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
2
Q
What functional groups are present at the active catalytic site of an enzyme?
A
- Co-enzymes
- Metal ions
- Amino acid residues
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
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
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
6
Q
What does the transition state complex bind more tightly to?
A
Enzyme
7
Q
What are the catalytic properties of an enzyme usually dependent on?
A
Cofactors/co-enzymes
i.e. NAD+, NADP+, FAD
8
Q
What are prosthetic groups?
A
Tightly bound cofactors
9
Q
What are the 2 general cofactor classes?
A
Activation-transfer
Oxidation-reduction
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
11
Q
What happens during oxidation-reduction?
A
- Coenzyme involved in oxidation from compound
- Coenzyme involved in reduction of a compound
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
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
14
Q
What are isoenzymes?
A
- Enzymes that differ in amino acid sequence
- Catalyse same chemical reaction
- May show different kinetic parameters
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
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
17
Q
What factors affect clinical exploitation of enzymes?
A
- Organ specificity
- Existence of isoenzymes
- Reference ranges
- Variable rate of increase in serum activity
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
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
20
Q
What happens when creatine kinase levels rise?
A
Myocardial infarction
21
Q
What is the Michaelis-Menten equation?
What are the assumptions?
A
- Number of molecules is large
- Low % enzyme-bound substrate
22
Q
What does it indicate when [S]>>Km?
A
- All active sites are occupied
- Reaction rate independent of [substrate]
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]
24
Q
What is Km?
A
Michaelis constant
Concentration of substrate which permits enzyme to acheive half of Vmax
25
What does low and high Km mean?
Low = high substrate affinity
High = low substrate affinity
26
What is Kd?
Dissociation constant
27
How do you calculate cayalytic efficiency (η)?
η = Kcat / Km
Kcat = turnover number
28
What does Lineweaver-Burke allow us to work out on a graph?
29
What is a reversible inhibitor?
* Not covalently bound to enzyme
* Can be removed by dialysis
* Characterised by Ki (inhibition constant)
* Can be competitive, non-competitive or uncompetitive
30
What are competitive inhibitors?
* Compete with substrate
* Close structural analogue'
* Can be overcome by increasing substrate concentration
* Increase apparent Km
* No effect on Vmax
31
What are non-competitive inhibitors?
* Doesn't compete with substrate
* Lowers enzyme Vmax as it lowers [active enzyme]
* No effect on Km
32
What are uncompetitve inhibitors?
* Can only bind to ES
* Creates dead-end complex (ESI)
* Cannot be overcome by increasing substrate concentration
33
What is irreversible inhibition?
* 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
What is the relationship between penicillin and bacterial cell walls?
* 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
What are suicide inhibitors?
* Unreactive until they bind to enzyme active site
* Converted into a reactive compound
36
what is African sleeping sickness?
* 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
What are the 2 main methods for enzyme regulation?
* Substrate repsonse
* Product inhibition
38
What mechanisms control rate-limiting enzymes?
* Allosteric activation/inhibition
* Phosphorylation
* Protein-protein interactions
* Proteolytic cleavage
39
What is allosteric regulation?
* 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
What are the advantages of allosteric regulation?
* 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
How do you distinguish between an allosteric activator and inhibitor?
Activator = enzyme activity increases when effector binds
Inhibitor = enzyme activity decreases when effector binds
42
What is the difference between and hetero and homotropic effector?
Homotropic effector = substrate serves as allosteric effector
Heterotropic effector = effector is different from substrate
43
What is positive and negative co-operativity?
_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
What is the Concerted Model?
* 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
What is the role of muscle glycogen phosphorylase in glycogenolysis?
* 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
What happens during phosphorylation?
* 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
What affect does adrenaline have on cAMP?
Increases intracellular concentrations
48
What do protein-protein interactions lead to?
Conformation change in the active site
49
How does the calcium-calmodulin family of modulator proteins work?
* Bind to other proteins
* Modulate activity
* Via steric hindrance and conformational change of catalytic site
* Can modulate activity of glycogen phosphorylase kinase too
50
What are the properties of G proteins?
* 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
What is proteolytic cleavage?
* Enzymes can be irreversibly activated or inactivated by proteolytic enzymes
52
What do membranes have a central role in?
* Reaction sequences
* Energy conservation
* Cell-to-cell communication
53
What biological activities are derived from cell physical properties?
* Exocytosis etc.
* Flexible
* Self-sealing
* Selectively permeable
54
How are ion fluxes restricted in cells?
Hydrophobic interior of cell membrane
55
Where do ion concentrations vary between in a cell?
Extracellular fluid and cell
Cell cytoplasm and compartments
56
What is the structure of a phospholipid?
57
What are micelles?
Clusters of phospholipids to prevent water contact with hydrophobic iner layer and molecule entry into cell
58
What happens when edges are exposed in cell membrane?
Vesicles form
59
What are the properties of fatty acids?
* Hydrophobic, hydrocarbon chain
* Have terminal carboxyl group
60
What are the 2 main types of lipids and their proeprties?
_Phospholipids_
* Have phosphate group in hydrophillic part
* Joined by phosphodiester bonds
_Glycolipids_
* Contains covalently attached carbohydrate
61
What are the 3 classes of membrane lipids?
* Phosphoglycerides
* Sphingolipids
* Cholesterol
62
What are the properties of phosphoglycerides?
* 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
What are the properties of sphingolipids?
* 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
What are the properties of cholesterol?
* 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
What are some proeprties of the plasma membrane?
* 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
What is the role of flippase?
Moves phospholipids from outer to cytosolic leaflet
67
What is the role of floppase?
Moves phospholipids from cytosolic to outer leaflet
68
What is the role of scramblase?
Moves lipids in either direction, toward equilibrium
69
What are the properties of membrane proteins?
* 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
What is the glycocalyx?
* 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
