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Organic Chemistry > 3.3.13 Amino acids, Proteins and DNA (A2) > Flashcards

3.3.13 Amino acids, Proteins and DNA (A2) Flashcards

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1
Q

what is the formula of the amine group?

A

H2N

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2
Q

what is the formula of the carboxyl group?

A

COOH

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3
Q

what does bifunctional mean?

A

molecule has two functional groups

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4
Q

how many different side chains are there? (amino acids)

A

20

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5
Q

what is a chiral carbon?

A

carbon with 4 different functional groups attached

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6
Q

how many of the 20 amino acids are chiral?

A

19

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7
Q

what are zwitterions?

A

molecules with both a positive and negative charge

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8
Q

what are the properties of zwitterions?

A

ionically bond due to charges
highly soluble in water
high melting points
white solids at room temp.

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9
Q

which end of an amino acid do we name it from?

A

carboxyl group end

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10
Q

state why each amino acid has a different Rf value when using TLC

A

each amino acid has different (relative) affinity/attraction to/solubility in
stationary and mobile phases

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11
Q

how can the amino acids be made visible after a TLC experiment?

A

UV light/lamp

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12
Q

which two bases in DNA form 3 hydrogen bonds between them?

A

cytosine and guanine

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13
Q

which bases in DNA form 2 hydrogen bonds between them?

A

adenine and thymine

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14
Q

what is the functional group of an amide?

A

RCONR’R’’

R - C - N - R’
O R’’

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15
Q

what is the functional group of an amine?

A

nitrogen atom with a lone pair

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16
Q

Suggest a suitable reagent for the hydrolysis of a protein (in TLC)

A

Conc HCl

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17
Q

what do amino acids react together to form?

A

peptides

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18
Q

what type of reaction happens between two amino acids?

A

condensation reaction

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19
Q

what is released in a condensation reaction?

A

molecule of water

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20
Q

what is a peptide bond?

A

secondary amide group

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21
Q

what is a peptide bond also called?

A

amide bond

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22
Q

what is a polypeptide?

A

a polymer of up to 50 amino acid residues

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23
Q

what is a protein?

A

a polymer of more than 45 amino acid residues

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24
Q

what is an amino acid residue?

A

what’s left after H2O is lost

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25
Q

how can a peptide bond / amide bond be broken?

A

heating with moderately concentrated acid or alkali

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26
Q

in living organisms how are proteins hydrolysed?

A

enzymes

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27
Q

what amount of bonds gives nitrogen a single positive charge?

A

4

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28
Q

why does nitrogen have a positive charge when it has 4 bonds attached?

A

forms a dative / coordinate bond

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29
Q

how is the alpha helix structure held together?

A

hydrogen bonds

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30
Q

what do hydrogen bonds form between in amino acid secondary structure?

A

d+ hydrogen in the N-H bond
the oxygen lone pair in the C=O bond in another amino acid residue

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31
Q

what are not included in hydrogen bonding in amino acids?

A

the R groups

32
Q

are hydrogen bonds amino acid specific? why?

A

no
R groups not involved in H bonds

33
Q

what level of protein structure is amino acid specific?

A

tertiary

34
Q

what do ionic bonds form between in tertiary structure?

A

R groups which can be ionised

35
Q

what do disulphide bridges (covalent bonds) form between in tertiary structure?

A

cysteine side chains

36
Q

what is the process of disulfide bridges forming between cysteine side chains called?

A

oxidation ( loss of H2 )

37
Q

are the hydrogen bonds involved in protein tertiary structure amino acid specific? why?

A

yes
occur between R groups containing O/N

38
Q

what happens when an amino acid is put in alkaline solution?

A

the hydrogen ion is removed from the -NH3+ group
no longer a zwitterion
only has a negative charge on the COO

39
Q

what happens when an amino acid is put in an acidic solution?

