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First Year Semester One > Biochemistry 1 > Flashcards

Biochemistry 1 Flashcards

1
Q

What are the electron orbitals?

A

s = 2
p = 6
d = 10
f = 14

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2
Q

How many electrons in each shell?

A

1st = 2
2nd = 8
3rd = 18
4th = 32

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3
Q

What is the shape of the 2p orbitals?

A

2pz = /
2py = l
2px = –
x then y then z

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4
Q

What is the nodal plane?

A

The region around a nucleus which the probability of finding an electron is zero.

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5
Q

What is the electron octet?

A

Noble gas configuration.
Full outer shell.
E.g. F gains an electron from Na - both will have electron octet

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6
Q

What are waves?

A

Electrons can be presented as waves - in phase = same wave.

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7
Q

What is a covalent bond?

A

2 electrons shared in 2 overlapping orbitals from 2 atoms with orbitals of similar energy.

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8
Q

What happens when 2 atomic orbitals combine in phase?

A

They form a bonding orbital which is lower than the original orbitals = bonding molecular orbital.

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9
Q

What happens when 2 atomic orbitals combine out of phase?

A

They form an antibonding molecular orbital which is higher in energy.

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10
Q

What is a sigma bond?

A

Strongest covalent bond.
Formed when 2 orbitals (s.p or hybrid) overlap along a line between the two nuclei.
Allows for free rotation around axis.

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11
Q

What is a pi bond?

A

Formed when two p orbitals overlap laterally - NOT ON BOND AXIS.
Usually occurs in addition to sigma - in double/triple.
Restrict rotation and weaker.

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12
Q

What is a hybrid orbital?

A

An orbital formed by combination of two or more atomic orbitals.

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13
Q

What is sp3?

A

Orbital formed from one s orbital and 3 p orbitals from the same atom - this forms four equivalent sp3 hybrid orbitals = tetrahedral (109.5).
Unsymmetrical - one lobe bigger than other.

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14
Q

What are the bonds in methane?

A

Sigma bond - 1s orbital from H overlaps with sp3 of C

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15
Q

What are examples of sp3 hybridized atoms?

A

Oxygen in water
Nitrogen in ammonia
1s of H overlaps the sp3 orbital, some sp3 orbitals have lone pairs

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16
Q

What is a molecular orbital?

A

Combination of atomic orbitals of similar energy - can be bonding or antibonding

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17
Q

What does in and out of phase mean?

A

In = electron waves are the same
Out = electron waves are different

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18
Q

What is an ionic bond?

A

Electron transferred - orbitals far apart in energy.

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19
Q

What does the excited state mean?

A

Ground - normal
Excited - moves to higher energy level e.g. s electrons move to p = hybridisation to sp3

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20
Q

Why can oxygen bind to 2 things?

A

The electrons are excited to sp3 orbitals - two have 2 electrons, 2 have 1 electron so can only make 2 covalent bonds.

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21
Q

How is the c-c bond formed in ethane?

A

Overlap of 2 carbon sp3 orbitals = sigma

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22
Q

What is an sp2 orbital?

A

Trigonal arrangement
1 s blends with 2 p

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23
Q

What is the bonding in ethene?

A

Sigma bond between c-c (sp2-sp2)
Sigma bond between c-h (sp2-s)
pi bond between c-c (p-p)

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24
Q

What is the bonding ethyne?

A

Sigma bond between c-c (sp-sp)
Sigma bond between c-h (sp-s)
2 pi bonds between c-c (py-py and pz-pz)
Triple bond

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25
Q

What are the bond angles?

A

single c-c = 109.6
double c-c = 121.7
triple c-c = 180

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26
Q

What is non-polar covalent bonding?

A

Equal sharing of electrons

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27
Q

What is polar covalent bonding?

A

Sharing electrons between atoms of different electronegativities.

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28
Q

What is the difference between sp2 vs sp3?

A

sp2 = one s and two p = 3 sp2
sp3 = one s and three p = 4 sp3

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29
Q

What does the A with a circle on top mean?

A

0.1 nm
Angstrum

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30
Q

What are the shapes of sp orbitals?

A

sp = linear
sp2 = trigonal
sp3 = tetrahedral

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31
Q

What effect does s character have?

A

More character - shorter, stronger and larger bond angle

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32
Q

What aa’s are proteins made of?

A

L amino acids (d is an isomer but not used - but just as good)

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33
Q

What types of side chains do amino acids have?

