Gloss Flashcards
1
Q
2* protein structure
A
Alpha helices or beta sheets, often based on the “preference” of the residue. Key structures based on properties of the residues in a small section of the primary structure, especially their psi or phi angles - “allowed” planes of the r residue. Stretches with similar angles will have regular secondary structure. Glycine and proline interfere with these structures, and many problematic mutations change them. Stabilized by the delocalization of electrons in formed pi orbitals of the n-c bond.
2
Q
3* protein structure
A
Polypeptide folding, often assisted by chaperone proteins. Always spontaneous due to the hydrophobic effect! Only about 2000 known ways to fold but these few scaffolds can have infinite functions. Stabilization from bonds, van der waals, salt bridges and the hydrophobic effect.
3
Q
4* protein structure
A
Association of multiple polypeptide structures due to h bonds, van der waals forces, and salt bridge formation.
4
Q
Alpha helix
A
Secondary structure. Can be left or right handed. Hydrogen bonds between the n-c backbones form the structure.
5
Q
Beta sheet
A
Secondary structure, usually formed from hydrophobic residues. N-c backbone helps form h bonds. Usually antiparallel but can be parallel (unstable and far less linear)
6
Q
Four major protein functions
A
- Enzymes catalize reactions 2. Information transmission via binding (ligands, Dna, other prot) 3. Transport (inter and extra cellular) 4. Structural integrity of cells or tissues
7
Q
What chirality are the amino acids in proteins?
A
L. All amino acids except glycine (ch3) are chiral. Mirror images are d (dexter) amino acids.
8
Q
What is the n-c backbone bond of a peptide called?
A
Amidepeptide bond
9
Q
What are the types of side chains that amino acids can have?
A
Polar Charged Uncharged Non-polar Aromatic Aliphatic
10
Q
Positively charged amino acid residues
A
K: lysine R: arginine H: histidine All of these can be post-translationallly modified to have regulatory roles in chromatin structure and gene transcription
11
Q
Negatively charged amino acid residues
A
D: aspartate (forms b sheets) (methylene branched, steric hinderence to a helices) E: glutamate (forms a helices) Structurally are very different!
12
Q
Uncharged amino acid residues
A
N: asparagine (derivative of d) Q: glutamine (derivative of e) S: serine T: Threonine (sterically hindered so less reactive, no a helices) C: cysteine (cysteine cross links or di-sulfide bonds)
13
Q
Aliphatic amino acid residues
A
G: Glycine (hates any secondary structure) A: Alanine P: Proline (hates any secondary structure) V: Valine (methylene branched, steric hinderence to a helices) L: Leucine I: Isoleucine (methylene branched, steric hinderence to a helices) M: methionine
14
Q
Aromatic amino acid residues
A
Y: tyrosine W: tryptophan F: phenylalanine
15
Q
The hydrophobic effect
A
Causes folding of proteins to be spontaneous. Hydrophobic residues bundle to face inwards, greatly increasing the entropy of the surrounding water, which was previously pretty ordered around residues that repelled it.
16
Q
What are the major categories of tertiary folding structure?
A
Class : major 2* elements. A? A&b? B? Architecture: spatial arrangement of 2* elements - many in each class (packing of 2* elements) Topology: connectivity of 2* elements and the order in which shape is created. CAT pyramid!
17
Q
Oligomer
A
Stable complex of more than one polypeptide chain Stabilization : h bonds Van der waals forces Salt bridges (all the same as 3* without hydrophobic)
18
Q
Subunit
A
One polypeptide chain in an Oligomer
19
Q
Homooligomer
A
Oligomer with identical subunits Homodimer, homotrimer, etc
20
Q
Heterooligomer
A
Different subunits
21
Q
What are some reasons the body might form oligomers?
A
A. Less genetic info needed for large structures B. Easier and cheaper repair by swapping just one subunit C. Enhanced stability of many proteins (folate reductase is a single protein normally but a dimmer is a thermophilic homologue) D. Substrate channeling - when one enz is done the next is right there to continue the rxn without refinding the substrate E. Regulation by cooperation and allostery (hgb, mgb) F. Coordinate regulation
22
Q
What were the old vs new thoughts about protein folding and stability?
