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Chapter 5 Ground Rules of Metabolism Sections 1-5. Energy. We define energy as the capacity to do work One form of energy can be converted to another Familiar forms of energy include light, heat, electricity, and motion ( kinetic energy )

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  • We define energy as the capacity to do work
  • One form of energy can be converted to another
  • Familiar forms of energy include light, heat, electricity, and motion (kinetic energy)
  • The energy in chemical bonds is a type of potential energy, because it can be stored
energy disperses
Energy Disperses
  • First law of thermodynamics
    • Energy is neither created nor destroyed, but can be transferred from one form to another
  • Second law of thermodynamics
    • Entropy (a measure of dispersal of energy in a system) increases spontaneously
    • The entropy of two atoms decreases when a bond forms between them (endergonic reaction)
energy conversion
Energy Conversion
  • Only about 10% of the energy in food goes toward building body mass, most is lost in energy conversions
energy s one way flow
Energy’s One Way Flow
  • The total amount of energy available in the universe to do work is always decreasing
    • Each time energy is transferred, some energy escapes as heat (not useful for doing work)
  • On Earth, energy flows from the sun, through producers, then consumers
    • Living things need a constant input of energy
chemical bond energy
Chemical Bond Energy
  • Reaction
    • A chemical change that occurs when atoms, ions, or molecules interact
  • Reactant
    • Atoms, ions, or molecules that enter a reaction
  • Product
    • Atoms, ions, or molecules remaining at the end of a reaction
reactions require or release energy
Reactions Require or Release Energy
  • We can predict whether a reaction requires or releases energy by comparing the bond energies of reactants with those of products
  • Endergonic (“energy in”)
    • Reactions that require a net input of energy
  • Exergonic(“energy out”)
    • Reactions that end with a net release of energy
why the earth doesn t go up in flames
Why the Earth Doesn’t Go Up in Flames
  • Activation energy
    • The minimum amount of energy needed to get a reaction started
    • Some reactions require a lot of activation energy, others do not
activation energy
Activation Energy




Activation energy

Free energy

Products: 2H2O

Difference between free energy of reactants and products


take home message how do cells use energy
Take-Home Message:How do cells use energy?
  • Activation energy is the minimum amount of energy required to start a chemical reaction
  • Endergonic reactions cannot run without a net input of energy
  • Exergonic reactions end with a net release of energy
  • Cells store energy in chemical bonds by running endergonic reactions that build organic compounds; they harvest energy by breaking the bonds
5 4 how enzymes work
5.4 How Enzymes Work
  • Enzyme
    • In a process called catalysis, an enzyme makes a specific reaction occur much faster than it would on its own
    • Enzymes are not consumed or changed by participating in a reaction
    • Most are proteins, some are RNA
  • Substrate
    • The specific reactant acted upon by an enzyme
the transition state
The Transition State
  • Enzymes lower the activation energy required to bring on the transition state, when substrate bonds break and reactions run spontaneously
  • Active sites
    • Locations on the enzyme molecule where substrates bind and reactions proceed
    • Complementary in shape, size, polarity and charge to the substrate
mechanisms of enzyme mediated reactions
Mechanisms of Enzyme-Mediated Reactions
  • Binding at enzyme active sites may bring on the transition state by four mechanisms
    • Helping substrates get together
    • Orienting substrates in positions that favor reaction
    • Inducing a fit between enzyme and substrate (induced-fit model)
    • Shutting out water molecules
effects of temperature ph and salinity
Effects of Temperature, pH, and Salinity
  • Raising the temperature boosts reaction rates by increasing a substrate’s energy
    • But very high temperatures denature enzymes
  • Each enzyme has an optimum pH range
    • In humans, most enzymes work at ph 6 to 8
  • Salt levels affect the hydrogen bonds that hold enzymes in their three-dimensional shape
take home message how do enzymes work
Take-Home Message:How do enzymes work?
  • Enzymes greatly enhance the rate of specific reactions.
  • Binding at an enzyme’s active site causes a substrate to reach its transition state. In this state, the substrate’s bonds are at the breaking point
  • Each enzyme works best at certain temperatures, pH, and salt concentration
types of metabolic pathways
Types of Metabolic Pathways
  • Ametabolic pathway is any series of enzyme-mediated reactions by which a cell builds, rearranges, or breaks down an organic substance
    • Anabolic pathways build molecules
    • Catabolic pathways break apart molecules
    • Cyclic pathways regenerate a molecule from the first step
controls over metabolism
Controls Over Metabolism
  • Concentrations of reactants or products can make reactions proceed forward or backward
  • Feedback mechanisms can adjust enzyme production, or activate or inhibit enzymes
  • Regulatory molecules can bind to an allosteric siteto activate or inhibit enzymes
    • Feedback inhibition



