Bioc lec 5 Flashcards
1
Q
What is Chargaff’s rule regarding the composition of DNA?
A
In all cellular DNA, the number of adenosine residues equals the number of thymidine residues, and the number of guanosine residues equals the number of cytosine residues.
2
Q
Which scientists used X-ray crystallography to study the secondary structure of DNA?
A
Rosalind Franklin and Maurice Wilkins.
3
Q
Why is it difficult to form well-ordered crystals of DNA for high-resolution X-ray diffraction?
A
Forming well-ordered DNA crystals is hard because DNA molecules are very long and often break into fragments during isolation. These fragments don’t align well enough to create clear patterns in high-resolution X-ray diffraction.
4
Q
What key discovery was made through Rosalind Franklin’s X-ray diffraction studies of DNA?
A
Franklin’s studies, including “Photo 51,” revealed that DNA molecules are helical and have two periodicities along the long axis.
5
Q
What are the two periodicities of DNA revealed by Franklin’s X-ray diffraction studies?
A
A primary periodicity of 3.4 Å and a secondary periodicity of 34 Å along the long axis.
6
Q
What structure is formed by two helical DNA chains?
A
They wind around a single axis, forming a right-handed double helix.
7
Q
Where is the sugar-phosphate backbone located in the DNA double helix?
A
The hydrophilic sugar-phosphate backbone is on the outside of the helix, facing the surrounding water
8
Q
How are the bases oriented inside the DNA double helix?
A
The hydrophobic bases are stacked inside the double helix, perpendicular to the helix axis.
9
Q
How are bases paired within the DNA double helix?
A
Each base of one strand is paired in the same plane with a complementary base of the other strand: adenine (A) pairs with thymine (T), and cytosine (C) pairs with guanine (G).
10
Q
What is the orientation of the two strands in the DNA double helix?
A
The two strands are antiparallel, meaning their 3’ to 5’ phosphodiester bonds run in opposite directions.
11
Q
What is the spacing between vertically stacked base pairs in the DNA helix?
A
The base pairs are 3.4 Å apart.
12
Q
How many base pairs are present in each turn of the DNA helix, and what is the length of one turn?
A
Each turn of the helix contains 10 base pairs, measuring 34 Å in length.
13
Q
What is the diameter of the DNA double helix?
A
The diameter of the double helix is 20 Å, which equals 2 nm.
14
Q
What is the essential feature of the Watson-Crick model of DNA?
A
Self-complementarity.
15
Q
How does self-complementarity function in DNA replication?
A
It allows each pre-existing strand of a double helix to serve as a template for synthesizing new daughter strands.
16
Q
What biological processes does self-complementarity help explain?
A
It explains mitosis, meiosis, heredity, and genetics.
17
Q
How does self-complementarity contribute to DNA repair?
A
It provides a mechanism, in principle, for the cell to repair damaged DNA by using the complementary strand as a template.
18
Q
What type of bonds hold Watson-Crick base pairs together in DNA?
A
Sets of hydrogen bonds.
19
Q
How many hydrogen bonds form between cytosine (C) and guanine (G)?
A
Three hydrogen bonds (GC 3).
20
Q
How many hydrogen bonds form between adenine (A) and thymine (T)?
A
Two hydrogen bonds (AT 2).
21
Q
What does a higher GC-to-AT ratio indicate about DNA stability?
A
A higher GC-to-AT ratio makes it more difficult to separate the two DNA strands, as GC pairs have stronger bonding.
22
Q
How are the two strands of the double helix coiled around each other?
A
They are plectonemically coiled, meaning they are wrapped around each other.
23
Q
How can the two strands of the double helix be separated?
A
The strands can only be separated by unwinding from an end.
24
Q
What is supercoiling in DNA?
A
Supercoiling occurs when the double helix undergoes additional twisting, resulting in very compact structures.
25
What are the two grooves present in double-helical DNA?
The major groove and the minor groove.
26
Why do major and minor grooves form in DNA?
The glycosidic bonds of a base pair are at an angle, creating a large angle (major groove) and a small angle (minor groove).
27
What causes the formation of a major and minor groove as the double helix winds?
The two strands winding around each other create a wider gap (major groove) on one side and a narrower gap (minor groove) on the opposite side of the helix.
28
What lines the major and minor grooves in DNA?
