Aug 28, 2010

Sample Respiration Q


Diagram 6.1 shows the part of the regulatory mechanism of oxygen and carbon dioxide contents in the body.

i) Based on the diagram, explain how the concentration of carbon dioxide in the blood is regulated during a vigorous activity.
[8 marks]
Sample answer
P1- During vigorous activity, the concentration / the partial pressure of carbon dioxide increases as a result of active cellular respiration
P2- the carbon dioxide react with water to form carbonic acid which results in a drop in the pH level of the blood and tissue fluid that bathing the brain
P3- The drop in pH is detected by the central chemoreceptors in the medulla oblongata
P4- and detected by peripheral chemoreceptors ( carotid bodies and aortic bodies )
P5-The central chemoreceptors and pheripheral receptors send nerve impulses to the respiratory centre in the medulla oblongata
P6- The respiratory centre sends nerve impulses to the diaphragm and the intercostal muscles, causing the respiratory muscle to contract and relax faster
P7- As a result, the breathing and ventilation rate increase causes more oxygen inhaled and the oxygen concentration return to the normal level
P8- As excess carbon dioxide is eliminated from the body, the carbon dioxide concentration and pH value of the blood return to normal level

ii) Explain why the pulse rate takes several minutes to return to normal after a vigorous activity.
[4 marks]
Sample answer
P1- After vigorous activity, the pulse rate takes several minutes to return to normal because during the activity the oxygen intake is not able to meet the oxygen demand of the body.
P2- Respiration has to take place anaerobically/anaerobic respiration occur
P3- As a result, lactic acid accumulates in the muscle.
P4- So more oxygen is needed to oxidize the lactic acid and to provide the energy for the recovery of the muscle

Trial Bio SPM 2010

Trial Bio SBP 2010
http://www.scribd.com/doc/36512821/Trial-Bio-SPM-SBP-2010

Aug 26, 2010

Oxygen and Carbon dioxide Transport

Oxygen Transport

A diversity of respiratory pigments have evolved in various animal taxa. One example, haemocyanin, found in arthropods and many molluscs, has copper as its oxygen–binding component, coloring the blood bluish. The respiratory pigment of almost all vertebrates and a wide variety of invertebrates is the protein haemoglobin, contained in the erythrocytes of vertebrates.

Haemoglobin consists of four subunits, each with a cofactor called a heme group that has an iron atom at its centre. The iron binds the O2; thus, each haemoglobin molecule can carry four molecules of O2. Like all respiratory pigments, haemoglobin must bind O2 reversibly, loading O2 in the lungs or gills and unloading it in other parts of the body

This process depends on cooperation between the subunits of the haemoglobin molecule. Binding of O2 to one subunit induces the others to change shape slightly, with the result that their affinity for O2 increases. And when one subunit unloads its O2, the other three quickly unload too as a shape change lowers their affinity for O2.

Cooperative O2 binding and release is evident in the dissociation curve for haemoglobin.



Over the range of O2 partial pressures (PO2) where the dissociation curve has a steep slope, even a slight change in PO2 cau2ses haemoglobin to load or unload a substantial amount of O2. Notice that the steep part of the curve corresponds to the range of O2 partial pressures found in body tissues. When cells in a particular location begin working harder—during exercise, for instance—PO2 dips in their vicinity as the O2 is consumed in cellular respiration. Because of the effect of subunit cooperativity, a slight drop in PO2 is enough to cause a relatively large increase in the amount of O the blood unloads.

As with all proteins, haemoglobin′s conformation is sensitive to a variety of factors. For example, a drop in pH lowers the affinity of haemoglobin for O2, an effect called the Bohr shift. Because CO2 reacts with water, forming carbonic acid (H2CO3), an active tissue lowers the pH of its surroundings and induces haemoglobin to release more O2, which can then be used for cellular respiration.

Carbon Dioxide Transport
In addition to its role in oxygen transport, haemoglobin also helps transport CO2 and assists in buffering—that is, preventing harmful changes in blood pH. Only about 7% of the CO2 released by respiring cells is transported in solution in blood plasma. Another 23% binds to the multiple amino groups of haemoglobin, and about 70% is transported in the blood in the form of bicarbonate ions (HCO3−). Carbon dioxide from respiring cells diffuses into the blood plasma and then into the erythrocytes.


The CO2 first reacts with water (assisted by the enzyme carbonic anhydrase) and forms H2CO3, which then dissociates into a hydrogen ion (H+) and HCO3−. Most of the H+ attaches to haemoglobin and other proteins, minimising the change in blood pH. The HCO3− diffuses into the plasma. As blood flows through the lungs, the process is rapidly reversed as diffusion of CO2 out of the blood shifts the chemical equilibrium in favor of the conversion of HCO3− to CO2.

Aug 25, 2010

Tips for Studying Bio



Studying for Biology class is a little different from studying for the other sciences. Physics is story problems: you're given a situation and you must pick out the relevant data to solve the problem. Chemistry is algebra; both sides of a chemical equation must balance just as both sides of an algebraic equation must balance. Biology? Biology is like foreign language: you have to know the words to speak the language. In fact, some educational research suggests that students learn more new terms in a year of biology than they do in a year of high school French.

There's more to learning Biology than memorising vocabulary, however. The words are packets of meaning that may contain huge concepts. Understanding the concepts requires a lot of work and a willingness to let go of what you think the words ought to mean.

I've taught Biology for many years, and studied it myself for many years. There are some study techniques for Bio class that I and my students have found useful for mastering the concepts. Try these out and see what works for you.

VOCABULARY CARDS
You'll have a lot of new vocabulary to learn. Make flash cards just as you would if you're studying another language. Print the term on one side of the card and its definition on the other. If the definition your teacher gives you is a worded differently from the one in the glossary of your textbook, use your teacher's definition. The wording probably fits the concepts the teacher wants you to master. Flip through your flash cards every day, any time you have a few minutes to spare.

CONCEPT MAPS
Research on human learning shows that when people think and try to reason their way through a problem, they can only hold a few ideas at a time in working memory. However, there's no limit to the size of those ideas. If you learn facts in biology as isolated bits of information, you can only think with a few small bits. When you link those facts to other facts, that whole linked network is one "item" to your working memory. You can also remember facts better when they're linked to other facts. One way to make a concept map is to use your vocabulary cards. Write the vocabulary words on small slips of paper. Arrange them on a large sheet of paper. With a pencil, sketch lines linking vocabulary words together. On the line, write in a phrase that defines the link. For example, if two of your words are "atoms" and "molecules," you might connect them this way: [atoms] - linked together make up -> [molecules]. Find as many conceptual connections between the vocabulary terms as you can.

