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Medicine 1 > Week 3 - Biochemical Basis > Flashcards

Week 3 - Biochemical Basis Flashcards

1
Q

What does enzyme under or over expression lead to?

What’s a clinical example of when this occurs?

A

Cell dysfunction

Heart attack

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2
Q

What functional groups are present at the active catalytic site of an enzyme?

A
  • Co-enzymes
  • Metal ions
  • Amino acid residues
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3
Q

What are the key points to remember about the lock-and-key theory?

A
  • Substrate binds through hydrophobic, electrostatic interactions and hydrogen bonds
  • Steric hindrance and charge repulsion can prevent binding
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4
Q

What are the key points to remember about the induced-fit model?

A
  • Enzymes undergo conformational changes
  • Repositioning of amino acid side chains
  • Dynamic surface
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5
Q

What to remember about the transition state complex?

A
  • Point at which bonds become maximally strained
  • Unstable, high-energy complex with strained electronic configuration
  • Activation energy of formation is reduced compared to non-catalysed reaction
  • Transition state decomposes to products
  • Enzyme then returns to original form
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6
Q

What does the transition state complex bind more tightly to?

A

Enzyme

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7
Q

What are the catalytic properties of an enzyme usually dependent on?

A

Cofactors/co-enzymes

i.e. NAD+, NADP+, FAD

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8
Q

What are prosthetic groups?

A

Tightly bound cofactors

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9
Q

What are the 2 general cofactor classes?

A

Activation-transfer

Oxidation-reduction

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10
Q

What happens during activation-transfer?

A
  • Directly participate in catalysis by forming covalent bond with substrate
  • Performed by coenzyme’s function group
  • Separate protion binds to enzyme
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11
Q

What happens during oxidation-reduction?

A
  • Coenzyme involved in oxidation from compound
  • Coenzyme involved in reduction of a compound
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12
Q

What are the properties of lactate dehydrogenase?

A
  • Catalyses transfer of electrons from lactate to NAD+
  • Uses coenzyme NAD+
  • ADP portion binds to enzyme and alters conformation
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13
Q

What are the properties of metal ions in catalysis?

A
  • Positive metal ions act as electrophiles
  • Assist in substrate binding or stabilise anions
  • Can accept or donate electrons in oxidation-reduction reactions
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14
Q

What are isoenzymes?

A
  • Enzymes that differ in amino acid sequence
  • Catalyse same chemical reaction
  • May show different kinetic parameters
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15
Q

What are multi-enzyme complexes and their advantages?

A

Enzymes promote consecutive reactions in a metabolic pathway

  • Transit time via diffusion reduced
  • Less interference as products are acted upon by correct enzyme
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16
Q

What are the 3 categories of enzymes in serum?

A
  • Serum specific enzymes –> normal location
  • Secreted enzymes –> i.e. pancreatic lipase or salivary amylase
  • Non-serum specific enzymes –> no role in serum, released due to cell turnover, damage or malignancy
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17
Q

What factors affect clinical exploitation of enzymes?

A
  • Organ specificity
  • Existence of isoenzymes
  • Reference ranges
  • Variable rate of increase in serum activity
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18
Q

What are the key points relating to ischaemic heart disease?

A
  • Oxygen to heart is compromised by cholesterol-rich atheromatous plaques
  • Blockages lead to:
    • Temporary ischaemia and angine pectoris
    • Myocardial infarction
    • Irreversible damage to cardiac cells
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19
Q

What are the properties of creatine kinase?

A
  • Dimeric protein –> M=muscle, B=brain
  • 3 isoforms
  • Heart = mainly MM
  • Skeletal muscle = mainly MM
  • Brain, stomach, intestine, bladder = mainly BB
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20
Q

What happens when creatine kinase levels rise?

A

Myocardial infarction

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21
Q

What is the Michaelis-Menten equation?

What are the assumptions?

A
  • Number of molecules is large
  • Low % enzyme-bound substrate
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22
Q

What does it indicate when [S]>>Km?

A
  • All active sites are occupied
  • Reaction rate independent of [substrate]
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23
Q

What does it indicate when [S]<<km></km>

A
  • Active site occupancy is low
  • Reaction rate directly related to number of sites occupied
  • Rate proportional to [substrate]
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24
Q

What is Km?

