Unit 3 Flashcards
(146 cards)
1
Q
What is Gibbs free energy?
A
π«G=available energy in a system (usable energy)
2
Q
What does π«G<0 mean?
A
spontaneous reaction
exergonic reaction
releases energy (cellular respiration)
3
Q
What does π«G>0 mean?
A
nonspontaneous reaction
requires an input of energy (absorbs energy)
endergonic reaction
(photosynthesis)
4
Q
What does π«G=0 mean?
A
system is in equilibrium
5
Q
What does enthalpy mean?
A
π«H=total energy in the system
Temperature (heat), pressure, volume
Reactants have high potential energy, products have low potential energy
exothermic and endothermic
6
Q
What does exothermic mean?
A
π«H is negative (releases heat)
7
Q
What does endothermic mean?
A
π«H is positive (absorbs heat)
8
Q
Where is enthalpy in biological systems?
A
potential energy is stored in chemical bonds
Glucose = energy storage molecule
Glucose monomers link up to form glycogen in animals
Glucose monomers link up to form starch in plants
9
Q
What is entropy?
A
π«S=amount of disorder in a system
10
Q
Are molecules with chemical bonds high or low ordered?
A
high
11
Q
How can chemical bonds be broken?
A
Can be broken down through metabolism or macromolecule recycling
individual atoms are formed
12
Q
Are individual atoms more or less ordered than a macromolecule?
A
less (increase in π«S)
13
Q
What is the cellular respiration (mitochondria) equation?
A
Glucose + oxygen + water β carbon dioxide + water + ATP
More highly ordered β less order
Low entropy β high entropy
14
Q
What is the photosynthesis (chloroplasts) equation?
A
CO2 + H2O + sunlight β glucose + O2
15
Q
Where do prokaryotes have machinery for photosynthesis?
A
in their outer cell membrane
16
Q
What is metabolism?
A
catabolic pathways that involve the breakdown of nutrient molecules into usable forms. Anabolic pathways build new molecules out of the products of catabolism and these pathways use energy
Energy is stored in energy molecules for later use or released as heat
17
Q
Do catabolic reactions release or absorb heat?
A
release
18
Q
Do anabolic pathways require an input of energy?
A
yes
19
Q
How are polymers restored into macromolecules?
A
Polymers (proteins, nucleic acids) get reduced to monomers (amino acids, nucleotides) and are restored into macromolecules through anabolic pathways
20
Q
Why do catabolic and anabolic pathways act in balance?
A
to control the level of metabolites and to make sure the cell has enough energy to do all of its functions
21
Q
What is a catalyst?
A
substance that speeds up a chemical reaction without being a reactant
22
Q
What are enzymes?
A
catalysts that speed up chemical reactions
Usually proteins and bring reactants in close physical contact so bonds can break/form
23
Q
What is the active site of an enzyme?
A
Location where a substrate binds to the enzyme
Enzyme changes shape when substrate binds to it
Called a conformational change
24
Q
What is a conformational change?
A
Enzyme is functioning to bring the molecules together in an orientation that bonds can be formed or broken to produce a reaction
25
Why are enzymes highly specific?
because the active site has a unique combination of amino acids in a specific conformation
26
1) What do lysozymes target?
2) What is their active site designed to do?
1) Lysozymes target peptidoglycan found in bacteria
Only function at a specific pH
Acid hydrolases need an acidic environment to function properly
These enzymes are found in human saliva
2) to bind to bacterial peptidoglycan to break it down
27
What are the 2 categories of active sites?
binding sites and catalytic sites
28
What are binding sites?
enzyme binds its substrate
29
What do catalytic sites do?
reduces the activation energy of the reaction
30
How do enzymes go about catalyzing a reaction?
initiation
transition state
termination
31
What is initiation?
Substrates bind to the active site in a specific orientation, forming an enzyme-substrate complex
32
What is the transition state?
Interactions between enzyme and substrate lower the activation energy
33
What is termination?
