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Bioc 192 > Bioc 192 2-21 > Flashcards

Bioc 192 2-21 Flashcards

1
Q

Are proteins branching or non-branching polymers??

A

Non-branching

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2
Q

What bonds bind amino acids together??

A

Peptide bonds

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3
Q

How does the different patterns of the amino acids do??

A

determine the folding and shape of the protein

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4
Q

What amino acid forms disulfide bonds?

A

Cystine

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5
Q

what 3 processes determine protein shapes?

A

crystallography, cryo-electron microscopy, NMR.

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6
Q

what does ‘ase’ mean in the protein name?

A

the protein is an enzyme

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7
Q

What is the basic function of hemoglobin?

A

protein that transports oxygen by binding to it from the lungs and carries it in the blood to tissues for use

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8
Q

What is the basic function of insulin?

A

protein hormone that binds to insulin receptors signalling cells to take up glucose.

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9
Q

what is the basic functions of hexokinase?

A

protein used for metabolism by adding a phosphate to glucose in the cell.

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10
Q

What do kinase add to molecules?

A

phosphates

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11
Q

what is the basic function of trypsin?

A

protein used for digestion by breaking down proteins

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12
Q

what are enzymes called that break down proteins?

A

proteases

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13
Q

what is the basic function of HIV protease?

A

essential for HIV replication as viruses and bacteria make proteins too

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14
Q

what is the basic function of amylase?

A

protein used in digestion, enzyme that breaks down starch into sugars

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15
Q

where is the amylase found in the body?

A

salivary glands and the pancreatic juices

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16
Q

what is the basic functions of alcohol dehydrogenase?

A

protein that is used in metabolism and helps to metabolize ethanol

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17
Q

what is the basic functions of ATP synthesis?

A

a membrane protein that generates ATP that is used in cellular functions

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18
Q

what is the basic functions of antibody?

A

protein used in immune protection by binding to cellular invaders to stop infections

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19
Q

what is the basic functions of DNA polymerase?

A

the protein used in replication and maintenance as it binds to one strand and adds a complementary strand.

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20
Q

what is the basic functions of RNA polymerase?

A

protein used in replication and maintenance as it creates a single strand of RNA that is complementary to one of the strands of duplex DNA

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21
Q

what is the dumb down version of a cell?

A

a bag of proteins, lipids and nucleic acids.

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22
Q

what does chiral mean?

A

can form mirror images

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23
Q

what is the two mirror images produced in chiral amino acids?

A

L-form dominates
D-form can appear

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24
Q

what is a zwitterion?

A

has a negative and positive charge attached to it

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25
Q

what are the 4 groups of the amino acids side chains?

A

polar, non-polar, positive, negative

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26
Q

what are non-polar amino side chains?

A

mostly hydrocarbon side chains
they are hydrophobic
when the side chain loops back around it makes the amino acid very rigid.

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27
Q

what are 2 polar amino side chains?

A

can be charged or uncharged

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28
Q

what 2 things can charged amino acid side chains be?

A

either positive or negative

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29
Q

what are uncharged amino side chains?

A

at pH 7 which are important for hydrogen bonding
they are hydrophillic

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30
Q

are negatively charged side chains acidic or basic?

A

acidic

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31
Q

are positively charged side chains acidic or basic?

A

basic

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32
Q

what happens in ionisable amino acids?

A

we change the pH of the environment of the amino acid.
this changes the protein
the charge can change depending on the pH

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33
Q

how do we classify ionisable side chains?

A

by their pKa value

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34
Q

what does a smaller pKa mean?

A

a stronger acid

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35
Q

what is pI (isoelectric point)?

A

where the pH at which the net charge on an amino acid is zero

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36
Q

can non-polar amino acids be ionizable?

A

nope

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37
Q

what does PTM do?

A

helps modify the protein to behave differently

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38
Q

what is a post-translational modification (PTM)?

A

a chemical group that can be added to an amino acid residue after translation has occured.
this is added via covalent attachment

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39
Q

what is phosphorylation?

A

PTM
often used to control enzyme activity like a chemical on/off switch

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40
Q

what is hydroxylation?

A

PTM
needed to prevent connective tissues diseases and scurvy

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41
Q

what is carboxylation?

A

PTM
needed for blood clotting

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42
Q

what is glycosylation?

A

adds sugar to the haemoglobin and can be used to detect diabetes

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43
Q

what are peptides?

