Exam 3 Flashcards
(156 cards)
1
Q
When does a chemical reaction occur
A
When atoms have enough energy to combine or change bonding partners
2
Q
Metabolism
A
Sum of all chemical reactions in a biological system at a given time
3
Q
Anabolic Reaction
A
Type of metabolism; complex molecules are made from simple molecules; energy is required
4
Q
Catabolic Reaction
A
Type of metabolism; complex molecules are broken down to simpler ones; energy is released
5
Q
Kinetic Energy
A
One of the two types of energy; the energy of movement (like temperature)
6
Q
Potential Energy
A
One of the two types of energy; energy stores as chemical bonds, concentration gradient, or charge imbalance
7
Q
First Law of Thermodynamics
A
Energy is neither created or destroyed; when energy is converted from one form to another, the total energy before and after is the same; total energy in the universe is constant
8
Q
Second Law of Thermodynamics
A
When energy is converted from one form to another, some of that energy becomes unavailable to do work; no energy transformation is 100% effective since some is lost to disorder
9
Q
Entropy (S)
A
A measure of the disorder/randomness in a system (takes energy to impose order on a system; unless energy is applied to system it will be disordered)
10
Q
How do we find out whether there’s energy available for a reaction
A
By considering the unusable energy
11
Q
Total Energy Equation
A
Total Energy = free energy + temp*entropy
H = G + TS
Enthalpy = Usable Energy + unusable energy
12
Q
Gibbs Free Energy Change
A
Used to predict whether a reaction will occur spontaneously
13
Q
Gibbs Free Energy Change Formula
A
change in G = change in H - T*Change in S
14
Q
If change in G<0
A
Energy is released (reaction occurs spontaneously)
15
Q
If change in G>0
A
Energy is required (reaction can’t occur on its own)
16
Q
Exergonic Reactions
A
Release E (change in G<0)
17
Q
Are catabolic reactions exergonic or endergonic
A
Exergonic
18
Q
Polar Molecules
A
Shortest, strongest bonds
19
Q
Nonpolar molecules
A
Longest, weakest bonds
20
Q
In molecules, what is potential energy directly related to
A
The electron positioning in nuclei; Nonpolar molecules have more potential energy
21
Q
Endergonic reactions
A
Consume energy (change in G>0)
22
Q
Are anabolic reaction usually endergonic or exergonic
A
Endergonic
23
Q
Chemical reaction proceed until they reach
A
Equilibrium (change in G = 0)
24
Q
Enzymes
A
Catalysts that increase the rate of chemical reaction by reducing the activation energy; made of proteins
25
What does "~" symbolize
High energy bond
26
Is ATP formation endergonic or exergonic?
Endergonic
27
Why does the P~O bond that links phosphate groups in ATP store/release so much energy?
1. There's a lot of energy stored in P~O; it cost a lot of energy to create in the first place
2. O~P stores more potential energy than the new bonds formed; the leftover energy must be released
28
What can happen to Pi after ATP hydrolysis
- Incorporated into a product that will serve as a reactant/provide fuel for an endergonic reaction
- Incorporated into a protein product, which changes its shape and activity
29
Is ATP hydrolysis reversible?
Yes
30
The more negative change in G is
The more fully it proceeds to completion
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The closer change in G is to 0
The more fully reversible the reaction is
32
Why are some reactions with change in G less than 0 slow
They have a high activation energy
33
How do enzymes cause substrates to adopt transition states?
- Orientation
- Physical strain (makes easier to break)
- Adding chemical groups (charge)
34
How do R groups of an enzymes composite amino acids directly participate in adding chemical groups
- Acid base catalysis: Enzyme acts like an acid
- Covalent catalysis
- Metal ion catalysis: Metal ions lose or gain electrons without detaching from the enzymes
35
Enzymes are highly what to their substrates
Specific
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What determines the specificity of an enzyme
Its 3D shape (structure = function)
37
Induced Fit
Some enzymes change shape when bound to their substrate, which alters the shape of the active site
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Do enzyme chemical compositions change before and after catalysis?
No; but substrates do change as a result of the reaction
39
Ribozymes
Enzymes made of RNA
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Oxidoreductases
One of the six categories of enzymes; moves electrons between molecules
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Transferases
One of the six categories of enzymes; transfers functional groups between molecules
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Hydrolases
One of the six categories of enzymes; Adds water to covalent bonds to break molecules
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Lyases
One of the six categories of enzymes; catalyzes nonhydrolytic bond breakage, often forming a new bond in the process (ex: adenylyl cyclase aka ATP diphosphate-lyase; atp-->PPi)
44
What is another name for adenylyl cyclase?