enzyme 1


enzyme 2


enzyme 3


Stepped Art

Figure 5-14 p84

redox reactions
Redox Reactions
  • Oxidation-reduction reactions(paired reactions)
    • A molecule that gives up electrons is oxidized
    • A molecule that accepts electrons is reduced
    • Coenzymes can accept molecules in redox reactions (also called electron transfers)




carbon dioxide



Figure 5-16 p85









carbon dioxide +




Figure 5-16 p85

take home message what are metabolic pathways
Take-Home Message:What are metabolic pathways?
  • Metabolic pathways are sequences of enzyme-mediated reactions; some are biosynthetic; others are degradative
  • Control mechanisms enhance or inhibit the activity of many enzymes; the adjustments help cells produce only what they require in any given interval
  • Many metabolic pathways involve electron transfers, or redox reactions.
  • Redox reactions occur in electron transfer chains; the chains are important sites of energy exchange in photosynthesis and aerobic respiration
cofactors and coenzymes
Cofactors and Coenzymes
  • Cofactors
    • Atoms or molecules (other than proteins) that are necessary for enzyme function
    • Example: Iron atoms in catalase
  • Coenzymes
    • Organic cofactors such as vitamins
    • May become modified during a reaction
catalase and cofactors
Catalase and Cofactors
  • Catalase is an antioxidant that neutralizes free radicals (atoms or molecules with unpaired electrons that attack biological molecules)
  • Catalase has four hemes (small organic compound with an iron atom at its center)
  • Catalase works by holding a substrate molecule close to one of its iron atoms (cofactors)
  • Iron pulls on the substrate’s electrons, bringing on the transition state
atp a special coenzyme
ATP—A Special Coenzyme
  • ATP(adenosine triphosphate)
    • A nucleotide with three phosphate groups
    • Transfers a phosphate group and energy to other molecules
  • Phosphorylation
    • A phosphate-group transfer
    • ADP binds phosphate in an endergonic reaction to replenish ATP (ATP/ADP cycle)


three phosphate groups









energy in

energy out


ADP + phosphate

Figure 5-18 p87

take home message how do cofactors work
Take-Home Message:How do cofactors work?
  • Cofactors associate with enzymes and assist their function.
  • Metal ions stabilize the structure of many enzymes. They also participate in some enzymatic reactions by donating or accepting electrons
  • Many coenzymes carry chemical groups, atoms, or electrons from one reaction to another
  • The formation of ATP from ADP is an endergonic reaction; ADP forms again when a phosphate group is transferred from ATP to another molecule – energy from such transfers drives cellular work
the fluid mosaic model
The Fluid Mosaic Model
  • Fluid mosaic model
    • Describes the organization of cell membranes
    • Phospholipids drift and move like a fluid
    • The bilayer is a mosaic mixture of phospholipids, steroids, proteins, and other molecules
cell membrane organization
Cell Membrane Organization

one layer of lipids

one layer of lipids

types of membrane proteins
Types of Membrane Proteins
  • Each type of protein in a membrane has a special function
    • Adhesion proteins
    • Recognition proteins
    • Receptor proteins
    • Enzymes
    • Transport proteins (active and passive)
types of membrane proteins1
Types of Membrane Proteins

B Recognition proteins such as this MHC molecule tag a cell as belonging to one’s own body.

c Receptor proteins such as this B cell receptor bind substances outside the cell. B cell receptors help the body eliminate toxins and infectious agents.

D Transport proteins bind to molecules on one side of the membrane, and release them on the other side. This one transports glucose.

E This transport protein, an ATP synthase, makes ATP when hydrogen ions flow through its interior.

Extracellular Fluid

Lipid bilayer


take home message what is a cell membrane
Take-Home Message:What is a cell membrane?
  • The structural foundation of all cell membranes is the lipid bilayer
  • Adhesion proteins, recognition proteins, transport proteins, receptors, and enzymes embedded in or associated with the lipid bilayer impart functionality to a cell membrane
5 8 diffusion and membranes
5.8 Diffusion and Membranes
  • Ions and molecules tend to move spontaneously from regions of higher to lower concentration
  • Water diffuses across cell membranes by osmosis
  • Diffusion
    • The net movement of molecules down a concentration gradient
    • Moves substances into, through, and out of cells
    • A substance diffuses in a direction set by its own concentration gradient, not by the gradients of other solutes around it
the rate of diffusion
The Rate of Diffusion
  • Rate of diffusion depends on five factors
    • Size
    • Temperature
    • Steepness of the concentration gradient
    • Charge
    • Pressure
concentration gradients
Concentration Gradients
  • Concentration
    • The number of molecules (or ions) of substance per unit volume of fluid
  • Concentration gradient
    • The difference in concentration between two adjacent regions
    • Molecules move from a region of higher concentration to one of lower concentration
  • Tonicity
    • The relative concentrations of solutes in two fluids separated by a selectively permeable membrane
  • For two fluids separated by a semipermeable membrane, the one with lower solute concentration is hypotonic, and the one with higher solute concentration is hypertonic
  • Isotonic fluids have the same solute concentration
  • Osmosis
    • The movement of water down its concentration gradient – through a selectively permeable membrane from a region of lower solute concentration to a region of higher solute concentration

