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Molecular Biology BSc First Year > MBB11001 -Biochemistry 1 > Flashcards

MBB11001 -Biochemistry 1 Flashcards

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1
Q

What happens to the waves when waves are added in phase?

A

they increase

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2
Q

What happens to the waves when waves are added out of phase?

A

they decrease

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3
Q

What happens when atomic orbitals are combined constructively?

A

-combine in phase
-bonding molecular orbital

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4
Q

What happens when atomic orbitals are combined destructively?

A

-combine out of phase
-antibonding molecular orbital

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5
Q

What is a sp3 hybridised orbital?

A

four atomic orbitals (one s orbital, three p orbitals) hybridised
-has one bigger lobe (so is unsymmetrical about nucleus)
-in excited state (so can form 4 bonds)

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6
Q

What arrangement are sp2 hybridised orbitals in?

A

trigonal planar

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7
Q

What arrangement are sp hybridised orbitals in?

A

linear

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8
Q

Which isomers of amino acids do proteins use?

A

L-isomer (never D-isomers)

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9
Q

Why do proteins only ever have L-isomers of amino acids?

A

to ensure the proteins are always produced the same
-diff isomers of aas would cause a diff arrangement and therefore a diff function of the protein

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10
Q

Which direction are polypeptide sequences written in?

A

from N-terminus to C-terminus

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11
Q

What is a residue (in respect to polypeptides)?

A

an amino acid in a polypeptide

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12
Q

What bonds are formed between amino acids?

A

peptide bond
-C(=O)-N(H)-

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13
Q

What are peptide bonds cleaved by?

A

proteolytic enzymes
-proteases or peptidases

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14
Q

What are the properties of peptide bonds?

A

-planar
-very stable
-partial double bond character
-no rotation around C-N but free rotation around N-Cα and Cα-C bonds (of main chain) -gives protein flexibility so it can fold in different ways

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15
Q

What does the Ramachandran plot show?

A

-beta sheet and alpha sheet are very favoured
-native conformation of protein is determined by types of side chains and their sequence in the polypeptide

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16
Q

Which amino acids have non-polar side chains?

A

glycine
alanine
proline
valine
leucine
isoleucine
methionine
tryptophan
phenylalanine

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17
Q

Which amino acids have polar, uncharged side chains?

A

tyrosine
asparagine
glutamine
serine
threonine
cysteine

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18
Q

Which amino acids have polar, positively charged side chains?

A

lysine
arginine
histidine

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19
Q

Which amino acids have polar, negatively charged side chains?

A

aspartate
glutamate

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20
Q

What are disulphide bonds in proteins?

A

covalent bond between 2 sulphur atoms (in 2 cysteine residues)
-only covalent bond formed after polypeptide is made
-requires oxidative conditions to form
-usually only forms in extracellular domains of proteins
-gives extra stability in harsh conditions

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21
Q

What are hydrogen bonds?

A

-interaction between polar groups (𝛿- charge on electronegative atoms like oxygen or nitrogen and 𝛿+ of hydrogen)
-much weaker and longer than covalent bonds but stronger than other non-covalent forces

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22
Q

What forces are involved in protein structure after the polypeptide is made?

A

-disulphide bonds
-hydrogen bonds
-ionic interactions
-van der waals interactions (dipole-dipole, dipole-induced dipole, London)
-hydrophobic effects

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23
Q

E =
(energy of association -ionic interactions)

A

kq1q2
_______
Dr

where E=energy of association
k=9x10^9JmC^-2
q=electric charge
D=dielectric constant
r=distance

-relating to ionic interactions

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24
Q

What is the dielectric constant?

A

a solvent’s ability to keep charges apart
-vacuum = 1 (smallest possible)
-polar solvent high vs unpolar solvent low

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25
Q

What are Van der Waals interactions?

A

weak interactions categorised into three types:
-dipole-dipole interactions
-dipole-induced dipole interactions
-London dispersion forces

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26
Q

What are the three types of Van der Waals interactions?

A

dipole-dipole interactions
dipole-induced dipole interactions (permanent dipole causes an induced dipole in a non-polar group for a brief instant in time)
London dispersion forces (induced dipole causes another induced dipole for a brief instant in time -both in non-polar groups)

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27
Q

What is the hydrophobic effect?

A

influences that cause non-polar groups to minimalise their contact with water and amphipathic molecules to form micelles in aqueous solutions

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28
Q

What does grouping non-polar molecules together do to the entropy of a solvent?

A

increases entropy of solvent

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29
Q

How does entropy change as a protein is folded?

A

increases
-due to water molecules in caged structures around hydrophobic side chains

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30
Q

Why do we know enthalpy is not involved in protein folding?

A

no bond breaking or forming
-covalent bonds stay the same
-hydrogen bonds, ionic bonds and van der Waals forces only change slightly

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31
Q

What is the primary structure of a protein?

A

the linear sequence of amino acids in a polypeptide chain

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32
Q

What is the secondary structure of a protein?

A

the folding of the polypeptide’s backbone into regular structures, like an alpha helix, beta sheet or turns and loops, by hydrogen bonding

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33
Q

What is an alpha helix?

A

coiled structure where all the main chain CO and NHs are hydrogen bonded (NH 4 residues along from CO)
-example of secondary structure (commonly right-handed helix)
-amphiphilic (hydrophobic and hydrophilic character)
-tightly packed core (due to all main chain atoms being involved in van der Waals forces)

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34
Q

What is the structure of an alpha helix like?

A

-dipoles of each peptide bond are aligned
-side chains point away and down from helix
-all main chain atoms involved in van der Waals forces (causing a tightly packed core)

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35
Q

What is a beta sheet?

A

secondary structure where 2+ polypeptide strands (beta strands) are hydrogen bonded to eachother
-strands in beta sheet can be parallel and/or antiparallel
-sheet can be flat or twisted
-side chains of consecutive residues are on opposite faces of sheet

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36
Q

What is a supersecondary structure of a protein?

A

common parts of secondary structures
-aka motifs
-smaller than a subunit or domain
-typically 10-40 residues in length
Eg. beta-alpha-beta unit, beta hairpin, alpha-alpha motif, helix-turn-helix, beta barrel

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37
Q

What are some examples of supersecondary structures?

A

-beta-alpha-beta unit
-beta hairpin
-alpha-alpha motif
-helix-turn-helix
-beta barrel

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38
Q

What is the tertiary structure of a protein?

A

the assembly of secondary structures into a native protein structure
-remaining segments in amino acid sequence form connecting loops (functional residues are often in interconnecting loops)

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39
Q

What is the quaternary structure of a protein?

A

the assembly of 2+ polypeptide chains into multi-subunit structures
-subunits are usually associated non-covalently

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40
Q

What is a homo-oligomer?

A

a molecule consisting of a few identical repeating units
eg. bacteriophage γ’s cro protein is a dimer of identical subunits

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41
Q

What is a hetero-oligomer?