A

Non polar
Polar
Polar positively charged
Polar negatively charged

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34
Q

What is a disulfide bond?

A

Between two cysteines to make a cystine

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35
Q

What direction do polypeptides go?

A

Written from N to C terminus

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36
Q

What are the features of a peptide bond?

A

Very stable and planar (can’t move due to partial double bond character)
Partial double character
Cleaved by proteolytic enzymes
c–o = sp2

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37
Q

What rotation is in amino acids?

A

N-C = phi (line in circle)
C-C = psi (trident)

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38
Q

What did Ramachandran say?

A

Many combinations of phi and psi are not found because of steric clashes

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39
Q

What are the bond lengths?

A

Single = 1.54 A
Double = 1.33 A
Triple = 1.20 A

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40
Q

Why can’t the peptide bond rotate?

A

Due to the delocalisation of electrons from the double-bonded oxygen to the peptide bond.

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41
Q

What is the denaturation of ribonuclease A?

A

It is reversible.
Native catalytically active state + urea & beta mercaptoethanol –> unfolded inactive with disulfides reduced to Cys –> removal of urea & mercaptoethanol = restored.

This showed that the instructions to fold in in the protein sequence.

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42
Q

What is the free energy required to denature AA’s?

A

0.4 kJ/mol per Amino Acid

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43
Q

What free energy is needed to overcome hydrogen bonds?

A

12 kJ/mol

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44
Q

What group does cysteine have?

A

SH = thiol

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45
Q

What covalent bond do adjacent cysteines make?

A

A disulphide bond s-s
Requires oxidative conditions
Only bond formed between side chains
Can provide extra stability

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46
Q

What are the non-covalent forces which hold proteins together?

A
  • ionic interaction
  • van der waal interactions
  • hydrogen bond
  • hydrophobic effect
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47
Q

What is the energy of association?

A

E = k q1 q2 /Dr
q1 & 2 = electric charges
r = distance
k = 9 x 10^9 JmC-2
D = dielectric constant

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48
Q

What is one electrical charge?

A

1.6 x 10^-19 C

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49
Q

What is D?

A

Dielectric constant of a solvent.
Is a measure of its ability to keep opposite charges apart.
Vacuum = 1
Water (polar) = 80
Non-polar (interior of protein) = 4

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50
Q

What are the three wan der Waal interactions?

A

Dipole-dipole interactions
Dipole-induced dipole interactions
London dispersion forces

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51
Q

What is a dipole-dipole interaction?

A

Occur between polar molecules which have permanent dipoles.
e.g. between c–o, c–o

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52
Q

What is a dipole-induced dipole interaction?

A

Between polar and non-polar (creates temporary dipole)
e.g. c–o, h3c

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53
Q

What is a london dispersion force?

A

Present in all molecules due to fluctuating asymmetric distribution of electrons.
e.g. ch3, ch3

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54
Q

What is a hydrogen bond?

A

Interaction between polar groups (H and FON)
Partial negative on O/N/F - partially positive on H.
Strongest non-covalent in aqueous medium
Strongest tend to be linear with lone pair orbital

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55
Q

What is the energy association of non-covalent interactions?

A

Hydrogen bonding = 4-13 kJ/mol
Ionic interactions = 5 kJ/mol
Van der waal = 2 kJ/mol

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56
Q

Which is longer: covalent or hydrogen bonding?

A

Hydrogen

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57
Q

What is the hydrophobic effect?

A

Influences which cause nonpolar substances to minimise their interaction with water - form micelles in aqueous solutions.
Non-polar

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58
Q

What can water solubilise?

A

Polar, ionic and hydrophilic

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59
Q

How does water act with hydrophobic parts?

A

Forms ‘cages’.
When buried - caged water molecules are released which increases entropy.

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60
Q

How do proteins fold?

A

Spontaneous - gibbs needs to be negative.
Enthalpy change is slightly negative.
Entropy change is positive as caged water is released.

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61
Q

What is the gibbs equation?

A

^g = ^h - t^s
gibbs free energy = enthalpy change - T entropy change
negative = feasible

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62
Q

Which non-covalent interactions stabilise proteins?

A

Hydrogen bonds = strong
Ionic = strong but don’t stabilise well
Dipole-dipole = weak but stabilise well

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63
Q

Why do proteins need to fold?