CATEGORISING TABLES
A categoriSing table is used to sort ideas into different categories. For example, if you're in the middle of a diversity unit and you need to remember the different phyla of animals, make a table where you list the different phyla across the top. Use your textbook, the internet, and other resources to look up all the examples you can find of members of each phylum. If you're studying the biomolecules, list the categories of biomolecules across the top of the table (proteins, lipids, carbohydrates, nucleic acids), then list examples of each underneath (be sure you know the difference between a type of protein, such as hemoglobin, and a nutritional source of protein, such as meat).

DEFINING FEATURES TABLES
You've just finished learning about mitosis and meiosis, and you just know that your teacher is going to test you over the differences between the two. Text yourself by making a defining features table. Down the side of the table, list all the features that your teacher will test you over, such as "produces two cells at the end," or, "produces haploid cells." Across the top, write "Mitosis" and "Meiosis." Now put a check underneath "Mitosis" or "Meiosis" to indicate which feature goes with which.

READ ACTIVELY
Have you ever had the sensation, while you're reading the textbook, that the information is just bouncing off of your forehead? The problem is that reading alone is too passive. If you want the information to stick, you need to be more active. Get out some paper and a pen and take notes as you read. If the book is yours and you don't mind marking it up, jot summaries of each section in the margin. Are there questions at the end of the chapter? Use these to review the chapters.

OUTLINE
An outline helps organise information into a framework that helps you make more sense of it. Use outlining to merge the information from your textbook with the information from class and labs. As you read your textbook, create an outline of the information. The chapter headers and subheaders will help you organise your outline. Then go through your notes and add in any information that's not in your textbook outline. This is a much better way of studying your notes than simply reading or rewriting them.

LEARN TO TAKE GOOD NOTES
I can stand in front of my class and talk for five minutes straight, and while my students listen attentively, I don't see one pencil moving.

If I turn and write a single word on the board, all heads go down and everyone dutifully copies that word. How useful is this as a notetaking system? Not very - I'm sure my students go home and wonder what in the world that word meant.

When I show presentations, I see a similar phenomenon. My students carefully copy the words on each slide, but few of them jot down the ideas as I explain what the concepts mean. If I show a figure, a picture, or an animation and talk about, the pencils are all still.

Instead of copying presentation slides word-for-word, learn to summarise the concepts. As your teacher talks, you should jot down the ideas in your own words. Develop a few shorthand abbreviations so you can write faster. Use a good note-taking system, such as the Cornell system (example: http://www.bucks.edu/~specpop/ Cornl-ex.htm), where you use one side of your paper to write detailed notes, and the other side to summarise main ideas, sketch pictures, or create small concept maps.

LEARN ABOUT MISCONCEPTIONS
Misconceptions about science are common, and they can be a real barrier to learning. So many common misconceptions just seem to "make sense," even though they're contrary to what we know about the world. Some misconceptions arise from the specific way science uses a word that has many different meanings outside of science. For example, the word "dominant" in genetics refers to a form of a gene whose trait is expressed even if you only inherit one copy of that gene. With recessive genes, you have to inherit two copes to show the trait. "Dominant" in this sense does not mean "most common," nor does it mean the gene will "take over" in a population. Other misconceptions arise from things we've heard all of our lives. For example, most people know that plants give off oxygen, which leads them to believe that the purpose of photosynthesis is to produce oxygen. Be aware that all of us, everyone, even your instructor, has misconceptions about something. Don't be embarrassed about your own. Be aware that you'll learn something that's contrary to what you thought was true about the world, and be open to changing your ideas.

STUDY IN GROUPS
Put social learning to work for you. Meet other people in your class and see if you can get together with them to study. Drill each other on vocabulary, quiz one another using your notes and the textbook, and go over study guides together. Many studies have shown that social learning increases student comprehension, especially in the sciences.

SEE YOUR TEACHER OFTEN
Your teacher is there to teach you, not just test you. If you're in college, find out when your instructor's office hours are and use them. If you're in school, arrange a time after school when you can see your teacher. Bring specific questions, such as concepts you're not clear on. Try drawing a picture of the concept and show it to your instructor to see if you've got the main idea. If you do poorly on an exam, ask the instructor to go over the questions you missed with you so you can understand them better.

Give each of these study techniques a good, sincere try. You may find that an idea that you thought was not for you actually gives you a big boost on the next quiz or exam. Soon you'll find which techniques work best for you, and you may even find they're helping you in your other classes.

Good luck...

Aug 24, 2010

Trial Science PMR 2010

Trial SBP 2010 P1 and P2 (Got some errors in the questions and the mark scheme. Consult your teacher).
http://www.scribd.com/full/36351918/P1-and-P2-2010

Trial Johor 2010 (P2)
http://www.scribd.com/full/36353750/P2-Johor-2010

Mark scheme Johor 2010
http://www.scribd.com/full/36353988/Mark-Scheme-Johor-2010

Trial Johor 2010 (P1)
http://www.scribd.com/doc/36382728/P1-Johor-2010

Trial Sabah 2010 (P2)
http://www.scribd.com/doc/36382994/Trial-Sabah-2010-P2

Mark scheme Sabah 2010
http://www.scribd.com/doc/36383064/Mark-scheme-Sabah-2010

Trial Kelantan 2010 (P2)
http://www.scribd.com/doc/3638539/Trial-Kelantan-2010-P2

Mark scheme Kelantan 2010
http://www.scribd.com/doc/36385600/Mark-scheme-Kelantan-2010

Trial Terengganu 2010 (P2)
http://www.scribd.com/doc/36385701/Trial-Terengganu-2010-P2

Mark scheme Terengganu 2010
http://www.scribd.com/doc/36385775/Mark-scheme-Terengganu-2010-P2

Trial Perlis 2010 (P2)
http://www.scribd.com/doc/36385912/Trial-Perlis-2010-P2

Trial Perak 2010 (P2)
http://www.scribd.com/doc/36389523/Trial-Perak-2010-P2

Aug 23, 2010

Leptospirosis

Description
Leptospirosis is a disease caused by Leptospira bacteria. Also known as Weil’s or Canecutter’s disease, it is contracted when grazed or cut skin (most commonly hands or feet) is infected by animal urine or other animal fluid, or soil or water contaminated by urine or other animal fluid. It has an incubation period of between two and 30 days but normally about 10 days. Most commonly, people infected are individuals whose work includes contact with animals and/or soil or water contaminated with the urine of infected animals.

