BIOLOJOY

Digestive System

2012-06-20T11:58:00.000+08:00

Why is digestion important?

When you eat foods—such as bread, meat, and vegetables—they are not in a form that the body can use as nourishment. Food and drink must be changed into smaller molecules of nutrients before they can be absorbed into the blood and carried to cells throughout the body. Digestion is the process by which food and drink are broken down into their smallest parts so the body can use them to build and nourish cells and to provide energy.

Tests for Chemical Components of Food

CHEMICAL	TEST	POSITIVE RESULT
Protein	Add a few drops of copper sulphate solution to the food sample, then a few drops of sodium hydroxide solution and mix well.	Blue-purple
Starch	Add a few drops of iodine solution to the food sample.	Blue-black
Glucose	Add an equal volume of Benedict's solution to the food sample and warm in a very hot water bath for a few minutes.	Orange-red
Lipid (Fats and Oils)	Rub a food sample onto brown paper and allow it to dry.	Translucent spot

3 Processes in Digestion

Ingestion - the mechanical taking in of food, chewing and swallowing
Digestion - The breakdown of food into smaller particles by physical or chemical means
Absorption - the absorption of these smaller food particles from the digestive tract into the blood

2 Types of Food Breakdown

Physical or Mechanical Breakdown - e.g. chewing, mixing with bile
Chemical Breakdown - e.g. enzymes, hydrochloric acid

Parts and Functions of the Human Digestive System

Mouth

Ingests food
Teeth physically break down food by chewing
Saliva lubricates food
The enzyme, salivary amylase also called ptyalin, breaks down starch into simple sugar, glucose

The Tooth

A tooth is a hard structure, set in the upper or lower jaw, that is used for chewing food. Teeth also give shape to the face and aid in the process of speaking clearly. The enamel that covers the crown (the part above the gum) in each tooth can be broken down by acids produced by the mouth for digestive purposes. This process is called "decay". To prevent decay, good oral hygiene, consisting of daily brushing and flossing, is necessary. The hardest substance in the human body is one of the four kinds of tissue which make up the tooth. It is enamel and covers the crown (area above the gum line) of the tooth. A bony material called "cementum" covers the root, which fits into the jaw socket and is joined to it with membranes. "Dentin" is found under the enamel and the cementum, and this material forms the largest part of the tooth. At the heart of each tooth is living "pulp," which contains nerves, connective tissues, blood vessels and lymphatics. When a person gets a toothache, the pulp is what hurts.

Pharynx

At the back of the mouth cavity
Both food and air pass through here

Oesophagus

Tube between mouth and stomach
A flap called the epiglottis closes over the top of the windpipe or trachea when swallowing, so that food does not enter the respiratory tract
The walls of the digestive tract from the oesophagus to the anus are muscular, and contract rhythmically to move food. The muscular contractions are called peristalsis.

Stomach

2 circular muscles called sphincters surround the entry and exit of the stomach to control the flow of food
Food remains in the stomach for about 3 hours where it physically broken down by the churning muscular contractions of the stomach wall muscles
Gastric juice contains hydrochloric acid and has a pH of 1 without food, and 3 with food.
HCl helps to kill bacteria, and works in association with the enzyme, pepsin, to partially break down proteins.
The stomach lining contains mucus to prevent damage from the acid
Only alcohol and a few drugs can be absorbed through the stomach wall into the blood

Small Intestine

Long tube that is about 7 metres long and 2.5 cm in diameter
3 parts of the small intestine are duodenum, jejunum and ileum
Most of digestion occurs in the small intestine
The enzymes of the small intestine do not function on the acidic stomach contents. First, an alkaline substance from the pancreas is secreted into the duodenum to neutralise the stomach acid.
A green substance called bile that is made in the liver and stored in the gall bladder is released into the duodenum to break the large fat particles into smaller fat particles
Enzymes from the pancreas also break down food chemically. Amylase breaks starch into simple sugars. Lipase breaks lipids into fatty acids and glycerol. Peptidases and Trypsin break down proteins into amino acids.
After the food into broken into smaller particles, it is absorbed through finger-like projections called villion the walls of the small intestine into blood capillaries.

Large Intestine

Thicker in diameter than the small intestine
Water is absorbed from the remains of undigested food to make faeces

Bacteria produce Vitamin B in the large intestine
Mucus lubricates the faeces
The appendix is attached to part of the large intestine. It may be part of the body's immune system.
Diarrhoea is the condition of more liquid faeces when the large intestine is infected.

Rectum

Storage area for faeces at the end of the large intestine
There is a sphincter surrounding the anus, the hole through which faeces passes on defaecation.
Constipation is the condition of dry hard faeces as a result of low fibre in the diet.

The Role of the Liver in Digestion

Bile - The liver produces bile which is stored temporarily in the gall bladder, and then secreted into the duodenum (first part of the small intestine) for the emulsification of lipids. Bile is also alkaline and aids in the neutralisation of stomach acid in the small intestine.
Sugar Conversion - After a meal, excess simple sugars in the bloodstream pass to the liver and are converted and stored as glycogen. However, between meals, the glycogen is converted back to simple sugars and released into the bloodstream. In this way, the blood sugar remains constant.

Appendix

Digestion takes place almost continuously in a watery, slushy environment. The large intestine absorbs water from its inner contents and stores the rest until it is convenient to dispose of it. Attached to the first portion of the large intestine is a troublesome pouch called the (veriform) appendix. The appendix has no function in modern humans, however it is believed to have been part of the digestive system in our primitive ancestors.

Additional hormones in the digestive system regulate appetite:

Ghrelin is produced in the stomach and upper intestine in the absence of food in the digestive system and stimulates appetite.
Peptide YY is produced in the digestive tract in response to a meal in the system and inhibits appetite.

Both of these hormones work on the brain to help regulate the intake of food for energy. Researchers are studying other hormones that may play a part in inhibiting appetite, including glucagon-like peptide-1 (GPL-1), oxyntomodulin (+ ), and pancreatic polypeptide.

Nerve Regulators

Two types of nerves help control the action of the digestive system.

Extrinsic, or outside, nerves come to the digestive organs from the brain or the spinal cord. They release two chemicals, acetylcholine and adrenaline. Acetylcholine causes the muscle layer of the digestive organs to squeeze with more force and increase the “push” of food and juice through the digestive tract. It also causes the stomach and pancreas to produce more digestive juice. Adrenaline has the opposite effect. It relaxes the muscle of the stomach and intestine and decreases the flow of blood to these organs, slowing or stopping digestion.

The intrinsic, or inside, nerves make up a very dense network embedded in the walls of the esophagus, stomach, small intestine, and colon. The intrinsic nerves are triggered to act when the walls of the hollow organs are stretched by food. They release many different substances that speed up or delay the movement of food and the production of juices by the digestive organs.

Together, nerves, hormones, the blood, and the organs of the digestive system conduct the complex tasks of digesting and absorbing nutrients from the foods and liquids you consume each day.

Comparison between the Digestive Tracts of
Herbivores and Carnivores

Cellulose is a complex carbohydrate that is a major component of leaves and grasses. Humans refer to cellulose as fibre, as it stimulates peristalsis and passes out in the faeces. Humans cannot digest cellulose.
Only a few organisms, such as fungi, protozoans and bacteria, can break down cellulose with anenzyme called cellulase.
Herbivores have a symbiotic relationship with these organisms that live in the herbivores' digestive tracts. The micro-organisms receive food and shelter and, in return, digest cellulose anaerobically into smaller molecules that the host can absorb.
Some herbivores have a caecum or hind-gut, where the small and large intestines join and where further breakdown of cellulose can occur. However, the faeces of these animals (e.g. horses, koalas, possums and rabbits) contain much cellulose.
Other herbivores have a more effective rumen or fore-gut before the stomach, where partly digested plant matter can be regurgitated into the mouth for further chewing and swallowed again. Ruminants mammals include cattle, sheep, kangaroos and wallabies.

PHYLUM CHORDATA

2012-01-09T22:20:00.001+08:00

All chordates have a number of structures in common:

A notochord (noto = the back; chord = string) is present in all embryos, and may be present or absent/reduced in adults. This is the structure for which the phylum was named.

A dorsal, hollow, ectodermal nerve cord (compare with Annelida and Arthropoda which have ventral, solid, mesodermal nerve cords) typically forms by an infolding of the ectoderm tissue, which then “pinches off” and becomes surrounded by mesoderm. Spinal bifida is the failure of the nervous system to close.

The pharangeal slits (pharynx = throat) originally functioned in filter feeding: water is taken into the mouth and let out via the pharangeal slits. The slits filter out food particles and keep them in the animal’s body so they can be put into the digestive tract. In fish, these have become modified as gills, and in humans as our ears and eustachian tubes.

