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Introduction to Molecular Biochemical Techniques > Module 2 - Proteins > Flashcards

Module 2 - Proteins Flashcards

1
Q

Do saturated fatty acids have double bonds?

A

No

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2
Q

Do unsaturated fatty acids have double bonds?

A

Yes

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3
Q

What is the role of double bonds in fatty acids?

A

They make unsaturated fats fluid, ensuring the smooth functioning of the membrane

No double bonds -> long + rigid chain blocking chemicals into cell -> floats around body as cholestrol

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4
Q

Which can be used by the body for energy: glucose or fructose?

A

glucose

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5
Q

How are ring monosaccharides formed?

A

The aldehyde or ketone group of a sugar molecule reacts with a hydroxol (-OH) group closing the molecule into a ring

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6
Q

Isomers

A

Molecules with differences in the arrangement of atoms resulting in changes in chemical properties

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7
Q

Example of 2 isomers

A

glucose and galactose

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8
Q

Hydrolysis

A

the addition of a water molecule

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9
Q

Condensation

A

the removal of a water molecule

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10
Q

What are the building blocks of proteins?

A

amino acids

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11
Q

What are the building blocks of fats?

A

fatty acids

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12
Q

What are the building blocks of nucleic acids?

A

nucleotides

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13
Q

What are the building blocks of polysaccharides?

A

sugar units

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14
Q

Signalling molecules (ligands)

A

molecules carrying a message that bind to specific receptors

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15
Q

Ion channels

A

pore-forming membrane proteins allowing ions to pass through

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16
Q

Ion pumps

A

modulate ion transport in + out of a cell or organelle

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17
Q

Transmembrane carriers

A

involved in the movement of ions + molecules across the membrane

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18
Q

What are molecuels accompanied by when passing through a membrane?

A

proteins

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19
Q

Chaperones

A

helps hydrophilic molecules to travel over hydrophobic membrane by binding to partially folded polypeptide chains, helping them to progress along the most energetically favourable folding pathway

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20
Q

Example of chaperon

A

insulin for glucose

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21
Q

Enzymes

A

protein acting as a catalyst in the movement of ions and molecules across the membrane

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22
Q

Antibodies

A

protein made by plasma blood cells (a type of white blood cell) in response to an antigen (= substance causing the body to make a specific immune response)

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23
Q

What happens if even 1 of the components of a receptor changes?

A

neurotransmitter loses affinity for it

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24
Q

What happens when a ligand (e.g. NT) binds to a receptor?

A

ligand-gated ion channel opens allowing ion to flow across the plasma membrane, ultimately changing the configuration of the receptor

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25
Q

What determines the 3D shape of a protein?

A

amino acid sequence

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26
Q

What determines the function of a protein?

A

its shape

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27
Q

What is the structure of an amino acid?

A

1) general core structure
2) side chain making it a unique amino acid

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28
Q

What makes up the general core structure of an amino acid?

A

1) amino group (H2N)
2) carboxyl group (COOH)
3) H atom

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29
Q

What happens when an amino acid is ionized?

A

It becomes neutral - H from the carboxyl group moves to the amino group resulting in COO (-) and H3N (+)

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30
Q

What do isomers have in common?

A

Identical melting + boiling temperatures, densities and solubilities - differ in chemical reactivity

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31
Q

What are the 2 types of isomers of amino acids?

A

D and L amino acids

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32
Q

What amino acid isomer is used by the body

A

L amino acids

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33
Q

Are hydrophilic amino acids polar/covalent or non-polar?

A

polar (unequal sharing of electrons btw atoms)

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34
Q

Are hydrophobic amino acids polar or non-polar?

A

non-polar (electron pair is shared equally between the two bonded atoms)

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35
Q

What are the 3 categories of hydrophilic amino acids?

A

1) basic
2) polar with uncharged R groups
3) acidic

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36
Q

Example of basic hydrophilic amino acid

A

lysine

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37
Q

Example of hydrophilic polar amino acid with uncharged R group

A

asparaginine

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38
Q

Example of hydrophilic acidic amino acid

A

aspartic acid

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39
Q

Example of hydrophobic amino acid

A

trytophan

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40
Q

Example of special amino acid

A

glyceine

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41
Q

Covalent bond

A

two atoms share electrons between themselves

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42
Q

Non-covalent bond

A

either exchange electrons or do not exchange electrons at all

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43
Q

Where are hydrophobic amino acids located?

