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IB Categories Archives: Topic 2: Molecular biology

2.8 – Photosynthesis

2.8 – Photosynthesis

2.8.1 – State that photosynthesis involves the conversion of light energy into chemical energy

Photosynthesis takes place in the chloroplast. These are found in the green leaves of plants, algae and some bacteria. Chlorophyll is the pigment found in the chloroplast, and is what causes plants to appear green.

Photosynthesis synthesises the compounds required more life, mainly glucose. Photons of light are trapped in the chlorophyll, which is then converted into chemical energy. There are both prokaryotic and eukaryotic organisms undergo photosynthesis to obtain their food.

The reaction requires CO2 and H2O, and produces sugar and O2. The entire process is divided
into the light-dependent reactions and the light-independent reactions.

2.8.2 – State that light from the Sun is composed of a range of wavelengths (colors)

The white light that comes from the sun is a combination of many different wavelengths of light, which blur to white light. They are found on a continuous spectrum, each wavelength representing a different colour. Light itself is simply electromagnetic radiation.

Along the entire electromagnetic spectrum, humans are only able to see a small portion of it. Chlorophyll absorbs light of specific wavelengths to varying degrees, so not all light is absorbed equally. In fact, some wavelengths are reflected altogether.

 

2.8.3 – State that chlorophyll is the main photosynthetic pigment

 

In green plants, there are a number of pigments that are able to help in photosynthesis; however chlorophyll is the predominant one. It is not soluble in water.

 

 

2.8.4 – Outline the differences in absorption of red, blue and green light by chlorophyll

Chlorophyll is able to absorb red and blue light, and reflects green light. This is why leaves and plants appear green. Its chemical structure is what allows it to absorb some colours, but not others.

 

2.8.5 – State that light energy is used to produce ATP, and to split water molecules (photolysis) to form oxygen and hydrogen

The chlorophyll molecules on the chloroplast membrane absorb and trap photons of light. This energy causes them to release electrons, or chemical energy, with oxygen released as a waste product. 

Water molecules are then split using this energy, through the process called photolysis. The hydrogen atoms are retained on hydrogen acceptor molecules. The light energy is also used to generate ATP from ADP and phosphate.

 

 

2.8.6 – State that ATP and hydrogen (derived from the photolysis of water) are used to fix carbon dioxide to make organic molecules

Once the water molecules have undergone photolysis, their electrons combine with carbon dioxide to form organic compounds. This process is called fixing CO2. The energy from ATP is used to form bonds between the carbon, hydrogen and oxygen, making sugars and carbohydrates.

 

2.8.7 – 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

There are a number of ways we can experimentally measure how much is produced during photosynthesis. One of these is through measuring the increasing biomass of the plant. Samples are taken at time intervals and the rate of increase in biomass is used to determine the rate photosynthesis However, this is very inaccurate due to the number of factors that affect photosynthesis, and energy is used or lost. A more accurate way of measuring it is

A more accurate way of measuring it is destarching the leaves. This involves leaving them in
the dark for 48 hours. Alternatively, the amount of oxygen produced can be measured. For water plants, the

Alternatively, the amount of oxygen produced can be measured. For water plants, the volume of oxygen bubbles produced is measured, while a data logger with a sensor is used for land plants.Another way is by measuring how much CO2 has been taken up by the plant using pH change in the water. 

Another way is by measuring how much CO2 has been taken up by the plant using pH change in the water. A pH probe is placed in the water and any increase in pH
can be detected.

 

2.8.8 – Outline the effects of temperature, light intensity and carbon dioxide concentration on the rate of photosynthesis

 

Temperature

As the temperature in the environment increases, the rate of photosynthesis increases. However, each plant has an optimum temperature, after which the rate of photosynthesis falls off steeply. This is because the enzymes and chlorophyll denature or become unstable.

 

 

Light Intensity
Since light is essential for photosynthesis to occur, the rate of photosynthesis increases as light intensity increases. However, the relationship plateaus when a certain temperature is reached. On the other hand, if there is no light, the plant can only respire. Chlorophyll can actually become damaged if the light is too intense.

