biology chapters 6,7,8

When considering a cell’s use of energy, it is helpful to also consider the cell’s sources of

carbon

what are the 2 ways in which organisms acquire their energy from their environment

from the sun or chemical compounds

organisms that capture energy from sunlight are called

phototrophs

ex: plants

the basics of how photosynthesis works

plants use energy from the sun to convert CO2 and water into sugar and oxygen. the oxygen is a byproduct of the reaction and the chemical bonds in the sugar can be broken down to make ATP

organisms that derive their energy directly from chemical compounds

chemotrophs

ex: animals

explain simply how chemotrophs make their energy

they ingest other organisms , obtaining glucose and other organic molecules that they then break down the chemical bonds of the organic molecules in the presence of oxygen to produce ATP and make CO2 and water as a byproduct

what is an autotroph

they are “self feeders” an organism that is able to convert CO2(an unorganic form of carbon) into glucose (an organic form of carbon).

ex: plants

heterotrophs

obtain their carbon from organic molecules synthesized by other organisms

ex: animals

are the terms chemotroph and a heterotroph interchangable?

no. although they are both used to describe the same organisms. chemotroph refers to where the organism gets its energy, heterotroph refers to where the organism sources its carbon.

same goes from phototroph v.s autotroph

do all organisms fit into the catagories of photoautotrophs and chemoheterotrophs?

no there are many exceptions such as photoheterotrophs and chemoautotrophs

define metabolism

the set of chemical reactions that convert molecules into other molecules and transfer energy in living organisms.

2 branches of metabolism, what do they mean?

catabolism: the set of chemical reactions that break down molecules into smaller units and produce ATP (think, cats always be breaking stuff)

anabolism: the set of chemical reactions that build molecules from smaller units and require an input of energy, usually ATP (think anabolic steroids help you build muscles)

kinetic energy

the energy of motion

in addition to things that move kinetic energy is also associated with light, electricity, and thermal energy

this is because all of these things have to do with the movement of photons/molecules

potential energy

Stored energy that is released by a change in an object’s structure or position

Stored energy that is released by a change in an object’s structure or position relative to a field (gravitational, electrical, magnetic)

energy definition

the capacity to do work

is CO2 considered organic?

no

as kinetic energy increases, potential energy

decreases

1st law of thermodynamics states that the

energy in the universe is constant, it cannot be created or destroyed, only the format of the energy can change

what is chemical energy

a type of potential energy coming from chemicals

what has more potential energy, and electron closer to the nucleus or further from it

further

in ATP or other molecules energy is stored in

phosphate bonds that occur in the 3rd electro shell

the energy currency of the cell

ATP

how many phosphates does ATP have

3

how many phosphates does ADP have

2

covalent bonds have different/same amount of energy when broken

different, some covalent bonds have more potential energy than others

how do you release the energy of ATP

hydrolysis

what has higher potential energy? ATP or ADP?

ATP because it has more phosphate to break

when one energy type is transformed to another, the energy available to do work decreases, this is because

some of the energy is lost as thermal energy that can’t be used to do work

2nd law of thermodynamics

A transformation in energy always leads to an increase in entropy (disorder) in

the universe

entropy

disorder

thermal energy leads to an increase in

entropy

gibbs free energy

energy that can be converted into work at a uniform temperature as in a living cell

Δ (delta)G

the change in free energy from the beginning to the end of a reaction

ΔG = G of products – G of reactants

- ΔG = energy is released

+ ΔG = energy is required

exergonic reaction (spontaneous)

you start with more potential energy than you end with

energy is released

endergonic reaction (non-spontaneous)

requires energy

you end with more potential energy than you start with

is catabolism exergonic or endergonic

exergonic

is anabolism exergonic or endergonic

endergonic

what do we mean when we say spontaneous or non-spontaneous

is there more energy in products or reactants

reactants

how many energy is released from converting ATP to ADP

ΔG = -7.3 kcal/mol

what is energetic coupling

Spontaneous reactions (-ΔG) can provide the energy to drive non-spontaneous reactions (ΔG)

Net of the two reactions must be negative

Could the hydrolysis of ATP

(ΔG = -7.3) provide enough

energy to phosphorylate

glucose (ΔG = +3.3)?

yes

enzymes decrease

activation energy

enzymes can speed up the reaction rate by a factoe of

1 mil

what are enzymes

proteins

At average human body temperatures, chemical reactions do/do not happen quickly enough to sustain life

do not, they need enzymes to help speed up the reactions

if ∆G is negative that mean

energy is produced

if a reaction is exergonic, is an

initial energy input is still needed?

yes Activation Energy (EA) is still needed

How do enzymes work to lower the EA

The active site can lower an EA barrier by

• Bonding to the substrates and make it more likely that two

molecules come in contact

• Orienting substrates correctly (so the substrate is oriented perfectly to bind to the active site)

• Straining substrate bonds (the bonds are more likely to break)

• Providing a favorable microenvironment

(hydrophilic/hydrophobic, acidic/basic)

qualities of enzymes

Not consumed (re-used)

• Highly specific

• Reduce activation energy

Activators (+) & Inhibitors (-)

Form transient associations with enzymes by forming weak bonds

• Reversible

• Competitive

• Allosteric

Competitive inhibitors

Substrate and inhibitor compete for the same site

Allosteric inhibitors

Substrate and inhibitor bind to different

sites and changes the shape of the enzymes binding site

-ΔG means

energy released

+ΔG

energy is required

More Energy in Products or Reactants?

