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A-Level Organic Chemistry AQA (Paper 2) > Amino Acids, Proteins, DNA And Chromatography > Flashcards

Amino Acids, Proteins, DNA And Chromatography Flashcards

1
Q

What functional groups make up amino acids? (2)

A
  • A carboxylic acid.

* A primary amine.

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2
Q

How many important occurring amino acids are there? (2)

A
  • 20 naturally occurring - all alpha-amino acids (2-amino acids).
  • Amine group is on carbon next to -COOH.
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3
Q

Since alpha-amino acids have a chiral carbon, all naturally occurring amino acids exist as…

A

•The negative (-) (left) enantiomer.

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4
Q

What are the acid and base properties of amino acids due to? (2)

A
  • Carboxylic acid group has a tendency to lose a proton (act as a Brønsted-Lowry acid).
  • Amine group has a tendency to accept a proton (act as a Brønsted-Lowry base)
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5
Q

What are bifunctional compounds?

A

•Compounds with two functional groups.

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6
Q

What do amino acids exist as?

A

•Zwitterions.

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7
Q

What are zwitterions? (2)

A
  • Ions with a permanent +ive charge and a permanent -ive charge.
  • Neutral compound overall.
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8
Q

Since amino acids are ionic… (2)

A
  • They have high melting points.

* They dissolve well in water but poorly in non-polar solvents.

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9
Q

Describe a typical amino acid at room temperature.

A

•White solid that behaves like an ionic salt.

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10
Q

What happens when an amino acid is in strongly acidic conditions? (2)

A
  • The lone pair on the H2N-group accepts a proton to form the positive ion.
  • Amino group has gained a hydrogen ion (protonated).
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11
Q

What happens when an amino acid is in strongly basic conditions? (2)

A
  • The -OH group loses a proton to form the negative ion.

* -COOH group has lost a hydrogen (deprotonated).

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12
Q

What are polypeptides?

A

•Molecules containing up to about 50 amino acids.

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13
Q

What are proteins?

A

•Molecules containing more than 50 amino acids.

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14
Q

Give some examples of proteins.

A

•Enzymes, wool, hair and muscles.

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15
Q

When the amine of one amino acid reacts with the carboxylic acid group from another, it forms… (2)

A
  • An amide/peptide linkage -CONH-.

* And a water molecule.

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16
Q

What are peptides?

A

•Compounds formed by the linkage of amino acids.

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17
Q

What is a dipeptide? (2)

A
  • A peptide with two amino acids.

* Dipeptide still retains -NH2 and -COOH groups and can react to further give tri-, tetra-peptides.

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18
Q

What is the primary structure of the protein?

A

•When a particular protein has a fixed sequence of amino acids in its chain.

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19
Q

Why are proteins biodegradable?

A

•They can be hydrolysed.

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20
Q

What does hydrolysis usually involve?

A

•A reaction with water (often boiling) catalysed by an acid, an alkali, or an enzyme.

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21
Q

Why are polypeptides and proteins condensation polymers?

A

•A small molecule (usually) water is eliminated as each amide/peptide linkage is formed in the chain.

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22
Q

How is a protein/peptide hydrolysed? (3)

A
  • By boiling it with hydrochloric acid of a 6 mol dm^-3 conc for about 24 hours.
  • It breaks down to a mixture of all the amino acids that made up the original protein/peptide.
  • All peptide linkages are hydrolysed by acid.
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23
Q

What is the structure of proteins?

A

•Complex shapes held in position by hydrogen bonds, other intermolecular forces and sulfur-sulfur bonds.

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24
Q

What are the shapes of proteins important for?

A

•Their functions e.g. as enzymes and structural materials in living things (think biology!- specific active site etc).

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25
Q

What are the structures of proteins either? (3)

A
  • Alpha-helix.
  • Beta-pleated sheet.
  • Held together by hydrogen bonds.
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26
Q

What is wool?

A

•A protein fibre with a helix held together by hydrogen bonds.