A
Old: proteins must fold completely to be stable and functional, and then can work. Pasteurs lock and key model. New: the native state is often an ensemble of related conformations, and flexibility is often essential for activity.
23
Q
1* protein structure
A
Amino acid order from n terminus to c terminus. Ultimately determines folding and stability of the protein. Functionally important residues are some of the most conserved DNA sequences.
24
Q
What are some takeaway points from this graph?
A
Native state is lowest energy = spontaneous folding
Energy wells get narrower as protein folds = less conformations as move towards native state
Native state only marginally stable - only about energy change of 1 ATP hydrolysis so that proteins can have necessary turnover and conformational change
25
Delta H, Delta S, and Delta G of protein folding
Delta H is enthalpy, energy of the aa system. Not always favorable
Delta S is the entropy of the solvent and is ALWAYS favorable (hydrophobic effect).
Delta G is
Delta G is negative (spontaneous) but is typically small
26
Intrinsically Disordered Protein (IDP)
A protein that undergoes conformational changes when binding its substrate
Accounts for 1/3 human proteins
lack hydrophobic cores to prevent aggregation (amyloid fibrils) while not in the native state
27
Why wouldn't an IDP have a hydrophobic core?
They spend most of their time incompletely folded.
If incomplete with a hydrophobic core they may aggregate into amyloid fibrils and cause amyloidgenic diseases.
28
PONDR
Predictor of Naturally Disordered Proteins
Developed at WSU
looks at the DNA genome to find non hydrophobic regions, especially those rich in charged residues or proline.
29
Two possible effects of protein misfolding
Gain of function mutations (often worse)
Loss of function mutations
30
Why chaperone assisted folding?
A child has the map, but needs an adult to help read it.
1. accelerates slow reactions, especially by shuffling disulfide bonds or interconverting cis/trans proline bonds.
2. Provides a favorable environment for folding
3. Prevents accumulation of 1/2 folded proteins - MAINTAINS PROTEOSTASIS
31
Hsp70
eukaryotic chaperone protein that binds to unfolded proteins as they exit the ribosome to prevent accumulation of 1/2 foldeds
Binds to protein sequences rich in hydrophobic side chains then performs ATP hydrolysis and releases. Can rebind if incorrect still.
32
GroEL/GroES
prokaryotic chaperone proteins that bind unfolded proteins as they exit the ribosome
Prevent aggregation from accumulation of 1/2 folded protein
Gives an encapsulated area for folding
EL = 2 rings + ES - cap, protecting from solvent
33
Why do most amyloidogenic diseases become more prevalent with age?
An age-related loss of chaperone proteins
Often, decline in ability to up-regulate chaperones in response to stress.
Less chaperones = more accumulation of 1/2 folded proteins.
34
Cystic fibrosis - what kind of protein mutation?
Loss of function mutation
Deletion of Phe508 in CFTR, a Cl- conductor. Misfolding = protein is not inserted into the membrane, less Cl- across the membrane.
Decrease in mucus linings of the respiratory tract
Increase in opportunistic infectsion (MRSA, pseudomonas)
Reoccuring infection = lung damage
35
Aggregation - what type of mutation?
EITHER
LOF of the chaperone proteins
GOF of an oligomer structure
36
Sickle cell anemia - what kind of mutation?
GOF mutation
Glu to Val mutation
Affects 4\* structure of Hgb, creation of chains of tetramers
Chains = "sickling" and lysis of RBCs, o2 binding is diminished
37
Amyloid fibrils
Insoluable, low energy strucutres formed by beta-sheet rich (hydrophobic) misfolded or half folded proteins
Array of b-sheets in a right handed helix.
38
Amyloidogenic disease - in general
40 or more human diseases, mostly caused by endogenous proteins going "bad"
Fibrils are diagnositic of these diseases
SMALL aggregations of amyloids seem to be toxic element
39
Prion diseases
Only transmissible type of amyloidogenic diseases
Diseased proteins can "corrupt" endogenous proteins and cause fibril formation
Zoonotic only if prions are of similar size in two species
Examples: Mad cow, kuru, CWD
40
Familial amyloid polyneuropathy - dx and drug
Affects transthyretin, which normally carries 4 thyroxin
Disease = destabalizes. amyloids form, no thyroxin carried
Drug: Tafamidis. Small ligand that attaches to the protein and stabalizes it enough to stop aggregation and carry 2 thyroxine. (Enough for no phenotype)
41
General rules for catalysts
1. unchanged at the end of a reaction
2. effect rate by LOWERING energy barrier of the transition state
3. DO NOT effect equilibrium - cannot make the rxn spontaneous
4. Especially useful if conditions lead to a slow reaction (provide a closed environment and/or stero/regio specificity).