ATP diphosphate-lyase (its a type of lyase enzyme)
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Isomerases
One of the six categories of enzymes; moves functional groups from one place to another within the same molecule (same atoms, different bonds)
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Ligases
One of the six categories of enzymes; ties two molecules together
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Coenzymes
AKA cofactors; small c-containing molecules that are not permanently bound to an enzyme (helps enzymes function)
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Prosthetic Groups
Non-amino acid groups bound to enzymes (helps enzymes function)
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Inorganic Compounds
Ions permanently bound to an enzyme (helps enzyme function)
50
What affects reaction rate?
Substrate concentration (until maximum rate is reached)
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How are chemical reactions in cells organized
In metabolic pathways that are interconnected
52
What helps organize and regulate metabolic pathways
Enzymes
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Cyclooxygenase (COX2)
An enzyme that normally produces prostaglandin from the substrate arachidonic acid which leads to an inflammatory response (vasodilation)
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Irreversible Inhibition
Inhibitor covalently binds to side chains in the active site, which permanently inactivates the enzyme (ex: aspirin permanently inhibits COX2)
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Aspirin
Binds to cyclooxgenase and transfers and acetyl group, which binds to its active site; prostaglandins can no longer be produced
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Cyclooxgenase cells produce (more/less) prostaglandin when aspirin is present
Less
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Reversible Inhibition
Inhibitor bonds noncovalently to the active site of enzyme and prevents substrate from binding
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Competitive Inhibition
Type of reversible inhibition; competes with the natural substrate for binding sites; binds before substrate
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ESPS
Enzyme in weed killer RoundUp
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Glyphosate
Competitive inhibitor of ESPS
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Competitive inhibitors can be overcome by
Adding more substrates
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Competitive Inhibitors have structures similar to
The enzyme's substrate
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Uncompetitive Inhibitors
Type of reversible inhibition; binds to the enzyme-substrate complex, preventing release of products; binds after the actual substrate binds to the enzyme
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Noncompetitive Inhibitors
Type of reversible inhibition; binds to an enzyme at a different site that isn't the active site; the enzyme changes shape and alters the active site
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PKA being activated by high concentration of cAMP is an example of
Noncompetitive inhibition; catalytic subunits have the active site
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Allosteric Regulation
A non-substrate molecule binds enzyme at a site different from the active site, which changes enzyme shape
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Allosteric Inhibitor
A molecule that stabilizes the inactive conformation of an enzyme
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Allosteric Activator
A molecule that stabilizes the active conformation of an enzyme
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Regulatory Subunits
Regulatory sites where inhibitors and activators bind to on polypeptides during allosteric regulation (PKA is an allosteric enzyme that has multiple subunits; cAMP is an allosteric activator)
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Feedback Inhibition
Final product acts as a noncompetitive inhibitor of the first enzyme, which shuts down the pathway (type of allosteric inhibition)
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Enzymes can be regulated by
- Gene expression changes
- Regulation of enzyme activity
- Phosphorylation
- Environmental Conditions (pH, temperature)
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Commitment Step
One of the first reactions in a metabolic pathway, other reactions then occur in sequence
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How are enzymes regulated by reversible phosphorylation?
If an enzyme is inactivated when a protein kinase adds a phosphate group, it might be activated by a protein phosphatase
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How are enzymes regulated by pH
Every enzyme is most active at a particular pH, which influences ionization of functional group; the rates of most enzyme-catalyzed reactions depend on the pH of the solution they're in
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How are enzymes regulated by temperature
Since noncovalent bonds break at high temperatures, which affects protein structure, temperature affects enzyme activity (there is an optimal temperature)
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ATP synthesis formula
ADP + Pi + free energy --> ATP + H20
Change in G = 7.3
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Is ATP synthesis endergonic or exergonic
Endergonic
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What releases enough energy to drive the formation of ATP?
