biol1000 units 3-4

energy

the capacity to cause change

kinetic energy

the energy of motion

thermal energy

kinetic energy associated with the random motion of atoms or molecules

heat

thermal energy transferred from one object to another

light energy

kinetic energy harnessed for photosynthesis

potential energy

energy that matter possesses based on its location or structure

chemical energy

potential energy available for release in a chemical reaction

how much (in percentage) can potential energy in gasoline be transformed into kinetic energy? what happens to the rest of the energy?

25% … rest of energy is lost as heat

how much (in percentage) can potential energy in cell's fuel is transformed into kinetic energy for cellular processes?

34% … rest of energy is lost as heat

ATP is the abbreviation of what?

adenosine triphosphate

what is ATP?

energy-carrying molecule and primary energy currency of all living cells … used for muscle contraction

chemically equivalent of a compressed spring ... tail end of 3 phosphates are all negatively charged + highly unstable = stores energy

why is ATP described as a compressed spring?

holds high potential energy which is released immediately when bond to the third phosphate group is broken

how can ATP be broken down easily

hydrolysis

what is hydrolysis and what does ATP release through this process?

the addition of water

releases ADP

exergonic reaction

reaction that produces/releases energy … the breaking down of glucose to produce ATP is exergonic

endergonic reactions

reactions that require an input of energy

phosphorylation

the phosphate group broken off of ATP is transferred to another molecule… this process is also endergonic (requires energy input)

what does ATP do in mechanical work?

hydrolysis of ATP when attached to motor proteins in muscle cells causes the proteins to change shape and pull on other protein filaments, therefore causing cells to contract

activation barrier vs. activation energy

barrier: energy barrier that must be overcome for any chemical reaction to begin

energy: energy required to contrort or weaken bonds so that they can break and new bonds can be formed

what are enzymes?

enzymes: molecules that function as biological catalysts … increases rate of a reaction without being consumed by the reaction … almost all proteins

how do enzymes lower the activation barrier for a chemical reaction to take place?

an enzyme speeds up a reaction by lowering the activation energy needed for a reaction to begin… a lowered barrier allows enzyme-catalyzed reaction to proceed more rapidly

each enzyme is a lock that only a specific key can fit into. what is this "key"/reactant that the enzyme relies on?

substrate

what is the catalytic cycle (of an enzyme)

represets how a catalyst facilitates the conversion of reactants into products while being regenerated at the end

steps of the catalytic cycle (example: enzyme is sucrase)

1) enzyme starts as empty active site
2) substrate (sucrose) enters the site attaching by weak bonds... site changes shape to hold it snug (AKA induced fit)*
3) sucrose bonded with enzyme reacts with water = hydrolyzed* = converts to products (glucose and fructose)
4) enzymes releases the products and emerges unchanged from reaction

in the catalytic cycle is the enzyme consumed by the reaction or is it reused?

the enzyme is reused... can hold up to thousands of substrates in seconds

what is denaturation and why must this not happen/be regulated?

the protein unfolds so that its 3D shape is changed…

optimal temperature allows for the best possible matching of substrate to active site… protein becomes nonfunctional if this is not achieved

what are cofactors and what are some inorganic cofactors

non protein molecules that aid enzymes… binds to the active site and function in catalysis

inorganic cofactors: ions of zinc, iron, copper

coenzyme

cofactor that is organic (e.g. vitamins)

inhibitor

a chemical that interferes with an enzyme's activity

competitive inhibitor

some inhibitors that resemble substrates that compete for entry into the active site… reduces enzyme's productivity by blocking substrate molecules from entering active site

noncompetitive inhibitor

doesn't enter active site… instead binds to enzyme elsewhere changing the enzyme's shape so that substrate could not fit into enzyme

why is it important for a cell to be able to inhibit an enzyme?

cells use inhibitors to regulate cellular metabolism (feedback inhibition)

feedback inhibition

if a cell is producing more product than it needs the product may become an inhibitor... when the product is consumed by cell, none will be left to act as the inhibitor = enzyme can function once again

is inhibition reversible or is it a permanent process?

inhibition can be either reversible or permanent (irreversible) …

reversible - inhibitor binds weakly (non-covalently) to enzyme = enzyme regains its functions
irreversible - inhibitor bonds strongly (covalently) to enzyme = deactivates enzyme

photosynthesis

the energy of sunlight is used to rearrange the atoms of carbon dioxide (CO2) and water (H2O), producing organic molecules and releasing oxygen (O2)

energy (sunlight) + CO2 + H2O -> organic molecules (sugar) + O2

cellular respiration

the aerobic harvesting of energy from organic molecules … O2 is consumed as organic molecules are broken down to CO2 and H2O and the cell captures the energy released as ATP

organic molecules (sugar) + O2 -> CO2 + H2O + energy (ATP)

what cells and organelles perform cellular respiration? what about photosynthesis?

photosynthesis: chloroplasts in plants and some prokaryotes

cellular respiration: mitochondria in all eukaryotes, and many prokaryotes

how are photosynthesis and cellular respiration opposites of each other? what are the reactants and products of each?