 

 

 

 

Carbon Dioxide Concentration

As the concentration of CO2 increases, the rate of photosynthesis also increases. Like light intensity, this relationship reaches a plateau. The relationship is exactly like the relationship of a substrate and enzyme. The optimum CO2 concentration varies between plants.

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2.7 – Cell Respiration

2.7 – Cell Respiration

2.7.1 – Define cell respiration

The controlled release of energy from organic compounds in cells in the form of ATP

 

2.7.2 – State that, in cell respiration, glucose in the cytoplasm is broken down by glycolysis into pyruvate, with a small yield of ATP

Cells transfer energy by breaking down nutrients, mainly carbohydrates like glucose, through the process of cell respiration. Plants synthesis these nutrients using sunlight in photosynthesis, while heterotrophs will digest them from their food.
Cell respiration takes place in a number of steps, which helps to control the release of energy. There are multiple enzymes which catalyze these reactions, and the energy is able to be trapped in the molecule ATP (adenosine triphosphate). It is a nucleotide that carries three phosphate groups. The nature of the molecule means that it is soluble and small enough to pass through the cell membrane quite easily. It contains a lot of chemical energy within its structure.

The first step is glycolysis, which takes place in the cytoplasm of the cell. Once broken down, the glucose molecule (which has six carbon atoms) forms two pyruvate molecules (each with three carbon atoms). A small yield of two molecules of ATP are produced.

 

2.7.3 – 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

Anaerobic respiration is also called fermentation (a process which is important in making wine, beer, bread, etc). It occurs when there is no oxygen available.
Some organisms will still respire anaerobically, even when there is oxygen available. The most important one is yeast, which has applications mentioned above.

𝒈𝒍𝒖𝒄𝒐𝒔𝒆 → 𝒆𝒕𝒉𝒂𝒏𝒐𝒍+𝒄𝒂𝒓𝒃𝒐𝒏 𝒅𝒊𝒐𝒙𝒊𝒅𝒆+𝑨𝑻𝑷

When a vertebrate uses anaerobic respiration, it instead produces lactic acid (which then ionises in the cell to form lactate). This will mainly take place in the muscle fibres during high demand for energy.

𝒈𝒍𝒖𝒄𝒐𝒔𝒆 → 𝒍𝒂𝒄𝒕𝒂𝒕𝒆+𝑨𝑻𝑷

The pyruvate remains in the cytoplasm and gets further broken down into lactate.
Anaerobic respiration can be seen as wasteful because only two molecules of ATP are produced, making far less energy available to the cell after aerobic respiration.

 

2.7.4 – 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
Aerobic respiration is summed up in the equation:

𝒈𝒍𝒖𝒄𝒐𝒔𝒆+𝒐𝒙𝒚𝒈𝒆𝒏 → 𝒄𝒂𝒓𝒃𝒐𝒏 𝒅𝒊𝒐𝒙𝒊𝒅𝒆+ 𝒘𝒂𝒕𝒆𝒓+𝑨𝑻𝑷

In the first stage of respiration, glycolysis, two molecules of ATP are formed from two molecules of ADP. The ATP is then used in other reactions for muscle movement, condensation, and movement across the membrane. It may also react with water through hydrolysis. During glycolysis, a glucose molecule in broken up into pyruvic acid, which then becomes pyruvate ions. This takes place in the cytoplasm.

If there is available oxygen, the pyruvate is then oxidised into carbon dioxide. The pyruvate moves into the mitochondria (organelles inside cells) by facilitated diffusion.

The pyruvate is oxidised by the removal of hydrogen atoms by hydrogen acceptors, and the addition of oxygen to the carbon atoms to form carbon dioxide. The reduced hydrogen acceptor molecules then react with oxygen to form water. ATP is produced in the process.

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2.6 – Enzymes

2.6 – Enzymes
2.6.1 – Define enzyme and active site
Enzyme – A biological catalyst made of globular protein
Enzymes speed up the reactions by influencing the stability of bonds in the reactants. They may also provide an alternative reaction pathway, and reduce the energy needed for the reaction.
Active Site – The region of an enzyme molecule surface where the substrate molecule binds and catalysis occurs
The substrate is drawn in to the active site. It has both binding and catalytic regions. The molecules are positioned to promote the reaction.