A

Residues need to come close to eachother to help function

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64
Q

NEED TO KNOW ALL PROTEINS?

A
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65
Q

What is the primary structure of a protein?

A

Linear sequence on amino acids
From N terminus to C terminus

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66
Q

What is the secondary structure of a protein?

A

Stabilised by hydrogen bonding
- alpha helix and beta pleated sheet

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67
Q

What is an alpha helix?

A

CO and NH hydrogen bonded - every 4 aa’s
1.5 angstrum rise per aa
100 degree rotation
3.6 aa per turn
RIGHT HANDED
Dipoles of each peptide bond align

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68
Q

What is the alpha helix terminator?

A

Pro (proline)

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69
Q

Are alpha helices hydrophobic or hydrophilic?

A

Amphiphilic - have both
Helix has a hydrophobic and hydrophilic sides
Occur in globular proteins - hydrophobic face interior, hydrophilic face solvent.

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70
Q

What is a beta sheet?

A

Can be parallel and antiparallel
Side chains occur on opposite faces of the sheet.
Can be flat - sometimes twisted due to steric repulsion.
Can have a beta turn.

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71
Q

What is the supersecondary structure of a protein?

A

Combination of secondary structures (e.g. beta-alpha-beta, alpha-alpha)

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72
Q

What is the tertiary structure?

A

Assembly of secondary elements into native protein structure

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73
Q

What is the quaternary structure of a protein?

A

Multiple polypeptide chains assemblied
homooligomer - identical monomers
heterooligomer - different

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74
Q

What is an allosteric interaction?

A

Ligand binds to quaternary structure - alter affinity of ligand to another subunit

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75
Q

What are domains?

A

Independent units - binding sites in clefts between domains
e.g. DNA polymerase - polymerase domain (synthesises new DNA), exonuclease domain (degrades incorrect DNA)

76
Q

What is an immunoglobulin?

A

Each domain in IgG is similar - antiparallel beta sheets surrounding hydrophobic core

77
Q

What is a conformative change?

A

Many proteins change their shape when binding to a ligand (on active site) - non-covalent bonds form
e.g. lactoferrin changes shape to show when it is bound to iron.

78
Q

What is phophorylation?

A

OH of ser, thr and Tyr can be reversibly phosphorylated

79
Q

What is glycosylation?

A

Addition of carbohydrates - increases hydrophilicity and ability to interact with other molecules.

80
Q

What is hydroxyproline?

A

OH group added to proline - this stabilises collagen fibres - Vit C deficiency can inhibit this

81
Q

What is y-carboxyglutamate?

A

Vitamin K deficiency can result in low carboxylation of glutamate in prothrombin - can cause haemorrhage.

82
Q

What are protein families?

A

AAs with a closely related amino acid sequence - arises from common ancestor

83
Q

What are serine proteases?

A

Family of enzymes which all contain - asp-his-ser
Includes: chymotrypsin, trypsin and elastase
Have very similar structures and include digestive enzymes and blood clotting

84
Q

What is a reaction mechanism?

A

1) determine where the electrons are
2) determine what bonds are made/broken
3) describe flow of electrons

85
Q

What is a lewis structure?

A

1) draw molecular skeleton
2) assume bonds are covalent
3) count electrons
4) add sigma bonds
5) add pi if necessary

86
Q

What is an electro and nucleophile?

A

Electrophile - accepts electrons
Nucleophile - supplies electrons

87
Q

How would we draw a sigma bond being made?

A

e.g. when an anion and cation encounter
Arrow is from lone pair of electrons to where they move to.
Reversible

88
Q

What is substitution nucleophilic bimolecular?

A

A nucleophile attacks an electrophile - substitutes a different group which is opposite to the attack.
There’s a single transition state where they are both partially bonded
e.g. bromine replacing iodine

89
Q

What is a lysozyme?

A

Enzyme - first line of defense as cleaves peptidoglycan (in cell walls of gram-positive bacteria - no effect on gram negative)
Part of glycosidase enzyme group
Hen egg-white lysozyme was first crytallography of any enzyme

90
Q

How do lysozymes work?

A

Cuts a glycosidic bond between NAM and NAG sugars (have similar structure) in peptidoglycan
Glycosidic bond between 4th and 5th sugars break

91
Q

What is the structure of a lysozyme?

