, which stimulate responses leading to a decrease in temperature. These responses include:

· Vasodilation of arterioles in the skin so that more heat is lost from the blood by radiation and conduction through the skin.

· Relaxation of the erector pili muscles to lower the hairs so that less insulating air is trapped.

· Increasing activity of the sweat glands (actually under sympathetic control) releasing sweat which evaporates, thus cooling the skin by removing latent heat of vaporisation.

As the body temperature falls back to the set point, the heat losing centre is no longer activated. Thus no further impulses are generated and the adjusting mechanisms are damped or switched off by negative feedback.

The norm or set point of body temperature actually fluctuates between set limits (between 36.5 and 37.50C) over a 24 hour period. The temperature is highest at around 1500 hrs and lowest around 0300 hrs and is a result of a similar fluctuation in basal metabolic rate which generates heat as a byproduct. This is an example of a circadian rhythm which is endogenous, although the precise internal reason for it is unknown.

During infections, the body temperature may be temporarily controlled by positive feedback. Diseased organisms often produce certain toxins called pyrogens (heat makers) which have the effect of raising the norm of body temperature, and the temperature is raised above the norm by positive feedback. This is of value, since the higher temperature may inhibit the enzymes of the bacteria or viruses, preventing their growth, whilst the enzymes of the host are less affected and can continue to work. Once the bacteria or viruses die and stop producing pyrogens, the control of body temperature reverts to the normal negative feedback.

Students usually learn and revise their Biology notes topic by topic - often in the same order that they were taught. However, feedback control mechanisms is a good example of a topic which requires students to be able to integrate in-depth knowledge of several different parts of a syllabus. This is, therefore, a popular topic.

Kidney Disease

10 Symptoms of Kidney Disease

Many people who have chronic kidney disease don't know it, because the early signs can be very subtle. It can take many years to go from chronic kidney disease (CKD) to kidney failure. Some people with CKD live out their lives without ever reaching kidney failure.

However, for people at any stage of kidney disease, knowledge is power. Knowing the symptoms of kidney disease can help you get the treatment you need to feel your best. If you or someone you know has one or more of the following symptoms of kidney disease, or you are worried about kidney problems, see a doctor for blood and urine tests. Remember, many of the symptoms can be due to reasons other than kidney disease. The only way to know the cause of your symptoms is to see your doctor.

1: Changes in Urination

Kidneys make urine, so when the kidneys are failing, the urine may change. How?

You may have to get up at night to urinate.

Urine may be foamy or bubbly. You may urinate more often, or in greater amounts than usual, with pale urine.

You may urinate less often, or in smaller amounts than usual with dark colored urine.

Your urine may contain blood.

You may feel pressure or have difficulty urinating.
What patients said:

"When you go to use the restroom, you couldn't get it all out. And it would still feel just like tightness down there, there was so much pressure."

"My urine is what I had started noticing. Then I was frequently going to the bathroom, and when I got there, nothing's happening. You think, 'Hey, I've got to go to the john,' and you get there: two, three drops."

"I was passing blood in my urine. It was so dark it looked like grape Kool-Aid. And when I went to the hospital they thought I was lying about what colour it was."

2: Swelling

Failing kidneys don't remove extra fluid, which builds up in your body causing swelling in the legs, ankles, feet, face, and/or hands.

What patients said:

"I remember a lot of swelling in my ankles. My ankles were so big I couldn't get my shoes on."

"My sister, her hair started to fall out, she was losing weight, but her face was really puffy, you know, and everything like that, before she found out what was going on with her."

"Going to work one morning, my left ankle was swollen, real swollen, and I was very exhausted just walking to the bus stop. And I knew then that I had to see a doctor."

3: Fatigue

Healthy kidneys make a hormone called erythropoietin that tells your body to make oxygen-carrying red blood cells. As the kidneys fail, they make less erythropoietin. With fewer red blood cells to carry oxygen, your muscles and brain become tired very quickly. This condition is called anaemia, and it can be treated.

What patients said:

"I was constantly exhausted and didn't have any pep or anything."

"I would sleep a lot. I'd come home from work and get right in that bed."

