Unknown Material Exam Three Flashcards
What are the forms of energy?
- Chemical energy - stored in bonds
- Heat energy - transfer due to temp difference
- Electrical energy - separation of charges
- Light energy - electromagnetic radiation stored as photons
- Mechanical - energy of motion
What are the laws of thermodynamics?
in biology, they are a set of laws that help us understand how cells harvest and transform energy to sustain life
What is the difference between potential and kinetic energy?
- Potential energy - stored energy (chemical bonds, concentration gradient, or an imbalance in charges)
- Kinetic energy - energy of movement
What is the second law of thermodynamics?
when energy is converted from one form to another, some of that energy becomes unavailable to do work i.e no energy transformation is 100% efficient, some energy is lost to disorder (entropy)
What is free energy?
it is the usable energy that can do work unit is (G)
How is a change in energy measured?
it is measured in calories or joules, delta symbol (triangle) means (a change in)
formula for change in free energy goes as follows:
∆ G = ∆H - T∆S
What does a -∆G mean?
when the change in energy is negative, energy is released
What does +∆G mean?
when the change in energy is positive, energy is required
What is meant by coupling reactions?
When the free energy RELEASED from one reaction (exergonic) and is used for/ coupled with another reaction that REQUIRES (endergonic) OR when one molecule is reduced SO THAT another can be oxidized.
What are the two characteristics of ATP that allow so much energy to be released?
- phosphate groups have negative charges and repel each other - the energy that is needed to get them close is in the P-O bond
- The free energy of the P-O bond is much higher in ATP than is the O-H bond that forms after hydrolysis on the ADP
How do enzymes do what they do?
enzymes lower the energy barrier E(a) AKA activation energy AKA the amount of ΔG needed to jumpstart the reaction
When activation energy is lowered, the reactions speed up
What do enzymes not do?
enzymes do not make a reaction happen that could not already happen
enzymes do not change the difference in Δ G between the reactants and the products i.e the final equilibrium
What are transition state intermediates?
are unstable substates/reactants with higher free energy, any substate with a +ΔG
What are substrates?
are the reactants or molecules that the enzyme exerts its catalytic function i.e lowering the activation energy.
What are the three mechanisms of enzyme action?
- Chemical change - enzymes can temporarily add chemical groups to itself
- Orientation - enzymes can align/position the substrate so they can react
- Physical strain - enzymes can induce strain by stretching substrate, and by consequence make the bonds of the substrate more reactive
What are the two ways enzymes can be regulated?
- Regulation of gene expression - how many enzyme molecules are made (works slowly)
- Regulation by the enzyme itself - enzyme shape may change (adding phosphate group/enzyme inhibitor may close/open the active site)
What is a competitive inhibitor?
reversible inhibitor that directly COMPETES with natural substrate for the active site / binding site.
the degree of the inhibition depend on what type of substrate and what type of inhibitor
What is an uncompetitive inhibitor?
reversible inhibitor that binds to the enzyme substrate complex (when the enzyme has substrate bound to it) and prevents the substrates release, freezes the reaction of substrates
UN = eNzyme sUbstrate
What is a competitive inhibitor?
a reversible inhibitor that binds to the enzyme at site that isn’t the active (allosteric site)
this changes the shape of the shape of the enzyme and alters the active site (allostery)
What is allosteric regulation?
when an effector (non competitive inhibitor) binds an enzyme at the allosteric site (different from the active site), changing the shape
active form - can bind substrate = product
inactive form - can’t bind substrate = no product
What is feedback inhibition?
when the final product acts as a noncompetitive inhibitor of the first enzyme, which shuts down the pathway.
this makes sure we don’t make too much of something or waste energy/materials making something in excess
what is the transition state?
it is the reactive status of the substrate/reactant, after there has been a good enough input of energy to start the reaction.
What are the principles of metabolic pathways?