Products have a lower affinity for active site and are released
Enzyme is unchanged after the reaction
34
Are enzymes adapted to function at a specific temperature range?
yes
35
Do molecules lose or gain kinetic energy as temperature increases?
gain
rate of collisions increase
reaction rate increases
36
What happens to the rate of reaction as enzymes reach optimum temperatures?
the rate of reaction plateaus and the reaction rate declines after
37
When do enzymes denature?
when temperature goes above optimum temperature
38
Do changes in pH denature enzymes?
yes, so enzymes adapt to function at a specific pH or pH range
39
What is pepsin?
enzyme found in the digestive tract and functions at a very acidic pH
40
What is salivary amylase?
enzyme found in saliva that functions at a neutral pH
41
What do enzymes do to the activation energy?
lower it
42
What is activation energy?
amount of energy required to start a chemical reaction
43
What do enzymes do to the transition state?
lowers/stabilizes it
44
Do enzymes change the Gibbs free energy of the reaction?
no
45
What happens to the rate of reaction when concentration of substrate increases?
increases
When there or more substrate molecules, more enzyme molecules bind them to speed up the reaction
46
What happens to rate of reaction when concentration of enzymes increases?
increases
When there are more enzyme molecules, more of the substrate can be bound to form product
47
Does increasing substrate or enzyme concentration affect the reaction rate at saturation?
no
48
How are enzymes regulated by other molecules?
competitive inhibition
allosteric activation
allosteric inhibition
49
What is competitive inhibition?
Regulatory molecule fits into the active site of an enzyme and prevents more reactions from occurring with that enzyme
Regulatory molecule competes for active site
50
What does allosteric mean?
Another molecule binds to the enzyme in a region outside of the active site and controls whether the enzyme is active or inactive
51
What is allosteric activation?
Activator turns the enzyme on by binding to an area other than the active site causing the active site to change shape so it can bind to its substrate and the reaction can proceed
52
What is allosteric inhibition?
Inhibitor binds to the enzyme at an allosteric site and causes the active site to change shape so substrate cannot bind
53
Are enzymes proteins and also RNA?
yes
54
What is Brownian motion?
random energy in everything
55
Is there enough energy to push reactions along if an enzyme is in too cold of an environment?
no
56
What happens to enzymes when they are at a temperature higher than their optimal range?
they denature
57
What do enzymes do at the transition state?
change shape for optimum conformation for bond breakage and formation
58
What happens when there are more substrate molecules?
they bind to more enzymes and speed up the rate of reaction
59
What happens when there are more enzyme molecules?
more of the substrate can be bound to form products
60
What makes the enzyme active site highly specific for a given substrate?
the unique arrangement and chemical properties of the amino acid residues within the site
61
How does temperature affect enzyme activity?
if temperatures are too low, the rate of reaction slows, making reactions unable to proceed, but if they are too high, this causes the enzyme to denature
62
What organisms are autotrophs?
almost all plants, some bacteria and protists
63
What are autotrophs?
organisms that generate their own organic matter through photosynthesis
64
What is energy from sunlight transformed into?
potential energy stores in chemical bonds
65
How do heterotrophs get sugars and macromolecules?
through other organisms
66
Where does photosynthesis take place?
the thylakoid membrane of chloroplasts
67
What is the makeup of chloroplasts?
inner and outer membranes, thylakoids, granum, lumen, and stoma
68
What are thylakoids?
flattened, sac-like structures (site of photosynthesis)
69
What are granum?
Interconnected thylakoids
70
What is lumen?
Interior of a thylakoid
71
What is stroma?
the fluid-filled space between the thylakoids and the inner membrane
72
What kind of energy is light?
electromagnetic energy that radiates in the form of waves
73
Does light behave as a wave and a particle?
yes
74
Do shorter or longer wavelengths have more energy?
shorter
75
Do photons have different characteristics of wavelength and energy levels?
yes
76
Do different pigments absorb different wavelengths of light?
yes
77
What wavelengths does white have?
all
78
How can photons be moved?
absorbed, transmitted, or reflected when it hits a surface
79
What are the 2 major pigment classes?
Chlorophyll and Carotenoids
80
What are the types of chlorophyll? What kind of lights do they absorb?