A postanal tail (post = behind, after; anal refers to the anus) is present and extends behind the anus in many taxa, thus the anus isn’t at posterior tip of body. In humans, the tail is present during embryonic development, but is subsequently resorbed.

The main taxa within Phylum Chordata include:

Subphylum Cephalochordata (cephalo = head), which doesn’t have a “head.” This subphylum includes Lancets, so-named for their shape. These are in genus Branchiostoma (branchio = gill, fish; stoma = mouth) which was formerly know as genus Amphioxus (amphi = on both sides, double) Lancets look a lot like the generic chordate described above. They have a notochord, but no bones. They are about one inch long, and live in the muddy ocean floor.

Subphylum Urochordata (uro = tail) are called the tunicates. Their larvae show typical chordate characteristics, but the adults have lost many of these organs, and what they do still have have become highly-modified.

Subphylum Vertebrata may have come from an Amphioxus-like ancestor, however vertebrates have a definite head and Amphioxus doesn’t. Another theory suggests that vertebrates may have come from a larval form similar to tunicate larvae that were capable of reproduction in the larval stage, that is, they are sexually mature prior to metamorphosis, which is referred to as paedogenesis (paedo = child — same root as in pediatrician; genesis = origin, birth), defined as the precocious attainment of sexual maturity in a larva. Vertebrate characteristics include:

vertebrae, the skeletal units surrounding the nerve cord

a brain, enclosed within a skull

an endoskeleton which will grow along with the animal (unlike arthropods which must molt).

a closed circulatory system with a ventral heart

excretion via kidneys

separate males and females with sexual reproduction in most, with a few cases of parthenogenesis

The Classes in Subphylum Vertebrata include:

Class Agnatha (a- = not, without; gnatho = jaw) which is the lampreys. They do not have jaws, are eel-shaped, prey on fish, and have larval forms which are different from the adults.

Class Chondrichthyes (chondro = cartilage; ichthys = fish) which includes sharks and rays. They have a cartilage skeleton, not bone. They are not buoyant like other fish so they must swim or sink. Like other fish they have a lateral line system which detects differences in water pressure, the equivalent of our hearing.

Class Osteichthyes (osteo = bone) is the bony fish. This is the most numerous of all vertebrate classes. In fish, O2 is exchanged via the gills, which are covered by an operculum which helps to draw water across/through the gills. Their swim bladder is an air sac used to control buoyancy, thus unlike the sharks, bony fish can hold still at any depth and not sink.

Class Amphibia (amphi = on both sides, double; bios = life) is frogs, newts, and salamanders. They were the first land vertebrates. Frogs, especially, go through metamorphosis. Their eggs have no egg shells, so the sperm can swim through the water to the eggs, and the embryos must develop in water.

Class Reptilia (reptili = creeping) is the dinosaurs (dino = terrible ), snakes, turtles, crocodiles, and lizards. Reptiles have scales and are dry to the touch. Their eggs have leathery shells. Reptiles areexothermic (exo = out, outside), that is they maintain their body temperature through external means such as sunning on a rock or seeking shade. Reptiles need less food/energy to live and live longer than a comparable-sized mammal. Some dinosaurs may have been endothermic.

Class Aves (avi = a bird) is the birds. It is thought that birds are descended from dinosaurs, as evidenced, in part, by the scales on their feet. Also, feathers are modified scales: a key characteristic of birds is that they have feathers. Birds’ bones are light weight for flight. Birds are endothermic (endo = within, inner), that is, they control their body temperature from within (they’re “warm-blooded”). Birds’ vision is the best of all vertebrates: soaring hawks can spot small mice scrambling through the grass in a field far below them. Birds have shelled eggs and so must have internal fertilization — the egg muct be fertilized before the hen’s reproductive tract secretes an eggshell. Generally, mating is accompanied by an elaborate courtship ritual. Eggs and often young birds are more exothermic (are not able to control their body temperatures from within) and so must be brooded/incubated by parents.

Class Mammalia (mamma, mammil = teat, nipple) is the mammals. Key characteristics of mammals are the presence of fur/hair and mammary glands, derived from modified sweat glands, which produce milk for the young. Mammals have a diaphragm to aid in respiration. They are endothermic. Most mammals bear live young.

Animal Groups	Description (Which group do you like best?)	Details
	Subclass :egg-laying mammals (monotremata) (trema = hole) Playtypuses, echidnas. Generally regarded as the most primitive mammals since they lay eggs (like reptiles) and do not give birth to formed young. These mammals lays eggs like reptiles, but do have fur and milk. However, they have no nipples: their mammary glands just secrete milk onto the fur, from which the babies lick it. They have one posterior opening for their digestive, urinary, and genital tracts, hence the subclass name.	Families: 2 Genera: 3 Species: 3 show species
	Subclass:marsupials or pouche mammals (marsupialia) marsupi = a bag, pouch) Includes kangaroos, wallabies, wombats, opossums, dunnarts, bandicoots, cuscuses. The young are born as very immature embryos and must crawl to their mother’s pouch to continue their development. Typically, once in the pouch (marsupium) a baby would find a nipple there. Because of continental drift, there is a wide variety of marsupials in Australia, yet few elsewhere on Earth.	Families: 19 Genera: 83 Species: 295 show species
	Subclass Placentals (placent = a round, flat cake) contains most of the animals with which we are familiar. In this taxon, young complete embryonic development within the mother’s uterus and are nourished across a placenta. Some of the Orders in Subclass Placentals include:
	Order: edentata Some of the worlds most bizarre animals - anteaters, armadillos, sloths. They have reduced or no teeth.	Families: 4 Genera: 13 Species: 29 show species

	monkeys and apes (primates) Includes lemrus, bushbabies, lorises, pottos, tarsiers, marmosets, tamarins, monkeys, apes, humansOrder Primates (prima = first) includes lemurs, monkeys, apes, and humans. These have opposable thumbs and eyes that face forward.	Species: 180 show species
	pangolins (pholidota) Seven living species of mammal are included in the Pholidota, the pangolins or scaly anteaters.	Species: 7 show species
	insectivores (insectivora) Includes shrews, moles, golden moles, desmans, hedgehogs, moonrats, solenodons, tenrecsOrder Insectivora (vora = to eat, devour) includes moles, shrews, and hedgehogs which eat insects.	Species: 375 show species
	aardvark (tubulidentata) Aardvark	Species: 1 show species
	carnivores (carnivora) carni = flesh; vore = eat, devour) Includes big and small cats, dogs, foxes, wolves, hyenas, bears, pandas, raccoons,weasels, stoats, badgers, skunks, otters,mongooses, civets. These are carnivorous and have pointed canine teeth and molars.	Species: 230 show species
	seals (pinnipedia) Seals, sea lions, walruses	Species: 33 show species
	colugos (dermopetera) Also called flying lemurs.	Species: 2 show species
	bats (chiroptera) Includes flying foxes (fruit bats), vampires, and all other bats. (chiro = a hand, like chiropractor; ptera = wing, feather) is the bats. Their fingers are webbed to create wings.	Families: 18 Genera: 177 Species: 993 show species
	rodents (rodentia) Includesrats and mice, dormice, gerbils, beavers, squirrels, porcupines, chinchillas, pacas, voles, hamsters,chipmunks. Order Rodentia (roden = gnaw, gnawing) includes squirrels, beavers, rats, porcupines, woodchucks, guinea pigs, and mice. These have chisel-like, constantly-growing incisors	Species: 1700 show species
	rabbits and hares (lagomorpha) includes rabbits, cottontails, jackrabbits, hares, pikas. which have chisel-like incisors and hind legs modified for jumping.	Species: 80 show species
	whales and dolphins (cetacea) ceta = a whale) toothed whales, baleen, (whalebone) whales, dolphins, propoises. Their front legs (equivalent to our arms) are fin-like, and they have no hind legs. They have a thick layer of blubber for insulation.	Species: 78 show species
	even-toed hoofed mammals (artiodactyla) Includes hippos, pigs, peccaries, camels, llamas, giraffes, deer, chevrotains, gazelles, antelopes, cattle, sheep, goats. which have even-toed hooves and are herbivorous.	Species: 220 show species
	odd-toed hoofed mammals (perissodactyla) horses, asses, zebras, rhinos, tapirs. which have odd-toed hooves and are herbivorous.	Species: 17 show species
	hyraxes (hyracoidea) bush hyraxes, tree hyraxes, rock hyraxes, dassies.	Species: 7 show species
	elephants (proboscidea) African and Indian elephantswhich have long, muscular trunks and thick, loose skin. Their upper incisors are elongated as tusks.	Species: 3 show species
	sea cows (sirenia) Dugongs, manatees. Their front legs (“arms”) are fin-like, and they have no hind legs.	Species: 4 show species
	scandentia tree shrews, tupais, and dendrogales or tree squirrels	Species: 18 show

Nine Phyla of the Animal Kingdom

2012-01-09T21:59:00.001+08:00

1. Phylum Porifera - The Sponges:

a.) Habitat: mainly marine (salt water)

b.) Sponges have a porous body wall. The pores or holes allow water to pass through this animal. Floating food particles are caught once they are inside the sponge.

c.) Adult sponges are sessile feeders which means these animals are attached to shells or rocks on the ocean floor as they feed.

d.) Shape: asymmetrical which means no definite shape.

