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Chemistry > 6.4 - Amino Acids, Proteins and DNA > Flashcards

6.4 - Amino Acids, Proteins and DNA Flashcards

1
Q

What are the two functional groups of amino acids?

A
  • NH₂ and COOH
  • amine and carboxylic acid
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2
Q

How many naturally occurring 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

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

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4
Q

Draw a general formula ɑ-amino acids.

A
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5
Q

Are ɑ-amino acids chiral? Why?

A
  • Yes, one carbon has 4 different substituents
  • Except glycine, where R = H
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6
Q

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

A

(-) enantiomer

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7
Q

How can amino acids be synthesized industrially?

A
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8
Q

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

A
  • No
  • racemic mixture is formed as the CN‾ ion can attack from above or below the planar C=O bond with equal likelihood.
  • An equal amount of each enantiomer is formed, so no net effect on plane polarised light
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9
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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10
Q

What colour solids are most zwitterions at room temperature?

A
  • white solids
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11
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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12
Q

Define a zwitterion?

A
  • ions which have both a permanent positive and negative charge, but are neutral overall.
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13
Q

How do zwitterions occur in amino acids? Draw a general structure of one.

A
  • COOH is deprotonated → COO‾
  • NH₂ is protonated → NH₃⁺
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14
Q

What happens to amino acids in acidic conditions? Draw this.

A
  • NH₂ group is protonated
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15
Q

What happens to amino acids in alkaline conditions? Draw this.

A
  • COOH group is deprotonated
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16
Q

What is the peptide linkage?

A
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17
Q

What is a dipeptide? Draw a general one for amino acids?

A
  • two amino acids bonded together (a dimer)
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18
Q

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

A
  • polypeptides
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19
Q

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

A
  • proteins
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20
Q

What are polypeptides and proteins found in?

A
  • enzymes
  • wool
  • hair
  • muscles
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21
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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22
Q

What conditions are needed for hydrolysis to occur?

A
  • add aqueous 6 mol dm‾³ HCl
  • relux for 24 hours
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23
Q

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

A
  • sequence of amino acids in a long chain
  • bonded by covalent bonds
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24
Q

How is the primary structure represented?

A
  • sequence of 3 letter abbreviations of the amino acids
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25
Q

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

A
  • hydrolysis
  • 6 mol dm‾³, reflux for 24 hours
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26
Q

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

A
  • sequence of amino acids in a long chain
  • bonded by covalent bonds
  • forms hydrogen bonds between peptide links (meaning chain isn’t a straight line)
27
Q

What are the two options for the secondary structure?

A
  • ɑ-helix or beta-pleated sheets
28
Q

What is the tertiary shape of a protein?

A
  • ɑ-helix or beta-pleated sheet folded into a complex 3D shape
  • this is the tertiary structure
29
Q

How is the tertiary structure held together?

A
  • hydrogen bonding
  • disulfide bridge
30
Q

How does disulfide bonding occur in tertiary structures of proteins?

A
  • occurs between cysteine residues
  • cysteine contains a thiol group (-SH)
  • these groups lose their hydrogens and join together to form a disulfide bond.
31
Q

Why is the tertiary structure important?

A
  • the shape of protein molecules is vital in their function
  • e.g. for enzymes
32
Q

How can amino acids bond/be attracted to each other?

A
  • covalent bonding
  • hydrogen bonding
  • disulfide bonding
  • ionic interactions between groups on side chains
33
Q

What is a TLC plate made of?

A
  • metal or plastic plate coated with silica (SiO₂) - This is the stationary phase (solvent is mobile phase)
34
Q

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

A

solvent carries amino acids up the plate. The rate of movement depends on:
- amino acids solubility in the solvent
- its affinity for the stationary phase

35
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
36
Q

How can Rf values verify which amino acid is which?

A
  • by comparing the experimental Rf values to known/accepted values in the same solvent
  • or run pure amino acids in the same solvent and compare results to identify amino acids
37
Q

How do you find the primary structure of a protein?

A
  • hydrolyis with 6 mol dm‾³ HCl and reflux for 24 hours
  • carry out TLC to find the number and type of amino acids present
38
Q

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

A
  • various techniques, e.g. X-Ray and Diffraction
39
Q

What is an enzyme?

A
  • protein based catalysts that speed up reactions in the body
40
Q

How many reactions is each enzyme designed to catalyse?

A
  • one reaction
41
Q

What is the structure of an enzyme?

A
  • protein with tertiary structure
  • contains an active site which is specific to a certain molecule that they break down (called a substrate)
42
Q

What does the stereospecifity of enzymes mean?

A
  • the enzymes will only work on one enantiomer of a substrate
43
Q

How are enzymes denatured?

A
  • change in temperature or pH
44
Q

How does enzyme inhibition work?

A
  • a molecules with a very similar shape and structure to the substrate is devised
  • binds to enzyme’s active site
  • blocks active site therefore substrate cannot absorb to the active site - so reaction cannot be catalysed
45
Q

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

A
  • penicillin
46
Q

What are the benefits of modelling new molecules on computers?

A
  • now we understand factors that affect the shapes of complex proteins
  • we can model drugs that haven’t been synthesised, predicts their properties and design drugs that will treat a range of medical conditions
47
Q

What does DNA stand for?

A
  • Deoxyribonucleic acid
48
Q

What does DNA do?

A
  • it is present in all cells and is a blueprint from which all organisms are made
49
Q

What structure does DNA take?

A
  • a polymer with 4 monomers
  • they can be combined different
50
Q

What constitutes a nucleotide?

A
  • a phosphate ion
  • a sugar (2-deoxyribose)
  • a base (A - (adenine), C - (cytosine), G - (guanine) and T - (thymine))
51
Q

Draw a nucleotide.

A
52
Q

What forms between bases of adjacent nucleotides?

A
  • hydrogen bonding
53
Q

Which bases pair up between nucleotides?

A
  • guanine with cytosine (C and G)
  • adenine with thymine (A and T)
54
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 H₂0
55
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
56
Q

What defines the properties of the DNA molecules?

A
  • the order of the bases
57
Q

Why does DNA have a double helix shape?

A
  • 2 strands exist - these strands are held together by hydrogen bonding (between C and G, A and T)
  • the complementary DNA molecule has bases that hydrogen bond in the same order to those on another molecules → double helix shape is formed
58
Q

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

A
  • because it codes for proteins and makes all cells
59
Q

Draw the structure of cisplatin.

A
60
Q

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

A
  • Anti-cancer drug
  • bonds to strands of DNA to distort shape and prevent cell replication
  • it bonds to the nitrogen (N) atoms on 2 adjacent guanine bases
  • N atoms replace the Cl‾ ligands in a ligands substitution reaction
61
Q

What are the drawbacks of using cisplatin?

A
  • affects healthy cells that are replicating quickly
  • e.g. hair follicles - causing hair loss
  • kidney damage
62
Q

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

A
  • CH₃Br is in excess, so every H on the N atoms (and the lone pair) is replaced by a CH₃
63
Q

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

A
  • methyl ester forms the COOH groups → COOCH₃
  • NH₂ is protonated by the acid → NH₃⁺

Chemistry (24 decks)

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