BIOL10002: Topic 2 Cells and Energy

a chemical reaction occurs when…

atoms have sufficient energy to combine or change their bonding partners

energy

the capacity to do work

occurs when a force operates on an object over a distance

bioenergetics

the study of how organisms manage their energy resources

forms of energy (5)

chemical-bond: stored in bonds

electrical: separation of charges

heat: transfer dur to temperature difference

light: electromagnetic radiation stored as photons

mechanical: energy of motion

types of energy in biology can be categorised as…

potential or kinetic energy

potential energy

the energy of state or position

can be stored in covalent bonds, as concentration gradient, as electrical charge imbalance

kinetic energy

energy of movement that does work or makes things change

heat causes molecular motions and can break chemical bonds

thermodynamics

the study of energy transformations

thermodynamics - closed system

In a closed system is isolated from its surroundings

thermodynamics - open system

energy and matter can be transferred between the system and its surroundings

most of the time biological systems are open systems as organisms exposed to external environments

first law of thermodynamics

energy can be transferred and transformed but cannot be created or destroyed

principle of conservation of energy

second law of thermodynamics

every energy transfer or transformation increases the entropy of the universe

during every energy transfer, some energy is unusable (often lost as heat)

role of ATP

Captures and transfers free energy

Can be hydrolysed to ADP and P_i -> releases a lot of energy for endogonic reactions

Can also phosphorylate other molecules -> molecules gain some energy

structure of ATP

three phosphate groups bonded to a carbon if a ribose molecules → nucleotide

end bond in triphosphate group can by hydrolysed to produce an inorganic phosohate → ADP, inorganic phosphate, free energy

exergonic reaction w example

release of energy

hydrolysis of ATP produces ADP, inorganic phosphate and energy

endergonic reactions w example

input of energy

condensation of ADP and inorganic phosphate produces ATP

ATP for chemical work example

Glutamic acid to glutamine = endergonic → not spontaneous

conversion reaction coupled with ATP hydrolysis → phosphorylated intermediate

• ATP phosphorylates glutamic acid → less stable with more free energy

• ammonia displaces phosphate group → glutamine formed

overall delta G = negative

ATP for kinetic work example - transport work

ATP hydrolysis causes shape and binding affinity change in some proteins embedded in cellular membrane

allows transport of solutes

ATP for kinetic work example - mechanical work

ATP binds noncovalently to motor proteins → hydrolysed

causes shape change that ‘walks’ the motor protein forward along cytoskeletal track

coupling reactions with ATP

ATP hydrolysis = exergonic and provides the input of energy for endergonic reactions to proceed

change in free energy always negative → more energy has to be released than consume

biological order and disorder

cells create ordered structures from less ordered materials

organisms also replace ordered forms of matter with energy with less ordered forms

energy flows into an ecosystem in the form of life and exits in the form of heat

How does the evolution of more complex organisms not violate the second law of thermodynamics

entropy may decrease in an organism but the total entropy of the universe increases → the more we try to order cells or the inside of living organisms → the more energy is released into the universe, increasing chaos

what is free energy

the amount of energy available to do work

all chemical reactions affect free energy

measures the instability of a system → tendency to change to a more stable state

equilibrium and energy

equilibrium =state of max stability

spontaneous reactions can perform only when it is moving towards equilibrium

ATP for chemical work → glutamic acid to glutamine (no atp)

endergonic reaction → not spontaneous

glutamic acid + ammoni → glutamine delta G = +ve kJ/mol

ATP for chemical work → glutamic acid to glutamine coupled with ATP hydrolysis steps

2 steps coupled by phosphorylation intermediate → ATp phosphorylates glutamic acid → less stable with more free energy → ammonia displaces phosphate group → glutamine, ADP, Pi

ATP for chemical work → glutamic acid to glutamine coupled with ATP hydrolysis free energy change

exergonic reaction → spontaneous

delta G (Glu) + delta G (ATP) = delta G (net) => -ve kJ/mol

ATP for kinetic work key example (2)

