Topic 2: Molecular Biology

Question 1

Vitalism

Answer 1

• It was believed that living organisms are composed of organic chemicals that could only be produced in living organisms because a vital force was needed.
• Falsified by a series of discoveries including synthesising urea artificially.
• No vital force has been found and natural selection is preferred.

Question 2

Synthesis of urea

Answer 2

• Discovered in human urine in 18th century.
• An organic compound.
• In 1828, a German chemist synthesised urea artificially- helped to falsify the theory of vitalism but did not disprove it completely.
• Several pieces of evidence were needed.

Question 3

Atoms and molecules

Answer 3

Atom- a single particle of an element.

Molecule- a group of two or more atoms held together by covalent bonds.

Question 4

Metabolism

Answer 4

• The sum of all chemical reactions in an organism.
• Metabolic pathways consist of chains of reactions or cycles of reactions.
• Anabolism- synthesis of complex molecules from simpler ones including condensation reactions because water is produced.
• Catabolism- breakdown of complex molecules into simpler ones including hydrolysis.
• Macromolecules- larger molecules
• Monomers- single subunits

Question 5

Polarity of water

Answer 5

• Water molecules are polar (hydrophilic)- hydrogen nuclei are less attractive to electrons than oxygen nuclei, so the two hydrogen atoms have a slight positive charge and the oxygen atom has a slight negative charge.
• Water molecules have two poles and are therefore dipoles- show dipolarity.

Question 6

Hydrogen bonding in water

Answer 6

• An intermolecular bond can form between the positive pole of one water molecule and the negative pole of another- hydrogen bond.
• These hydrogen bonds give water its properties.
• Energy is released when a hydrogen bond is made, and used when it is broken.

For ex. when a water molecule evaporates, hydrogen bonds must be broken, heat energy is used for this- explains sweat as a coolant, evaporation of sweat removes heat.

Question 7

Solubility in water

Answer 7

• Attractive to water- hydrophilic.
• Hydrophilic- ionic, polar.
• Not as attracted to water- hydrophobic. Hydrophobic substances are insoluble in water.
• Hydrophobic- non-polar.

Question 8

Transport in blood

Answer 8

• Sodium chloride- soluble in water and is transported dissolved as sodium and chloride ions.
• Glucose and amino acids- polar and transported dissolved.
• Oxygen- non-polar and the amount dissolved is insufficient so red blood cells are needed with haemoglobin to which oxygen binds.
• Cholesterol and fats- non-polar and insoluble in water so transported in small droplets called lipoproteins (cholesterol and fats inside, coated by phospholipids and proteins).

Question 9

Properties of water

Answer 9

Cohesive- water molecules cohere (stick to each other) because of the hydrogen bonds- ex. xylem.
Adhesive- dipolarity of the water molecules makes them adhere to surfaces that are polar- ex. water drawn out of xylem vessels to keep the wall moist.
Thermal- due to hydrogen bonding, water has high melting and boiling points, high latent heat of vaporisation and high specific heat capacity- ex. suitable habitat oceans.
Solvent- many substances dissolve in water due to its polarity- ex. dissolved substances for chemical reactions/metabolism.

Question 10

Condensation and hydrolysis

Answer 10

Condensation- joins two molecules together to form a larger molecule plus a molecule of water. Anabolic reactions.
Hydrolysis- reverse, a large molecule is broken down into smaller molecules. Water is used up in the process.

Question 11

Carbohydrates

Answer 11

Monosaccharides- sugars that consist of a single sub-unit/monomer. Ex. glucose, galactose, fructose (GIVES GOOD FLAVOUR).
Disaccharides- two monosaccharides linked together. Ex. lactose, sucrose, maltose (LENGTH SUPPORTS MOVEMENT).
Polysaccharides- many monosaccharides linked together. Ex. cellulose, glycogen, starch (CAN GET STORED).

