IB Bio HL Unit 5 - ATP, etc.

Adenosine Triphosphate

Molecule that serves as the energy currency of the cell

• Energy can be transported, exchanged, etc.

Monomer of ATP

modified RNA nucleotide

Process that produces ATP

Mitocondria produce ATP during aerobic (using oxygen) cellular respiration

processes that use ATP

Used whenever a cell process needs energy

• Active transport

• Anabolic reactions

• Muscle contractions

• Movement of cells or cell parts

Reasons for ATP’s spring-like structure

• the 3 phosphates groups have negative charges

• the neg. phosphate charges repel eachother

• If a bond between the phosphates breaks they will spring apart

How is energy released from ATP

• Energy is released by breaking the 2nd and 3rd phosphate bonds (called ATP hydrolysis)

• Creates Adenosine DI-phosphate and one phosphate group (ATP → ADP + P)

what is ADP?

• Adenosine Diphosphate

• has some energy but less then ATP

How is ATP regenerated from ADP

• ADP Phosphorylation ( addition of a phosphate group to an ADP to transform it into an ATP)

• Energy needed to perform ADP phosphorylation is obtained by humans through food

ATP hydrolysis

• ATP → ADP

• Triphosphate → Diphosphate

• exergonic - energy is released from the breaking of the 2nd/3rd phosphate bond

• the energy is then used in the cell

ADP phosphorylation

• ADP → ATP

• Diphosphate → Triphosphate

• Endergonic (energy absorbed - from energy from food)

Structure of ATP

• RNA Nucleotide

• Ribose sugar (pentose → 5 carbons)

• Adenine nitrogenous base

What is Photosynthesis?

• Transformation of light energy (from the sun) into chemical energy (glucose)

Autotroph/photoautotroph

• Autotroph: Organisms that produce their own chemical energy

• Photoautotroph: Use light to produce their own chemcial energy

Autotroph’s role in the ecosystem

Supply chemical energy to the entire ecosystem

• energy created by autotrophs (or photoautotrophs) is passed down the food chain to fuel the ecosystem

Examples of Photoautotrophic organisms

• Plants

• Algae

• Cyanobacteria

Location of photosynthesis in plants

On the leaves

• in mesophyll cells (which have lots of chloroplasts)

Double membrane of chloroplast

• inner and outer membrane

• formed by endosymbiosis

Thylakoid structure

Inside of Chloroplasts

• Flattened membrane-bound sac

• surrounded by thylakoid membrane

• Thylakoid space → inner part of the membrane

• High efficiency and SA;V ratio because of flat shape

Thylakoid function

• Contains chlorophyll (embedded in the thylakoid membrane)

• location of the light reactions

Configuration of Thylakoids in the chloroplasts

• Arranged in ‘Grana’ (Stacks)

• maximises light absorption as light passes through the stacks

Location of the stroma

• Fluid filled space between the inner membrane of the chloroplasts and the thylakoid membrane

  

Function of the Stroma

• Contains enzymes and materials needed for the Calvin cycle

• location where the calvin cycle occurs

3 spaces within a chlorplast

• Intermembrane space: in between inner and outer membranes of the chloroplast

• Stroma: between inner membrane of chloroplast and thylakoid membrane

• Thylakoid Space: withen thylakoid membrane, lamaelle connect the grana to make them continuous

reduction reaction

• gaining electrons

• charge reduced (more neg.)

• leo says GER

Oxidation

• losing electrons

• LEO says ger

photosystem

• integral protein complex located in the phospholipid bilayer

• Located in thylakoid membrane of choloplast

• Location in cell membrane of cyanobacteria

How can photosystems absorb light?

• Photosystems contain chlorophyll and other accessory pigments to absorb light energy

Photoactivation of photosystems

• protons of light strike the pigment molecules in the photosystem making the electrons excited

• excited electrons are transfered through pigments in the photosystem

• electrons reach the reaction centre (Chlorophyll a)

• at the reaction center the electron is emitted from the photosystem

• Photosystem → oxidized (loses electrons)

• Emitted electron goes to first ETC

Photosystem I and II

• Photosystem II - 680 nm

• Photosystem I - 700 nm

  PSII undergoes photoactivation first in light reaction

Important particle of light reaction

• electrons

Electron transport chain

-electron eitted from PSII during photoactivation is transfered to the 1st electron transport chain (ETC)

Photolysis

• After electron is lost from PSII in photoactivation, photolysis replaces the electron

• water broken down into electrons, protons, and oxygen

• oxygen emmited

• protons start concentration gradient

Photolysis location

• in the thylakoid space near PSII

• What happens to the H+s produced during photolysis

• remaining protons stay in the thylakoid space beginning the concentration gradient

What happens to the O2 produced during photolysis

• o2 that is broken down from h20 is diffused out of the cell

what happens to e- produced during photolysis

• e- from H2o are transfered to the PSII

Structure of 1st electron transport chain

• a series of integral (amphipathic) protein complexes within the thylakoid membrane

• recieves the excited (filled with energy) electron from PSII following photoactivation

Functions of the 1st ETC

• Transfer electrons from PSII to PSI

• Harness the energy from excited electrons and use it to pump the H+ (protons) into the thylakoid space

• Creates a proton concentration gradient

Proton gradient (Light reaction)

• High concentration of H+ in the thylakoid space (1st ETC pumps the H+ into the thylakoid space to begin concentration gradient)

• Low concentration of H+ in stroma

THe ways proteins are concentrated in the thylakoid

• H+ produced in the thylakoid during photolysis

• H+ are pumped (active transport) into thylakoid space by 1st ETC

• thylakoids are small spaces, they fill up with H+ quickly

purpose of H+ concentration gradient (light reaction)

• to allow for passive transport of protons out of the thylakoid space

• Concentration gradient allows for passive transport (no use of energy)

CHemiosmosis

• diffusion of H+ down the concentration gradient through ATP synthase

ATP Synthase functions

• transmembrane integral protein (enzyme)

• preforms adp phosphorylation to create ATP

How does chemiosmosis drive ATP synthesis

• The movement of the protons creates energy allowing for the extra phosphate to be put onto the ADP

ADP → ATP

Process that occors in PSI

Photoactivation

What happens to electrons in PSI

• excited by light

• transfered between pigments

• reaction centre

• emitted from the photosystem and transfered to NADP+ reductase

How are electrons replaced in PSI after they are emitted?

