Biochemistry Final Exam prep Flashcards
1
Q
Synthesis of Acetyl CoA requires three enzymes and five coenzymes.
What are the three enzymes and their Abbreviation code?
A
Pyruvate dehydrogenase component (E1) Dihydrolipoyl transacetylase (E2) Dihydrolipoyl dehydrogenase (E3)
2
Q
There are five coenzymes needed in the synthesis of Acetyl CoA…
What are the three catalytic coenzymes?
What are the two stoichiometric coenzymes?
A
Catalytic coenzymes: TPP, lipoamide and FAD
Stoichiometric coenzymes: CoA and NAD+
3
Q
What is the Prosthetic group of E1, E2, and E3
A
E1 is TPP
E2 is Lipoamide/lipoic acid
E3 FAD
4
Q
In the Synthesis of Acetyl CoA, what is the reaction catalyzed by Pyruvate dehydrogenase component (E1)?
A
Oxidative decarboxylation of pyruvate
5
Q
In the Synthesis of Acetyl CoA, what is the reaction catalyzed by Dihydrolipoyl transacetylase (E2)?
A
Transfer of acetyl group to CoA
6
Q
In the Synthesis of Acetyl CoA, what is the reaction catalyzed by Dihydrolipoyl dehydrogenase E3?
A
Regeneration of the oxidized form of lipoamide
7
Q
The conversion of pyruvate to acetyl CoA involves three
reactions:
A
- Decarboxylation
- Oxidation and
- Transfer of acetyl group
8
Q
What Coenzyme is Derived from vitamin B1?
A
TPP
9
Q
Where does the Conversion of Pyruvate to acetyl CoA occur in eukaryotes?
A
In mitochondrial matrix.
10
Q
What are the functional chemical groups common to any amino acid?
A
α carbon, carboxyl, and amino groups
11
Q
What is the precursor for all nucleotide synthesis?
A
Pyrophosphate (PRPP)
12
Q
Name 4 characteristics of Michaelis-Menten Enzymes:
A
1) Catalytic activity is not regulated
2) activity is controlled by mass action,
3) lack quaternary structure
4) enzyme kinetics plot is hyperbolic
13
Q
Name characteristics of Allosteric enzymes: , usually have quaternary structure with multiple active sites in each enzyme (some could be monomeric and lack quaternary structures).
A
1) Catalytic activity regulated by environmental signals (regulatory molecules and end products in the pathway)
2) kinetics more complex than Michaelis-Menten enzymes
3) kinetics plot is sigmoidal
4) USUALLY have quaternary structure with multiple active sites in each enzyme
4) could be monomeric and lack quaternary structures).
14
Q
Functions of Enzymes:
A
Enhance rates of reactions (applies to all enzymes) Information sensors (applies only to allosteric enzymes)
15
Q
Enzyme Kinetics is:
A
Study of the rates of enzyme-catalyzed chemical reactions
16
Q
Enzyme kinetics reaction V= k[A], what does each letter mean?
A
V= rate/velocity of the reaction k= rate constant [A] = substrate concentration
17
Q
Where is the Electron Transport chain is located in eukaryotes and bacteria
A
eukaryotes: inner membrane of mitochondria
bacteria: located in the plasma membrane.
18
Q
Michaelis-Menten model describes the kinetics of enzymes and is based on the premise:
A
that a specific ES complex is a necessary intermediate in catalysis.
19
Q
When is Vmax attained?
A
ONLY when all enzymes (total enzyme or Et) are saturated/bound to substrate [S]
20
Q
What does Km stand for and what are 3 characteristics of Km?
A
Km stands for Michaelis constant
1) KM is unique to each enzyme,
2) is independent of enzyme concentration
3) depends on specific substrate and environmental conditions.
21
Q
What is a compilation of rate constants?
A
Km, or Michaelis Constant
22
Q
How do you find the Km, or Michaelis Constant?
A
Km= (K-1 + K2) / K1
23
Q
Is Vmax directly or indirectly dependent on enzyme concentration?
A
Directly dependent
24
Q
When is Km equal to the substrate concentration?
A
When the reaction velocity is half its maximal value.