Potential hydrogen-bond donors and acceptors from the bases line each groove, enabling specific interactions with proteins.
29
Why are major grooves more accessible to proteins?
The larger size of the major grooves makes them more accessible for interactions with proteins that recognize specific DNA sequences.
30
How does the secondary structure of DNA relate to its sequence?
This is because the two kinds of base pairs have very similar
shapes and properties.
31
What is the primary force that stabilizes the double helix by hiding hydrophobic bases?
The hydrophobic effect, which buries the hydrophobic bases in the core of the helix.
32
What type of bonding contributes to the stabilization of the double helix through base pair interactions?
Hydrogen bonding between base pairs.
33
What non-covalent interaction helps stabilize the double helix by stacking the bases?
Van der Waals interactions through base stacking.
34
What is the central dogma of molecular biology?
DNA is transcribed into RNA, and RNA is translated into protein.
35
What is transcription?
Transcription is the process of making an RNA copy of a DNA sequence.
36
What is translation?
Translation is the process of using RNA to build a protein.
37
What type of bonds hold the phosphate groups in ATP together?
Phosphoanhydride bonds.
38
What happens when phosphoanhydride bonds in ATP are broken?
Breaking these bonds releases a large amount of energy.
39
What are the components of an ATP molecule?
A base (adenine), a sugar (ribose), and three phosphate groups labeled alpha (α), beta (β), and gamma (γ).
40
Is ATP a store of chemical energy?
No, ATP is not a store of chemical energy; it links catabolism and anabolism.
41
How is ATP synthesized in cells?
Cells break down nutrients (catabolism) and use the free energy to synthesize ATP from ADP.
42
How rapidly does ATP turnover in cells?
ATP is broken down and synthesized very rapidly, with a lifetime of seconds to minutes.
43
What is the free energy change (ΔGnotprime) for the hydrolysis of ATP?
The free energy change is large and negative, approximately -30.5 kJ/mol under standard conditions.
44
How does the ΔG of hydrolysis for ATP compare to other bonds?
G for ATP hydrolysis (~-50 kJ/mol) is much greater than for amides, esters, and phosphoesters (~15–20 kJ/mol).
45
Where do energy-releasing and energy-requiring processes involving ATP occur?
At the phosphate groups of ATP.
46
What happens to the electrostatic repulsion in ATP during hydrolysis?
Hydrolysis releases the electrostatic repulsion among the negative charges in ATP.
47
Why does the inorganic phosphate (Pi) produced in ATP hydrolysis have greater stability than ATP?
The inorganic phosphate has greater resonance stabilization than ATP.
48
What is the formula for calculating the free energy change (ΔG°')?
ΔG°' = Free energy of products - Free energy of reactants.
49
How many high-energy bonds are present in ATP?
ATP contains two high-energy bonds, which are phosphoanhydride linkages.
50
Which bond in ATP is broken during hydrolysis?
The bond between the gamma (γ) and beta (β) phosphates is broken during hydrolysis.
51
What type of reaction occurs during the hydrolysis of ATP?
A nucleophilic attack on the gamma phosphate occurs during ATP hydrolysis.
52
What are the products of ATP hydrolysis?
The products are ADP (adenosine diphosphate) and inorganic phosphate (Pi).
53
How much energy is released during the hydrolysis of ATP?
Approximately 30 kJ of energy is released during ATP hydrolysis.
54
What happens during the hydrolysis of the alpha-beta linkage in ATP?
A nucleophilic attack on the alpha phosphate occurs, resulting in the breakdown of ATP to AMP and pyrophosphate (PPi).
55
What are the products of hydrolyzing the alpha-beta linkage in ATP?
The products are AMP (adenosine monophosphate) and pyrophosphate (PPi).
56
What happens to pyrophosphate (PPi) in the cell?
Pyrophosphate (PPi) is immediately hydrolyzed by the enzyme pyrophosphatase, producing two moles of inorganic phosphate (Pi).
57
: How does the hydrolysis of ATP to AMP + PPi compare to the hydrolysis of ATP to ADP + Pi?
The hydrolysis of ATP to AMP + PPi releases twice as much energy as the hydrolysis of ATP to ADP + Pi, because it breaks both phosphoanhydride bonds in ATP.
