CH3 Biological Molecules

3.1 Biological Elements

1. What are molecules?
2. What are elements?
3. Name the 6 key elements in living organisms.
4. What is a covalent bond?
INORGANIC IONS
5. What are ions? Name the 2 types.
6. What are macro- and micronutrients? Give examples
7. What happens if sufficient macronutrients are not consumed?
8. Name 4 cations important in living things.
9. Why are calcium ions necessary?
10. Why are sodium ions necessary?
11. Why are potassium ions necessary?
12. Why are hydrogen ions necessary?
13. Why are ammonium ions necessary?
14. Name 5 anions necessary in living things.
15. Why are nitrate ions necessary?
16. Why are hydrogen carbonate ions necessary?
17. Why are phosphate ions necessary?
18. Why are hydroxide ions necessary?
19. Why are chloride ions important?
20. What elements/atoms are carbohydrates made of?
21. What elements/atoms are lipids made of?
22. What atoms/elements are proteins made of?
23. What atoms/elements are nucleic acids made of?
24. Define polymers and monomers.

3.2 WATER
25. Describe the structure of a water molecule.
26. Explain the polarity of water.
27. Define polar(ity).
28. Why are most organic molecules polar?
29. What are hydrogen bonds?
30. Draw a water molecule showing hydrogen bonds.
31. State 5-7 properties of water and explain how they are essential for living
organisms?
32. What happens to hydrogen bonds as water molecules constantly move around?
33. Water is liquid at room temperature, give 4 reasons why this is important for living
organisms.
34. Describe the density of water (at what temperature does this density change?)
35. State 2 ways in which the density of water is important to living organisms.
36. Why is ice less dense than water (structure)?
37. What makes water a good solvent?
38. How is the solvent property of water useful for living organisms?
39. What is meant by solvent and solute?
40. Name 2 polar solutes.
41. What is cohesion?
42. What is surface tension?
43. State 2 ways in which cohesion and surface tension are useful to living organisms.
44. What is meant by specific heat capacity?
45. What is the specific heat capacity of water?
46. What is water temperature a measure of?
47. Does the SHC of water mean it cools/heats very easily?
48. How is the SHC of water essential for living organisms?
49. What is latent heat of vaporisation?
50. Explain why water has a high latent heat of vaporisation?
51. What is the difference between SHC and LHV?
52. How is the latent heat of vaporisation of water important for living organisms?
53. Name a property of water that does not depend on its polarity.
54. Why is water good as a reactant?
3.3 CARBOHYDRATES
1. What are carbohydrates?
2. What is the general formula of carbohydrates?
3. What else are carbs known as?
4. Define monosaccharide.
5. Define disaccharide.
6. Define polysaccharide.
7. Define oligosaccharide.
8. What is glucose? + chemical formula
9. What type of monosaccharide is glucose?
10. How many structural isomers does glucose have?
11. What is the difference between a and B glucose? -Draw .
12. Why is glucose soluble in water and why is this solubility important for living
organisms?
13. What is meant by condensation reactions?
14. What is a glycosidic bond?
15. Describe the condensation reaction between 2 a glucose molecules.
16. What is meant by 1,4 glycosidic bond?
17. Name 2 other hexose monosaccharides.
18. Which 2 monosaccharides form the following disaccharides:
-maltose
-sucrose
-lactose
-cellobiose
19. Draw the structure for ribose and deoxyribose (what type of monosaccharide)?
STARCH AND GLYCOGEN
20. What is starch?
21. Why does not starch affect the water potential of plant cells?
22. Which 2 polysaccharides is starch a mixture of?
23. How is amylose formed?
24. Why is amylose more compact than individual a-glucose monomers?
25. What is amylopectin and how is it different to amylose?
26. How often do the branching points (1-6) occur?
27. What is glycogen?
28. Why is glycogen more compact than amylopectin and why?
29. How does the branching/coiling make polysaccharides ideal for storage?
30. Why is the branching of glycogen important for animals?
31. Define hydrolysis?
32. What type of reaction is hydrolysis?
33. What is cellulose?
34. Why are B glucose molecules unable to join like a? How is this overcome?
35. How does the bonding affect their ability to coil?
36. What are microfibrils?
37. What are macrofibrils?
38. What are (cellulose) fibres?
39. How is cellulose adapted for its function?