- Complex transformations occur in a series of separate reactions
- Each reaction is catalyzed by a specific enzyme
- Many metabolic pathways are similar in all organisms
- In Eukaryotes are compartmentalized in specific organelles
- Key enzymes can be inhibited or activated to alter the rate of the pathway
The transfer of electrons is often associated with?
the transfer of hydrogen ions
a hydrogen atom is H+ ion plus a negatively charged electron
When a molecule loses H atoms what does it mean?
it becomes more oxidized
less hydrogens = more oxidized = less free energy
What is the oxidized form of NADH, and how many electrons / protons does the molecule transfer?
the oxidized form is NAD+ and it transfers 2 electrons and one proton (H+)
When NADH loses an electron to O2, which is oxidized and which is reduced? Is this exergonic or endergonic?
{NADH + (H+) + (.5)O2 –> (NAD+) + H2O}
The oxygen is reduced and the NADH is oxidized.
This reaction is exergonic because the NADH loses an electron and therefore releases energy.
What are the five energy-yielding metabolic pathways?
- Glycolysis
- Pyruvate Oxidation
- Fermentation
- Krebs Cycle
- ETC and Chemiosmosis (Oxidative Phosphorylation)
Where does glycolysis occur and does it occur when oxygen is present or in the absence?
glycolysis occurs in the cytoplasm (cytosol) of the cell outside the mitochondria
glycolysis is anaerobic (it does not require oxygen), but functions the same even if oxygen is available
Where does fermentation occur and does it function with or without the presence of oxygen?
fermentation occurs in the cytoplasm
it occurs in the absence of oxygen
Where does pyruvate oxidation occur and does it function with or without the presence of oxygen?
it occurs in the mitochondrial matrix
it ONLY functions in the presence of oxygen.
Where does the citric acid cycle occur and does it function with or without the presence of oxygen?
it occurs in the mitochondrial matrix
it ONLY functions in the presence of oxygen
Where does the electron transport cycle / respiratory chain occur and does it function with or without the presence of oxygen?
it occurs in / through the inner membrane of the mitochondrial matrix - why the cristae has folds
it ONLY functions with the presence of oxygen
Define glycolysis and explain.
it is separate from cellular respiration, but is required to perform cell respiration
catabolic process that converts glucose into 2 pyruvate molecules
involves energy investment phase (1-5)
involves energy payoff phase (6-10)
What are the input / output of glycolysis?
Input: 2 ATP, 2 NAD+, 1 Glucose (6 carbon), 2 Pi
Output 4 ATP, 2 NADH, 2 Pyruvate (3 carbon)
Net yield: 2 ATP, 2 NADH, 2 Pyruvate
Where are glycolysis’ products used, i.e how is it connected to the other pathways?
The 2 NADH produced are used down the line in the ETC
The 2 Pyruvate are the input for the next pathway, pyruvate oxidation
Without glycolysis, no other pathway has a chance.
Every pathway requires many specific (…….)
all of the reactions inside each pathways have their own specific enzyme that catalyses
What are the inputs and outputs of pyruvate oxidation?
Inputs: 2 pyruvate, 2 NAD+ 2 Coenzyme A
Outputs: 2 Acetyl CoA (2 carbon), 2 NADH, 2 CO2
Where are the products of pyruvate oxidation used, i.e how is it connected to other pathways?
The CO2 is released outside of the cell
The acetyl CoA is used in the citric acid cycle
The 2 NADH are used later in the ETC
What are the inputs and outputs of the krebs cycle?
Inputs: 2 Acetyl CoA, 6 NAD+, 2 FAD, 2 ADP, and 2P(i) water
Outputs 4 CO2, 2 ATP, 6 NADH, 2 FADH2
Where are the products of the krebs cycle used, i.e how it is connected to other pathways?
The CO2 is released
The NADH, and FADH2 are used in the ETC
The krebs cycle relies on pyruvate oxidation to provide the acetyl CoA
What are the inputs and outputs of oxidative phosphorylation (ETC + ATP synthesis)?
