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Chemistry > Unit 3: Section 8 - Amino Acids, Proteins and DNA > Flashcards

Unit 3: Section 8 - Amino Acids, Proteins and DNA Flashcards

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1
Q

What are the 2 functional groups of amino acids?

A

NH2 and COOH (amine and carboxylic acid)

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2
Q

How many naturally occuring amino acids are there in the body?

A

20

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3
Q

What type of amino acids are found in the body? What does this mean about their structure?

A

α - amino acids (alpha) it means that NH2 is always on the carbon next to COOH

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4
Q

Are α-amino acids chiral? Why?

A

Yes, one carbon has 4 different substituents - except glycerine where R = H

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5
Q

Which enantiomer do α-amino acids exist as in nature?

A

(-) enantiomer

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6
Q

How can amino acids be synthesised naturally?

A

RCHO + NH4CN -> RCH(NH2)CN via nucleophilic addition
RCH(NH2)CN + HCl + 2H2O -> RCH(NH2)COOH + NH4Cl - hydrolysis, HCl is dilute - need to reflux the reaction mixture

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7
Q

Is the product from amino acids being synthesised naturally optically active? Why?

A

No, a racemic mixture is formed as the CN- ion can attack from above or below the planar C=O bond with equal probablitity
An equal amount of each enantiomer is formed, so no net effect on the plane polarised light

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8
Q

In what form do amino acids exist as solids? What consequences does this have?

A

Zwitterions (ionic lattice) - high melting and boiling points

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9
Q

What colour solids are most zwitterions at room temperature?

A

White solids

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10
Q

Do zwitterions dissolve in water? Non-polar solvents? Why?

A

Yes, but not in non-polar solvents - due to ionic nature/polar bonds

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11
Q

What is the definition of a zwitterion?

A

Ions which have both a permanent positive and negatice charge, but are neutral overall

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12
Q

How do zwitterions occur in amino acids?

A

COOH is deprotonated -> COO-
NH2 is protonated -> NH3+

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13
Q

What happens to amino acids in acidic conditions?

A

Gains a proton on NH2 group

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14
Q

What happens to amino acids in alkaline conditions?

A

Loses a proton from COOH group

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15
Q

What is the peptide bond?

A

-CONH-

O H
= -
-C-N-

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16
Q

What is a dipeptide?

A

Two amino acids bonded together (a dimer)

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17
Q

What name is given to chains of amino acids up to 50 amino acids?

A

Polypeptides

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18
Q

What name is given to chains of amino acids with more than 50?

A

Proteins

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19
Q

What are polypeptides and proteins found in?

A

Enzymes
Wool
Hair
Muscles

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20
Q

What is the process called by which polypeptides or proteins can be broken down into their constituent amino acids?

A

Hydrolysis

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21
Q

What conditions are needed for hydrolysis to occur?

A

6 moldm^-3 HCl, reflux for 24 hours

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22
Q

What is the primary structure of a protein? How is it bonded?

A

The sequence of amino acids along the protein chain - bonded by covalent bonds

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23
Q

How is the primary structure represented?

A

Sequence pf 3 letter abbreviations of the amino acids

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24
Q

How can the primary structure of a protein be broken up?

A

Hydrolysis, 6M HCl, 24 hour reflux

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25
Q

What is the secondary strucutre of a protein?

A

The shape of the protein chain?

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26
Q

What are the 2 options for the secondary protein strucuture?

A

Alpha-helix shape or beta-pleated sheets

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27
Q

How is the secondary structure held together?

A

Hydrogen bonding e.g. between C=O and N-H groups

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28
Q

What is the tertiary shape of a protein?

A

Alpha-helix or beta-pleated sheet is folded into a complex 3D shape

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29
Q

How is the tertiary protein strucutre held together?

A
  • Hydrogen bonding (mainly)
  • Ionic interactions between R groups
  • Sulfur-sulfur bonding (disulfide bridges)
  • Van der Waals forces of attraction
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30
Q

Why is the tertiary structure of proteins important?