A

a molecule consisting of a few non-identical repeating units
eg. haemoglobin is a tetramer of 2 identical alpha subunits and 2 identical beta subunits

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42
Q

What is an oligomer?

A

a molecule consisting of a few repeating units
(less units than in a polymer)

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43
Q

What is a domain?

A

globular clusters in a protein
-proteins of 200+ residues fold into multiple domains
-each domain has a specific function
-structurally independent units

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44
Q

What are binding sites in terms of domains?

A

clefts between domains

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45
Q

What is a conformational change?

A

when a macromolecule (eg. protein) changes its 3D shape when a small ligand binds eg. substrate binding, phosphorylation, etc

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46
Q

How can additional functionality be added to proteins?

A

covalent modification of side chains via post translational modification of amino acids

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47
Q

Where does phosphorylation (as a post-translational modification) typically occur in a protein?

A

hydroxy groups of serine, threonine and tyrosine

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48
Q

Where does glycosylation (as a post-translational modification) typically occur in a protein?

A

asparagine, serine and threonine residues

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49
Q

What post-translational modification occurs to form hydroxyproline?

A

hydroxy group added to proline
-stabilises fibres of newly synthesised collagen
-when there is a lack of vitamin C, this is inhibited so the fibres weaken -results in scurvy

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50
Q

What post-translational modification occurs to produce carboxyglutamate?

A

carboxylation of glutamate residues
-when there is a lack of vitamin D, there is insufficient carboxylation in prothrombin (clotting protein) -results in haemorrhage

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51
Q

What is a protein family?

A

a group of proteins with closely related amino acid sequences and 3D structure but different functions
-most likely arises from divergent evolution from a common ancestor

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52
Q

What are serine proteases?

A

a family of proteolytic enzymes including digestive enzymes and proteases involved in blood clotting
-contains catalytic triad: Asp-His-Ser
eg. chymotrypsin, trypsin, elastase (sim aa seq and 3D structure but have diff substrate binding sites and cut substrates at different points)

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53
Q

How do you draw Lewis structures?

A

-write the molecular skeleton
-assume all bonds covalent
-count the available valence e-
-add sigma bonds and give each atom 8 e- (2 for H)
-if the number of electrons in structure is the same then description is correct –otherwise introduce pi bonds

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54
Q

What do curly arrows show?

A

direction of e- movement

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55
Q

What is lysozyme?

A

glycosidase enzyme which cleaves peptidoglycan by breaking the glycosidic bond between NAM and NAG sugars as a defence against bacterial attack

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56
Q

What is the structure of lysozyme?

A

-129aas
-4 disulphide bridges
-2 domains separated by deep cleft -left domain is small ß-sheet of mainly hydrophilic residues, right domain has a hydrophobic core surrounded by short α helices
-active site is top half of cleft (Glu35 and Asp52 residues) and can bind 6 sugars

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57
Q

What state is the Glu35 residue in the active site of lysozyme?

A

protonated (in hydrophobic environment)
-acts as an acid (glutamic acid rather than glutamate)

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58
Q

What state is the Asp52 residue in the active site of lysozyme?

A

deprotonated
-acts as a nucleophile

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59
Q

What happens in the mechanism of lysozyme?

A

-Asp52 undergoes a nucleophilic attack to form acyl-enzyme intermediate
-Glu35 donates H+ and sugars E-F (first product) diffuse away
-water attacks, adding an OH to sugar D’s C1 and a H+ to Glu35
-sugars A-B-C-D produced (second product)

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60
Q

What are enzymes?

A

biological catalysts
-specific
-enhance rate w/o altering eqm
-unchanged by rxn cycle
-regulated
-have active site
-often pH sensitive

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61
Q

Ka =
Dissociation constant

A

[H+][A-]
_______
[HA]

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62
Q

What is the Henderson Hasselbalch equation?

A

pH= pKa + log([A-]/[HA])

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63
Q

How can the Henderson Hasselbalch equation be used to calculate the percentage of protonated and deprotonated forms of a group in solution?

A

-rearrange equation so that:
pH-pKa = log([A-]/[HA])
-input pH and pKa values
-do 10^(pH-pKa) to get rid of log to get [A-]/[HA]
-use this fraction to get a ratio and convert into percentage (HA=protonated, A-=deprotonated)

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64
Q

How do enzymes enhance rate?

A

-bring substrates closer together and hold them in optimal orientation for rxn
-turns intermolcular rxns into intramolecular rxns

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65
Q

What is the induced fit model of enzyme action?

A

-conformation of enzyme is altered to match better to the structures of substrates/transition states
-substrate is bound non-optimally
-enzyme is strained when substrate binds, this energy (from the strain) is relieved when transition state is reached

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66
Q

What catalytic mechanisms can enzymes use?

A

-acid-base catalysis
-covalent catalysis
-catalysis using metal ions

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67
Q

What do enzymes do in acid-base catalysis?

A

act as an acid by donating H+ or a base by removing H+

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68
Q

What do enzymes do in covalent catalysis?

A

form covalent bonds with substrates to generate transient reactive intermediates
-enzyme generally has a strong nucleophile

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69
Q

How do enzyme carry out catalysis using metal ions?

A

-metals can generate nucleophile to participate in rxn
-metal ions can stabilise transition state
-metals can increase binding interaction
-changes in the metal’s oxidation states can facilitate catalysis (oxidation and reduction)

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70
Q

How can metal ions be bound in enzymes?

A

tightly -typically transition metal ions =>known as metalloenzymes
loosely -typically alkali metal ions =>known as metal activated enzymes

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71
Q

What are metalloenzymes?

A

enzymes with a metal ion tightly bound
-typically transition metal ions eg.Fe2+, Fe3+, Cu2+, Zn2+

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72
Q

What are metal activated enzymes?

A

enzymes with a metal ion loosely bound
-typically alkli metal ions eg.Na+, K+, Ca2+, Mg2+

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73
Q

What is a cofactor?

A

metal ion/small molecule required by some enzymes to carry out catalytic function
-reused and recycled
-enzymes w/similar cofactors often have similar function

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74
Q

What are coenzymes?

A

small organic cofactors
-loosely bound =cosubstrates
-tightly bound =prosthetic groups

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75
Q

What are cosubstrates?

A

loosely bound coenzymes (small organic cofactors)
-can dissociate

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76
Q

What are prosthetic groups?

A

tightly bound coenzymes (small organic cofactors)

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77
Q

What is an apoenzyme?

A

an enzyme without a cofactor bound

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78
Q

What is a holoenzyme?

A

an enzyme with a cofactor bound

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79
Q

What is a protein cofactor?

A

an additional protein required for an enzyme’s full catalytic activity

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80
Q

What is nicotinamide adenine dinucleotide (NAD)?