selectively permeable membrane

membrane permeability
Membrane Permeability
  • Selective permeability
    • The ability of a cell membrane to control which substances and how much of them enter or leave the cell
    • Allows the cell to maintain a difference between its internal environment and extracellular fluid
    • Supplies the cell with nutrients, removes wastes, and maintains volume and pH
selective permeability of lipid bilayers
Selective Permeability of Lipid Bilayers

glucose and other polar molecules; ions


lipid bilayer


effects of fluid pressure
Effects of Fluid Pressure
  • Hydrostatic pressure (turgor)
    • The pressure exerted by a volume of fluid against a surrounding structure (membrane, tube, or cell wall) which resists volume change
  • Osmotic pressure
    • The amount of hydrostatic pressure that can stop water from diffusing into cytoplasmic fluid or other hypertonic solutions
take home message what influences the movement of ions and molecules
Take-Home Message: What influences the movement of ions and molecules?
  • Molecules or ions tend to diffuse into an adjoining region of fluid in which they are not as concentrated
  • he steepness of a concentration gradient as well as temperature, molecular size, charge, and pressure affect the rate of diffusion
  • Osmosis is a net diffusion of water between two fluids that differ in water concentration and are separated by a selectively permeable membrane
  • Fluid pressure that a solution exerts against a membrane or wall influences the osmotic movement of water
how substances cross membranes
How Substances Cross Membranes
  • Gases and nonpolar molecules diffuse freely across a lipid bilayer
  • Ions and large polar molecules require other mechanisms to cross the cell membrane
    • Passive transport
    • Active transport
    • Endocytosis and exocytosis
passive transport
Passive Transport
  • Passive transport (facilitated diffusion)
    • Requires no energy input
    • A passive transport protein allows a specific solute (such as glucose) to follow its concentration gradient across a membrane
    • A gated passive transporter changes shape when a specific molecule binds to it
active transport
Active Transport
  • Active transport
    • Requires energy input (usually ATP)
    • Moves a solute against its concentration gradient, to the concentrated side of the membrane
  • Calcium pumps
    • Active transporters move calcium ions across muscle cell membranes into the sarcoplasmic reticulum
active transport calcium pump
Active Transport: Calcium Pump

Extracellular Fluid


  • Cotransporter
    • An active transport protein that moves two substances across a membrane at the same time
    • Example: The sodium-potassium pump moves Na+ out of the cell and K+ into the cell
cotransport sodium potassium pump
Cotransport: Sodium-Potassium Pump

Extracellular Fluid



take home message how do molecules or ions cross a cell membrane
Take-Home Message: How do molecules or ions cross a cell membrane?
  • Transport proteins help specific molecules or ions to cross cell membranes
  • In passive transport, a solute binds to a protein that releases it on the opposite side of the membrane; he movement is driven by a concentration gradient
  • In active transport, a transport protein pumps a solute across a membrane, against its concentration gradient; the movement is driven by an energy input, such as ATP
5 10 membrane trafficking
5.10 Membrane Trafficking
  • By processes of endocytosis and exocytosis, cells take in and expel particles that are too big for transport proteins, as well as substances in bulk
  • Requires formation and movement of vesicles formed from membranes, involving motor proteins and ATP
exocytosis and endocytosis
Exocytosis and Endocytosis
  • Exocytosis
    • The fusion of a vesicle with the cell membrane, releasing its contents to the surroundings
  • Endocytosis
    • The formation of a vesicle from cell membrane, enclosing materials near the cell surface and bringing them into the cell



A Molecules get

concentrated inside coated pits at the plasma membrane.

coated pit

D Many of the sorted molecules cycle to the plasma membrane.

B The pits sink inward and become endocytic vesicles.

E Some vesicles are routed to the nuclear envelope or ER membrane. Others fuse with Golgi bodies.

C Vesicle contents are sorted.

F Some vesicles

and their contents are delivered to lysosomes.



Stepped Art

Figure 5-27 p94

take home message how do cells take in large particles and bulk substances
Take-Home Message: How do cells take in large particles and bulk substances?
  • Exocytosis and endocytosis move materials in bulk across plasma membranes
  • In exocytosis, a cytoplasmic vesicle fuses with the plasma membrane and releases its contents to the outside of the cell
  • In endocytosis, a patch of plasma membrane sinks inward and forms a vesicle in the cytoplasm
  • Phagocytosis is an endocytic pathway by which cells engulf particles such as microorganisms