Question 12

Polysaccharides

Answer 12

• Cellulose- unbranched polymer of beta-glucose. Glucose units alternate. Cellulose microfibrils have a lot of strength.
• Starch- a polymer of alpha-glucose with the glucose units in the same orientation. Two types of starch.
  Amylose: only 1,4 linkages so unbranched.
  Amylopectin: some 1,6 linkages in addition to 1,4 linkages so branched.
• Glycogen- branched polymer of alpha-glucose, however more 1,6 linkages than in amylopectin (a type of starch).

Question 13

Lipids

Answer 13

Lipids- carbon compounds made by living organisms, almost entirely hydrophobic.
Three main types:
- Triglycerides- 3 fatty acids and 1 glycerol (three hydrocarbon tails).
- Phospholipids- 2 fatty acids and 1 glycerol and phosphate group. Only partly hydrophobic.
- Steroids- four fused rings in their molecule. Cholesterol, progesterone, oestrogen and testosterone are all steroids.
Molecules can be identified as lipids if they have two or three hydrocarbon chains or the quadruple ring structure of steroids.

Question 14

Types of fatty acid

Answer 14

• Saturated- all of the carbon atoms in the chain are connected by a single bond- the nr of hydrogen atoms cannot be increased.
• Unsaturated- contain one or more double bonds.
  1. Monounsaturated- only one double bond.
  2. Polyunsaturated- two or more double bonds.
  3. Cis unsaturated- hydrogen atoms are bonded to carbon atoms on the same side of a double bond.
  4. Trans unsaturated- hydrogen atoms are bonded to carbon atoms on opposite sides of a double bond.

Question 15

Amino acids

Answer 15

• Hydrogen atom
• Amine group
• Carboxyl group
• R group (20 in most living organisms but hundreds of different ones can be synthesised).

Question 16

Polypeptides

Answer 16

Unbranched chain of amino acids.
The number of amino acids is variable, can be over 10,000, mostly between 50 and 2,000.
Chains of fewer than 40 amino acids are usually called peptides.
The amino acid sequence is coded for by a gene.
A protein consists of either a single polypeptide or more than one polypeptide linked together.

Question 17

Proteome

Answer 17

All of the proteins produced by a cell, a tissue, or an organism.
Proteome is variable while genome is fixed.

Question 18

Peptide bonds

Answer 18

Amino acids are linked together by condensation reactions- a peptide bond is formed between the amine group of one amino acid and the carboxyl group of the next.

Question 19

Denaturation

Answer 19

The conformation can be changed and damaged easily.

1. Heat causes vibrations within protein molecules, breaking intermolecular bonds and causing conformation to change. Heating egg white, albumins denature- turns into solid.
2. Every protein has an ideal optimum pH- if increased by adding alkali or decreased by adding acid, the conformation of the protein may initially stay the same, but denaturation will eventually occur- intramolecular bonds break.

Question 20

Functions of proteins

Answer 20

• Rubisco- catalysis photosynthesis reaction- fixes carbon dioxide from the atmosphere.
• Insulin- hormone that is carried dissolved in blood and binds to insulin receptors, causing the cells to absorb glucose and lower the blood glucose concentration.
• Immunoglobulins- antibodies that bind to antigens on pathogens. Many different ones.
• Rhodopsin- a pigment that makes the rod cells on the retina light sensitive.
• Collagen- a structural protein that prevents fractures and tearing in tendons, ligaments.
• Spider silk- structural protein used to make webs for catching prey.

Question 21

Immobilised enzymes

Answer 21

Enzymes are widely used in industry for catalysing specific reactions. The enzymes are usually immobilised, by attachment of enzymes to another material or entrapment in a membrane/gel or aggregation by bonding them together to restrict their movement.

Enzyme immobilisation has benefits:

• Catalysis can be controlled
• Enzyme concentrations can be higher
• Enzymes can be reused, saving money
• Enzymes are resistant to denaturation over greater ranges of pH and temperature

Question 22

Lactose-free milk

Answer 22

Lactose can be hydrolysed into glucose and galactose by the enzyme lactase.
- Lactose-free milk is got by adding lactase to the milk.
Benefits:
- For lactose-intolerant people
- Glucose and galactose are sweeter- no need for sugar
- Smoother
- Bacteria ferment glucose and galactose faster- production of yoghurt and cottage cheese is faster