• electrons from PSII via the 1st ETC

Function of NADP+/H

electron carrier

Difference between NADP+ and NADPH

• NADP+ → oxadized form of NADPH (doesnt have electrons and therefore plus charge)

• NADPH → reduced form (has electrons and lower charge)

How is NADP+ reduced?

• reduced when it picks up 2 electrons

• Electrons come from PSI and 1st ETC

• Reduction happens in NADP+ reductase

NADP+ + 2e- → NADPH

What happens to NADPH produced in light cycle?

• Goes to calvin cycle to drop off electrons

Electron flow during noncyclic photophosphorylation

Water → PSII → 1st ETC → PSI → NADPH

Flow of electrons during cyclic photophosphorylation

PSII → 1st ETC → PSI

What makes Cyclic Photophosphorylation Cyclic

• Electrons are lost from and return to the same photosystem

enzyme that performs carbon fixation

• RuBisCO

Carbon fixation (calvin cycle)

• process of attaching a CO2 to a RUBP (5 carbons)

• makes it 6 carbons

why is there high concentration of Rubisco in stroma

• not efficient enzyme at carbon fixation

• calvin cycle has high energy requirement

photorespiration

• when rubisco accidentally fixates an o2 instead of a co2

• molecule can no longer be processed through the calvin cycle

Glycerate 3 phosphate (GP)

• after carbon fixation

• 6 carbon compound breaks into 2 × 3 carbon compounds

• creates 6 GP out of 3 × 6-carbon compounds

reduction phase of calvin cycle

• GP (glycerate 3 phosphate) converted to triose phosphare (TP)

• each molecule being converted requires energy from 1 ATP, and electrons from one NADPH

What happens after the reduction phase

• 1 TP (aka glyceraldehyde 3 phosphate of G3P) will exit the cycle

• 5 TP will remain in cycle for regeneration

regeneration phase of calvin cycle

• 5 TP (or G3P) remain

• carbons in G3P/TP are rearranged into 3xRuBP (the first compound in the calvin cycle)

• requires energy from 3 atp

effect on photosynthesis if no light

• light reaction: ATP and NADPH cant be produced

  • O2 byproduct cant be produced

• Calvin cycle: cant happen w/o ATP NADPH

Effect on photosynthesis if no CO2

• GP and consequently TP cant be produced because there is no way for RUBISCO to carbon fixate the 6th carbon onto the RuBP

aerobic

requiring O2

anaerobic

not using O2

Outer membrane of mitocondria

transport proteinds for getting pyruvate into mitocondrian

inner membrane mitocondria

contains ETC and ATP synthase for OX phos

highly folded

cristae

folds of inner membrane

high SA;V ratio

Intermembrane space of mitocondria

inbetween inner and outer membranes

small space

proton gradient accumulates fast

mitocondrial matrix

space inside inner membrane

has ideal PH/enzymes for krebs cycle

Glycolysis

breaking down 2 glucose molecules into 2 pyruvate molecules

happens in cytoplasm

doesnt need O2

energy investment phase of glycolysis

• phosphorylation: 2 atp phosphorylate glucose (add phosphates to it) making it unstable

• lysis: phosphorylated glucose is split into 2 TP molecules

energy yielding phase of glycolysis

• oxidation: electrons from hydrogen are removed from the 2 TP molecules

• dehydrogenation: electrons and hydrogens are transferred into 2 NAD+ to make 2 NADH

NAD+/NADH

• electron carriers of glycolysis

Substrate level phosphorylation

• enzyme takes phosphate group from substrate and attatches it to ADP to make ATP

link reaction location

in the mitocondrial matrix

oxidative dexarboxylation

• Co2 and electrons removed from pyruvate

goes from 3 carbon to 2 carbon

electrons removed allow NAD+ → NADH

Coenzyme-A

• produces 1 Acetyl-COa per Pyruvate

location of the krebs cycle

• mitocondrial matrix

goal of krebs cycle

• finish breaking down glucose

  • electron carriers

formation of citrate

acetyl co A (2c) + oxaloacetate (4C) = citrate (6c)

how ATP is formed during the krebs cycle and glycolysis

• substrate level phosphorylation

location of mitocondrial etc

inner membrane of mitocondria

Proton motive force (photosynthesis and oxphos)

• diffusion of H+ down concentration gradient give ATP synthase the energy needed to phosphorylation ADP

pro/con of substrate level phosphorylation

• pro: no oxygen or special structure needed (happens in the cytoplasm)

• Con: not a lot of ATP produced

pro/con of oxidative phosphorylation

• pro: makes a lot of ATP

  • con: needs o2 and needs to happen in the mitocondrian

goal of fermentation

• regenerates NAD+ to allow glycolysis to continue without o2\

  • keeps glycolysis running by creating NAD+

inputs and outputs of alcohol fermentation

glucose → 2 ethanol +2co2 + 2ATP

ethanol is waste product

Lactic acid fermentation

• glucose → 2lactase +2atp

• lactase is waste product