A

cofactor used in enzyme-catalysed oxidation or reduction rxns
-converted between NAD+ and NADH

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81
Q

What are the different classes of enzymes?

A

-oxioreductases/dehydrogenases
-transferases
-hydrolases
-lysases
-isomerases
-ligases

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82
Q

What do dehydrogenases/oxioreductases do?

A

oxidation reduction rxns
-often using a cofactor

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83
Q

What do transferases do?

A

transfer groups between molecules
-nucleophilic substitution
-involves movement of electrophilic group

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84
Q

What do hydrolases do?

A

transfer groups involving water between molecules
-cleave rxns by adding water

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85
Q

What do lyases do?

A

aid the formation of double bonds
-add or remv=ove groups

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86
Q

What do isomerases do?

A

intramolecular group transfer
-interconversion of isomeric forms of components
-isomerisation rxns
eg. racemases convert L-amino acid to D-amino acid (racemization)

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87
Q

What do racemase enzymes do?

A

carry out racemization (isomerisation when converting from L-amino acid to D-amino acid)

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88
Q

What do ligases do?

A

join molecules using a chemical energy source (eg. ATP)

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89
Q

What are the roles of biological membranes?

A

-site of rxns (oxidative phosphorylation, photosynthesis)
-separate cells from environment/organelles from eachother
-control movement (highly selective permeability)

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90
Q

What are biological membranes permeable to?

A

-gases (eg. O2, CO2, N2)
-small, uncharged, polar molecules (eg. ethanol)

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91
Q

What are biological membranes impermeable to?

A

-large, uncharged, polar molecules (eg. glucose, fructose)
-ions (eg. K+, Ca2+, Cl-)
-charged polar molecules (eg. amino acids, proteins, ATP, G6P)

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92
Q

What do lipid types within a membrane influence?

A

-curvature
-fluidity
-thickness

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93
Q

What is the structure of phospholipids?

A

-glycerol backbone
with…
-2 fatty acids (hydrocarbon chains = hydrophobic)
-phosphate
-alcohol bound to phosphate (alcohol = hydrophilic)

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94
Q

What different phospholipids are there?

A

-phosphatidyl serine
-phosphatidyl choline
-phosphatidyl ethanolamine
-phosphatidyl inositol

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95
Q

What is the structure of cholesterol?

A

-steroid rings and chains
-OH group at C3

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96
Q

How does cholesterol interact with phospholipids in biological membranes?

A

-steroid rings and chains of cholesterol interacts with fatty acid chains of phospholipids
-hydroxy group at C3 interacts with phosphate head of phospholipid

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97
Q

What do phospholipids and glycolipids form in aqueous media?

A

bimolecular sheets
-no hydrophobic hydrocarbon chains exposed
-complete compartment formed

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98
Q

What does the curvature of a biological membrane depend on?

A

relative sizes of polar heads and non-polar tails of phospholipids
-cylindrical phospholipids (eg. phosphatidyl choline) have relatively large heads so form flat bilayers
-cone-shaped phospholipids (eg. phosphatidyl ethanolamine) have relatively small heads so form curved bilayers

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99
Q

What does the fluidity of a biological membrane depend on?

A

-fatty acid composition
-cholesterol content (more cholesterol = more rigid)

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100
Q

What does biological membrane thickness depend on?

A

lipid composition
-cholesterol has a lipid-ordering effect on phosphoglyceride bilayers

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101
Q

Why do biological membranes appear to have uneven surfaces on electron micrographs

A

due to embedded/associated proteins

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102
Q

How do proteins in bilayers have mobility?

A

-mobility within plane (can move around surface, can’t flip)
-due to fluidity of phospholipids
-depends on thickness and lipids (could encourage clustering of proteins)

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103
Q

What are the roles of membrane proteins?

A

-regulates ionic balance of cell and for processes (ion pumps)
-transport larger molecules across
-receive signals (receptors)
-convert energy stimuli
-convey cell identity (self vs non-self)
-metabolic processes

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104
Q

What is FRAP?

A

FRAP = fluorescence recovery after photobleaching
technique used to visualise lateral movement of membrane proteins

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105
Q

How is fluorescence recovery after photobleaching carried out?

A

-cells are labelled with fluorescent reagent, which is bound to specific lipid/protein
-a laser light is focused on small area of surface of cell, irreversibly bleaching the bound reagent (that area is no longer fluorescent)
-cell is observed over time: fluorescence of bleached area increases as lipids/proteins with bleached reagent move out of bleached area and lipids/proteins with fluorescent reagent move into bleached area

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106
Q

How do proteins conserve asymmetry of membranes?

A

-proteins have a unique orientation so are synthesised and inserted into membrane in an asymmetric manner
-proteins don’t rotate so asymmetry is conserved

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107
Q

What 3 classes are membrane proteins classed into?

A

-integral membrane proteins (intrinsic)
-peripheral/membrane-associated proteins (extrinsic)
-lipid-anchored membrane proteins

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108
Q

What are the properties of integral (intrinsic) membrane proteins?

A

-all/partially embedded in membrane -usually transmembrane (use alpha helices to span membrane but can be beta sheets)
-residues interact with interior hydrophobic regions of membrane
-often extra domains in aqueous space
-require detergent to release from membrane

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109
Q

Do integral (intrinsic) membrane proteins require detergent to be released from membrane?

A

yes

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110
Q

Do peripheral (extrinsic) membrane proteins require detergent to be released from membrane?

A

no

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111
Q

What are the properties peripheral (extrinsic) membrane proteins?

A

-interact with membrane via polar lipid head groups or integral protein
-readily dissociate from membranes (don’t require detergent to do so)

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112
Q

What are the properties of lipid-anchored membrane proteins?

A

-phospholipid (hydrophobic tail) embedded in membrane (no amino acids)
-protein polypeptide remains in aqueous space

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113
Q

What are the types of membrane transfer proteins?

A

-channels(/pores)
-transporters (passive/active)

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114
Q

What do channel proteins transport?

A

ions or molecules

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115
Q

Which direction do channel proteins transport substances?

A

either direction depending on concentration gradient (diffusion)

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116
Q

What do passive transporter proteins transport?

A

specific solutes

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117
Q

Which direction do passive transporter proteins transport substances?

A

in direction of concentration gradient (diffusion)

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118
Q

Which direction do active transporter proteins transport substances?

A

against concentration gradient

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119
Q

What is uniport transport?

A

transport of a single type of solute

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120
Q

What is symport transport?

A

transport of two types of solute in the same direction

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121
Q

What is antiport transport?

A

transport of two types of solute in opposite directions

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122
Q

What is primary active transport?

A

transport directly coupled to energy source

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123
Q

What is secondary active transport?

A

transport coupled to an ion concentration gradient

124
Q

What are ATP-binding cassette (ABC) transporters?

A

transporters which carry substrates across a membrane by using the hydrolysis of ATP
-have a transmembrane channel domain, ATP binding domain, substrate binding domain

125
Q

Why do cells need to be able to receive signals?