A

short, single amino bonds
a polypeptide is a long chain that it folds up and forms a protein.

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44
Q

what are amino acid residues?

A

amino acids covalently joined together in a peptide or protein.
this is because they are no longer complete, individual amino acids.

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45
Q

are proteins more long straight chains or more globular?

A

globular

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46
Q

what are the 4 levels of protein structure?

A

primary, secondary, tertiary and quanternary

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47
Q

what is a primary protein structure?

A

the linear sequence of amino acids that make up a polypeptide.

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48
Q

what is a secondary protein structure?

A

the 3-D arrangment of a protein chain over a short stretch

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49
Q

2 examples of secondary protein strutures?

A

A-helices and B-sheets

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50
Q

what is a tertiary protein structure?

A

the 3-D structure of a complete protein chain

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51
Q

what is a quanternary protein structure?

A

interchain packing that contains multiple polypeptide chains

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52
Q

what is a phi angle?

A

rotation angle around the N-Ca bond

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53
Q

what is a psi angle?

A

rotation angle around the Ca-C bond

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54
Q

what is the rotation angle around the peptide bond called?

A

omega

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55
Q

what is the purpose of the bond angles?

A

to not have polypeptide colliding and causing a steric hindrance.

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56
Q

what do phi rotation lead to?

A

O-O collision

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57
Q

what do psi rotation lead to?

A

NH-NH collision

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58
Q

why are peptide bond usaully trans but can sometimes be cis?

A

to avoid steric hinderance

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59
Q

what leads to its overall 3-D structure?

A

the combination of all the rotations and twists around all the bonds
this inturn leads to the function of the protein.

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60
Q

what are the 2 dominant secondary protein structures?

A

A-helices, B-sheets

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61
Q

what is an alpha helix?

A

the main chain spirals around the central axis with non-covalent interactions

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62
Q

why are there non-covalent interactions in a-helices?

A

this is because there is a small charge so they form non-covalent interactions themselves.

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63
Q

what direction do alpha helices point in a protein?

A

outwards of the helix

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64
Q

what way do the a-helix dipoles run?

A

in the same direction

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65
Q

what does the negativly charged end of the A-helix bind to?

A

phosphate groups

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66
Q

what are B-strands?

A

stretches of amino acids that extend further than the a-helix

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67
Q

what stabilizes B-sheets?

A

hydrogen bonds which occur between adjacent strands

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68
Q

around how many amino acids are in each of the B-strands?

A

around 6 amino acids

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69
Q

what decides if the B-strand is parrallel or antiparallel?

A

the hydrogen bonding pattern

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70
Q

what are the 2 alternative B-strands?

A

polar, non-polar

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71
Q

what does a parallel B-strands look like?

A

when the strands run in the same direction

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72
Q

what does an anti-parallel B-strand look like?

A

when the strands run in opposite directions

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73
Q

what is a B-pleated sheet?

A

like a paper fan shape with a slight twist to the left

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74
Q

what are turns?

A

turns are an element that links together to change the direction of a polypeptide

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75
Q

what are the 2 things that allow turns to happen?

A

phi and psi angles

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76
Q

what are coils?

A

just longer turns

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77
Q

what are supersecondary structures?

A

a collection of secondary structure but not the entire fold of the protein

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78
Q

what is a helix-turn-helix?

A

2 alpha helices that are connected by a turn

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79
Q

what is a B-hairpin?

A

they are antiparallel sheets that are connected by a small turn
they look like hairpins

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80
Q

what is a greek key?

A

has 4 anti-parallel strands that start in the middle and is connected by small loops to make a B-sheets

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81
Q

what is a strand-helix-strand?

A

a combination of alpha helices and beta structures
the B-strand runs parallel
the B-strand can still form hydrogen bonds as the helix is on a different plane

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82
Q

what do super secondary structures form?

A

domains

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83
Q

what are domains?

A

independantly folded regions of super secondary structures that have a specific function

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84
Q

what are the 3 types of domain functions?

A

a-domain
a-domain family globin
a/b family

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85
Q

what are a-domains?

A

consists of 4 a-helical structures which forms a 4 helix bundle
they have a hydrophobic core and a hydrophillic outside
the helical structures are connected by small loops

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86
Q

what are a-domain family globins?

A

a fold that is an amphipathic helices with side chains packed closely within the hydrophobic core

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87
Q

what are a/b family domains?

