Topic 3: The Chemistry of Life

3.1.1 The most frequently occurring elements in living organisms are nitrogen, hydrogen, oxygen and carbon

3.1.2 A variety of other elements are needed by living organisms including calcium, sulphur, sodium, iron and phosphorous.

3.1.3 State one role for the elements above.

Name of element	Prokaryotes	Plants	Animals
Calcium	Flagella movement. Co-factor for certain enzymes.	Cell plate formation during cytokinesis. Co-factor for certain enzymes	Present in bones, shells and teeth. Involved in synaptic transmission and muscle fibre contraction. Co-factor for certain enzymes.
Sodium	Involved with potassium in membrane function	Involved with potassium in membrane function	Involved with potassium in membrane function.  Involved in nerve impulse conduction.
Phosphorous	Nucleotide synthesis	Nucleotide synthesis	Nucleotide synthesis
Sulphur	Formation of proteins	Formation of proteins	Formation of proteins
Iron	Constituent of electron transport molecules.	Constituent of electron transport molecules. Chlorophyll synthesis.	Present in haemoglobin. Constituent of electron transport molecules.

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

3.1.5 Explain how the properties of water are significant to living organisms.

Water functions as a coolant in plants and animals when it evaporates. This is due to its high latent heat of vaporization, which means that water releases a lot of heat energy when it converts from a liquid to a gas.

Water also functions as a universal solvent, allowing It to dissolve minerals and sugars which it transports up the xylem and phloem tubes in plants, respectively.  Water is also a medium for many metabolic reactions that occur in the cytoplasm of animal cells.

The strong hydrogen bonds between water molecules results in water’s cohesiveness. This is useful for plants to transport water in long columns up the roots of plants.

Water is also transparent, allowing light to pass through water, which in turn enables photosynthesis in plants which require sunlight. Other motile living organisms underwater need to be able to see their predators and their prey, made possible by water’s transparency.

water is transparent / light passes through water;
this allows organisms to live below the surface / plants to photosynthesize;
hydrogen bonds between water molecules make water cohesive;
this gives water a high surface tension allowing animals to live on the
surface
helps in water movement through plants/transpiration;
water has a high latent heat of vaporization / OWTTE;
evaporation/sweating/transpiration leads to cooling;
water has a high specific heat capacity / OWTTE;
this provides a stable environment for water organisms;
water is a universal solvent;
can transport materials around organisms/plants/animals;
can be a solvent for chemical reactions in organisms;
ice is less dense than water / water has a maximum density at 4°C;
surface (pond/lake/ocean) freezes first, allowing organisms to survive
in the water below;

3.2.1 Distinguish between inorganic and organic compounds.

Organic compounds contain carbon (except for hydrogen carbonates,carbonates and oxides of carbon which are inorganic compounds)whereas inorganic compounds do not contain carbon

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

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

Monosaccharides – Glucose, fructose, ribose and galactose

Disaccharides – Sucrose, lactose and maltose

Polysaccharides – Glycogen, starch and cellulose

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

Glucose – Used in cellular respiration

Lactose – Present in mammals milk providing energy to offspring

Glycogen –Energy store in liver and skeletal muscles

Fructose – Present in flow nectar, attracting pollinators

Sucrose – Transport form of carbohydrates in phloem tubes

Cellulose – Component of cell wall.

3.2.5      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.

Outline the role of hydrolysis in the relationships between monosaccharides, disaccharides and polysaccharides.

Hydrolysis is the splitting of a large molecule into smaller fragments with the addition of water. Monosaccharides are single sugars, disaccharides are made up of two sugars and polysaccharides are made up of multiple sugars.
In order for a disaccharide or a polysaccharide to be hydrolysed, the peptide bond(s) between molecules must be broken. Thereafter -H is added to one unit and -OH is added to the other unit causing the molecule to split.
For example the disaccharide lactose is hydrolysed into the monosaccharides glucose and galactose. Polysaccharides on the other hand are broken down into disaccharides.
Hydrolysis is largely dependent on enzymes present in living organisms, such as pepsin, amylase and lipase.

n

monosaccharides are single sugars and disaccharides are two sugars and polysaccharides are multiple sugars;
hydrolysis is the addition of water to split a molecule into smaller fragments;
–OH and –H are added to the fragments;
disaccharides are split/digested into two single sugars;
polysaccharides are broken/digested into smaller fragments (e.g. disaccharides);
process depends on enzyme control (in organisms);

Outline the role of condensation in the relationships between monosaccharides, disaccharides and polysaccharides.

• Monosaccharides are single sugars whereas disaccharides are made up of two sugars.
• Condensation involves the combination of two fragments (monosaccharides) to form a disaccharide with the release of water.
• OH and H is released resulting in a glycosidic linkage betweeen the two monosaccharides, resulting in a disaccharide.
• For example, glucose and galactose combine to form the disaccharide lactose, producing water in the process.
• Condensation reactions can also occur between disaccharides to form a polysaccharide.
• Condensation reactions are dependent on enzymes present in organisms.