A

129 aa’s - four disulphide bridges
Has 2 domains seperated by deep cleft (active site and can bind to 6 sugars- ABCDEF)
L - beta sheet with hydrophilic residues
R - hydrophobic core surrounded by a-helices

92
Q

What is the lysosyme active site?

A

Binds to peptidoglycan so a NAM ring is at D and NAG at E.
The D-E bond is next to Glu35 and Asp52 - Glu35 has a carboxylic acid chain (as its in unusual hydrophobic environment) and Asp52 has a carboxylate at pH 6 (optimum)

93
Q

What is the lysozyme mechanism?

A

1) Nucleophilic attack from ASP 52 - forms covalent acyl-enzyme intermediate
2) Glu35 donates proton and sugars E, F diffuse away
3) Water now attackes - OH to D and proton to Glu35 - ABCD released

DRAW MECHANISM

94
Q

What are the products of a lysozyme reaction

A

Sugars E,F
Sugars ABCD

95
Q

What do enzymes do?

A

Enhance rate - don’t alter equilibrium
Have active sites - for their job
Unchanged by end of cycle - may have to use ions from water ect. to get back to normal

96
Q

What is the difference between pH, Ka and pKa?

A

pH = conc of hydrogen ions
pKa = strength of acid
ka = dissociation constant

97
Q

What is the dissociation constant?

A

Ka = [H][A]/[HA]

98
Q

What is pKa?

A

pKa = - log(Ka)
pKa basically turns Ka into a nice number

99
Q

What is the Henderson-Hasselbalch equation?

A

pH = pKa + log([A]/[HA])
We can use it to work out the % of protonated and deprotonated forms of a group.

pKa>pH = protonated vice versa

e.g. Histidine side chain pKa = 6, so at pH 7
log([A]/[HA]) = 1
[A]/[HA] = 10
for every histidine sidechain in HA form, there’s 10 in A- form
10/11 = 91% of sidechains deprotonated

100
Q

How does pH change as hydroxide is added?

A

pH increases - cation (nh3+) then zwitterion then anion (coo-)
Some plateaus in graph - pK1, pl (around 6-9), pK2

101
Q

What is pl?

A

Isoelectric point - zwitterion

102
Q

How many pKa values in an amino acid?

A

2 or 3 if the side chain is titratable
Amino group - pKa = 9-10
Carboxyl group - pKa = 2-3

103
Q

What effect does the side chain of histadine have on pKa?

A

The chain has a pKa of 6 - makes it very sensitive to pH under normal conditions

104
Q

Are most enzyme reactions pH sensitive?

A

e.g. Cholinesterase increases and plateaus
e.g. Chymotrypsin normal bell curves
e.g. pepsin is high at low then decreases to 5

The protonation state of side chains are usually responsible for this

105
Q

Why can the local environment influence sidechain pKa?

A

In lysozymes - Glu35 has a pKa is 4.1 but the pH that it usually works at is 7.4 - expect it to be unprotonated - BUT IT’S NOT

106
Q

What is the name of a protonated and unprotonated form of the histidine side chain?

A

Protonated = imidazolium ion
Unprotonated = Imidazole

107
Q

What groups do papain have?

A

Cys25 - wants to be unprotonated - 4.2
His15 - wants to be protonated - 8.2
Has bell-shaped curve

108
Q

How does an enzyme make a reaction faster?

A

Turns a intermolecular reaction into a faster intramolecular one.
Holds them in an optimum orientation so they have react.
This is rate enhancement

109
Q

Are there intermediates from substrate to product?

A

Yes!
There may be intermediates or transition states - intermediates are more stable.
Enzymes prefer to bind transition states

110
Q

How do enzymes bind to substrates?

A

They bind to transition state.
They do not bind too strongly (hypothetically great) as that would increase the activation energy to the non enzyme levels
E+S - ES - ES’

111
Q

How does the induced fit theory work?

A

Substrate binds non-optimally and is stressed when bound - enzyme strained but the strain energy is released when transition state is reached

112
Q

What is catalysis?

A

The process that increases the rate at which a reaction approaches equilibrium

113
Q

What steps occur in enzyme catalyzed reactions?

A

1) general acid-base catalysis - donation/gain of proton
2) covalent catalysis
3) metal ions in catalysis

Lower free energy pathway

114
Q

What is an example of acid-base catalysis?

A

Lysozyme - Glu35 donates a proton to the substrate and cleaves the glycosidic bond - acts as an acid. Glu35 then takes a proton from water - acts as a base, OH from water adds to substrate - complete cycle

115
Q

What is Vmax and km?