A

Michaelis constant

Concentration of substrate which permits enzyme to acheive half of Vmax

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25
Q

What does low and high Km mean?

A

Low = high substrate affinity

High = low substrate affinity

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26
Q

What is Kd?

A

Dissociation constant

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27
Q

How do you calculate cayalytic efficiency (η)?

A

η = Kcat / Km

Kcat = turnover number

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28
Q

What does Lineweaver-Burke allow us to work out on a graph?

A
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29
Q

What is a reversible inhibitor?

A
  • Not covalently bound to enzyme
  • Can be removed by dialysis
  • Characterised by Ki (inhibition constant)
  • Can be competitive, non-competitive or uncompetitive
30
Q

What are competitive inhibitors?

A
  • Compete with substrate
  • Close structural analogue’
  • Can be overcome by increasing substrate concentration
  • Increase apparent Km
  • No effect on Vmax
31
Q

What are non-competitive inhibitors?

A
  • Doesn’t compete with substrate
  • Lowers enzyme Vmax as it lowers [active enzyme]
  • No effect on Km
32
Q

What are uncompetitve inhibitors?

A
  • Can only bind to ES
  • Creates dead-end complex (ESI)
  • Cannot be overcome by increasing substrate concentration
33
Q

What is irreversible inhibition?

A
  • Bind covalently to enzyme
  • Cannot be removed by dialysis
  • Reduces amount of enzymes available for reaction
  • Can target functional group or metal atom of active site
34
Q

What is the relationship between penicillin and bacterial cell walls?

A
  • Bacterial cell wall allows them to live in hypotonic environments
  • Penicillin binds to and inactivates transpeptidase
  • Balance between cell wall biosynthesis and degradation disrupted
35
Q

What are suicide inhibitors?

A
  • Unreactive until they bind to enzyme active site
  • Converted into a reactive compound
36
Q

what is African sleeping sickness?

A
  • Caused by trypanosome
  • Cell coat covered by a single protein and antigen sensed by immune system
  • Host develops fever
  • Cycle repeats until patient dies
37
Q

What are the 2 main methods for enzyme regulation?

A
  • Substrate repsonse
  • Product inhibition
38
Q

What mechanisms control rate-limiting enzymes?

A
  • Allosteric activation/inhibition
  • Phosphorylation
  • Protein-protein interactions
  • Proteolytic cleavage
39
Q

What is allosteric regulation?

A
  • Activity modulation via reversilbe, non-covalent binding of small molecules
  • Small molecules = effectors
  • Bind at allosteric site (NOT active site or substrate binding site)
  • Changes catalytic site conformation
  • Rapid process
40
Q

What are the advantages of allosteric regulation?

A
  • Effectors can be activators as well as inhibitors
  • Effectors don’t need to resemble substrate or product
  • Rapid regulation –> effect as soon as [effector] changes
41
Q

How do you distinguish between an allosteric activator and inhibitor?

A

Activator = enzyme activity increases when effector binds

Inhibitor = enzyme activity decreases when effector binds

42
Q

What is the difference between and hetero and homotropic effector?

A

Homotropic effector = substrate serves as allosteric effector

Heterotropic effector = effector is different from substrate

43
Q

What is positive and negative co-operativity?

A

Positive = when substrate binds to one subunit it can enhance the catalytic properties of other subunits

Negative = catalytic properties of other subunits are reduced when substrate binds to subunit

44
Q

What is the Concerted Model?

A
  • Model suggesting reason for positive co-operativity behaviour
  • Initial substrate has difficulty binding to subunit as is in T state
  • Once binding occurs, adjacent subunits change to R state
  • Activators increase fraction of enzyme from T to R state
45
Q

What is the role of muscle glycogen phosphorylase in glycogenolysis?

A
  • Degrades glycogen to glucose 1-phosphate
  • Regulated by activator [AMP]
  • Increases in cell as ATP used for muscular contraction
  • Signals need for more fuel and ATP generation
46
Q

What happens during phosphorylation?