58
Why does the hydrolysis of ATP to AMP + PPi release more energy than ATP to ADP + Pi?
The hydrolysis of ATP to AMP + PPi breaks two phosphoanhydride bonds, while ATP to ADP + Pi only breaks one, leading to more free energy being released.
59
What is the result of the hydrolysis of ATP?
ATP is hydrolyzed into ADP (adenosine diphosphate) and inorganic phosphate (Pi).
60
What is the free energy change (ΔG) for the hydrolysis of ATP?
The hydrolysis of ATP has a negative ΔG, meaning it releases energy, making it an exergonic reaction.
61
How does the hydrolysis of ATP drive energetically unfavorable reactions?
Although ATP hydrolysis itself has a negative ΔG, some reactions require an input of energy to get started. ATP hydrolysis provides that energy, driving unfavorable reactions by coupling them with favorable ones.
62
What does ATP = ADP + Pi mean?
The equation ATP → ADP + Pi represents the breakdown of ATP into ADP (Adenosine Diphosphate) and an inorganic phosphate (Pi).
63
What chemical mechanism allows ATP hydrolysis to drive reactions forward?
ATP hydrolysis drives reactions forward by coupling energy-releasing ATP breakdown to energy-requiring processes, such as the synthesis of biomolecules.
64
Give an example of a reaction driven by ATP hydrolysis.
The synthesis of glutamine by glutamine synthetase.
65
How does the cell drive the synthesis of glutamine forward?
The reaction is coupled to ATP hydrolysis, where ATP is converted to ADP and Pi (ATP → ADP + Pi).
66
What is the first step in the mechanism of glutamine synthetase?
ATP reacts with glutamate to produce a covalent intermediate, a mixed anhydride of phosphate and glutamate.
67
What is the second step in the mechanism of glutamine synthetase?
Ammonia (NH₃) acts as a nucleophile and reacts with the electrophilic carbonyl carbon atom of the intermediate, displacing Pi as the leaving group.
68
How does ATP provide energy to drive reactions forward?
ATP provides energy not by simple hydrolysis but through group transfer.
69
What makes ATP chemically versatile?
ATP's phosphate group can participate in a variety of chemical reactions with common organic functional groups.
70
Besides transferring a phosphoryl group, what other groups can ATP transfer?
ATP can transfer a pyrophosphoryl (PPi) group or an adenylate (AMP) moiety.
71
What role does ATP's group transfer capability play in biochemical reactions?
Group transfer from ATP helps to drive reactions forward by modifying substrates or enzyme amino acid residues.
72
What are the 5 high energy compounds (highest to lowest
1. Phosphoenol pyruvate,
2. 1,3-biphosphoglycerate,
3. creatine phosphate
4. Acetyl-CoA,
5. ATP
73
What are the two low energy compounds (highest to lowest)
1. Glucose 6 - Phosphate
2. Pi (no energy)
74
How is metabolism divided?
Metabolism is divided into two halves: catabolism and anabolism.
75
What is catabolism?
Catabolism is the breakdown of large molecules and foodstuffs into simpler products.
76
What is anabolism?
Anabolism is the process of building up larger and more complex molecules from simple precursors.
77
What are the main inputs and outputs for catabolism?
In:Carbohydrates, fats, and proteins.
Out:CO₂, H₂O, and NH₃
78
What energy-related molecules are involved in catabolism?
Catabolism produces ATP and reduced cofactors while consuming ADP and oxidized cofactors.
79
What are the main inputs and outputs of anabolism?
In: Amino acids, sugars, and fatty acids.
Out: Proteins, lipids, and nucleic acids
80
What energy-related molecules are involved in anabolism?
Anabolism consumes ATP and reduced cofactors while producing ADP and oxidized cofactors.
81
What happens to carbon skeletons in catabolic pathways?
The carbon skeletons of most sugars, fats, and amino acids are converted into a single, centrally-important metabolite called acetyl coenzyme A (acetyl CoA).
(converge into acetyl coA)
82
What is the role of acetyl CoA in metabolism?
Acetyl CoA serves as a precursor for building fatty acids, steroids, components of proteins, and nucleic acids.
83
What happens in anabolic pathways?
Anabolic pathways diverge, meaning they use common precursors to build a variety of complex molecules.(diverge into complex molecules)
84
What can acetyl CoA be used to build?