A

a mixture of a-helices and b-structures to form a barrel shape with a hydrophobic center and a hydrophillic outside

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88
Q

what domains are mostly used to transport molecules?

A

b-barrel
these are mostly b-structures as the interior is hydrophobic

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89
Q

what do domains fold into?

A

tertiary structures

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90
Q

what does nature do with domains?

A

reuses them and combines them with other domains to make proteins with different functions

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91
Q

what is the anfinsen experiment?

A

breaking of the ribonuclease by breaking the disulfide bonds and making a long chain and watching it fold back to its original shape

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92
Q

what forces folding pathways of amino acids?

A

hydrophobic molecules forming hydrophillic walls

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93
Q

what are 2 factors that stabilise protein folding?

A

non-covalent interactions and disulfide bonds

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94
Q

what are chaperone proteins?

A

able to help polypeptides fold
can put the polypeptide in a bin to apply extra help to fold

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95
Q

how does protein unfolding occur?

A

when the non-covalent bonds break and denature

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96
Q

how to denature a protein?

A

by using heat or changing the pH

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97
Q

what can misfolding a protein do?

A

changes the shape and can aggregate the protein which can lead to brain damage

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98
Q

what are misfolded proteins called?

A

prions

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99
Q

what are prions?

A

a to b transformation and can cause diseases
there is no treatment and can be fatal

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100
Q

how much more oxygen can hemoglobin carry compared to saline?

A

25 times

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101
Q

where does haemoglobin reside?

A

in the muscle

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102
Q

how much oxygen can haemoglobin store for?

A

enough for around a 7 second sprint

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103
Q

what is myoglobin?

A

a 8 a-helices structure that folds to make a hydrophobic pocketto bind the haem molecule which gives the molecule its function

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104
Q

what is the structure of haem?

A

4 pyrrole rings linked together in a plane where they bind an iron atom
this binds to the nitrigen atom of histidine F8 and the other side binds to the O2 groupi

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105
Q

is the binding of the O2 group reversible?

A

yes

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106
Q

what do we use to find the concentration of oxygenated haemoglobin?

A

spectroscopy

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107
Q

what does the spectroscopy of haemoglobin find?

A

2 peaks in the oxygenated state and 1 in the deoxygenated state

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108
Q

why do proteins change shape?

A

to allow oppotunity to change activity

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109
Q

what does allosteric control mean?

A

controlling without overlapping
can be used by any protein to change shape

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110
Q

why is myoglobin easier to be saturated than haemoglobin?

A

Myoglobin binds to oxygen better and tighter
myoglobin does not need as much before it soaks up the molecules

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111
Q

why does haemoglobin change shape?

A

to release the oxygen that is binded to the haemoglobin eaiser

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112
Q

what is co-operativity when talking about haemoglobin?

A

when all 4 structures of the haemoglobin symaltaneouslyget used instead of working one at a time.

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113
Q

what are the2 states of haemoglobin?

A

T state
R state

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114
Q

what is the T state?

A

Tense state

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115
Q

what is the R state?

A

Relaxed state

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116
Q

what is the ‘KNF’ sequential model show?

A

the first subunits that bind making it harder for the other subunits to bind
MWC model works better

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117
Q

what structures make haemoglobin a tertramer?

A

2 copies of an alpha chain and 2copies of a beta chain

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118
Q

what does the tetrameric state allow?

A

communication between chains as a change of shape

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119
Q

what does oxygen binging deform?

A

the shape of the chain which tells the next shape that is oxygen bound

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120
Q

what shape is deoxygenated haem?

A

a dish shape

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121
Q

what shape is oxygenated haem?

A

a planar shape

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122
Q

how does the oxygen binding to the haem change its shape?

A

the Fe atom is dragged down which pulls the histine F8 and distorts the shape of the protein

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123
Q

why does the R state of heme have a high affinity?

A

because the heme has oxygen bound to it
(oxyhaemoglobin)

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124
Q

why does the T state of heme have a low affinity?

A

because the heme is most likely not binded to an oxygen atom (deoxyhaemoglobin)

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125
Q

how do the interactions between the chains lead to the main change of heme?

A

the subunits get further apart as the oxygen binds which changes the shape and the angle which leads to a change in interactions of subunits.

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126
Q

what happens when subunits get further apart?

A

they form a binding site for biphosphoglycerate invetween all the subuits

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127
Q

what is biphosphogylcerate (BPG)?

A

its highly negatively charged signalling molecule which tells haemoglobin what ti do such as move to the T state

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128
Q

where does BPG bind?

