Chapter 03. Energy Light to Life Overview: Energy from the sun is used to make ATP ATP is used to activate molecular bonding Energy is stored in bonds

Chapter 03

EnergyLight to Life

Overview:• Energy from the sun is used to make ATP• ATP is used to activate molecular bonding• Energy is stored in bonds• Energy is released when bonds are broken

The structure of atoms

An atom is:

• The smallest unit of a pure substance (element) which cannot be broken down by ordinary chemical means

• Composed of protons, neutrons and electrons


• Protons: mass = 1, + charge, found in nucleus

• Neutrons: mass = 1, no charge, found in nucleus

• Electrons: mass negligible, - charge, orbit the nucleus


Chemical behavior is determined by electron number and arrangement :

• Electrons arranged in energy levels• Highest energy level electron shells are

farthest from nucleus • Octet Rule: atoms bond in ways to achieve 8

electrons in the highest energy level

The Structure of AtomsAn atom is made of negatively-charged electrons orbiting

around a positively-charged nucleus.

Biological molecules are organic (carbon-based) compounds

Common elements in living systems:

• C, O, H, N

• Important ions: Ca, K, P, Na, S, Cl, Mg

• Trace ions and minerals: I, Zn, Mn, Cu, and others

Carbon

• Basis of all organic compounds• Forms four bonds• Enables molecules to add backbone

length• Enables molecules to connect unique

side groups; provide character and informational value

• Forms bonds most often with O, H, or N

Example of an Organic CompoundLine structure and space-filling model of the dipeptide glycine-

serine

Making Bonds

Bonds:

• forces that hold atoms together

• form when atoms with correct fit collide with sufficient force

• store energy

Making Bonds

• Covalent bond: atoms collide and electrons rearrange so that some of the electrons are shared by the two atoms

Making Covalent BondsAtoms collide and electrons are rearranged and shared.

Two electron orbits are joined.

Making BondsOxygen forms covalent bonds with two hydrogen atoms

to form water

Molecular ChangesBreaking Bonds

• Bonds break when molecules collide with enough force and at appropriate angles

• Shared electrons return to their original orbits and release the stored energy in the bond

• Bond energy can be lost as heat or transferred to other molecules and preserved in a new bond

Transferring EnergyMolecules collide, bonds break, and energy is transferred to

the bonds of the new molecule.

Life and the Laws of Energy

All matter and energy in the universe follow the Laws of Thermodynamics:

• First Law: Energy can be gained or lost in chemical processes, but it can’t be created or destroyed.

• Second Law: Energy disperses and ordered structures become disordered (entropy increases).

Energy Flow and change in living systems

How the laws of thermodynamics apply to cells:

• Over time, all things in the universe tend toward disorder

• Cells need a continual, external source of useful energy to do work, overcome entropy and remain organized

Energy Flow and Equilibrium

• Equilibrium: energy flows as readily backwards as forwards in a chemical reaction

• Cells become inactive and die in equilibrium conditions

• Cells maintain far-from-equilibrium conditions by adding reactants and removing products

EquilibriumNO2 molecules collide to form N2O4. When sufficient N2O4 accumulates, the reverse reaction begins and N2O4 fragments into NO2. Equilibrium is reached when the forward and reverse reactions occur at the same rate.

Energy Flow and Equilibrium

ATP – The Energy Molecule

Each ATP molecule has three subunits:

• ribose sugar • adenine• three phosphate

groups (PO4) linked to form a triphosphate group


• ATP is a high-energy donor molecule

• Energy is released by breaking ATP’s phosphate bonds (hydrolysis)

• ATP is reassembled by reattaching its phosphates with an input ? energy


Some of ATP’s JobsMaking information chains

Some of ATP’s JobsMaking proteins contract

Some of ATP’s JobsTransporting small molecules

Enzymes

Enzymes:• Catalysts that speed up and facilitate

chemical reactions• Molecules fit into active sites (docking

sites)• Chemically interact with molecules and

force them to react in aided collisions• Large protein molecules

Enzymes bind substrates at active sites

Active site:

• groove or cleft on enzyme formed by tertiary structure of protein

• binds, orients, strains substrate

• has shape specific for substrate

Enzymes

Energy Flow Through LifeMacro View

Food Chain:• Primary Producers: convert energy from sun

into chemical bonds of sugar (photosynthesis)• Herbivores: obtain energy directly from plants• Carnivores: obtain energy from flesh of

herbivores• Decomposers: obtain energy by breaking down

waste and dead bodies of above groups



Plants play an important role:

• produce fuel (sugar)

• produce oxygen to burn fuel

• consume carbon dioxide waste

Energy Flow Through Life Macro View

Energy Flow Through LifeMicro View

Sugar (glucose)

• energy source

• building material for other molecules such as amino acids and nucleotides

Glucose

Glucose is a small carbohydrate called a monosaccharide (mono = “one”, saccharide is from saccharum = “sugar”)

Starch

Glucose molecules link together to form

starch, a polysaccharide

(“many sugar units”). Amylopectin is a type

of plant starch.