2.6.2 – Explain enzyme-substrate specificity
A substrate is the starting substance, which is converted to the product.
Enzymes are very specific, and will only catalyse one type of reaction or a very small group of similar reactions. They recognize the substrate as the active site had a precise shape and
distinctive chemical properties. Hence, only particular substrate molecules will be attracted to the active site and fit there. Others cannot fit and will not bind.
Enzymes can have high specificity (when it will only bind to a single type of substrate) or low specificity (when it will bind to a range of related substances). When they bind, the enzyme substrate complex is formed. In the lock and key model, it is suggested that the enzyme and substrate possess specific, complementary shapes that fit exactly into each other.

 

2.6.3 – Explain the effects of temperature, pH and substrate concentration on enzyme
activity
Temperature -Each enzyme has an optimal temperature for function. When at this temperature, the enzyme will work at its peak, speeding up the reaction. After the temperature reaches its optimum level, the reaction rate abruptly declines. Many enzymes are adversely affected by high temperatures, at which point denaturation occurs. Many enzymes only have a narrow range of conditions under which they operate properly. This is usually at low temperatures for plant and animal enzymes.

pH -Enzymes also have an optimal pH. At this point, it works best and the reaction occurs the fastest, as the enzyme is the most active. There is lower activity above and below the optimum pH (see graph). Extremes in pH will usually result in a complete loss of activity for most enzymes as it leads to a change in shape of the active site. The H+ ions interfere with hydrogen and ionic bonds within the protein structure, which means that the substrate cannot bind. The optimum pH for each enzyme varies greatly. For example, pepsin has an optimum pH of 1.5, but lipase has an optimum pH of 8.0.

Substrate Concentration – If the amount of the enzyme is kept constant and the substrate concentration is increased, the reaction velocity will increase until it hits its maximum. After that, the velocity plateaus. At this point, all of the enzymes have formed complexes with the substrates.

Enzyme Concentration – The rate of reaction, so long as there is excess substrate, will continue to increase as the concentration of the enzyme increases

 

2.6.4 – Define denaturation
Denaturation is a structural change in a protein that alters its shape and results in a loss of biological properties. This can be caused by pH or temperature. This is when the protein loses its three-dimensional structure, usually along with function. It is often permanent. The bonds in the secondary and tertiary structure are altered, although the sequence is unchanged.
This can result from strong acids and alkalis, which disrupt ionic bonds, resulting in coagulation. Long exposure will eventually break down the primary structure. Heavy metals also disrupt ionic bonds, and form bonds with the carboxyl groups of the R group, reducing the charge of the protein. This generally causes the protein to precipitate. Heat and radiation (such as UV rays) disrupt the bonds because of the increased energy provided to the atoms. Detergents and solvents form bonds with the non-polar groups in the protein, which disrupts hydrogen bonding.

2.6.5 – Explain the use of lactase in the production of lactose-free milk
The production of lactose-free milk is an example of industrial use of biotechnology, which is of huge and increasing economic importance. People who cannot digest lactose are lactose intolerant and do not produce lactase. They must instead drink lactose-free milk, which is made by using lactase from bacteria.
This used to be done through whole-cell preparations. This is not efficient, however, and inappropriate for a food like liquid milk. Cell-free preparation is also used, although the enzymes cannot be re-used, and removal can be expensive.
Instead, immobilized enzymes are used. The advantages of this method are:

  • The enzyme preparation can be re-used
  • The product received is enzyme-free
  • The enzyme may be more stable and long lasting due to protection by the inert matrix

Today, lactose free milk is produced by passing milk over lactase enzyme, bound to an inert carrier. The enzyme is obtained from bacteria, purified, and enclosed in capsules. Once the molecule is cleaved, there are no lactose ill-effects. Alternatively, a harmless bacterium may be added (such as L. Acidophilus), which affects the lactose in milk and yoghurt.

