# The Chemistry of Life
## Chemical Elements and Water
### State one role for each of the elements mentioned in 3.1.2.

* Sulfur: Needed for the synthesis of two amino acids.
* Calcium: Acts as a messenger by binding to calmodulin and a few other proteins which regulate transcription and other processes in the cell.
* Phosphorus: Is part of DNA molecules and is also part of the phosphate groups in ATP.
* Iron: Is needed for the synthesis of cytochromes which are proteins used during electron transport for aerobic cell respiration.
* Sodium: When it enters the cytoplasm, it raises the solute concentration which causes water to enter by osmosis.

### Outline the thermal, cohesive and solvent properties of water.

and

### Explain the relationship between the properties of water and its uses in living organisms as a coolant, medium for metabolic reactions and transport medium.

Thermal properties:
* large heat capacity:
** Temperature of water tends to remain relatively stable.
** Beneficial for aquatic animals as they use water as a habitat.
** Water can be used as a thermal medium, like blood in humans.
* Boiling and freezing points.
** High boiling and freezing point.
** Water is less dense in the solid phase than in the liquid phase.
** Ice on the surface of water also insulates the liquid water underneath, enabling survival of organisms in colder climates.
* Cooling effect of evaporation.
** Water can evaporate at temperature below boiling point.
** This is an endothermic physical change, and therefore has a cooling effect.
Cohesive properties:
* Water has hydrogen bonding, giving its molecules cohesion.
** Plants can transport water to their upper foliage because of this property.
Solvent properties:
* Because of the polarity of water molecules, many substance can dissolve in it.
** Organisms can use water as a medium for metabolic reactions.

## Carbohydrates, lipids and proteins
### Distinguish between organic and inorganic compounds.

* Organic compounds are compounds that contain carbon.
** Exceptions include carbon dioxide, carbonates and hydrogen carbonates.
* Inorganic compounds don’t contain carbon.

### List three examples each of monosaccharides, disaccharides and polysaccharides.

‘’’Monosaccharides:’’’
* Glucose
* Galactose
* Fructose
‘’’Disaccharides’’’
* Maltose
* Lactose
* Sucrose
‘’’Polysaccharides’’’
* Starch
* Glycogen
* Cellulose

### State one function of glucose, lactose and glycogen in animals, and of fructose, sucrose and cellulose in plants.

‘’’Animals’’’
| Sugar | Function |
| Glucose | Energy source |
| Lactose | Sugar found in milk Provides energy to newborns until they are weaned |
| Glycogen | short term energy source stored in muscles and the liver |
‘’’Plants’’’
| Sugar | Function |
| Fructose | Makes fruits taste sweet which attracts animals which eat the fruits and disperse the seeds found in the fruits |
| Sucrose | Sugar found in milk Energy source |
| Cellulose | Used in plant cell wall structure |

### State three functions of lipids.

* Energy storage in the form of fat in humans and oil in plants.
* Heat insulation as fat under the skin reduces heat loss.
* Allow buoyancy as they are less dense than water and so animals can float in water.

### Compare the use of carbohydrates and lipids in energy storage.

| Feature | Carbohydrates | Lipids |
| Energy storage | Short term stores | Long term stores |
| Water solubility | Solubility allows rapid transportation through circulatory systems | Insolubility makes transportation difficult, but does not affect osmosis |
| Speed of digestion | Very rapid, so carbs are better for energy needed quickly | Slow |
| Energy density | Low energy per gram | Higher energy per gram, makes lipids a lighter energy source |

## DNA structure
### Outline DNA nucleotide structure in terms of sugar (deoxyribose), base and phosphate.

Made of:
* deoxyribose
* a nitrogenous base (which can be either adenine, guanine, cytosine or thymine)
* a phosphate group.
[image]

### State the names of the four bases in DNA.

Adenine, Guanine, Cytosine and Thymine.

### Outline how DNA nucleotides are linked together by covalent bonds into a single strand.

Below is a diagram showing how nucleotides are linked to one another to form a strand. A covalent bond forms between the sugar of one nucleotide and the phosphate group of another nucleotide. [image]

### Explain how a DNA double helix is formed using complementary base pairing and hydrogen bonds.

* DNA is made up of two nucleotide strands.
* The nucleotides are connected together by covalent bonds within each strand.
* The sugar of one nucleotide forms a covalent bond with the phosphate group of another.
* The two strands themselves are connected by hydrogen bonds.
* The hydrogen bonds are found between the bases of the two strands of nucleotides.
* Adenine forms hydrogen bonds with thymine whereas guanine forms hydrogen bonds with cytosine (this is called complementary base pairing)
* Below is a diagram showing the molecular structure and bonds within DNA.
[image]

### Draw and label a simple diagram of the molecular structure of DNA.
## DNA replication
### Explain DNA replication in terms of unwinding the double helix and separation of the strands by helicase, followed by formation of the new complementary strands by DNA polymerase.