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27
Q

What happens when wool is stretched? (2)

A
  • The hydrogen bonds stretch and the fibre extends.
  • Releasing the tension allows the hydrogen bonds to return to normal length and the fibre returns to its original shape.
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28
Q

What happens when wool is washed at high temperatures?

A

•It permanently breaks the hydrogen bonds causing the garment to permanently lose its shape.

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29
Q

What does the bonding between amino acids in a protein chain consist of? (3)

A
  • Hydrogen bonding between C=O groups and -N-H- groups: C=O—H-N.
  • Ionic attractions between groups on the side chains of amino acids e.g. -COO^- (on glutamic acid) and -NH3^+ (on lysine).
  • Sulfur-sulfur bonds (disulfide bridging) between two cysteine amino acid molecules.
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30
Q

Describe sulfur-sulfur bridging/a disulfide bridge. (3)

A
  • Amino acid cysteine has a side chain with a -CH2SH group.
  • Under suitable oxidising conditions, two cysteine molecules may react together to form a sulfur-sulfur bond that forms a bridge between the two molecules.
  • Creates a double amino acid, cystine.
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31
Q

What is the primary structure of a protein? (2)

A
  • The sequence of amino acids along a protein chain.

* Represented by three-letter names of amino acids.

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32
Q

What is the primary structure of a protein held together by? (2)

A
  • Covalent bonds - making it relatively stable.

* Requires harsh conditions e.g. 6 mol dm^-3 of hydrochloric acid to break amino acids apart.

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33
Q

What is the secondary structure of a protein?

A

•When a protein forms an alpha-helix (coiled) or a beta-pleated sheet (folded).

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34
Q

What is the secondary structure of a protein held together by? (2)

A
  • Hydrogen bonding between C=O groups and -N-H groups.
  • Hydrogen bonds are weaker than covalent bonds, so it can be relatively easily be disrupted by gentle heating or changes in pH.
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35
Q

What is the tertiary structure of a protein?

A

•When the alpha-helix or beta-pleated sheet is folded into a 3D shape.

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36
Q

What is the tertiary structure of a protein held together by?

A

•A mixture of hydrogen bonding, ionic interactions and sulfur-sulfur bonds (as wells as van der Waals forces which exist in all molecules).

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37
Q

What do many proteins fold into?

A

•Globular shapes.

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38
Q

How do you find the structure of proteins? (2)

A
  • X-ray diffraction, which locates the actual positions of atoms in space.
  • Thin-layer chromatography.
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39
Q

How do you determine the primary structure of a protein? (3)

A
  • Finding the number of each type of amino acid present in the protein.
  • Protein is refluxed with 6 mol dm^-3 of hydrochloric acid (hydrolysis).
  • Breaks the amide bonds between amino acids and results in a mixture containing all the individual amino acids in the original protein.
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40
Q

After, hydrolysis how are the amino acids separated and identified? (3)

A
  • By thin-layer chromatography (TLC).
  • Using a thin chromatography plate consisting of a thin, flexible plastic sheet coated with a thin layer of silica (silicon dioxide, SO2).
  • White powder is the stationary phase.
41
Q

What are the alternative materials for the stationary phase?

A

•Glass or aluminium sheets.

42
Q

Why are plastic sheets usually convenient to use?

A

•They can be cut to size easily.

43
Q

Describe and explain the method for the thin layer chromatography practical. (7)

A
  • 1). A small spot containing the mixture of amino acids to be separated is placed on a line 1 cm up the plate.
  • 2). Plate is placed in a tank containing a suitable solvent to a depth of 1/2 cm above the initial solvent.
  • 3). A lid is placed inside on the tank, so the inside is saturated with solvent vapour and the solvent is allowed to rise up the plate.
  • 4). When the solvent rises up it carries amino acids with it, each amino acid lags behind the solvent front to an extent that depends on its affinity for the solvent compared with its affinity for the stationary phase.
  • 5). When the solvent has almost reached the top of the plate, the plate is removed from the tank and the position to which the solvent front has moved is marked.
  • 6). Amino acids are colourless, so the positions they have moved are made visible by spraying the plate with a developing agent e.g. ninhydrin, which reacts with amino acids to form a purple compound, or by shining ultraviolet light on the plate, if the solvent is suitable, the amino acids will be completely separated.
  • 7). Calculate Rf (retention factor) values + each amino acid in the mixture is identified by comparing Rf values of each spot with the values obtained by known pure amino acids run in the same solvent mixture.
44
Q

What is the solvent (or a mixture of solvents) known as in TLC?