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2.5 – Transcription and Translation

2.5 – Transcription and Translation

2.5.1 – Compare the structure of RNA and DNA

 

 

2.5.2 – Outline DNA transcription in terms of the formation of an RNA strand complementary to the DNA strand by RNA polymerase

A complimentary copy of the DNA is made in the nucleus to form the mRNA. This process is catalysed by the enzyme RNA polymerase. To copy the mRNA, the DNA double helix is unwound by DNA helicase, with the hydrogen bonds breaking between the base pairs to be copied. The DNA opens at the transcription site, or position of the gene that needs to be copied.

The coding strand, or the sense strand, is the template for the mRNA. However, the mRNA is actually built against the anti-sense strand. It has the same pattern as the opposite strand due to complimentary base pairing.

The free nucleotides pair with the DNA nucleotides. The only difference is that uracil replaces thymine, bonding to adenine. The RNA polymerase forms the phosphodiester bonds to make the backbone of the mRNA molecule. The mRNA then detaches and leaves the nucleus via the nuclear pores in the membrane. It enters the cytoplasm for reading at the ribosomes. The DNA double helix reforms.

2.5.3 – Describe the genetic code in terms of codons composed of triplets of bases

Each sequence of three bases codes for one amino acid, called a triplet code. These groups of three are called codons.

For every amino acid, it has two or three triplets which code for them. Other triplets act as the ‘start’ or ‘stopcodons, which define where to begin and end the polypeptide sequence.

There are also multiple triplets which code for these ‘punctuation’ codons.

 

2.5.4 – Explain the process of translation, leading to polypeptide formation

The amino acids are activated by combining with tRNA (transfer RNA) in the cytoplasm. tRNA molecules are in the shape of a clover leaf. Each molecule binds to a specific amino acid codon, the other end binding to the amino acid. The other end has an anticodon, which
is the complimentary codon for the mRNA. The tRNA binds to the amino acid, catalysed by an enzyme. This process uses ATP.

 

Once the mRNA molecule has been transcribed, it is sent to the ribosome in the cytoplasm or endoplasmic reticulum for translation. The protein is formed from the polypeptides, which are built up at the ribosomes. The ribosomes move along the mRNA the ‘read’ the code, beginning at the start codon.

From here, the tRNA molecules, with their amino acids, find their complimentary codon on the mRNA. The amino acids are bound in the ribosomes to form the polypeptide chains. The tRNA then separates from the amino acid and the mRNA, and is sent back to the cytoplasm to find more amino acids. This process continues until a stop codon is reached, at which point the polypeptide chain is released.

 

In order to provide enough free amino acids for translation, heterotrophs consume them in the protein of their diet.

 

The first codon on the mRNA molecule is AUG, the start codon, which bonds to the anti codon [UAC] on the tRNA molecule. This tRNA molecule carries the amino acids Methionine. Codon to anti-codon binding is anti-parallel.

The polypeptides formed with fold into their shape for the protein as a result of various intermolecular forces.

The process continues until the complete polypeptide is formed.

2.5.5 – Discuss the relationship between one gene and one polypeptide

The theory is that one gene forms one polypeptide. This is true in most cases, however there are a few exceptions:

  • Some genes code for types of RNA that do not produce polypeptides
  • Some control the expression of other genes
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2.4 – DNA Replication

2.4 – DNA Replication

2.4.1 – 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

The first stage is when the DNA double helix unwinds. This is catalysed by the enzymes helicase, which causes the breaking of the hydrogen bonds between the base pairs. The two strands separate and are held apart. Both of the exposed strands are then copied. Free nucleotides in the nucleus are attached to their complementary base pairs on the parent strands. The strands are still antiparallel.

The hydrogen bonds reform and the sugar and phosphate on the free nucleotides condense to form the “backbone” on the new DNA molecules.

DNA polymerase is the enzyme that catalyses the reaction.

 

Along one strand of DNA, there are multiple replication forks. This allows the entire process of replication to occur more quickly.