42
General functions of catalysts
1. entropy reduction: bring molecules closer together
2. change orientation (especially in side chains - reduce entropy of the shape)
3. specificity - sterio/regio side rxns are minimized
4. desolvation - move into a more favorable (often hydrophobic) environment
43
What are some of the main takeaways of this graph? ![]()
By themselves: ATP and glucose would join but VERY SLOWLY
With Pi: One transition state may happen quickly, but then caught in a "energy well" - rest of the reaction would occur incredibly slowly
with enzyme: dramatically reduces energy barrier of the transition state = MUCH FASTER
44
Enzymes bind to the transition state generally
Draw two graphs - one with preferential binding to the substrate and one with preferential binding to the transition state to show why the second is more favorable.
If bound to the substrate, a massive energy well would be formed, so the reaction would be incredibly unfavorable and slow.
45
Should drugs targeting enzymes appear like their substrate or the transition state?
Transition state - preferential binding.
46
![]()
What is k1?
What is k2?
Which is the rate limiting step?
k1 = enzyme binding to the substrate, REVERSIBLE
k2 = chemistry to create the product, IRREVERSIBLE
EITHER can be the rate limiting step.
47
Perfect enzyme
In which the k-1 (dissolution of enzyme/sub) is much smaller than k2 (chemistry)
(essentially, chemistry is not the rate determining step - if it binds, it does its job)
a HIGHLY EFFICIENT enzyme
48
Assumptions of a steady-state
Rate of formation = rate of decay (by all possible pathways)
SO
The [intermediate/E.S] is constant over time
49
Draw a progress curve in a steady state over time for:
[enzyme]
[E.S]
[Product]
[Substrate]
Including the pre-steady state and steady state time periods
![]()
50
ternary complexes
Protein with three or more molecules
Most enzymes have two or more substrates
If rxns are ordered, enzyme said to have no ternary complex (first one is generated, then second, no complex needed)
If rxns are random, the enzyme has a ternary complex (both products are released at the same time, complex needed)
51
For our purposes, what are the parameters of the Michaelis-Menten equation telling us?
1. We are in a steady state
2. Chemistry is the rate-determining step
3. We can now solve for the velocity of the chemisty rxn based on [E.S] and k2
52
Two versions of the Michaelis-Mickelsen equation
v0 = (vmax . [S]) / (kM + [S])
or
vo / [E]tot = (k2 . [S]) / (KM + [S])
53
vmax and kcat are?
Measures of speed of the reaction
Relatively interchangable BUT kcat is corrected for the amount of enzyme in an experiment (1 animal's vs 2 animal's enzymes) or vmax/[e]assay
Units = 1/s
54
kM is?
SATURATION. amount of substrate that gets you to 1/2 of vmax.
(k-1 + k2) / k1 or rate of decay/rate of formation
Not a direct measure of binding affinity, but a good indicator.
55
kcat/km is?
EFFICIENCY.
measures the rate when [s] approaches 0. Can tell us whether [s], [e], or chemistry is the limiting step.
56
Draw an M-M plot - rate vs [substrate]
Mark kcat and kcat/km
![]()
Two asymptotes: kcat and [s]=0
57
How can natural inhibitors change the M-M plot?
Two ways:
can change efficiency (kcat/cm slope is lower but kcat is the same. Think of the affinity of biscuits and kibble - dog like biscuits better, more efficient, higher kcat/km slope but same result)
can change kcat (lower asymptote, kcat/km changed by this but not as the direct effect)
58
Why would enzymes typically work better targeting kcat/km than targeting kcat?