"It's just like when you're extremely tired all the time. Fatigued, and you're just drained, even if you didn't do anything, just totally drained."

4: Skin Rash/Itching
Kidneys remove wastes from the bloodstream. When the kidneys fail, the buildup of wastes in your blood can cause severe itching.
What patients said:
"It's not really a skin itch or anything, it's just right down to the bone. I had to get a brush and dig. My back was just bloody from scratching it so much."
"My skin had broke out, I was itching and scratching a lot."

5: Metallic Taste in Mouth/Ammonia Breath

A buildup of wastes in the blood (called uremia) can make food taste different and cause bad breath. You may also notice that you stop liking to eat meat, or that you are losing weight because you just don't feel like eating.

What patients said:

"Foul taste in your mouth. Almost like you're drinking iron."

"You don't have the appetite you used to have."

"Before I started dialysis, I must have lost around about 10 pounds."

6: Nausea and Vomiting

A severe buildup of wastes in the blood (uremia) can also cause nausea and vomiting. Loss of appetite can lead to weight loss.

What patients said:

"I had a lot of itching, and I was nauseated, throwing up all the time. I couldn't keep anything down in my stomach."

"When I got the nausea, I couldn't eat and I had a hard time taking my blood pressure pills."

7: Shortness of Breath

Trouble catching your breath can be related to the kidneys in two ways. First, extra fluid in the body can build up in the lungs. And second, anemia (a shortage of oxygen-carrying red blood cells) can leave your body oxygen-starved and short of breath.

What patients said:

"At the times when I get the shortness of breath, it's alarming to me. It just fears me. I think maybe I might fall or something so I usually go sit down for awhile."

"I couldn't sleep at night. I couldn't catch my breath, like I was drowning or something. And, the bloating, can't breathe, can't walk anywhere. It was bad."

"You go up a set of stairs and you're out of breath, or you do work and you get tired and you have to stop."

8: Feeling Cold
Anaemia can make you feel cold all the time, even in a warm room.
What patients said:
"I notice sometimes I get really cold, I get chills."
"Sometimes I get really, really cold. It could be hot, and I'd be cold."

9: Dizziness and Trouble Concentrating
Anaemia related to kidney failure means that your brain is not getting enough oxygen. This can lead to memory problems, trouble with concentration, and dizziness.
What patients said:
"I know I mentioned to my wife that my memory—I couldn't remember what I did last week, or maybe what I had 2 days ago. I couldn't really concentrate, because I like to work crossword puzzles and read a lot."
"I was always tired and dizzy."
"It got to the point, like, I used to be at work, and all of the sudden I'd start getting dizzy. So I was thinking maybe it was my blood pressure or else diabetes was going bad. That's what was on my mind."

10: Leg/Flank Pain

Some people with kidney problems may have pain in the back or side related to the affected kidney. Polycystic kidney disease, which causes large, fluid-filled cysts on the kidneys and sometimes the liver, can cause pain.

What patients said:

"About 2 years ago, I was constantly going to the bathroom all the time, the lower part of my back was always hurting and I was wondering why...and they diagnosed that kidney problem."

"And then you're having to get up all time through the night, and then you have the side ache, a backache, and you can't move."

"At night, I would get a pain in my side. It was worse than labor pain. And I'd be crying and my husband would get up, everybody, rubbing my legs."

Sep 11, 2010

Respiration (2)

Cellular respiration is the process by which the energy contained in organic molecules is made available for all of the active processes within a cell. The usual substrate (the organic substance from which energy is released) is glucose, although fats, amino acids and other substrates can be used if necessary. The energy which is released is stored - in the short term - in molecules of ATP.

The process of respiration can occur with oxygen (aerobic) or without oxygen (anaerobic). For every glucose molecule which is broken down, aerobic respiration produces nineteen times as much ATP than anaerobic respiration.

Aerobic respiration can be divided into four stages:

1. Glycolysis (G)

2. The Link reaction (LR)

3. Kreb’s cycle (K)

4. The electron transfer chain (ETC)

These take place in different parts of the cell (Table 1) and the detailed biochemistry of these reactions is shown.