A

•The mobile/eluent phase.

45
Q

What does the affinity of amino acids for the solvent compared with its affinity for the stationary phase depend on? (2)

A
  • The intermolecular forces that act between the amino acid and the solvent.
  • The stronger they are, the closer the amino acid is to the solvent front.
46
Q

How do you calculate Rf?

A

Rf = distance moved by the spot/distance moved by the solvent

47
Q

What are the units of Rf values?

A

•No unit - both measurements are in cm and cancel out.

48
Q

All Rf values must be…

A

•Less than 1 because the spot cannot travel further than the solvent.

49
Q

Draw and label a diagram of thin-layer chromatography. (4)

A
  • Lid.
  • Solvent front.
  • Solvent mixture.
  • Baseline above the level of the solvent (line drawn by graphite pencil).
50
Q

What is the solvent front?

A

•The furthest point reached by the solvent.

51
Q

Why is the baseline drawn in pencil?

A

•Graphite has no interaction with the mobile phase, it will not rise up.

52
Q

Why should the TLC plate be handled with gloves?

A

•To avoid contamination from the grease/skin residue/oils affecting the Rf values.

53
Q

What happens when amino acids have very similar Rf values in a particular solvent? (4)

A
  • Use 2-dimensional TLC - plate is spotted and chromatogram is run in usual way to separate the spots.
  • Plate is turned through 90º and chromatogram is run again with a different solvent.
  • Makes it easier to see the separation between the spots and gives two Rf values (for each solvent).
  • Both values should match a known amino acid.
54
Q

What are enzymes?

A

•Protein-based catalysts found in living things.

55
Q

What is the usual structure of enzymes? (2)

A
  • Globular proteins.

* Shape has a cleft or crevice = active site where reaction takes place.

56
Q

What is the lock and key model?

A

•Substrates fit precisely in the active site of an enzyme and are held in the right orientation to react.

57
Q

What happens when an enzyme and its complementary substrate come into contact? (2)

A
  • Substrate bonds temporarily by intermolecular forces.
  • Whilst bonded, IMFs promote the movement of electrons within the substrate that lower the activation energy for the reaction.
58
Q

What is stereospecificity? (2)

A
  • When the active site of an enzyme can be so selective of the shape of a substrate that many enzymes only catalyse reactions of one or other of enantiomers.
  • = Stereoisomers.
59
Q

Draw and label a diagram to show a substrate bonding to the active site of an enzyme. (5)

A 
•Substrate. 
•Active site. 
•Hydrogen bonds. 
•Positive and negative attraction. 
•Variable R groups. 
(See textbook page 466)
60
Q

What can enzymes be denatured by?

A

•Changes in temperature and pH = different hydrogen/ionic/sulfide bonds made in tertiary structure.

61
Q

What is enzyme inhibition? (2)

A
  • Devising a molecule of a similar shape to the enzyme’s substrate.
  • Molecule will bind to enzyme’s active site.
62
Q

Draw and label a diagram for competitive inhibition of an enzyme. (4)

A

•Substrate molecule occupying active site of enzyme.
•Substrate molecule unable to occupy the active site.
•Enzyme molecule.
•Inhibitor molecule occupying the active site of enzyme.
(See textbook page 466)

63
Q

What does the drug penicillin inhibit?

A

•Enzymes that control the building of cell walls in bacteria.

64
Q

How are chemists beginning to understand factors that influence the shapes of proteins? (3)

A
  • Computer modelling techniques to predict the shapes of proteins before they have been synthesised.
  • Properties predicted.
  • Helps to design drugs used in treatment of medical conditions.
65
Q

What is a single strand of DNA?

A

•A polymer made from four different monomers.