A

Vmax = maximum velocity (rate)
Km = 1/2 Vmax

116
Q

What are enzyme inhibitors usually?

A

Transition state analogs

117
Q

What is covalent catalysis?

A

Some enzymes can form covalent bonds with substrates - generate impermanent intermediates

Usually involves a strong nucleophile on enzyme

118
Q

How does a lysozyme use covalent catalysis?

A

Forms an intermediate between Asp52 and the oxonium ion on NAM - a water will donate oxygen to break bond - don’t worry about details for exam

119
Q

What metal ions are used in catalysis?

A

Good as don’t alter pH

Metal can be tightly bound - metalloenzymes
e.g. Fe2+/3+, Cu2+, Zn2+, Mn2+

Or loosely bound - metal activated
e.g. alkali earth metals - Na+, K+, Ca2+, Mg 2+

Metals have coordination shells

120
Q

How are metals used in catalysis?

A
  • can generate nucleophilic species to participate in reaction e.g. carbonic anhydrase uses Zn to generate OH- nucleophile to attack CO2
  • can stabilise transition state charge e.g. DNA polymerase I has Mg2+ or Mn2+ bound to active site which stabilises phosphate transtition state
  • can increase binding interaction e.g. Mg2+ can bind to ATP and indirectly to the enzyme via water
  • can use oxidation state to facilitate catalysis e.g. Fe-S clusters can change from Fe2+ and Fe3+
121
Q

What are cofactors?

A

Additional metal ions or small molecules which help enzymes with their function.
- usually recycled and used again

Usually are coenzymes (small organic)
- tightly bound (prosthetic group)
- loose or dissociate (cosubstrate)

122
Q

What are coenzymes?

A

Small organic cofactors

can be tightly bound (prosthetic group)
can be loose or can dissociate (cosubstrate)

123
Q

What are the cofactor + enzyme called?

A

Enzyme alone = apoenzyme
Together = holoenzyme

124
Q

Can proteins help enzymes?

A

Yes!
They are a protein coenzyme and usually involved in transport

125
Q

What is AMP?

A

Adenosine monophosphate
- building block in cofactors
- phophate group, adenine ring (2) and ribose ring

126
Q

What are nucleoside triphosphates?

A

ATP, GTP (guanine) ect.
- know structure

127
Q

What is NAD?

A

Nicotinamide adenine dinucleotide
- nicotinamide ring, adenine ring, 2 ribose, 2/3 phosphates
- cofactor
- can be NAD+/NADH/NADP+/NADPH
- the nicotinamide ring is what gets reduced
- Used to accept or donate hydride group
- need to know this structure (especially nicotinamide)!!!

128
Q

What are the different classes of enzymes?

A

Oxidoreductases - redox
Transferases - transfer things
Hydrolases - transfer things involving water
Lyases - make double bond
Isomerases - intramolecular group transfer
Ligases - joining molecules by ATP

129
Q

What are oxidoreductases?

A

Often use a cofactor e.g. NAD
Carries out REDOX
Half equations can show this

130
Q

What are transferases?

A

Transfers a group between molecules e.g. nucleophilic substitution

131
Q

What is a group transfer reaction?

A

Transfer of electrophiles from one nucleophile to another

132
Q

What is a hydrolase enzyme?

A

Cleavage reaction via addition of water
e.g. aryl sulphatase

133
Q

What is a lyase enzyme?

A

Also known as synthases
Add or remove groups to make double bond
e.g. enolase

134
Q

What is an isomerase enzyme?

A

Interconversion of isomeric forms of compounds
When converting L-AA to D-AA - racemization

135
Q

What is a ligase enzyme?

A

Joining two molecules requiring ATP
e.g. CO2 + pyruvate –> oxaloacetate needs pyruvate carboxylase - requires biotin cofactor

136
Q

What is a membranes permeability?

A

Permeable: gases, ethanol
Slightly permeable: water, urea (small uncharged polar)
Permeable: glucose, ions, charged polar molecules (AA, ATP)

137
Q

What fats are in membranes?

A

Phospholipids - glycerol + 2 FAs + phosphate attached to alcohol

  • phosphatidyl serine
  • phosphotidyl choline
  • phosphotidyl ethanolamine
  • phosphotidyl inositol

Know structure??

Can influence fluidity, curvature and thickness

138
Q

How does membrane composition change between cell types?