A

-to receive info from environment so that they can adjust cellular activity to ensure survival/maximise use of conditions
-to communicate with other cells to coordinate activities (regulate cell divison)

126
Q

What is quorum sensing?

A

cell-cell communication in unicellular prokaryotes (bacteria)
where they produce, secrete and detect autoinducers
-low concs of autoinducer => individual behaviour
-high concs of autoinducer => group behaviour (collaborative or antagonistic)

127
Q

What do bacteria do when they detect low concentrations of autoinducer (in quorum sensing)?

A

individual behaviour

128
Q

What do bacteria do when they detect high concentrations of autoinducer (in quorum sensing)?

A

group behaviour
-if signal was from same species, collaborative group behaviour
-is signal was from other species, antagonistic group behaviour (against eachother)

129
Q

What are first messenger chemical signals?

A

signals produced in a cell released by diffusion or exocytosis which are detected by intracellular receptors or target cell surface receptors
-molecule produced is known as a ligand
-hormones (endocrine) or local mediates (paracrine)

130
Q

What are the key features of signals?

A

-unique (relay defined signal, detected by specific receptors)
-small (travel easily)
-can be synthesised, released or altered quickly (to quickly start signalling)
-can be degraded or re-sequenced quickly (to quickly stop signalling)

131
Q

What are hormones?

A

first messenger involved in endocrine (long distance) signalling

132
Q

What are local mediators?

A

first messenger involved in paracrine (short distance) signalling

133
Q

What are some examples of endocrine signalling?

A

-adrenaline released by adrenal gland
-insulin released by pancreas
-testosterone released by testes
-oestrogen released by ovaries

134
Q

What affect does adrenaline have in its target cells?

A

heart cells -increases contractions (heart rate)
liver cells -increases breakdown of glycogen
-diff response induced in diff target cells

135
Q

What are some examples of paracrine signalling?

A

-histamine released by most cells as an immune response
-acetylcholine (neurotransmitter) released by nerve terminals

136
Q

What is autocrine signalling?

A

highly localised signalling where the first messenger is released and detected by the same cell
eg. quorum sensing in bacteria, growth factors released by cancer cells

137
Q

What is contact dependent signalling?

A

highly localised signalling between adjacent cells
-membrane bound signals bind to specific receptors on adjacent cells
-in early development eg. delta/notch in nerve cell specification

138
Q

What are the ideal properties of a receptor?

A

-high specificity
-high affinity for ligand (in some situations, low affinity may be ideal)

139
Q

What mediates a receptor’s affinity for a signal?

A

non-covalent bonds

140
Q

What gives receptors specificity for a ligand?

A

complex tertiary structure (3D shape) of protein

141
Q

What happens when a ligand binds to a receptor?

A

-receptor undergoes a conformational change
-receptor is activated and can convert extracellular signal into an intracellular signal by inducing a change in the cell cytoplasm

142
Q

What are the classes of receptors in animals?

A

-ligand gated ion channels
-G-protein coupled receptors
-receptors associated with enzyme acitivity

143
Q

What are secondary messengers?

A

signals produced by effectors associated with receptor to generate a response within a cell
-regulate cell metabolism, gene transcription, cell differentiation, changes in cytoskeleton (to transport), cell development
eg. Ca2+

144
Q

What are ligand gated ion channels?

A

multi-subunit, transmembrane proteins forming a pore that specific ions can travel through down an electrochemical gradient
-channels can be opened or closed (regulatory ligands)
eg. present in post-synaptic knob in neuronal synapses in response to neurotransmitter ligands -sodium channel in response to acetylcholine

145
Q

What are receptors with enzymic activity?

A

single pass transmembrane proteins with a domain with enzymic activity in cytoplasm
-operate as dimers
-most act as protein kinases

146
Q

What do protein kinases do?

A

add a phosphate group to serine, histidine, tyrosine and threonine residues in eukaryotic cells
-added phosphate group alters protein charge, which changes its conformation => switches protein activity on/off

147
Q

What does ligand binding cause in receptor tyrosine kinases?

A

-dimerization of receptor
-activation of kinase domain

148
Q

What intracellular signalling pathways are activated by receptor tyrosine kinases?

A

-kinase cascades (activated receptor acts as docking site which proteins can bind to)
-secondary messengers (phospholipase C docking causes Ca2+ release)

149
Q

How does the Ras switch work?

A

-guanine exchange factor (GEF) causes Ras-GDP (off) to release GDP and by GTP, causing a conformational change which switches Ras on
-Ras-GTP (on) activates specific kinases, causing cell proliferation
-GTPase activating protein (GAP) binds to Ras-GTP (on) and hydroluses GTP to GDP, causing a conformational change which switches Ras off

150
Q

What switches Ras on?

A

guanine exchange factor (GEF)
-causes Ras to release GDP and bind GTP
-conformation change

151
Q

What switches Ras off?

A

GTPase activating protein (GAP)
-hydrolyses GTP to GDP
-conformational change

152
Q

What hapens in a kinase cascade?

A

-phosphorylated receptor dimers act as a docing site for other proteins
-these proteins arecognise and bind to the phosphorylated tyrosine (may act as adaptor proteins)

153
Q

What is an oncogene?

A

a mutated protooncogene causing a normal cell to become cancerous

154
Q

What mechanisms can happen in receptor tyrosine kinases when there is cancer?

A

-gain of function mutations (change in regulation)
-amplification (increased expression)
-kinase domain duplication (auto-activation)
-autocrine activation

155
Q

How can mutation in Ras lead to cancer?

A

-Ras can still bind GTP but can’t hydrolyse it so is stuck in on position
-causes uncontrolled growth and proliferation

156
Q

What happens to cause the calcium release as a secondary messenger signalling pathway activated by receptor tyrosine kinases?

A

-phospholipase C (PLC) docks directly onto phosphorylates tyrosine residues in RTK
-RTK phosphorylated PLC, increasing its activity
-as a result, PLC cleaves PI2P into IP3 and DAG
-IP3 binds to receptors on ER membrane, causing a release in Ca2+
-increase in Ca2+ activates specific proteins (DAG also affects the activity of these proteins)
-both IP3 and DAG cause and amplify signals inside cells

157
Q

What are G-protein coupled receptors?

A

receptors which have a seven-pass transmembrane structure and are coupled to G protein on their cytosolic side

158
Q

What is the signalling mechanism of G-protein coupled receptors?

A

-ligand binding causes a conformational change in G-protein coupled receptor
-this increases the G-protein coupled receptor’s affinity for ligand, so the ligand can interact with the G-protein
-this interaction causes the G-protein to release GDP => switches G-protein on
-activated G-protein moves away and activated an effector enzyme

159
Q

How do the speeds of receptors vary

A

fastest to slowest:
ligand-gated ion channels
G-protein coupled receptors
receptor tyrosine kinases

160
Q

What do interactions between signalling pathways enable?