the products for one are the reactants (inputs) for the other

… photosynthesis releases sugar + O2 after inputs of sunlight energy + CO2 + H2O

… cellular respiration releases O2 + H2O + ATP energy after inputs of sugars and O2

respiration

the exchange of gases / breathing

… organisms gain O2 from the environment -> releases CO2 as a waste product

aerobic vs. anaerobic

aerobic: oxygen requiring

anaerobic: not requiring oxygen

how are respiration and cellular respiration linked?

breathe -> take up O2 -> carried by bloodstream into muscle cells -> used in cellular respiration to produce ATP -> powers the muscle cells

basal metabolic rate

the body's resting rate of energy output

kilocalories (kcal or C)

a measure of the quantity of heat required to raise the temperature of 1 kg of water by 1 degree Celsius

what process require energy in our body? how does the intake and burning of kcal affect weight gain and loss?

energy from ATP is needed for all bodily activities

consuming more calories than the body expends (surplus) = weight gain … consuming fewer calories = weight loss, as the body burns stored fat for energy

redox reaction

the transfer of electrons from one reactant to another (oxidation + reduction)

oxidation

the loss of electrons from one substance … a molecule is 'oxidized' when it loses one or more electrons … always paired with reduction

reduction

the gaining/addition of electrons to another substance … a molecule is said to be 'reduced' when it gains one or more electrons… always paired with oxidation

in cellular respiration which reactants are oxidized and reduced? what products do oxidation and reduction result in?

OIL RIG (oxidation is losing reduction is gaining) … glucose LOVES hydrogen atoms as it is OXIDIZED to CO2

NAD+ vs NADH

NAD+ is OXIDIZED (loses electrons)… it shuttles electrons in redox reactions

NADH is REDUCED (gains electrons)

NADH becomes NAD+ if electrons are lost

what is the role of NAD+ and NADH in cellular respiration?

NAD+ (oxidized) acts as an electron acceptor during glycolysis and the Citric Acid Cycle. It becomes NADH (reduced), which transports high-energy electrons to the electron transport chain (ETC) to produce ATP

Dehydrogenase

an enzyme that catalyzes the removal of hydrogen atoms from a molecule, particularly in the electron transport chain (ETC) reactions of cell respiration

How are electrons transferred to NAD+?

dehydrogenase (enzyme) strips 2 hydrogen atoms from the organic fuel molecule (e.g. glucose) and transfers 2 electrons and 1 proton to NAD+ (which in turn reduces it to NADH)

electron transport chain (ETC)

chain of carrier molecules that receive electrons from the NADH… series of redox reactions makes electrons go down from one carrier to another (like a staircase), which releases energy to make ATP

what is at the end/bottom of the electron transport chain?

it is oxygen which, receives the electrons = ends up making H2O (aka REDUCES O2 to H2O)

where are the ETC carrier molecules embedded/located?

mostly in the inner mitochondrial membrane

what are the 3 stages of cellular respiration

1) glycolysis
2) pyruvate oxidation + citric acid ccylce
3) oxidative phosphorylation

what is glycolysis and where does it take place in the cell?

it begins cellular respiration by splitting glucose into 2 molecules of pyruvate… small amount of ATP is released

it takes place in the cytosol

what is the starting reactant and the final product in glycolysis?

starting reactant: glucose
final product: pyruvate

substrate level phosphorylation

explains how ATP is formed in glycolysis + citric acid cycle

enzyme transfers a phosphate group from a substrate molecule to ADP

how many chemical steps are there in glycolysis?

9 steps… product of one reaction is reactant for next reaction… different enxyme used for each step

intermediates

compounds formed in the steps between the starting reactant and the final product

what is the net gain of ATP and NADH in glycolysis?

2 NADH and 2 ATP

4 ATP produced in payoff phase but 2 used for investment stage = left with 2 ATP

2 NAD+ are REDUCED to 2 NADH

steps of glycolysis can be grouped into two main phases, which are:

energy investment and energy payoff

energy investment phase

CONSUMING energy … 2 ATP molecules are used to energize the glucose molecule … glucose is split into 2 smaller molecules

energy payoff phase

PRODUCING energy … 4 ATP and 2 NADH makes 2 pyruvate molecules

is glycolysis an aerobic or anaerobic process?

anaerobic process… no oxygen needed to break down glucose into pyruvate and produce ATP

how do we know that glycolysis might have evolved very early in the history of life?

occurs in cytosol… does NOT need membrane bound organelles and oxygen (used long before there was oxygen in the atmosphere)

what organisms and cells can live off glycolysis alone? what organisms and cells need to continue through the rest of cellular respiration to produce enough energy to survive?

organisms who are adapted to anaerobic environments or lack mitochondria

complex, multicellular organisms

pyruvate oxidation

Conversion of pyruvate to acetyl CoA and CO2 that occurs in the mitochondrial matrix in the presence of O2.

citric acid cycle (aka Krebs Cycle)