A

The shape of protein molecules is vital in their functions e.g. enzymes

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31
Q

How can amino acids bond/be attracted to each other? (3 main ways)

A
  1. Hydrogen bonding
  2. Ionic interactions between groups on side-chains
  3. Sulfur-sulfur bonds/disulfide bridges; 2 S atoms oxidised to form an S-S bond
32
Q

What is wool? How is it held together?

A

Protein fibre with secondary alpha-helix structure held together by hydrogen bonds

33
Q

What does wool’s structure and bonding mean for wool’s properties?

A
  • Can be stretched, H bonds extend
  • Release it and it returns to its original shape
  • Wash too hot and H bonds permanently break so garment loses its shape
34
Q

What is a TLC plate made of?

A

Plastic sheet coated with silica, SiO2
This is the stationary phase

35
Q

Describe how you would carry out thin layer chromatography

A
  1. Spot the samples onto a pencil line a few cm above the base of the TLC plate
  2. Place this in a beaker or tank, with solvent level below the pencil line
  3. Ensure there is a lid on the beaker to keep the inside saturated with solvent vapour
  4. Wait until the solvent front is almost at the top od the TLC plat; then remove from the beaker and analyse
36
Q

Why does TLC separate amino acids (or other molecules)?

A
  1. Solvent carries amino acids up the TLC plate
  2. The rate of movement depends on the balance between that amino acid’s affinity for the solvetn (solubility in it) and affinity for the stationar phase (attraction to the silicon with hydrogen bonding)
37
Q

What do you often have to do to enable the amino acids to be seen on the chromatogram?

A

Spray with ninhydrin (amino acids are colourless, ninhydrin turns their spots purple
Shine UV light on them

38
Q

How do you calculate an Rf value?

A

Distance moved by that substance divided by the distance moved by the solvent front

39
Q

How can Rf values verify which amino acid is which?

A
  1. Compare the experimental Rf values to known/accepted values in the same solvent
  2. Run pure amino acids int the same solvent and compare results to identify amino acids
40
Q

What is 2D TLC?

A
  • Uses a square TLC plate
  • Spot the amino acids in one corner, then run TLC in first solvent
  • Flip the plate through 90° and repeat TLc in a separate solvent
41
Q

What are the benefits of 2D TLC (2 main ones)?

A
  1. Separates the spots more - it is extremely unlikely that 2 amino acids will have identical Rf values in 2 solvents
  2. Gives you 2 Rf values for each amino acids; you can be more confident in verifying the identity of the amino acids when comparing to known values, as 2 Rf values can be verified
42
Q

How do you find the primary structure of a protein?

A
  1. Reflux with 6M HCl and reflux for 24 hours
  2. Carry out TLC to find the number and types of amino acids present
43
Q

How you find the secondary and/or tertiary structure of a protein?

A

Various techniques e.g. X-ray diffraction

44
Q

What is an enzyme?

A

Protein based catalyst that speed up rate of reaction by factors of up to 10^10

45
Q

How many reactions is each enzyme designed to catalyse?

A

One reaction - they are very specialised

46
Q

What is the structure of an enzyme?

A

Globular protein with a creft/crevice in it, known as an “active site” - very particular shape

47
Q

How does its structure help the function of the enzyme? What is this hypothesis known as?

A

The reacting molecules fit precisely into the active site and are held at exactly the right orientation to react
This is the lock and key hypothesis

48
Q

How else do enzymes increase the rate of reaction?

A
  • Reacting molecules form temporary bonds (via intermolecular forces) to the enzyme
  • This weakens the bonds in the molecules, promotes electron movement and lowers EA
49
Q

What does the stereospecificity of enzymes mean?

A

Active sites are so selective of the shape of substrates that only reactions involving one enantiomer are catalysed

50
Q

How does enzyme inhibition work?

A
  1. A molecule with a very similar shape and structure to the substrate is devised
  2. Binds to the enzyme’s active site
  3. Blocks the active site (does not desorb easily)
  4. Substrate cannot absorb to the active site, so reaction cannot be catalysed
50
Q

What does stereospecificity mean for most naturally occurring molecules?

A

Most naturally occurring molecules only occur as one enantiomer due to stereospecific enzymes

50
Q

How are enzymes denatured?

A

Change in temperature or PH

50
Q

What is an example of a drug that works through enzyme inhibition?