2. Phylum Coelenterata – The Coelenterates: jellyfish, hydras, corals

a.) Habitat: marine

b.) Body wall: Their body wall is made of 2 cell layers called the ectoderm and endoderm. The ectoderm is the outside layer while the endoderm is found on the inside layer. A jellylike material is found between these 2 layers.

c.) Digestive System: The digestive system is incomplete which means that coelenterates have just one opening to the digestive cavity. This single opening serves as both its mouth and anus.

d.) Symmetry: radial

e.) Specialized Cells: 1.Most coelenterates have tentacles that contain stinging cells that are used for protection and capturing food. 2. Their bodies contain a nerve network that allows movement of the tentacles and body.

3. Phylum Platyhelminthes – The Flatworms: planaria, tapeworms

a.) Habitat: fresh and salt water; terrestrial(land)

b.) Body Plan: These animals are given their name because of their flattened bodies. Flatworms have 3 distinct tissue layers called the ectoderm, endoderm, and mesoderm or middle layer. Each layer gives rise to the various organs and systems of this animal.

c.) Digestive System: In free-living species of flatworms the digestive system is incomplete which means that the digestive cavit y has only a single opening. The parasitic tapeworm has no need for a digestive system because it absorbs nutrients that are already digested by the host in which it lives.

d.) Symmetry: Flatworms have bilateral symmetry and they have a definite head and tail region.

e.) Specialized Structures: 1. The planaria has a pair of eyespots at its anterior or front end. These eyespots detect light which the planaria avoids so they are less visible to their predators. 2. The tapeworm like other parasitic worms has a thick protective cuticle on the outside of its body. The cuticle protects the worm from being digested by the strong digestive enzymes of its host.

4. Phylum Nematoda – The Roundworms

a.) Habitat: fresh and salt water; terrestrial

b.) Body Plan: The body of a roundworm is long, smooth and unsegmented. Their cylindrical bodies are tapered at both ends and are covered by a protective cuticle. Three tissue layers; ecto, endo and mesoderm.

c.) Digestive System: Roundworms have a complete digestive system which means their digestive tract has 2 openings; a mouth to ingest food and an anus to egest waste.

d.) Symmetry: Bilateral symmetry with an anterior end and a posterior end.

e.) Interesting Facts: 1. Free-living roundworms are extremely plentiful in soil and are essential in producing quality soil. 2. Pinworms are common parasitic roundworms found in children.

5. Phylum Annelida – The Segmented Worms: earthworm, leech, sandworm

a.) Habitat: marine, freshwater, terrestrial

b.) Body Plan : similar shape as the roundworm but the body is segmented both internally and externally which allows for a quicker response for movement.

c.) Digestive System: Segmented worms have a complete digestive system and this set-up is often referred to as a tube-within-a-tube body plan.

d.) Symmetry: Bilateral; anterior and posterior ends; dorsal and ventral surfaces.

6. Phylum Arthropoda – The Arthropods: insects, spiders, crustaceans

a.) Habitat: arthropods are found in all environments.

b.) Numbers: Arthropods are the most successful of any animal group. This is mainly due to the success of insects, which has more than a million different species.

c.) Body Plan: Arthropods have a segmented body with paired jointed appendages that provide excellent movement for walking, swimming, flying, grabbing, fighting, digging and biting just to name a few. In most arthropods the body is divided into a head, abdomen and thorax.

d.) Exoskeleton: The outside skeleton of arthropods is made of chitin which protects the soft body of this animal and prevents water loss allowing them to live successfully on land.

e.) Symmetry: Bilateral

7. Phylum Mollusca – The Mollusks: clams, snails, oysters, octopus

a.) Habitat: marine and fresh water; terrestrial

b.) Body Plan: Mollusks have a soft, unsegmented body and often move with a strong muscular foot on its ventral surface.

c.) The radula: Mollusks are well known for their tongue-like organ called the radula which has many rows of teeth and is used to scrape food from the surface of plants and rocks.

d.) The mantle: The mantle is a fold of skin that surrounds the body organs. The mantle acts like a gland because it is capable of secretion. These secretions harden to help form the shells of mollusks.

e.) Symmetry: bilateral

8. Phylum Echinodermata – The Echinoderms: sea stars, sea urchins

a) Habitat: all are marine living mainly on the ocean floor.

b) Body: Echinoderms have an internal, limy skeleton and a spiny outside surface or skin. These structures give both support and protection.

c) Water-vascular System: Echinoderms like sea stars and sea urchins are well known for their water-vascular system which consist of water-filled tubes that run through their body. By moving water in and out of these tubes echinoderms can move on “jets” of water or use their tubed feet as suction cups.

d) Digestive System: complete

e) Symmetry: Radial

9. Phylum Chordata – The Chordates: fish, reptiles, amphibians, birds, mammals

a.) Habitat: marine, freshwater, or terrestrial

b.) Symmetry: bilateral

c.) Dorsal nerve cord.

d.) Chordates have a flexible, supporting rod or notochord on their dorsal side. In the invertebrates the notochord remains stiff and flexible. In the vertebrates, cartilage or bone replaces the notochord to form a supporting backbone.

Central Dogma of Biology

2011-12-31T07:29:00.002+08:00

Molecular Genetics

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DNA and Chomosomal basis of heredity

2011-12-30T13:46:00.001+08:00

Chromosomal basis: please click on the link:
Chromosomes, Karyotyping, Sex determination, Sex Linkage and Pattern of Inheritance

DNA and molecular genetics:

BIOL 102 Chp 16 PowerPoint
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Review about heredity

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Bab 3 F 4 Part 1

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Heredity

2011-12-30T13:30:00.000+08:00

Heredity

Genetics and heredity

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Introduction to the Human Body

2011-12-30T09:28:00.000+08:00

1. The human body is made up of a head, neck, torso, two arms and two legs. The average height of an adult human is about 5 to 6 feet tall. The human body is made to stand erect, walk on two feet, use the arms to carry and lift, and has opposable thumbs (able to grasp).
2. The adult body is made up of: 100 trillion cells, 206 bones, 600 muscles, and 22 internal organs.

3.  There are many systems in the human body: Circulatory System (heart, blood, vessels) Respiratory System (nose, trachea, lungs) Immune System (many types of protein, cells, organs, tissues) Skeletal System (bones) Excretory System (lungs, large intestine, kidneys) Urinary System (bladder, kidneys) Muscular System (muscles) Endocrine System (glands) Digestive System (mouth, esophogus, stomach, intestines) Nervous System (brain, spinal cord, nerves) Reproductive System (male and female reproductive organs)

4. Every square inch of the human body has about 19 million skin cells.

5. Every hour about 1 billion cells in the human body must be replaced.

6. The average human head has about 100,000 hairs.

7. The circulatory system of arteries, veins, and capillaries is about 60,000 miles long.

8. The heart beats more than 2.5 billion times in an average lifetime.

9. There are about 9,000 taste buds on the surface of the tongue, in the throat, and on the roof of the mouth.

10.  The strongest muscle in the body is the tongue.

11. The human heart creates enough pressure when it pumps out to the body to squirt blood 30 feet.

12. You blink over 10,000,000 times a year.

13. The human brain weighs about 3 pounds.

14. It takes about 20 seconds for a red blood cell to circle the whole body.
15. Only 10% of the population are left handed.

16.  One fourth of the bones in your body are in your feet.

17. Children tend to grow faster in the spring.

18. The most sensitive finger on the human hand is the index finger.

19. More men are color-blind than women.

20. More people have brown eyes than any other color.

Animal Behavior

2011-12-30T09:05:00.000+08:00

Animal Behavior is the scientific study of the wild and wonderful ways in which animals interact with each other, with other living beings, and with the environment. It explores how animals relate to their physical environment as well as to other organisms, and includes topics such as how animals find and defend resources, avoid predators, choose mates, reproduce, and care for their young.

Behaviors exist on a continuum from being to a large extent contingent on genetic factors (i.e., instinctive), to others which are mostly acquired through experience. Instinctive components are those that are exhibited without the benefit of, or need for, prior experience. They come to the fore when, for instance, newly hatched, inexperienced individuals of a particular species of spider construct their webs with little variation, despite the lack of a tutor. Learned behaviors are those that are acquired through interactions with the surrounding world.