A and B
Both strongly absorb blue and red light
81
Why are plants green?
presence of chlorophyll makes plants look green because they reflect green light
82
What are the structures of photosynthetic (chlorophyll) pigments and where are they inserted?
contain ring structures and are inserted into the thylakoid membrane
83
What are the 2 linked components of photosynthesis?
light reactions and the calvin cycle
84
1) What are light reactions?
2) Where does water and light go, what is it absorbed by, and what does it produce?
3) What are water and light converted into?
4) What is that transferred to?
1) Light energy from the sun interacts with chlorophyll and chlorophyll absorbs the energy and converts photons to chemical energy to feed the Calvin cycle
2) into the thylakoid membrane, absorbed by chlorophyll molecules, and produces oxygen as a waste product
3) NADPH and ATP
4) the Calvin cycle
85
1) What does the Calvin cycle synthesize?
2) Where does the Calvin cycle take place?
3) What goes in and what comes out?
4) What is water, light, and carbon dioxide convert into?
1) Synthesises sugars or organic compounds as a food source
2) Takes place in the stoma
3) Carbon dioxide comes in and glucose goes out
4) Water, light, and carbon dioxide are converted into sugar and oxygen
86
Where do plants take in water and where do they take in carbon dioxide?
roots
leaves
87
How do leaves absorb carbon dioxide?
through stomata that opens and closes
88
1) What is stomata?
2) What goes in and what goes out?
1) Sites of gas exchange (CO2, Oxygen, water vapor)
2) Carbon dioxide enters the stomata, oxygen and water vapor exit the stomata
89
Does the thylakoid membrane have a lipid bilayer?
yes
90
What are photosystems?
large complexes of proteins and pigments (light-absorbing molecules) that are optimized to harvest light
91
How is energy absorbed by lights through the pigments transferred?
transferred from one pigment molecule to another, to the reaction center of the photosystem
92
What do photons of light transfer?
electrons through the photosystem
93
What does Chlorophyll A do?
helps boost the energy level of the electrons to the electron acceptors
94
What is Non-cyclic photophosphorylation?
electrons are removed from water and passed through PSII (photosystem II) and PSI (photosystem I) before ending up in NADPH
95
1) What is the electron transported through in non-cyclic photophosphorylation?
2) What do they attach to and what does this create?
3) What do they carry?
1) transported through the electron transport chain through the photosystems
2) gets attached to NADP+ to create NADPH
3) and NADPH carries chemical energy into the Calvin cycle
96
1) What does each photosystem need?
2) What is light captured by?
1) input of light and that light energy
2) captured by the photosystems and the electron transport chain
97
What does light energy power in non-cyclic photophosphorylation?
an enzyme called ATP synthase
98
What does ATP synthase work through?
the activity of proton pumping to convert ADP to ATP
99
What are the 3 steps of the Calvin cycle?
fixation of carbon dioxide, reduction of 3PGA to G3P, regeneration of RuBP from G3P
100
What are the steps of carbon fixation?
Takes in CO2 from the atmosphere through the leaf stomata
Convert that ATP and NADPH produced in the light-dependent reactions to fix the carbon from carbon dioxide
101
What is the step of reduction of 3PGA to G3P?
Goes through reduction to build the building blocks for sugars (glucose)
102
What are pigments classified as?
lipids
103
What wavelengths does chlorophyll b absorb?
higher energies
wavelengths at the lower end of the spectrum
104
What wavelengths does chlorophyll a absorb?
lower energies
wavelengths at the higher end of the spectrum
105
Where is the hydrocarbon tail of photosynthetic pigments inserted?
into the membrane
106
1) Where do light capturing reactions take place in?
2) Where does the photon enter, what is it absorbed by and what does this set up?
3) Where are electrons transferred?
4) What are the purpose of proton pumps and what powers them?
5) What do proton pumps transfer electrons to?
1) thylakoid membrane
2) chloroplast, absorbed by pigment molecules in thylakoid membrane, sets up transport chain that powers a pump
3) throughout the electron transport chain
4) electron transport chain powers them to pumps protons into thylakoid lumen that generates a high concentration of protons in the thylakoid and they want to flow down their oncentrtation gradient that powers the production of ATP
5) electron carrier that powers reactions in the Calvin cycle
107
What do light-capturing reactions convert light energy into?
chemical energy
108
What are the products of light-capturing reactions?