Acetyl CoA can be used to build fatty acids, steroids, and components of proteins and nucleic acids.
85
What is a metabolic pathway?
A metabolic pathway is a series of enzyme-catalyzed reactions that converts a precursor (A) into a product (E) through intermediates known as metabolites.
86
What happens at each step of a metabolic pathway?
Each step involves a small, specific chemical change, such as the removal, addition, or transfer of an atom or functional group. When all steps are strung together, the pathway achieves a transformation that may not be obvious from individual steps.
87
Why are metabolic pathways considered irreversible?
They contain at least one reaction that is thermodynamically very favorable, making the pathway essentially irreversible.
88
How are metabolic pathways regulated?
1. Transcriptional control of enzyme levels.
2. Inhibition or activation of enzyme activity, such as feedback inhibition by products or reversible phosphorylation.
89
What is feedback inhibition?
Feedback inhibition occurs when the end product of a pathway inhibits an earlier enzyme, regulating the pathway's activity.
90
What is reversible phosphorylation in metabolism?
Reversible phosphorylation is the addition or removal of a phosphate group to enzymes, regulating their activity.
91
What happens when wild-type E. coli or yeast (prototrophs) are exposed to a mutagen?
Exposure to a mutagen can inactivate a gene encoding a specific enzyme, leading to auxotrophic mutants.
92
How are auxotrophic mutants identified?
their requirement for the end product of the metabolic pathway that is blocked due to the inactivation of a specific enzyme.
93
How can you identify the metabolites that accumulate in a mutant?
By analyzing the metabolites, you can identify which ones accumulate in the mutant due to a blocked pathway (e.g., metabolite B could accumulate).
94
What types of radioactively labeled substrates are commonly used in metabolic studies?
Common radioactively labeled substrates include ³H, ¹⁴C, ³²P, and ³⁵S.
95
How does ¹⁴C behave in terms of its chemistry?
¹⁴C behaves like regular ¹²C in chemical reactions, but it can be traced because it releases a small flash of energy when it decays.
96
Why is ¹⁴C useful in metabolic experiments?
¹⁴C is useful because it can be incorporated into compounds, and its radioactive decay makes it easily traceable, allowing scientists to track the compound and any products derived from it.
97
What advantage does using ¹⁴C for tracing provide in experiments?
It allows for sensitive detection of very small amounts of a compound, even in complex mixtures, due to the ability to trace the radioactive carbon.
98
is NADH reduced or oxidized?
reduced
99
is NAD+ reduced or oxidized
oxidized
100
Where does the equilibrium lie in a redox reaction?
The equilibrium lies toward the species with the higher standard reduction potential (E₀').
101
Why do you need to know the standard reduction potential (E₀') of the two half-reactions?
To determine which species has a greater tendency to accept the available electron.
102
How can E₀' be used in a redox reaction?
E₀' can be used to predict the direction of electron flow.
103
Where do electrons always flow in a redox reaction?
Electrons always flow to the half-reaction with the higher reduction potential.
104
What does ΔE₀' represent in a redox reaction?
ΔE₀' represents the difference in reduction potentials and indicates the strength of the tendency for electron flow.
105
When can redox reactions proceed spontaneously?
Redox reactions can proceed spontaneously if ΔE₀' > 0.
106
How can this be calculated?
ΔE₀' = ?
ΔE₀' = E₀' of the electron acceptor - E₀' of the electron donor
107
108
Is an electron donor a reducing agent or oxidizing agent
reducing agent
109
Is an electron acceptor an oxidizing agent or reducing agent?
Oxidizing agent
110
What are enzyme cofactors?
Enzyme cofactors are additional chemical compounds required by some enzymes to carry out their functions.
111
What are some examples of inorganic ions that act as enzyme cofactors?
Examples include Fe²⁺, Mg²⁺, Mn²⁺, Zn²⁺, and Cu²⁺.
112
What are coenzymes?
Coenzymes are complex organic or metalloorganic compounds that act as transient carriers of specific functional groups.
113
What is the relationship between coenzymes and adenosine?
Many coenzymes are derivatives of adenosine.
114
What is the role of ATP in metabolism?
ATP acts as a carrier/donor of phosphate groups, used to phosphorylate molecules such as sugars, lipids, and proteins.
115
What is the function of a kinase?