A

RBCs - equal amounts of cholesterol and the phospholipids
Neurones - more P-ethanolamine and P-serine and cholesterol
E.coli - only P-ethanolamine and P-serine
Endoplasmic reticulum - more P-choline
Mitochondria - more P-serine, P-ethanolamine, P-choline

don’t need to know well

139
Q

What does cholesterol do to membranes?

A

Makes them thicker as it has a lipid-ordering effect
Has hydrophilic (OH at end) and phobic parts (steroid rings)

140
Q

What causes membrane curvature?

A

Segregation of lipids - depends on size of heads and tails
P-choline - cylindrical lipids - bilayers flat
P-ethanolamine - cone shaped - curved

141
Q

What determines membrane fluidity?

A

Fatty acid composition and cholesterol
Cholesterol - stiffens the structure and makes thicker

142
Q

How much proteins do membranes have?

A

25-50% lipid and 50-75% protein by mass
Many membrane proteins diffuse rapidly in the plane - fluid mosaic model is used for the organisation of everything

143
Q

What is a leaflet?

A

Half of a phospholipid bilayer

144
Q

How can we visualise the movements of proteins in the bilayer?

A

Fluorescence recovery after photobleaching

1) cells are labelled with a fluorescent reagent binding with specific lipid or protein
2) laser light is focused on a small area - reduces fluorescence and bleaches
3) the fluorescence will increase as unbleached surface molecules diffuse into it

145
Q

How do proteins provide functional asymmetry of membranes?

A

Inserted asymmetrically e.g. Na+/K+ pump is orientates so Na comes out and K+ goes in.

The asymmetry is preserved as proteins can’t rotate - just move side to side

146
Q

What are the three types of membrane proteins?

A
  • integral (intrinsic)
  • peripheral (extrinsic)
  • lipid anchored
147
Q

What are integral membrane proteins?

A

All or partially embedded in membrane - require detergent to release them
Often transmembrane

Often use alpha helices to span membrane
Can use beta sheets wrapped around to form beta barrels - usually pores or receptors

Interact with hydrophobic interior

148
Q

What are peripheral membrane proteins?

A

Interact with membrane via polar heads of integral proteins

149
Q

What are lipid-anchored membrane proteins?

A

Protein polypeptide remains in aqueous phase

Can be fatty acid anchored, isoprenoid anchored or glycosylphosphatidyl-inositol anchored

150
Q

What are the two classes of membrane transfer proteins?

A

Channels/pores - central passage for ions/molecules
Transporters - passive and active

151
Q

What are the transporters transfer process?

A

Uniport - single solute
Symport - same direction
Antiport - opposite direction

152
Q

What are the two types of active transport?

A

Primary - coupled to energy source
Secondary - coupled to ion conc gradient created by primary

153
Q

What is ModABC?

A

ATP-binding cassette transporter

154
Q

What is the work equation?

A

work (J) = force x distance

e.g. dropping apple from string

Starts at rest then moves in the direction needed to reduce potential energy

155
Q

What is pico?

A

x 10-12

e.g. piconeutons per nanometre

156
Q

What is kinetic energy?

A

KE = 1/2mv2

Energy is conserved

If a ball bangs into another - kinetic energy remains the same before and after

157
Q

What is the Boltzmann distribution?

A

P directly proportional e^-PE/kbT

P = probability of energy
e = exponential
PE = potential energy
kb = boltzman constant
T = temp (kelvin)

We can use this equation to find the difference in probability of energies

158
Q

What is KbT?

A

Typically the energy of one molecule

Boltzmann constant (Kb) x T (temp)

Units = JK-1

To find energy per moles - do RT (gas constant)

159
Q

Is PE the same from folded to unfolded?

A

Yes!
e.g. if increased by 10 when folded, decreased by 10 when unfolded

Change of potential energy = change of enthalpy

160
Q

Does an unfolded or folded protein have more entropy?

A

Unfolded - at higher temperatures get more probable - still not as likely as folded

161
Q

How is free energy useful?

A

Allows coupling - favourable can drive unfavourable e.g. ATP synthase uses H+ concentration to try to increase ATP when the conditions would want to decrease it. Overall delta g = delta g of H transfer + delta g of ADP-ATP reaction

Overall delta G must be negative enough for reactions to occur

Delta g for H would be negative, delta g for making ATP is positive - add together should be negative

162
Q

What is the entropy of mixing?