• • The following reactions below are examples of condensation and hydrolysis reactions.
  •                                    hydrolysis
  • Maltose + water        glucose + glucose
  •                            condensation    
  •                                    hydrolysis
  • Lactose + water        glucose + galactose
  •                            condensation    

Outline the role of condensation and hydrolysis in the relationships between fatty acids, glycerol and triglycerides.

• Condensation is the combination of smaller fragments to form a molecule with the release of water.
• Conversely, hydrolysis occurs when a molecules is split with the addition of water to form smaller fragments.
• The following reactions below are examples of condensation and hydrolysis reactions.
•                                            hydrolysis
• Monoglyceride + water        fatty acids + glycerol
•                                     condensation    
•                                            hydrolysis
• Diglyceride + water        Monoglyceride + Monoglyceride
•                                   condensation    

•                                              hydrolysis
• Triglyceride + water       Diglyceride + Diglyceride
•                                     condensation    
• 
  
• Triglycerides are made up of several fatty acids, whereas a fatty acid is only one fatty acid
• Enzymes break the ester linkage and OH joins to one molecule and H joins to the other and they are split. This is called hydrolysis.
• Condensation involves the creation of an ester linkage and the removal of water, resulting in a molecule, e.g. a triglyceride.
• Both condensation and hydrolysis reactions are dependent on enzymes in organisms.

Outline the role of condensation and hydrolysis in the relationships between amino acids and polypeptides.

• Condensation reactions are the combination of individual fragments to form one molecule with the release of water.
• Amino acids are the building blocks of polypeptides. 
• Dipeptides are made up of two amino acids whereas polypeptides are made up of several amino acids.
• When two single amino acids combine in a condensation reaction, the OH from one amino acid and the H from the other amino acid are removed and a peptide bond is formed, resulting in a dipeptide.
• In the reverse reaction called hydrolysis, the peptide linkage is broken and water is added, thereby splitting the molecule to form two molecules.
• For instance, a dipeptide is split into two separate amino acids. 
• In the process of translation, amino acids are combined together using condensation reactions to form a long polypeptide chain.
• For hydrolysis and condensation reactions to occur, enzymes present in organisms are needed.

3.2.6 State three functions of lipids.

• Thermal insulation
• Energy storage
• Buoyancy in aquatic animals

3.2.7 Compare the use of carbohydrates and lipids in energy storage

• Both lipids and carbohydrates are primary energy sources for living organisms.
• Although, lipids are used for long-term energy storage whereas carbohydrates are used for short-term energy storage.
• Lipids contain more energy per unit mass.
• Lipids contain 38 kJ of energy per gram whereas carbohydrates contain only 17 kJ of energy per gram.
• Complete oxidation of fats and oils produces a larger amount of water than for the same mass of carbohydrate. 
• Desert animals such as the camel and the desert rat use this to help them survive when there is a lack of water available for drinking.
• However carbohydrates are easier to transport than lipids making their energy more accessible.
• This is because lipids are insoluble in water whereas small carbohydrates are soluble in water.
• Carbohydrates are also taken more easily out of carbohydrate stores and thus provide a quicker release of energy.

both lipids and carbohydrates are primary sources of energy for

organisms;

lipids store more energy per unit mass

lipids provide 38 kJ g–1 whereas carbohydrates have 17 kJ g–1

carbohydrates are easier to transport (than lipids) making their

energy more accessible;

because lipids are insoluble (in water) whereas (small) carbohydrates are soluble (in water);

carbohydrates are more easily taken out of storage making their energy more quickly available;

carbohydrates are short-term storage molecules, whereas lipids

provide long-term storage;

3.3 Explain the structure of a DNA Double Helix

• A DNA double helix are made up of nucleotide subunits.
• Each nucleotide contains one phosphate, connected to one deoxyribose via a covalent bond. The deoxyribose sugar is also connected to one nitrogenous base via a covalent bond.
• This nitrogenous base can be either adenine, thymine, guanine or cytosine.
• Nitrogenous bases form complementary base pairs with nitrogenous bases on the opposite strand and stay connected by hydrogen bonds.
• Adenine bonds with thymine and guanine bonds with cytosine.
• This way two strands of nucleotides are linked together.
• The resulting DNA double helix is described as antiparallel because the sugar phosphate backbone face opposition directions.