25
At very low substrate concentrations, what happens when the Substrate (S) is much less than the value of Km?
The velocity will be directly proportional to the substrate concentration.
26
What happens when the substrate is much greater than Km?
When Substrate is greater than Km, Vo= (Vmax/Km)[S]
| Velocity will be maximal and independent of substrate concentration
27
Allosteric sites
1) always catalyze the committed steps of metabolic pathway.
2) Binds regulatory molecule (activators or inhibitors)
3) often have a shape different from the substrate molecule.
4) substrate binding site and allosteric site communicates with each other by conformational change of the protein.
5) regulated by products of the pathways under their control.
28
Concerted model (Monod, Wyman and Chaneaux model)
show that allosteric enzymes depend on changes in the quaternary structure and is built on four premises.
29
What is the rate of catalysis symbol?
Kcat (or aka K2) is equal to the rate constant, or rate of Catalysis
30
What is the definition of Vmax (maximum velocity)
Is the turnover number of an enzyme which is the number of substrate molecules that an enzyme can convert into product per unit time when the enzyme is fully saturated with substrate.
31
What is the specificity constant or catalytic efficiency?
Kcat/Km = measures the catalytic efficiency because it takes into account both the rate of catalysis with a particular substrate (Kcat) and the nature of the enzyme-substrate interaction (Km)
32
What are the four stages of Cellular Respiration?
1) Glycolysis 2) Pyruvate oxidation 3) Citric acid cycle
| 4) Oxidative phosphorylation
33
What happens in Glycolysis?
a six carbon is transformed into molecules of pyruvate, a three carbon organic molecule. ATP is made, NAD+ is reduced to NADH
34
What happens in Pyruvate oxidation?
Each pyruvate from glycolysis enters the mitochondrial matrix (innermost compartment of mitochondria) where it is converted to Coenzyme A, or acetyl CoA. CO2 is released and NADH is generated
35
What happens in the Citric acid cycle?
The acetyl CoA combines with a 4 carbon molecule to produce citrate (in the presence of Oxalacetate). At the end, regenerating a 4 carbon molecule, ATP, NADH and FADH2 and CO2 is released.
36
What happens in Oxidative phosphorylation?
The NADH and FADH2 that were made in the other sets, deposit their electrons in the electron transport chain (ETC) converting back to their oxidized forms (NAD+ and FAD). As Electrons move down the chain, energy is released and used to pump protons out of the matrix creating a gradient. Protons flow back into the matrix through a port called ATP synthase, making ATP. At the end to eh chain, Oxygen accepts electrons and takes up protons to form water
37
What is substrate-level phosphorylation?
a phosphate group is transferred from a pathway intermediate straight to ADP
38
What is a kinase?
an enzyme that catalyzes the transfer of phosphate groups from high-energy, phosphate-donating molecules to specific substrates.
39
What is phosphorylation?
high-energy ATP molecule donates a phosphate group to the substrate molecule
40
What are the two enzymes that are involved in the substrate level phosphorylation in glycolysis?
Phosphoglycerate kinase and pyruvate kinase
41
what is oxidative phosphorylation?
When the H+ flows back down the gradient from the electron transport chain. As the H+ passes through the ATP synthase, it drives the synthesis of ATP
42
What is cellular respiration?
When glucose is broken down using an electron transport chain, the breakdown is called cellular respiration
43
What does the mnemonic "LEO goes GER"?
Lose Electrons, Oxidized; Gain Electrons, Reduced.
44
what is a redox reaction?
When one molecule loses electrons and is oxidized, while another molecule gains electrons (the ones lost by the first molecule) and is reduced.
45
What is the electron transport chain?
series of 4 membrane embedded proteins and organic molecules found in the inner membrane of the mitochondria. Electrons are passed from one member of the transport chain to another in a series of redox reactions. Energy is released in the downhill electron transfers and is used to pump protons from mitochondrial matrix to intermembrane space to create the gradient.
46
What is chemiosmosis?
Any process in which energy stored in a proton gradient is used to do work. Energy released from the ETC reactions is captured as a proton gradient, which is then used to make ATP.