Energy Flow Through LifeProducing Sugar - Photosynthesis

Chloroplasts:

• organelle found in plant cells

• produces sugar using energy from sunlight

Energy Flow Through LifeBreaking Down Sugar - Respiration

Mitochondria:

• organelles found in both plant and animal cells

• break down sugar and produce ATP

Energy Flow Through LifeMicro View

Life’s molecules are continuously recycled:

• Chloroplasts:

carbon dioxide + water sugar + oxygen

• Mitochondria:

sugar + oxygen carbon dioxide + water

Capturing Light Energy

• Light: electromagnetic energy that travels in waves of varying lengths

• Photons: packets of light• Pigments: molecules which absorb some

light wavelengths and reflect others• The colors we observe correspond to the

wavelengths that are reflected by the pigment

The Electromagnetic Spectrum

Pigments absorb some visible wavelengths of light and reflect others.

Capturing light energy in chemical bonds

Photosynthetic pigments:

• Chlorophylls: primary pigments· Absorb photons of violet-blue and red

• Antenna pigments (carotenoids) · Absorb photons of green, blue, violet · Increase range of energy absorption

Chlorophylls absorb violet-blue and red light. They reflect green and

yellow light.

Photosynthesis Takes Place in Chloroplasts

Chlorplast

• Double outer membrane• Stroma: inner chamber• Thylakoids: flattened sacs• Grana: stacks of thylakoids

PhotosynthesisLight-Dependent Reactions

(“Electron Bounce”)1. Photons hit

chlorophyll molecules (photosytem II) in leaves, exciting electrons to higher-energy orbits.


(“Electron Bounce”)• 2. Electrons

bounce along chlorophyll molecules and onto small carrier molecules (an electron transport chain) in the thylakoid membrane.


(“Electron Bounce”)

• 3. Electrons lost from chlorophyll are replaced by electrons from water. Oxygen atoms from the water pair up with hydrogen and are released as an important byproduct.


(“Ion Shuffle”)

• 4. Electrons on carrier molecules attract hydrogen ions from the stroma.


(“Ion Shuffle”)

• 5. Carrier molecules bring hydrogen ions to an enzyme which ejects them into the thylakoid sac.


(“Ion Shuffle”)

• 6. Hydrogen ions exit the thylakoid sac through a channel in an ATP-producing enzyme (ATP synthase).


(“Ion Shuffle”)• 7. Spent

electrons replace electrons bouncing off a new set of energized chlorophyll molecules (photosystem I).


(“Ion Shuffle”)

• 8. Energized electrons unite with hydrogen ions on NADP to form reactive “hot” hydrogens (NADPH).

Overview of Light-Dependent Reactions

PhotosynthesisLight-Independent Reactions – Calvin Cycle

Overview:• Team of five

enzymes uses ATP, carbon dioxide, and “hot” hydrogens from NADPH to produce half-molecules of sugar in the stroma of the chloroplast (carbon fixation or Calvin Cycle).

Calvin Cycle

• Enzyme A: attaches three carbon dioxides to three 5-C sugars

Calvin Cycle

• Three 6-C sugars break into six 3-C sugars

• Enzyme B: energizes 3-C sugar fragments with ATP

Calvin Cycle

• Enzyme C: attaches hydrogens from NADPH to six 3-C sugars and releases one

• Released 3-C sugars (half-sugars) exit chloroplast and pair up to form 6-C glucose in cytoplasm

Calvin Cycle

• Enzyme D: rearranges remaining five 3-C sugars to form three 5-C sugars

Calvin Cycle

• Enzyme E: energizes 5-C sugars with ATP

• Repeat cycle

Calvin Cycle

Respiration Takes Place in the Mitochondria

Respiration Overview

Three main stages:

• Glycolysis: cytosol

• Krebs Cycle: mitochondrial matrix

• Electron Transport Chain: mitochondrial inner membrane

Overview of Respiration

Glycolysis

• From greek: lysis = “to break apart”, glyco = “sugar”

• Glucose is broken into smaller fragments by a series of enzymes

• Generates two ATP• Requires no oxygen (anaerobic)• Prepares glucose for Krebs Cycle• Emergency energy source• Early metabolic pathway

Glycolysis

RespirationKrebs Cycle

• Enzymes extract energetic hydrogens from 2-C sugar fragments (from glycolysis of glucose) [1]

• Carbon and oxygen combine and are discarded as carbon dioxide (animals exhale)

The Krebs Cycle

RespirationElectron Transport Chain

• “Hot” hydrogens (from NADPH) give up their electrons to an enzyme in the mitochondrion inner membrane.

• Electrons pass along carriers in the inner membrane, picking up hydrogen ions [2]


• Enzymes eject hydrogen ions into intermembrane space [3]


• Hydrogen ions force their way out through a channel in an ATP-producing enzyme [4] ATP is the end result


• Spent electrons combine with hydrogen ions and oxygen to form water – a waste product [5]

Respiration – The Electron Transport Chain

MetabolismBuilding up and breaking down materials

Community Energy

Within an organism:

• Groups of cells have special roles that require additional energy

• Specialized cells divert ATP to duties that benefit whole organism

Documents

Chapter 03. Energy Light to Life Overview: Energy from the sun is used to make ATP ATP is used to activate molecular bonding Energy is stored in bonds