A

-regulation
-signal amplification

161
Q

What intracellular responses are caused by signals?

A

-protein phosphorylation
-production or release of secondary messengers
-activation of enzyme or transcription factors

162
Q

What can thermodynamics tell you?

A

whether a rxn can happen in specific conditions
-tell you nothing about time scale (kinetics does)

163
Q

What is potential energy?

A

the energy depending on the position of object based on other forces
work = force x distance

164
Q

work (J) =

A

force (N) x distance (m)

165
Q

kinetic energy (J) =

A

1/2 x mass x velocity^2

166
Q

How does the kinetic energy change in a collision?

A

stays the same before and after collision

167
Q

What is kbT?

A

the typical kinetic energy of one molecule
units: J

168
Q

How can kb be used?

A

to compare energy to see how strong/weak interaction is

169
Q

Why is it more likely for a protein to go from its unfolded state to its folded state?

A

-attractive forces aid it to go from unfolded to folded
-going from folded to unfolded would require lots of unfavourable rxns

170
Q

ΔG =

A

ΔH - TΔS

171
Q

What does the free energy of a state take into account?

A

-the likelihood of microstates (PE of microstates ≈ enthalpy)
-number of microstates

172
Q

for conc gradient across a membrane
ΔG a->b =
for one molecule

A

kbTln(Cb/Ca)

173
Q

for conc gradient across a membrane
ΔG a->b =
for one mole

A

RTln(Cb/Ca)

174
Q

Keq =

A

[prods]eq
___________
[reacts]eq

175
Q

Γ =
(mass action ratio)

A

[prods]
________
[reacts]

176
Q

What does ΔG depend on?

A

-intramolecular configurational entropy (how many configurations are available)
-some conc independent terms
-some conc dependent terms

177
Q

energy change (J) =

A

charge on object (C) x potential difference (JC^-1 or V)

178
Q

for H+ across a membrane
ΔG =

A

e x ΔΨ
where e = charge on electron
ΔΨ=membrane potential

179
Q

for moving charges
ΔG =

A

NA x e x ΔΨ
where NA= Avogadro’s constant
e= charge on electron
(F=NAxe)
ΔΨ= membrane potential

180
Q

Why are initial rates usually used in practicals?

A

-might not know initial conc
-prods may inhibit
-may have small pH changes
-enzymes may be unstable

181
Q

rate =

A

d[A]
_____
dt

182
Q

What do rates depend on?

A

-temp
-pressure
-pH
-ionic strength
-reagent concs
-sequence of events
-rxn mechanism

183
Q

What order are irreversible unimolecular rxns?

A

first
v=k[A]

184
Q

What order are irreversible biomolecular rxns?

A

second
v=k[A][B]

185
Q

What does Kd represent?

A

ligand binding
-the lower Kd is, the stronger the binding (better ligands, stronger interactions, etc)

186
Q

Kd =

A

koff
_____
kon

187
Q

What is the correlation between Kd and binding strength?

A

higher Kd = weaker binding

188
Q

Michaelis Menten equation
rate =

A

kcat x [E]T x ([S]/[S]+KM)
where kcat =rate constant for rxn of ESC
[E]T = total enzyme conc
KM =Michaelis constant

189
Q

Using Michaelis Menten equation
Vmax=

A

kcat x [E]T

190
Q

What are competitive inhibitors?

A

molecules that bind to an enzyme and prevent substrate binding
-typically bind in active site
-so need higher [substrate] to compete against inhibitor ∴KM increases
-once substrate is in active site, enzyme can act as normal ∴kcat is unchanged

191
Q

How do competitive inhibitors affect the Michaelis constant (KM)?

A

KM increases

192
Q

How do competitive inhibitors affect the rate constant for rxn of ESC (kcat)?

A

kcat doesn’t change

193
Q

What are allosteric inhibitors?

A

molecules that bind to an enzyme somewhere other than the active site but (generally) alter the shape of the active site
-can affect binding and chemistry ∴KM and/or kcat can change

194
Q

What does metabolism involve?

A

-anabolism (endergonic processes)
-catabolism (exergonic processes)

195
Q

What is anabolism?

A

synthesis of substances
-endergonic (non-spontaneous) processes
eg. protein synthesis

196
Q

What is catabolism?

A

breakdown of substances
-exergonic (spontaneous) processes
-provide energy and precursors for anabolism
eg. glucose oxidation

197
Q

What are endergonic processes?

A

non-spontaneous processes
-have +ΔG

198
Q

What are exergonic processes?

A

spontaneous processes
-have -ΔG

199
Q

What is a metabolic pathway?

A

series of linked rxns usually involving a discrete enzyme at each step which catalyses the conversion of one molecule to another

200
Q

What must metabolic pathways be?

A

-thermodynamically likely (net -ΔG)
-kinetically feasible (aided by enzymes)
-physically possible (all enzymes present and accessible)
-shielded from unwanted side rxns (regulatory pathways -switches on/off, shielding active site, separate compartments)

201
Q

What are the benefits of metabolic pathways?

A

-make complex transformations kinetically possible
-allow energy production site by releasing free energy in manageable amounts by coupling them to synthesis in activated carriers
-generate diverse range of chemical structures (flexibility)
-have a high level of control (more steps=more possible control sites)

202
Q

What are the common features of metabolism in different organisms?

A

-many common pathways (eg. glycolysis)
-common set of regulatory principles
-common set of co-factors
-use of ATP
-6 types of rxns in cells

203
Q

What are heterotrophs?

A

organisms which obtain energy by oxidising reduced carbon sources (eg. sugars, fats)
-rxns occur in small steps -low Ea (kinetically feasible), controlled

204
Q

Why do rxns in heterotrophs occur in small steps?

A

-low Ea ∴kinetically feasible
-controlled -can be captured and stored in activated carriers

205
Q

What common activated carrier molecules are there?

A

-ATP (carries Pi)
-NADH/NADPH/FADH2 (carry e-/H)
-acetyl coA (carries acetyl group)
-carboxylated biotin (carries carboxy group)
-S-adenosylmethionine (carries methyl group)
-uridine diphosphate glucose (carries glucose)

206
Q

How are carrier molecules activated?

A

via catabolism

207
Q

How are carrier molecules deactivated?

A

via anabolism

208
Q

Why is ATP less stable than ADP and Pi?

A

-phosphates’ -ve charges repel eachother
-increased entropy
-ADP and Pi are stabilised by water
-free Pi is stabilised by resonance structures not possible when bound in ATP

209
Q

What is a rxn’s capacity to do work down to?

A

mass action ratio (Γ -ratio of prods to reacts) being displaced from eqm
-not ATP having that attribute but [ADP][Pi]/[ATP] ratio being away from eqm so rxn acts as energy store

210
Q

What are the substances in glycolysis?