A

centre of a protein

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44
Q

Where are hydrophilic amino acids located?

A

surface of a protein

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45
Q

Hydrophobic amino acids have __ side chains

A

long

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46
Q

Hydrophilic amino acids have __ side chains

A

short

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47
Q

Why is water polar?

A

Because of its shape - H ends of the molecule are (+) charged and the O end is (-) charged

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48
Q

Why do H2O molecules attract each other and other polar molecules?

A

Because of its shape - H ends of the molecule are (+) charged and the O end is (-) charged

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49
Q

Peptide bonds aka

A

amide bond

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50
Q

How is a peptide/amide bond formed?

A

amine group (H3N) of one amino acid bonds with the carboxyl group (COOH) of another -> condensation reaction -> peptie bond formed

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51
Q

What kind of bond links amino acids?

A

peptide/amine bonds

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52
Q

What are proteins (chain of amino acids) made up of?

A

1) polypeptide backbone
2) amino terminus (N-terminus)
3) carboxyl termines (C-terminus)
4) amino acids linked by peptide bonds

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53
Q

What are the 2 ends of a chain of amino acids?

A

1) amino/N terminus
2) carboxyl/C terminus

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54
Q

What is the backbone of a chain of amino acids

A

polypeptide backbone

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55
Q

What kind of bonds are involved in the folding of a protein (tertiary structure)?

A

non-covalent (e.g. hydrogen) between side chains

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56
Q

Primary level of protein structure

A

linear sequence of amino acids

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57
Q

Secondary level of protein structure

A

the localized organisation of parts of a polupeptide chain (e.g. the alpha helix or beta sheet)

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58
Q

Tertiary level of protein structure

A

3D arrangement of polpeptide chain

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59
Q

Quaternary level of protein structure

A

association of 2 or more polypeptides into a multi-subunit complex

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60
Q

How are alpha-helices formed?

A

Hydrogen bonds: the N-H of every peptide bond is hydrogen bonded to the C = O of the neighbour peptide bond, forming a spiral helix

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61
Q

Where are alpha-helices found?

A

cell membrane proteins e.g. receptors

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62
Q

What determines whether a protein’s secondary structure is an alpha helix or beta sheet?

A

ribosomes

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63
Q

What determines where proteins are used

A

ribosomes

free ribosomes -> protein used in the cell

endoplasmic reticulum ribosomes -> proteins out of the cell are packaged to be used in the cell membrane

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64
Q

How are beta sheets formed?

A

Hydrogen bonds (H + O) formed in a polypeptide chain in a way that forms either a chain running in the direction opposite to that of its neighbours (antiparallel chains - so it folds on itself) OR neighbouring segments o the polypeptide backbone running in the same orientation (parallel chains)

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65
Q

What is a coiled-coil motif?

A

2 or more helices wound around one another

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66
Q

How are coiled-coil motifs formed?

A

form when 2 (or more) helices have most of their non-polar (hydrophobic) side chains on one side, so they can twist around eachother with these side chains facing inwards

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67
Q

What kind of bonds help proteins maintain folding?

A

covalent bonds (e.g. disulfide)

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68
Q

How are proteins secreted from a cell?

A

through the extracellular matrix

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69
Q

What are protein domains?

A

functional protein domains - complex structure + unique function

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70
Q

Example of a quaternary level structure protein

A

Hemoglobin = 2 alpha-globins and 2 beta-globins

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71
Q

Protein families

A

a similar structure (amino acid sequence) but differ in function

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72
Q

Native state of protein

A

molecules of any protein adopt a single conformation known as the native state, which is the most stably form of the molecule

72
Q

Native state of protein

A

molecules of any protein adopt a single conformation known as the native state, which is the most stably form of the molecule

72
Q

Native state of protein

A

molecules of any protein adopt a single conformation known as the native state, which is the most stably form of the molecule

73
Q

Proteasome

A

proteins that degrade unneeded or damaged proteins through the ubiquitination process