A kinase is an enzyme that phosphorylates molecules with the help of ATP.
116
What is Coenzyme A (CoA/CoASH)?
Coenzyme A is a cofactor that acts as a carrier of acyl (acid) groups.
117
From which vitamin is Coenzyme A derived?
Coenzyme A is derived from the vitamin pantothenic acid (B5).
118
Who discovered Coenzyme A?
Coenzyme A was discovered by Fritz Lipmann.
119
What does CoASH form derivatives with?
CoASH forms derivatives with organic acids (R-COOH).
120
What is a thioester?
A thioester is like an ester, but it has a sulfur (S) atom instead of an oxygen (O) atom in one part of its structure. It’s a compound where a sulfur atom is bonded to a carbonyl group.
121
What is an "acyl" group?
An "acyl" group refers to an acid functional group within a molecu
122
What is the CoA derivative of acetic acid called?
The CoA derivative of acetic acid is called acetyl CoA (CoASAc).
123
What are the key cofactors involved in oxidation reactions?
The key cofactors are NAD+, NADP+, FAD, and FMN.
124
What role do cofactors like NAD+ and FAD play in oxidation reactions?
These cofactors act as electron acceptors, accepting electrons removed from substrates, which reduces them and conserves the energy of oxidation.
125
What is the role of NAD+ and FAD in beta-oxidation?
NAD+ and FAD are involved in beta-oxidation, where they accept electrons during the breakdown of fatty acids.
126
What are NAD+ and NADP+ also known as?
NAD+ and NADP+ are also known as the pyridine nucleotides.
127
From which vitamin are NAD+ and NADP+ derived?
NAD+ and NADP+ are derived from the vitamin niacin (B3).
128
What is similar about the redox chemistry of NAD+ and NADP+?
The redox chemistry of NAD+ and NADP+ is similar, and both occur at the nicotinamide ring.
129
What happens during the oxidation of substrates in reactions involving NAD+ or NADP+?
During oxidation, two hydrogen atoms are removed from the substrate (dehydrogenation).
130
Why are enzymes involved in these reactions called "dehydrogenases"?
They are called dehydrogenases because they catalyze the removal of hydrogen atoms (dehydrogenation).
131
How does NAD+ or NADP+ become reduced?
NAD+ or NADP+ accepts a hydride ion (H-) (equivalent to a proton and two electrons) to become reduced to NADH or NADPH.
132
What happens to the other proton during the reduction of NAD+ or NADP+?
The other proton is released into the aqueous environment.
133
Despite their similar redox chemistry, how do NAD+ and NADP+ differ in their roles?
NAD+ is used as the oxidizing agent in catabolic processes, while NADPH is used as the reducing agent in biosynthesis.
134
What role does NAD+ play in the cell?
NAD+ is used as the oxidizing agent in catabolic processes (e.g., fatty acid oxidation, TCA cycle), and the resulting NADH is reoxidized via the electron transport chain to generate energy.
135
What role does NADPH play in the cell?
NADPH is used as the reducing agent in biosynthesis (e.g., fatty acid synthesis, steroid synthesis).
136
What are FAD and FMN also known as?
FAD and FMN are known as the flavin nucleotides.
137
From which vitamin are FAD and FMN derived?
FAD and FMN are derived from the vitamin riboflavin (B2).
138
What is the typical role of flavin nucleotides (FAD and FMN)?
Flavin nucleotides usually act as prosthetic groups, tightly bound to the enzyme.
139
How can flavin nucleotides (FAD and FMN) accept electrons?
Flavin nucleotides can accept one or two electrons in the form of one or two hydrogen atoms (each hydrogen atom is an electron plus a proton) from substrates undergoing oxidation.
140
What are the fully reduced forms of FAD and FMN?
The fully reduced forms of FAD and FMN are FADH₂ and FMNH₂.
141
What happens when flavin nucleotides accept only one electron?
When only one electron is accepted, they form the stable semiquinone radical forms FADH· and FMNH·.
142
Why are FMN and FAD involved in a greater diversity of reactions compared to NAD(P)-linked dehydrogenases?
FMN and FAD can participate in either one-electron or two-electron transfers, allowing them to be involved in a greater diversity of reactions.
143
Why is fat the most concentrated store of metabolic energy?