A

to the positive sidechains of the beta chains and the BPG stabilizes the hemoglobin and can move the haemoglobin from the R state to the T state to release the oxygen atoms

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129
Q

when is BPG produced?

A

through respiration and is found where the oxygen is required more

130
Q

what is the bohr effect?

A

CO2 or low pH pushes haemoglobin to the T state to release the oxygen

131
Q

how do foetuses recieve oxygen?

A

they catch it as it moves across the placenta so they have a higher affinity than there mothers.

132
Q

why do foetuses use gamma subunits rather than beta subunits?

A

this is a less positive binding site for the BPG so it a weaker bind so the protein spends more time in the R state
so the foetus can draw what it needs across the placenta

133
Q

what is methaemoglobin?

A

the oxidation from Fe2+ to Fe3+
this only occurs if we strip the electrons off the heme and we get a non-functioning heme
this decreases the amount of oxygen the protein can carry

134
Q

what can be used to reduce the metgaemoglobin?

A

an enzyme will make the Fe3+ go to Fe2+

135
Q

what does it mean if the delta G is less than 0?

A

negative
spontaneous
energy released

136
Q

what does it mean if the delta G is greater than 0?

A

positive
non-spontaneous
energy required

137
Q

what does it mean if the delta G is equal to 0?

A

Its at equilibrium and nothing works

138
Q

what do spontaneous reactions pass through?

A

high-energy transition states

139
Q

what is the activation energy?

A

the energy difference from reactants to the transitional state

139
Q

how do we get to the transitional state?

A

we have the achieve the activation energy

140
Q

how do enzymes catalyse the reaction?

A

by lowering the transitional state

141
Q

what does lowering the transitional state do?

A

speeds up the rate of reaction

142
Q

what do we call the enzyme that lowers the transitional state?

A

protein catalyst

143
Q

what do proteins require to help catalyse reactions?

A

non-protein factors that are called co-factors

144
Q

what are the 2 main classes of co-factors?

A

metal ions
co-enzymes

145
Q

what are metal ions?

A

good electron receptors so they help with acid/base catalysis
they also co-ordinate compounds so reactants are positioned well

146
Q

what are co-enzymes?

A

small organic molecules that come from vitamins
good at donating a proton to a phosphate group that needs it

147
Q

what is pyridoxal phosphate (PLP)?

A

a co-enzyme of glycogen phosphorylase

148
Q

what are enzyme active sites?

A

where enzymes bind to substates
they have amino acid side chains projecting into it
binds to substates via several weak interactions

149
Q

why do we want weakish bonds between the enzymes and the substate?

A

makes it easier for the complex to met the transitional state

150
Q

what are ionic bonds?

A

these make use of charged side chains

151
Q

what are hydrogen bonds?

A

side chains or backbone of O and N atoms can often act as hydrogen bond donor and acceptors

152
Q

what are Van der waals interactions?

A

between any protein and substrate atoms in close proximity
these are the weakiest of the interactions

153
Q

what are covalent bonds?

A

these are relatively rare and are stronger than the other bonds

154
Q

what happens when the active site becomes substrate bound?

A

changes shape as the enzyme induced a fit for the substrate

155
Q

what are the 2 factors that decrese the activation energy?

A

ground state destabilisation
transition state stabilisation
both of these reduce the amount of activation energy for the reaction

156
Q

what are catalytic mechanisms?

A

preferential binding of the proximity and orientation effects are both common to all entry ways

157
Q

what is preferential binding of the transitional state?

A

is when an enzyme should bind, the transitional state more tightly than it binds to the substrate

158
Q

what is proximity and orientation effects?

A

needs 2 molecules that are going to react to be close together and in correct orientation

159
Q

what does acid-base catalysis require?

A

involves proton transfer which requires side chains that can donate or accept protons

160
Q

what is metal ion catalysis?

A

its cofactors at active sites
these metals provide substate orientation so will interact as specific co-ordination geometry
they are able to act as a lewis acid (electron acceptor) to polarise functional groups

161
Q

what is covalent catalysis?

A

less common
these involve the formation of a reactive, short-lived intermediate, which is covalently attached to the enzyme

162
Q

what is spectrophotometry?

A

gives us a way of measuring compounds in a solution

163
Q

how do we compare enzymes to another?

A

we measure the progress curve

164
Q

what is the Vmax of a curve?