74
Q

3 steps of an enzymatic reaction

A

1) substrate binding (-> enzyme-substrate complex)
2) product formation (-> enzyme-product complex)
3) product release (-> product released from enzyme)

75
Q

Hydrolases

A

catalyze hydrolytic cleavage reaction

76
Q

Nucleases

A

break down nucleic acids by hydrolizing bonds between nucleotides

77
Q

Proteases

A

break down proteins by hydrolyzing bonds between amino acids

78
Q

Isomerases

A

catalyze the rearrangement of bonds with a single molecule

79
Q

Polymerases

A

catalyze polymerization reactions e.g. synthesis of RNA

80
Q

Kinases

A

catalyze the addition of a phosphate group to molecules

81
Q

Phosphatases

A

catalyze hydrolytic removal of a phosphate group from a protein i.e. dephosphyrylation

82
Q

Oxido-reductase

A

one molecule is oxidized while the other is reduced

83
Q

ATPases

A

hydrolyze ATP

84
Q

As concentration increases, the rate of an enzymatic reaction

A

increases and then plateaus when substrate-binding sites on the enzyme molecules are occupied

85
Q

What is the relevane of enzyme kinetics?

A

can we inhibit or slow them down

86
Q

Thorium

A

a rate-limiting enzyme in SE synthesis that determines how much SE will be produced

87
Q

Competitive inhibitor

A

competes with substrate at the active site of an enzyme - it linearly increases the rate of the reaction in contrast to if there was no inhibitor present (which eventually plateaus)

88
Q

What are the 2 ways in which proteins are regulated?

A

1) reversible binding of other molecules
2) protein phosphorylation: covalent addition of a phosphate group to 1 or more of its amino acid side chains

89
Q

Non-competitive inhibitor (allosteric modulator)

A

does not bind to active site but another site -> works similar to if there was no inhibitor present but it slows down the reaction and plateus at a lower point

90
Q

What 4 ways can enzyme activity be regulated?

A

1) allosteric transitions
2) phosphorylation/dephosphorylation
3) proteolytic activation
4) compartmentalization

91
Q

Purpose of phosphorylation

A

vital for cellular storage + transfer of free energy using energy carrier molecules

92
Q

Proteolytic activation

A

activating an enzyme by peptide cleavage i.e. breaking peptide bonds

93
Q

Compartmentalization

A

storing enzymes in specific compartments to keep them from doing damage or provide the right conditions for activity

94
Q

How do antibodies function?

A

bind tightly with high specificity to a target molecule, inactivating it directly or making it for destruction

95
Q

Antigen

A

target of antibody

96
Q

What is the purpose of cell lysis?

A

to free the content of the cell so proteins are in the solution

97
Q

What do you need for cell lysis?

A

lysis buffer

98
Q

What components of the lysis buffer enable the solubilizing of the cell membrane?

A

Igepal + triton

99
Q

What component of the lysis buffer stabilizes the protein?

A

glycerol

100
Q

What components of the lysis buffer enable enzyme inhibition?

A

EDTA + EGTA

101
Q

What components of the lysis buffer inhibits the removal of a phosphate group i.e. acts as a phophatase inhibitor?

A

Trisodium vanadate + sodium fluoride

102
Q

Denatured proteins are

A

looser + more random in structure

102
Q

Denaturation

A

modifying protein structure by breaking weak hydrogen links

103
Q

What is the purpose of bicinchoninic acid (BCA) sodium salt?)

A

interacts with copper in a complex non-covalent interaction in a basic environment (BCA-Copper reaction) to give a blue colour

104
Q

Blueness is proportional to

A

amount of peptide bonds present in proteins

105
Q

Steps of BCA-copper reaction

A

1) Peptide bonds of a protein in a basic environment complex a bivalent Cu2+ ion in a way that it become monovalent, Cu1+, and stabilizes the bond
2) BCA molecules take over Cu1+ ion to make a complex with 2 BCA molecules which turn blue by absorbing a lot of light

106
Q

What is sodium dodecylsulphate (SDS)?

A

denaturing agent that is (-) charged enabling proteins to migrate into electrical field

107
Q

Polyacrylamide Gel Electrophoresis (PAGE)

A

induction of movement by an electric field

108
Q

What is the goal of SDS-PAGE?