NADPH and ATP (required to power Calvin cycle)
109
What is the Calvin cycle?
Taking in carbons from carbon dioxide and the chemical intermediates are modified to create G3P (building block for sugars)
Takes some of the G3P product and generates it back to the original starting product so the cycle can flow
Wonβt flow without light-dependent reactions
110
What kind of reaction is carbon fixation?
redox (gain of electrons)
111
What are electron carriers?
reducing agents
112
What is the NADPH reaction?
NADP+ + e- + H+ β NADPH
Reduction reaction
NADPH is used in Calvin cycle (chemical energy is used from NADP+ and e-)
Reaction is reverse in the Calvin cycle
NADPH is going to be oxidized (lose electrons) to regenerate NADP+
113
What is the cellular respiration NADH reaction?
NAD+ + e- + H+ β NADH
Reduction reaction
NADH can be oxidized to regenerate NAD+
114
What is FADPH sub 2 reaction?
FADP+ + 2e- + 2H+ β FADPHsub2
Reduction reaction
FADPHsub2 can be oxidized to regenerate FADP+
115
What is the difference in between stroma and stoma?
Stroma: interior space of the chloroplast
Stoma: openings in leaves for gas exchange
116
What is the role of water in photosynthesis?
Pigment molecules absorb photon of light that passes the energy to reaction center (2 chlorophyll molecules close together), absorbs energy to increase kinetic energy that gives away an electron, that electron is transported through the electron transport chain to power proton pumps (chloroplast pumps protons from stroma into thylakoid lumen and free protons from water are being built up in the lumen creating a high proton concentration in the lumen, things want to diffuse out of the lumen and back into the stroma, they do that through ATP synthase), electron needs to be obtained from water, breaks bonds in water to form hydrogen atoms and oxygen gas, this drives ATP synthase (channel that allows protons to flow down their concentration gradient) to make ATP
117
What 2 products of the light reactions are used in the Calvin cycle?
ATP: provides energy to drive chemical reactions
NADPH: reducing agent that donates electrons to convert CO2 into glucose
118
What is the role of redox in photosynthesis?
NADP+ turns into NADPH
NADPH gains electrons
Electrons are transferred from water to carbon dioxide, making oxygen and glucose
119
What ultimately happens to the sugars created by the calvin cycle?
G3P build glucose, stores energy for later use, and sugars are combined to form plant's food source
120
Where is G3P released, and what is it used for? Give an example
into the cytoplasm, used as a building block to produce other sugars
Animals: glucose
121
What does glucose do and how is it made usable?
Stores chemical energy for use in cellular processes
Made usable by energy stored in glucose bonds are transferred to ATP
122
What does the process of cellular respiration start with?
the breakdown of glucose and extracting that chemical energy so it can be transferred to ATP for cells to use
123
Where does cellular respiration start?
cytoplasm and continues in mitochondria
124
What does cellular respiration result in?
the complete oxidation of glucose into carbon dioxide and water
125
What is produced as glucose molecules are broken down?
ATP is produced by substrate-level phosphorylation
126
What do electrons from the bonds in glucose get transferred to?
electron carriers that fuel oxidative phosphorylation to produce large amounts of ATP
127
What are the 4 stages of cellular respiration?
glycolysis
pyruvate oxidation
citric acid cycle
electron transport chain
128
Describe glycolysis
Takes place in the cell cytoplasm
Glucose goes through a series of chemical transformations and is converted into two molecules of pyruvate
3 carbon molecule
Some ATP is produced through substrate-level phosphorylation
Electron carrier (NAD+) is reduced to form NADH
Pyruvate gets transferred into the mitochondrial matrix
129
Describe pyruvate oxidation
Gets converted into 2 carbon molecules bound to coenzyme A (acetyl CoA)
Releases carbon dioxide and transfers electrons to electron carrier, NAD+
NAD+ gets reduced to form NADH
Acetyl CoA feeds into the citric acid cycle
130
Describe the citric acid cycle
Acetyl-CoA gets oxidized to carbon dioxide, producing more ATP through substrate-level phosphorylation
Transfers electrons to electron carriers (NAD+ to produce NADH and FAD to produce FADH2)
131
Describe the electron transport chain step in cellular respiration
All of these electron carriers transfer electrons through the electron transport chain in the mitochondrial matrix membrane
Electrons get passed down their gradient and transfer electrons as they go
Powers proton pumps
Protons get pumped out of the matrix
Forms gradient (buildup of protons outside the matrix)
Want to flow back down gradient through ATP synthase enzyme
Synthesizes large amounts of ATP
132
What is glycolisis regulated through?