A

the top point of the progress curve
this is the maximum possible velocity when we have as much substrate as possible

165
Q

what is the initail velocity of the progres curve?

A

the linear phase of the progress curve

166
Q

what is it when the curve becomes non-linear?

A

when the reactants are running out and products are reduced over time

167
Q

what is the Vo proportional to?

A

the enzyme concentration

168
Q

what is the first order kinetics?

A

rate depends on substrate concentration

169
Q

what is the zero order kinetics?

A

rate does not depend on substate concentration

170
Q

what is the Km?

A

the substrate concentration at half of the Vmax
this is called the Michaelis constant

171
Q

what happens if we have a lower Km?

A

the less substrate the enzyme needs to hit the Vmax
this means its an efficient enzyme

172
Q

how do we get a lineweaver-burk plot?

A

if we plot one over the velocity by one over the substrate concentration

173
Q

what are the intercepts on a lineweaver burk plot?

A

y-intercept is 1 over the Vmax
x-intercept is -1 over Km

174
Q

what does the Km mean?

A

characterize one enzyme-substrate pair

175
Q

what does the Kcat mean?

A

the turnover number which is the number of substrate molecules converted into a product

176
Q

why do we want a higher Kcat?

A

to have the higher ability to turnover a lot of substrate into product per second

177
Q

why do we want a high Km?

A

to have a low substrate concentration required to get up to speed

178
Q

what do enzyme inhibitors do?

A

bind to enzymes and reduces its activity when the enzymes isn’t necessary

179
Q

examples of inhibitors in nature?

A

drugs, piosons and toxins

180
Q

what are the 2 classes of enzyme inhibitors?

A

irreversible and reversible

181
Q

what do irreversible enzyme inhibitors do?

A

bind to the enzyme and are permanently inactivated the enzyme is no longer working

182
Q

what do reversible enzyme inhibitors do?

A

bind to the enzyme but then can subsequently be released so the enzyme can continue working

183
Q

what are competitive inhibitors?

A

competes directly with the substrate for the active site of the enzyme
enzymes cant bind to both at the same time

184
Q

what are transition state analouges?

A

these are competitive inhibitors

185
Q

what are non-competitive enzyme inhibitors?

A

they bind at a different site than the substrate
can bind to the substrate and the inhibitor at the same time

186
Q

what happens to Vmax and the Km in the presence of non-competitive present?

A

the Vmax decreases and the Km does not change

187
Q

how is AMP a mode of enzyme regulation?

A

AMP binds to an allosteric binding site which allows feedforward activation

188
Q

5 methods of enzyme regulation?

A

covalent modification
allosteric effects
proteolytic cleavage
turn gene expression on and off
degrades the enzyme

189
Q

what can be activated or inhibited by different substrates?

A

proteins

190
Q

what is pharmocology?

A

the study of effects of drugs on b iological systems from a molecular level through to a patient study

191
Q

what is toxicology?

A

closely related to pharmacology but specializes in the study of the harmful effects of drugs and other chemicals

192
Q

what is the definition of binding or reception?

A

chemical substance interacts with its target protein
the binding event affects the protein to either activate it or inhibit it and leads to a cellular response

193
Q

what is a receptor?

A

a chemical protein that control chemical signalling between and within cells

194
Q

at least one third of drugs activate or inhibit what?

A

receptors

195
Q

what are enzymes?

A

have one active site that binds to substrates
they change the substrate into a product and can be membrane bound or free in cytosol

196
Q

what are receptors?

A

have several binding sites that binds to ligands
they release ligands unchanged and can be membrane-bound or free in cytosol

197
Q

what are the 3 receptor classes?

A

ligand-gated ion channels
G protein-coupled receptor
receptor tyrosine kinase

198
Q

what is a ligand?

A

a chemical substance that specifically binds to a receptor
They are very diverse in chemical structure

199
Q

what is the first step of reception?

A

chemical substances

200
Q

what is the second step of reception?

A

binding to reception protein

201
Q

where are most of the receptors on the cell located?

A

on the outer cell membrane so the receptors are in the extracellular enviroment

202
Q

what is the third step of reception?

A

causes activation or inhibition

203
Q

what is the chemical substance (ligand) called that binds to a receptor?

A

agonist

204
Q

what is the fourth step of reception?

A

changes cellular response (activation)

205
Q

what is signal transduction?

A

active receptor starts a chain of events where messages are passed on through the cell

206
Q

what is the name of the ligand that binds to a receptor and prevents activation of an agonist?