A

to separate protein based on molecular weight

109
Q

Upper part (stacking) of gel is _ charged

A

negatively

110
Q

Lower part (running) of gel is _ charged

A

positively

111
Q

What 2 gels are used in SDS-PAGE

A

1) running
2) stacking

112
Q

What is the pH of the running gel and what does that contribute?

A

The pH of the running gel is 8.8 (more acidic)

113
Q

What is the purpose of the stacking gel being negatively charged?

A

causes them proteins to move slower

114
Q

What is the purpose of the running part of the gel being positively charged?

A

causes them to more faster through the gel leaving proteins behind

115
Q

What causes proteins to move through the gel?

A

negative charge

116
Q

What is the function of TEMED in SDS-PAGE

A

acts as a catalyst of the chemical reaction, reduces need for energy in the reaction

117
Q

What is the function of ammonium persulfate (APS) in SDS-PAGE?

A

initiate reaction

118
Q

What is the function of Polymerized acrylamide (polyacrylamide) in SDS-PAGE?

A

forms a mesh-like matrix suitable for the separation of proteins of typical size

119
Q

What are the components of the running/stacking gel in SDS-PAGE?

A

1) milliQ water
2) acrylamide
3) tris hydrochloride (8.8 + 6.8)
4) SDS
5) APS
6) TEMED

120
Q

Large proteins move __ through the gel

A

slower

121
Q

Small proteins move __ through the gel

A

faster

122
Q

What determines how quickly proteins move through the gel in SDS-PAGE?

A

size

123
Q

Purpose of glycine in SDS-page?

A

pushes proteins into running gel

124
Q

What is Coomassie staining? What is its purpose

A

It is a blue dye that stains proteins - the more faint the less protein bonds present, the more blue the more present

125
Q

What molecular weight marker do we look at in Coomassie staining?

A

kDa (1kDa = 100 Da)

126
Q

How do you calculate dilution factor of a concentration of lysate?

A

substitute average absorption of the 3 wells for each dilution as y into the line of best fit

127
Q

How do you calculate the total protein concentration?

A

add dilution factors together

128
Q

How do you prepare lysate?

A

1) aspirate medium (move to another tube)
2) wash cells left with PBS twice gently to remove external proteins
3) add lysis buffer to flask and incubate on use for 2 minutes
4) scrape external proteins using cell scraper on bottom of flask)
5) triturate the lysate and transfer to eppendorf tube
6) incubate for 30 mins on ice vortexing every 5 minutes

129
Q

How do you prepare dilutions of lysate?

A

combine with lysis buffer in eppendorf tubes depending on desired concentration e.g. 50% would be 25 ul of lystae + 25 ul of lysis buffer

130
Q

What protein standard was used in protein determination of SDS-PAGE?

A

Bovine Serum Albumin (BSA)

131
Q

How do you make dilutions of your protein?

A

Mix 50 ul BSA with 450 ul lysis buffer to get a concentration of 4mg/ml, then mix 250 ul BSA with 250 ul lysis buffer to get a concentration of 2mg/ml and continue A-H dilutions

132
Q

How do you measure the absorptions of your protein assay?

A

Biorad plate reader

133
Q

Ideal wavelength for SDS-PAGE?

A

655nm

134
Q

Why is TEMED added last minute to gels?

A

Will start polymerizing the protein if added before

135
Q

What do the chemical properties of the protein depend on?

A

sequence of side-chain group

136
Q

How are disulfide bridges made?

A

oxidation - adding an oxidant

137
Q

How are disulfide bridges broken?

A

reduction - adding a reductant

138
Q

Ubiquitin

A

small molecule placed on the protein that marks misfolded proteins to be broken down

139
Q

Michaelis constant (Km)

A

amount of substrate we must add to have half of the enzyme’s activity

140
Q

Substrate inhibition

A

too much substrate -> enzyme loses activity, slows down

141
Q

Product inhibition

A

the product of the enzyme interferes with the binding site of the substrate

142
Q

What property of proteins do we use to measure the total amount of proteins?

