Chapter 6 Flashcards
energy
- allows biological work
- fundamental to all biological processes
- energy can be used to…do work and supply heat
potential energy
- due to structure or position
- energy that is not being used at a given moment but there is potential of it being used
Chemical Bonds: Potential energy
- stored in the arrangement of the atoms bonded together to form a molecule
- can be “harnessed” during chemical reactions
- critical for understanding metabolism
- bonds between two molecules within an atom are a form of PE
- net energy is stored in how bonds are arranged
energy transformers
- organisms
- converting one type of energy into another type
- ex: cellular respiration
- PE stored in glucose released and used for chemical work
Organisms are energy transformers..
- all energy came from light (sun) and was “fixed” into an organic molecule by a plant
- energy that comes in from the sun is being fixed by plants into organic molecules
first law of thermodynamics
- energy cannot be created or destroyed
- only transformed (not making new energy, energy is not going away, we just convert into different forms)
- conservation of energy
- this is the heart of metabolism
- energy is transformed by chemical reactions
Spontaneous Chemical Reaction
- without input of free energy; proceed on their own
- does not mean “speed”
- ex: sucrose -> CO2 and water
Nonspontaneous Chemical reaction
-requires free energy
Reactions are spontaneous if…
- Products have lower potential energy than reactants
ex: methane reacts with oxygen - Product molecules are less ordered than reactants
- entropy- amount of disorder
enthalpy
difference in potential energy (delta H)
exothermic
releases heat (- delta H)
endothermic
absorbs heat (+ delta H)
entropy
amount of disorder (delta S)
Second Law of Thermodynamics
-the amount of disorder, or entropy (delta S), increases in an isolated system over time
Chemical processes favor…
- direction w/ lower PE
- increased disorder
- ex: glucose oxidation: Reactants: high PE, ordered. Products: low PE, disordered
- for reaction to occur spon, the system must either give up enthalpy (-delta H) or increase entropy (+delta S) or both
H=G+TS
- total energy- usable energy +unusable energy
- H= enthalpy or total energy
- G= free energy/usable energy
- S= entropy or unusable energy
- T = absolute temperature in Kelvin (K)
Gibbs Free Energy (G) & Spontaneity
-to determine if reaction is spon, we can look at change in entropy (delta S) and change in enthalpy (potential energy, delta H)
(delta G= delta H -T delta S)
Exergonic reaction
- delta G less than O or negative free energy change
- spontaneous
Endergonic reaction
- delta G greater then 0 or positive free energy change
- requires addition of free energy
- not spontaneous
Free energy & Equilibrium
- for a reaction at equilibrium, delta G=0
- Reactants Products
- if a cell is in equilibrium, no work is being done
- the cell is DEAD
- life is a process of dis-equilibrium: it requires a constant inout and processing of energy
How do we used free energy to do work?
- ATP (adenosine triphosphate)
- ribonucleotide (ribose + adenine)
- 3 phosphate group
ATP: energy molecule
- ATP can release this energy when needed for some activity
- muscle activity, active transport
- 3rd phosphate bond is a high-energy bond
Hydrolysis of ATP
- delta G= -7.3 kcal/mole
- reaction favors formation of products
- energy liberated can drive a variety of cellular processes
ATP hydrolysis for energy coupling
- an endergonic reaction can be coupled to an exergonic reaction
- endergonic reaction will be spontaneous if net free energy change processes is negative
- how we get an endergonic reaction to proceed
Rate of chemical reactions
- spontaneous reactions are not fast
- molecules must come into contact with each other for a reaction to occur- requires energy
- most reactions under physiological conditions happen slow
Rate of chemical reactions: temperature and concentration
- increase temp, molecules move faster/collide more often
- increase concentration=more collisions
- both speed up reactions
enzymes are catalysts
- speeds up rate of reaction
- not consumed during reaction
- proteins
- metabolism= all chemical reactions within a cell
- mediated by the actions of enzymes
enzymes
- we possess thousands of enzymes
- each enzyme facilitates a specific reaction
- lactase: lactose -> glucose + galactose
- sucrose: sucrose -> glucose + fructose
- RNA polymerase: nucleotides-> RNA
- ____-ase: substrate -> product
Enzymes: disorders
- many inherited disorders are caused by the inability to produce a specific enzyme
