Biology 1002B Lecture Notes - Lecture 6: Spontaneous Combustion, Endergonic Reaction, Protein Folding
28 Jun 2018
School
Department
Course
Professor
Cells%are%islands%of%low%entropy%
Living&cells& are&open&systems&exchanging&energy&and&matter&with&environment&
Energy&coming&in&as&photons&+&CO2&as&matter&
○
-
If&you&are&a&human&then&the2&arrows&are&the&same&arrow&(energy&and&matter=&
food)&this&is&called&a&heterotroph
-
Plants&use&matter&they&bring&in&to&do&cellular&work&and&energy&used&to&combine&
the&molecules&in&order&structured&(ex. Protein%synthesis,&balls&are&amino&acids&
and&then&there&all&connected&together&in&a&peptide-1&ATP/peptide&bond&,&
peptide&bonds&connecting&amino&acids&together)
-
Half&life&of&mammal&protein&is&46&hours-everything&breaks&down&(highly&ordered&
to&spread&out&in&living&systems&and&everything&has&a&half&life&
-
Entropy=&energy&spreading&,&moving&to&ordered&to&disordered&,&energy&spread&out&on&
different&molecules
Sugar&breaks&down&and&energy&is&spread&out&on&more&molecules&,&entropy&is&
increasing&-7&molecules&on&left&to&12&on&the&right&=&more&disordered&
-
This&is&why&you&need&to&keep&eating,&you&don’t&make&all& hexokinase&in&the&world&
to&start,&you&eat&to&make&sure&stuff&doesn’t&break&down&and&to&restore&it&
(enzymes,&protein)&
-
You&always&have&to&bring&in&energy&to&do&cellular& work&to&counteract&the&second&
law&which&is&breaking&stuff&down&,&by&doing&this&we&keep&the&entropy&in&the&cells&
lower&
-
Life: systems&that&bring&in&energy&to&maintain&a&state&of&low&entropy&
-
2nd&law&says&entropy&must&go&up&but&we&counteract&it&by&repairing&stuff&(but&
entropy&of&the&surroundings&must&go&up-releasing&heat&and&waste&into&
environment&so&the&entropy/disorder&of&the&environment&goes&up)&
-
Free%energy%(G)%
Amount&of&energy&something&has&that&WE&CAN&USE&TO&DO&WORK&,&G&explains&
metabolism&and&energy&transport&(why&some&molecules&move&across&a&
membrane&and&some&don’t-why&we&actually&care&about&G)&&,&flow&of&energy&of&
carbon&and&glucose&is&explained&by&free&energy&change&
-
H&is&enthalpy&:&free&energy&of&bond&energy&products-free&energy&of&bond&energy&
of&reactants&(-=exothermic,&energy&released&+=&endothermic,&energy&absorbed&)
-
S&id&entropy=&change&of&disorder&(steals&thunder)&(+&more&space,&-less&space)&
-
G=&+&endergonic,&-exergonic&(spontaneous&,&the&reaction&will&proceed&as&written&
and&A&will&be&converted&to&b,&free&energy&of&products&is&LESS&then&the&free&
energy&of&reactants)&
-
A&to&B&will&this&reaction&proceed&or¬??