reactants have higher potential energy

energetic coupling

Spontaneous reactions (-ΔG) can provide the energy to drive non-

spontaneous reactions (ΔG)

basically, using the energy released from something like ATP to power something else

• Net of the two reactions must be negative

Could the hydrolysis of ATP (ΔG = -7.3) provide enough energy

to phosphorylate glucose (ΔG = +3.3)?

active site

Forms transient bonds

• Formed in 3-D shape (tertiary structure)

• Proper folding essential for enzyme function

are enzymes consumed?

no they’re reused

what are all the ways you could increase the rate of a reaction

increase the temp: makes molecules move faster

increase the substrate

why does a reaction with a fixed amount of enzymes level off no matter how much substrate you add

all the enzymes get busy

are enzymes active all the time?

no, their activity is modulated by the needs of a cell

are the bonds between competitive and allosteric inhibitors and the active site reversible

yes

Can you recover enzyme

activity (# of products

produced) by adding

more substrate, if the

inhibitor is a competitive inhibitor?

yes, because at some point there will be more substrate than competitive inhibitors

Can you recover enzyme

activity (# of products

produced) by adding

more substrate, if the

inhibitor is a noncompetitive inhibitor

no, because the substrate isn’t competing for the same binding site so it doesn’t matter ow much substrate you have

possitive feedback loop

A positive feedback loop occurs when the outcome of a process increases or accelerates the very process that produced it. In other words, A produces more of B, which in turn produces more of A, creating a self‑reinforcing cycle

something is happening, let’s make it happen MORE

possitive feedback

when there a bunch of car parts, the car part assembler knows to make more cars

negative feedback

too many cars, the car assembly is turned down

stimulatory allosteric effect

we need more of ___! SAE attaches to enzyme and makes it work faster

inhibitory allosteric effect

we have enough of __, STOP! IAE attaches to enzymes and stops it.

what is a toxin, what does it do?

can irreversibly alter enzyme activity

Irreversible inhibitors of enzymes

bind covalently to the active site and permanently inactivate it

aerobic cell respiration

taking a large molecule like a glucose and breaks it down via catabolism

the potential energy in the carbohydrate is coverted to either ATP or electron carriers (mostly electron carriers)

the electron carriers then make ATP

max ATP yield: 32 ATP, -233.6 kcal

cell respiration formula

C6H12O6 + 6O2=>6CO2 + 6 H2O + 32 ATP

final electron acceptor

oxygen

oxidation

a chemical loses an electron

reduction

a chemical gains an electron

NAD+

small molecule (2 attaches nucleotides) oxidized, accepts electrons. when it accepts electrons, it becomes its reduced ofrm NADH

FAD

oxidized form, electron acceptor, becomes FADH2 when reduced

glycolysis

glucose is broken down into 2 pyruvates

1. Takes place in cytoplasm

2. Multi-step process

3. 6 carbon sugar is broken down into 2 3-carbon molecules (pyruvate)

4. Some ATP is used but there is a net gain of 2 ATP

5. Electrons are transferred from glucose to NAD+ yielding 2 NADH

6. Allosterically controlled by AMP and ATP

pyruvate oxidation

pyruvates lose a CO2

pyruvate is oxidized, coenzyme A is made and hold onto Acetyl, making Acetyl CoA

NAD+ takes the electron that thpyruvate loses and becomes reduced to NADH

can only happen with oxygen present

yield CO2, NADH and acetyl CoA

citric acid cycle

1. Takes place in mitochondrial matrix

2. 2 pyruvate are completely broken down and released as

4 molecules of CO2

3. From each molecule of glucose 6 NADH and 2 FADH2 are generated

4. 2 ATP are made per

molecule of glucose

how many membranes does a mitochondria have?

2

outer membrane: normal membrane

inner membrane: squiggles in the mitochondria

in prokaryotes cell respiration occurs where?

in the cytoplasm and the cell membrane

do strong covalent bonds contain a lot of chemical energy

no, they contain relatively little chemical energy

what makes a weak covalent bond weak

These bonds are easily broken because the arrangement of orbitals in these molecules is only somewhat more stable than if the two atoms did not share electrons

what is ATP made of

adenine, the nucleotide base

a 5 carbon ribose sugar

3 phosphates

do catabolic reactions increase or decrease entropy

increase

do anabolic reactions increase or decrease entropy

net increase on entropy due to heat from the energy transfer

gibbs free energy

do catabolic reactions increase or decrease entropy

enthalpy

the total amount of energy

energy that can do work + energy that can’t do work

absolute temperature

temperature measured on the kelvin scale

total amount of energy equation

total energy=( energy available to do work) +(energy lost to entropy x absolute temp)

explain the equation delta G= delta H -T delta S

this equation measures how spontaneous a reaction is

so, delta H is heat (+ means the reaction requires heat, - means it’s releasing heat) the T is temperature and delta S is the entropy

if delta G is less than 0 the reaction is spontaneous, if it’s more that 0 the reaction is not spontaneous, if it’s equal to 0 it’s at equalibrium (it’s doesn’t not want to happen but it always doesn’t want to happen either)

free energy difference for ATP hydrolysis (in a lab) is

-7.3 kcal per mole

free energy difference for ATP hydrolysis (in a cell) is

-12 kcal per mol

do weak bonds have a lot of potential energy or a little

a lot because they require more energy to hold together

what is the energy barrier

another word for the hump of activation energy

when activation energy is lowered, what happens to free energy?

decreased

are enzymes specific or unspecific

specific

lock-and-key model of active site

the substrate fits into the active site in the same way that a key fits into a lock