A

peptide bonds

143
Q

Purpose of antibodies

A

used by the immune system to identify and neutralize foreign objects

144
Q

What are the 2 regions of an antibody

A

1) constant
2) variable

145
Q

Purpose of constant region of an antibody

A

contains antigen binding sites

146
Q

Purpose of variable region of an antibody

A

binds to immune cell receptor

147
Q

Constant region has __ chain

A

heavy

148
Q

Variable region has __ chain

A

light

149
Q

What are antibodies made up of?

A

multiple proteins joined by disulfide bridges

150
Q

Hypervariable loop of the variable region

A

light chain; sequence of amino acids different between antibodies (each antibody is specific to one kind of antigen); present at the end of both arms

151
Q

Specificity of binding of a monoclonal antibody

A

Binds to a specific epitope on an antigen

152
Q

Specificity of polyclonal antibodies

A

aspecific binding: binds to all epitopes because they can recognize other molecules that are only a little bit different

153
Q

Specificity of monoclonal anitbodies is __ and of polycloncal is __

A

high, low

154
Q

Sensitivity of monoclonal antibodies is __ and of polyclonal is __

A

low, high

155
Q

Monoclonal antibodies are used in

A

smaller animals e.g. mice

156
Q

Polyclonal antibodies are used in

A

larger animals e.g. rabbits

157
Q

What are antibodies produced from

A

B/immune cells

158
Q

How are monoclonal antibodies formed?

A

1) mouse injected with a specific antigen coupled to an immunogenic carrier protein -> production of antibodies induced
2) mouse sacrificed to enable isolation of immune cells (each with one kind of antibody)
3) immune cells are coupled to tumorous cells to form hybridomas (can live forever)
4) Hybridomas are screened for the production of desired antibody
5) anti-body producing hybridomas are cloned -> monoclonal antibodies

159
Q

How are polyclonal antibodies formed?

A

1) animal injected with antigen coupled to immunogenic carrier protein
2) after 12 weeks, blood taken, blood purified to get different antibodies, they recognize different parts and sides of 1 antigen

160
Q

Primary antibodies

A

bind directly to epitope of antigen they are built against

161
Q

Secondary antibodies

A

bind to heavy chain of primary antibody they are built against

162
Q

Direct detection of antibody

A

primary antibody is directly conjugated to a label

163
Q

Indirect detection of antibody

A

primary antibody is bound by a labelled secondary antibody that has been against the host species of the primary antibodies

164
Q

Pro + con of direct antibody detection

A

high specificity, low sensitivity

165
Q

Pro + con of indirect antibody detection

A

high sensitivity, low specificity

166
Q

Chromogenic detection (enzyme labelling)

A

work through chromogenic reactions i.e. soluble + colourless substrate (e.g. DAB) is converted into an insoluble chromogenic (colorful) product

167
Q

Example of chromogenic detection

A

Horseradish peroxidase (HRP) - hydrogen peroxide H2O2 (which is produced in the mitochondria and is highly reactive) is transformed into water by peroxidase

  1. Secondary antibody is conjugated with HRP
  2. A solution with DAB and hydrogen peroxide is added
  3. A side chain group of one amino acid from HRP binds to the hydrogen peroxide, converting the hydrogen peroxide into water resulting in a cascade of reactions
168
Q

Fluorescence detection

A

fluorescent molecules capture energy from a light source and release it in the form of a photon - when receiving energy, their electrons will move to a higher orbit and will then fall back, releasing the energy they got in the form of light

169
Q

Which one is more durable? chromogenic or fluorescence detection

A

chromogenic since fluorescent molecules decay over time

170
Q

Which one only shows one target? chromogenic or fluorescence

A

chromogenic

171
Q

What happens if more targets are done in chromogenic?

A

risk of overlap

172
Q

Why can multiple targets be used in fluorescence detection?

A

shows different colours

173
Q

Which can be analysed quicker? chromogenic or fluorscence

A

chromogenic (other is more complicated but more accurate)

174
Q

Which is cheaper? chromogenic or fluorescence?

A

chromogenic

175
Q

How do we decide between chromogenic and fluorescence detection?

A

depends on which the primary antibody we are looking at works best with

Introduction to Molecular Biochemical Techniques (4 decks)

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