47
What are the two most important functions of ETC?
Regenerates electron carriers (NADH and FADH2) pass electrons to the ETC turning back into NAD+ and FAD (Oxidized forms are used in Glycolysis and the Citric Acid Cycle and are needed to keep processes running
Makes a proton gradient with higher H+ concentration in intermembrane space and lower concentration in matrix.
48
What are the Complexes I, III, IV of the ETC?
Proton pumps capture the H+ ions from released as the electrons flow through the chain to pump H+ ions from the matrix to the intermediate space.
49
What is another name of Proton-motive force?
The proton gradient
50
Both complex I and complex II pass their electrons to a small, mobile electron carrier called:
ubiquinone (Q)
51
What does ubiquinone (Q) get converted to and where does it go?
Reduced to form QH2, it travels through the membrane and delivers electrons to complex III
52
What happens to electrons as they move through Complex III?
More H+ ions are pumped across the membrane and are ultimately delivered to the mobile carrier cytochrome C (Cyt C)
53
What does the mobile carrier cytochrome C do?
Carries the electrons to complex IV where the final H+ ions are pumped across the membrane.
54
What does Complex IV of the ETC do?
It passes the electrons to O2, which splits into 2 oxygen atoms and accepts protons from the matrix to form water. Four electrons are needed to reduce each molecule of )2 and two water molecules are formed.
55
What is the allosteric constant (Lo)?
It is the T:R ratio in the concerted model. With T being the tense or less reactive stage and R being the relaxed or active conformation stage.
56
When there is a lack of substrate or signal molecules in the concerted model, what is happening with the T:R?
In the absence of signal molecules or substrate, R and T are in equilibrium with T being the more stable state and therefore more common state.
57
An example of a negative feed back loop would be ATP which is an allosteric inhibitor of, and a substrate for:
Phosphofructokinase, telling it we have enough ATP, glycolysis isn't needed.
58
Because ATP is both an allosteric regulator and a substrate for phosphofructokinase, it is called a:
Homotropic inhibitor (because the substrate and inhibitor is the same molecule)
59
What is an activator for phosphofructokinase
AMP
60
What is an example of a heterotropic activator?
AMP is a regulating molecule but it is not an active site substrate for phosphofructokinase, it is a heterotropic activator.
61
How many steps in glycolysis?
10
62
Best committed steps in a pathway are ones that have a very high:
Negative Delta G value
63
IN the sequential model , the binding of substrate causes conformational change, which makes other subunits with to what state?
R state
64
In the concerted model, the binding of the substrate effects the probability that the enzyme (as a whole) is:
T or R state
65
In the breakdown of amino acids for energy, the final acceptor of the α-amino group(Nitrogen group) is what?
Alpha ketoglutarate. During the breakdown of amino acids for energy, the final acceptor of the α-amino group is α-ketoglutarate, forming glutamate.
66
What does the central metabolism consist of?
includes the Embden-Meyerhof-Parnas (EMP) pathway of glycolysis, the pentose phosphate pathway, and the citric acid cycle
67
For Alanine to enter the Krebs cycle, it has to be converted to:
Pyruvate
68
TO get any amino acids to enter the central metabolism, we have to get rid of the nitrogen group and replace it with a carbonyl group, the amine group (Ammonia) is toxic for the cells, what can accept a nitrogen group?
Alpha-ketoglutarate
69
How does Glutamate play a central role in mammalian nitrogen flow?
Serves as both a nitrogen donor and nitrogen acceptor using glutamate dehydrogenase and glutamine synthetase.
70
How is transamination involved in the gluconeogenic pathway?
Transamination of amino acid alanine to pyruvate allows pyruvate to form glucose through the gluconeogenic pathway.
71
What is the only organ that can safely get rid of nitrogen from the body?
Liver (it uses transamination to form glutamate which enters Urea cycle and is disposed of in urine)
72
Once a chemical is converted to Acetyl CoA, is it reversible?
No it is not, it is the committed step into the cycle in glycolysis, gluconeogenesis and from keto acids(Keto acids can also form Acetyl CoA) but then it is one direction and enters the cycle.
73
What is involved in the anaplerotic pathway?