Respiratory quotients

The respiratory quotient (RQ) is defined as the ratio of carbon dioxide produced to oxygen consumed per unit time by an organism:

RQ = volume of CO2 produced per unit time.

volume of O2 consumed

Different substances give different RQ values.

Anaerobic respiration

If oxygen is unavailable the Kreb’s cycle and electron transfer chain cannot operate. This is because without oxygen there would be no way of disposing of the hydrogen at, for example, the end of the electron transfer chain. However, even in anaerobic conditions, glycolysis occurs so reduced NAD still forms. If glycolysis is to continue, the reduced NAD must be reoxidized, that is, the hydrogen must be removed and disposed of. Anaerobic organisms have developed two ways of doing this:

1. In yeast, pyruvate is decarboxylated to produce ethenal. Ethenal then accepts the hydrogen from NAD and forms ethanol. This releases the NAD to be reused in glycolysis. The conversion of pyruvic acid to ethanol with the release of carbon dioxide is called alcoholic fermentation.

2. In mammals, the pyruvate accepts the hydrogen from NAD and is reduced to lactate. The NAD is then available for further use in glycolysis. If oxygen later becomes available, the lactate is reoxidised.

Since anaerobic respiration only involves glycolysis, only the 2 ATP produced in glycolysis are formed.

Glycolysis - occurs in the cell cytoplasm in both aerobic and anaerobic conditions.

1. Glucose is phosphorylated, i.e. ATP is used to add a phosphate group to glucose. This makes the glucose more reactive, allowing it to be broken down. A six carbon (6C) phosphorylated sugar is produced called hexose bisphosphate.

2. The hexose bisphosphate is converted into two molecules of a 3C sugar phosphate called Triose Phosphate (TP)

3. Hydrogen is removed from each of the TP molecules, i.e. the TP molecules are oxidised. The hydrogen is passed to NAD, a coenzyme which, by definition, is said to be reduced.

Remember - any substance that gains oxygen or loses hydrogen or electrons is said to be oxidised. Any substance that loses oxygen or gains hydrogen or electrons is said to be reduced. The enzymes which remove hydrogen from substances are called dehydrogenases. The hydrogen atoms picked up by NAD are used to generate four molecules of ATP. The removal of hydrogen from TP produces pyruvic acid (PA).

The Link Reaction - occurs only if oxygen is available.

4. PA enters the mitochondrion

5. Carbon dioxide and hydrogen are removed from the PA by decarboxylase and dehydrogenase enzymes respectively. The PA is combined with coenzyme A (CoA) to form a 2C compound called acetylcoenzyme A (AcCoA).

Kreb's Cycle - only occurs if oxygen is available.

5. AcCoA (2C) is combined with oxaloacetate (4C) to form citrate (6C). Citrate enters the Kreb’s cycle. This involves a series of decarboxylation and dehydrogenation reactions.

6. The carbon dioxide is released. The hydrogen which is removed is passed to coenzymes such as NAD and FAD (i.e. the coenzymes are reduced).

7. 2ATP molecules are generated directly in the Kreb’s cycle.

8. Eventually the 4C compound (oxaloacetate) is regenerated. This then combines with more AcCoA and the whole cycle begins again.

The electron transfer chain - only occurs if oxygen is available.

9. The reduced coenzymes NAD and FAD are reoxidized, i.e. hydrogen is removed from them by dehydrogenase enzymes located on the cristi of the inner membrane of the mitochondrion.

10. Each hydrogen atom is split into a hydrogen ion (H+) and an electron (e-).

11. The electrons then pass through a series of electron carriers. Just as in the electron transfer chain in the light-dependent stage of photosynthesis, the electron carriers are at successively lower energy levels. As the electron passes down from one electron carrier to another, some of their energy is released. This energy is used to convert ADP into ATP, i.e. to phosphorylate ADP. Since the removal of hydrogen or electrons from substance is defined as oxidation, the overall reactions of the ETC are known as oxidative phosphorylation.

12. Finally, each electron is reunited with a hydrogen ion (H+) and the hydrogen which forms immediately combines with oxygen to form water.