66
Q

What are nucleotides?

A

•Monomers of DNA.

67
Q

What is a DNA nucleotide made up of? (3)

A
  • Phosphate group.
  • Organic base (G, C, A or T).
  • Pentose sugar - 2-deoxyribose.
68
Q

How do two nucleotides link together?

A

•Condensation polymerisation - when an -OH group of a phosphate on one nucleotide reacts with an -OH group on a sugar molecule on another nucleotide molecule to eliminate a water molecule.

69
Q

When many nucleotides are linked together…

A

•A sugar-phosphate backbone is formed

70
Q

How does a DNA molecule exist? (2)

A
  • As two strands held together by hydrogen bonding to form a double helix.
  • G and C (3 hydrogen bonds); A and T (2 hydrogen bonds) = complementary base pairs for hydrogen bonding.
71
Q

Hydrogen bonds are only about 10% strength of covalent bonds, what does this mean for DNA?

A

•They can break under conditions that leave the covalent bonds of the DNA chain unaffected.

72
Q

Describe a brief summary of semi-conservative replication. (3)

A
  • Hydrogen bonds of DNA double helix break and strand starts to unravel but covalently bonded chains remain intact retaining the sequence of bases.
  • Cell contains free nucleotides which pair with complementary bases on the exposed template = linked together by sugar-phosphate backbone.
  • Results in two new DNA molecules.
73
Q

What is the DNA sequence used for?

A

•To transcribe and translate new proteins which could be enzymes involved in the control of metabolic reactions.

74
Q

What is Cisplatin?

A

•An anti-cancer drug.

75
Q

What is the shape of Cisplatin?

A

•Square planar.

76
Q

How does cisplatin work? (6)

A
  • By bonding to strands of DNA, distorting their shape and preventing replication of the cells.
  • Molecule bonds (platinum) to nitrogen atoms on two adjacent guanine bases on a strand of DNA.
  • Nitrogen atoms of guanine molecules have lone pairs of electrons, which form dative covalent bonds with the platinum.
  • Chloride ion ligands in cisplatin are displaced by water.
  • Water ligands are then displaced by nitrogen on guanine as nitrogen is a better ligand. (Ligand substitution reaction)
  • Pt binds to N in two guanines in DNA in place of chloride ligand, preventing cell replication.
77
Q

What are the side effects of cisplatin? (2)

A
  • It will bond to DNA in healthy cells as well as cancerous ones, but cancerous cells replicate faster = greater effects on cancer.
  • Cells that replicate quickly e.g. hair follicles are significantly affected, so results in hair loss.
78
Q

What is chromatography? (2)

A
  • Describes a whole family of separation techniques.
  • Depend on the principle that a mixture can be separated if it is dissolved in a solvent and the resulting solution (mobile phase) moves over a solid (stationary phase).
79
Q

What is the mobile phase? (3)

A
  • Carries the soluble components of the mixture with it.
  • The more soluble the component, the faster it moves.
  • Solvent known as eluent (in column chromatography).
80
Q

What is the stationary phase? (2)

A
  • Will hold back components in the mixture that are attracted to it.
  • The more affinity a component in the mixture being separated has for the stationary phase, the slower it moves with the solvent.
81
Q

What is thin-layer chromatography? (2)

A
  • Filter paper is replaced by a glass, metal or plastic sheet coated with a thin layer of silica gel (silicon dioxide, SiO2) or alumina (aluminium oxide, Al2O3) - acts as stationary phase.
  • Known as plates which can be cut to size.
82
Q

What are the advantages of TLC over paper chromatography? (4)

A
  • Runs faster.
  • Smaller amounts of mixtures can be separated.
  • Spots usually spread out less.
  • Plates are more robust than paper.
83
Q

What is column chromatography? (4)

A
  • Uses a powder e.g. silica, aluminium oxide or resin as stationary phase.
  • Packed into a narrow tube, column, and solvent (eluent) is added to the top.
  • As the eluent moves down the column, the components of the mixture move at different rates and can be collected separately in flasks at the bottom.
  • More than one eluent may be used for better separation.
84
Q

What is the advantage of using column chromatography?