Nature vs. Nurture describes a debate about the degree to which individual differences in physical and behavioral traits are the product of an individual's innate qualities ("nature") versus those shaped by personal experiences ("nurture"). This dichotomy aims to delineate how much of the human (psychological) make-up is the result of environmental influences and how much is a result of phylogenetic heritage. In today's view there are multiple problems with phrasing the issue in this either-or form. Most significant of all, as the two are NOT mutually exclusive concepts. It is now clear that in every instance both influences play significant roles as all development represents a complex interaction between inherited factors and environmental conditions.

Inherited and Learned Behavior:

Ap chap 51 animal behavior
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Kingdom Animalia

2011-12-30T07:45:00.000+08:00

Animal APBio

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Vertebrates

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Seeds and Fruits

2011-12-30T06:49:00.000+08:00

Plants in the division Anthophyta (angiosperms) have evolved complex mechanisms to provide for protection and dispersal of their offspring. The two key features of this system are the production of embryos within seeds, and the enclosing of these seeds in ovaries which mature into fruits. Both the hard seed coat and internal nutrient supplies of seeds, and the hard or fleshy fruit create an effective buffer preventing harsh environmental conditions from causing damage to the enclosed embryo. In addition, both seeds and fruits often include specific mechanisms to facilitate seed dispersal..

Seeds

In angiosperms, seeds consist primarily of the external seed coat, the embryo, and a nutritive tissue called the endosperm. The embryo consists of a primary root (radicle) one or two embryonic leaves (cotyledons) , a stem-like portion below the cotyledons (thehypocotyl) , and a stem-like portion above the cotyledons (the epicotyl). Plants in the class Monocotyledones (monocots) contain just one cotyledon; plants in the class Dicotyledones (dicots) contain two cotyledons. In many of the monocots, the epicotyl and any developing leaves it bears are surrounded by a protective sheath called a coleoptile; the radicle is surrounded by another protective sheath called a coleorhiza.

The endosperm results from divisions of a primary endosperm nucleus. This nucleus arises when the two polar nuclei of the megagametophyte fuse with a sperm nucleus, a process which occurs simultaneously with the fusion of the egg with the other sperm nucleus. In the seeds of some plants, such as corn, the endosperm forms a large portion of the mature seed and serves as the major source of nutrition for the embryo during seed germination. In the seeds of other plants, such as pea and bean, the endosperm has been almost entirely consumed by the time the seed is mature. In these seeds the cotyledons are enlarged and fleshy and serve as the major nutrient source during germination.

Fruits

Fruits are formed when an ovary undergoes changes, becoming either dry and hardened or enlarged and fleshy. This maturation process is generally triggered by signals accompanying seed formation. The nature of the fruit in a particular plant will depend, to a large extent, on the nature of the ovary from which it develops. For example, the placentation of the ovules carried in a particular ovary will determine the eventual placement of seeds within the fruit. Also, the number of locules in the ovary will be apparent in the fruit.

There are several key features which are used to classify fruits. These include:

1. The composition of the fruit A true fruit is one that forms from ovary tissue alone, while an accessory fruit is one that includes modified tissue of other floral parts (usually the receptacle). 2. The origin of the fruit A simple fruit is one that forms from a single ovary; an aggregate fruit (e.g. the raspberry, the strawberry with its development from flower to fruit) forms from several ovaries of a multipistillate flower; a multiple fruit (e.g. the pineapple) forms from the ovaries of several different flowers within an inflorescence. 3. The texture of the fruit Some fruits are dry, whereas others are fleshy.

The following is a key to some specific fruit types.

I. Dry fruits

A. Indehiscent fruits (these are fruits which do not open at maturity)

1. Achene - a small, dry, hard, indehiscent fruit, one-seeded, nut-like, often mistaken for a seed. Examples: sunflower, lettuce, strawberry, buttercup. 2. Caryopsis (grain) - an achene in which the ovary wall and seed coat are inseparable. Examples: wheat, corn. 3. Nut - a large, indehiscent achene, commonly one-seeded. Examples: chestnut, acorn of oak. 4. Samara - a winged achene or nut. Examples: maple, elm, ash.

B. Dehiscent fruits (these are fruits which do open at maturity to shed their seeds)

1. Follicle - derived from one carpel, several seeded, opening along one side at maturity. Examples: milkweed, proboscidea, larkspur. 2. Legume - derived from one carpel, usually several-seeded, opening along two sides at maturity. Examples: bean, pea. 3. Capsule - developed from a pistil of two or more united carpels, each opening at maturity. Examples: lily, iris.

II. Fleshy or partly fleshy fruits

A. Berry - ovary wall becomes fleshy throughout, one to many seeds. Examples: grape, eggplant, persimmon, tomato, carambola, kiwi fruit. B. Pepo - an accessory berry, in which the ovary wall and floral tube are adherent, with a hard rind. Applied to fruits of the gourd family. Examples: cucumber (also cucumber in c.s.), squash, pumpkin, cantaloupe. C. Hesperidium - a modified berry, in which the outer part of the ovary wall becomes leathery. Applied to fruits of the citrus family. Examples: grapefruit, lemon. D. Drupe - a fruit from a single carpel, in which the outer wall of the ovary has become fleshy and the inner part stony at maturity. Often termed a "stone fruit". Examples: plum, peach, almond, cherry. E. Pome - an accessory fruit derived from a compound pistil of several carpels, parts of which are stony or membranous and parts of which are fleshy; the whole permanently enclosed in the fleshy floral tube or receptacle. Examples: pear, apple, quince, hawthorn.

The Flower

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The Flower:
The flower is the reproductive unit of some plants (angiosperms). Parts of the flower include petals, sepals one or more carpels (the female reproductive organs), and stamens (the male reproductive organs).

The Female Reproductive Organs:
The pistil is the collective term for the carpel(s). Each carpel includes an ovary (where the ovules are produced; ovules are the female reproductive cells, the eggs), a style (a tube on top of the ovary), and a stigma (which receives the pollen during fertilization).

The Male Reproductive Organs:
Stamens are the male reproductive parts of flowers. A stamen consists of an anther (which produces pollen) and a filament. The pollen consists of the male reproductive cells; they fertilize ovules.

Fertilization:
Pollen must fertilize an ovule to produce a viable seed. This process is called pollination, and is often aided by animals like bees, which fly from flower to flower collecting sweet nectar. As they visit flowers, they spread pollen around, depositing it on some stigmas. After a male's pollen grains have landed on the stigma during fertilization, pollen tubes develop within the style, burrowing down to the ovary, where the sperm fertilizes an ovum (an egg cell), in the ovule. After fertilization, the ovule develops into a seed in the ovary.

Types of Flowers:
Some flowers (called perfect flowers) have both male and female reproductive organs; some flowers (called imperfect flowers) have only male reproductive organs or only female reproductive organs. Some plants have both male and female flowers, while other have males on one plant and females on another. While Complete flowers have stamens, a pistil, petals and sepals. Incomplete flowers lack one of these parts.

Pollination and flower structure

Although many angiosperms have the potential to self-fertilize, most plants cross-fertilize. To transfer pollen from flower to flower, angiosperms make use of wind dispersal and animal pollinators. Animals which pollinate flowers include insects, birds, and mammals. One of the important functions of flowers is to attract animal pollinators. Because of this, flower structure, color, and odor vary dramatically in correlation with the primary pollinators. For example, flowers which are pollinated by flies smell like rotting meat, while some flowers pollinated by wasps mimic the appearance of a female wasp (potential mate). The benefits to pollinators include nutrition from nectar and pollen.

It is often possible to determine what type of pollination/pollinator a plant uses by the structure, color, shape, and smell of the flower. You should be familiar with this table:

Flower Trait	Pollinator
Reduced sepals and petals	Wind
Large sepals or petals	Animal
Petals white	Moth or bat
Petals colored
Flower tubular
Sweet odor	Butterfly
No odor	Hummingbird
Flower not tubular	Bee or beetle

Inside the anther, microspores are produced through meiosis. These microspores give rise to themicrogametophyte – the pollen grain.

The female reproductive organ, the ovary, contains developing ovules. Each ovule produces megaspores (haploid) through meiosis. One megaspore survives in each ovule and develops into a multi-nucleated megagametophyte.

When pollen reaches the stigma, it grows a pollen tube to extend down the style. Two sperm nuclei enter the ovule: one fuses with the egg to produce the zygote, the other fuses with two polar nuclei to make the 3n endosperm. The endosperm is part of the seed and provides nutrition for the sporophyte embryo. The fusion of two sperm nuclei with megagametophyte nuclei is called double fertilization.

Following fertilization, the zygote develops into an embryo, the endosperm grows, the ovule forms a seed, and the ovary develops into a fruit.

Leaves

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Add caption

Terrariums

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Terrariums are a great way to bring life to your tiny cubbyhole in the office, or a bare space at home. They are very easy and inexpensive to make. Basically, all you need is a clear container, sand, pebbles, gravel, activated charcoal, potting soil, plants, and decorative elements.