Fat is the most concentrated store of metabolic energy because it is chemically reduced, with most of the carbon atoms being CH₂, which releases maximum free energy when oxidized to CO₂.
144
How does the chemical structure of fat differ from sugars in terms of energy release?
Fat is more chemically reduced than sugars, as most of the carbon atoms in sugars are CH₂O, meaning they are already partially oxidized. In contrast, fat releases more energy when oxidized to CO₂.
145
Why can fat be stored nearly water-free?
Fat is hydrophobic, so it can be stored nearly water-free, whereas polysaccharides store much of their weight as water (due to solvation).
146
How is each biomolecule formed in relation to oxidation?
Each molecule is formed by the oxidation of the molecule immediately preceding it.
147
What is the most oxidized form of carbon found in living systems?
CO₂ is the most oxidized form of carbon found in living systems
148
What are human energy reservoirs?
Human energy reservoirs are stores of energy that the body uses, moving from readily available but limited reserves to larger, more difficult-to-mobilize stores.
149
What happens during fasting in terms of energy reservoirs?
During fasting, the body moves from readily-available but limited capacity energy reservoirs to much larger stores of energy, which are harder to mobilize.
150
How many stages are involved in the complete oxidation of fatty acids to CO₂ and H₂O?
The complete oxidation of fatty acids occurs in three stages.
151
What experimental method did Franz Knoop use to study beta oxidation?
He tagged the terminal (ω) carbon atom of fatty acids with a phenyl group and fed them to dogs.
He collected and analyzed the aromatic products excreted in the dogs' urine.
152
How are fatty acids prepared for catabolism?
Fatty acids are activated to fatty acyl CoA for catabolism.
153
Where is acyl CoA synthetase located?
Acyl CoA synthetase is located in the outer mitochondrial membrane.
154
What is equivalent to the hydrolysis of 2 moles of ATP to ADP + Pi?
The conversion of 1 mole of ATP to AMP + 2 Pi is equivalent to this.
155
What is the difference between synthetase and synthase?
Synthetase: Combines two small molecules into a larger molecule with ATP energy.
Synthase: Combines two small molecules into a larger molecule without ATP energy.
156
How many steps are involved in fatty acid activation?
Fatty acid activation occurs in two steps.
157
What happens in the second step of fatty acid activation?
The thiolate anion form of coenzyme A (nucleophile) reacts with the acyl adenylate, releasing AMP and forming a fatty acyl-CoA thioester.
158
What is the overall ΔG°′ of fatty acid activation?
The overall ΔG°′ is -34 kJ/mol.
159
Where does β oxidation take place in the cell?
β oxidation occurs in the mitochondrial matrix.
160
How permeable is the outer mitochondrial membrane?
The outer mitochondrial membrane is freely permeable to small molecules and ions.
161
How permeable is the inner mitochondrial membrane?
The inner mitochondrial membrane is highly impermeable to most solutes.
162
Why does the mitochondrial matrix have a different chemical composition from the cytosol?
Due to the high impermeability of the inner mitochondrial membrane to most solutes.
163
How are fatty acids with more than 12 carbons transported into the mitochondrial matrix?
They are transported as acyl-carnitine esters via the acyl-carnitine/carnitine transporter.
164
What happens to fatty acyl CoA once it enters the mitochondrion?
Once inside the mitochondrion, fatty acyl CoA is committed to undergo beta-oxidation.
165
What are the four steps of beta-oxidation?
The four steps of beta-oxidation are:
Oxidation
Hydration
Oxidation
Thiolysis
166
What is removed with each pass through beta-oxidation?
Each pass through beta-oxidation removes one acetyl moiety in the form of acetyl-CoA.
167
What occurs in Step 1 of beta-oxidation?
In Step 1 of beta-oxidation, oxidation by FAD forms a double bond between the α and β carbons of fatty acyl CoA, changing it from alkane to alkene.
168
What enzyme oxidizes FAD in step 1 of beta oxidation?
Acyl-coA dehydrogenase
169
What happens in Step 2 of beta-oxidation?
In Step 2 of beta-oxidation, hydration occurs across the double bond, forming an alcohol at the beta carbon (hydration of the alkene to an alcohol).
170
What happens in Step 3 of beta-oxidation?
In Step 3 of beta-oxidation, the alcohol is oxidized by NAD+ to form a keto group at the beta carbon.