Symptoms
Normally a sudden-onset illness, symptoms include fever, headaches, severe muscle pain nausea, vomiting and bloodshot eyes. The fever may fluctuate, and in some cases, a skin rash, impaired liver function resulting in jaundice (yellowing of the skin), confusion, depression, kidney failure or even meningitis may occur. The severity of symptoms can vary in each case. Further complications due to infection include kidney, heart and lung damage. In some instances, these complications can cause death.

The illness normally lasts from three days to three weeks, however if left untreated, it can take several months to recover from the disease.

Treatment
A person with leptospirosis is usually admitted to hospital and treated with appropriate antibiotics.

Health Outcome
People with leptospirosis normally recover well after antibiotic treatment. In some cases, intensive care treatment is required.
Prior infection with leptospirosis does not guarantee future immunity as there are a number of different types which can cause infection.
Treatment is recommended to avoid further complications and persistence of the disease. Recovery, if the disease is left untreated, may take serveral months.

Prevention
People most at risk include farmers, abattoir workers, people cleaning up after rodents, bushwalkers, campers, canoeists and gardeners. To prevent contracting leptospirosis, employ the Cover-Wash-Clean Up strategy:
Cover consists of protecting all cuts, grazes and abrasions with waterproof dressings or band-aids and wearing dry, full-cover boots or shoes, gloves and long sleeve shirts when handling animals (eg. milking, trimming, tagging and birthing), soil, vegetation or animal feed that is possibly contaminated.
Wash involves thoroughly washing hands regularly, particularly before any hand to mouth, nose or eye action such as smoking or eating, and showering after work. Any contact with animals or carcasses (eg. aborted material or rat traps), or with liquids that are potentially contaminated with urine, faeces and blood from animals, should be followed by washing of hands and arms in soapy water and washing of contaminated clothes.
Clean Up involves controlling rodents around the home by securing rubbish lids, cleaning up bench tops with bleach solution, and generally keeping the workplace and home clean to discourage rodents. You can also prevent the contamination of living and recreational areas by keeping potentially infected animals away from such zones, for example keeping working dogs away from the house and yard, and not letting them inside. Also, do not feed dogs raw offal as it may contain bacteria which can cause the disease.

For individuals who are at high occupational risk, there is the possibility of implementing animal vaccination (for cattle and pigs), which reduces the shedding of bacteria. This can be a key strategy for large scale farms and businesses.

Aug 22, 2010

Aerobic and Anaerobic Respiration

Respiration is one of the imperative functions of the body that are of crucial importance for all the living organisms be it human being, or the microscopic bacteria. In general the process of respiration serves two basic purposes in living organisms, the first one being disposal of electrons generated during catabolism and the second one being production of ATP. The respiration machinery is located in cell membranes of prokaryotes whereas it is placed in the inner membranes of mitochondria for eukaryotes. Respiration requires a terminal electron acceptor. Simply put, the respiration process, which uses oxygen as its terminal electron acceptor, is called aerobic respiration and the one, which uses terminal electron acceptors other than oxygen, is called anaerobic respiration.

Differences between Aerobic and Anaerobic Respiration
Starting from the bio-chemical pathway used to utilize bio-molecules, to the amount of energy produced in the respiration process, there exist a lot of differences between aerobic and anaerobic respiration. Let us discuss the two respiration processes separately with respect to the process, outcome and the chemical reactions involved in aerobic and anaerobic respiration.

Aerobic Respiration
Aerobic respiration is the process that takes place in presence of oxygen. Aerobic respiration is the metabolic process that involves break down of fuel molecules to obtain bio-chemical energy and has oxygen as the terminal electron acceptor. Fuel molecules commonly used by cells in aerobic respiration are glucose, amino acids and fatty acids.. The process of obtaining energy in aerobic respiration can be represented in the following equation:
Glucose + Oxygen →Energy + Carbon dioxide + Water

The aerobic respiration is a high energy yielding process. During the process of aerobic respiration as many as 38 molecules of ATP are produced for every molecule of glucose that is utilized. Thus aerobic respiration process breaks down a single glucose molecule to yield 38 units of the energy storing ATP molecules.

Anaerobic respiration
The term anaerobic means without air and hence anaerobic respiration refers to the special type of respiration, which takes place without oxygen. Anaerobic respiration is the process of oxidation of molecules in the absence of oxygen, which results in production of energy in the form of ATP or adenosine tri-phosphate. Anaerobic respiration is synonymous with fermentation especially when the glycolytic pathway of energy production is functional in a particular cell. The process of anaerobic respiration for production of energy can occur in either of the ways represented below:
Glucose (Broken down to) →Energy (ATP) + Ethanol + Carbon dioxide (CO2)

Glucose (Broken down to) →Energy (ATP) + Lactic acid

The process of anaerobic respiration is relatively less energy yielding as compared to the aerobic respiration process. During the alcoholic fermentation or the anaerobic respiration (represented in the first equation) two molecules of ATP (energy) are produced. for every molecule of glucose used in the reaction. Similarly for the lactate fermentation (represented in the second equation) 2 molecules of ATP are produced for every molecule of glucose used. Thus anaerobic respiration breaks down one glucose molecule to obtain two units of the energy storing ATP molecules.
 
video
video

Photosynthesis (Higher Level)

The Two Stages of Photosynthesis: A Preview

The equation for photosynthesis is a deceptively simple summary of a very complex process. Actually, photosynthesis is not a single process, but two processes, each with multiple steps. These two stages of photosynthesis are known as the light reactions (the photo part of photosynthesis) and the Calvin cycle (the synthesis part).



The diagram above is an overview of photosynthesis: cooperation of the light reactions and the Calvin cycle. In the chloroplast, the thylakoid membranes are the sites of the light reactions, whereas the Calvin cycle occurs in the stroma. The light reactions use solar energy to make ATP and NADPH, which function as chemical energy and reducing power, respectively, in the Calvin cycle. The Calvin cycle incorporates CO2 into organic molecules, which are converted to sugar. A smaller version of this diagram will reappear in several subsequent figures as a reminder of whether the events being described occur in the light reactions or in the Calvin cycle.