-completes breakdown of glucose to CO2
-takes place in mitochondrial matrix (eukaryotic) /cytosol (prokaryotic) … small amount of ATP produced

steps of pyruvate oxidation

1) carboxyl group is removed from pyruvate = released as CO2
2) remaining two carbon molecules are oxidized to REDUCE NAD+ to NADH
3) a compound called coenzyme A (CoA) joins with the two carbon molecule to form the final product: acetyl CoA

what are the reactants + products of pyruvate oxidation?

reactants: pyruvate

products: CO2, NADH, acetyl CoA

Hans Krebs

studied the cycle; the person the Krebs Cycle (aka the citric acid cycle) is named after

what is FADH2?

electron and H+ ion carrier… produced in CAC… ‘middleman’ to help move electrons

brief steps of the Krebs cycle/CAC/TCA cycle?

• acetyl CoA is combined with oxaloacetate to make citrate

• redox reactions remove two carbon atoms and releases them as CO2

• oxaloacetate is regenerated

what are the reactants of the CAC?

acetyl CoA, NAD+, FAD, ADP, H2O, oxaloacetate

what are the products of the CAC?

2 CO2, 3 NADH, 1 FADH2, 1 ATP

output is doubled to account for the production per glucose molecule (4, 6, 2, 2)

what is the net gain of ATP, NADH, FADH2, and CO2 from pyruvate oxidation and the citric acid cycle? (per single PYRUVATE molecule)

pyruvate oxidation: 1 NADH, 1 CO2, 0 ATP or FADH2

CAC: 1 ATP, 3 NADH, 1 FADH2, 2 CO2

what is the net gain of ATP, NADH, FADH2, and CO2 from pyruvate oxidation and the citric acid cycle? (per single GLUCOSE molecule)

pyruvate oxidation: 2 NADH, 2 CO2, 0 ATP or FADH2

CAC: 2 ATP, 6 NADH, 2 FADH2, 4 CO2

at what stages of cellular respiration are the reactants used? at what stages are the products produced?

stages where reactants are used: glycolysis (glucose), ETC (oxygen)

stages where reactants are produced: glycolysis (ATP), CAC (ATP, CO2), ETC (ATP, H2O), pyruvate oxidation (CO2)

oxidative phosphorylation

final stage of cellular respiration… takes place in mitochondria… divided into two parts (electron transport chain and chemiosmosis)

***where 90% of the ATP of cellular respiration is produced

Role of ETC (oxidative phosphorylation)

first component of oxidative phos.

• NADH and FADH2 shuttle electrons to the ETC

• H+ ions are pumped across the inner mitochondrial membrane into the intermembrane space (active transport… results in H+ concentration gradient that holds potential energy)

• terminal electron acceptor is O2, which is REDUCED to H2O

where do we find a high concentration of H+ ions?

in the intermembrane space during oxidative phosphorylation

chemiosmosis

the potential energy of the H+ concentration gradient is used to make/synthesize ATP

how does chemiosmosis result in ATP production?

H+ atoms are driven back down their concentration gradient through the enzyme complex called ATP synthase … ADP is phosphorylated to ATP

what is the final net energy generation (ATP) of celluular respiration based on a single glucose molecule?

32 ATP

fermentation

the process of harvesting energy from organic matter without using oxygen as a terminal electron acceptor … an ANAEROBIC form of respiration

What fermentation pathways result in NAD+ regeneration? Why is this necessary?

lactic acid fermentation and alcohol fermentation

necessary because regeneration of NAD+ from fermentation ensures glycolysis can happen so ATP can be produced (glycolysis requires constant supply of NAD+)

lactic acid fermentation

animal muscle cells and certain bacteria can regenerate NAD+… NADH is oxidizes back to NAD+ as pyruvate is reduced to lactate

alcohol fermentation

yeasts and certain bacteria recycle their NADH back to NAD+ while converting pyruvate to CO2 and ethanol

what organisms undergo lactic acid fermentation? alcohol fermentation?

lactic acid fermentation: animal muscle cells and some bacteria

alcohol fermentation: yeasts + some bacteria

3 types of anaerobes

anaerobes, obligate anaerobes, facultative anaerobes

anaerobes

organisms that can live in anaerobic conditions

obligate anaerobes

require anaerobic conditions

facultative anaerobes

can live in anaerobic or aerobic conditions

under what conditions will a facultative anerobe produce ATP using fermentation? what conditions are needed for them to produce ATP using oxidative phosphorylation

facultative anaerobe will produce ATP using fermentation if O2 IS NOT PRESENT

can also produce ATP using oxidative phosphorylation if O2 IS PRESENT

autotrophs

"self-feeders" … organisms that make their own food … ultimate source of organic molecules for almost all life on Earth

photoautotrophs

autotrophs that use energy from light… primary producers of the biosphere

heterotrophs

the consumers of the biosphere

• cannot make their own food

• consumes plants, animals and decomposes organic material

• dependent on photoautotrophs for organic fuel + oxygen to maintain life

where do photosynthetic organisms fit into the food chain?

primary producers … first in the trophic level