Cells typically aren't high in [s] naturally
If [s] is high, adding more won't change the m-m plot
if [s] is low, adding more will SIGNIFICANTLY change the m-m plot
if [s] is constant at a low point, changing kcat/km will change rate much more dramatically than changing kcat.
59
What is the rule of thumb betwen [s] and kM?
[s] and kM tend to be on the same order of magnitude (microM vs mM, etc.)
60
What are mechanism based inhibitors?
Irreversible inhibitiors, "suicide" inhibitors, or "trojan-horse" inhibitors.
Caused by the covalent modification of an enzyme, hijacking the enzyme's mechanism to trap reactive intermediates ad prevents completeion of normal catalytic cycles.
Usually powerful and potent but SPECIFIC inhibitors
61
What are the three types of reversible inhibition and what distinguishes them?
- Competative inhibition
- Uncompetative inhibition
- Mixed (Noncompetative) inhibition
Depends on what state of the enzyme they bind
62
Clavamox mechanism of action
Mechanism based inhibitor (irreversible)
Normal bacterial wall: transpeptidase carries out a two part rxn to create a cross-linkage between two peptidoglycan chains to make an essential protein in the bacterial cell wall.
1st, beta-lactam (-cillins). Have an aromatic R group with a lactam ring active site. Mimicks the ser active site that transpeptidase would normally bind, but there is no leaving group and so the transpeptidase is irreversibly bound.
Bacterial cell response: beta-lactamases that cleave lactam rings of -cillins and regenerate the beta-lactamase.
2nd, clavulanic acids: Irreversible covalently bind to the b-lactamases, allowing the -cillins to do their job.
63
What would an energy/time chart look like for a suicide inhibitor?
Gigantic energy well from the covalent modification.
64
Competative inhibition
Type of reversible inhibition
Binds to E, and E.I and E then compete for S
65
Uncompetative inhibition
Type of reversible inhibition
I binds to E.S, preventing chemistry
66
Mixed inhibition
Type of reversible inhibition, aka noncompetative
Binds to both E and E.S
67
Which M-M parameter is affected by competative inhibition? How is it affected?
Increases Km, and so decreases Kcat/Km
- leads to a decrease in efficiency and slope of kcat/km on the M-M plot
Think: Change to efficacy of E by competition with E.I when high [S] = 0
Change to efficacy of E by competition with E.I when low [S] = high
equation: 1/v = (1/vmax) + (alpha)(km/vmax.[s])
68
alpha (in M-M parameters)
alpha = 1+([i]/ki)
A term for the inhibitor
The placement of alpha in an M-M equation will tell you what type the inhibitor is if you look at what term it is multiplied by.
69
What is the effect of having a low Kcat/Km?
A much larger substrate concentration is needed to reach saturatuation (0.5vmax)
70
What are methotraxate, trimethoprim sulfa, and sulfa drugs all an example of?
Competative inhibitors that target dihydrofolate reductase in bacteria - make the bacteria unable to replicate DNA.
71
Which M-M parameter does Uncompetative Inhibition affect?
Kcat; Also affects Kcat/Km because Kcat is changed
If [E.S] is bound, inhibitor has a large effect at a large [S]
Inhibitor has a much smaller effect at lower [S]
In equation: alpha multiplied by [S]
Rarest type of inhibition: very few real world examples
72
What M-M parameter will mixed inhibition affect?
BOTH kcat and Km, so affects both kcat and kcat/km (not changed proportionally)
Effective at both low [substrate] (binds E) and at high [substrate] (binds E.S)
alpha multiplied by [S] AND kcat in equation.
Note: the inhibitor may not bind with equal affinity to E vs E.S but will still bind both.
73
What is the difference between mixed and non-competative inhibition?
Both have the same effects on the M-M parameters and non-competative is a type of mixed. Noncompetative inhibitors bind E and E.S with EXACTLY EQUAL affinity, mixed inhibitors still bind both but maybe not with the same affinity.
74
Where do competative inhibitors bind to an enzyme?
Where do uncompetative inhibitors bind to an enzyme?
Competative inhibitors: look like substrate and bind to the active site.
Uncompetative inhibitors: the majority of the time bind to another, non-active site so that they can bind regardless of if E has bound S.