The light reactions are the steps of photosynthesis that convert solar energy to chemical energy. Light absorbed by chlorophyll drives a transfer of electrons and hydrogen from water to an acceptor called NADP+ (nicotinamide adenine dinucleotide phosphate), which temporarily stores the energized electrons. Water is split in the process, and thus it is the light reactions of photosynthesis that give off O2 as a by–product. The electron acceptor of the light reactions, NADP+, is first cousin to NAD+, which functions as an electron carrier in cellular respiration; the two molecules differ only by the presence of an extra phosphate group in the NADP+ molecule. The light reactions use solar power to reduce NADP+ to NADPH by adding a pair of electrons along with a hydrogen nucleus, or H+. The light reactions also generate ATP, using chemiosmosis to power the addition of a phosphate group to ADP, a process called photophosphorylation. Thus, light energy is initially converted to chemical energy in the form of two compounds: NADPH, a source of energised electrons (“reducing power”), and ATP, the versatile energy currency of cells. Notice that the light reactions produce no sugar; that happens in the second stage of photosynthesis, the Calvin cycle.

The Calvin cycle is named for Melvin Calvin, who, along with his colleagues, began to elucidate its steps in the late 1940s. The cycle begins by incorporating CO2 from the air into organic molecules already present in the chloroplast. This initial incorporation of carbon into organic compounds is known as carbon fixation . The Calvin cycle then reduces the fixed carbon to carbohydrate by the addition of electrons. The reducing power is provided by NADPH, which acquired energized electrons in the light reactions. To convert CO2 to carbohydrate, the Calvin cycle also requires chemical energy in the form of ATP, which is also generated by the light reactions. Thus, it is the Calvin cycle that makes sugar, but it can do so only with the help of the NADPH and ATP produced by the light reactions. The metabolic steps of the Calvin cycle are sometimes referred to as the dark reactions, or light–independent reactions, because none of the steps requires light directly. Nevertheless, the Calvin cycle in most plants occurs during daylight, for only then can the light reactions provide the NADPH and ATP that the Calvin cycle requires. In essence, the chloroplast uses light energy to make sugar by coordinating the two stages of photosynthesis.

The thylakoids of the chloroplast are the sites of the light reactions, while the Calvin cycle occurs in the stroma. In the thylakoids, molecules of NADP+ and ADP pick up electrons and phosphate, respectively, and then are released to the stroma, where they transfer their high–energy cargo to the Calvin cycle. The two stages of photosynthesis are treated in this figure as metabolic modules that take in ingredients and crank out products. Our next step toward understanding photosynthesis is to look more closely at how the two stages work, beginning with the light reactions.
The light reactions convert solar energy to the chemical energy of ATP and NADPH.

Chloroplasts are chemical factories powered by the sun. Their thylakoids transform light energy into the chemical energy of ATP and NADPH. To understand this conversion better, we need to know about some important properties of light.

Chlorophyll and light absorption
Chlorophyll absorbs light from the visible part of the electromagnetic spectrum. Chlorophyll is made up of a number of different pigments: chlorophyll a, chlorophyll b, chlorophyll c along with other pigments such as carotenoids. Each of these absorb different wavelengths of light so that the total amount of light absorbed is greater than if a single pigment were involved. Not all wavelengths of light are absorbed equally. An absorption spectrum is a graph showing the percentage absorption plotted against wavelength of light (Fig 1). An action spectrum is a graph showing the rate of photosynthesis plotted against wavelength of light (Fig 1). The similarity between the absorption spectrum and the action spectrum shows that red (650- 700nm) and blue (400-450nm) wavelengths, which are absorbed most strongly, are also the wavelengths which stimulate photosynthesis the most. Green light (550mm) is mostly reflected.





1. Light energy is absorbed by chlorophyll molecules in PSI and PSII.
2. The electrons in the chlorophyll molecules are boosted to a higher energy level and are emitted.
3. The loss of electrons from PSII stimulates the loss of electrons from water i.e. it stimulates the splitting or photolysis of water. O2 is given off.
4. The electron from PSII passes through a series of electron carriers. At each transfer some energy is released.
5. This energy is used by cytochromes to pump protons (H+ ions) from the stroma across the thylakoid membranes. This sets up an electrochemical or H+ gradient. The H+ ions then diffuse back through a protein which spans the thylakoid membrane. Part of this protein acts as an enzyme - ATP synthetase - which uses the diffusion of H+ to synthesise ATP.
6. The electrons emitted from PSI may:
a) Pass down through the same carrier molecules as the electrons from PSII, again generating ATP. Before returning to PSI. Thus electrons are cycled (PSI i carriers i PSI i carriers etc. The energy to begin this cycle came from light (photo) and is used to convert ADP to ATP i.e. to phosphorylate ADP (add a phosphate). Hence this process is called cyclic photophosphorylation (CPP). Or
b) Combine with the hydrogen ions (protons) released from the photolysis of water to reduce nicotinamide adenine dinucleotide phosphate (NADP), forming NADPH. Non cyclic photophosphorylation (NCP) occurs when electrons are emitted from water and then pass to PSII i carrier (with ATP production) i PSI i carriers i NADPH.
7. Reactions 1-6 make up the Light Dependent Stage. The ATP and NADPH produced diffuse into the stroma where the Light Independent Stage occurs (7-11).
8. CO2 combines with a 5C compound called ribulose bisphosphate. This reaction is catalysed by the enzyme RuBPC.
9. The 6C compound formed immediately splits into two molecules of glycerate-3-phosphate (GP).
10. The GP molecules are converted into molecules of triose phosphate (TP) using energy from ATP and the hydrogen atom from NADPH i.e. the two useful products of the LDS are now used up in the LIS.
11. Some of the TP is used to regenerate RuBP.
12. The rest of the TP is used to produce other essential substances which the plant needs - fats, proteins etc.

Aug 21, 2010

Photosynthesis (SPM level)



Photosynthesis – takes place in the chloroplast.
Light reaction (occurs in grana; splitting up water molecules – photolysis of water)
Dark reaction (occurs in stroma; fixation of carbon dioxide)

Light reaction - occurs in the grana (contained chlorophyll) - takes place in the presence of sunlight and chlorophyll - chlorophyll absorbs light; then it becomes activated and this energy is used to :
i) produce energy in the form of – ATP (used for dark reaction)
ii) split up water molecules (photolysis) into hydroxyl ions(OH-) and hydrogen ions (H+) - oxygen is released; but hydrogen enters dark reaction.