A

glucose
glucose-6-phosphate
fructose-6-phosphate
fructose-1,6-bisphosphate
(dihyroxyacetate phosphate)
glyceraldehyde-3-phosphate
1,3-bisphosphoglycerate
3-phosphoglycerate
2-phosphoglycerate
phosphoenolpyruvate
pyruvate

211
Q

What stages in glycolysis use ATP?

A

-phosphorylation of glucose, producing glucose-6-phosphate (step 1)
-phosphorylation of fructose-6-phosphate, producing fructose-1,6-bisphosphate (step 3)

212
Q

What stages in glycolysis produce NADH?

A

-oxidation of glyceraldehyde-3-phosphate, producing 1,3-bisphosphoglycate (step 6)

213
Q

Which stages in glycolysis produce ATP?

A

-conversion of 1,3-bisphospholycerate to 3-phosphoglycerate (step 7)
-conversion of phosphoenolpyruvate to pyruvate (step 10)

214
Q

What was Harden and Young’s experiment on glycolysis?

A

-homogenised yeast cells
-homogenate still carried out fermentation but dialysed cell didn’t
∴something smaller than protein needed to work with enzymes -cofactors!

215
Q

What enzyme is needed for glucose phosphorylation (step 1 of glycolysis)?

A

hexokinase

216
Q

Why does adding a phosphate to glucose (producing glucose-6-phosphate) prevent it from leaving the cell?

A

-makes it -vely charged -can’t easily cross membrane

217
Q

How does hexokinase work?

A

-glucose binding causes conformational change
-cleft closes, making active site (around glucose and ATP) more polar -excludes water (preventing unwanted ATP hydrolysis) and favours direct transfer of Pi from ATP to glucose

218
Q

What is the mechanism of hexokinase?

A

-active site contains Asp residue which deprotonates C6 OH of glucose
-deprotonated O:- acts as nucleophile and attacks gamma Pi of ATP
-Pi is directly transferred to glucose

219
Q

What enzyme is needed for glucose-6-phosphate isomerisation to produce fructose-6-phosphate (step 2 of glycolysis)?

A

phosphoglucose isomerase

220
Q

Which steps in glycolysis are control steps (driving rxns)? And why?

A

-glucose phosphorylation (step 1)
-fructose-6-phosphate phosphorylation (step 3)
-conversion of phosphoenolpyruvate to pyruvate (step 10)

because they have -ΔG (providing thermodynamic driving force) giving glycolysis a net -ΔG

221
Q

What enzyme is needed for the phosphorylation of fructose-6-phosphate (step 3 of glycolysis)?

A

phosphofructokinase

222
Q

How is glycolysis regulated?

A

At rest:
glycolysis inhibited
-ve feedback
-glucose-6-phosphate inhibits hexokinase
-high energy charge of ATP/AMP inhibit phosphofructokinase and pyruvate kinase

During exercise:
glycolysis stimulated
+ve feedback
-low energy charge of ATP/AMP activated phosphofructokinase
-fructose-1,6-bisphosphate forward stimulates pyruvate kinase

223
Q

What enzyme is needed for the cleavage of fructose-1,6-bisphosphate (step 4 of glycolysis)?

A

aldolase

224
Q

What enzyme is needed for the conversion of dihydroxyacetate to glyceraldehyde-3-phosphate (step 5 of glycolysis)?

A

triose phosphate isomerase

225
Q

What is the mechanism of triose phosphate isomerase?

A

-10aa loop region moves over active site
-this blocks exit of enediol (intermediate) so that it can’t form methyl glyoxal (toxic)

226
Q

What enzyme is needed for the oxidation of glyceraldehyde-3-phosphate (step 6 of glycolysis)?

A

glyceraldehyde-3-phosphate dehydrogenase

227
Q

How does glyceraldehyde-3-phosphate dehydrogenase work?

A

-couples oxidation of aldehyde to acid (energetically favourable) with the formation of acyl-phosphate group (energetically unfavourable) via thioester intermediate

228
Q

What enzyme is needed for the conversion of 1,3-bisphosphoglycerate to 3-phosphoglycerate (step 7 of glycolysis)?

A

phosphoglycerate kinase

229
Q

What does the Mg2+ in phosphoglycerate kinase’s active site do?

A

activate ADP

230
Q

What is substrate level phosphorylation?

A

transfer of phosphate group from a compound of high phosphoryl transfer potential to ADP

231
Q

What enzyme is needed for the isomerisation of 3-phosphoglycerate to 2-phosphoglycerate (step 8 of glycolysis)?

A

phosphoglycerate isomerase

232
Q

What enzyme is needed for the removal of water from 2-phosphoglycerate (step 9 of glycolysis)?

A

enolase

233
Q

What enzyme is needed for the conversion of phosphoenolpyruvate to pyruvate (step 10 of glycolysis)?

A

pyruvate kinase

234
Q

What happens to pyruvate and NADH in an absence of oxygen?

A

fermentation
-to lactate by lactase dehydrogenase in muscle
-to acetylaldehyde and then ethanol by pyruvate decarboxylase and alcohol dehydrogenase in yeast and bacteria

-converts NADH back to NAD so it can enter glycolysis again

235
Q

What enzyme converts pyruvate to lactate in the absence of oxygen in muscles?

A

lactase dehydrogenase

236
Q

What enzymes convert pyruvate to ethanol in the absence of oxygen in yeast and bacteria?

A

pyruvate decarboxylase
alcohol dehydrogenase

237
Q

What enzymes are present in the pyruvate dehydrogenase complex?

A

-pyruvate decarboxylase
-dihydrolipoyl transacetylase
-dihydrolipoyl dehydrogenase

238
Q

Which cofactors can the pyruvate dehydrogenase complex bind?

A

-NAD
-FAD
-Coenzyme A
-lipoamide
-thiamine pyrophosphate

239
Q

What happens in the link reaction?

A

-pyruvate is decarboxylated to CO2 and a hydroethyl fragment, which gets bound to a thiamine pyrophosphate (TPP) cofactor in pyruvate decarboxylase
-hydroxyethyl-TPP is oxidised to an acetyl fragment, which gets bound to a lipoamide cofactor on dihydrolipoyl transacetylase
-acetyl-dihydrolipoamide reacts with CoA to form acetyl CoA and dihydrolipoamide, which is oxidised by FAD, forming FADH2 which goes on to reduce NADH to NAD by dihydrolipoyl dehydrogenase

240
Q

What enzyme decarboxylates pyruvate (in step 1 of the links reaction)?

A

pyruvate decarboxylase

241
Q

What enzyme oxidises hydroxyethyl-TPP (in step 2 of the links reaction)?

A

dihydrolipoyl transacetylase

242
Q

What enzyme converts acetyl-dihydrolipoyl transferase to acetyl CoA to reduce FAD and NADH (in step 3 of the links reaction)?