Enzymes
These&are&all&spontaneous&reactions&don’t&need&to&put&energy&in:
Spontaneous&doesn’t&mean&reaction&goes&fast&
-
In&red:&if&you&add&an&enzyme&(biological&catalysts&are&proteins)&reaction&happens&
faster
-
2&types&of&catalysts: ribozyme&(rna&molecule)&and&enzyme&(protein)&
-
Enzyme&functions
G&+&(products&have&MORE&free&energy&then&the&reactants)
-
Enzyme&CANT&give&free&energy&away&BY&THEMSELVES&
-
Enzyme&can&help&is&energy&is&added
-
Exergonic%reaction%energy%profile
Free&energy&to&get&to&transition&state&its&just&molecular&motion-molecules&bump&
into&each&other&-random&molecular&motion&(THIS&IS&RARE&THO&and&is&why&it&
takes&a&long&time&for&most&reactions&to&go)&
-
For&reaction&to&proceed&it&needs&to&get&free&energy&to&allow&bonds&of&reactants&
to&break&(that’s&the&transition%state)&this&requires&energy&that&the&reactant&
molecules&don’t&have&themselves&(this&is&activation%energy to&get&reactants&to&
transition&state&-and&this&energy&is¬&a&fixed&amount)
-
Don’t&care&how&tall&hump&is&or&anything&all&that&matters&is&G&none&of&this&stuff&
changes&G&(free&energy&of&p-free&energy&of&r)&
-
EA&represents&a&barrier&,&a&kinetic&barrier&-to&get&to&transition&may&take&A&LOT&of&
energy&-this&restricts&the&rate&of&the&energy&
-
Propane=&lots&of&energy&in&propane&and&in&presence&of&o2&it&will&combust&
spontaneously&
Its&thermodynamically&unstable&because&it&has&a&G=-BUT&its&kinetically&
stable&(if&you&open&propane&tanks¬hing&will&happen)&because&FEW&
propane&molecules&will&get&to&transition&state(the&few&that&do&are&because&
of&random&molecular&motion&)&,&if&you&add&a&spark&then&the&energy&comes&
from&spark&and&transition&state&goes&faster&
○
-
Enzymes&lower&activation&energy&(energy&requirement&for&reaction&to&
process)&does&this&all&by&itself&:)&BUT&ENZYME&DOESN’T&CHANGE&THE&G&OF&
THE&REACTION -path&and&kinetics&are&different&but&doesn’t&change&G&
-
Rate&of&reaction&is&proportional&to&the&number&of&activated&
molecules/molecules&that&can&get&to&the&transition&state
If&lots&of&molecules&can&get&to&transition&state&then&the&rate&of&the&
reaction&increases&
§
If&few&molecules&can&get&to&TS&then&rate&is&slower
§
Both&spontaneous&BUT&kinetics&are&different&
§
-
Why%does%life%need%enzymes?
Enzymes are&proteins&that&control&the&speed&of&chemical&reactions&in&your&body&
at&low&temperatures(0-100)&in&body&.&Without enzymes,&these&reactions&would&
take&place&too&slowly&to&keep&you&alive.&
-
In&chemistry&we&can&make&reactions&go&faster&by&just&increasing&the&temperature&
but&in&biology&you&cant&do&that&because&it&could&denature&proteins&so&we&have&
enzymes&instead&:)&
-
HOW&does&enzyme&actually&lower&activation&energy(&pic&4.23&)&-what&enzyme&does&to&
a&substrate
Protein&(enzyme)&folding
After&translation&peptide&folds&into&protein&and&most&functional&(some&undergo&
post-translational&modifications)&
-
What&is&required&for&protein/enzyme&fold?&
Anfinsen's&dogma&experiment,&in&test&tub&enzyme=&protein&folding&is&
spontaneously&-no&energy&needed!&Protein&folding&(3D&sturcture)&
determined&entirely&from&primary&protein&sequence!
-
-
-
Urea&denatures&enzyme&(it&competes&with&amino&acid&for&H&bonding)&it&causes&
protein&to&unfold&
-
If&you&get&rid&of&urea&then&the&protein&comes&back&
-
Enzyme&are&big&and&substrates&are&small
-
Enzymes&are&flexible& it&has&tertiary&structure&and&eats&and&folds&around&the&
substrate&
-
Where&catalysis&happens&is&active&site&
-
Enzymes%and%growth%rate-E.coli%
Why&e.coli&grows&faster&at&37&from&catalytic& cycle&
-
What&cells,&when&you&shift&them&to&low&temps&what&could&they&do&to&help&,&so&
the&reaction&doesn’t&slow&down&