Dark reaction (Light independent reaction) - takes place in the stroma -ATP combined with hydrogen atoms (from the light reaction) are used to reduce carbon dioxide to form glucose.

Glucose produced –
i) converted to starch (stored),
ii) transformed - sucrose ; transported to other parts
iii) synthesis of cellulose
iv) converted to a. acids and fatty acids.

Aug 17, 2010

Ruminants and Rodents


The stomach of a ruminant has four chambers. Because of the microbial action in the chambers, the diet from which a ruminant actually absorbs its nutrients is much richer than the grass the animal originally ate. In fact, a ruminant eating grass or hay obtains many of its nutrients by digesting the symbiotic microorganisms, which reproduce rapidly enough in the rumen to maintain a stable population.

The chewed food is passed --> rumen --> cellulose, broken down (enzyme cellulase produced by microbes).
Food enters reticulum (undergoes further hydrolysis). The food now is called cud --> regurgitate bit by bit into mouth --> then rechewed
Reswallow into omasum. Food --> further broken down into smaller pieces (peristalsis)
Food particles move into abomasum (the true stomach). Gastric juices contain digestive enzymes complete the digestion of proteins and other food substances.
The food --> small intestine --> digested & absorbed.
Rodent – large caecum and appendix – shelter for bacteria – produce enzyme cellulase
Rodent chews food – pass through alimentary canal – broken down by cellulase – produced by bacteria
Soft and watery faeces – produced at night
Rodent eats again the faeces – repeat the breakdown process – digested products are absorbed
Defecation – during the day – faeces harder and drier

Similarities
Both do not produce cellulase on their own to digest cellulose. They depend on cellulase-producing microbes for digestion.
They swallow food twice.


Aug 14, 2010

Coccyx (Tulang Sulbi)


Coccyx (tulang sulbi) adalah tulang terbawah dari vertebral column. Disebutkan dalam banyak hadith bahawa tulang ini adalah asal mula manusia, bahawa dari tulang inilah mereka akan dibangkitkan pada hari Kiamat, dan bahawa tulang ini tidak hancur di dalam tanah.

Hadith-Hadith Nabi Saw:
1. Abu Hurairah meriwayatkan bahwa Rasul s.a.w bersabda, ‘Semua bahagian tubuh anak Adam akan dimakan tanah kecuali tulang sulbi yang darinya ia mulai diciptakan dan darinya dia akan dibangkitkan.’ (HR Bukhari, Nasa’i, Abu Dawud, Ibnu Majah dan Ahmad in Musnad-nya, dan Malik in kitab al-Muwaththa’).

2. Diriwayatkan Abu Hurairah bahwa Rasul saw bersabda, ’Ada satu tulang pada anak Adam yang tidak dimakan tanah.’ Mereka bertanya, ‘Apa itu, ya Rasulullah?’ Beliau menjawab, ‘Tulang sulbi.’ (HR Bukhari, Nasa’i, Abu Daud, Ibnu Majah, Ahmad dalam kitabnya al-Musnad, and Malik dalam kitabnya al-Muwaththa’).

Jadi, hadits-hadits tersebut jelas dan memuat fakta-fakta sebagai berikut:
1. Manusia diciptakan mulai dari tulang sulbi.
2. Tulang sulbi tidak hancur.
3. Pada hari Kiamat, kebangkitan manusia bermula dari tulang sulbi.

Tahap-Tahap Pembentukan Janin
Ketika sperma bercantum dengan ovum, maka pembentukan janin dimulai. Zigot terbelah menjadi dua sel, dan masing-masing sel itu membahagimenjadi dua sel lagi. Pembahagian dan perkembangan sel itu berlangsung hingga terbentuknya embryonic disk (lempengan embrio) yang memiliki dua lapisan.

Tulang Punggung dan Tulang Sulbi:
• External Epiblast yang terdiri dari cytotrophoblasts yang membekalkan nutriens embrio pada dinding uterus, dan menyalurkan nutrisi dari darah dan cairan kelenjar pada dinding uterus.
• Internal Hypoblast: Dimulai sejak janin terbentuk dengan izin Allah. Pada hari ke-15, lapisan sederhana muncul pada bahagian belakang embrio dengan bahagian belakang yang tirus, dan disebut primitive node (gumpalan sederhana).

Sisi unsur primitif yang muncul itu diketahui sebagai bahagian belakang dari embrio. Dari unsur primitif dan gumpalan sederhana ini seluruh jaringan dan organ janin terbentuk sebagai berikut:

• Ectoderm, membentuk kulit dan sistem saraf pusat.
• Mesoderm, membentuk otot halus sistem pencernaan, otot kerangka, sistem sirkulasi, jantung, tulang pada bahagian kelamin, dan sistem urinari, jaringan subcutaneous, sistem limpa, limpa, dan kulit luar.
• Endoderm membentuk lapisan pada sistem pencernaan, sistem pernafasan, organ-organ yang berhubungan dengan sistem pencernaan (seperti hati and pankreas, kelenjar tiroid dan saluran pendengaran.

Jadi, lapisan dan gumpalan sederhana itu merupakan tulang sulbi yang dijelaskan Nabi s.a.w kepada kita. Cacat pada janin merupakan bukti bahwa tulang sulbi itu mengandungi sel-sel induk bagi seluruh jaringan manusia.

Kesimpulannya, tulang sulbi itu merupakan gumpalan sederhana, dan ia bisa berkembang dengan menghasilkan tiga lapisan yang membentuk janin: ectoderm, mesoderm and endoderm. Ia juga membentuk seluruh organ tubuh.

Tulang Sulbi tidak boleh hancur:
Berbagai kajian menemukan bahawa pembentukan dan pengorganisasian sel-sel janin itu disokong sepenuhnya oleh lapisan dan gumpalan sederhana, dan sebelum pembentukannya tidak ada pembezaan sel-sel. Salah seorang saintis terkemuka yang membuktikan hal ini adalah ilmuwan Jerman yang bernama Hans Spemann.