Sep 7, 2010

Food Test

Food tests and chromatography are techniques used for the recognition of biologically important chemical compounds. The use of these techniques is not limited only to the food industry. Detectives can use chromatography to analyse fibres found at a crime scene and when used in conjunction with sniffer dogs, gas chromatography is a common way to identify explosives in airports, it has also been used in schools to perform drug screening.

Why do we need two methods for identifying foods?

Food tests are less precise, they basically identify foods into the category of proteins, lipids, starch, cellulose, reducing sugars or non-reducing sugars, whereas paper chromatography can identify specific molecules, for example, finding out which amino acids or monosaccharides are contained in a mixture.

Three tips on food tests with sugars

1. To distinguish between reducing and non-reducing sugars, first test a sample for reducing sugars, to see if there are any present, if no positive result is achieved test for non-reducing sugars.
2. When testing for a reducing sugar it is not possible to distinguish between glucose and fructose, paper chromatography would need to be used.
3. When testing for a non-reducing sugar the solution will be neutralised when it stops fizzing.

Sep 6, 2010

Gas exchange in animals

All living organisms respire. They need to do this so that energy can be transformed into a form that cells can use. In aerobic respiration, oxygen is used by cells and carbon dioxide is a waste product. In anaerobic respiration, although oxygen is not used, carbon dioxide is still a waste product. Gas exchange is the diffusion (passive movement) of these gases into and out of cells and it is essential for respiration to take place.

For gas exchange to occur efficiently, organisms require:

a large surface area over which gas exchange may take place rapidly

a concentration gradient down which gases may diffuse

a thin surface across which gases may diffuse rapidly
a moist surface on which gases may dissolve and diffuse into and out of cells

Such surfaces are called gas exchange surfaces.

Unicellular organisms

The gas exchange surface of unicellular (single-celled) organisms is the cell surface membrane. Although this is not a specialised gas exchange surface (as in the case of many multicellular organisms) it achieves efficient gas exchange because it has a large surface area to volume ratio. Fig 1 demonstrates how the surface area to volume ratio of a cube decreases as its volume increases. The same is true of living organisms. The small size of unicellular organisms means that they have a large surface area over which gas exchange may take place. In other words, the smaller the organism, the greater its surface area to volume ratio and the greater the efficiency of diffusion of gases through the outer cell surface membrane

The build up of carbon dioxide inside a respiring unicellular organism sets up a concentration gradient so that the gas diffuses out of the cell. If the organism respires aerobically then oxygen diffuses down a concentration gradient into the cell as the oxygen is used up.

The cell surface membrane of unicellular organisms is thin ensuring rapid gas exchange and it is moist to allow gases to dissolve.

Multicellular organisms

Most multicellular organisms respire aerobically. This is because the energy requirements of multicellular organisms tends to be great and aerobic respiration provides nineteen times more ATP (Adenosine triphosphate) per molecule of glucose respired than anaerobic respiration. Multicelluar organisms therefore require an efficient supply of oxygen so that their energy needs can be met.

To achieve efficient gas exchange, multicellular organisms have large gas exchange surfaces. In small multicellular organisms the outer surface of their bodies is usually sufficient. Larger multicellular organisms require specialised surfaces such as lungs or gills.

Maintaining a concentration gradient for gases is a problem that large organisms face because diffusion becomes less efficient over larger distances. Transport systems (e.g. circulatory systems) are needed to ensure that dissolved gases can move to and from respiring tissues rapidly.

Terrestrial (land-living) organisms often have internal gas exchange surfaces to reduce evaporation losses. The following examples illustrate some of the gas exchange surfaces of animals.

Animals without specialised gas exchange surfaces
Many small terrestrial animals use their outer body surfaces efficiently for gas exchange. The earthworm, Lumbricus terrestris, achieves this with:
an elongated body to increase surface area to volume ratio
a primitive circulatory system to maintain a concentration gradient a moist outer body surface

The outer body surface of the earthworm is supplied with a dense capillary network, which join up to form contractile blood vessels. The earthworm does not contain a heart but the circulatory system transports oxygen to and carbon dioxide away from respiring tissues, thereby increasing the efficiency of diffusion.