The first step to making a terrarium is to select a clear container. Anything can be used as the home of your terrarium as long as it is clear. Popular choices include a fishbowl, an empty aquarium, or any large glass container. You can also use dishes, soda bottles, and glass jars. Of course, your container of choice will depend on whether you want to create an open-air terrarium, or a closed environment terrarium.

2. Once you have selected your container, the next step is to create a drainage layer for your terrarium. This is important because it will ensure that your plants will thrive inside your terrarium. You can use pebbles, sand and gravel to make the drainage layer. Adding activated charcoal is also recommended, especially if you are making a closed environment terrarium. The charcoal will filter the air and keep it fresh. Activated charcoal can be bought at any pet shop that sells aquarium supplies.

3. You may also opt to add sphagnum moss on top of your drainage layer. Why? The sphagnum moss will prevent the soil from falling through the cracks in your drainage layer once you start watering the plants. You can also use a very fine screen as an alternative to sphagnum moss. However, this will need to be replaced as it will rust over time.

4. Now that we're done with the drainage layer, the next step is to add the potting soil up to 3 inches deep. Create hills and angles by distributing the potting soil unevenly. Any potting soil will do. Just make sure that the potting soil you are using is fresh. You can buy this at any garden store. A world of caution though: if you are planning on creating a desert terrarium, make sure to pick the right potting soil for such plants. Use a long handled spoon to dig holes for the roots of your plants.

5. Now, you are ready to add plants to your terrarium. Do not just put any plant you want. Create a theme for your terrarium. If you like the tropics, then you can use tropical plants like African violets. For a desert feel, you can use cacti and other succulents.

6. Once you have decided on a theme, do not put the plants in just yet. Think how you want your terrarium to look. Here is where your artistic side comes in. You can sketch a design, or you can try arranging the plants inside the container to see which layout appeals to you the most. Once you have found the perfect lay out, then you can start adding your plants in the terrarium. Plant your plants in the dirt, gently spreading out their roots, and replace the dirt over their roots. After planting them in, Mist the inside walls of your terrarium with an ounce or two of distilled water. Do not water your terrarium again until it has begun to dry out. Keep your terrarium in indirect sunlight.

Roots and Types of roots

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Roots are the principal water-absorbing organs of a plant.
There are three primary functions of roots: (1) to anchor the plant to a substrate, (2) to absorb water and dissolved minerals, and (3) to store food reserves. Typically we see roots in soil, but there are specialized types of aerial roots (air roots) that enable climbing plants and epiphytes to become attached to rocks, bark, and other nonsoil substrates. In addition, parasitic plants may form specialized haustorial roots that form an attachment disc to the host during the first stage of colonization.

TYPES OF ROOTS:

OTHER TYPES OF ROOTS:

Photosynthesis VS Cellular Respiration

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Photosynthesis vs Respiration

Photosynthesis and respiration are reactions that complement each other in the environment. They are in reality the same reactions but occurring in reverse. While in photosynthesis carbon dioxide and water yield glucose and oxygen, through the respiration process glucose and oxygen yield carbon dioxide and water.
They work well since living organisms supply plants with carbon dioxide which undergoes photosynthesis and produces glucose and these plants and bacteria give out oxygen which all living organisms need for respiration.

Comparison chart

Improve this chart	Photosynthesis	Respiration
Main function:	Production of food. Energy Capture.	Breakdown of food. Energy release.
Electron Carrier:	NADPH	NADH
Electron source:	Oxidation H2O at PSII	NADH + FADH2
What pumps protons across the membrane:	C	Complex I, III, IV
What powers ATP synthesase:	H+ gradient across thylakoid membrane. High H+ concentration in the thylakoid space	H+ gradient across the inner mitochondria membrane. High H+ concentration in the intermembrane space
Process:	The production of organic carbon (glucose and starch) from inorganic carbon (carbon dioxide) with the use of ATP and NADPH produced in the light dependent reaction	The production of ATP from the oxidation of organic sugar compounds.
Fate of oxygen and carbon dioxide:	Carbon dioxide is absorbed and oxygen is released.	Oxygen is absorbed and carbon dioxide is released.
Occurrence:	Occurs in plants and some bacteria.	Occurs in all living organisms.
Location:	chloroplasts	mitochondria
Product:	C6H12O6 and O2	CO2 and H2O
Reactants:	CO2 and H2O	C6H12O6 and O2
Equation:	6CO2 + 6H2O light --> C6H12O6 + 6O2	6O2 + C6H12O6 --> 6CO2 +6H2O + energy
Production of ATP:	yes	yes, 36-38
Requirement of sunlight:	Can occur only in presence of sunlight	Occurs at all times.
Chemical reaction:	Carbon dioxide and water combine in presence of sunlight to produce glucose.	Glucose is broken down into water and carbon dioxide.
Final electron receptor:	NADP+	Oxygen
Catalyst:	Reaction takes places in presence of chlorophyll.	No catalyst is required for respiration reaction.
Stages:	2 stages (The light dependent reaction, light independent reaction).	3 stages (Glycolysis, Link reaction, Krebs cycle).

Photosynthesis is a process that converts carbon dioxide into organic compounds in presence of sunlight. Respiration is the set of metabolic reactions that take in cells of living organisms that convert nutrients like sugar into ATP (adenosine tri phosphate) and waste products.

Processes in photosynthesis are divided on basis of requirement of sunlight while respiration processes are divided on basis of requirement of oxygen. Hence in photosynthesis you have the light dependent reactions and the dark reactions while in respiration there is aerobic respiration and anaerobic respiration.
In photosynthesis light dependent reactions, ultra violet light strikes chlorophyll pigments which excites electrons leading to separation of oxygen molecules from carbon dioxide. In the dark reactions, carbon molecules now independent of oxygen are converted into carbohydrates and stored in plant cells as energy and food source. In aerobic cellular respiration oxygen is utilized to convert organic compounds into energy and in anaerobic respiration converts organic compounds into energy without using oxygen.

Photosynthesis takes place in the chloroplasts and organelles of a plant cell. Respiration takes place in the cytoplasm and mitochondria in the cell of a living organism.

Reaction kinetics

The electron acceptor in photosynthesis is NAD+ while in respiration the electron acceptor is NADH. In cellular respiration reaction 36 molecules of ATP are produced in complete oxidation of one molecule of glucose.

Electron Transport Chain

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ELECTRON TRANSPORT SYSTEM

Introduction:

The majority of the energy conserved during catabolism reactions occurs near the end of the metabolic series of reactions in the electron transport chain. The electron transport or respiratory chain gets its name from the fact electrons are transported to meet up with oxygen from respiration at the end of the chain. The overall electron chain transport reaction is:

2 H⁺ + 2 e⁺ + 1/2 O₂ ---> H₂O + energy

Notice that 2 hydrogen ions, 2 electrons, and an oxygen molecule react to form as a product water with energy released in an exothermic reaction. This relatively straight forward reaction actually requires eight or more steps. The energy released is coupled with the formation of three ATP molecules per every use of the electron transport chain.

Complex I

In Complex I (NADH dehydrogenase, also called NADH:ubiquinone oxidoreductase; two electrons are removed from NADH and transferred to a lipid-soluble carrier, ubiquinone (Q). The reduced product, ubiquinol (QH₂) freely diffuses within the membrane, and Complex I translocates four protons (H⁺) across the membrane, thus producing a proton gradient. Complex I is one of the main sites at which premature electron leakage to oxygen occurs, thus being one of the main sites of production of harmful superoxide.
The pathway of electrons occurs as follows:
NADH is oxidized to NAD⁺, by reducing Flavin mononucleotide to FMNH₂ in one two-electron step. FMNH₂ is then oxidized in two one-electron steps, through a semiquinone intermediate. Each electron thus transfers from the FMNH₂ to an Fe-S cluster, from the Fe-S cluster to ubiquinone (Q). Transfer of the first electron results in the free-radical (semiquinone) form of Q, and transfer of the second electron reduces the semiquinone form to the ubiquinol form, QH₂. During this process, four protons are translocated from the mitochondrial matrix to the intermembrane space.

Complex II

In Complex II (succinate dehydrogenase; EC 1.3.5.1) additional electrons are delivered into the quinone pool (Q) originating from succinate and transferred (via FAD) to Q. Complex II consists of four protein subunits: SDHA, SDHB, SDHC, and SDHD. Other electron donors (e.g., fatty acids and glycerol 3-phosphate) also direct electrons into Q (via FAD).