The anaplerotic pathways include: (1) carboxylation of pyruvate by pyruvate carboxylase; (2) carboxylation of phosphoenolpyruvate by PEP carboxylase; (3) oxidation of malate to pyruvate by the malic enzyme; and (4) the glyoxylate cycle.
74
What Amino acids are catabolized into pyruvate?
| look for the Amino acids that contain three carbon atoms
alanine, serine, glycine (via serine), and cysteine, are converted into pyruvate, (the entry point for the citric acid cycle OR gluconeogenesis).
75
Alanine is converted into pyruvate by a reaction catalyzed by the enzyme
alanine aminotransferase, which reversibly transfers the amino group from the amino acid alanine to 2-oxoglutarate to produce pyruvate and glutamate.
76
Cysteine can be converted into pyruvate:
The three carbons of cysteine can be converted into cystathionine that in turn is transformed into pyruvate and homocysteine.
77
Threonine is an amino acid that is both glucogenic and ketogenic. The most common pathway of degradation involves the formation of:
Acetyl-CoA and glycine. Glycine is then converted into serine (by serine hydroxymethyl transferase) and then into pyruvate by serine dehydratase.
78
What Amino acids are catabolized to oxaloacetate?
Aspartate and asparagine are both readily catabolized to oxaloacetate.
79
What Amino acids are catabolized into acetyl-CoA and acetoacetate?
Lysine and leucine are the only purely ketogenic amino acids,
80
In the Beta oxidation of odd fatty acids, the last segment will contain propionyl Co-A, how is that used in gluconeogeneis?
Propionyl-CoA is converted to succinyl-CoA, which is oxidized or converted to glucose by way of oxaloacetate and pyruvate
81
How are Sphingolipids (membrane lipids) different than phospholipids?
The backbone is serine instead of glycerol.
In sphingosine, the carboxylic acid of serine is attached to palmitic acid in a carbon-carbon bond, rather than the ester bond as seen in phospholipids.
82
How are Sphingolipids (membrane lipids) different than phospholipids?
The backbone is serine instead of glycerol.
In sphingosine, the carboxylic acid of serine is attached to palmitic acid in a carbon-carbon bond, rather than the ester bond as seen in phospholipids.
83
What is a universal donor of nitrogen?
Glutamate
84
How can glutamate help make aspartatate?
Donates a nitrogen to Oxaloacetate to form aspartatate
85
What is the universal methyl donor?
S-adenosylmethionine (SAM) is the major methyl donor in the cell. It is involved in DNA methylation and synthesis of phosphatidylcholine, and in reactions involving neurotransmitters, creatine, carnitine, and antioxidants (such as glutathione and taurine).
86
What does Vitamin C and E do for homocysteine?
vitamins C and E can act within hours.
87
What is another (more traditional way) to lower homocysteine levels?
Use of vitamins B6, B12 and folic acid.
88
Phenylalanine is a precursor to synthesis of (in order):
tyrosine, L-dopa, dopamine, norepinephrine, and epinephrine.
89
Tryptophan is made with low efficiency so it needs to obtained from our diet, but it is a precursor to the synthesis of:
Serotonin and melatonin.
90
histamine is an important biogenic amine with regulatory roles in:
neurotransmission, gastric acid secretion and immune response.
91
How is histidine converted to histamine?
```
Histidine decarboxylase (HDC) is an enzyme responsible for catalyzing the decarboxylation of histidine to form histamine.
Histamine cannot be generated by any other known enzyme.
```
92
Trivalent Chromium is an essential mineral that the body needs in TRACE amounts (too much and it can interfere with medications and biological functions), what is a BIG benefit of Chromium?
Chromium enhances the action of the hormone insulin.
93
Is Riboflavin water or lipid soluble, and how is it attained?
Riboflavin is a water-soluble small organic molecule that is not synthesized by humans.
94
How is Riboflavin connected to Succinate Dehydrogenase?
Riboflavin is metabolically converted in our body into a substance called flavin adenine dinucleotide ( FAD ), which is required by succinate dehydrogenase to function.