171
What happens in Step 4 of beta-oxidation?
In Step 4 of beta-oxidation, the bond between the α and β carbons is broken by thiolysis, producing acetyl-CoA and a shortened fatty acyl-CoA.
172
What happens during each round of beta-oxidation?
Each round of beta-oxidation produces acetyl-CoA and shortens the fatty acyl-CoA chain by two carbons.
173
How many times are the four steps of β-oxidation repeated for complete oxidation of palmitic acid?
The four steps of β-oxidation are repeated 7 times to fully oxidize palmitic acid into 8 molecules of acetyl-CoA.
174
What is produced during each pass of beta-oxidation?
Each pass of beta-oxidation produces:
1 FADH2
1 NADH
In total, 7 FADH2 and 7 NADH are produced.
175
What happens to the FADH2 and NADH produced during beta-oxidation?
The FADH2 and NADH are oxidized via the electron transport chain to generate ATP.
176
What happens to acetyl-CoA after it is produced in beta-oxidation?
Acetyl-CoA enters the citric acid cycle and is further oxidized into CO2, producing more GTP, NADH, and FADH2.
177
What is the overall stoichiometry for the oxidation of palmitoyl-CoA through beta-oxidation?
The overall stoichiometry is:
Palmitoyl-CoA + 7 CoASH + 7 FAD + 7 NAD+ + 7 H2O → 8 Acetyl-CoA + 7 FADH2 + 7 (NADH + H+).
178
What are the three stages involved in the complete oxidation of glucose to CO2 and H2O?
The three stages are:
Glycolysis + Pyruvate dehydrogenase
TCA Cycle
Electron Transport Chain (ETC)
179
How does glucose enter cells?
Glucose is a highly polar molecule and cannot enter cells by passive diffusion. It is transported into cells by GLUTs (GLUcose Transporters), which are transporter proteins in the cell membrane.
180
What role does insulin play in glucose uptake?
Insulin stimulates GLUT-mediated glucose uptake in skeletal muscle and adipose tissue.
181
What happens in diabetes with respect to glucose uptake?
In diabetes, the body "starves in the midst of plenty" because blood glucose is not adequately taken up into cells.
182
What is the fasting blood glucose concentration?
The fasting blood glucose concentration is around 5 mM, making it one of the most abundant small molecules in the body.
183
Which tissues and cell types are solely dependent on glycolysis for energy?
Red blood cells, renal medulla, brain (which consumes about 100 grams of glucose daily), and sperm are solely dependent on glycolysis for energy provision.
184
Why is glycolysis important for anaerobic conditions?
Glycolysis is the only pathway that can provide energy under anaerobic conditions. Anaerobic microorganisms are completely dependent on glycolysis for energy generation.
185
Where does glycolysis occur?
Glycolysis occurs in the cytosol of the cell.
186
How many steps are involved in glycolysis?
Glycolysis consists of 10 different steps.
187
What happens in the first five reactions of glycolysis?
The first five reactions of glycolysis make up the preparatory phase, where ATP is used to phosphorylate and activate glucose.
188
What happens in the next five reactions of glycolysis?
The next five reactions of glycolysis make up the payoff phase, leading to the net generation of ATP.
189
What happens in Step I of glycolysis? What does glucose become?
In Step I, glucose is phosphorylated by ATP which is oxidized to ADP, which acts as a cofactor and donor of phosphate groups. This process helps activate glucose for further metabolism.
Glucose becomes glucose 6-phosphate
190
What enzyme helps ATP phosphorylate glucose in step 1 of glycolysis?
hexokinase
191
How many different isozymes of hexokinase are there?
There are four different isozymes of hexokinase (I-IV).
192
How does hexokinase IV (glucokinase) differ from the other hexokinases?
Hexokinase IV (glucokinase) differs from the other hexokinases in its kinetic and regulatory properties.
193
What are isozymes?
Isozymes are two or more enzymes that catalyze the same reaction but are encoded by different genes.
194
What happens in step two of glycolysis?
Glucose 6-phosphate becomes fructose 6-phosphate by phosphohexose isomerization by phosphohexose isomerase enzyme
195
What happens in step 3 of glycolysis?
the second phosphorylation,
Fructose 6-phosphate becomes fructose 1,6-biphosphate.