75
Saint John's Wort
Natural supplement that acts as a mixed inhibitor of the liver cytochrome P450. Have the same function as many liver Rxs and can cause problems with the steady state if both are taken at the same time.
76
What type of pathways do allosteric enzymes regulate?
Mostly metabolic pathways
77
What is cooperativity in terms of enzyme function?
Binding at site A affects the binding at site B
Usually in oligomers.
78
Equilibrium of inactive and active oligomers.
Oligomers are always in a mix between active and inactive state proteins
R = relaxed = active state = promoted by activators
T = taut = inactive state = promoted by inhibitors
different ligands and activators can bind and shift the equilibrium from more T to more R with allosteric reactions.
79
Homotropic effectors
The two states R (active) and T (inactive) of a protein caused by a ligand that binds at the normal binding site
Example: Hgh and oxygen. O2 shifts towards R state.
80
Why regulate with allostery?
Fine tunes the sensitivity of a system - doesn't have to be all on or all off.
Sensitivity can be based on multiple types of stimuli (ATP vs GTP, etc)
Enables cross-talk between metabolic pathways (if the cell has high or low energy)
81
How will inhibitors and activators effect the protein equilibrium state?
Inhibitiors = push towards the T state
Activators = push towards the R state
82
Heterotropic effectors
Switch a protein from T to R by binding somewhere besides the active site
83
Draw a M-M chart that depicts allostery.
![]()
Sigmoidal graph
Will still be reaching the same kcat but the amount of substrate needed to get to 1/2kcat will be higher in the sigmoidal plot due to the low activity of the T state.
84
Draw the two lines that make up the sigmoidal shape of an allosteric response. Why does the sigmoidal shape happen in actuality?
![]()
In actuality, T state will dominate at low [S] while R state will dominate at high [S]
Will see the same sigmoidal graph by adding effectors non-dependent on [S]
85
Why do homotropic effectors help Hgb do its job in the body?
In the tissues: we want Hgb to be more in the T state so that it drops O2 off
In the lungs: we want Hgb to be more in the R state so it picks O2 up
If Hgb was all R or T it wouldn't pick up and drop off effectively - the pO2 of the tissues and the lungs is not different enough. But, because R-T equilibrium changes sigmoidally with pO2 it can function well in both tissues.
86
The Bohr effect
The effect of pH on O2 affinity or Hgb R/T equilibrium
Increased pH encourages the R state, decreased encourages the T state
CO2 is acidic. H+ is a NEGATIVE heterotropic effector - encourages the inactive state of the protein and causes affitnity to drop.
As more active cells release CO2, Hgb drops off more oxgen at those tissues
87
Fetal vs maternal Hgb
Maternal Hgb : alpha and beta subunits
Fetal Hgb: alpha and gamma subunits. Gamma subunits have a His to Ser substitution which WEAKENS the T state of the fetal Hgb so that the R state is slightly more favored and so has a higher affinity for O2 than maternal Hgb. This sub also DECREASES the Bohr effect by decreasing affinity for H+ protons (negative heterotropic effector)
88
Anabolism
The synthesis of macromolecules
Consumes energy to create necessary molecules
89
Catabolism
The degradation of molecules to produce energy
90
Reciprocal regulation
What activates one pathway will repress an opposite pathway
Ex: high ATP or NADH turns off catabolism, and turns on anabolism
91
Redox potential of anabolism
Anabolism favors METABOLITE REDUCTION
Uses NADPH as a reducing equivalent
NADP+ : NADPH ratio very very low (keep product low!)
92
Redox potential of catabolism
Catabolism favors METABOLITE OXIDATION
Produces NADH
NAD+ : NADH ratio very very high (keeps product low)
93
NADPH and NADH structures and functions
Structures: incredibly similar. Nicotinamide rings where the chemistry occurs. The phosphate group of NADPH is NOWHERE NEAR where chemistry occurs
Functions: Very different - not interchangable. NADPH = used in ANABOLIC pathways and NADH is formed in catabolic pathways.
94
Catabolic pathway to key intermediate
All linear pathways tend to converge into one or two main metabolic substrates that can then be used by cyclical pathways (TCA, glycolysis) to create energy
95
Anabolic pathway from intermediate
Tends to be linear and diverging. Take something, build it into one of hundreds of different macromolecules. Can also use cyclic pathways to create new molecules.