95
When substrate concentration is not saturating, but much greater than KM, the catalytic rate is almost equal to:
K2
96
What conclusion can be drawn concerning an inhibitor if the Vmax = Vmaxapp?
The inhibitor binds to the active site of the enzyme
97
What are some characteristics of double displacement type of reactions?
Some products have to leave the active site before other substrates can bind, Transient chemical modification of the enzyme.
98
When [S] < KM and k2 is greater than k-1, what is happening with Kcat and Km?
1) kcat/KM approaches k1
| 2) kcat/KM is controlled by the diffusion rate
99
What are some characteristics of Km of an enzyme?
1) Depends on ion concentrations
2) Varies with different substrates
3) Depends on pH and temperature
100
Name 3 Premises for the concerted model?
1) Allosteric constant (Lo) is high in the absence of the substrate
2) allosteric enzymes have multiple subunits
3) all subunits of the allosteric enzyme are in the same state
101
If we have a mutation in cytoplasmic acetaldehyde dehydrogenase, we will be
insensitive to ethanol
102
Bonding/Interactions between side chains of the amino acids, W(Tryptophan) and F(Phenylalanine), at neutral pH would be:
Hydrophobic
103
NADH and pyruvate binds to the active site of the enzyme alcohol dehydrogenase and forms a complex. **After all substrates bind**, catalysis occurs and the products, ethanol and NAD+ and CO2 are released from the active site. What can you predict about this reaction?
It would be a sequential reaction
104
Sequential reactions are one of the classes involved in multiple substrate reactions. In these types of reactions, all the substrates involved are bound to the enzyme:
before catalysis of the reaction takes place to release the products.
105
Sequential reactions can be:
either ordered or random.
106
Allosteric effectors:
can cause large changes in enzyme activity near Km
107
A mutation in an allosteric enzyme changed the Allosteric constant (Lo) value to zero. The enzyme will:
1) Will be always catalytically active as long as enough substrate is present
2 Will behave like a Michaelis-Menten enzyme
108
The enzyme concentration is 5 nM, the substrate concentration is 5 mM, and the KM is 8 mM. Which of the following is true under the following conditions?
Many of the enzyme molecules do not have a bound substrate.
109
When [S] is way below KM:
[E] = [ET]
110
What vitamin is a necessary cofactor in the conversion of L-phenylalanine to L-tyrosine?
Vitamin B6
111
What vitamin is a necessary cofactor in the conversion of L-DOPA to dopamine?
Vitamin B6
112
If an enzyme with a high Km and a low affinity for its substrate, what does it need to get to Vmax?
It requires a greater concentration of substrate to achieve Vmax
113
What amino acid lacks a beta carbon?
Glycine
114
What is the approximate pOH of water that has a H+ concentration of 6.50 X10^-10?
4.8
115
You have been observing an inset that defends itself from enemies by secreting a caustic liquid. Analysis of the liquid shows it to have a total concentration of formats plus formic acid (Ka= 1.8 x 10^ -4) of 1.8M; the concentration of formate ion is .45 M. What is the pH of the secretion?
3.2
116
IN a hospital lab, a 4.0 mL sample of gastric juice obtained several hours after meal, was titrated with .2 M NaOH to neutrality; 5mL of NaOH was required. The patients stomach contained no ingested food or drink, thus assume no buffers were present. What was the pH of the gastric juice?
.60
117
What amino acid is incapable of displaying optical isomerism?
Glycine
118
The pKa of the organic acid, oxalic acid is 3. At pH of 8, the acid is:
Predominately deprotonated, and exists predominately as oxalate
119
How many stereoisomers are there for an amino acid that has 3 chiral carbons? What is the formula?
8
Formula is 2^n
Where n = chiral carbons.
So it would be 2^3 or 2x2x2=8
120
What amino acid is also an imino acid?
proline
121
If an enzyme requires maximum ionization of both the aspartic acid and a lysine side chains to be fully active The pKa of the side chain of the ASP and the side chain of Lys are 4 and 11, respectively. At what pH will the enzyme show maximum activity? ( pH of 2, 4, 6, 14)
6
122
What amino acids contain sulfur ?
Cysteine and methionine