-
Growth&rate&of&E.coli
Explain&this&curve
-
Growth&rate&on&y&axis&-growth&rate=&enzyme&activity&
-
L6-Energy*&*Enzymes*
Wednesday,& January&24,&2018
1:47&AM
Cells%are%islands%of%low%entropy%
Living&cells& are&open&systems&exchanging&energy&and&matter&with&environment&
Energy&coming&in&as&photons&+&CO2&as&matter&
○
-
If&you&are&a&human&then&the2&arrows&are&the&same&arrow&(energy&and&matter=&
food)&this&is&called&a&heterotroph
-
Plants&use&matter&they&bring&in&to&do&cellular&work&and&energy&used&to&combine&
the&molecules&in&order&structured&(ex. Protein%synthesis,&balls&are&amino&acids&
and&then&there&all&connected&together&in&a&peptide-1&ATP/peptide&bond&,&
peptide&bonds&connecting&amino&acids&together)
-
Half&life&of&mammal&protein&is&46&hours-everything&breaks&down&(highly&ordered&
to&spread&out&in&living&systems&and&everything&has&a&half&life&
-
Entropy=&energy&spreading&,&moving&to&ordered&to&disordered&,&energy&spread&out&on&
different&molecules
Sugar&breaks&down&and&energy&is&spread&out&on&more&molecules&,&entropy&is&
increasing&-7&molecules&on&left&to&12&on&the&right&=&more&disordered&
-
This&is&why&you&need&to&keep&eating,&you&don’t&make&all& hexokinase&in&the&world&
to&start,&you&eat&to&make&sure&stuff&doesn’t&break&down&and&to&restore&it&
(enzymes,&protein)&
-
You&always&have&to&bring&in&energy&to&do&cellular& work&to&counteract&the&second&
law&which&is&breaking&stuff&down&,&by&doing&this&we&keep&the&entropy&in&the&cells&
lower&
-
Life: systems&that&bring&in&energy&to&maintain&a&state&of&low&entropy&
-
2nd&law&says&entropy&must&go&up&but&we&counteract&it&by&repairing&stuff&(but&
entropy&of&the&surroundings&must&go&up-releasing&heat&and&waste&into&
environment&so&the&entropy/disorder&of&the&environment&goes&up)&
-
Free%energy%(G)%
Amount&of&energy&something&has&that&WE&CAN&USE&TO&DO&WORK&,&G&explains&
metabolism&and&energy&transport&(why&some&molecules&move&across&a&
membrane&and&some&don’t-why&we&actually&care&about&G)&&,&flow&of&energy&of&
carbon&and&glucose&is&explained&by&free&energy&change&
-
H&is&enthalpy&:&free&energy&of&bond&energy&products-free&energy&of&bond&energy&
of&reactants&(-=exothermic,&energy&released&+=&endothermic,&energy&absorbed&)
-
S&id&entropy=&change&of&disorder&(steals&thunder)&(+&more&space,&-less&space)&
-
G=&+&endergonic,&-exergonic&(spontaneous&,&the&reaction&will&proceed&as&written&
and&A&will&be&converted&to&b,&free&energy&of&products&is&LESS&then&the&free&
energy&of&reactants)&
-
A&to&B&will&this&reaction&proceed&or¬??
Enzymes
These&are&all&spontaneous&reactions&don’t&need&to&put&energy&in:
Spontaneous&doesn’t&mean&reaction&goes&fast&
-
In&red:&if&you&add&an&enzyme&(biological&catalysts&are&proteins)&reaction&happens&
faster
-
2&types&of&catalysts: ribozyme&(rna&molecule)&and&enzyme&(protein)&
-
Enzyme&functions
G&+&(products&have&MORE&free&energy&then&the&reactants)
-
Enzyme&CANT&give&free&energy&away&BY&THEMSELVES&
-
Enzyme&can&help&is&energy&is&added
-
Exergonic%reaction%energy%profile
Free&energy&to&get&to&transition&state&its&just&molecular&motion-molecules&bump&
into&each&other&-random&molecular&motion&(THIS&IS&RARE&THO&and&is&why&it&
takes&a&long&time&for&most&reactions&to&go)&
-
For&reaction&to&proceed&it&needs&to&get&free&energy&to&allow&bonds&of&reactants&
to&break&(that’s&the&transition%state)&this&requires&energy&that&the&reactant&
molecules&don’t&have&themselves&(this&is&activation%energy to&get&reactants&to&
transition&state&-and&this&energy&is¬&a&fixed&amount)
-
Don’t&care&how&tall&hump&is&or&anything&all&that&matters&is&G&none&of&this&stuff&
changes&G&(free&energy&of&p-free&energy&of&r)&