A

Penicillin

51
Q

What are the benfits of modelling new molecules on computers?

A

Now we understand factors that affect shapes of extremely complex proteins, we can model drugs that haven’t even been synthesised, predict their properties and design drugs that will treat a range of medical conditions

52
Q

What does DNA stand for?

A

Deoxyribonucleic acid

53
Q

What does DNA do?

A

It is present in all cells and is a blueprint form which all organisms are made

54
Q

What structure does DNA take?

A

A polymer with 4 monomers; they can be combined differently

55
Q

What constitutes a nucleotide?

A

A phosphate ion
A sugar (2-deoxyribose)
A base (A - adenine, C- cytosine, G - guanine, T - thymine)

56
Q

What forms between bases of adjacent nucleotides?

A

Hydrogen bonding

57
Q

Which bases pair up between nucleotides?

A

Adenine with thymine (A and T)
Guanine with cytosine (C and G)

58
Q

How does DNA polymerise?

A

OH on phosphate group and OH on number 3 carbon of 2-deoxyribose react to eliminate a molecule of H2O

59
Q

What kind of polymer does the polymerisation of DNA lead to?

A

Condensation polymer chain -> backbone of phosphate and sugar molecules, with bases attached

60
Q

What defines the properties of the DNA molecule?

A

The order of the bases

61
Q

Why does DNA have a double helix shape?

A
  • Exists as 2 strands; held together by hydrogen bonding between C and G and A and T
  • The complementary DNA molecule has bases that hydrogen bond in the same order to those on another molecule -> double helix shape is formed
62
Q

Why is it important that DNA is exactly copied when cells divide?

A

It codes for proteins and makes all cells

63
Q

How is DNA exactly copied when cells divide?

A
  • Hydrogen bonds between base pairs break
  • Covalent bonds in polymer chains remain intact
  • The sequence fo bases is maintained
  • Separate nucleotide molecules that have been created move to hydrogen bond to their relevant bases
  • They polymerise
64
Q

How does the body use information that is stored in DNA?

A
  • Template for arranging amino acids into protein chains - codes for proteins
  • “Recipe” for proteins that make up all living things; enzymes, flesh
65
Q

What is the structure of cisplatin?

A

cCntral platinum atom surrounded by two ammonia (NH₃) molecules and two chloride (Cl) ions in a square planar arrangement

66
Q

What is cisplatin’s function? How does it do this?

A
  • Anti-cancer drug
  • Bonds to strands of DNA to distort shapeand prevent cell replication
  • It bonds to the N (nitrogen) atoms on 2 adjacent G bases
  • The N atoms replace the Cl- ligands in a ligand substitution reaction
67
Q

Why are CL- ions able to be replaced by N on the base?

A
  • N atoms on the G base have lone pairs of electrons that can co-ordinately bond the the Pt ion
  • N atoms are better ligands that Cl- so replace them
68
Q

What are the drawbacks of using cisplatin?

A
  • Affects healthy cells that are replicationing quickly e.g. hair follicles
  • Thought to damage kidneys
69
Q

What happens when excess bromomethane is added to an amino acid?

A

CH3Br is in excess, so every H on the N atom and the lone pair on the N atom is replaced by a CH3 group -> quaternary ammonium ion (makes a salt with Br-)

70
Q

What happens if an amino acid is added to an excess of methanol in the presence of concentrated sulfuric acid?

A

Methyl ester forms with COOH group -> COOCH3
NH2 is protonated by the acid -> NH3+

71
Q

What does NMR stand for?

A

Nuclear Magnetic Resonance

72
Q

What are the basic principles of NMR?

A
  • Structures of complex molecules by placing them in a magnetic field and applying EM waves of radio frequency to them
  • If radio waves of the right frequency are absorbed, the nuclei flips from parallel to applied magnetic to field to anti-parallel
  • This energy change can be monitored and recorded
  • Use the resonance of nuclei with spin
73
Q

How would you carry out NMR spectroscopy?

A
  • Dissolve the liquid sample in suitable solvent, put in a tube along with a small amount of TMS and put the tube in an NMR machine
    *

Chemistry (20 decks)

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