3.4 TESTING FOR CARBOHYDRATES

1. What are reducing sugars?
2. What is reduction?
3. What is the chemical test for reducing sugars?
4. What chemical is reduced?
5. Describe the process of the benedict’s reagent test for reducing sugars.
6. Explain the molecular basis of the test?
7. What do different results mean in terms of colour?
8. Is the benedict’s test qualitative or quantitative?
9. What are non-reducing sugars? Give examples.
10. How do you test for non-reducing sugars?
11. Name and describe the test for starch?
12. What are reagent strips?
13. What do quantitative tests tell you about a substance in a sample?
14. Name 2 quantitative tests for carbohydrates?
15. What is a colorimeter?
16. What are biosensors?
17. Describe the steps of colorimetry.
18. What affect does a high concentration of substance have on absorbance and
transmission?
19. What are biosensors?
20. What is an analyte?
21. Describe and name the 3 steps when using biosensors?
22. What else can biosensors be used for (Pearson)?

3.6 LIPIDS
1. Define lipids + what elements do they contain?
2. What are macromolecules?
3. Are lipids polar. Why?
4. What are macromolecules?
5. What are liquids vs solid lipids?
6. Define triglycerides.
7. Describe the structure of triglycerides?
8. What organic group does glycerol belong to?

9. What group do fatty acids belong to?

10. Describe the condensation reaction in triglycerides? What is it called?
11. How many ester bonds formed?
12. Draw and annotate a diagram showing formation of ester bonds in triglycerides.
13. Describe the hydrolysis reaction in triglycerides? How many h20 molecules needed/
14. Define saturated fatty acids?
15. Draw a saturated fatty acid.
16. Define unsaturated fatty acid and draw.
17. What is meant by monounsaturated and polyunsaturated?
18. Why are lipids containing unsaturated fatty acids liquid at room temperature?
19. Define phospholipids.
20. Describe the structure of phospholipids and how is it different to triglycerides?
21. What is meant by hydrophobic/hydrophilic?
22. What part of a phospholipid is hydrophobic/hydrophilic?
23. Describe and explain the behaviour of phospholipids in water. What structure do
they form?
24. What is meant by amphipathic?
25. Are membrane lipids amphipathic?
26. Are storage lipids amphipathic?
27. How does a phospholipid bilayer form?
28. Describe the movement of lipids inside the bilayer?
29. What are sterols? Give an example.
30. Describe the structure of sterols.
31. What is the role of cholesterol in the plasma membrane?
32. Name 3 substances manufactured using cholesterol.
33. State and describe the roles of lipids due to non-polar nature.
34. How can you test for lipids?

3.6 PROTEIN STRUCTURE

1. Define protein.
2. Define amino acid.
3. State 3 functions of proteins and why they are suitable for these roles?
4. How do plants vs animals get their proteins?
5. How do amino acids join to form polypeptides?
6. Between which two groups/atoms does the condensation reaction occur and what
bond is formed?
7. Draw the general structure of amino acid.
8. How is a peptide bond broken?
9. What enzymes break down peptide bonds and where?
 LEVELS OF PROTEIN STRUCTURES
10. Define primary structure.
11. How many possible ways are there of ordering 100 amino acids?
12. What determines the primary structure?
13. Why is the order of amino acids in primary structure important?
14. What type of bonds are involved at this stage?
15. Define secondary structure.
16. What are the 2 possible secondary structures?
17. Define alpha helix and beta pleated sheet.
18. How is the alpha helix held together?
19. How are beta pleated sheets held together?
20. Hydrogen bonds are relatively weak, but alpha helix and beta pleated sheets are
stable structures. Why?
21. What are the main bonds in secondary structure?
22. Can a protein only have one secondary structure?
23. Define tertiary structure.
24. What groups interact in tertiary structure and how does the secondary structure
make this possible?
25. State and describe the 4 interactions involved in tertiary structure. Put them in order
of strength.
26. Define quaternary structure.
27. Name the interactions involved in Q.S and how it is different to tertiary structure.
28. How are primary, secondary, and tertiary different to quaternary?
29. Where do the hydrogen bonds occur between amino acids?
30. Where do ionic bonds occur between amino acids?
31. What are disulphide bonds and where do these occur?
32. Describe hydrophobic/hydrophilic interactions of R groups and how this affects
shape/structure of protein.
33. Do all polypeptides have to be identical in a protein. Give different examples.
34. Name and describe the identification test of proteins.
35. What does a positive and negative result show?
36. What is the molecular basis of a protein test?
37. What does a biuret reagent contain?

