Foundations of Biology Topic 2

energy

is the capacity to do work or cause change, where work occurs when a force acts over a distance

main types of energy in biology

• Chemical energy → stored in bonds (e.g. ATP, glucose)

• Electrical energy → charge differences across membranes

• Heat (thermal energy) → molecular motion/temperature

• Light energy → photons used in photosynthesis/vision

• Mechanical energy → movement (muscles, cytoskeleton)

two broad categories of energy

• Potential energy → stored energy (bonds, gradients, charges) → chemical bonds, ion gradients, ATP

• Kinetic energy → energy of movement (heat, motion, particles) → muscle movement, diffusion, heat energy

thermodynamics

study of energy transformations and transfers in systems

open vs closed energy systems

• Closed system: no matter/energy exchange (e.g. thermos)

• Open system: exchanges energy + matter (e.g. organisms)

first law of thermodynamics

Energy cannot be created or destroyed, only transferred or transformed.

second law of thermodynamics

Every energy transfer increases entropy (disorder) because some energy is lost as heat

ATP

• Adenosine triphosphate → a high-energy molecule used to transfer energy in cells.

• energy rich → 3 negatively charged phosphate groups that repel each other

• bonds are unstable → energy released when broken

ATP hydrolysis

• water added

• ATP → ADP + Pi

• releases energy (exergonic)

• energy is used in the cell for work

phosphorylation

addition of phosphate group to a molecule, changes its shape and energy shape

Gibbs free energy

ΔG symbol, represents energy (useful energy)

exergonic and endergonic reactions

• Exergonic: releases energy, spontaneous (-ΔG)

• Endergonic: requires energy, non-spontaneous (+ΔG)

equilibrium in energy

state of maximum stability where no net energy change occursstate of maximum stability where no net energy change occurs

catabolic and anabolic reactions

• Catabolic: breakdown large molecules into smaller ones, release energy (exergonic), -ΔG, usually hydrolysis and oxidation

• Anabolic: build complex molecules from simple ones, uses energy (endergonic), +ΔG, usually condensation and reduction

• are interconnected

oxidation

Loss of electrons

reduction

Gain of electrons

redox reactions

• changes in electron transfer or charge of molecules

• coupling of oxidation + reduction

• transfer energy via electrons for work, driving processes like respiration and photosynthesis

enzymes

act as biological catalyst to increase reaction (metabolic and digestive) rate by lowering activation energy without being consumed

activation energy

the minimum energy required for reactants to reach the transition state and begin a reaction. lowering it means more molecules reach the transition state, more successful collisions per second thus faster reaction rate.

active site

specific region where the substrate binds and the reaction occurs, involving specific amino acid R groups.

active side models

• Lock and key: rigid and fixed active site shape, perfect fit

• Induced fit: active site changes shape to fit substrate (more accurate model)

steps is enzyme catalysis

1. substrate binds to active site

2. enzyme stabilises transition state

3. activation energy is lowered

4. products are released, enzyme unchanged

substrate concentration on enzyme activity

• rate increases as substrate increases

• at saturation point all active sites are full → maximum rate (Vmax)

temperature on enzyme activity

• Low temp → slow activity

• Optimal temp (~37°C in humans) → max activity

• High temp → denaturation → loss of function

pH on enzyme activity

• Low temp → slow activity

• Optimal temp (~37°C in humans) → max activity

• High temp → denaturation → loss of function

cofactors

• Non-protein helpers required for enzyme function

• can be inorganic ions or organic molecules

coenzymes

• non protein organic molecules, transfer chemicals from active site of an enzyme to active site of another enzyme

prosthetic groups

• permanently bind to active site to transfer chemicals from active site of enzyme to some other substance

inhibitors

molecules that reduce enzyme activity by blocking or altering active sites

• Competitive: compete with substrate

• Non-competitive: bind elsewhere, change enzyme shape

• Irreversible: permanently inactivate enzyme

how to measure enzyme reaction rate

• Decrease in substrate concentration

• Increase in product concentration

• Change per unit time (kinetic measurement)

feedback inhibition

A regulatory mechanism where the end product of a metabolic pathway inhibits an enzyme earlier in the pathway, slowing or stopping further production.

importance:

• prevent overproduction of products

• conserves energy and resources

how does feedback inhibition work

1. final product accumulates

2. binds to an enzyme early in the pathway, often allosterically

3. enzyme activity decreases → pathway slows or stops

feedback activation

when a product or molecule activates an enzyme, increasing pathway activity and directs metabolic flow.

how can biological pathways be regulated by feedback + example

• Products from one pathway can:

  • Inhibit their own pathway

  • Activate other pathways

• Helps balance metabolic needs

example:
Phosphofructokinase (glycolysis enzyme):

• Activated by AMP (low energy)

• Inhibited by ATP and citrate (high energy)

adjusts respiration rate based on energy demand

allosteric regulation

Regulation where a molecule binds to a site other than the active site (allosteric site), causing a shape change that alters enzyme activity.

allosteric enzyme

An enzyme with:

• Multiple subunits

• Multiple binding sites

• Ability to switch between active and inactive forms

allosteric activators

• Bind to allosteric site

• Stabilise active form

• Increase enzyme activity

allosteric inhibitors

• Bind to allosteric site

• Stabilise inactive form

• decrease enzyme activity

metabolism

the sum of all biochemical reactions in a cell, often organised into metabolic pathways where products of one reaction become substrates for the next

metabolic pathways

• reactions occur in stepwise sequences

• each step is catalysed by a specific enzyme

• pathways are regulated at key steps

catabolism and anabolism

• Catabolism: breakdown of large molecules to smaller ones, usually hydrolysis and oxidation, releasing energy (exergonic, -ΔG)

• Anabolism: Synthesis of complex molecules from simpler ones, usually condensation and reduction, requiring energy (endergonic, +ΔG).

they are interconnected

lipid metabolism

catabolism: energy production

1. lipolysis: triglycerides → glycerol + fatty acids, occurs in adipose tissue

2. fatty acids bind to coenzyme A → fatty acyl-Co, tranport to mitochondria for energy production or lipid synthesis

3. β-oxidation (mitochondrial matrix): fatty acids broken down into acetyl-CoA (TCA cycle), NADH, FADH₂ (ETC)

anabolism: energy storage

lipogenesis: when energy is abundant, acetyl-CoA from excess glucose or amino acids → fatty acids → triglycerides stored in adipose tissue

gluconeogensis

production of glucose within a cell, it is almost a reversal of glycolysis. making new glucose from a non carb source.

protein metabolism reasons

3 key points:

1. there is no storage form of proteins, all proteins consumed is turned into carbs or fat and the nitrogen from the amino group must be eliminated through the urea cycle

2. essential amino acids must be consumed daily for proteins to be made

3. proteins are always degraded, therefore there is a constant need for quality protein to maintain the product’s structure

How are proteins catabolised?

• amino acids undergo:

  • Transamination (transfer NH₂ group to a keto acid)

  • Deamination (remove NH₂ → ammonium ion is removed)

• Carbon skeleton enters glycolysis or citric acid cycle

urea cycle

takes 2 metabolic waste products, ammonium ions and carbon dioxide and produces urea, a relatively harmless soluble compound that is excreted in urine

why are proteins not a preferred energy source

• no storage form

• requires nitrogen removal (urea cycle)

• complex, slower

how are proteins synthesised

• Amino acids formed via amination (ammonium ion used to form an amino group) and transamination (amino group transferred to keto acid)

• Assembled into proteins

aerobic cellular respiration

• metabolic process in which cells break down glucose using oxygen to produce energy in the form of ATP, releasing carbon dioxide and water as waste

C6H12O6(glucose)+6O2(oxygen)→6CO2(carbondioxide)+6H2O(water)+ATP(energy)

1. glycolysis: in cytoplasm, break down glucose to pyruvate and makes 2 tap

2. TCA cycle: in mitochondrial matrix, producing carbon dioxide and transfer electrons

3. ETC: in inner mitochondria membrane, produce majority of ATP through oxidative phosphorylation

glycolysis

• in cytosol

• 10 step pathways

• inputs: glucose, ATP, NAD+, ADP + Pi

• steps 1-5: (energy investment) use ATP to phosphorylate glucose

• steps 6-10: (energy pass off): produces ATP and NADH

• outputs: pyruvate, 2 ATP (net), NADH

regulation of glycolysis

key enzyme in glycolysis: phosphofructokinase

reaction in pathway: fructose-6-phosphate → fructose-1,6-bisphosphate

Regulation:

• Activated by: AMP, ADP → when low energy → ↑ glycolysis

• Inhibited by: ATP, citrate → when high energy → ↓ glycolysis

TCA cycle/citric acid/krebs cycle

inputs: acetyl CoA, NAD+, FAD, ADP + Pi, H2O

outsputs: CO2, NADH, FADH2, ATP

cycle spins twice per glucose, making 2 ATP

TCA cycle regulation

• High NADH/FADH₂ inhibits enzymes

• Slows cycle when energy is abundant

energy generation in TCA cycle

• Energy (electrons and H+)captured as NADH and FADH₂ (electron carriers)

• Small ATP via substrate-level phosphorylation

• Electron carriers go to electron transport chain → major ATP production

Electron transport chain

• inner mitochondrial membrane

• inputs: NADH, FADH2 (electron carriers), O2 (final electron accepter)

• NADH and FADH₂ are oxidised → release high-energy electrons

• Electrons pass through a series of protein carriers

• Energy released is used to pump H⁺ (protons) from matrix → intermembrane space
  
  process done through chemiosmosis

ATP Synthesis:

• H⁺ flows back into matrix via ATP synthase

• Drives ADP + Pi → ATP
  👉 This is oxidative phosphorylation
  
  outputs: 30-32 net ATP, water, NAD+, FAD

chemiososis

from a proton gradient

• Creates electrochemical gradient (high H⁺ outside, low inside)

• This stores potential energy

anaerobic cellular respiration

• without O2, no ETC

• cells use: glycolysis and fermentation (lactic acid and alcoholic)

• fermentation regenerates NAD+ for glycolysis

lactic acid fermentation

pyruvate → lactate

in muscle cells

2 atp

alcoholic fermentation

pyruvate → ethanol + CO2

in yeast and plants cells

2 atp