Question 23

Factors affecting enzyme activity

Answer 23

• Temperature
• pH
• Substrate concentration
• Light intensity

Question 24

DNA replication

Answer 24

1. Helicase unwinds the double helix and separates the two strands by breaking hydrogen bonds. Single-stranded binding proteins keep the strands apart.
2. Gyrase moves ahead of Helicase to relieve the strain it puts on the DNA molecule.
3. On the leading strand: DNA polymerase III adds nucleotides in a 5’ to 3’ direction on the leading strand.
4. On the lagging strand: DNA primase adds a short length of RNA (primer) attached by base pairing to the template strand. DNA polymerase III adds nucleotides next to RNA primer away from the replication fork. DNA polymerase I removes the RNA primer and replaces it with DNA. DNA ligase seals up the nick left between the nucleotides.
5. The daughter DNA molecules each rewind into a double helix.
6. The 2 daughter molecules are identical to each other and the parent molecule, because of complementary base pairing. Adenine will only pair with thymine and cytosine will only pair with guanine. Each of the new strands is complementary to the template strand on which it was made and identical to the other template strand.

Question 25

Transcription

Answer 25

The copying of the base sequence of a gene by making a RNA molecule.

In prokaryotes:

• RNA polymerase binds directly to the promoter in prokaryotes.
• Repressor proteins can bind to the promoter and prevent transcription. Blocking transcription switches genes off.

In eukaryotes:

• The control of gene expression is more complicated in eukaryotes.
• The sense strand- the strand that is not transcribed but has the same base sequence as the mRNA except for having T instead of U.
• The antisense strand- the transcribed strand.
• Proteins called transcription factors bind to the promoter- allows RNA polymerase to bind and then start transcription. Repressor proteins can prevent transcription as well.
• RNA polymerase moves along the gene, assembling an RNA molecule one nucleotide at a time. RNA polymerase adds a nucleotide to the 3’ end of the growing mRNA molecule (in 5’ to 3’ direction).
• Transcription is terminated at the end of the gene and the DNA, RNA and RNA polymerase separate.

Question 26

Translation

Answer 26

The synthesis of polypeptides on ribosomes, using mRNA and tRNA.

• Translation depends on complementary base pairing between codons on mRNA and anticodons on tRNA.

1. mRNA binds to a site on the small subunit of the ribosome.
2. tRNA molecules bind to three binding sites on the large subunit of the ribosome. 3 sites- E, P, A. tRNA can only bind if it has the anticodon complementary to the codon on the mRNA. The complementary bases link by hydrogen bonding (same as in replication and transcription).
3. The amino acids carried by the tRNA molecules are bonded together by a peptide linkage. A dipeptide is formed, attached to the tRNA on the right. The tRNA on the left detaches and the ribosome moves along the mRNA to the next codon. A chain of amino acids is formed and this continues until a polypeptide is formed.

Question 27

Meselson and Stahl and DNA replication

Answer 27

Soon after discovery of structure of DNA, evidence for semi-conservative replication was found.

• Cultured E. Coli bacteria for generations in 15N
• Then transferred the bacteria to 14N isotope.
• Used a centrifuge to separate
• After one generation the DNA was intermediate in density
• In the next generation, two equal bands, 14N and 15N
• Then less dense 14N band became stronger and the 14N/15N band weaker

Question 28

Model making and the structure of DNA

Answer 28

Complementary base pairing found by Crick and Watson by using the ideas from the X-ray diffraction (helical shape) by Franklin (not acknowledged).

Question 29

Production of human insulin in bacteria

Answer 29

• Human insulin- a protein that consists of only 51 amino acids.
• The gene that codes for insulin has been transferred from humans to E. Coli to produce insulin needed to treat diabetes.
• The amino acid sequence of the insulin in these organisms using the transferred gene is identical to the sequence produced in humans- universality of the genetic code.

Question 30

Polymerase chain reaction (PCR)

Answer 30

For gene transfer procedures, many copies of the desired gene are needed. Also useful if more needed for forensic analysis.