Mammals

Mammals are examples of large terrestrial animals. They do not rely on their outer body surface for gas exchange but have specialised internal gas exchange surfaces, called lungs, which have the following features:

a large surface area due to numerous air sacs called alveoli a highly developed circulatory system

a short distance between alveoli and the circulatory system ensuring rapid diffusion across the gas exchange surface

the surface of the alveoli is covered by a thin layer of fluid.

Fig 2 shows a diagram of a human alveolus. Note the numerous capillaries and their close proximity to the gas exchange surface.

The concentration gradients of carbon dioxide and oxygen in the alveoli are maintained by the highly efficient blood transport of the capillaries surrounding each alveolus and by ventilation (breathing), which ensures that air moves in and out of the lungs regularly. Diffusion becomes less efficient over larger distances, so the transport system prevents the build up of carbon dioxide or oxygen, thus maintaining the necessary concentration gradient. Red blood cells contain the protein haemoglobin, which associates strongly with oxygen and carbon dioxide providing greater efficiency.

The partial pressures of oxygen (pO2) and carbon dioxide (pCO2) at the gas exchange surface, show how the concentration gradient is established (Fig 3).

Partial pressure is a way of expressing the concentration of a gas and is measured in kilopascals (KPa).

e.g. Oxygen represents about 21% of the atmosphere. The total pressure of the atmosphere is 101.3KPa.

The partial pressure of oxygen (pO2) is therefore 21% of 101.3KPa, which is 21.2KPa.

Oxygen inside the lungs has a partial pressure (pO2) of 13.3KPa. This is less than the pO2 in the atmosphere because the inhaled air has mixed with the air already in the lung (residual air) which has a lower pO2. Blood in capillaries travelling towards the alveoli (afferent capillaries) has a pO2 of about 5.3kPa. There is therefore a concentration gradient between the oxygen in the alveoli and oxygen in the capillaries and oxygen diffuses into the capillary. The blood travelling away from the alveoli (efferent capillary) has a pO2 of 13.3KPa, thus equilibriating with oxygen inside the alveolus.

The converse is true of carbon dioxide. The pCO2 in afferent capillaries is 6.0kPa, which is higher than the pCO2 inside the alveoli because the blood is carrying carbon dioxide produced by respiring tissues. A concentration gradient is set up so that carbon dioxide diffuses into the alveolus. The efferent capillary has a pCO2 of 5.3kPa (the same as the pCO2 of the alveolus). Therefore, the carbon dioxide inside the capillary and alveolus have also reached equilibrium.

Insects

The hard exoskeleton of insects is unsuitable for gas exchange but their internal gas exchange surfaces differ significantly from those of mammals. The most significant difference is the lack of a transport system.

Fig 4 shows a diagram of the insect’s gas exchange surface. Note that the tracheoles join up to trachea. The trachea lead to the outside via pores on the insect’s outer body surface (spiracles).

Fig 4. The insect tracheal system

The main features of insect gas exchange are:

a large surface area achieved by an extensive network of tubes (tracheoles) which penetrate deep into tissues

small bodies which enable gases to get in and out of tissues by diffusion alone, in some cases aided by rhythmical body movements thin, fluid filled tracheoles which allow gases to dissolve and diffuse into tissues efficiently.

The extensive network of tracheoles in the gas exchange system of the insect resembles the mammalian circulation system. Gases diffuse passively through the spiracles, trachea and tracheoles directly to the tissues. Some species of insect produce rhythmical muscle contractions to assist the passive diffusion of gases. This is a type of ventilation.

Insects can control their rate of gas exchange. When respiration levels are high, the concentration of lactic acid in tissues increases. This sets up an osmotic pressure causing fluid to diffuse from the tracheoles into the tissues by osmosis. Gas exchange then occurs more rapidly because the gases can diffuse at a faster rate through a gaseous medium (the residual air in the tracheoles) rather than a liquid medium.

Fish

Fish use water as a gas exchange medium instead of air. The properties of both media are summarised in Table 1.