 

2.4.2 – Explain the significance of complementary base pairing in the conservation of the base sequence of DNA

Complementary base pairing means that the new DNA strands are perfect copies of the original one. The complete genome of the organism is successfully copied. All the genes remain intact and are passed on to the next generation. Opposite pairs are attracted to each other, and their structure means that the DNA polymerase can “back check” for mistakes in replication. Adenine (A) and Thymine (T) will always bond, and Cytosine (C) and Guanine (G) will bond.

 

2.4.3 – State that DNA replication is semi-conservative 

On every DNA double helix, one of the strands of DNA came from the parent chromosome. The other strand was newly synthesised during replication from the free nucleotides. Therefore, every time DNA replication occurs, half of the original molecule is conserved.

 

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2.3 – DNA Structure

2.3 – DNA Structure

2.3.1 – Outline DNA nucleotide structure in terms of sugar (deoxyribose), base and phosphate

Nucleotides are formed from a pentose sugar, phosphate, and a base.

  • Phosphate links neighboring sugars together (PO43-)
  • The sugar is either ribose for RNA or deoxyribose for DNA, which has one less oxygen
  • Four types of bases, which comprise the coded genetic message
  •  Nitrogen-based ring structures
  •  Cytosine (C), Guanine (G), Adenine (A), Thymine (T)
  • Nucleotides form sequences, which are instructions for the organism
  • Changes to nucleotides cause mutations

 

2.3.2 – State the names of the four bases in DNA

Purines – Two Ringed Bases

  • Adenine (A)
  • Guanine (G)

Pyrimidines – Single Ringed Bases

  • Cytosine (C)
  • Thymine (T)
  • Uracil replaces Thymine in RNA (U)

 

 

2.3.3 – Outline how DNA nucleotides are linked together by covalent bonds into a single strand

  • DNA composed of two polynucleotide chains
  • Nucleotides are covalently bonded
  • Bond is a phosphodiester
  •  Two covalent bonds between the OH- and acidic phosphate group
  • Nucleotides bond at the 3l (three prime) end of the molecule
  • To form the polynucleotide, the nucleotides condense together one at a time, giving water in the reaction

2.3.4 – Explain how a DNA double helix is formed using complementary base pairing and hydrogen bonds

Complementary means matching

  • A double helix is made up of two anti parallel polynucleotide chains
  • Bases pair and are bonded with hydrogen bonds
  • Adenine and thymine are the same distance apart as guanine and cytosine

 

2.3.5 – Draw and label a simple diagram of the molecular structure of DNA

  • DNA is made up of two anti-parallel polynucleotide chains
  • They form the double helix (“spiral” structure)
  • The DNA has a sugar-phosphate backbone
  • Bonded with complementary base pairs
  •  Adenine to Thymine
  •  Cytosine to Guanine

 

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2.2 – Carbohydrates, Lipids and Proteins

2.2 – Carbohydrates, Lipids, and Proteins

2.2.1 – Distinguish between organic and inorganic compounds

Organic compounds are based on carbon and can be found in living things. Exceptions include HCO₃, CO₂ and CO. These are classed as non-organic carbon. Three types of organic compounds widely found in living organisms are lipids, proteins and carbohydrates. Inorganic compounds are any compounds that do not fall into the category of organic compounds.

 

2.2.2 – Identify amino acids, glucose, ribose and fatty acids from diagrams showing their structure

Amino acids
There are 20 common amino acids found in the protein structures of living things. These are monomers, and combine to form larger polypeptides, which in turn form proteins. These are the basis of enzymes, as well as many cellular and extracellular components. All amino acids are soluble. Each common amino acid has the same structure, except for the R group.

 

 

Glycine (below) is the smallest amino acid. A common source of it is sugar cane. Glycine has an amino group, a carboxylic acid group and an R group (H).

 

 

 

 

Alanine (below) is a common amino acid, similar to glycine, but the R group is CH₃. The R group of each amino acid is different, and the amino acids have very different characteristics as a result (and consequently the proteins containing them).