A

its called an antagonist

207
Q

what does the antagonist do?

A

prevents the agonist from activating so signal transduction does not work

208
Q

what are chemical signals called?

A

second messengers or through sequential phosphorylation

209
Q

what are second messengers?

A

they transmit the signals from a receptor to other molecules because they are not attached to the membrane

210
Q

are ligands first or second messengers?

A

first

211
Q

what is phosphorylation?

A

a widespread mechanism for regulating protein activity where protein kinase transfer phosphates from ATP to a protein

212
Q

what is dephosphorylation?

A

the removal of a phosphate group from a protein to control signal transduction

213
Q

what is a phosphorylation cascade?

A

where multiple protein kinase are being active at once to make a cellular response

214
Q

what is internalisation?

A

where the receptor is removed from the cell surface through endocytosis so it can no longer respond to a ligand

215
Q

what does GPCR mean?

A

G protein coupled receptor

216
Q

what happens when the G protein starts transduction?

A

this activates the G protein which communicates with other proteins in the cell

217
Q

what is Gai?

A

inhibitory G protein that decreases the activity of adenylate cyclase

218
Q

what is a G protein?

A

guanine nucleotide-binding protein
it has a heterotrimeric shape which has 3 different sub units (alpha, beta, gamma)

219
Q

what is alpha s?

A

stimulatory of the adenylate cyclase

220
Q

what is alpha i?

A

inhibitory of the adenylate cyclase

221
Q

what does an activated adenylate cyclase?

A

produces our secondary CAMP

222
Q

what does CAMP do?

A

activates the protein kinase which begins the phosphorylation cascade

223
Q

what is glycogen receptor signal transduction?

A

when the receptor activation causes G protein activation and further signal tranduction events, leading to the breakdown of glycogen breakdown

224
Q

what does GLP-1 receptor signal tranduction do?

A

when the receptor activation causes G protein activation and further signal transduction events, leading to insulin secretion

225
Q

what does receptor tyrosine kinase?

A

phosphorylation of adaptor proteins to start signal transduction
when the ligand binds, the receptor changes conformation and becomes activates.

226
Q

what do adaptor proteins do?

A

communicate with other proteins within the cell

227
Q

what is ligand gated ion channels?

A

they don’t have relay proteins as ions directly to produce effects so this signal transduction is faster than the other

228
Q

What is DNA?

A

a double helical structure that encodes proteins within a cell

229
Q

what does the cell do within the enviroment?

A

break molecules, generates energy, and maintain itself

230
Q

what are the percentages of cells within a human?

A

50% protein
40% lipids
10% carbohydrates

231
Q

what forms macromolecules?

A

building block proteins

232
Q

what building blocks make what macromolecules?

A

carbon chains - lipids
sugars - complex carbohydrates
amino acids - proteins
sugar + base - nucleic acids

233
Q

what do macromolecules make?

A

supramolecular assemblies and they go on and make our organelles

234
Q

what does our DNA encodes proteins?

A

puts mechanisms together to make more complex structures

235
Q

what is regulation to do with proteins?

A

being able to control and regulate within a cell to help make things happen

236
Q

how are proteins made from DNA?

A

bits of DNA transcribe and translate to form the protein

237
Q

what is transcriptional control?

A

determines when and in what cell a gene is transcribe to produce the mRNA

238
Q

what are the transcription factors?

A

they are proteins that bind to a specific DNA sequence and control the rate of transcription (DNA to RNA)

239
Q

what is the promotor region?

A

the region of the gene that proteins can bind to

240
Q

what is the transcribed region?

A

the sequence of DNA that are copied into RNA (transcribed)

241
Q

what is RNA polymerase?

A

an enzyme that is at the beginning of the transcribed region

242
Q

how are mRNA made?

A

transcription factors interact with eachother and recruits the RNA polymerase to make mRNA

243
Q

what is leptin?

A

a hormone that binds to a receptor which changes the confirmation of the protein
this can be used to regulate a gene within a cell

244
Q

what are mendels 3 laws?

A

law of segregation
law of independant assortment
law of dominance

245
Q

where are the 2 genetic instructions from?

A

one from our mum and one from our dads

246
Q

what is the differences in our genes called?

A

alleles

247
Q

what is the law of segregation?

A

The alleles are separated so that the gametes carries only one allele from each gene

248
Q

what is the law of independant assortment?