The breakdown of glucose
79
How do cells harvest energy from glucose
A series of metabolic pathways
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Breakdown of glucose formula
C6H12O6 + 6O2 --> 6CO2 + 6H2O + free energy
Change in G = -686
81
What are the three catabolic processes that harvest energy from glucose
- Glycolysis (always first)
- Cellular Respiration
- Fermentation
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Glycolysis
The first of three catabolic processes that harvest energy from glucose; a series of chemical rearrangements in which 1 molecule of glucose is converted into 2 molecules of pyruvate
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What are the end products of glycolysis
2 pyruvate, 2 ATP, 2 NADH
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True or false: Both prokaryotes and eukaryotes harvest energy from glucose
True
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Five Principles of Metabolic Pathways
1. Complex transformation occur in a series of separate reactions
2. Each reaction is catalyzed by a specific enzyme
3. Many metabolic pathways are similar in all organisms
4. In eukaryotes, metabolic pathways are compartmentalized in specific organelles
5. Key enzymes can be inhibited or activated to alter the rate of the pathway
86
What are the two types of reaction that occur repeatedly in many metabolic pathways
Oxidation-Reduction and Substrate-Level Phosphorylation
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Oxidation-Reduction Reaction
One substance transfers electrons and energy to another substance (exergonic)
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Oxidation
Loss of electrons
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Reduction
Gain of electrons
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What happens in redox reactions where it doesn't involve a complete transfer of electrons
Electrons aren't gained or lost, but an atom's share of electrons is changed due to polar vs nonpolar bonds
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What is the transfer of electrons often associated with
Transfer of H+ ions (reduction is gain of H+, oxidation is loss of H+)
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Reducing Agent
The reactant that will become oxidized in a redox reaction
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Oxidizing Agent
The reactant that will become reduced in a redox reaction
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Are oxidation reactions endergonic or exergonic
Exergonic; the more reduced a molecule is, the more energy it has stored in its covalent bonds
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Are reduction reactions endergonic or exergonic
Endergonic
96
NAD+/NADH
A coenzyme that is an electron carrier in redox reactions
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When do electrons have more potential energy
When paired with less electronegative atoms (ex: glucose has high potential energy because of many high energy C-C and C-H bonds vs low potential energy CO2 with low energy C-O bonds)
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What are the reducing/oxidizing agents in glucose metabolism?
Glucose is the reducing agent, oxygen is the oxidizing agent
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The more reduced a molecule is
The more energy it has
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Substrate-Level Phosphorylation
Exergonic reaction that releases less energy than redox reactions, but still enough to convert ADP to ATP; a phosphate group on a substrate is phosphorylated to ADP
101
What goes in/out of glycolysis
In: Glucose, 2ATP, 2NAD+
Out (net): 2 ATP, 2 NADH, 2 Pyruvate
102
Where does the energy from the partial oxidation of glucose in glycolysis go
Energy from this exergonic reaction goes to substrate-level phosphorylation for creation of ATP and reduction of NAD+ to NADH
103
Pyruvate Oxidation
Second step of cellular respiration after glycolysis; glucose is fully oxidized if oxygen is present (vs in glycolysis where glucose is partially oxidized)
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What goes in/out of pyruvate oxidaition
In: 2 pyruvate
Out: 2 NADH, 2CO2, 2 Acetyl CoA
105
Site of pyruvate oxidation
Mitchondrial matrix
106
What is pyruvate oxidation catalyzed by
The pyruvate dehydrogenase complex; three enzymes that catalyze the three intermediate steps in the process
107
In pyruvate oxidation, what is pyruvate oxidized to?
CO2 and Acetate
108
True or false: pyruvate oxidation is also regulated by feedback inhibition
True
109
Starting point of the citric acid cycle
Acetyl CoA
110
What goes in and out of the citric acid cycle
In: 2 acetyl CoA
Out: 6 NADH, 4 CO2, 2 FADH2, 2 ATP
111
In the citric acid cycle, what does the acetyl group completely oxidize to
2 molecules of CO2
112
What is the energy released in the citric acid cycle captured by
GDP, NAD+, and FAD
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What is regenerated in the last step of the citric acid cycle, showing that the citric acid cycle is a cycle
Oxaloacetate
114
What is crucial in all pathways
Regeneration of substrates
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Step 8 of citric acid cycle
Example of redox reaction in the citric acid cycle; the oxidation of malate is exergonic and the energy released is trapped in the reduction of NAD+ to NADH
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What happens to the energy in GTP in the citric acid cycle
It is transferred to ATP; GTP can transfer its high-energy phosphate to form ATP
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Where does the energy from glucose oxidation go in the citric acid cycle?
The energy is harvest by phosphorylation of ATP (from GTP) and by reduction of NAD+ and FADH
118
What does the activity of phosphofructokinase change in response to
Cellular energy demands (cellular concentration of ATP); this is an example of allosteric regulation and feedback inhibition
119
Site of citric acid cycle
Mitochondrial matrix
120
Between NADH, FADH2 and ATP, which molecule carries the most free energy?
NADH, then FADH2, then ATP
121
What provides energy for electron transport chain?