The enzyme phosphofructosekinase-1 does this and ATP is oxidized to ADP as a cofactor
196
What happens in step 4 of glycolysis?
Fructose 1,6-biphosphate which has six carbons is split into two 3 carbon units.
1. Dihydroxyacetone phosphate
2. Glyceraldehyde 3-phosphate
197
In step 5 of glycolysis, What happens to DHAP (dihydroxyacetone phosphate) in glycolysis?
DHAP is immediately isomerized to G3P (Glyceraldehyde 3-phosphate), and glycolysis continues with G3P only. (2 G3P molecules are formed)
198
How is the mechanism of triose phosphate isomerase similar to phosphohexose isomerase?
The mechanism of Triose Phosphate Isomerase is essentially the same as phosphohexose isomerase.
199
After the interconversion of triose phosphates, how many triose molecules are catabolized for each glucose molecule?
From this point onwards, two triose molecules must be catabolized for each molecule of glucose.
200
In step 6 of glycolysis, What happens in the reaction catalyzed by Glyceraldehyde 3-Phosphate Dehydrogenase?
G3P is oxidized (from aldehyde to carboxylic acid) and then phosphorylated to form a mixed anhydride bond.
201
What cofactor is required in the Glyceraldehyde 3-Phosphate Dehydrogenase reaction?
The reaction requires NAD+ as a cofactor.
202
Why must NADH be re-oxidized in glycolysis?
NADH must be re-oxidized to allow glycolysis to continue as an ongoing process.
203
is 1,3-Biphosphoglycerate a high energy compound
yes
204
What type of reaction is catalyzed by phosphoglycerate kinase in step 7 of glycolysis?
A substrate-level phosphorylation, transferring a phosphate group from 1,3-BPG to ADP to form ATP.
205
What happens to the free energy of hydrolysis from the anhydride bond in 1,3-Biphosphoglycerate?
It is recovered in the form of ATP.
206
How many ATP molecules are generated from this reaction per molecule of glucose in step 6 of glycolysis
Two ATP molecules are generated per glucose because two moles of 1,3-BPG are formed from one mole of glucose.
207
In step 6 of glycolysis, what does 1,3-Biphosphoglycerate become?
3-phosphoglycerate
208
What type of enzyme catalyzes the conversion of 3-phosphoglycerate to 2-phosphoglycerate in step 8 of glycolysis?
A mutase, a subclass of isomerase.
209
What do mutases specifically catalyze?
They catalyze reactions where a functional group is moved between different positions within the same molecule.
210
what does 3-phosphoglycerate become in step 7 of glycolysis, and using what cofactor?
becomes 2-phosphoglycerate, using phosphoglycerate mutase as a cofactor
211
What reaction occurs in Step IX of glycolysis?
Dehydration of 2-phosphoglycerate to form phosphoenolpyruvate (PEP).
212
What enzyme catalyzes the dehydration of 2-phosphoglycerate?
Enolase.
213
What is the significance of forming phosphoenolpyruvate? is pep a high energy compound.
PEP is a high-energy compound that drives the next substrate-level phosphorylation step in glycolysis. yes pep is a high energy compound
214
What reaction occurs in Step X of glycolysis?
Transfer of the phosphoryl group from phosphoenolpyruvate pyruvate enol form and then pyruvate keto form. ATP is also formed
215
What enzyme catalyzes the transfer of the phosphoryl group from PEP to pyruvate enol form?
Pyruvate kinase.
216
What gives this reaction a large negative ΔG?
Hydrolysis of PEP forms enolpyruvate, which quickly tautomerizes to the more stable keto form (pyruvate). This tautomerization lowers the product concentration and drives the reaction forward.
217
How does pyruvate exist in solution?
As an equilibrium mixture of keto (predominant) and enol (minor) tautomers.
218
If an inhibitor (X) blocks phosphoglycerate mutase in an anaerobic system metabolizing glucose, which compound would accumulate?
3-phosphoglycerate would accumulate, as the enzyme responsible for converting it to 2-phosphoglycerate is inhibited.
219
Which enzyme catalyzes the first reaction in glycolysis that forms an energy-rich compound?
Glyceraldehyde 3-phosphate dehydrogenase catalyzes this step, forming 1,3-bisphosphoglycerate, a compound with a highly negative ΔG'° of hydrolysis.