* DNA replication is semiconservative: both of the DNA molecules produced are formed from an old strand and a new one
* Unwinding of the DNA double helix and separating them by breaking the hydrogen bonds between the bases.
** This is done by the enzyme helicase.
** Each separated strand now is a template for the new strands.
* Free nucleotides around the replication fork bond to the template strands.
** The free nucleotides form hydrogen bonds with their complementary base pairs on the template strand.
** Adenine will pair up with thymine and guanine will pair up with cytosine.
** DNA polymerase is the enzyme used for DNA polymerization.
* The new DNA strands then rewind to form a double helix. The replication process has produced a new DNA molecule which is identical to the initial one.

### Explain the significance of complementary base pairing in the conservation of the base sequence of DNA.

* Complementary base pairing is very important in the conservation of the base sequence of DNA.
* Adenine always pairs up with thymine and guanine always pairs up with cytosine.
* DNA replication is semiconservative (see above); this complementary base pairing allows the two DNA molecules to be identical to each other as they have the same base sequence.
* New strands formed are complementary to their template strands but also identical to the other template.

### State that DNA replication is semi-conservative.
## Transcription and translation
### Compare the structure of RNA and DNA.

| Feature | DNA | RNA |
| Sugar in nucleotide | Deoxyribose | Ribose |
| Nucleotides | Adenine, guanine, cytosine, thymine | Guanine, adenine, uracil, cytosine |
| Shape | Double stranded helix | Single strand |

### Outline DNA transcription in terms of the formation of an RNA strand complementary to the DNA strand by RNA polymerase.

* DNA transcription is the formation of an RNA strand which is complementary to the DNA strand.
* Uncoiling of the DNA double helix.
* Free RNA nucleotides start to form an RNA strand by using one of the DNA strands as a template.
** Uses complementary base pairing; however, in the RNA chain the base thymine is replaced by uracil.
** RNA polymerase is the enzyme involved in the RNA polymerization and the uncoiling of the DNA double helix.
** RNA strand then elongates and then separates from the DNA template.
** DNA strands then reform a double helix.
* Strand of RNA formed is called messenger RNA (mRNA).

### Describe the genetic code in terms of codons composed of triplets of bases.

* A triplet of bases (3 bases) forms a codon.
* Each codon codes for a particular amino acid.
* Amino acids in turn link to form proteins.
* DNA and RNA regulate protein synthesis.
* The genetic code is the codons within DNA and RNA, composed of triplets of bases which eventually lead to protein synthesis.
* DNA → RNA → Protein

### Explain the process of translation, leading to polypeptide formation.

* Translation is the process through which proteins are synthesized.
* Involves ribosomes, messenger RNA (mRNA) - which is composed of codons - and transfer RNA (tRNA), which has a triplet of bases called the anticodon.
* The first stage of translation is the binding of mRNA to the small subunit of the ribosome.
* The tRNA molecules have a specific amino acid attached to them which corresponds to their anticodons.
* A tRNA molecule will bind to the ribosome; its anticodon must match the codon on the messenger RNA.
* This is done through complementary base pairing. These form a hydrogen bond together.
* Another tRNA molecule then bonds.
* Two transfer RNA molecules can bind at once.
* Then the two amino acids on the two transfer RNA molecules form a peptide bond.
* The first transfer RNA then detaches from the ribosome and the second one takes it’s place.
* The ribosome moves along the messenger RNA to the next codon so that another transfer RNA can bind.
* Again, a peptide bond is formed between the amino acids and this process continues.
* This forms a polypeptide chain and is the basis of protein synthesis.

### Discuss the relationship between one gene and one polypeptide.

* A polypeptide is formed by amino acids liking together through peptide bonds.
* There are 20 different amino acids so a wide range of polypeptides are possible.
* Genes store the information required for making polypeptides.
* The information is stored in a coded form by the use of triplets of bases which form codons.
* The sequence of bases in a gene codes for the sequence of amino acids in a polypeptide.
* The information in the genes is decoded during transcription and translation leading to protein synthesis.

## Enzymes
### Define enzyme and active site.

‘’’Enzymes:’’’ Globular proteins which act as catalysts of chemical reactions. ‘’’Active site:’’’ Region on the surface of an enzyme to which substrates bind and which catalyses a chemical reaction involving the substrates.