A

dihydrolipoyl dehydrogenase

243
Q

What are the substances in the Krebs cycle?

A

oxaloacetate
citrate
isocitrate
α-ketoglutarate
succinyl-coA
succinate
fumarate
malate

244
Q

Which steps of the Krebs cycle produce NADH?

A

-oxidation of isocitrate (step 3)
-decarboxylation of α-ketoglutarate (step 4)
-regeneration of oxaloacetate from malate (step 8)

245
Q

Which steps of the Krebs cycle produce ATP?

A

-conversion of succinyl-CoA to succinate (step 5)

246
Q

Which steps of the Krebs cycle produce FADH2?

A

-oxidation of succinate (step 6)

247
Q

What enzyme is needed for citrate formation (step 1 of the Krebs cycle)?

A

citrate synthase

248
Q

What is the intermediate in citrate formation from acetyl CoA and oxaloacetate (step 1 of the Krebs cycle)?

A

S-citryl CoA

249
Q

What happens in citrate formation (step 1 of the Krebs cycle)?

A

-citrate synthase removes a H+ from acetyl CoA’s methyl group, to generate CH2 – which acts as a nucleophile and attacks carbonyl group of OAA
-S-citryl CoA intermediate formed
-intermediate is hydrolysed (energetically favourable) by water to regenerate CoA

250
Q

What enzyme is needed for citrate isomerisation (step 2 of the Krebs cycle)?

A

aconitase

251
Q

What happens in citrate isomerisation (step 2 of the Krebs cycle)?

A

-aconitase isomerises citrate to isocitrate by removing water and then adding back to move OH from C3 to C4
-via cis-aconitate intermediate

252
Q

What is the intermediate in citrate isomerisation (step 2 of the Krebs cycle)?

A

cis-aconitate intermediate

253
Q

What enzyme is needed for the oxidation of isocitrate (step 3 of the Krebs cycle)?

A

isocitrate dehydrogenase

254
Q

What happens in the oxidation of isocitrate (step 3 of the Krebs cycle)?

A

-isocitrate dehydrogenase catalyses OH on C4 to be oxidised (to a carbonyl group) by reducing NAD
-unstable oxalosuccinate intermediate formed
-intermediate decarboxylated, producing α-ketoglutarate and CO2

255
Q

Why is it important CO2 is produced in steps of the Krebs cycle?

A

-creates a strong thermodynamic pull
-CO2 is very stable
-CO2 easily leaves rxn site (bc it’s v soluble in water and is membrane soluble) -pulls rxn to right

256
Q

What enzyme is needed for the decarboxylation of α-ketoglutarate (step 4 of the Krebs cycle)?

A

α-ketoglutarate dehydrogenase complex

257
Q

What happens in the decarboxylation of α-ketoglutarate (step 4 of the Krebs cycle)?

A

-α-ketoglutarate dehydrogenase catalyses C5 to be oxidised from +3 to +4 via decarboxylation and C4 to be oxidised from +2 to +3
-oxidation is coupled to formation of NADH

258
Q

What enzyme is needed for the conversion of succinyl-CoA to succinate (step 5 of the Krebs cycle)?

A

succinyl-CoA synthetase

259
Q

What happens in the conversion of succinyl-CoA to succinate (step 5 of the Krebs cycle)?

A

-thioester bond is hydrolysed (using water) and replaced with phosphodiester bond (using Pi from the soln -not from ADP) which is catalysed by succinyl-CoA synthetase
-phosphate is then transferred to ADP to produce ATP (substrate level phosphorylation)

260
Q

What is the mechanism of succinyl-CoA synthetase?

A

-Pi in active site acts as nucleophile towards carbonyl group, severing the thioester bond
-succinyl phosphate intermediate forms,
-His side chain in active site acts as a nucleophile towards phosphate, which severs the phosphodiester bond
-the phosphate group is then transferred to ADP, forming ATP and regenerating the His side chain

261
Q

What enzyme is needed for the oxidation of succinate (step 6 of the Krebs cycle)?

A

succinate dehydrogenase

262
Q

What happens in the oxidation of succinate (step 6 of the Krebs cycle)?

A

-succinate is oxidised to fumarate by succinate dehydrogenase, using FAD as a cofactor (reducing it to FADH2)

263
Q

What enzyme is needed for the hydration of fumarate (step 7 of the Krebs cycle)?

A

fumarase

264
Q

What happens in the hydration of fumarate (step 7 of the Krebs cycle)?

A

-fumarase adds water to C=C bond to form OH group (avoids C≡C bond forming which helps oxidation in step 8)

265
Q

What enzyme is needed for the oxidation of malate (step 8 of the Krebs cycle)?

A

malate dehydrogenase

266
Q

What happens in the oxidation of malate (step 8 of the Krebs cycle)?

A

-malate dehydrogenase converts OH group to carbonyl group, using NAD as a cofactor, to regenerate oxaloacetate

267
Q

What happens in the oxidation of malate (step 8 of the Krebs cycle)?

A

-malate dehydrogenase converts OH group to carbonyl group, using NAD as a cofactor, to regenerate oxaloacetate

268
Q

What does it mean that the Krebs cycle is an amphibolic cycle?

A

-both anabolism and catabolism occurs
-intermediates provide precursors for anabolic reactions

269
Q

What can oxaloacetate go on to produce?

A

-glucose
-amino acids -purines and pyramidines

270
Q

What can succinyl-coA go on to produce?

A

-chlorophyll
-porophyins
-heme

271
Q

What can α-ketoglutarate go on to produce?

A

-glutamane -other aas -purines

272
Q

What can citrate go on to produce?

A

-fatty acids
-sterols

273
Q

How is a β-cleavage site generated in the Krebs cycle? And what does this allow to occur?

A

-β-cleavage site is generated by condensing acetylCoA with OAA
-allows full oxidation to occur

274
Q

How was the Krebs cycle discovered?

A

-Krebs observed that adding acids (citrate, malate, etc) to homogenates of minced pigeon muscle stimulated an unusually large uptake of oxygen
-each acid was acting catabolically to stimulate oxidation of an endogenous substance (sugars in pyruvate) in the muscle tissue
-when malonate (comp inhibitor of succinate dehydrogenase) was present, succinate would always accumulate -suggesting it was a cycle

275
Q

How can stimulatory effects in the Krebs cycle be explained?

A

-if one of the intermediates is in low supply, rate is limited and there’s a low oxygen uptake as only small amounts of NADH and FADH2 are produced and can be used in oxidative phosphorylation
-if any of the intermediates is acid, O2 uptake is stimulated as large amounts of NADH and FADH2 are produced and can be used in oxidative phosphorylation

276
Q

How did Krebs measure the uptake of oxygen?

A

using a Warburg manometer
-measures changes in pressure caused by O2 uptake (CO2 is absorbed by filter paper soaked in KOH)
-substrates added in side flask and tipped to mix

277
Q

What is the energy released from the transfer of electrons from NADH/FADH2 to O2 used for?