3.7 TYPES OF PROTEINS

GLOBULAR
1. Define globular proteins.
2. How are globular proteins formed?
3. Are globular proteins soluble in water. Why?
4. What are the roles of globular proteins? Give 3 examples.
5. What is insulin? + role?
6. Why does insulin have to be soluble?
7. How does insulin cause uptake of glucose by muscle and fat cells?
8. Describe the structure of insulin. Is it tertiary or quaternary?
9. Define conjugated protein.
10. Define prosthetic group.
11. Name a conjugated protein.
12. What is the prosthetic group found in haemoglobin (what iron does it contain)?
13. Describe the structure of a haemoglobin molecule.
14. What is the role of Hb?
15. What does the oxygen bind to in Hb?
16. What happens to colour of Hb as O2 binds?
17. Name a globular protein that is an enzyme.
18. What is the role of catalase?
19. Describe the structure of catalase.
20. Is catalase a conjugated protein? Why?
21. What does the presence of fe2+ allow?
FIBROUS PROTEINS
22. Define fibrous proteins.
23. Describe the sequences of amino acids in fibrous proteins and how it is reflected in
their roles.
24. Are fibrous proteins soluble in water. Why?
25. Name 2 fibrous proteins that are found in connective tissues.
26. What is keratin and where is it found?
27. State 2 properties of keratin and how the structure gives it these properties?
28. What is the role of keratin other than being found in hair, horns etc.?
29. What is elastin?
30. Role of elastin?
31. Name 4 places in our body where elastin is found?
32. Describe structure of elastin.
33. What is collagen?
34. What is the function of collagen?
35. Name 4 places where collagen is found and its role there.
36. State the properties of collagen.
COMPUTER MODELLING OF PROTEIN STRUCTURE
37. Name the 2 approaches to computer modelling of protein structure.
38. What is ab initio protein modelling?
39. What is comparative protein modelling?

PRACTICAL 3 -CHROMOTOGRAPHY (biological molecules)

1. What is the aim/principle of chromatography?
2. What is the stationary phase?
3. What is the chromatography paper and TLC plate made of?
4. What is the mobile phase?
5. What is the mobile phase for polar vs non-polar molecules?
6. Describe step by step how a chromatography practical is carried out.
7. Describe the set up of thin layer chromatography?
8. How do you measure and calculate Rf value?
9. When should the distance of solvent front be measured and why?
10. Sometimes molecules are colourless so cannot be seen name 3 ways in which this
problem may be overcome.
11. How is UV light used in TLC to make the spots visible?
12. What is ninhydrin used for?
13. What and how is iodine used?
HOW TLC WORKS?
14. What does speed of molecules travelling along TLC plate depend upon?
15. Describe the movement of polar vs non-polar molecules up the plate and explain
why this happens?
16. What should you do if 2 molecules travel exactly at the same speed?
17. Where can TLC be used in real life?

3.8 NUCLEIC ACIDS

1. What are nucleic acids? Give 2 examples.
2. What are nucleotides and polynucleotides?
3. What does a nucleotide consist of?
4. How is a polynucleotide formed (describe the condensation reaction)?
5. Name the nucleotide pentose sugar in RNA and DNA.
6. How is deoxyribose different to ribose?
7. How many possible nucleotides of DNA are possible and why?
8. What are phosphorylate nucleotides? Give examples.
9. Why are phosphorylated nucleotides important? (2 reasons)
10. What is the difference between a nucleotide and nucleoside?
11. Which of the following are nucleoside and nucleotide?
-ADP
-AMP
-ATP
-Adenosine
12. What is DNA?
13. Describe the structure of DNA:
-monomers -strands (direction) (name) -nucleotide made of -bonds
between nucleotides -what they carry
14. Define purine. Which bases are purines?
15. Define pyrimidine. Which bases are pyrimidines?
16. What are the (complementary) base pairing rules?
17. How many hydrogen bonds to A and T form?
18. How many hydrogen bonds to C and G form?
19. Why are hydrogen bonds important in the structure of DNA?
20. What is the 5’ end of the molecule?
21. What is the 3’ end of molecule?
22. How is DNA organised in E.Cs?
23. How is DNA organised in P.Cs?
24. How is DNA organised in viruses?
RNA
25. What is the role of RNA?
26. Describe the nucleotides of RNA.
27. What are the base pairing rules in RNA?
28. What bonds are formed between RNA nucleotides?
29. What happens to RNA molecules in cytoplasm after used?
DNA EXTRACTION
30. State some sources of DNA extraction.
31. Describe the step-by-step process by which DNA can be extracted from a
plant?
32. What is role of each of the following:
-detergent
-salt
-protease enzyme
-ethanol