A
  • Addition of phosphate to serine, threonine and tyrosine residues
  • Negatively charged residues
  • Alters ionic interactions and hydrogen bond patterns
  • Mediated by protein kinases (ATP = phosphate donor)
  • Phosphate groups removed by protein phosphatases via hydrolysis
47
Q

What affect does adrenaline have on cAMP?

A

Increases intracellular concentrations

48
Q

What do protein-protein interactions lead to?

A

Conformation change in the active site

49
Q

How does the calcium-calmodulin family of modulator proteins work?

A
  • Bind to other proteins
  • Modulate activity
  • Via steric hindrance and conformational change of catalytic site
  • Can modulate activity of glycogen phosphorylase kinase too
50
Q

What are the properties of G proteins?

A
  • Contain an ‘internal clock’
  • Act as GTPases which slowly hydrolyse GTP
  • Change conformation
  • Dissassembly of complex formed
  • Activity can be regulated by accessory proteins
51
Q

What is proteolytic cleavage?

A
  • Enzymes can be irreversibly activated or inactivated by proteolytic enzymes
52
Q

What do membranes have a central role in?

A
  • Reaction sequences
  • Energy conservation
  • Cell-to-cell communication
53
Q

What biological activities are derived from cell physical properties?

A
  • Exocytosis etc.
  • Flexible
  • Self-sealing
  • Selectively permeable
54
Q

How are ion fluxes restricted in cells?

A

Hydrophobic interior of cell membrane

55
Q

Where do ion concentrations vary between in a cell?

A

Extracellular fluid and cell

Cell cytoplasm and compartments

56
Q

What is the structure of a phospholipid?

A
57
Q

What are micelles?

A

Clusters of phospholipids to prevent water contact with hydrophobic iner layer and molecule entry into cell

58
Q

What happens when edges are exposed in cell membrane?

A

Vesicles form

59
Q

What are the properties of fatty acids?

A
  • Hydrophobic, hydrocarbon chain
  • Have terminal carboxyl group
60
Q

What are the 2 main types of lipids and their proeprties?

A

Phospholipids

  • Have phosphate group in hydrophillic part
  • Joined by phosphodiester bonds

Glycolipids

  • Contains covalently attached carbohydrate
61
Q

What are the 3 classes of membrane lipids?

A
  • Phosphoglycerides
  • Sphingolipids
  • Cholesterol
62
Q

What are the properties of phosphoglycerides?

A
  • Polar head groups attached to phosphate
  • 2 fatty acids esterified to a glycerol backbone
  • Phosphate attached to position 3 of glycerol
  • Phosphate-head group in hydrophillic
63
Q

What are the properties of sphingolipids?

A
  • Simple fatty acid joined to sphingosine (a fatty amine)
  • Some are phospholipids, some glycolipids
  • Often in neuron membranes
  • 2 hydrophobic tales (1 = fatty acid residue, 1 = hydrocarbon tail of sphingosine)
64
Q

What are the properties of cholesterol?

A
  • Sterols = compounds characterised by 4 fused hydrocarbon rings
  • Structurally more rigid than other membrane lipids
  • >10% of total lipid in PM and golgi
  • Cholesterol = minor component of bilayer but helps maintain membrane fluidity
65
Q

What are some proeprties of the plasma membrane?

A
  • Bilayer is asymmetric
  • High phosphatidylcholine and sphingomyelin in outer leaflet
  • High phosphatidylserine and phosphatidylethanolamine in inner leaflet
  • Dynamic membrane composition
  • Slow lipid diffusion between leflets
66
Q

What is the role of flippase?

A

Moves phospholipids from outer to cytosolic leaflet

67
Q

What is the role of floppase?

A

Moves phospholipids from cytosolic to outer leaflet

68
Q

What is the role of scramblase?

A

Moves lipids in either direction, toward equilibrium

69
Q

What are the properties of membrane proteins?

A
  • Asymmetric orientation
  • Integral ones contain transmembrane domains
  • Peripheral proteins can be released by ionic solvents
  • Lipid anchored proteins bound to inner or outer membrane surface
70
Q

What is the glycocalyx?

A
  • Short chains of oligosaccharides on surface proteins and lipids extend into aqueous medium
  • Protects cell from digestion
  • Restricts hydrophobic compound uptake
  • Glycoproteins contan blacnhed 15 sugar residues

Medicine 1 (28 decks)

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