- ex: lactose intolerance
Ribozymes
- RNA molecules with catalytic function
- almost all enzymes are proteins
- Ribozymes RNA molecules that can facilitate chemical reactions (speed up) catalytic function
Activation energy
- all reactions require initial input of energy to start
- breaks chemical bonds in reactants
- once bonds have become unstable enough to break
the activation energy barrier
- critical for life
- most macromolecules are “energy rich”
- ex: glucose oxidation
- releases a LOT of energy
- would be released immediately without barrier
- the molecules would spon “combust” if we didn’t have this
- this is BAD
- doesn’t happen at normal cell temps
substrate
reactants in enzyme mediated reactions
- enzymes are substrate specific
- form enzyme-substrate complex
Active site
- pocket on surface where substrate fits
- not rigid
Substrate-specific
- lock and key model
- key fitting in the lock, its the exact fit
induced fit
enzyme changes shape when the substrate binds
- enzyme hugs around the molecule
enzyme structure
- position reactants together to facilitate bonding
- weaken chemical bonds to make it easier to reach transition state
- provides specific microenvironment
- direct participation in reaction
- covalent bonds made and broken
- then returns to original state
enzymes are affected by environment
- function best within a narrow rage of temp and pH
- otherwise function decreases (or stops)
inhibitors
- selectively block enzyme action
- enzymes stop facilitating to let you know you made enough of that product
- ex: DDT in nervous system- band in the US
- used to use as pesticide, but it builds up on body tissue, acts as an enzyme inhibitor in your NS and blocks signals
Cofactor
- inorganic ion
- metals like iron, Mg and zinc ions
- nonprotein molecules or ions
- required for catalysis
Coenzyme
- organic molecules
- many come from diet
- vitamins or derivatives
- nonprotein molecules or ions
- required for catalysis
enzymes & metabolism
- chemical reactions occur in metabolic “pathways”
- some are catabolic, some are anabolic
- each step coordinated by a specific enzyme
anabolis; pathways
- biosynthetic
- endergonic
- requires energy (ATP)
- ex: protein synthesis
catabolism; pathways
- breaks down
- exergonic
- energy stored in energy intermediates (ATP or NADH)
- ex: cellular respiration
energy coupling
- energy released from catabolism used to drive anabolic synthesis of macromolecules
- coupling a exergonic reaction with an endergonic one and getting the endergonic reaction to run
- what cell does when it wants to build something
energy intermediates
- provide a mechanisms for coupling reactions
- Here we have Catabolic reaction we have our food being broken down into smaller bits. This is going to release energy. We have some sort of molecule acting as a carrier, taking that energy so you can use it for anabolic reactions so now we are
- Taking molecules and building something bigger requires an input of energy. So now we have exhausted our energy intermediate and it Has to go back to this catabolic reaction to pick up more energy and carry it to an anabolic reaction
How do we make ATP to power endergonic reactions (anabolic pathways)?
- Substrate level phosphorylation: enzyme directly transfers phosphate from one moelcule to another
- most enzymatic reactions - Chemiosmosis: energy stored in an electrochemical gradient is used to make ATP from ADP and Pi
- photosynthesis and cellular respiration
NADH
- another energy intermediate used in energy coupling
- stores energy in electrons
- donates them during synthesis reactions
- supplies electrons fro ATP synthesis
Redox reactions
- redox- electron removed from one moelcule and added to another
- oxidation- removal of electrons; often during breakdown, positive
- reduction: addition of electrons; often during building, negative
energy intermediates & redox
- during oxidation of organic molecules
- electrons are removed & used to create energy intermediates (NADH)
Gene regulation
- turn genes “on” or “off”
- changes amount of enzyme present
Cellular regulation
- cell signaling pathways like hormones change activity of enzyme
- ex: insulin, glucagon
Biochemical regulation
- enzyme inhibition
- direct change in enzyme activity
feedback inhibition
- major mechanism to control metabolism
- pathway is switched off by product formation
- when product levels low again, inhibition is relieved
allosteric inhibition
bonds to enzyme in area separate from active site
Feedback inhibition: Rate-limiting step
- the slowest enzyme in a pathway
- regulation of this step can have the largest effect