Setelah melakukan eksperimen-eksperimen terhadap lapisan dan gumpalan sederhana yang mengatur penciptaan janin, dan kerana itu ia menyebutnya ‘primary organiser’, maka ia memotong bahgian ini dari satu janin dan mengimplantasinya pada janin lain pada tahap permulaan embrio (minggu ketiga dan keempat). Ini membawa kepada pembentukan janin sekunder pada guest body segera sesudah pencampuran dan pembentukan yang disokong oleh sel-sel  pada implantasi itu.

Pada tahun 1931, ketika Spemann memotong ‘primary organiser’ dan mengimplantasinya, maka potongan itu tidak memengaruhi eksperiman lagi, sementara embrio skunder itu tetap berkembang.

Pada tahun 1933, Spemann dan ilmuwan lain mengadakan eksperimen yang sama, tetapi kali ini primary organiser itu dipanaskan. Embrio sekunder itu tetap berkembang meskipun primary organiser itu dipanaskan, dan itu menunjukkan bahawa sel-sel tersebut tidak terpengaruh. Pada tahun 1935, Spemann dianugerahi Nobel atas penemuannya tentang Primary Organiser tersebut.

Dr Othman Al Djilani dan Syaikh Abdul Majid melakukan beberapa eksperimen terhadap tulang sulbi pada bulan Ramadhan 1423 di Rumah Sheikh Abdul Majid Azzandani, di Sanaa, Yaman.

Keduanya memanggang tulang punggung berikut tulang sulbi dengan gas selama sepuluh minit hingga benar-benar terbakar (tulang-tulang berubah merah lalu hitam). Kemudian keduanya meletakkan potongan-potongan yang telah gosong itu pada kotak steril, dan membawanya ke makmal analisa terkenal di Sanaa (Al Olaki Laboratory). Dr Al Olaki, professor bidang histologi dan pathologi di Sanaa University, menganalisa potongan-potongan tersebut dan menemukan bahwa sel-sel pada jaringan tulang coccyx tidak terkesan, dan ia dapat bertahan terhadap pembakaran (hanya otot, jaringan lemak, dan sel-sel sumsum tulang saja yang terbakar, sementara sel-sel tulang tidak terpengaruh).

Adaptasi dari Dr. Mohamad Daudah

Human Digestive System

Each organ of the mammalian digestive system has specialised food–processing functions.

The general principles of food processing are similar for a diversity of animals, so we can use the digestive system of mammals as a representative example. The mammalian digestive system consists of the alimentary canal and various accessory glands that secrete digestive juices into the canal through ducts

After food is chewed and swallowed, it takes only 5–10 seconds for it to pass down the oesophagus and into the stomach, where it spends 2–6 hours being partially digested. Final digestion and nutrient absorption occur in the small intestine over a period of 5–6 hours. In 12–24 hours, any undigested material passes through the large intestine, and faeces are expelled through the anus.

The general principles of food processing are similar for a diversity of animals, so we can use the digestive system of mammals as a representative example. The mammalian digestive system consists of the alimentary canal and various accessory glands that secrete digestive juices into the canal through ducts.

Peristalsis, rhythmic waves of contraction by smooth muscles in the wall of the canal, pushes the food along the tract. At some of the junctions between specialized segments of the digestive tube, the muscular layer is modified into ringlike valves called sphincters, which close off the tube like drawstrings, regulating the passage of material between chambers of the canal. The accessory glands of the mammalian digestive system are three pairs of salivary glands, the pancreas, the liver, and the gallbladder, which stores a digestive juice.

Using the human digestive system as a model, let′s now follow a meal through the alimentary canal, examining in more detail what happens to the food in each of the processing stations along the way.

The Oral Cavity, Pharynx, and Oesophagus
Both physical and chemical digestion of food begin in the mouth. During chewing, teeth of various shapes cut, smash, and grind food, making it easier to swallow and increasing its surface area. The presence of food in the oral cavity triggers a nervous reflex that causes the salivary glands to deliver saliva through ducts to the oral cavity. Even before food is actually in the mouth, salivation may occur in anticipation because of learned associations between eating and the time of day, cooking odors, or other stimuli. Humans secrete more than a liter of saliva each day.

Saliva contains a slippery glycoprotein (carbohydrate–protein complex) called mucin, which protects the lining of the mouth from abrasion and lubricates food for easier swallowing. Saliva also contains buffers that help prevent tooth decay by neutralizing acid in the mouth. Antibacterial agents in saliva kill many of the bacteria that enter the mouth with food.

Chemical digestion of carbohydrates, a main source of chemical energy, begins in the oral cavity. Saliva contains salivary amylase, an enzyme that hydrolyses starch (a glucose polymer from plants) and glycogen (a glucose polymer from animals). The main products of this enzyme′s action are smaller polysaccharides and the disaccharide maltose.

The tongue tastes food, manipulates it during chewing, and helps shape the food into a ball called a bolus. During swallowing, the tongue pushes a bolus to the back of the oral cavity and into the pharynx.

The region we call our throat is the pharynx, a junction that opens to both the oesophagus and the windpipe (trachea). When we swallow, the top of the windpipe moves up so that its opening, the glottis, is blocked by a cartilaginous flap, the epiglottis. You can see this motion in the bobbing of the “Adam′s apple” during swallowing. This tightly controlled mechanism normally ensures that a bolus is guided into the entrance of the oesophagus.

From mouth to stomach: the swallowing reflex and esophageal peristalsis.

Food or liquids may go “down the wrong pipe” because the swallowing reflex didn′t close the opening of the windpipe in time. The resulting blockage of airflow (choking) stimulates vigorous coughing, which usually expels the material. If it is not expelled quickly, the lack of airflow to the lungs can be fatal.

The oesophagus conducts food from the pharynx down to the stomach by peristalsis. The muscles at the very top of the oesophagus are striated (voluntary). Thus, the act of swallowing begins voluntarily, but then the involuntary waves of contraction by smooth muscles in the rest of the esophagus take over.

The Stomach
The stomach stores food and performs preliminary steps of digestion. This large organ is located in the upper abdominal cavity, just below the diaphragm. With accordionlike folds and a very elastic wall, the stomach can stretch to accommodate about 2 L of food and fluid. It is because the stomach can store an entire meal that we do not need to eat constantly. Besides storing food, the stomach performs important digestive functions: It secretes a digestive fluid called gastric juice and mixes this secretion with the food by the churning action of the smooth muscles in the stomach wall.