Inputs: 10 NADH, 2 FADH2, H+, 28 ADP, Pi
Outputs: 10 NAD+, 2 FAD, H2O, 28 ATP
How else is oxidation phosphorylation connected to the rest of the pathways, specifically the last step of the ETC?
For the first three pathways in aerobic respiration to continue, NADH must be oxidized again, and FADH2 must as well.
Since they donate their electrons to O2, if oxygen is low, they can’t donate them and the “aerobic” pathway gets backed up
What is oxidative phosphorylation?
Two Stages:
1. Electron Transport
2. Chemiosmosis
What is the electron transport cycle?
when the electrons from NADH and FADH2 pass through a series of protein complexes inside the inner membrane
the electrons flow results in a (high potential energy) proton concentration gradient across the membrane
(inner-membrane space high and mitochondrial matrix low)
What is chemiosmosis?
when protons naturally flow back across the membrane through a channel protein ATP synthase (uniporter) (facilitated diffusion) which couples this diffusion with ATP synthase
Where do the electrons that are responsible for pumping H+ ions into the inter-membrane space come from and what are they used for?
In complex 1 they come from NADH
In complex 2 they come from FADH2
They are used for their potential energy to transfer hydrogen ions into the inner membrane compartment
What is the proton-motive force and what are the two components
The force generated across a membrane that consists of a chemical potential plus an electrical potential due to the positivity of the H+
What the two types of fermentation?
Lactic Acid
Alcoholic
Explain glycolysis and lactic acid fermentation.
It occurs in microorganisms and some vertebrate muscle cells - PYRUVATE IS FINAL ELECTRON ACCEPTOR
key enzyme is lactate dehydrogenase
Input is Glucose, 2 ADP, 2 Pi, 2 NAD+
Output is 2 lactate, 2 NAD+, 2 ATP
Explain glycolysis and alcoholic fermentation.
It occurs in yeasts and some plant cells - PYRUVATE IS THE FINAL ELECTRON ACCEPTOR
two enzymes are required
Input is Glucose, 2 ADP, 2 Pi, 2 NAD+
Output is 2 ethanol, 2 ATP, 2 CO2, 2 NAD+
What is light?
energy that can be kinetic or potential, and is electromagnetic radiation stored as photons.
What is electromagnetic radiation?
radiation propagated as waves and particles
the amount of energy in the wave is inversely proportional to wavelength (small wavelength -> greater energy)
What is a photon?
they are packets that store energy, (particles of light)
What does absorbed energy do?
absorbed energy adds energy to the molecule (makes it excited)
it boosts an electron in the molecule into a shell farther from the nucleus which makes it more unstable and reactive
What do pigments do with the sun’s light?
they absorb specific wavelengths in the visible range
the other light / wavelengths are scattered or transmitted which imparts the colors we see
Explain what are absorbed wavelengths.
Light can be absorbed only in certain wavelengths and it all depends on the PIGMENT
chlorophyll a and b absorb red and blue wavelengths
carotenoids absorb blue and violet
Only absorbed light is useful for photsynthesis
Explain the reflected wavelengths.
Hardly no wavelength is absorbed from 500-625
No pigment absorbs pure green light, so it is reflected, which is why we perceive leaves to be green
What is the importance of photosynthesis?
The primary function / importance of photosynthesis is to convert solar energy into chemical energy and then store that chemical energy for future use, but it also makes oxygen as a byproduct.
Without photosynthesis, cellular respiration wouldn’t have a hope in functioning i.e it sustains all the food chains in an ecosystem
What are the two pathways of photosynthesis?
- Light reactions (dependent)
- Carbon fixation (light independent) Calvin Cycle
What is the input and output of light reactions?
Input: Sunlight, 6H2O, ADP, Pi, NADP+
Output: 6 O2, ATP, NADPH
What is the input and output of the carbon fixation (light independent reactions?)