ATP hydrolysis can cause changes in the shapes and binding affinity of proteins

• transport work

• mechanical work

ATP for kinetic work - transport work

can change the shape of a protein embedded in the cellular membrane by phosphorylating it → shape change allows transport oof solutes

ATP for kinetic work - mechanical work

ATP binds non-covalently to motor proteins → hydrolysed

causes shape change that walks the motor protein forward

coupling of reactions

endergonic reactions often coupled with exergonic reactions so that energy produced from hydrolysis of ATP can push the endergonic reaction

delta G is always negative as overall reaction has to be exergonic

catabolic reactions w example

may break down an ordered structure into smaller more randomly distributed products

Those that release energy = exergonic

hydrolysis of sucrose into glucose and fructose

anabolic reactions w example

may make a single highly ordered product out of many smaller less ordered reactants

those that absorb free energy = endergonic

synthesis of sucrose from glucose and fructose

equilibrium and metabolism (closed v open systems)

reactions in a closed system eventually reach equilibrium and then do no work

cells are not in equilibrium → open systems experience constant flow of materials

metabolism is never at equilibrium

define cellular metabolism

a series of numerous chemical reactions that are occurring to enable cells to exist

occurs within the cell

enzymes are the only biological catalysts

False

enzymes as biological catalysts

act as a framework where reactions can take place by reducing activation energy → more unstable forms with higher free energy

increases proportion of reactants in transition state

process of enzyme catalysts

1. substrate approaches enzyme’s active site → active site R groups are specific for the substrate and allow it to enter

2. substrate binds to the enzyme’s active site forming enzyme-substrate complex → R groups of amino acids in active site react with bonds int he substrate → environment of isntabiity → easier to break apart

3. products are released and enzyme returns to its original shape, ready to catalyse a new reaction

enzymes alter the change in free energy of a reaction

false.

enzyme catalyse reactions have a lower activation energy than uncatalysed reactions but do not influence the overall change in delta G

enzyme substrate interaction types - overview (3)

orientation

physical strain

chemical charge

enzyme substrate interaction types - orientation

active site allows substrates to be orientated in a way that the bonds between molecules can occur → single molecule released

enzyme substrate interaction types - physical strain

position of R groups in the active site allow pressure to be placed ont he substrate → less stable → easier to change

enzyme substrate interaction types - chemical charge

enzyme adds charges, change or manipulate polarity of bonds → change molecule state

how is reaction rate measured (2)

decrease of concentration of the substrate

increase of concentration of product

rate of change = amount of products produced or reactants consumed in a defined time

define kinetic measurements

measurement of change in a defined time interval

rate of catalysed reactions depend on…

substrate concentration until all enzymes are saturated and max rate is achieved

define reaction rate in terms of enzyme kinetics

measure and effects of varying conditions of the reaction

what does the michaelis-menten model explain

how the rate of reaction varies with substrate concentration

explain the variables int he equation

v = michaelis menten constant → always the same for each particular enzyme but varies from one enzyme to another

• measure of affinity of the enzyme for its substrate → low constant = high affinity

v max = max velocity achieved by a system at max substrate concentration

KM = substrate concentration where reaction velocity is 50% of Vmax

s = substrate

how does temperature influence enzyme activity

• Optimum temp of most enzymes in humans is usually 37

  • Little activity at low temps

  • Lose activity at temps above 50 -> denaturation -> loss of active site conformation and catalytic activity

• Thermophilic bacteria have higher optimal temp than humans

how does pH influence enzyme activity

Optimum pH of most enzymes in humans is usually 7.4

• Depends on where enzyme is located

  • Enzymes in stomach will usually have lower pH

  • Enzymes in liver will usually have higher pH

Enzymes contain R groups of amino acids with proper charges at optimum pH -> lose activity in low or high pH (tertiary structure disrupted)

cofactors overview (3)

non-rotein enzyme helpers that may be inorganic or organic

• activators

• co-enzymes

• prosthetic groups

activators as cofactors

increase rate of enzymatic catalysed reactions by promoting formation of active site or other reactants

eg. magnesium ion, calcium ion, potassium ion

coenzymes as cofactors

complex non-protein organic molecules that transfer chemicals from active site of one enzyme to the active site of another