 

 

 

Carbohydrates

Monosaccharides are carbohydrates with relatively small molecules. They taste sweet and are soluble in water. All the bonds in these molecules are covalent. Glucose is an important monosaccharide as:

  • All green leaves manufacture glucose using light energy
  • Our bodies transport glucose in the blood
  • All cells use glucose in respiration – it is called one of the respiratory substrates
  • Glucose is the building block for many larger molecules in cells and organisms

 

 

 

The molecular formula of glucose is C₆H₁₂O₆

 

 

Ribose is an example of a pentose, or 5-carbon sugars. Deoxyribose is a modified version of

ribose, and is known for its role in DNA as part of the sugar phosphate backbone. Its chemical
properties are very different to ribose.

 

 

 

Fatty acids

These are the basis of triglycerides and many other types of lipid. They are also the basis of the phospholipid molecules of the phospholipid bilayer of the cell membrane. Lipids are insoluble in water, often described as hydrophobic. This is a basic saturated (no double bonds) fatty acid. There is a methyl group (CH₃) at one end of the chain. The chains are made up of covalently bonded carbons, saturated with hydrogens. The chain is non-polar and hydrophobic. These are typically made up of 16-18 carbon atoms, but can be anywhere from 14-22. The carboxyl group is polar, making the end of the molecules hydrophilic.


In water, fatty acid molecules arrange into spheres called micelles. The tails are at the centre, away from water. This is important to fat digestion and membrane structure.

 

2.2.3 – List three examples each of monosaccharides, disaccharides, and polysaccharides

 

Monosaccharides

Glucose – [animal] transported to cells in the blood plasma, and used as a respiratory substrate. In plants, it is a first product of photosynthesis

Galactose – [animal] used in the production of lactose

Fructose – [plant] this is produced in cellular respiration, and in the production of sucrose

 

Disaccharides

Lactose – [animal] produced in mammary glands and secreted into the milk as an important component in the diet of very young mammals

Sucrose – [plant] produced in green leaves from glucose and fructose. It is transported in the plant in solution, in the vascular bundles

Maltose – [plant] this is a breakdown product in the hydrolysis of starch
Polysaccharides

Glycogen – [animal] this is a storage carbohydrate formed from glucose in the liver and other cells (except brain cells) when glucose is not immediately required for cell respiration

Cellulose – [plant] this is manufactured in cells and laid down externally, in bundles of fibres, as the main component of the cell walls

Starch – [plant] this is a storage carbohydrate

 

2.2.4 – State one function of glucose, lactose and glycogen in animals, and of fructose, sucrose and cellulose in plants

Animals

 Glucose

  • Respiratory substrate

 Lactose Dietary component for young mammals, secreted from the mammary glands in

  • Dietary component for young mammals, secreted from the mammary glands in the milk

 Glycogen

  • Storage carbohydrate for when glucose is not immediately needed

Plants
 Fructose

  • Used in the production sucrose, and also an intermediate of glucose breakdown

 Sucrose

  • Produced from glucose and fructose, and transported in the plant in solution

 Cellulose

  • The main component of cell walls, laid down in bundles of fibres

 

2.2.5 – Outline the role of condensation and hydrolysis in the relationships between monosaccharides, disaccharides, and polysaccharides; between fatty acids, glycerol and triglycerides; and between amino acids and polypeptides

A polymer consists of large molecules made up of a linked series of repeated simple monomersA

A monomer is a simple molecular unit.

Condensation is the process of two monomers into a dimer or polymer. A molecule of water will also be formed as a product. This is a condensation reaction. The link between them after the removal of H₂O is called a glycosidic linkage, which comprises of strong, covalent
bonds. This reaction is brought about by an enzyme.

The reverse, a hydrolysis reaction, is when a molecule of water is added and the glycosidic linkage is split. It is also catalysed by an enzyme, but a different one from in the condensation reaction.

 

 

 

Sugars

Below is a condensation reaction between two molecules of glucose
to form maltose. This can be reversed in a hydrolysis reaction.
To form polysaccharides, many monosaccharides are joined.
Polysaccharides form in the same way as disaccharides.

 

 

 

Fats and oils

Fats and oils are triglycerides (simple lipids). At 20oC, fats are solid and oils are liquid. Oils have a lower density and melting point due to bends in their tails and unsaturated bonds. Fats tend to have longer fatty acid tails and saturated bonds. This makes them denser and raises the melting point. Triglycerides are not formed as in above. Instead, the chains are bonded to the molecule glycerol. The triglyceride formed is insoluble.