Gastric juice is secreted by the epithelium lining numerous deep pits in the stomach wall. With a high concentration of hydrochloric acid, gastric juice has a pH of about 2—acidic enough to dissolve iron nails. One function of the acid is to disrupt the extracellular matrix that binds cells together in meat and plant material. The acid also kills most bacteria that are swallowed with food. Also present in gastric juice is pepsin, an enzyme that begins the hydrolysis of proteins. Pepsin breaks peptide bonds adjacent to specific amino acids, cleaving proteins into smaller polypeptides, which are later digested completely to amino acids in the small intestine. Pepsin is one of the few enzymes that works best in a strongly acidic environment. The low pH of gastric juice denatures (unfolds) the proteins in food, increasing exposure of their peptide bonds to pepsin.

What prevents pepsin from destroying the cells of the stomach wall? First, pepsin is secreted in an inactive form called pepsinogen by specialised cells called chief cells located in gastric pits

Other cells, called parietal cells, also in the pits, secrete hydrochloric acid. The acid converts pepsinogen to active pepsin by removing a small portion of the molecule and exposing its active site. Because different cells secrete the acid and pepsinogen, the two ingredients do not mix—and pepsinogen is not activated—until they enter the lumen (cavity) of the stomach. Activation of pepsinogen is an example of positive feedback: Once some pepsinogen is activated by acid, activation occurs at an increasingly rapid rate because pepsin itself can activate additional molecules of pepsinogen. Many other digestive enzymes are also secreted in inactive forms that become active within the lumen of the digestive tract.

The stomach′s second defense against self–digestion is a coating of mucus, secreted by the epithelial cells of the stomach lining. Still, the epithelium is constantly eroded, and mitosis generates enough cells to completely replace the stomach lining every three days. Gastric ulcers, lesions in this lining, are caused mainly by the acid–tolerant bacterium Helicobacter pylori

Though treatable with antibiotics, gastric ulcers may worsen if pepsin and acid destroy the lining faster than it can regenerate.

About every 20 seconds, the stomach contents are mixed by the churning action of smooth muscles. You may feel hunger pangs when your empty stomach churns. (Sensations of hunger are also associated with brain centres that monitor the blood′s nutritional status and levels of the appetite–controlling hormones discussed earlier in this chapter.) As a result of mixing and enzyme action, what begins in the stomach as a recently swallowed meal becomes a nutrient–rich broth known as acid chyme.

Most of the time, the stomach is closed off at both ends. The opening from the oesophagus to the stomach, the cardiac orifice, normally dilates only when a bolus arrives. The occasional backflow of acid chyme from the stomach into the lower end of the oesophagus causes heartburn. (If backflow is a persistent problem, an ulcer may develop in the esophagus.) At the opening from the stomach to the small intestine is the pyloric sphincter, which helps regulate the passage of chyme into the intestine, one squirt at a time. It takes about 2 to 6 hours after a meal for the stomach to empty in this way.

The Small Intestine
With a length of more than 6 m in humans, the small intestine is the longest section of the alimentary canal (its name refers to its small diameter, compared with that of the large intestine). Most of the enzymatic hydrolysis of food macromolecules and most of the absorption of nutrients into the blood occur in the small intestine.

Enzymatic Action in the Small Intestine

The first 25 cm or so of the small intestine is called the duodenum. It is here that acid chyme from the stomach mixes with digestive juices from the pancreas, liver, gallbladder, and gland cells of the intestinal wall itself

The pancreas produces several hydrolytic enzymes and an alkaline solution rich in bicarbonate. The bicarbonate acts as a buffer, offsetting the acidity of chyme from the stomach. The pancreatic enzymes include protein–digesting enzymes (proteases) that are secreted into the duodenum in inactive form. In a chain reaction similar to the activation of pepsin in the stomach, the pancreatic proteases are activated once they are safely located in the extracellular space within the duodenum
 
The liver performs a wide variety of functions in the body, including the production of bile, a mixture of substances that is stored in the gallbladder until needed. Bile contains no digestive enzymes, but it does contain bile salts, which act as detergents (emulsifiers) that aid in the digestion and absorption of fats. Bile also contains pigments that are by–products of red blood cell destruction in the liver; these bile pigments are eliminated from the body with the feces.

The epithelial lining of the duodenum, called the brush border, is the source of several digestive enzymes. Some of these enzymes are secreted into the lumen of the duodenum, but other digestive enzymes are actually bound to the surface of epithelial cells.

Enzymatic digestion is completed as peristalsis moves the mixture of chyme and digestive juices along the small intestine.
 
 
Most digestion is completed early in this journey, while the chyme is still in the duodenum. The remaining regions of the small intestine, called the jejunum and ileum, function mainly in the absorption of nutrients and water
 
Absorption of Nutrients
To enter the body, nutrients in the lumen must cross the lining of the digestive tract. A few nutrients are absorbed in the stomach and large intestine, but most absorption occurs in the small intestine. This organ has a huge surface area—300 m2, roughly the size of a tennis court. Large circular folds in the lining bear fingerlike projections called villi, and each epithelial cell of a villus has many microscopic appendages called microvilli that are exposed to the intestinal lumen
 
(The microvilli′s shape is the basis of the term brush border for the intestinal epithelium.) This enormous microvillar surface is an adaptation that greatly increases the rate of nutrient absorption.

Penetrating the core of each villus is a net of microscopic blood vessels (capillaries) and a small vessel of the lymphatic system called a lacteal. (In addition to their circulatory system, vertebrates have an associated network of vessels—the lymphatic system—that carries a clear fluid called lymph. Nutrients are absorbed across the intestinal epithelium and then across the unicellular epithelium of the capillaries or lacteals. Only these two single layers of epithelial cells separate nutrients in the lumen of the intestine from the bloodstream.

In some cases, transport of nutrients across the epithelial cells is passive. The simple sugar fructose, for example, apparently moves by diffusion down its concentration gradient from the lumen of the intestine into the epithelial cells and then into capillaries. Other nutrients, including amino acids, small peptides, vitamins, and glucose and several other simple sugars, are pumped against concentration gradients by the epithelial membranes. This active transport allows the intestine to absorb a much higher proportion of the nutrients in the intestine than would be possible with passive diffusion.

