practice questions

Question 1

would binding of a fluorescently labelled small molecule to a protein result in an increase or decrease in the FP signal

Answer 1

increase

Question 2

for a useful fluorescence polarization (FP) assay should the fluorescence lifetime be longer or shorter than the molecular tumbling time

Answer 2

longer

Question 3

would a competing ligand that displaces a bound fluorescent ligand increase or decrease the signal in an FP competition assay

Answer 3

decrease

Question 4

would a rapidly tumbling exited molecule exhibit low or high fluorescence polarisation

Answer 4

low

Question 5

what happens when the fluorescently labeled protein is small during FP

Answer 5

the molecule will rotate more rapidly in solution leading to lower polarisation because the emitted florescence is less likely to be aligned with exitation light

Question 6

what happens when the fluorescently labeled protein is large during florescence polarisation

Answer 6

the molecule will rotate more slowly resulting in higher polarisation

Question 7

do low frequency electromagnetic waves have high or low:
wavelength
energy
wavenumber

Answer 7

high (long) wavelength
low energy
low wavenumber

Question 8

do high frequency electromagnetic waves have low or high:
wavelength
energy
wavenumber

Answer 8

low (short) wavelength
high energy
high wavenumber

Question 9

what can uv/visible absorption spectroscopy be used to do

Answer 9

measure concentration of a protein
measure rate of reaction
study the secondary structure of proteins by circular dichroism

Question 10

A protein sample has an absorbance at 280nm of 0.3. Approximately what percentage of the incident light is transmitted by the sample?

Answer 10

(use beer lambert law)
50%

Question 11

A protein sample has an absorbance at 280nm of 0.1. Approximately what percentage of the incident light is transmitted by the sample?

Answer 11

(use beer lambert law)
79%

Question 12

what is the delta G value for irreversible reactions

Answer 12

non-zero

Question 13

define an irreversible reaction

Answer 13

the reactants/products are held away from equilibrium

Question 14

are irreversible reactions used as regulation points in metabolic pathways

Answer 14

yes

Question 15

are proteins thermodynamically stable

Answer 15

no

Question 16

are proteins kinetically stable

Answer 16

yes

Question 17

are proteins dynamic

Answer 17

yes

Question 18

is the conformational space of a polypeptide highly restricted

Answer 18

yes

Question 19

do secondary structures utilise the full hydrogen bonding potential of the amino acid side chains

Answer 19

no

Question 20

do secondary structures promote protein folding by compensating for loss of hydrogen bonding interactions with water

Answer 20

yes

Question 21

are secondary structures only stable in the context of the folded protein

Answer 21

yes

Question 22

do secondary structures promote formation of favorable side chain interactions

Answer 22

yes

Question 23

for alpha helixes what is the number of residues per turn

Answer 23

3.6

Question 24

for beta sheets what is the number of residues per turn

Answer 24

3.2

Question 25

roughly what angles are found in beta sheets and strands

Answer 25

-120, 120

Question 26

'The carbonyl group of residue n Hydrogen bonds with the amide group of residue n + 4' is this a feature of beta sheets or alpha helix

Answer 26

alpha helix

Question 27

are beta pleated sheets or beta strands more extended

Answer 27

beta pleated sheets

Question 28

are parallel or antiparallel beta sheets more stable

Answer 28

antiparallel

Question 29

can beta sheets be amphipathic

Answer 29

yes

Question 30

what is the molten globule state

Answer 30

an early intermediate in the protein folding pathway

Question 31

does hydrophobic collapse significantly reduce the conformational space of the polypeptide chain

Answer 31

yes

Question 32

does the secondary structure formation promote protein folding

Answer 32

yes

Question 33

does protein folding promote secondary structure formation

Answer 33

yes

Question 34

can protein folding get trapped in local minima

Answer 34

yes

Question 35

what is the kyte and doolittle hydropathy scale

Answer 35

method used to estimate the hydrophobicity or hydrophilicity of amino acids based on their chemical properties by quantifying them

Question 36

is the kyte and doolittle hydropathy scale based on experimental free energy values

Answer 36

yes

Question 37

is the kyte and doolittle hydropathy scale based on the average syrface accessibility of different amino acid side chains in protein crystal structures

