bio will ace

metabolism

all of the chemical reactions in an organism

metabolic pathways

series of chemical reactions that either build complex molecules or breakdown complex molecules

a series of steps to produce a product- catalyzed by a specific enzyme

ex. substrate>enzyme1.> intermediate reaction>enzyme2.> intermediate reaction>product

two types of metabolic pathways

catabolic (cat-astrophe, breakdown, release)

anabolic (A na, A te, build up, consume)

catabolic pathways

pathways that release energy by breaking down complex molecules into simpler compound

ex. cellular respiration-breaking down glucose when O2 is present to make  ATP

anabolic pathways

pathways that consume energy to build complicated molecules from simpler compounds

ex. synthesizing proteins from put together amino acids, putting monosaccharides together to build a disaccharide 

energy

the ability to do work

necessary to survive and function

must be transferred from one form to another to live

a loss of energy results in

death

kinetic energy

associated with motion

thermal energy

associate with the movement of atoms or molecules

heat

type of kinetic (at the molecule scale)

heat

thermal energy that transfers from one object to another)

potential energy

stored energy

because of location or structure

chemical energy

type of potential energy (structure)

released in a chemical energy 

thermodynamics

study of energy transformation in matter

its laws apply to all the universe

3 laws

1) energy cannot be created or destroyed, it can be transferred or transformed (principle of conservation of energy)

2) energy transformation increases entropy (disorder; [S]) of the universe, during transfers/transformations, some energy is unusable and is lost as heat

3) ?

entropy examples

heat

multiple pieces

solid(least) to liquid to gas (most disorder)

diffused particles/spaced apart

isolated system

unable to exchange energy or matter with its surroundings

open system

ex organisms

energy os transferred between the system and its surroundings

organisms pay for their complexity and organization by

creating disorder themselves

free energy

determines the likelihood of reactions in organisms or in the reactions are energetically favorable

delta G= delta H-TdeltaS

energy that can do wor is usable

delta G

change in free energy

high G

more free energy

less stable

greater work capacity

in spontaneous change

free energy of the system decreases (delta G<0)

system become more stable

released energy is harnessed to do work

low G

less free energy

more stable

less work capacity

delta H

change in total energy

T

absolute temp in kelvin

delta S

change in entropy

free energy change of reactions determine

whether reactions occur spontaneously (no outside input of energy is required)

based on this, reactions are classified as exergonic (expel) or endergonic (engorge??)

exergonic reactions

reactions that release energy (ex. cellular respiration)

delta G is less than 0

spontaneous

endergonic reactions

reactions that absord energy (ex. photosynthesis

delta G is greater than 0

not spontaneous (decrease entropy; require energy)

cells perform three kinds of work

mechanical

transport

chemical

mechanical work

movement

ex.beating cilia, movement of chromosomes, contraction of muscle cells

transport work

pumping substances across membranes against spontaeous movement

chemical work

synthesis of molecules

ex building polymers from monomers

ATP

adenosine triphosphate- molecule that organisms use for energy

couples exergonic to endergonic reactions to power cellular work

-the exergonic process drives the enderognic process

also used to make RNA

ribose, adenine (nitrogenous base) and three phosphate groups

ATP>ADP (hydrolysis)

organisms obtain energy by breaking the bond between the 2nd and 3rd phosphate in a hydrolysis reaction (addition of water)

energy come from lowering (-delta G) of free energy, not phosphate bonds (more pieces, greater entropy, -delta G)

phosphorylation

the released phosphate moves to another molecule to give energy

regeneration of ATP

ATP cycle

ADP +Pi uses energy from exergonic process to become ATP and water and energy is released in hydrolysic for cellular work to become ADP +Pi

spontaneous reactions are not necessarily fast

can be sped up with enzymes

enzymes

type of protein that catalyze or speed up reactions by lowering activation energy

ends in -ase

not consumed by reaction

enzyme acts on

active site of a reactant called a substrate

ways enzymes lower activation energy

substrates may be oriented to facilitate reaction

substrate stretched to make bonds easier to break

active site may provide a microenvironment that favors the reaction

amino acids in active site may participate in reactions

enzyme function

induced fit

enzymes will change the shape of their active site to allow the substrate to bind better

enzyme catabolism

enzyme break down complex molecule

enzyme anabolism

enzyme build complex molecules

shape of enzyme affected by

temperature

pH

chemicals

change in shape is a change in function

optimal conditions

best conditions (tmep and ph) for enzymes to function

cofactors

non-protein molecules that assist enzyme function

can consist of metals

can be tightly or loosely bound

holoenzyme: when enzyme has cofactor attached

coenzymes: organic cofactors (ex vitamins)

enzyme inhibitors

reduce enzyme activity

can be permanent (covalent bonds) or reversible (weak interactions)

competitive inhibitors

reduce enzyme activity by binding to active site before substrate

can be reversed with increased substrate concentration

noncompetitive inhibitors

bind to an allosteric site (not active site) and changes active sites shape to prevent binding

allosteric enzymes have 2 binding sites

active and allosteric (regulatory)

allosteric regulation

molecules bind noncovalently to allosteric site to change shape of active site

can help (stimulation of enzyme activity) or hinder (inhibition)

allosteric activator

substrate bonds to allosteric site and stabilizes shape of enzyme so that the active site remains open

allosteric inhibitor

substrate binds to allosteric site and stabilizes the enzyme shape so that the active sites are closed/inactive

cooperativity

substrate binds with one active site (enzyme that has multiple) which stabilizes active form

considered allosteric regulation since binding at one site changes shape of others