Phospholipids are the principle molecules in the cell membrane that form the bilayer. Their structure is similar to the triglyceride, except one of the fatty acids chains are replaced by a phosphate group.

 

𝑮𝒍𝒚𝒄𝒆𝒓𝒊𝒅𝒆 + 𝟑 𝑭𝒂𝒕𝒕𝒚 𝑨𝒄𝒊𝒅𝒔 → 𝑻𝒓𝒊𝒈𝒍𝒚𝒄𝒆𝒓𝒊𝒅𝒆 + 𝟑𝑯𝟐𝑶 

Amino Acids

In the formation of a dipeptide or polypeptide, two amino acid monomers will align to form peptide bonds by condensation reactions. This bond can form between the carboxyl group of the
first amino acid and the amino group of the second amino acid. Again, water is removed in the reaction. A dipeptide is formed when there is a bond between C-N. This pattern is true for all polypeptides.

𝟐 𝑮𝒍𝒚𝒄𝒊𝒏𝒆 → 𝑫𝒊𝒑𝒆𝒑𝒕𝒊𝒅𝒆 + 𝑯𝟐𝑶

Polypeptide chains fold into the complex, specific shapes of the protein seen below. The shape is determined by the hydrogen bonding and some covalent bonding between R groups. Polypeptides can be hydrolysed in the same way as polysaccharides by incubating with acids. They are digested into amino acids by peptidases.

2.2.6 – State three functions of lipids

  • Energy store – Fats and oils transfer twice as much energy as carbohydrates. They are also insoluble, so their presence does not cause osmotic water uptake
  • Metabolic water source – Energy and water are released when fats are used as a substrate in respiration.
  • Buoyancy aid – fat is not as dense as muscle or bone, so [for example, the blubber in whales] it will give buoyancy to the body.
  • Thermal insulation – Heat can be retained in the body through fat insulation
  • Water-proofing for hairs and feathers – this oil acts as a water repellent cuticle, and prevents hair and feathers from becoming waterlogged when wet.
  • Electrical insulation – Myelin lipid forms sheaths around the long fibres of nerve cells, electrically isolates the cell plasma membrane and facilitates the conduction of nerve impulses.
  • Hormones – Steroids can act as hormones in the body, examples include progesterone and testosterone
  • Cell receptors – Glycolipids on the surface of cells can act as receptors for hormones and other substances
  • Structure – Lipids like cholesterol are essential for maintaining the structure of cell membranes.

 

2.2.7 – Compare the use of carbohydrates and lipids in energy storage

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2.1 – Chemical Elements and Water

2.1 – Chemical Elements and Water

2.1.1 – State that the most frequently occurring chemical elements in living things are carbon, hydrogen, and oxygen

The most common elements in living things are carbon (C), hydrogen (H) and oxygen (O). Carbon is the most important element to life. It is a macronutrient, and basically our entire body is made up of it. It acts as a basic building block, which can be attached to form chains or to other elements. Carbon is essential for the big molecules to be built. They are based around chains of carbon atoms. Without them, we would be a pile of loose atoms with no way of being built into a person.

Hydrogen is also a macronutrient. It forms part of water, which we would die within a few days if we didn’t get any. Water is very important, with around 75% of our bodies (by weight) made up of it. It dissolves other important substances and can transport them. Important reactions also take place in water. Hydrogen bonds are what give water these amazing attributes. Hydrogen is almost always bonded to the carbon our bodies are made of. Also, crucial substances (i.e. Stomach acid – HCl) contain hydrogen. It is essential to life.

Oxygen is another macronutrient. It is needed by plants as well as humans. It forms a part of the water compound, which, of course, is essential to life. This versatile element is the single most important substance to life.

Nitrogen is another important element. It too is a macronutrient, and plays a role in digestion and growth. 80% of the air we breathe is made up of nitrogen, however it is in the wrong form, so we cannot use it. Instead, we get it from our food. It is extracted early to aid
us in growth. Nitrogen is especially useful during pregnancy, as it is necessary for foetus development. Nitrogen is one of the three main elements that make plant life possible.