phoshofructokinase
133
1) What does phosphofructokinase catalyze?
2) How does it do it?
1) third step of glycolysis
2) ATP bound in active site and 1 carbon intermediate (fructose 6 phosphate) is bound there too
Enzyme transfers one phosphate group from ATP onto fructose 6 phosphate to lead to the conversion of glucose into pyruvate
Once the cell has synthesized large amounts of ATP, it will bind to phophofructokinase (an allosteric site) and inhibit the activity of the enzyme
Feedback inhibition
End product of these redactions is ATP inhibiting the pathway from happening because the cell wants to make enough ATP to fuel its activities but wants to stop putting energy into synthesizing ATP until it needs more
Allows cell to always be able to synthesize proper amounts of ATP
134
What is the structure of mitochondria?
Outer and inner membrane
Inner membrane is folded to create cristae
Electron transport chain and ATP synthase are embedded in the inner membrane
Outer membrane has transmembrane proteins (porin) that allow things to get in and out of mitochondria
The innermost layer is the matrix
Location where 3 of the 4 reactions of cellular respiration take place
Has double-stranded circular DNA and possesses ribosomes so they can synthesize their own DNA and express needed proteins
135
What does cellular respiration convert?
glucose into ATP
136
What are the steps of glycolysis and where does it start?
Glycolysis
Takes place in the cytoplasm
6 carbon glucose undergoes multiple steps, making ATP and NADH, releasing an electron, to make 3 carbon pyruvate
137
What are the steps of pyruvate oxidation and where is it located?
Pyruvate oxidation
Takes place in the mitochondrial matrix
Pyruvate turns into acetyl CoA by releasing an electron from NAD+ to make NADH, and making CO2
138
What are the steps of the citric acid cycle and where does it take place?
Takes place in mitochondrial matrix
Starts with acetyl CoA, makes CO2, NADH, and ATP
139
What are the steps of oxidative phosphorylation, what does it produce, and where does it take place?
Production of ATP by ATP synthase
Electron carriers from steps 1-3 deliver electrons to the electron transport chain in the inner membrane of the mitochondria and powers proton pumps to pump protons from the interior of the matrix to the intermembrane space (space in between inner and outer membrane of mitochondria) making a high proton concentration in the inner membrane space, so protons want to flow back into the matrix through ATP synthase and produce ATP
Takes place in the inner mitochondrial membrane
140
What is the structure of ATP and what is it used for?
three phosphate groups with high-energy bonds
ATP is used to power reactions because of their high-energy bonds
141
What is phosphorylation?
adds a phosphate group to another molecule
142
How is oxidative phosphorylation an example of phosphorylation?
adds a phosphate group to ADP using ATP synthase
2 examples: 4th step of cellular respiration and the step in photosynthesis making ATP through ATP synthase
143
What is substrate level phosphorylation?
Where ATP is produced as part of the reaction, not using ATP synthase
144
What is phosphofructokinase?
catalyzes the third step of glycolysis
regulated by feedback inhibition
The product of the reaction inhibits the reaction
Glucose is broken down, ATP binds to an allosteric site
Once the cell makes enough ATP, it stops making glucose
When the concentration of ATP is high, it will bind to the enzyme (phosphofructokinase) and turn the enzyme off
This enzyme regulates glycolysis
ATP functions as a substrate and as an allosteric regulator
145
What is feedback inhibition?
The product of the reaction inhibits the reaction
146
How is photosynthesis connected to cellular respiration?
Photosynthesis produces glucose that is the start of cellular respiration