A

one gene occurs independantly to that of any other gene

249
Q

what is recombination of a gene?

A

the reshuffling of the DNA which provides more variation so alleles are assorted more independently

250
Q

what is the law of dominance?

A

some alleles are dominant while others are recessive
an organism with atleast one dominant allele will display this trait

251
Q

what is a dominant allele?

A

can mask not having a recessive allele and can compensate for not having the allele

252
Q

what are the consequences of not being able to breakdown pheylalanine?

A

leads to intellectual disability, seizures, behavioral problems an mental disorders

252
Q

what is phenotype?

A

is the physical trait that is shown

253
Q

what is translation?

A

when each tRNA carries an amino acid to be added to the polypeptide chain.

254
Q

what are the codons?

A

are within the coding region of the mRNA which specify the amino acid sequence of the polypeptide chain

255
Q

what is translation initiation?

A

starts with a small ribosomal subunit binds to mRNA

256
Q

what is elongation?

A

when the codon recognises and binds to the ‘A site’
the peptide bond formation changes from the ‘P site’ to the ‘A site’

257
Q

what is termination?

A

when the ribosome reaches a stop codonm on the mRNA
This release factor promotes hydrolysis and clears the other sites and everything dissociates

258
Q

what is PKU?

A

when your mum and dad have a mutation and cant form phenylalanine hydroxylase and results in phenylalanine

259
Q

what do pancreatic beta cells do?

A

sense how much glucose is in the blood and releases insulin when glucose is high

260
Q

what is glucokinase?

A

senses how much glucose is broken down therefore how much insulin is produced

261
Q

what happens if there is a mutation to the glucoskinase?

A

can lead to hyperglycaemia which is a type of diabetes

262
Q

what does PCR (polymerase chain reaction) do?

A

amplifies a specific gene sequence and then they detect genetic differences of intrest
it heats up the DNA to 95 degress to sequence the DNA strands then cools to 65 degress to anneal a DNA primer. the DNA is then heated to 72 degress to aloow taq DNA polymerase to copy the DNA

263
Q

what is a primer?

A

a short sequence that is chemically synthesized

263
Q

what is hindIII?

A

a restriction enzyme that specifically cuts the sequence AAGCTT
cuts and gives 2 DNA fragments

263
Q

what are the 2 types of mutations?

A

germline and somatic

264
Q

what are germline mutations?

A

occurs in a cell that go on to a gamete

264
Q

what are somatic mutations?

A

mutation that occur in other cells and cannot be passed on and can result in cancer

265
Q

how are our cells regulated?

A

its balanced by cell division (proliferation) and cell death (apoptosis)

266
Q

what are cancer cells?

A

cells that cant duplicate or die properly
over time they become resistant to cell regulatory control and divid more rapidly

266
Q

what is cancer?

A

a collection of related diseases and can start anywhere within the body
cells divide faster and this increases the chances of mutations to occur which is why older people are more prone to cancer

267
Q

what are the 2 classes of genes that are mutated and are related to cancer?

A

tumor suppressor genes
onco-genes

268
Q

what are tumor suppressor genes?

A

they encode proteins that normally prevent uncontrolled cell growth such as inhibitors

269
Q

what are onco-genes?

A

they encode proteins that promote cell growth such as proteins that stimulate cell division

270
Q

what are inactive transcription factors (E2F)?

A

the transcribed factor that binds to protein when it is not being used
when a signal for cell division occurs a ki9mnase is release to release the E2F then we lose control of when cells should divid

271
Q

what do proto-onco genes do?

A

release excess proteins which increases the cell growth

272
Q

what do mutations in stem cells lead to?

A

uncontrolled growth of the cells with the ability to keep dividing

272
Q

what is tyrosine kinase?

A

a normal ABL protein for the phosphorylation of the transcription factor for successful cell division

273
Q

what is radiation therapy?

A

targeted radiation treatment to kill cancer cells

274
Q

what is chemotherapy?

A

uses drugs to target dividing cells as cancer cells grow and divid rapidly but it also affects normal cells

275
Q

what is targeted therapy?

A

drugs that target changes in cancer cells that allow them to grow and divid
it can do this as BCR-ABL is only found in cancer cells

276
Q

whjat are the 2 forms of diabetes?

A

type 1
type 2

277
Q

what is type 1 diabetes?

A

a self-attacking illness where the host cant produce any insulin by the pancreas so it cant break down glucose

278
Q

what is type 2 diabetes?