Answer 37

yes

Question 38

is the kyte and doolittle hydropathy scale based on free energy calculations on protein structures

Answer 38

no

Question 39

did kyte and doolittle tweak the values on their hydropathy scale to reflect their own experiences

Answer 39

yes

Question 40

when an amide bond forms between amino acids is water released

Answer 40

yes

Question 41

is the formation of an amide bond between amino acids spontaneous

Answer 41

no

Question 42

does the formation of an amide bond between amino acids require ATP hydrolysis

Answer 42

yes

Question 43

are amide bonds kinetically stable

Answer 43

no

Question 44

does the formation of an amide bond between amino acids have a positive delta G value

Answer 44

yes

Question 45

do the names of all enzymes end in the suffix 'in'

Answer 45

yes

Question 46

how do enzymes speed up rates of reaction

Answer 46

by altering the position of equilibrium to favour products

Question 47

are all enzymes proteins

Answer 47

yes

Question 48

do enzymes speed up the rate of both the forwards and backwards reaction

Answer 48

yes

Question 49

is the rate of an enzyne catalysed reaction always directly proportional to temperature

Answer 49

yes

Question 50

is the rate of an enzyme catalysed reaction always directly proportional to pH

Answer 50

no

Question 51

does the free energy between transition state and the reactants have to be negative

Answer 51

no

Question 52

can the transition state be stabilised by covalent catalysis

Answer 52

yes

Question 53

does the transition state represent the ES complex

Answer 53

no

Question 54

does the transition state analougues convert the transition state to a stable thermodynamic state

Answer 54

yes

Question 55

what is michaelis constant (Km)

Answer 55

a measure of the enzyme-substrate binding affinity

Question 56

is Michaelis constant (Km) the [S] that half-saturates the enzyme

Answer 56

yes

Question 57

what state should enzymes preferentially bind to to increase rate

Answer 57

transition state

Question 58

can enzymes have optimal pHs at temperatures as high as 100 degrees

Answer 58

yes

Question 59

do enzymes reduce gibbs free energy change for the reaction

Answer 59

no

Question 60

do irrerversible enzyme inhibitors permanently inactivate the enzyme

Answer 60

no

Question 61

do irreversible enzyme inhibitors inhibit competitively

Answer 61

yes

Question 62

do irreversible enzyme inhibitors maximise product by minimising ES->E+P

Answer 62

yes

Question 63

can sufficiently high concentrations of substrate override inhibition from irreversible enzyme inhibitors

Answer 63

yes

Question 64

can irreversible enzyme inhibitors be reversed by removing the inhibitor

Answer 64

yes

Question 65

what is the substrate concentration if an enzyme has a Km value of 1mM and the initial rate is less than 76% of the maximal velocity

Answer 65

3.17mM

Question 66

does RNA occur primarily as single stranded molecules that can give rise to stem loops

Answer 66

yes

Question 67

what % A and C does a double stranded DNA fragment usually contain

Answer 67

A - 12% C - 38%

Question 68

how wide is a B-form DNA duplex

Answer 68

2nm

Question 69

is a double stranded DNA helix always right handed

Answer 69

no

Question 70

how long would a double stranded DNA need to be to encode a 100 residue protein

Answer 70

1020A

Question 71

how many turns of B-form DNA duplex are required to encode 187 residue protein

Answer 71

56

Question 72

is this statement true: a -form DNA duplex x nm long can encode a protein containing at most x amino acids

Answer 72

true

Question 73

is this statement true or false: a stretch of dsDNA 34nm in length is required to encode a 100 residue protein

Answer 73

false

Question 74

is this statement true or false: to encode a protein measuring x Å in size requires a B-form DNA duplex measuring at least 3x Å long

Answer 74

true

Question 75

does the DNA helix stabilise hydrogen bonds between phosphate groups

Answer 75

no

Question 76

does the DNA helix stabilise through stacking interactions

Answer 76

yes

Question 77

does the DNA helix stabilise hydrogen bonds between base pairs

Answer 77

yes

Question 78

does the DNA helix stabilise favorable electrostatic interactions

Answer 78

yes

Question 79

does the DNA helix stabilise hydrogen bonds between the 5' and 3' hydroxyl groups

Answer 79

no