A

the COO- part of the zwitterion picks up a hydrogen ion.
no longer a zwitterion
only has a positive charge on the NH3

39
Q

what method can we use to work out which amino acids are present once we have hydrolysed the peptide?

A

chromatography
separating compounds in a soluble mixture (all soluble)

39
Q

what is a technique used to determine the secondary and tertiary structure of a protein?

A

x ray diffraction

40
Q

what are the steps in using TLC?

A
  1. Get the TLC plate but only handle on the sides
  2. Using a pencil draw the base line around 1.5cm from the bottom of the plate
  3. Put a dot of your mixture in the middle of the baseline
  4. fill beaker with 1cm cubed of solvent
  5. put the TLC plate into the beaker and use watch glass as a lid
    6.Run the chromatogram until solvent reaches near the top
  6. Remove from beaker and mark solvent front
  7. leave to dry in a fumehood
41
Q

why do we only handle TLC plates from the side?

A

to not contaminate with the proteins from our hand

42
Q

why do we leave TLC chromatograms in a fumehood to dry?

A

solvents can be toxic

43
Q

why do we use a lid for TLC?

A

prevent evaporation of the solvent

44
Q

what is a TLC plate?

A

glass plate covered in a thin layer of silicon dioxide

45
Q

how can we visualise the amino acids after TLC?

A

UV light
ninhydrin - purple stain

46
Q

name an example of a protein.

A

enzymes such as
DNA helicase
DNA polymerase
amylase

47
Q

how many reactions does one enzyme catalyse?

A

one

48
Q

what are globular proteins?

A

proteins that have a compact spherical shape

49
Q

what is the main property of globular proteins?

A

soluble in water

50
Q

where does the reaction take place in an enzyme?

A

active site

51
Q

how does the substrate bind to the active site?

A

intermolecular forces

52
Q

what do the intermolecular forces form between in enzymes and substrates?

A

R groups in the enzyme’s active site and R groups of the amino acids in the substrate

53
Q

what do the intermolecular forces do when an enzyme binds to the substrate?

A

promote the movement of electrons within the substrate
lover the Ea of the reaction

54
Q

can enzymes tell the difference between E/Z isomers?

A

yes

55
Q

how can enzymes be stopped in their reaction?

A

denaturing
blocking their active site

56
Q

what do nucleotides contain?

A

deoxyribose sugar (5C)
phosphate group
nitrogen base

57
Q

why is the sugar called deoxyribose?

A

no oxygen bound to carbon number 2

58
Q

why are the nitrogenous bases basic?

A

they have nitrogen atom which can accept a proton

59
Q

what reaction is used to create nucleotides?

A

condensation reaction

60
Q

how many molecules of water are released in the condensation of nucleotides?

A

2 per nucleotide

61
Q

how many condensation reactions happen in the creation of one nucleotide?

A

2

62
Q

what direction do DNA strands run to each other?

A

anti parallel

63
Q

what does the 2 ring base hydrogen bond to?

A

a 1 ring base

64
Q

what does the 2 ring base binding to a 1 ring base ensure?

A

the DNA structure is straight and uniform

65
Q

why is urea effective at separating the complimentary strands in DNA?

A

the amino groups are able to substitute for the H bonds in the double helix

66
Q

where is the nitrogenous base located on a nucleotide?

A

on the first carbon

67
Q

where is the phosphate group located on a nucleotide?

A

on the third carbon

68
Q

why is cisplatin called so?

A

two different substituent groups next to each other around the transition metal

69
Q

what is cisplatin?

A

anti cancer drug

70
Q

what does cisplatin do?

A

binds to DNA
distorts the shape
prevents replication
prevents cell division

71
Q

where does cisplatin bind to DNA?

A

nitrogen in two adjacent guanine bases

72
Q

which is the better ligand? water or nitrogen?

A

nitrogen

73
Q

what are the side effects of cisplatin?

A

cannot discriminate between healthy and cancerous cells
hair follicles also effected because they replicate quickly - much like cancer cells

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