• For copying DNA artificially.
• DNA is copied in small tubes called eppendorfs and it is carried out at high temperatures.
• However, enzymes usually denature at high temperatures. TAQ Polymerase from a bacterium from hot springs is used.
• Millions of copies of the DNA can be produced by PCR in a few hours.

Question 31

Cell respiration

Answer 31

Controlled release of energy (in the form of ATP) from organic compounds (eg glucose).

• 1st stage: Glycolysis in cytoplasm. NAD is an electron carrier- it gains electrons and is reduced to NADH.
• Link reaction
• 2nd stage: Krebs cycle

Question 32

Glycolysis

Answer 32

1. Two phosphate groups are added to a molecule of glucose by ATP- hexose bisphosphate (Phosphorylation). The energy level of the hexose is raised, less stable.
2. The hexose bisphosphate is split to form two molecules of triose phosphate- Lysis (splitting molecules).
3. Two atoms of hydrogen are removed from each triose phosphate molecule- oxidation. The energy released by oxidation is used to convert two ADP molecules to ATP. The end product of glycolysis is pyruvate.

Question 33

Link reaction

Answer 33

• Enzymes in the matrix of the mitochondria remove carbon dioxide and hydrogen from the pyruvates.
• Oxidative decarboxylation
• The product acetyl group is attached to coenzyme A to form acetyl coenzyme A.

Question 34

Krebs cycle

Answer 34

1. Acetyl CoA transfers its acetyl group to a 4C compound to make a 6C compound.
   - Over a series of reactions, the 6C compound is broken down to reform the original 4C compound (hence, a cycle).
   - CO2 removed in 2 of the reactions- decarboxylations.
   - Hydrogen removed in 4 of the reactions- oxidations.
   - Accepted by hydrogen carriers (3 times accepted by NAD (reduction), 1 time by FAD). These oxidations release energy which is stored by the carriers and later released by the electron transport chain to make ATP.
   - ATP is produced in one of the reactions- substrate-level phosphorylation.

Question 35

Electron transport chain

Answer 35

A series of electron carriers, located in the inner membrane of the mitochondria (including the cristae).

• NADH supplies two electrons (from oxidation) to the first carrier in the chain.
• As the electrons pass along the chain from one carrier to the next they give up energy.
• Some of the electron carriers act as proton pumps and use this energy to pump protons against the concentration gradient from the matrix of the mitochondrion to the intermembrane space.
• FADH also feeds electrons into the electron transport chain, but slightly later.
• Chemiosmosis- the generation of ATP using energy released by the movement of hydrogen ions across a membrane.

Question 36

Using yeast in brewing and baking

Answer 36

1. CO2 and the baking industry: Yeast is used in baking bread as it is mixed into the dough before baking. The yeast rapidly uses up all oxygen present in the dough and then produces ethanol and CO2 by anaerobic respiration. The CO2 forms bubbles that make the dough rise. When the dough is baked, most of the ethanol evaporates and the CO2 bubbles give the bread a light texture.
2. Ethanol and the brewing and biofuel industries: Yeast can be used to produce ethanol by fermentation. The yeast is cultured in a liquid containing sugar and other nutrients, but not oxygen so it respires anaerobically. The ethanol concentration of the fluid around the yeast cells can rise to 15% before it becomes toxic to the yeast and the fermentation ends. Most of the CO2 bubbles out into the atmosphere and beer, wine and other alcoholic drinks are brewed this way. Ethanol is also produces by fermentation four use as a fuel.

Question 37

Photosynthesis

Answer 37

The production of carbon compounds in cells using light energy.

• Photosynthesis: light-dependent reactions, light-independent reactions / Calvin Cycle.
• Substrates for photosynthesis are simple inorganic substances including CO2 and water.
• CO2 is converted into carbohydrates and other carbon compounds. Energy from light is needed to do this.
• Light is absorbed by photosynthetic pigments.
• Electrons are needed to convert CO2 into carbohydrates. They are obtained by photolysis which is the splitting of water molecules. Oxygen is a waste product from the photolysis of water.

Question 38

Absorption spectra

Answer 38

A graph showing the range of wavelengths absorbed by a pigment is called an absorption spectrum.