### Explain enzyme-substrate specificity.

* The active site of an enzyme is very specific to its substrates as it has a very precise shape.
* This results in enzymes being able to catalyze only certain reactions as only a small number of substrates fit in the active site.
* This is called enzyme-substrate specificity.
* For a substrate to bind to the active site of an enzyme it must fit in the active site and be chemically attracted to it.
* This makes the enzyme very specific to its substrate.
* The enzyme-substrate complex can be compared to a lock and key, where the enzyme is the lock and the substrate is the key.

### Explain the effects of temperature, pH and substrate concentration on enzyme activity.

* Enzyme activity increases with an increase in temperature and usually doubles with every 10 degrees rise. This is due to the molecules moving faster and colliding more often together. However at a certain point the temperature gets too high and the enzymes denature and stop functioning. This is due to the heat causing vibrations within the enzyme destroying its structure by breaking the bonds in the enzyme.
* Enzymes usually have an optimum pH at which they work most efficiently. As the pH diverges from the optimum, enzyme activity decreases. Both acid and alkali environments can denature enzymes.
* Enzyme activity increases with an increase in substrate concentration as there are more random collisions between the substrate and the active site. However, at some point, all the active sites are taken up and so increasing the substrate concentration will have no more effect on enzyme activity. As long as there are active sites available, an increase in substrate concentration will lead to an increase in enzyme activity.

### Define denaturation.

Denaturation: a change to the structure of a protein so it can no longer carry out its function.

### Explain the use of lactase in the production of lactose-free milk.

* Lactose is the sugar found in milk.
* It can be broken down by the enzyme lactase into glucose and galactose.
* Some people lack this enzyme and so cannot break down lactose leading to lactose intolerance.
* Lactose intolerant people need to drink milk that has been lactose reduced. Lactose-free milk can be made in two ways:
* The first involves adding the enzyme lactase to the milk so that the milk contains the enzyme.
* The second way involves immobilizing the enzyme on a surface or in beads of a porous material. The milk is then allowed to flow past the beads or surface with the immobilized lactase. This method avoids having lactase in the milk.

## Cell Respiration
### Define cell respiration.

Cell respiration: the controlled release of energy from organic compounds in cells to form ATP.

### Explain that, during anaerobic cell respiration, pyruvate can be converted in the cytoplasm into lactate, or ethanol and carbon dioxide, with no further yield of ATP.

* In anaerobic cell respiration the pyruvate stays in the cytoplasm and in humans is converted into lactate which is then removed from the cell.
* In yeast the pyruvate is converted into carbon dioxide and ethanol. In either case, no ATP is produced.

### Explain that, during aerobic cell respiration, pyruvate can be broken down in the mitochondrion into carbon dioxide and water with a large yield of ATP.

* If oxygen is available, the pyruvate is taken up into the mitochondria and is broken down into carbon dioxide and water.
* A large amount of ATP is released during this process.

## Photosynthesis
### State that photosynthesis involves the conversion of light energy into chemical energy.

* Photosynthesis involves the conversion of light energy into chemical energy.

### Outline the differences in absorption of red, blue and green light by chlorophyll.

* Chlorophyll can absorb red and blue light more than green.
* Chlorophyll cannot absorb green light and so instead reflects it making leaves look green.

### Explain that the rate of photosynthesis can be measured directly by the production of oxygen or the uptake of carbon dioxide, or indirectly by an increase in biomass.

* Photosynthesis can be measured in many ways as it involves the production of oxygen, the uptake of carbon dioxide and an increase in biomass.
* Aquatic plants release oxygen bubbles during photosynthesis and so these can be collected and measured.
* Uptake of carbon dioxide is more difficult to measure so it is usually done indirectly.
* When carbon dioxide is absorbed from water the pH of the water rises and so this can be measured with pH indicators or pH meters.
* Photosynthesis can be measured through an increase in biomass. If batches of plants are harvested at a series of times and the biomass of these batches is calculated, the rate increase in biomass gives an indirect measure of the rate of photosynthesis in the plants.

### Outline the effects of temperature, light intensity and carbon dioxide concentration on the rate of photosynthesis.

* As temperature increases, the rate of photosynthesis increases more and more steeply until the optimum temperature is reached. If temperature keeps increasing above the optimum temperature then photosynthesis starts to decrease very rapidly.
* As light intensity increases so does photosynthesis until a certain point. At a high light intensities photosynthesis reaches a plateau and so does not increase any more. At low and medium light intensity the rate of photosynthesis is directly proportional to the light intensity.
* As the carbon dioxide concentration increases so does the rate of photosynthesis. There is no photosynthesis at very low levels of carbon dioxide and at high levels the rate reaches a plateau.