eg. NAD+ and CoA

prosthetic groups as cofactors

non-protein organic molecules that are attached to the enzme and act like built-in coenzymes

eg. vitamin b6

types of enzyme inhibitors (overview)

competitive

non-competitive

permanent

competitive inhibitors

similar shape to the substrate → bind to active site of an enzyme to compete with the substrate

can be reversed by increasing concentration of the susbtrate

non-competitive inhibitors

bind to allosteric sites of enzymes → causes enzyme to change shape, making active site less effective

cannot be reversed by increasing concentration of substrate

permanent inhibitors

forms covalent bonds with amino acid R groups that prevent catalytic activity

eg. toxins and poisons → nerve gas

allosteric regulation

non-substrate molecules bind an enzyme at a site away from the active site → changes shape

active in inactive forms can be interconverted depending on substrate molecules binding away from the active site

inhibitors and activators bind other polypeptides at regulatory sites to regulate metabolic processes

allosteric enzyme structure

typically have quaternary structure with active site on the catalytic subunit

Some allosteric enzymes have mutliple subunits with acitve sites

• substrate binding at one site has an allosteric effect and increases rate of reaction

• non-allosteric enzymes with one active site have different reaction rates at low substrate concentration

describe allosteric activators and inhibitors

active form oscillates with inactive form

activator binds away from the active site and stabilises the active form

inhibitor binds way from the active site and stabilises the inactive form

• even if substrate is around → will not bind to active site

describe cooperativity, the type of allosteric activation

relies on enzyme being in an inactive form

once substrate binds to the active site → active form is stabilised

will oscillate between active and inactive form until stabilised when substrate binds to one active site

how do allosteric enzymes regulate metabolism w example

Allosteric enzymes catalyse certain points in the respiratory pathway to regulate pace of glycolysis and the citric acid cycle

Phosphofructokinase catalyses the commitment step in glycolysis and is inhibited by ATP and citrate → feedback inhibition + negative feedback

principles of metabolic pathways (5)

1. complex transformation occur in a series of separate reactions

2. each reaction is catalysed by a specific enzyme

3. many metabolic pathways are similar in all organisms

4. in eukaryotes, metabolic pathways are compartmentalised in specific organelles

5. key enzymes can be inhibited or activated to alter the rate of the pathway

catabolic processes that harvest energy from glucose (overview)

1. glycolysis

2. cellular respiration

3. fermentation

where does glycolysis take place and what are the inputs and outputs

in the cytosol

6-carbon glucose -> 2 3-carbon sugars -> oxidised -> remaining atoms rearranged to form 2 pyruvate

produces net 2 ATP and 2 NADH

stages of glycolysis

first 5 steps = energy investment stage

• 2 ATP is needed and steps 1-3 are endergonic

last 5 steps = energy payoff stage

• 4 ATP and 2 NADH produced

regulation of glycolysis

phosphofructokinase catalyses commitment step of glycolysis → inhibited by ATP and citrate produced in citric acid cycle → activated by ADP

define anaerobic respiration

the production of ATP using a molecule other than oxygen as the final acceptor in the ETC

define fermentation

the production of energy in the absence of oxygen and without the ETC

different end products depend on what the starting compound was

consists of glycolysis and reactions that regenerate NAD+ by transferring electrons from NADh to pyruvate or derivatives of pyruvate

explain the key difference between anaerobic respiration and fermentation

Anaerobic respiration uses a molecule other than oxygen as the final electron acceptor whilst fermentation does not involve the ETC and uses pyruvate or its derivates as the final electron acceptor

lactic acid fermentation

pyruvate is electron acceptor

lactate = product

occurs in microorganisms and some complex organisms

lactate dehydrogenase catalyses fermentation

• in the presence of O2 → catalyses oxidation of lactate to pyruvate

during intensive exercise → oxygen cannot be delivered to cells fast enough for aerobic respiration → muscle cells break down glycogen for lactic acid fermentation