A

occurs later in life and can be caused by genetics and environment such as weight

279
Q

what is insulin?

A

an enzyme produced in the pancreatic beta cells that is used to break down glucose in the blood

280
Q

what are the 2 chains called in insulin?

A

alpha and beta chains

281
Q

what holds insulin chains together?

A

intermolecular disulfide bridges

282
Q

what are plasmids?

A

circular pieces of double stranded DNA and replicate independently of the hosts chromosomal DNA
they are common in bacteria and are found in eukaryotes so they can have anti-bacterial resistance

283
Q

how do we get plasmids?

A

we take them from the environment and genetically modify them for our own benefit

284
Q

why do we put antibiotic resistant gene in the plasmid?

A

allows us to select the cells to contain our plasmids

285
Q

why do put a promotor in the plasmid?

A

this is to express a particular gene

286
Q

why are there restriction sites in the plasmids?

A

to allow ourgene to fit in like a cut and paste mechanism

287
Q

what are restriction sites in plasmids?

A

used to degrade foreign DNA such as bacteriaphage DNA by using restriction enzymes

288
Q

what is complementary base pairing?

A

puts 2 strands together and we use DNA ligase to repair phosphodiester bond to make the strands one

289
Q

why do we use transformation on our recombinant plasmids?

A

it transfers our plasmids into bacteria to replicate on plates. the bacteria amplifies the DNA to be purified

290
Q

what is the universal genetic code?

A

used for taking our plasmid and expressing a gene

291
Q

what is UGA?

A

a stop codon
used to transform a human gene into bacteria and it will still make the same protein

292
Q

pros and cons of using mammilian cells?

A

they are food at being glycosylated and folding yet arent the cheapest option

293
Q

pros and cons of using bacterial cells?

A

they are cheap but arent great at being glycosylated and folding

294
Q

what is EPO?

A

a recombinant human protein that increases the production of RBC from stem cells which increases the transport of oxygen around the body which enhances the host endurance
this is a form of blood dopeing

295
Q

what is CHO?

A

chinese hamster ovary cells
they are used as they have similar glycosalation as humans

296
Q

how is cDNA made?

A

by reverse translation of mRNA

297
Q

what is thrombin?

A

it is blood clotting

298
Q

what is anti-thrombin (AT)?

A

is produced in goats and taken from goat milk as AT has a milk specific promotor to express human specific proteins

299
Q

why do we isolate the gene of intrest?

A

so we can use PCR and only amplify that gene

300
Q

step 1 of a recombinant protein?

A

to source the gene expressing protein

301
Q

how do we mature cDNA?

A

we seperate the 2 chains (A and B) with a lac Z gene fused to one of the 2
we transform these chains into bacteria and the promotor binds to lac Z which will express the gene
we then extract the lac Z by breaking the peptide bond and removing the lac Z
when then mix the A chain and the B chain togetherwhich will recombine and form disulfide bridges and will leave you with a mature protein

302
Q

what is the first cell to use for post-translational modification of a protein?

A

mammalian cells as they are cheap

303
Q

what is GFP?

A

normally found in jellyfish and is an illuminessence gene that illuminates when the host feels threatened

304
Q

what is optogenetics?

A

a light sensitive protein found in algae
when light is detected channels open up and let the photos transfer into the cell

305
Q

what is channelrhedopsin?

A

a form the algae cDNA

306
Q

how can we control epilepsy?

A

by inserting an optical light into the brain

307
Q

why was protein evolution done?

A

to improve their uses such as in detergents making the proteins work faster
or we can make GFP change to be a different colour

308
Q

how do we use protein evolution?

A

by using a PCR enzyme that cant proof read so no mistakes can be corrected so its prone to making errors so we will end up with many mutations
we then take the mutation we want and amplify the gene to then be purified

309
Q

what is gene therapy?

A

takes recombinant DNA and inserts it into a the patients cells and the host is producing the proteins that they need to treat their conditions
this would be a one off treatment

310
Q

why do we use viral vectors in gene therapy?

A

because viruses are good at getting genetic information into cells
it would have to be a disabled virus that no longer carries any pathogenic material
the gene is expressed under the control of an appropriate promoter

311
Q

what is ex-vevo genetherapy?

A

injects from outside the patient

312
Q

what is en-vevo genetherapy

A

where we inject into a patient

313
Q

what is crispa technology?

A

can correct diseases effecting people through gene editing

Bioc 192 (4 decks)

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