Complex III

In Complex III (cytochrome bc₁ complex; EC 1.10.2.2), the Q-cycle contributes to the proton gradient by an asymmetric absorption/release of protons. Two electrons are removed from QH₂ at the Q_O site and sequentially transferred to two molecules of cytochrome c, a water-soluble electron carrier located within the intermembrane space. The two other electrons sequentially pass across the protein to the Q_i site where the quinone part of ubiquinone is reduced to quinol. A proton gradient is formed by two quinol (4H+4e-) oxidations at the Q_o site to form one quinol (2H+2e-) at the Q_i site. (in total six protons are translocated: two protons reduce quinone to quinol and four protons are released from two ubiquinol molecules).
Cytochromes are very similar to the structure of myoglobin or hemoglobin. The significant feature is the heme structure containing the iron ions, initially in the +3 state and changed to the +2 state by the addition of an electron. The CoQH₂ (yellow)passes along the 2 electrons first to cytochrome (blue) b1 heme (magenta), then b2 heme , then to an iron-sulfur protein (green), then to cytochrome c1 (red with black heme), and finally to cytochrome c (not shown). Co Q is represented by the inhibitor antimycin (yellow) in the graphic
When electron transfer is reduced (by a high membrane potential or respiratory inhibitors such as antimycin A), Complex III may leak electrons to molecular oxygen, resulting in superoxide formation.

Complex IV

In Complex IV (cytochrome c oxidase;), sometimes called cytochrome A3, four electrons are removed from four molecules of cytochrome c and transferred to molecular oxygen (O₂), producing two molecules of water. At the same time, four protons are translocated across the membrane, contributing to the proton gradient. The activity of cytochrome c oxidase is inhibited by cyanide.

Coupling with oxidative phosphorylation

According to the chemiosmotic coupling hypothesis, proposed by Nobel Prize in Chemistry winner Peter D. Mitchell, the electron transport chain and oxidative phosphorylation are coupled by a proton gradient across the inner mitochondrial membrane. The efflux of protons from the mitochondrial matrix creates an electrochemical gradient (proton gradient). This gradient is used by the F_OF₁ ATP synthase complex to make ATP via oxidative phosphorylation. ATP synthase is sometimes described as Complex V of the electron transport chain.^{[citation needed]} The F_O component of ATP synthase acts as an ion channel that provides for a proton flux back into the mitochondrial matrix. This reflux releases free energy produced during the generation of the oxidized forms of the electron carriers (NAD⁺ and Q). The free energy is used to drive ATP synthesis, catalyzed by the F₁ component of the complex.^{[citation needed]}
Coupling with oxidative phosphorylation is a key step for ATP production. However, in specific cases, uncoupling the two processes may be biologically useful. The uncoupling protein, thermogenin—present in the inner mitochondrial membrane of brown adipose tissue—provides for an alternative flow of protons back to the inner mitochondrial matrix. This alternative flow results in thermogenesis rather than ATP production and generates heat.^{[citation needed]} Synthetic uncouplers (e.g., 2,4-dinitrophenol) also exist, and, at high doses, are lethal

Summary

In the mitochondrial electron transport chain electrons move from an electron donor (NADH or QH₂) to a terminal electron acceptor (O₂) via a series of redox reactions. These reactions are coupled to the creation of a proton gradient across the mitochondrial inner membrane. There are three proton pumps: I, III, and IV. The resulting transmembrane proton gradient is used to make ATP via ATP synthase.
The reactions catalyzed by Complex I and Complex III work roughly at equilibrium. This means that these reactions are readily reversible, by increasing the concentration of the products relative to the concentration of the reactants (for example, by increasing the proton gradient). ATP synthase is also readily reversible. Thus ATP can be used to build a proton gradient, which in turn can be used to make NADH. This process of reverse electron transport is important in many prokaryotic electron transport chains

Krebs Cycle

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The Krebs Cycle or the Citric Acid Cycle (TCA)

The citric acid cycle — also known as the tricarboxylic acid cycle (TCA cycle), the Krebs cycle, or the Szent-Györgyi-Krebs cycle^[1]^[2] — is a series of chemical reactions which is used by all aerobic living organisms to generate energy through the oxidization of acetate derived from carbohydrates, fats and proteins into carbon dioxide and water. In addition, the cycle provides precursors for the biosynthesis of compounds including certain amino acids as well as the reducing agent NADH that is used in numerous biochemical reactions. Its central importance to many biochemical pathways suggests that it was one of the earliest established components of cellular metabolism and may have originated abiogenically.^[3]
The name of this metabolic pathway is derived from citric acid which is first consumed and then regenerated by the pathway to complete the cycle. In addition, the cycle consumes acetate in the form of acetyl-CoA, reduces NAD⁺ to NADH, and produces carbon dioxide. The NADH generated by the TCA cycle is fed into the oxidative phosphorylation pathway. The net result of these two closely linked pathways is the oxidation of nutrients to produce energy in the form of ATP.
In eukaryotic cells, the citric acid cycle occurs in the matrix of the mitochondrion. Bacteria also use the TCA cycle to generate energy, but since they lack mitochondria, the reaction sequence is performed in the cytosol.
The components and reactions of the citric acid cycle were established in the 1930s by seminal work from the Nobel laureates Albert Szent-Györgyi ^[4] and Hans Adolf Krebs.^[5]

The citric acid cycle is a key component of the metabolic pathway by which all aerobic organisms generate energy. Through catabolism of sugars, fats, and proteins, a two carbon organic product acetate in the form of acetyl-CoA is produced. Acetyl-CoA along with two equivalents of water (H₂O) are consumed by the citric acid cycle producing two equivalents of carbon dioxide (CO₂) and and one equivalent of HS-CoA. In addition, one cycle of the pathway converts three equivalents of nicotinamide adenine dinucleotide (NAD⁺) into three equivalent of reduced NAD⁺ (NADH), one equivalent of ubiquinone (Q) of into one equivalent of reduced ubiquinone (QH₂), and one equivalent each of guanosine diphosphate (GDP) and inorganic phosphate (P_i) into one equivalent of guanosine triphosphate (GTP). The NADH and QH₂ that is generated by the citric acid cycle is in turn used by oxidative phosphorylation pathway to generate energy rich adenosine triphosphate (ATP).

One of the primary sources of acetyl-CoA are sugars that are broken down by glycolysis to produce pyruvate that in turn is decarboxylated by the enzyme pyruvate dehydrogenase generating acetyl-CoA according to the following reaction scheme:

CH₃C(=O)C(=O)O^– (pyruvate) + HSCoA + NAD⁺ → CH₃C(=O)SCoA (acetyl-CoA) + NADH + H⁺ + CO₂

The product of this reaction, acetyl-CoA, is the starting point for the citric acid cycle. Below is a schematic outline of the cycle:

The citric acid cycle begins with the transfer of a two-carbon acetyl group from acetyl-CoA to the four-carbon acceptor compound (oxaloacetate) to form a six-carbon compound (citrate).
The citrate then goes through a series of chemical transformations, losing two carboxyl groups as CO₂. The carbons lost as CO₂ originate from what was oxaloacetate, not directly from acetyl-CoA. The carbons donated by acetyl-CoA become part of the oxaloacetate carbon backbone after the first turn of the citric acid cycle. Loss of the acetyl-CoA-donated carbons as CO₂ requires several turns of the citric acid cycle. However, because of the role of the citric acid cycle in anabolism, they may not be lost, since many TCA cycle intermediates are also used as precursors for the biosynthesis of other molecules.^[8]
Most of the energy made available by the oxidative steps of the cycle is transferred as energy-rich electrons to NAD⁺, forming NADH. For each acetyl group that enters the citric acid cycle, three molecules of NADH are produced.
Electrons are also transferred to the electron acceptor Q, forming QH₂.
At the end of each cycle, the four-carbon oxaloacetate has been regenerated, and the cycle continues.

Products

Products of the first turn of the cycle are: one GTP (or ATP), three NADH, one QH₂, two CO₂.

Because two acetyl-CoA molecules are produced from each glucose molecule, two cycles are required per glucose molecule. Therefore, at the end of two cycles, the products are: two GTP, six NADH, two QH₂, and four CO₂

Description	Reactants	Products
The sum of all reactions in the citric acid cycle is:	Acetyl-CoA + 3 NAD⁺ + Q + GDP + P_i + 2 H₂O	→ CoA-SH + 3 NADH + 3 H⁺ + QH₂ + GTP + 2 CO₂
Combining the reactions occurring during the pyruvate oxidation with those occurring during the citric acid cycle, the following overall pyruvate oxidation reaction is obtained:	Pyruvate ion + 4 NAD⁺ + Q + GDP + P_i + 2 H₂O	→ 4 NADH + 4 H⁺ + QH₂ + GTP + 3 CO₂
Combining the above reaction with the ones occurring in the course of glycolysis, the following overall glucose oxidation reaction (excluding reactions in the respiratory chain) is obtained:	Glucose + 10 NAD⁺ + 2 Q + 2 ADP + 2 GDP + 4 P_i + 2 H₂O	→ 10 NADH + 10 H⁺ + 2 QH₂ + 2 ATP + 2 GTP + 6 CO₂

The above reactions are balanced if P_i represents the H₂PO₄^- ion, ADP and GDP the ADP^2- and GDP^2- ions, respectively, and ATP and GTP the ATP^3- and GTP^3- ions, respectively.