Sometimes, the end product of a metabolic pathway can act as an inhibitor to an early enzyme in the same pathway

prevents excess products

starch is the major fuel for animals

starch breaks down into glucose

cellular respiration is exergonic

oxidation of glucose transfers e- to a lower energy state, releasing energy to be used in ATP synthesis

downhill exergonic path:

glucose>nadh>etc>oxygen

Dehydrogenases

Oxidizing agent for glucose

take 2 e- and 2 protons from glucose

transfer 2e- and 1 proton to the coenzyme NAD+. Reduces to NADH (stores the energy, carries e- to the electron transport chain) last proton is release into surrounding solution

stages of cellular respiration

final e- acceptor aerobic

oxygen

makes h20 releases energy

nadh v nadph

nadh-cellular respiration

nadph-photosynthesis

photosynthesis

light energy to chemical

photosynthesis first developed in prokaryotic organisms

cyanobacteria: early prokaryotes capable of photosynthesis

Oxygenated the atmosphere of early Earth

foundation of eukaryotic photsynthesis

primary location of photosynthesis in most plants

leaves (mesophyll, the primary location of photosynthesis in most plants)

chloroplast

found in mesophyll’

surrounded by a double membrane

have stroma and thylakoid

stomata

pores in leaves that allow CO2 in and O2 out

stroma

aqueous internal fluid

Thylakoids

form stacks known as grana

Chlorophyll

green pigment in thylakoid membranes

simplified formula

6 CO2 + 6 H2O + light energy C6H12O6 + 6 O2

Redox reaction:

reaction involving complete or partial transfer of one or more electrons from one reactant to another

redox in photo synthesis

reduction co2 to glucose

water to oxygen

photo light reactions

in thylakoid

synthesis calvin cycle

in stroma

light

electromagnetic energy

Made up of particles of energy called photons

Travel in waves

Wavelength

the distance from the crest of one wave to the crest of the next

The entire range is known as the electromagnetic spectrum

380 nm to 750 nm is visible light

short wave high energy long wave low energy

cholorphyll a

Primary pigment

Involved in the light reactions

Blue/green pigment

Chlorophyll b:

• Accessory pigment

• Yellow/green pigment

cartotenoids

Broaden the spectrum of colors that drive photosynthesis

Yellow/orange pigment

Photoprotection- carotenoids absorb and dissipate excessive light energy that could damage chlorophyll or interact with oxygen

light reactions

light + H20 > O2 + ATP&NADPH

Occur in the thylakoid membrane in the photosystems

Converts solar energy to chemical energy(NADPH and ATP

The cell accomplishes this conversion by using light energy (photons) to excite electrons(

Chlorophyll absorbs a photon of light

e- is boosted from a ground state to an excited state

e- is unstable

Falls back to ground state

Releases energy as heat

Emits photons as fluorescence

Photosystems

reaction center and light capturing complexes
Photosystem 2: reaction center P680=Absorbs light at 680 nm

Photosystem 1: reaction center P700=Absorbs light at 700 nm

Reaction center:

a complex of proteins associated with chlorophyll a and an electron acceptor

Light capturing complexes

pigments associated with proteins

Think: antenna for the reaction centers

ps ii

PLight energy (photon) causes an e- to go from a ground state back to an excited state. This repeats until it reaches the P680 pair of chlorophyll a molecules (trapped energy travels till eventually reaches chlorophyll a)

The e- is transferred to a primary e- acceptor, forming P680+H2O is split into:

2 e- (Reduce P680+; go to ps I)

2 H+ (Released into thylakoid space)

1 oxygen atom (which immediately bonds to another oxygen atom)

Linear electron flow: each excited electron will pass from PS II to PS I via the electron transport chain (exits pq> cytochrome>pc)

The “fall” of electrons from PS II to PS I provides energy to form ATP

The H+ gradient is a form of potential energy

atp synthase

couples the diffusion of H+ to the formation of ATP

psi

Light energy excites electrons in the P700 chlorophyll molecules Become P700+

Electrons go down a second transport chain

NADP+ reductase catalyzes the transfer of e- from Fd to NADP+

reduces to NADPH

inputs and outputs of light reactions

in: H2O, ADP, NADP+

out: O2, ATP, NADPH

summary light reactions

converts solar to chemical (NADPH & ATP)

Water is split (hydrogen is source of electrons and protons H+, O2 released as by product)

light absorbed by chlorophyll drives transfer of electron and ions from water to NADP+ which is reduced to NADPH

ATP generated from ADP phosphorylated

calvin cycle

uses atp and nadph to reduce co2 to sugar (G3P)

for 1 G3P the cycle takes place 3 times

3 phases of calvin cycle

carbon fixation

reduction

regeneration of RuBP

carbon fixation

CO2 is incorporated one at a time

each attached to RuBP

this is catalyzed by rubisco (most abundant protein in chloroplasts)

forms 3-phocphoglycerate

reduction

each of 3-phosphoglycerate is phosphorylated by ATP(6 total)

becomes single bisphosphoglycerate which reduces to G3P

6 G3P are formed but only one is net cause other 5 r used to regen RuBP

regeneration of RuBP

5 G3P are used to regenerate 3 RuBP

uses 3 ATP

Cycle takes in CO2 again

inputs and outputs of calvin cycle

in: 3CO2, 9 ATP, 6 NADPH

out: 1 G3P, 9 ADP, 6 NADP+

calvin cycle summary

uses NADPH, ATP, and CO2

produces 2 C sugar G3P

three phases: carbon fixation 

reduction

regeneration of RuBP