• when lactic acid builds up → increase in hydrogen ions lowers pH → can cause muscle pain

alcohol fermentation

occurs in yeast and some plant cells

requires 2 enzymes to metabolise pyruvate to ethanol

reactions are reversible and used to produce alcoholic beverages

downfalls of fermentation

cellular respiration yields more energy than fermentation

glucose is only partially oxidised in fermentation → more energy remains in the product than in CO2

alternative names to citric acid cycle

krebs cycle

TCA cycle

outputs of citric acid cycle per glucose molecule

6 NADH, 2 GTP, 2FADH2, 2 oxaloacetate, 4 CO2, 2 H2O

GTP and ATP

GTP can easily transfer the phosphate group and energy to ADP to produce ATP

role of oxygen in the citric acid cycle

citric acid cycle does not directly use O2 but it has to be present as the final electron acceptor in the ETC so that NAD+ and FAD+ can be regenerated to be reduced in the cycle

oxidative phosphorylation involves what 2 processes

the electron transport chain and chemiosmosis

explain oxidative phosphorylation

the synthesis of ATP by reoxidation of electron carriers in the presence of oxygen → relies on proton gradient between hydrogen ion concentration in the mitochondria matrix and inter membrane space

explain the electron transport chain

the transfer of hdyrogen ions and electrons from NADH and FADH2 from one electron carrier to the next, coming it with oxygen to make H2O

occurs across the inner mitochondrial membrane

consists of a series of protein complexes

• Q mvoes between I and III

• Cytochrome C moves between I and IV

whilst electrons are passed through complexes, protons are pumped into the intermembrane space,e creating a highly positive environment and an electrochemical gradient

explain chemiosmosis

the movement of hydrogen ions back across the membrane to a relatively more neutral environment and electron movement through the ETC provides the energy need for synthesis of ATP from ADP

oxygenic photosynthesis is a ____ and an ______ reaction

redox; endergonic

photosynthesis reaction overall

6CO2 + 6H2O → C6H12O6 +6O2

structure of chloroplast (photosynthesis)

2 membranes surrounding dense fluid → stroma

thylakoids = sacs that form third membrane system suspended within stroma

chlorophyll in thylakoid membranes = green pigment

light absorbed by chlorophyll drives synthesis of organic molecules in the chloroplast

explain light as a form of energy

light = electromagnetic radiation

propagated as waves, energy is inversely proportional to wavelength

light behaves as particles

when a photon of light hits a molecule, it can… (3)

bounce off → scattered or reflected

pass through → transmitted

be absorbed → adding energy to molecule = excited s

when a photon of light hits a chlorophyll molecule…

absorbs blue and red light but scatters green

major pigment of photosynthesis

chlorophyll a

how does chlorophyll anchor itself in the thylakoid

chlorophyll has a hydrocarbon tail that anchors it in a protein complex in the thylakoid

light reactions overview

light energy comes in as a photon to drive electron flow along the electron chain

water is oxidised and electrons move through photosystem II then I to rpdoceu ATP and NADPH

describe photosystem

process by which heterotrophs use energy from sunlight to drive the synthesis of organic molecules from CO2 and water

what comes first, photosystem I or II

photosystem II

photosystem process: step 1 (photon hits)

photon of light strikes one of the pigment molecules in light-harvesting complexes → boosts one of the electrons to a higher energy level

as electron falls back to ground state, released energy transferred to a nearby pigment molecule → process continues until it is transferred to P680 pair in reaction centre

photosystem process: step 2 (P680+)

excited electrons transferred to priamry electron acceptor via redox reaction → leaves P680 missing its negative charge → P680+

P680+ is strongest biological oxidising agent known

photosystem process: step 3 (photolysis)

enzyme catalyses tge splitting of water into 2 hydrogen ions and 2 electrons

electrons replace on that was transferred to priamry electron acceptor one by one

hydrogen ions released to thylakoid space

oxygen atom immediately binds with another to form oxygen gas

photosystem process: step 4 (II to I)

excited electron passes from primary electron acceptor to photosystem I via electron transport chain

movement of electrons pumps protons into thylakoid membrane

photosystem process: step 5 (chemiosmosis)

protons move through ATP synthase to generate ATP

proton gradient stores potential energy

components of electron transport one

Pq, cytochrome complex, Pc