Input: 6 CO2, NADPH, 18ATP
Output: 2 G3P (can form one glucose), 12 NADP+, 18 ADP, and 18 Pi
How are the light dependent reactions connected to the carbon fixation reactions?
The ATP and NADPH made in the light dependent reactions are used in the carbon fixation reactions
What are photosystems?
multi-protein light harvesting complexes embedded in the thylakoid membrane
they contain pigment molecules, like chlorophyl that absorb the photon and make the molecule excited.
In which pathway are photosystems used?
They are used in the light dependent reactions
Explain light harvesting complexes and reaction centers.
When a pigment molecule absorbs a photon, the molecule becomes unstable and the energy is released quickly, so the energy is absorbed by other pigment molecules and is passed to the reaction centers, where it is converted to chemical energy (when the excited molecule gives up an electron to the electron acceptor
Chlorophyll in the reaction center is oxidized
The electron acceptor molecule is reduced
Explain the orientation of the light harvesting complexes and reaction centers.
A protein complex that includes chlorophyll molecules and carotenoid molecules make up the antenna system (light harvesting complex)
Inside the antenna system there are different proteins that contain other chlorophylls
This entire thing is embedded in the thylakoid membrane
What is light energy converted to and what is the final electron acceptor in the photosystems?
The light energy is converted into chemical energy in the form of potential energy.
The electron acceptor in the photosystem is only the first of many
*The final electron acceptor is NADP+
What photosystems are used in noncyclic electron transport?
Photosystem II - when an chlorophyll gives up its excited electron it is unstable and grabs another electron from water, and the water becomes oxidized (the H+ are dropped in the thylakoid place)
The electron is passed through an ETC which pumps H+ into the thylakoid space by using the energy of the electron and ATP synthase eventually synthesizes
Photosystem I - chlorophyll takes an electron from the last carrier in PS2 and the excited electron is passed through several other carriers and reduces NADP+ to NADPH
What photosystems are used in cyclic electron transport?
Photosystem I - when the chlorophyll gives up its excited electron, the energetic electron then passes through the ETC which pumps H+ into the thylakoid space by using the energy of the electron and then ATP synthase does its thing phosphorylate ADP (NADPH is not produced)
The electron is then accepted by the chlorophyll again and the process re-starts
How is ATP produced during light dependent reactions?
It is formed by photophosphorylation,
when H+ flows back across the membrane through ATP synthase, it uses that energy to synthesize ATP
What two things contribute to the H+ gradient?
Hint: (ones in the lumen and ones in the stroma)
Water oxidation in the lumen and NADP+ reduction in the stroma
Why is ATP synthase important?
The ATP produced in the light dependent reactions is needed for the light independent reactions
If ATP synthase isn’t woking correctly, the H+ concentration will just keep building up potential energy but there will no way to release it.
What is CO2 reduced to in the light independent (carbon fixation) reactions and where does the energy come from to do this?
it is reduced to carbohydrates, and it uses the energy stored as potential energy in ATP and NADPH
Where do the carbon fixations occur?
they occur in the stroma
What enzyme is involved in the Calvin Cycle?
Rubisco
For every turn of the Calvin Cycle, what happens?
One CO2 is fixed and One RuBP is regenerated
What is photorespiration?
It is when RuBP reacts with O2 in the Calvin Cycle when it is supposed to react with CO2
it consumes O2 and releases O2, and it happens only in night
it wastes ATP and NADPH and reduces the net carbon fixed by the Calvin cycle
How do C4 and CAM plants avoid photorespiration?
C4 plants they have physically separated the Calvin Cycle (mesophyll and bundle sheath cells) from O2 rich spaces in the leaf, so the rubisco always encounters high CO2
CAM plants only open their stomata at night
What are some examples of energy loses in photosynthesis?
- Wavelengths that couldn’t be absorbed - 50%
- Light energy not absorbed due to plant structure - 30%
- Inefficiency of light reactions 10%
- Inefficiency of CO2 fixation pathways 5%