Fish rely on specialised flaps of tissue called gills for gas exchange. Gills may be external or internal (see Fig 5). External gills usually have a higher surface area but they are less protected.

The gas exchange surface of fish has the following features:

gills have numerous folds which give rise to a large surface area

the concentration gradient is achieved by an efficient circulatory system

Ventilation of gills

External gills receive oxygen passively from the surrounding water. Internal gills however, are protected by an operculum (Fig 6) and therefore need to be actively ventilated. The fish takes water in through its buccal cavity which then flows through the pharynx and past the gill plates, leaving via the opercular openings on each side of the fishes head.

Parallel and counterflow mechanisms of gas exchange

Water which comes in contact with the gills may flow in the same direction as blood in the gill capillaries - parallel flow, or it may flow in the opposite direction - counterflow.

In the parallel flow mechanism, the pO of the blood in the efferent capillaries is about 50% of that of the water entering the buccal cavity of the fish. In other words, the pO of the blood and the water leaving the gills are the same and there is no longer a concentration gradient.

In the counterflow mechanism, the pO2 of the blood in the efferent capillaries is nearly 100% of that of the water entering the buccal cavity of the fish. This mechanism therefore maintains a concentration gradient between the water and the blood in the capillaries even when the blood is highly saturated with oxygen.

The counterflow mechanism is much more efficient because it ensures that there is always a diffusion gradient between the water which is flowing through the gill lamellae and the blood in the lamellae. As blood flows through the gill lamellae, it therefore absorbs more and more oxygen until the pO2 of the blood is almost the same as the pO2 of the incoming water.

By the time the water leaves the gills it has lost almost all of its oxygen the blood. This mechanism therefore results in the pO2 exceeding the pO2 of the blood across the entire gill plate and this ensures that a concentration gradient is maintained. Fig 7 shows the oxygen saturation of the blood and water across the gill plate in both the parallel flow and counterflow mechanisms.

Lailatul Qadr

There is night in the month of Ramadhan which is better than a thousand months (83 years, 4 months). This night is called Laitatul Qadr.

According to Hadith, this night occurs during the last ten days of Ramadhan on one of the odd numbered nights. Usually it is celebrated on the 27th night of this holy month. It is a night of great importance and enormous blessings for Muslims.

A night such as Lailatul Qadr was not granted to any religious community (Ummah) before Muslims. Only the Ummah of the Prophet Muhammad (peace and blessings of Allah be upon him) were favoured with a night of huge reward. Once reason, it was granted, was to enable Muslims to equal the worship of any people who lived before us. In the distant past it is said that people lived very long lives of hundreds of years. We, today, live much shorter lives. And so Allah gave us Laitatul Qadr to enable us to do as much worship as a man who lived even hundreds of years longer. If in a lifetime, you only worshipped on Lailatul Qadr ten times, you would have equaled in those ten nights 833 years of worship.

Signs of Laitul Qadr

There are some signs that reveal which night is Laitatul Qadr.

The night will be peaceful, neither hot nor cold, with a clear moon shinning but with no rays.

There will be no shooting stars in the night

At sunrise the sun will rise as just a disc without and radiant beams of light.

One companion of the Prophet reported that on Laitatul Qadr he tasted sea water and it was sweet.

Sep 1, 2010

Cancer

A clump of prostate cancer

Also called Carcinoma, Malignancy, Neoplasms, Tumour

Cancer begins in your cells, which are the building blocks of your body. Normally, your body forms new cells as you need them, replacing old cells that die. Sometimes this process goes wrong. New cells grow even when you don't need them, and old cells don't die when they should. These extra cells can form a mass called a tumour. Tumours can be benign or malignant. Benign tumors aren't cancer while malignant ones are. Cells from malignant tumours can invade nearby tissues. They can also break away and spread to other parts of the body.

Most cancers are named for where they start. For example, lung cancer starts in the lung, and breast cancer starts in the breast. The spread of cancer from one part of the body to another is called metastasis. Symptoms and treatment depend on the cancer type and how advanced it is. Treatment plans may include surgery, radiation and/or chemotherapy.