-
EA&represents&a&barrier&,&a&kinetic&barrier&-to&get&to&transition&may&take&A&LOT&of&
energy&-this&restricts&the&rate&of&the&energy&
-
Propane=&lots&of&energy&in&propane&and&in&presence&of&o2&it&will&combust&
spontaneously&
Its&thermodynamically&unstable&because&it&has&a&G=-BUT&its&kinetically&
stable&(if&you&open&propane&tanks¬hing&will&happen)&because&FEW&
propane&molecules&will&get&to&transition&state(the&few&that&do&are&because&
of&random&molecular&motion&)&,&if&you&add&a&spark&then&the&energy&comes&
from&spark&and&transition&state&goes&faster&
○
-
Enzymes&lower&activation&energy&(energy&requirement&for&reaction&to&
process)&does&this&all&by&itself&:)&BUT&ENZYME&DOESN’T&CHANGE&THE&G&OF&
THE&REACTION -path&and&kinetics&are&different&but&doesn’t&change&G&
-
Rate&of&reaction&is&proportional&to&the&number&of&activated&
molecules/molecules&that&can&get&to&the&transition&state
If&lots&of&molecules&can&get&to&transition&state&then&the&rate&of&the&
reaction&increases&
§
If&few&molecules&can&get&to&TS&then&rate&is&slower
§
Both&spontaneous&BUT&kinetics&are&different&
§
-
Why%does%life%need%enzymes?
Enzymes are&proteins&that&control&the&speed&of&chemical&reactions&in&your&body&
at&low&temperatures(0-100)&in&body&.&Without enzymes,&these&reactions&would&
take&place&too&slowly&to&keep&you&alive.&
-
In&chemistry&we&can&make&reactions&go&faster&by&just&increasing&the&temperature&
but&in&biology&you&cant&do&that&because&it&could&denature&proteins&so&we&have&
enzymes&instead&:)&
-
HOW&does&enzyme&actually&lower&activation&energy(&pic&4.23&)&-what&enzyme&does&to&
a&substrate
Protein&(enzyme)&folding
After&translation&peptide&folds&into&protein&and&most&functional&(some&undergo&
post-translational&modifications)&
-
What&is&required&for&protein/enzyme&fold?&
Anfinsen's&dogma&experiment,&in&test&tub&enzyme=&protein&folding&is&
spontaneously&-no&energy&needed!&Protein&folding&(3D&sturcture)&
determined&entirely&from&primary&protein&sequence!
-
-
-
Urea&denatures&enzyme&(it&competes&with&amino&acid&for&H&bonding)&it&causes&
protein&to&unfold&
-
If&you&get&rid&of&urea&then&the&protein&comes&back&
-
Enzyme&are&big&and&substrates&are&small
-
Enzymes&are&flexible& it&has&tertiary&structure&and&eats&and&folds&around&the&
substrate&
-
Where&catalysis&happens&is&active&site&
-
Enzymes%and%growth%rate-E.coli%
Why&e.coli&grows&faster&at&37&from&catalytic& cycle&
-
What&cells,&when&you&shift&them&to&low&temps&what&could&they&do&to&help&,&so&
the&reaction&doesn’t&slow&down&
-
Growth&rate&of&E.coli
Explain&this&curve
-
Growth&rate&on&y&axis&-growth&rate=&enzyme&activity&
-
L6-Energy*&*Enzymes*
Wednesday,& January&24,&2018 1:47&AM
Document Summary
Living cells are open systems exchanging energy and matter with environment. Energy coming in as photons + co2 as matter. If you are a human then the2 arrows are the same arrow (energy and matter= food) this is called a heterotroph. Plants use matter they bring in to do cellular work and energy used to combine the molecules in order structured (ex. Protein synthesis, balls are amino acids and then there all connected together in a peptide- 1 atp/peptide bond , peptide bonds connecting amino acids together) Half life of mammal protein is 46 hours- everything breaks down (highly ordered to spread out in living systems and everything has a half life. Entropy= energy spreading , moving to ordered to disordered , energy spread out on different molecules. Sugar breaks down and energy is spread out on more molecules , entropy is increasing - 7 molecules on left to 12 on the right = more disordered.