3.4.1 Explain DNA replication

• DNA replication occurs in the nucleus and begins when DNA helicase enzyme unwinds the DNA double helix into two separate strands, thereby breaking the hydrogen bonds between nitrogenous bases.
• DNA polymerase enzyme then adds complementary base pairs to the two separated template strands.
• These complementary nitrogenous bases are connected to nucleotides which are also added to the two single strands, resulting in two new strands of DNA.
• Adenine bonds with thymine, guanine bonds with cytosine.
• This results in two DNA double helices.
• Each DNA double helix is composed of the original template strand and a newly formed strand.
• For this reason, DNA replication is a semi-conservative process.

helix is unwound;
two strands are separated;
helicase (is the enzyme that unwinds the helix separating the two strands);
by breaking hydrogen bonds between bases;
new strands formed on each of the two single strands;
nucleotides added to form new strands;
complementary base pairing;
A to T and G to C;
DNA polymerase forms the new complementary strands;
replication is semi-conservative;
each of the DNA molecules formed has one old and one new strand;

3.4.2 Explain the significance of complementary base pairing in the conservation of the base sequence of DNA

• The process of DNA replication is semi-conservative, whereby DNA is split into two template strands.
• DNA polymerase adds nucleotides to each template, which attaches to the strand by forming complementary base pairs.
• Adenine bonds to thymine and cytosine bonds to guanine.
• This results in two DNA double helices that are each identical to the original DNA double helix.
• The strand newly formed on each template strand is identical to the other template strand in the original DNA double helix.

DNA replication is semi-conservative;

DNA is split into two single/template strands;

nucleotides are assembled on/attached to each single/template strand; by complementary base pairing;

adenine with thymine and cytosine with guanine / A with T and C with G;

strand newly formed on each template strand is identical to other

template strand;

DNA polymerase used;

Transcription and Translation

3.5.1 Compare the structure of RNA and DNA.

RNA	DNA
Contains ribose sugar	Contains deoxyribose sugar
Contains base uracil instead of thymine	Contains base thymine instead of uracil
Usually single-stranded	Double-stranded

Do not mention the highlighted statements if a question asks only for the chemical structure.

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

• DNA transcription occurs in nucleus
• Genetic code from DNA is transcribed to genetic code of RNA.
• DNA double helix is unzipped and hydrogen bonds broken by RNA polymerase enzyme.
• RNA polymerase adds complementary base pairs to one of the two strands.
• Adenine bonds with Uracil instead of Thymine, and Cytosine bonds with Guanine.
• RNA polymerase forms hydrogen bonds between the complementary base pairs
• and adds RNA nucleotides to the DNA strand.
• mRNA separates from DNA and DNA double helix reforms
• mRNA leaves nucleus via nuclear pores and travels to cytoplasm to begin translation.

Transcription is the formation of an RNA strand that is complementary to the DNA strand being transcribed by the enzyme RNA polymerase. Transcription occurs in the nucleus and begins when only one strand of the DNA double helix is unzipped and unwound by RNA polymerase into two separate strands. The template strand of DNA is then transcribed with complementary ribose nucleotides, forming hydrogen bonds between nitrogenous bases. In particular, the base uracil instead of thymine is used to form a complementary base pair with adenine on the DNA strand. The mRNA then separates from the DNA and the double helix is reformed. mRNA leaves nucleus via the nuclear pores and travels to the cytoplasm to begin the process of translation.

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

• Genetic code is made of mRNA base triplets named codons
• 64 different codons and each codes for a specific amino acid that is added to a polypeptide during translation
• Genetic code is degenerate meaning that several different codons can code for the same amino acid, e.g. codons GUU and GUC both code for amino acid valine.
• Genetic code is universal because it is present in nearly all living organisms.
• Some codons do not code for any amino acids, e.g. codons coding for mRNA, tRNA and rRNA.
• Introns are non-coding segments of DNA which are removed prior to translation.

Genetic code is composed of mRNA base triplets called codons. There are 64 different codons and each codes for the addition of a specific amino acid to a growing polypeptide chain during translation. Different codons can code for the same amino acid, for example the codons GUU and GUC both code for the amino acid valine. For this reason, the genetic code is described as being degenerate. Stop codons UAA, UAG and UGA all code for the end of translation, as well as the start codon AUG coding for the start of translation.This genetic code is also universal because nearly all living organisms use the same code. 

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

Translation is the process whereby the genetic code of the mRNA strand is used to code for amino acids that form a polypeptide chain. Translation begins when the mRNA strand from the nucleus attaches to the smaller ribosomal subunit in the cytoplasm. The mRNA is "read" by the ribosome one codon at a time. Each codon consists of three nitrogenous bases that code for a specific amino acid. This specific amino acid is brought to the ribosome by a tRNA molecule, which forms a hydrogen bond between the mRNA's codon and the tRNA's anticodon. RIbosome shifts one codon to the left, resulting in a second tRNA transporting an amino acid specific to that codon, and a hydrogen bond forms between the tRNA's anticodon and the mRNA's codon. A peptide linkage forms between adjacent peptide molecules and the first tRNA detaches.

Ribosome continuously reads the codons on the mRNA strand and the process is repeated until the stop codons UAA, UAG and UGA are reached. Thereafter the mRNA and ribosome separate and the completed polypeptide is released.

3.5.5 Discuss the relationship between one gene and one polypeptide.

• Polypeptide initially thought to have been coded from only one gene
• However a polypeptide may require more than two genes
• Each gene coding for a specific section of the polypeptide
• Some genes code for tRNA, rRNA and mRNA and not proteins
• Non-coding segments of DNA called introns do not code for polypeptides