A

•Fairly large amounts can be separated and collected e.g. a mixture of amino acids can be separated into its pure compounds.

85
Q

Draw and label a diagram of column chromatography. (4)

A 
•Eluent. 
•Powdered solid (stationary phase). 
•Components moving down column. 
•Mineral wool plug.
(See textbook page 497)
86
Q

What is gas-liquid chromatography? (3)

A
  • Stationary phase is powder, coated with oil, either packed into or coated onto the inside of a long capillary tube, up to 100m long and less than 1/2 mm in diameter coiled up and placed in an oven whose temperature can be varied.
  • Mobile phase = unreactive gas e.g. nitrogen or helium.
  • After injection, sample is carried along by the gas and the mixture separates as some of the components move along with the gas and some are retained by the oil each at a different degree.
87
Q

What is measured in gas-liquid chromatography? (2)

A
  • Retention times - components leave the column at different times after injection.
  • Identification is by matching retention time of component with a known substance under the same conditions, then by comparing the mass spectra of the two substances.
88
Q

Draw and label a diagram of gas-liquid chromatography. (6)

A 
•Sample injection. 
•Detector. 
•Carrier gas.
•Spiral tube containing stationary phase. 
•Variable temperature oven. 
•Detector to chart recorder/PC. 
(See textbook page 497)
89
Q

How are the results for gas-liquid chromatography presented? (2)

A
  • On a graph - detector measures thermal conductivity of emerging gas, area under each peak is proportional to the amount of the component.
  • Sometimes components are fed directly into a mass spectrometer, infrared spectrometer or NMR spectrometer for identification.
90
Q

What is gas-liquid chromatography used to separate and identify? (3)

A
  • Minute traces of substances in foodstuffs.
  • Link crude oil pollution found on beaches with its tank of origin, by comparing oil samples.
  • Athletes’ blood or urine for drug taking.
91
Q

What is gas chromatography-mass spectrometry (GCMS)? (3)

A
  • Mass spectrometer used as the detector for a gas chromatography system.
  • As each component of the mixture comes out of the gas chromatography column, the time it has taken to pass through the column (retention time) is noted.
  • Each component is fed automatically into mass spectrometer - enables compound to be identified by its fragmentation pattern or by measuring its accurate mass.
92
Q

*What is high pressure/performance liquid chromatography (HPLC)? (4)

A
  • When mixture to be separated is forced through a column containing the stationary phase by a solvent driven by a high-pressure pump.
  • Pump drives the solvent (eluent) rather than gravity.
  • Variety of materials can be used as the stationary phase including chiral ones that can separate optical isomers.
  • Detection methods vary e.g. UV light.
93
Q

Draw and label a schematic diagram of a HPLC system. (7)

A 
•1). Solvent (mobile phase) reservoir.
•2). Pump. 
•3). Sample injector. 
•4). HPLC column. 
•5). Detector. 
•6). Chromatogram computer. 
•7). Waste.
(See textbook page 499)
94
Q

Which nitrogens on the organic bases form hydrogen bonds in DNA? (2)

A
  • Nitrogen in 6 carbon ring in guanine and thymine.

* Nitrogen in 5 carbon ring in cytosine and adenine.

95
Q

Draw and label a diagram of a DNA nucleotide repeating unit. (2)

A
  • PO4, -O- coming off P.

* - Coming off deoxyribose sugar to show repeating unit.

96
Q

Why would trans-platin not stop DNA replication?

A

•It is in the wrong orientation/geometry to bind to two guanines on opposite strands so it cannot hold DNA strands together.

97
Q

What do 3 prime and 5 prime ends in DNA refer to?

A

•The number of carbon atoms the phosphate group is bonded to.

98
Q

Polypeptide chains are held together by hydrogen bonding. Explain how these hydrogen bonds form.

A

•The electron deficient hydrogen attracts a lone pair of electrons on the oxygen. (Between N-H and O=C)

A-Level Organic Chemistry AQA (Paper 2) (17 decks)

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