The reduced electron donors NADH and FADH2
122
What happens downstream of glycolysis in aerobic conditions (O2 available)
O2 is available as final electron acceptor; four metabolic pathways operate
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What happens downstream of glycolysis in anaerobic conditions (O2 not available)
The pyruvate produced by glycolysis is metabolized by fermentation
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Oxidative Phosphorylation
ATP is synthesized by reoxidation of electron carriers in the presence of O2; two components are electron transport and chemiosmosis
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What is the final electron acceptor in the in the electron transport chain
Oxygen
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Site of electron transport chain
Inner mitochondrial membrane
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Starting point of electron transport chain
NADH from glycolysis
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Do electrons lose or gain free energy stepwise as it travels through each complex in the electron transport chain
Loses; energy is released as electrons are passed between carriers
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What contains electron carriers and associated enzymes that carry out electron transfer
Four large protein complexes; complex I, II, III, and IV
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Complexes I, III, IV role
Active transport protons into the mitochondrial intermembrane space where they accumulate
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What provides energy for ATP synthase
The diffusion of H+ with its concentration and charge gradient by protein complexes I, III, and IV; when H+ diffuses through the channel, the potential energy (called protein-motive force) is converted to kinetic energy, causing the central polypeptide of ATP synthase to rotate
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Chemiosmosis
Diffusion of protons back across the membrane; it releases energy and is coupled to ATP synthesis
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ATP Synthase
The channel protein that captures energy that is released from chemiosmosis as ATP; it is the same in all species; ATP synthase can also act as ATPase, hydrolyzing ATP
134
Parts of ATP synthase
ATP synthase is a molecular motor with two parts:
- F0 Unit: A transmembrane H+ channel
- F1 Unit: Projects into the matrix; rotates to expose active sites for ATP synthesis
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Chemiosmotic Theory
The electron transport chain creates a proton gradient and ATP synthase uses the gradient to synthesize ATP
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Why is ATP synthesis favored
ATP leaves the matrix as soon as its made, keeping ATP concentration in the matrix low
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How is ATP harvested from glucose without O2
Some ATP can be harvested from glucose via glycolysis and fermentation; fermentation allows cells to make ATP only using glycolysis
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Lactic Acid Fermentation
Pyruvate from glycolysis is reduced to lactate and NADH is oxidized to NAD+
Formula:
C6H12O6+2ADP+2Pi-->2 lactate+2ATP
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Alcoholic Fermentation
Occurs in other types of eukaryotic cells (yeast and some plants cells)
Formula:
C6H12O6+2ADP+2Pi-->2 ethanol+2CO2+2ATP
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Site of fermentation
Cytoplasm
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What happens in both types of fermentation
NAD+ is regenerated to keep glycolysis going, and 2 ATP per glucose are produced by substrate-level phosphorylation
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Does cellular respiration or fermentation yield more energy
Cellular respiration
143
Glycolysis and fermentation formula summary
C6H12O6--> 2 lactate (or 2 ethanol+2CO2)+2ATP
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Glycolysis and cellular respiration summary
C6H12O6+6O2-->6 CO2+6H2O+32ATP
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What can carbon skeletons be used for
They can be broken down to release energy or used to build more complex molecules, depending on the cell's needs
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Catabolic interconversion
How polysaccharides, lipids, and proteins can be broken down to provide energy
147
What are polysaccharides like glycogen and starch hydrolyzed to (catabolic interconversion)
Glucose, which enters glycolysis
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What are lipids broken down to (catabolic interconversion)
Glycerol (glycolysis) and fatty acids (citric acid cycle)
- Glycerol-->DHAP-->Glycolysis
- Fatty acids-->Acetyl CoA--> CAC
149
B-oxidation
Way in which fatty acids are slowly converted to acteyl CoA, which enters CAC
150
What are proteins hydrolyzed to (catabolic interconversion)
Amino acids, which can enter glycolysis or citric acid cycle
151
Anabolic interconversion
Way in which intermediates from metabolic pathways may be used to build polysaccharides, lipids, and proteins
152
True or false: citric acid cycle intermediates can also be used to synthesize nucleic acid components
True
153
Fatty acid biosynthesis
Acetyl-CoA is used to form long-chain fatty acids like palmitate
154
Gluconeogensis
Glucose is produced from glycerol, pyruvate, lactate, or amino acids (same pathways in reverse)
155
True or false: Cellular respiration interacts with other catabolic and anabolic pathways
True
156
How do cells maintain a steady state between catabolism and anabolism
- Having less substrate available (use intermediates in other pathways)
- Making more/less enzyme present (transcription/translation)
- Turning enzyme activity on/off (covalent modifications, allosteric inhibition)
