Question 11
QPCR that employs a TaqMan probe also uses 2 standard, external [1]. During each cycle of PCR, after denaturation, the TaqMan probe anneals to the template DNA. During the extension stage, Taq DNA polymerase destroys the probe using the enzyme's [2]prime to [3]prime [4] activity. While the probe is intact (either in solution or annealed to template DNA) the fluor is in close proximity to a [5] (which is also part of the probe) and so no [6] is observed. However, once the probe has been destoyed, the [7] is released from the [8] and so can be detected by the QPCR machine. QPCR employing a TaqMan probe is specific to the gene/sequence of interest, because the probe can only [9] with that specific sequence. If that sequence is absent, the probe cannot be broken down by Taq and so no [10] is released.

Specified Answer for: 1primers
Specified Answer for: 2 5
Specified Answer for: 3 3
Specified Answer for: 4 exonuclease
Specified Answer for: 5 Quencher
Specified Answer for: 6 fluorescence
Specified Answer for: 7 fluorescence
Specified Answer for: 8 probe
Specified Answer for: 9 hybridise
Specified Answer for: 10 fluorescence

Question 12
Which eleven (11) of the following amino acids can form hydrogen bonds with their side groups? Please note that partial credit has been disallowed for this question (owing to BB marking anomalies) - you therefore need to get all 11 right in order to score the marks.

Selected Answers:

aspartic acid
glutamic acid
histidine
lysine
asparagine
glutamine
arginine
serine
threonine
tryptophan
tyrosine
Answers:
alanine
cysteine
aspartic acid
glutamic acid
phenylalanine
glycine
histidine
isoleucine
lysine
leucine
methionine
asparagine
proline
glutamine
arginine
serine
threonine
valine
tryptophan
tyrosine

Question 13
Chromatogrpahic strategies other than ion exchange chromatography include:

1. [1] chromatography, in which proteins stick to the column according to their [2] and are
eluted in a [3] gradient from [4] to [5] concentration at constant pH

2. [6] in which proteins elute from the column according to their [7] and are eluted on a [8]
gradient

3. [9] chromatography in which there is no gradient. Proteins are simly eluted according to
[10].

Specified Answer for: 1 Hydrophobic interaction
Specified Answer for: 2 hydrophobic interactions
Specified Answer for: 3 salt
Specified Answer for: 4 high
Specified Answer for: 5 low
Specified Answer for: 6 Isoelectric focusing
Specified Answer for: 7 isoelectric points
Specified Answer for: 8 pH
Specified Answer for: 9 Size exclusion
Specified Answer for: 10 size

Question 18
Fill in the following table concerning the number of proteins encoded when doing saturation mutagenesis:

No. of codons

No. of encoded proteins
1 [1]
2 [2]
3 [3]
4 [4]
5 [5]
6 [6]

Where the numbers to be completed represent the numbers of different protein sequences.

Your answers should be numerical and should be written out in ful (ie avoiding powers)

Specified Answer for: 1 20
Specified Answer for: 2 400
Specified Answer for: 3 8000
Specified Answer for: 4 160000
Specified Answer for: 5 3200000
Specified Answer for: 6 64000000

Question 11 QPCR that employs a TaqMan probe also uses 2 standard,...