96
Why are metabolic pathways irreversible no matter the pathway type?
Net value of the reaction will always be exergonic (spontaneous) with some low delta G steps and some highly negative delta G steps
Anabolic pathways ARE NOT just catabolic pathways in reverse. Require different enzymes to move past highly negative delta G steps, even if some of the low delta G steps are easily reversible.
Anabolic : A to B to C
Catabolic: C to X to Y to A (not just C to B to A)
97
What would be the best step at which to regulate a metabolic pathway?
Flux generating steps: anything with a large delta G. River and lake example - a small change will have a larger effect with higher flux.
Also must think of first committed steps - the only way to turn a pathway completely on or off. Think of fructose in glycolysis.
98
Levels of metabolic regulation
1. Location (organelle, cell type, or organ)
2. Amount of enzyme (transcriptional/translational regulation)
3. Activity of the enzyme (allostery, post-translational modification)
99
Feed forward activation
Precursors activate their pathway
100
Feed back inhibition
Products inactivate their pathway
101
Cell levels of
NAD+ vs NADH
NADP+ vs NADPH
More NAD+ (cell is poised for catabolism)
More NADPH (cell is poised for anabolism)
102
Why gluconeogenesis?
Lots of cells need glucose to function (brain, nervous system). The body stores enough glycogen for about a day and a half of use and then must do gluconeogenesis.
Some anabolic requirements (glucose to ribose, etc)
103
Where does gluconeogenesis occur?
Mainly liver, and to a lesser extent in the renal cortex and the small intestine epithelium.
104
True or false: metabolic pathways exist in a steady state.
True
105
What key intermediates are made into pyruvate for gluconeogenesis?
Animals: Lactate, gluconeogenic amino acids, and tri-acyl glycerols (only the glycerol).
Plants: no lactate but other two above plus CO2 fixation.
106
Amino acid catabolism provides far less energy for oxidation than amino acides, but in starvation conditions the breakdown of protein will start before the fat stores are depleted. Why?
Fas are converted to ACoA through beta oxidation. This is a good source of energy when used in the TCA cycle, but CANNOT be converted by any eukaryotic processes into glucose. This isn't good for the brain or nervous system, so something must be broken down into glucose for those cells.
107
What are the three regulatory steps in glycolysis?
1. Glucose to G-6-P with hexokinase
3. First commited step -regulatory. Fructose-6-P to F-1,6-biP with phosphofructokinase
10. PEP to pyruvate with PK
The first two steps require the use off ATP to ADP. PK regenerates one ADP to ATP.
108
What are the four regulatory steps in gluconeogenesis?
11. pyruvate to OAA with pyruvate carboxylase (ATP to ADP)
10. OAA to PEP with PEP carboxykinase (GTP - GDP)
3. F-1,6-biP to F-6-P with Fruc-bis phosphatase (release Pi) (regulatory step)
1. G-6-P to Glucose with Glu-6-P phosphatase (release Pi)
109
Anapleurotic reactions
Cause the system to "refill" OAA. OAA can be used for catabolic OR anabolic reactions, in many different pathways. Anapleurotic = refill the very useful intermediate.
110
Biotin
A CO2 carrying cofactor.
Bicarbonate + pyruvate uses enz pyruvate carboxylase with biotin to ATP to ADP +Pi and oxaloacetate. 1st step of the two-step bypass of PK.
111
Succinate importance in ruminates
In ruminant fermentation, propionate is produced
To get rid of, propionate + CO2 = succinate which can then be metabolized
112
Delta G of the two step bypass of PK
Gluconeogenic
Positive delta G = 0.9 kJ/mol
not spontaneous but close - just needs to get pushed down the rest of the pathway. Needs enzymes to push through and needs two steps just in case.
113
Why polymerize glycogen? Why not fat or glucose monomers?