The total number of ATP obtained after complete oxidation of one glucose in glycolysis, citric acid cycle, and oxidative phosphorylation is estimated to be between 30 and 38. A recent assessment of the total ATP yield with the updated proton-to-ATP ratios provides an estimate of 29.85 ATP per glucose molecule.

Glycolysis

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Glycolysis literally means "splitting sugars." Glucose, a six carbon sugar, is split into two molecules of a three carbon sugar. In the process, two molecules of ATP, two molecules of pyruvic acid and two "high energy" electron carrying molecules of NADH are produced. Glycolysis can occur with or without oxygen. In the presence of oxygen, glycolysis is the first stage of cellular respiration. Without oxygen, glycolysis allows cells to make small amounts of ATP. This process is called fermentation.

Cellular Respiration

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Once the energy that was in sunlight is transformed into chemical energy, often by photosynthesis, the organism has to now convert the chemical energy into a usable form. It may seem a bit odd for there still to be more steps. After all, when you eat a candy bar isn't the sugar in the candy bar "burnt" by the body to provide energy? Well the answer is yes and no. First of all when we burn something normally in the air we combine that substance with oxygen releasing energy from the substance. Indeed, an analogous process does happen in our bodies.

What goes on in living things is not really like burning because the molecules from which we harvest energy give up their energy in a controlled fashion rather than all at once as what happens in a fire. Think of your car. All the energy in the gas tank when you get in your car is not released all at once but rather in small bursts which allow you to control the car's movement. In the same way cells take the energy from the "food" and package that energy into manageable bursts that provide just the right amount of energy for the organism's activities be those activities driving a car or flashing a light to attract a mate.

The point of cellular respiration is to harvest electrons from organic compounds such as glucose and use that energy to make a molecule called ATP. ATP in turn is used to provide energy for most of the immediate work that the cell does. ATP can be thought of as being like a small package of energy that has just the right amount of energy that can be used in a controlled manner.

ATP: Adenosine tri-phosphate,ATP is a nucleotide with three phosphate groups instead of one phosphate group. The point of cellular respiration is to harvest chemical energy from food and store it in the chemical bonds of ATP. ATP is said to be the currency for energy.

Types of cellular respiration: There are two basic types of cellular respiration aerobic cellular respiration and anaerobic cellular respiration. Aerobic respiration requires the use of oxygen and anaerobic respiration which does not use oxygen. There are several types of anaerobic respiration, most familiar is a process called Fermentation. During fermentation, the pyruvic acid produced during glycolysis is converted to either ethanol or lactic acid. This continued use of pyruvic acid during fermentation permits glycolysis to continue with its associated production of ATP.

Aerobice Respiration on the other hand, has three main stages: glycolysis, the citric acid cycle, and electron transport.

Glycolysis can occur in either the absence or the presence of oxygen. Glycolysis occurs in the cytoplasm of cells, not in organelles, and occurs in all kinds of living organisms. Prokaryote cells use glycolysis and the first living cells most likely used glycolysis.

In glycolysis glucose is partially oxidized and broken down into two 3 carbon molecules called pyruvate or pyruvic acid. In the process, glycolysis produced 4 ATP for a net gain of two ATP and two molecules of NADH. Each NADH is carrying two energy rich electrons away from the glucose and these electrons can be used by the cell to do work.

After glycolysis the pyruvate is processed to harvest 2 more NADH molecules and remove one carbon per pyruvate. The carbon and two oxygens is removed since it no longer has any useful energy. So it is waste. This little step is the source of some of the carbon dioxide we produce.

Kreb's Cycle. The remaining two carbons from the pyruvate feed into a complicated set of reactions called the Kreb's cycle. The Kreb's cycle produces 8 more NADH molecules and two molecules of FADH2. Again both of these are carrying energy rich electrons.

Electron transport phosphorylation. Most of the NADH and FADH2 travel to special membranes in the cell which have a series of molecules called the electron transport system that harvest the energy rich electrons from the NADH and FADH2 and use that energy to male lots of ATP by a process called electron transport phosphosphorylation. If we are dealing with aerobic respiration this is where the oxygen becomes important.

Role of oxygen in Aerobic Respiration. As the energy rich electrons from food are used to make ATP by electron transport phosphorylation they loose energy and once they are no longer useful they have to be removed. Oxygen is a great electron acceptor and so the electrons are combined with hydrogen ions and oxygen to make water. This prevents electrons from building up in the electron transport system.

Some forms of anaerobic respiration also use the electron transport phosphoylation but differ in that they use other inorganic molecules as the final electron acceptor instead of oxygen.

In eukaryotic organisms aerobic respiration is compartmentalized, Glycolysis takes place in the cytoplasm and the Kreb's cycle and electron transport chein takes place in the mitochondrion.

Simply put:

Respiration is the opposite of photosynthesis, and is described by the equation:

C₆H₁₂O₆+6O₂ ----------> 6CO₂+6H₂O+36ATP

Simply stated, this equation means that oxygen combines with sugars to break molecular bonds, releasing the energy (in the form of ATP) contained in those bonds. In addition to the energy released, the products of the reaction are carbon dioxide and water.

** Note that photosynthesis is a reduction-oxidation reaction, just like respiration. In respiration energy is released from sugars when electrons associated with hydrogen are transported to oxygen (the electron acceptor), and water is formed as a byproduct. The mitochondria use the energy released in this oxidation in order to synthesize ATP. In photosynthesis, the electron flow is reversed, the water is split (not formed), and the electrons are transferred from the water to CO₂ and in the process the energy is used to reduce the CO₂ into sugar. In respiration the energy yield is 686 kcal per mole of glucose oxidized to CO₂, while photosynthesis requires 686 kcal of energy to boost the electrons from the water to their high-energy perches in the reduced sugar -- light provides this energy.

Nature of Sunlight and Pigment

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Nature of Sunlight and Pigments

The electromagnetic spectrum

GAMMA RAYS- X-RAYS - UV VISIBLE LIGHT INFRARED MICRO RADIO WAVES

VIOLET	INDIGO	BLUE	GREEN	YELLOW	ORANGE	RED
380 nm	450 nm	500 nm	550 nm	600 nm	650 nm	700 nm

Plants use light in the 450 and 700 nm range. Meaning the plants like indigo-blue and orange-red light.

Certain colors in light rays are important for proper plant growth. Leaves reflect and derive little energy from many of the yellow and green rays of the visible spectrum. Yet the red and blue parts of the light spectrum are the most important energy sources for plants, and plants require more rays from the red range than from the blue. Plants growing outdoors, in greenhouses or close to windows are exposed to a natural balance of the blue and red light rays that plants need. Where plants receive little or no natural light, you must provide additional light from artificial sources.

Most people are familiar with the incandescent light produced by ordinary light bulbs in our homes. As a single light source for plants, these bulbs are not particularly good. They are a good source of red rays but a poor source of blue. They produce too much heat for most plants and, if used, must be kept away from the plants, thus reducing the intensity of the light the plants receive. They are also about three times less efficient than fluorescent tubes inconverting electrical energy to light.

Photosynthesis occurs in organelles called CHLOROPLASTS.

More specifically, half of the photosynthesis chemistry stuff occurs in a liquid inside the chloropasts called STROMA, & the other half of photosynthesis occurs in stacks of membranes inside the chloroplast called GRANA.

What are the main structures of chloroplasts?

Chloroplasts are involved by two membrane layers, the outer and the inner membranes. Inside the organelle the formative unit is called the granum, a coin-shaped structure that, piled with others grana, forms several structures called thylakoids. The thylakoids fill the chloroplast and an intergrana membrane permeates the interior of the organelle.

Chlorophyll looks green because it absorbs red and blue light, making these colors unavailable to be seen by our eyes. It is the green light which is NOT absorbed that finally reaches our eyes, making chlorophyll appear green. However, it is the energy from the red and blue light that are absorbed that is, thereby, able to be used to do photosynthesis. The green light we can see is not/cannot be absorbed by the plant, and thus cannot be used to do photosynthesis.

Various plant pigments help use light. Carotenoids, chlorophyll a, b, and c. Chlorophyll a absorbs indigo and red lights, b absorbs blue and orange -red, c absorbs blue and orange in smaller amounts.

Chlorophyll is a molecule containing 2 main parts: a complex ring with a magnesium ion in the center and a nonpolar tail.