A

to drive the formation of proton motor force for ATP synthesis

278
Q

What are the five complexes used in oxidative phosphorylation?

A

-NADH dehydrogenase
-succinate dehydrogenase
-cytochrome bc1 complex
-cytochrome oxidase
-ATP synthase
(all in the inner mitochondrial membrane)

279
Q

What is complex 1 in oxidative phosphorylation?

A

NADH dehydrogenase

280
Q

What is complex 2 in oxidative phosphorylation?

A

succinate dehydrogenase

281
Q

What is complex 3 in oxidative phosphorylation?

A

cytochrome bc1 complex

282
Q

What is complex 4 in oxidative phosphorylation?

A

cytochrome oxidase

283
Q

What is complex 5 in oxidative phosphorylation?

A

ATP synthase

284
Q

What happens at complex 1 (NADH dehydrogenase) in oxidative phosphorylation?

A

-NADH dehydrogenase oxidises NADH to NAD, transferring e- to ubiquinone, reducing it to ubiquinol
-free energy released is used to pump 4H+ across the inner mitochondrial membrane (from the matrix to intermembrane space)

285
Q

What is the overall reaction at complex 1 (NADH dehydrogenase) in oxidative phosphorylation?

A

NADH + 5H+matrix + UQ -> UQH2 + NAD + 4H+ims

286
Q

What is redox potential?

A

measure of affinity of redox couple for e-
-the more -ve, the more likely redox couple is to release e- (reductant)
-the more +ve, the more likely redox couple is to accept e- (oxidant)

287
Q

What is the electron transport chain in term of redox potentials?

A

energetically favourable flow of e- from -ve to +ve redox potentials via series of sequential redox rxns

288
Q

How is the standard redox potential of a couple measured?

A

-using standard hydrogen half cell and substance’s half cell
-if e- flow to hydrogen half cell, its redox potential is more -ve than hydrogen’s

289
Q

How is electron transfer coupled to proton pumping (in complexes 1 and 4) in oxidative phosphorylation?

A

-NADH and UQ (in complex 1)/cytochrome c (in complex 4) binding causes a conformational change, promoting the uptake of H+
-when UQ/cytochrome c is reduced, another conformational change occurs, altering which side the bound H+ are exposed to
-as UQ/cytochrome c are released, the affinity for H+ decreases, causing them to be released
-complex’s confirmation is reset

290
Q

What happens at complex 2 (succinate dehydrogenase) in oxidative phosphorylation?

A

-succinate dehydrogenase oxidises succinate to fumarate, passing e- to FAD to form FADH2 (Krebs)
-2e- are passed onto ubiquinone, forming ubiquinol
-no H+ are directly pumped (FADH2 yields less H+ than NAD)

291
Q

What is the overall reaction at complex 2 (succinate dehydrogenase) in oxidative phosphorylation?

A

succinate + UQ + 2H+matrix -> fumarate + UQH2

292
Q

Why are no H+ directly pumped at complex 2 (succinate dehydrogenase) in oxidative phosphorylation?

A

FADH2 yields less H+ than NAD

293
Q

What happens at complex 3 (cytochrome bc1 complex) in oxidative phosphorylation?

A

-cytochrome bc1 complex oxidises ubiquinol to ubiquinone, transferring e- to cytochrome c, reducing it
-free energy released is used to pump 4H+ across the inner mitochondrial membrane (from the matrix to intermembrane space)

294
Q

What is the overall reaction at complex 3 (cytochrome bc1 complex) in oxidative phosphorylation?

A

UQH2 + 2cytCox + 2H+matrix -> UQ + 2cytCred + 4H+ims

295
Q

What is the difference between ubiquinone and ubiquinol?

A

-ubiquinone is the oxidised form (has 2 ketone groups)
-ubiquinol is the reduced form (has 2 hydroxy groups)

296
Q

What is cytochrome c?

A

-small soluble e- carriers in mitochondrial intermembrane space
-has haem cofactor
-Fe3+ (in haem cofactor) is reduced to Fe2+ each time cytochrome c binds 1 e-

297
Q

How is a translocating loop formed between complex 3 and complex 1/2 in oxidative phosphorylation?

A

-complex 3 oxidises ubiquinol, which is provided by complex 1/2
-2H+ are taken up from the matrix when ubiquinone is reduced to ubiquinol but when ubiquinol is oxidised, these 2H+ are released into the intermembrane space
-for every ubiquinol complex 3 oxidises, 2 extra H+ are moved from the matrix into the intermembrane space via Q-cycle

298
Q

What happens at complex 4 (cytochrome c oxidase) in oxidative phosphorylation?

A

-cytochrome c oxidase reduces cytochrome c, transferring its e- to oxygen, which is used with 2H+ from the matrix to produce water
- free energy released is used to pump 2H+ across the inner mitochondrial membrane (from the matrix to intermembrane space)

299
Q

What is the overall reaction at complex 4 (cytochrome c oxidase) in oxidative phosphorylation?

A

2cytCred + 4H+matrix + ½ O2 -> 2cytCox + H20 + 2H+ims

300
Q

What happens at complex 5 (ATP synthase) in oxidative phosphorylation?

A

-potential energy of proton motor force is used to drive energetically unfavourable ATP formation
-protons flowing through ATP synthase turns F0 rotor
-this drives the Fi ATP synthase head to turn, causing the synthesis of ATP
-1 full turn carries 8H+ and produces 3 molecules of ATP

301
Q

What is the overall reaction at complex 5 (ATP synthase) in oxidative phosphorylation?

A

8H+ims + 3ADP + 3Pi -> 3ATP + 8H+matrix

302
Q

What is the structure of ATP synthase?

A

-H+ carrier (rotor ring) -embedded in inner mitochondrial membrane
-central stalk
-together the H+ carrier and central stalk form the F0 rotor
-Fi ATP synthase head

303
Q

What is proton motor force?

A

force formed from the combination of membrane potential (difference in charge across membrane) and proton concentration difference (pH difference)

304
Q

Why is the actual H+/ATP higher than calculations would say it is?

A

-proton motive force also drives metabolic exchange between mitochondria and cytoplasm -metabolites need to be actively transported into mitochondria
-for each ADP, pyruvate and Pi imported costs the equivalent to one H+

305
Q

How much ATP is produced per one molecule of glucose in respiration?

A

26

2 from glycolysis
2 from Krebs cycle
22 from oxidative phosphorylation

306
Q

What did Mitchell suggest to explain how ATP is generated in oxidative phosphorylation?

A

electrochemical H+ gradient

307
Q

What is the Beer-Lambert law? (Abs=)

A

Abs = Ecl
when Abs = absorbance
E = extinction coefficient
c = conc (M)
l = length (cm)

Molecular Biology BSc First Year (10 decks)

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