 

2.1.2 – State that a variety of other elements are needed by living organisms, including sulfur, calcium, phosphorus, iron and sodium

Many other elements are necessary for the survival of living organisms. These include sulfur, calcium, phosphorus, iron and sodium.

2.1.3 – State one role of each of the elements mentioned above

Sulfur is also needed by living organisms. For example, it is an important element in some amino acids. It protects our cells from environmental hazards like pollution and radiation, as well as helping our liver to function properly. It is important for making blood clots, and keeps our skin supple and elastic.

Calcium is important, and can be found in our bones and teeth. This macronutrient is also important for other things like muscle growth, and electrical impulses in your brain. It maintains proper blood pressure and makes blood clot when you are cut. Calcium deficiency
can lead to muscle spasms, leg cramps and brittle bones.

Iron is found in hemoglobin, the part of our blood that carries oxygen. Hence, an iron deficiency would lead to fatigue and shortened attention span. This may lead to iron deficiency anaemia. It has many functions such as making tendons and ligaments, as well as controlling chemicals in our brains. It is needed for maintaining a healthy immune system.

Sodium is needed for nerve impulses to be sent. It also forms an important part of blood plasma, and without we cannot get the nutrients we need to survive. It maintains the correct amount of water in our blood. Our bodies therefore have various mechanisms to keep our sodium levels right, such as becoming thirsty when we have a lot of salt to dilute it and dispose of the excess.

Phosphorus is found in membrane structures, an integral part of the cell. It the most abundant mineral in our body, second only to calcium. It is needed for the healthy formation of bones and teeth, as well as processing food. It is part of our energy storage system. Contractions of the heart, normal cell growth and repair are all dependent of phosphorus. Deficiency leads to lowered energy levels and decreased attention span. Phosphorus is also one of the three main elements that make plant life possible. High intake from processed foods, etc, may lead to osteoporosis.

2.1.4 – Draw and label a diagram showing the structure of water molecules to show their polarity and hydrogen bond formation

The hydrogen atoms in a water molecule have a slight positive charge, and the oxygen atoms have a slight negative charge. The give water molecule two poles, which is called polarity.

 

Hydrogen bonds can form between the positive and negative poles of the molecules. In liquid water, many bonds will form to give the water its properties and making it useful for living organisms.

 

2.1.5 – Outline the thermal, cohesive and solvent properties of water

Thermal

  • Water has a large heat capacity, which means that large amounts of energy are required to raise its temperature. This is needed to break the hydrogen bonds.
  • The boiling point of water is high (100oC), as all the hydrogen bonds must be broken between the water molecules.
  • Water is able to evaporate at temperatures below boiling. The heat energy that breaks the hydrogen bonds is taken from the liquid, cooling it down.

Cohesive

Water molecules will stick together because of the hydrogen bonds between them.

Solvent

The polarity of water means that various substances will dissolve in it. Ions with positive or negative charges dissolve as they are attracted to the poles of water molecules. Many molecules are polar, so they will dissolve. Enzymes will also dissolve in water.

 

2.1.6 – 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

Blood (which is mainly composed of water) is able to carry heat from warmer parts of the body to cooler parts of the body. Thus, water can be used as a transport medium for heat. On earth, water is found below boiling point almost everywhere, and usually above freezing
point. Water is a medium for metabolic reactions as a liquid. Evaporation from plant leaves (transpiration) and from human skin (sweat) can have a cooling effect, thus water is useful as a coolant.

Cohesive

Strong pulling forces can be exerted to suck columns of water up to the tops of trees in their transport systems. These columns of water rarely break, so water is used as a transport medium in the xylem of plants. Water surfaces also have surface tension, meaning that it
can have enough structural strength to support the mass of insects.

Solvent

Most chemical reactions in living organisms with all of the substances dissolved in water. Hence, water is a medium for metabolic reactions. These properties also allow many substances to be carried dissolved in water in the blood of animals and the sap of plants.
Hence, it is a transport medium.

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