3.9 DNA REPLICATION AND GENETIC CODE

1. What is meant by DNA replication?
2. Define semi-conservative replication.
3. What happens to DNA each time a cell divides?
4. Describe the process of semi-conservative replication.
5. What is DNA helicase?
6. What is DNA gyrase?
7. Define DNA polymerase?
8. In what direction does DNA polymerase catalyse the addition of new
nucleotides?
9. What are the leading and lagging strands?
10. Where does the energy to make phosphodiester bonds come from?
11. Which enzyme is involved in the following:
-Unwinding
-Unzipping
-Formation of phosphodiester bonds
12. How does DNA helicase cause DNA molecule to unzip?
13. What is the product of semi conservative replication?
14. How do loops of DNA in prokaryotes and mitochondria/chloroplasts
replicate?
CONTINOUS VS DISCONTINUOUS REPLICATION
15. In what direction does DNA polymerase move? Why?
16. In what direction does DNA polymerase catalyse addition of new nucleotides
and why?
17. Which strand is continuously replicated (direction)?
18. Which strand is discontinuously replicated? (what direction)?
19. What are okazaki fragments?
20. How are these fragments joined?
MUTATIONS /REPLICATION ERRORS
21. How can a mutation occur during replication and how is this minimized?
22. Are mutations harmful?
23. What are alleles?
24. Define genetic code.
25. Define genes.
26. Why is the genetic code described as universal?
27. Why is the genetic code called degenerate? How does this reduce effect of
point mutation?
28. Why is the genetic code non-overlapping?
29. What is meant by triplet code?
30. What is meant by codon?
31. Why are their 64 different codons possible?

3.10 PROTEIN SYNTHESIS

1. Define gene.
2. Define transcription.
3. Define translation.
4. State 5 ways in which RNA is structurally different to DNA.
5. Why is it important for sequence of base triplets/primary structure to be
correct:
-enzyme
-antibody
-receptors
-ion channel protein.
6. What is the difference between DNA base triplet and codon?
TRANSCRIPTION
7. Why does transcription have to occur?
8. Describe the process of transcription.
9. What is meant by the sense strand? (what direction does it run?)
10. What is meant by anti-sense strand? direction
11. Which strand acts as a template strand and why?
12. Name the 2 enzymes involved in transcription.
13. Describe the base pairing in transcription? What nucleotides are
involved?
14. What happens to structure of DNA as mRNA leaves?
15. How does mRNA leave the nucleus?
TRANSLATION
16. Where are ribosomes made?
17. What are ribosomes made of?
18. What does mRNA bind to in the cytoplasm?
19. What catalyses the synthesis of polypeptides?
20. What is rRNA?
21. Define tRNA.
22. Where are tRNA molecules formed?
23. Describe the structure of tRNA.
24. What is anticodon?
25. Describe the process of transcription.
26. Which organelle causes the synthesis of polypeptides?
27. What is the role of tRNA?
28. What does the ribosome do as it moves along the mRNA?
29. How is energy supplied for polypeptide synthesis?
30. How is the polypeptide assembled?
31. What happens to mRNA strand after the polypeptide has been
synthesised?
32. What happens to the polypeptide chain after it has been synthesised?
33. What is a triplet of bases in DNA called?
34. What is the triplet of bases in mRNA called?
35. What is the triplet of bases in a tRNA called?

3.11 ATP
1. What are the 3 main activities that cells need energy for?
2. Define ATP.
3. Why is ATP known as the universal energy currency?
4. What happens in terms of energy when bonds break and bonds
form?
5. How does ATP release energy? (talk about breaking and forming
bonds)
6. Describe the hydrolysis reaction in ATP.
7. Write the equation of ATP hydrolysis.
8. Define ADP.
9. Why is ATP not a good long term energy storage molecule?
10. Name 2 long term energy storage molecules and how they can be
used to produce ATP.
11. What is phosphorylation?
12. What type of reaction is phosphorylation?
13. Why is ATP a good intermediate energy store?
PROPERTIES OF ATP
14. State 5 properties of ATP molecules.
15. Why is energy released by ATP not wasted?
16. Why is ATP suitable for reactions inside living organisms/cells?
17. Describe the bonds between phosphates of ATP molecules.