A

If we shake 2 solutions together of the same size and shaped particles - all microstates equally likely

Small number of states = low entropy = high free energy vice versa

More favourable to be mixed than ordered

162
Q

What is the free energy for transferring one molecule from a to b?

A

delta G = kb x T x ln (Cb/Ca)

in moles: kb changed to R (gas constant)

If Cb = Ca then ln = 0

163
Q

How do chemical reactions and free energy relate?

A

For a reaction to go forward - delta g for reactants must be higher than products (Forward < backward reaction)

164
Q

What is the equilibrium constant?

A

Keq = [product] eq x [product]eq/ [reactant]eq x [reactant]eq

165
Q

What is the mass action ratio?

A

r = [product][product]/[reactant][reactant]

166
Q

What does delta G depend on?

A

Concentration independent terms

Concentration dependent terms - entropic

167
Q

What are the features of delta g?

A

Free energy depends on concs
What at equilibrium = 0
Delta G values in tables are Arbitrary - depend on conditions
Delta G will change for different sets of conditions

168
Q

What is delta g ^o

A

Standard state - concs are all 1M - usually pH = 7 so we can ignore [h]

delta g = delta g^o + RT([P]/[R])

169
Q

How do we measure delta g^o

A

We let reaction reach equilibrium

0 = delta g ^o + RTlnk
delta g^o = -RTlnK

170
Q

How do we calculate energy change for ions moving across a membrane?

A

= charge of object [coulombs] x PD (JC-1)

for H+ = delta G = e (electron charge) x membrane potential

for moles = x avogadro’s number

If we see volts as a change - x by charge on object = energy

171
Q

What do reaction rates depend on?

A

Temperature
Pressure
pH
Ionic strength
Reagent conc

172
Q

What is the irreversible unimolecular kinetic model?

A

A -> B
not reversible

Rate is proportional to concentration of A

v = -delta A/deltaT = deltaB/deltaT

rate = k[A] - FIRST ORDER

173
Q

What is first order vs unimolecular?

A

First order - rates directly proportion to concentration
Unimolecular - A –> B

174
Q

What are the units for k?

A

first order - usually min-1 or s-1
second - usually conc-1time-1

175
Q

What is the reversible unimolecular kinetic model?

A

Rate of formation of B = k1[A] - k2[B]

176
Q

What is the irreversible bimolecular kinetic model?

A

A + B –> C

second order

rate to form C = k[A][B]

A+B need to collide - and needs to be right orientation and violent enough

177
Q

What is the average time a molecule stays in state a?

A

Average time = 1/k1

Same for B = 1/k2

178
Q

What is Keq in relation to k1 and k2?

A

Keq = k1/k2

179
Q

What is Keq when equilibrium shifts?

A

Keq = [product]/[reactant]

Keq gives you the proportion of how much of one state you have compared to another

e.g. we heat a reaction slightly, 100 um pf folded is turned into 40 unfolded, 60 folded = 2/3

180
Q

What is a way to work out the proportion of B?

A

[B]/[A]+[B]

this is the same as

([B]/[A])/ ([A]+[B])/[A]

this is the same as
Keq/1 + Keq

If we wanted A: 1/1+Keq

181
Q

What is a bimolecular reversible reaction?

A

A + B -><- C

These include binding reactions: drug & receptor binding, TFs, enzyme/substrates

Rate of formation of PL = k1[P][L]

Rate of loss of PL = k-1[PL]

182
Q

What is KD?

A

KD = koff/kon

Describes ligand binding

Stronger binding = lower KD

183
Q

What is the fraction of bound protein?

A

[P][L]/[PL] = Kd

[PL]/[P]total = [L]/[L] + Kd

[P] total = [P] + [PL]
[L] total = [L] + [PL]

184
Q

What are the rates of a bimolecular reversible reaction at equilibrium?

A

Rates equal

k1[P][L] = k-1[PL]

We write equilibrium as dissociation: PL -><- P + L

185
Q

How does the fraction of [PL] change as [L] changes?

A

1) if [L] = 0.1Kd

[PL]/[P] total = 0.1/1.1 = 0.091 meaning 1 in 11 is PL

2) if [L] = 10 Kd

[PL]/[P] = 10/11 meaning 10 in 11 is PL

3) if [L] = Kd

[PL] /[P] = 1/2 meaning that there is 0.5 binding

186
Q
A

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