1. Much lower osmotic pressure from one long strand than glucose monomers.
2. multiple non-reducing ends of glycogen - MUCH faster to break down than fat
3. glycogen can run anaerobic reactions, fat cannot
4. easier transport through blood than fat (fat has special mechanism)
5. More metabolically versitile than fate (fas to ACoA, glycogen to glucose)
114
Three general steps of glycogen synthesis
1. Activate glucose - UDP-glucose (costs eq. of 2 ATP, one will be released when broken down except at branch sites)
2. Add monomers to glycogen polymer with glycogen synthase
3. Incorporate branches into the polymer with branching enzyme
115
UDP-Glu-pyrophosphorylase
Enzyme for the activation step of glycogen synthesis
Rxn driven by the hydrolysis of pyrophosphate
116
Glycogen synthase
Enzyme in the linking step of glycogen synthesis
Releases UDP
Only can add in a straight line with alpha 1,4 linkages
\*This is the point of reciprocal regulation in glycogenolysis\*
117
Branching enzyme
Third branching step of glycogen synthesis
Occurs by transfer of an 8-12 monomer chain from the main.
Two functions: Hydrolysis of an alpha 1,4 bond from the non-reducing end of the polymer and formation of an alpha 1,6 bond as a branch.
118
Degradation of Glycogen (Glycogenolysis)
1. Cleave one monomer with glygogen phosphorylase to G-1-P
2a. Hydrolysis of alpha 1,4 bond with debranching enzyme and reformation of alpha 1,4 bond to the main polymer chain
2b. hydrolysis of the alpha 1,6 bond to release glucose with debranching enzyme.
119
Glycogen phosphorylase
First step of glycogenolysis
Breaks of one monomer from the chain by breaking bond with Pi (compare to hydrolysis with H2O) and creates one NTP equivalent, negating one of the ATPs used in synthesis
Product is G-6-P
This is the site of reciprocal regulation with glycogen synthesis
Released monomers must be at least 5 monomers for a branch or this enzyme will be sterically hindered
120
Debranching enzyme
Bifunctional - catalyzes two reactions, 2nd two of glycogenolysis. Common type of enzyme in metabolic processes = improved efficiancy because of sterospecificity.
Hydrolysis of the alpha 1,4 bond of the branch site and reconnection of the branch to the main polymer so that glycogen phosphorylase can chew on it
Hydrolysis of the final glucose's alpha 1,6 bond, released as glucose. Approximately 7% of monomers released as glucose.
121
Storage of glucose as glycogen uses a lot of energy. Is it worth it?
Yes! Return is much faster mobilization of glucose.
122
Glycogen storage diseases
Any disease that causes issues in glycogen metabolism. Common in both humans and animals. Examples - glycogen cannot be unbranched or glucose released has no protein to remove the phosphate group that is attached and so cannot be transported.
123
Isosyme
Enzymes with highly similar functions that are encoded in different tissues. Different tissues (liver vs muscle) will express different isosymes.
124
Should NADH activate or inhibit the TCA cycle?
Inhibit.
NADH = high amount of catabolism and so is a good indicator that the cell has plenty of energy.
TCA cycle produces energy. With high energy we don't need this, so NADH should inhibit the cycle.
125
Why is it good to have signal cascades and second messengers?
1. Signal amplification
2. Wider range of allosteric stimuli
3. Flexibility/sensitivity of control
126
Key regulators of the TCA cycle
Inhibitors: ATP, ACoA, NADH, fatty acids, succinyl-CoA, and citrate
Activators: AMP, ADP, CoA, NAD+, Ca2+ (the muscle needs energy)
127
PDH
Pyruvate dehydrogenase complex
Irreversibly converts pyruvate to ACoA for catabolism
Inhibited by ACoA mainly.
Inactivated by phosphorylation. When ATP is high it can donate a P, so it upregulates PDH kinase ("the regulator of the regulator") which phosphorylates PDH.
128
ACoA's role in regulation of the aerobic fate of pyruvate
Pyruvate can become OAA for anabolism or ACoA for catabolism. It can be derived from both glucose and amino acids.
Level of ACoA is "decision point" for what to turn pyruvate into. PDH is the first committed and irreversible step to catabolism if ACoA is low, but ACoA will deactivate this pathway if high. If high it will also activate pyruvate carboxylate to turn pyruvate to OAA (reversible) for anabolism.
129
Pyruvate carboxylase
pyruvate to OAA for anabolism. Reversible - not a real comitted step.