• Chlorophyll is the main photosynthetic pigment.
• a and b chlorophyll- absorb red and blue light most effectively.
• Most of green light is reflected- looks green.

Absorption spectrum shows which wavelengths are most absorbed by a specific molecule while Action spectrum for photosynthesis shows which wavelengths are used by plants in photosynthesis.

Question 39

Action spectra

Answer 39

The percentage use of the wavelengths of visible light in photosynthesis.
The action spectra shows that there is some use of green light in photosynthesis, even though chlorophyll absorbs little of it.

Question 40

Photosynthesis and the atmosphere

Answer 40

Oxygen is a waste product of photosynthesis.
It is produced when water is split by photolysis to provide the electrons needed to convert CO2 into carbohydrates and other carbon compounds.
First organisms to release oxygen from photosynthesis into atmosphere were bacteria.
At first- little oxygen- caused dissolved iron to precipitate in oceans as iron oxide- banded iron formation.
Until 750 million years ago, then oxygen levels started to rise.

Question 41

Chromatography

Answer 41

Separating photosynthetic pigments by chromatography

1. Tear up a leaf into small fragments
2. Grind pieces of leaf with sharp sand and propanone to extract the leaf pigments
3. Transfer sample of extract to a watch glass
4. Evaporate to dryness
5. Add a few drops of propanone to dissolve the pigments
6. Build a concentrated spot of pigment from the end of the strip
7. Suspend the strip in a tube
8. Remove the strip from the tube when the solvent has nearly reached the top
9. Calculate Rf values for each pigment spot

Question 42

Light absorption

Answer 42

• Pigments such as chlorophyll absorb certain wavelengths of light- cause an electron in the pigment to be raised to a higher energy level.
• Chlorophyll molecules in the chloroplast are part of large groups of pigment molecules called photosystems.
• The two types of photosystems- I and II are located in different parts of the thylakoid membranes.

Question 43

Light-dependent reactions

Answer 43

In the thylakoid membranes in the chloroplast.

1. Electrons are excited and gain energy.
2. Electrons move from PSII to PSI (along a chain of electron carriers).
3. Electrons lost from PSII are replaced from water (water is split by Photolysis producing oxygen as waste).
4. From PSI, electrons are used to reduce NADP to NADPH.
5. As electrons pass along the electron transport chain they lose energy- causes protons to be pumped into the thylakoid space- high concentration of protons builds up in the space.
6. Chemi-osmosis- Protons then flow down the electro-chemical gradient into the stroma through ATP synthase enzymes.
7. ATP synthase makes ATP from ADP and P - making ATP requires energy but it does not release it!!!

Question 44

Light-independent reactions / Calvin cycle

Answer 44

In the stroma of the chloroplast.

• CO2 is combined with a 5C compound called RuBP forming two molecules of 3C compound Glycerate 3-Phosphate.
  This is catalysed by Rubisco- carboxylation.
• Glycerate 3-phosphate is then converted into a 3C sugar, Triose Phosphate using ATP and NADPH (both from the light dependent stage)- known as reduction as glycerate 3-phosphate gains electrons from NADPH.
• 2 molecules of triose phosphate (⅙) can then be used to make glucose.
• ⅚ of triose phosphate is used to regenerate RuBP.

Question 45

Calvin’s experiment

Answer 45

• Chlorella placed in a thin glass vessel / lollipop vessel
• Supplied with CO2 and HCO3
• 12C replaced with 14C
• Took samples of the algae at very short intervals and immediately killed and fixed them with hot methanol
• Extracted the carbon compounds and separated them by double-way paper chromatography
• Results: Found that carbon compounds in the algae contained 14C by autoradiography. More labelled glycerate 3-phosphate- 1st product, triose phosphate- 2nd product.

Question 46

Improvements in apparatus

Answer 46

1. Radioactive labelling- radioisotopes like 14C.
2. Double-way chromatography- separating and identifying compounds using a solvent and chromatography paper.
3. Autoradiography- X-ray film to find the location of radioisotopes. Using two sheets, chromatography paper and a film paper, keeping them in darkness together for several weeks and developing an X-ray film. Black pathes appear where radioisotopes are located.