Chlorophyll is a complex molecule. Several modifications of chlorophyll occur among plants and other photosynthetic organisms. All photosynthetic organisms (plants, certain protistans, prochlorobacteria, and cyanobacteria) have chlorophyll a. Accessory pigments absorb energy that chlorophyll a does not absorb. Accessory pigments include chlorophyll b (also c, d, and e in algae and protistans), xanthophylls, and carotenoids (such as beta-carotene). Chlorophyll a absorbs its energy from the Violet-Blue and Reddish orange-Red wavelengths, and little from the intermediate (Green-Yellow-Orange) wavelength.
Did you notice that these main pigments do not absorb green light well? Chlorophyll a and b both absorb blue light and red light best, resulting in an overall green appearance, whereas beta-carotene absorbs blue and some green light best resulting in an orange color (carotene was first derived from carrots, hence its name). During the summer, chlorophylls dominate, resulting in leaves of plants being green. In the autumn, when deciduous plants are getting ready for winter, they digest their chlorophyll resulting in the accessory pigments like carotenes becoming dominant, hence the bright red and orange colors of fall foliage.

In Light dependent reaction, all the pigment molecules in the LHC are constantly absorbing light, and when light of a certain wavelength (<680 nm) is absorbed, the absorbed energy is transfered from one molecule to another until it reaches the reaction center. Because it works optimally with light of <680 nm, the core reaction center of photosystem II is called the P680 complex.

In Dark reaction, the proteins associated with the pair of special Chl a molecules in the reaction center are different, PSI functions optimally with photons of light with an wavelength of 700 nm, so the reaction center of PSI is called the P700 complex.

Photosynthesis- Light Independent Reaction or CALVIN CYCLE

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Light-independent or Dark Reaction

The Calvin Cycle

Main articles: Calvin cycle, Carbon fixation, and Light-independent reactions

In the light-independent or dark reactions the enzyme RuBisCO captures CO₂ from the atmosphere and in a process that requires the newly formed NADPH, called the Calvin-Benson Cycle, releases three-carbon sugars, which are later combined to form sucrose and starch. The overall equation for the light-independent reactions in green plants is:^[18]

3 CO₂ + 9 ATP + 6 NADPH + 6 H⁺ → C₃H₆O₃-phosphate + 9 ADP + 8 P_i + 6 NADP⁺ + 3 H₂O

CALVIN BENSON CYCLE DIAGRAM ( Note to my students: Below is the diagram for printing in tarpauline)

The Calvin Cycle:

ATP and NADPH produced by the light reactions are used in the Calvin cycle to reduce carbon dioxide to sugar.

The Calvin cycle is similar to the Krebs cycle in that the starting material is regenerated by the end of the cycle.
Carbon enters the Calvin cycle and leaves as sugar.
ATP is the energy source, while NADPH is the reducing agent that adds high energy electrons to form sugar.
The Calvin cycle actually produces a 3 carbon sugar glyceraldehyde 3-phosphate.
The Calvin cycle may be divided into 3 steps.

Step 1: Carbon Fixation. This phase begins when a carbon dioxide molecule is attached to a 5 carbon sugar, ribulose biphosphate (RuBP).

This reaction is catalyzed by the enzyme RuBP carboxylase (rubisco) one of the most abundant proteins on earth.
The products of this reaction is an unstable 6 carbon compound that immediately splits into 2 molecules of 3-phosphoglycerate.
For every 3 molecules of carbon dioxide that enter the cycle via rubisco, 3 RuBP molecules are carboxylated forming 6 molecules of 3-phosphoglycerate.

Step 2: Reduction. This endergonic reduction phase is a 2 step process that couples ATP hydrolysis with the reduction of 3-phosphoglycerate to glyceraldehyde phosphate.

An enzyme phosphorylates ( adds a phosphate) 3-phosphoglycerate by transferring a phosphate from the ATP. The product is 1-3-bisphosphoglycerate.
Electrons from the NADPH reduce the carboxyl group of the 1-3-bisphosphoglycerate to the aldehyde group of glyceraldehyde-3-phosphate.
For every three carbon dioxide molecules that enter the Calvin cycle,6 glyceraldehyde-3-phosphates are produced, only one can be counted as a net gain. The other 5 are used to regenerate 3 molecules of RuBP.

Step 3: Regeneration of RuBP. A complex series of reactions rearranges the carbon skeletons of 5 glyceraldehyde-3-phosphate molecules into 3 RuBP molecules.

These reactions require 3 ATP molecules.
RuBP is thus regenerated to begin the cycle again.

To be more specific, carbon fixation produces an intermediate product, which is then converted to the final carbohydrate products. The carbon skeletons produced by photosynthesis are then variously used to form other organic compounds, such as the building material cellulose, as precursors for lipid and amino acid biosynthesis, or as a fuel in cellular respiration. The latter occurs not only in plants but also in animals when the energy from plants gets passed through a food chain.
The fixation or reduction of carbon dioxide is a process in which carbon dioxide combines with a five-carbon sugar, ribulose 1,5-bisphosphate (RuBP), to yield two molecules of a three-carbon compound, glycerate 3-phosphate (GP), also known as 3-phosphoglycerate (PGA). GP, in the presence of ATP and NADPH from the light-dependent stages, is reduced to glyceraldehyde 3-phosphate (G3P). This product is also referred to as 3-phosphoglyceraldehyde (PGAL) or even as triose phosphate. Triose is a 3-carbon sugar (see carbohydrates). Most (5 out of 6 molecules) of the G3P produced is used to regenerate RuBP so the process can continue (see Calvin-Benson cycle). The 1 out of 6 molecules of the triose phosphates not "recycled" often condense to form hexose phosphates, which ultimately yield sucrose, starch and cellulose. The sugars produced during carbon metabolism yield carbon skeletons that can be used for other metabolic reactions like the production of amino acids and lipids.

Carbon concentrating mechanisms

C4 CARBON FIXATION

C₄Plants: Many plants begin the Calvin cycle with a 4 carbon compound instead of a 3 carbon compound. These are called the C₄plants. They include the grasses ( sugar cane and corn). These plants live in areas that are very hot and semiarid. The intermediate process is shown below and the product is then introduced to the bundle sheath cells where the Calvin cycle will take place.

In hot and dry conditions, plants close their stomata to prevent the loss of water. Under these conditions, CO₂ will decrease, and oxygen gas, produced by the light reactions of photosynthesis, will decrease in the stem, not leaves, causing an increase of photorespiration by the oxygenase activity of ribulose-1,5-bisphosphate carboxylase/oxygenase and decrease in carbon fixation. Some plants have evolved mechanisms to increase the CO₂ concentration in the leaves under these conditions.
C₄ plants chemically fix carbon dioxide in the cells of the mesophyll by adding it to the three-carbon molecule phosphoenolpyruvate (PEP), a reaction catalyzed by an enzyme called PEP carboxylase, creating the four-carbon organic acid oxaloacetic acid. Oxaloacetic acid or malate synthesized by this process is then translocated to specialized bundle sheath cells where the enzyme RuBisCO and other Calvin cycle enzymes are located, and where CO₂ released by decarboxylation of the four-carbon acids is then fixed by RuBisCO activity to the three-carbon sugar 3-phosphoglyceric acids. The physical separation of RuBisCO from the oxygen-generating light reactions reduces photorespiration and increases CO₂ fixation and, thus, photosynthetic capacity of the leaf.^[21] C₄ plants can produce more sugar than C₃ plants in conditions of high light and temperature. Many important crop plants are C₄ plants, including maize, sorghum, sugarcane, and millet. Plants that do not use PEP-carboxylase in carbon fixation are called C₃ plants because the primary carboxylation reaction, catalyzed by RuBisCO, produces the three-carbon sugar 3-phosphoglyceric acids directly in the Calvin-Benson cycle. Over 90% of plants use C₃ carbon fixation, compared to 3% that use C₄ carbon fixation^.

^{CAM PHOTOSYNTHSIS}

Xerophytes, such as cacti and most succulents, also use PEP carboxylase to capture carbon dioxide in a process called Crassulacean acid metabolism (CAM). In contrast to C₄ metabolism, which physically separates the CO₂ fixation to PEP from the Calvin cycle, CAM temporally separates these two processes. CAM plants have a different leaf anatomy from C₃ plants, and fix the CO₂ at night, when their stomata are open. CAM plants store the CO₂ mostly in the form of malic acid via carboxylation of phosphoenolpyruvate to oxaloacetate, which is then reduced to malate. Decarboxylation of malate during the day releases CO₂ inside the leaves, thus allowing carbon fixation to 3-phosphoglycerate by RuBisCO. Sixteen thousand species of plants use CAM.

In water

Cyanobacteria possess carboxysomes, which increase the concentration of CO₂ around RuBisCO to increase the rate of photosynthesis. This operates by carbonic anhydrase, producing hydrocarbonate ions (HCO₃^–), which are then pumped into the carboxysome, before being processed by a different carbonic anhydrase to produce CO₂.^[24] Pyrenoids in algae and hornworts also act to concentrate CO₂ around rubisco.