Amino acids and sugars pass through the epithelium, enter capillaries, and are carried away from the intestine by the bloodstream. After glycerol and fatty acids are absorbed by epithelial cells, they are recombined into fats within those cells. The fats are then mixed with cholesterol and coated with proteins, forming small globules called chylomicrons, most of which are transported by exocytosis out of the epithelial cells and into lacteals

The lacteals converge into the larger vessels of the lymphatic system. Lymph, containing chylomicrons, eventually drains from the lymphatic system into large veins that return blood to the heart.

In contrast to the lacteals, the capillaries and veins that drain nutrients away from the villi all converge into the hepatic portal vein, a blood vessel that leads directly to the liver. This ensures that the liver—which has the metabolic versatility to interconvert various organic molecules—has first access to amino acids and sugars absorbed after a meal is digested. Therefore, blood that leaves the liver may have a very different balance of these nutrients than the blood that entered via the hepatic portal vein. For example, the liver helps regulate the level of glucose molecules in the blood, and blood exiting the liver usually has a glucose concentration very close to 0.1%, regardless of the carbohydrate content of a meal (see Figure 41.3). From the liver, blood travels to the heart, which pumps the blood and the nutrients it contains to all parts of the body.



The large intestine or colon, is connected to the small intestine at a T–shaped junction, where a sphincter (a muscular valve) controls the movement of material. One arm of the T is a pouch called the caecum. Compared to many other mammals, humans have a relatively small cecum. The human cecum has a fingerlike extension, the appendix, which is dispensable. (Lymphoid tissue in the appendix makes a minor contribution to body defense.) The main branch of the human colon is about 1.5 m long.

A major function of the colon is to recover water that has entered the alimentary canal as the solvent of the various digestive juices. About 7 L of fluid are secreted into the lumen of the digestive tract each day, which is much more liquid than most people drink. Most of this water is reabsorbed when nutrients are absorbed in the small intestine. The colon reclaims much of the remaining water that was not absorbed in the small intestine. Together, the small intestine and colon reabsorb about 90% of the water that enters the alimentary canal.

The wastes of the digestive tract, the feces, become more solid as they are moved along the colon by peristalsis. The movement is sluggish, and it generally takes about 12 to 24 hours for material to travel the length of the organ. If the lining of the colon is irritated—by a viral or bacterial infection, for instance—less water than normal may be reabsorbed, resulting in diarrhea. The opposite problem, constipation, occurs when peristalsis moves the feces along the colon too slowly. An excess of water is reabsorbed, and the faeces become compacted.

Living in the large intestine is a rich flora of mostly harmless bacteria. One of the common inhabitants of the human colon is Escherichia coli, a favorite research organism of molecular biologists. The presence of E. coli in lakes and streams is an indication of contamination by untreated sewage. Intestinal bacteria live on unabsorbed organic material. As by–products of their metabolism, many colon bacteria generate gases, including methane and hydrogen sulfide. Some of the bacteria produce vitamins, including biotin, folic acid, vitamin K, and several B vitamins. These vitamins, absorbed into the blood, supplement our dietary intake of vitamins.

Faeces contain masses of bacteria, as well as cellulose and other undigested materials. Although cellulose fibers have no caloric value to humans, their presence in the diet helps move food along the digestive tract.

The terminal portion of the colon is called the rectum, where faeces are stored until they can be eliminated. Between the rectum and the anus are two sphincters, one involuntary and the other voluntary. One or more times each day, strong contractions of the colon create an urge to defecate.

Aug 2, 2010

Double Fertilisation


After landing on a receptive stigma, a pollen grain absorbs moisture and germinates; that is, it produces a pollen tube that extends down between the cells of the style toward the ovary.

The nucleus of the generative cell divides by mitosis and forms two sperm. Directed by a chemical attractant, possibly calcium, the tip of the pollen tube enters the ovary, probes through the micropyle (a gap in the integuments of the ovule), and discharges its two sperm near or within the embryo sac.

The events that follow are a distinctive feature of the angiosperm life cycle. One sperm fertilises the egg to form the zygote. The other sperm combines with the two polar nuclei to form a triploid (3n) nucleus in the centre of the large central cell of the embryo sac. This large cell will give rise to the endosperm, a food–storing tissue of the seed. The union of two sperm cells with different nuclei of the embryo sac is called double fertilisation. Double fertilisation ensures that the endosperm will develop only in ovules where the egg has been fertilized, thereby preventing angiosperms from squandering nutrients.

The tissues surrounding the embryo sac have prevented researchers from being able to directly observe fertilization in plants grown under normal conditions. Recently, however, scientists have isolated sperm from germinated pollen grains and eggs from embryo sacs and have observed the merging of plant gametes in vitro (in an artificial environment). The first cellular event that takes place after gamete fusion is an increase in the cytoplasmic calcium (Ca2+) levels of the egg, as also occurs during animal gamete fusion. Another similarity to animals is the establishment of a block to polyspermy, the fertilization of an egg by more than one sperm cell. Thus, maize (Zea mays ) sperm cannot fuse with zygotes in vitro. In maize, this barrier to polyspermy is established as early as 45 seconds after the initial sperm fusion with the egg.

From Ovule to Seed

After double fertilisation, each ovule develops into a seed, and the ovary develops into a fruit enclosing the seed(s). As the embryo develops from the zygote, the seed stockpiles proteins, oils, and starch to varying extents, depending on the species. This is why seeds are such major sugar sinks. Initially, these nutrients are stored in the endosperm, but later in seed development in many species, the storage function of the endosperm is more or less taken over by the swelling cotyledons of the embryo.

Endosperm Development

Endosperm development usually precedes embryo development. After double fertilisation, the triploid nucleus of the ovule’s central cell divides, forming a multinucleate “supercell” having a milky consistency. This liquid mass, the endosperm, becomes multicellular when cytokinesis partitions the cytoplasm by forming membranes between the nuclei. Eventually, these “naked” cells produce cell walls, and the endosperm becomes solid. Coconut “milk” is an example of liquid endosperm; coconut “meat” is an example of solid endosperm. The white fluffy part of popcorn is also solid endosperm.

In grains and most other monocots, as well as many eudicots, the endosperm stores nutrients that can be used by the seedling after germination. In other eudicots (including bean seeds), the food reserves of the endosperm are completely exported to the cotyledons before the seed completes its development; consequently, the mature seed lacks endosperm.