Chapter 8: An Introduction To Metabolism

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Chapter 8 An Introduction To
Metabolism
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Essential Knowledge

• 2.a.1 All living systems require constant input
  of free energy (8.1-8.3).
• 4.b.1 Interactions between molecules affect
  their structure and function (8.4 8.5).

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Metabolism

• The totality of an organisms chemical processes
• Concerned with managing the material and energy
  resources of the cell

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Catabolic Pathways

• Pathways that break down complex molecules into
  smaller ones, releasing energy
• Example Cellular respiration
• DOWNHILL!

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Anabolic Pathways

• Pathways that consume energy, building complex
  molecules from smaller ones
• Example Photosynthesis, condensation synthesis
• UPHILL!

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1st Law of Thermodynamics

• Energy cannot be created or destroyed
• It can be converted from one form to another
• The sum of the energy before the conversion is
  equal to the sum of the energy after the
  conversion

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2nd Law of Thermodynamics

• Some usable energy dissipates during
  transformations and is lost
• During changes from one form of energy to
  another, some usable energy dissipates, usually
  as heat
• The amount of usable energy therefore decreases

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Energy

• Ability to do work
• The ability to rearrange a collection of matter
• Forms of energy
• Kinetic
• Potential
• Activation

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Kinetic and Potential Energy

• Kinetic
• Energy of action or motion
• Ex heat/thermal energy
• Potential
• Stored energy or the capacity to do work
• Ex chemical energy

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Activation Energy

• Energy needed to convert potential energy into
  kinetic energy

Activation Energy
Potential Energy
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Free Energy

• The portion of a system's energy that can perform
  work
• Known as ?G

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Free Energy

• ?G ? H - T ? S
• ? change (final-initial)
• ?G free energy of a system
• ?H total energy of a system (enthalpy)
• T temperature in oK
• ?S entropy of a system

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Free Energy of a System

• If the system has
• more free energyless stable (greater work
  capacity)
• less free energymore stable (less work capacity)
• As rxn moves towards equilibrium, ?G will decrease

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Chemical Reactions

• These are the source of energy for living systems
• They are based on free energy changes
• Two types exergonic and endergonic

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Reaction Types

• Exergonic
• chemical reactions with a net release of free
  energy
• Ex cellular respiration
• - ?G , energy out, spontaneous
• Endergonic
• chemical reactions that absorb free energy from
  the surroundings
• Ex Photosynthesis
• ?G , energy in, non-spontaneous

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Exergonic/Endergonic
- ?G
?G
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Cell Energy

• Couples an exergonic process to drive an
  endergonic one
• ATP is used to couple the reactions together
• Types mechanical, transport, chemical

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ATP Description

• Adenosine Triphosphate
• Made of
• Adenine (nitrogenous base)
• Ribose (pentose sugar)
• 3 phosphate groups
• bonds can be broken to make ADP

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Keys to ATP

• Three phosphate groups and the energy they
  contain
• Negative charges repel each other and makes the
  phosphates unstable
• Tail is unstable more free energy more
  instability
• Works by energizing other molecules by
  transferring phosphate groups
• Hydrolysis of ATP free energy is released as
  heat (can be adv or not adv)

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ATP Cycle

• Energy released from ATP drives anabolic
  reactions
• Energy from catabolic reactions recharges ATP
• Very fast cycle
• 10 million made per second

Coupled RXN
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ATP Cycle
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ATP is Made

• Takes place in cytoplasm and mitochondria
• Using special process called substrate-level
  phosphorylation
• Energy from a high-energy substrate is used to
  transfer a phosphate group to ADP to form ATP

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Enzymes

• Biological catalysts made of protein
• Speeds up rxn without being consumed
• Cause the speed/rate of a chemical rxn to
  increase
• By lowering activation energy

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Basic Chemical Reaction

• AB CD AC BD
• AB and CD are reactants
• AC and BD are products
• Involves bond forming/breaking
• Transition state can be unstable

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Unstable state
Energy is released as heat
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Enzymes
Intro to Enzymes movie

• Lower the activation energy for a chemical
  reaction to take place
• Why do we need enzymes?
• Cells cant rely on heat to kick start rxns
• Why? Denaturation, heat cant decipher between
  rxns
• Enzymes are selective! Can only operate on a
  given chemical rxn

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Enzyme Terms

• Substrate
• the material the enzyme works on
• Enzyme names
• Ex. Sucrase
• - ase name of an enzyme
• 1st part tells what the substrate is (i.e.
  Sucrose)

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Enzyme Name

• Some older known enzymes don't fit this naming
  pattern
• Examples pepsin, trypsin

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Active Site

• The area of an enzyme that binds to the substrate
• Structure is designed to fit the molecular shape
  of the substrate
• Therefore, each enzyme is substrate specific

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Enzyme equation

• Enzyme Enzyme- Enzyme
• Subtrate Sub complex Product
• Notice Complex becomes product, but enzyme stays
  the same! Enzyme is NOT CONSUMED!

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Models of How Enzymes Work

• Lock and Key model
• Induced Fit model
• Reminder Enzymes and substrates are usually held
  together by weak chemical interactions (H/ionic
  bonds)

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Lock and Key Model

• Substrate (key) fits to the active site (lock)
  which provides a microenvironment for the
  specific reaction

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Induced Fit Model

• Substrate almost fits into the active site,
  causing a strain on the chemical bonds, allowing
  the reaction

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Enzymes

• Usually specific to one substrate
• Each chemical reaction in a cell requires its own
  enzyme
• Dont change during rxn
• Always catalyze in direction towards equilibrium

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Four Mechanisms to Lower EA

1. Active site is template for enzyme
2. Enzymes may break/stretch bonds needed to be
   broken/stretched
3. Active site is microenvironment
4. Active site directly participates in chemical rxn

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Factors that Affect Enzymes

• Environment
• Cofactors
• Coenzymes
• Inhibitors
• Allosteric Sites

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Environment

• Factors that change protein structure will affect
  an enzyme.
• Examples
• pH shifts (6-8 optimal)
• Temperature (up, inc activity)
• Salt concentrations

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Cofactors Coenzymes

• Cofactors
• Non-protein helpers for catalytic activity
• Examples Iron, Zinc, Copper
• Coenzymes
• Organic molecules that affect catalytic activity
• Examples Vitamins, Minerals, usually proteins

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Enzyme Inhibitors
Inhibitor video

• Competitive
• mimic the substrate and bind to the active site
  (compete for active site)
• Toxins/poisons Ex DDT
• Can be used in medicine painkillers,
  antibiotics
• Noncompetitive
• bind to some other part of the enzyme
• Causes active site to change shape

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Summary

• Identify forms of energy and energy
  transformations.
• Recognize the Laws of Thermodynamics.
• Recognize that organisms live at the expense of
  free energy.
• Relate free-energy to metabolism.
• Identify exergonic and endergonic reactions.
• Identify the structure and hydrolysis of ATP.
• Recognize how ATP works and is coupled to
  metabolism.
• Recognize the ATP cycle
• Relate enzymes and activation energy.
• Recognize factors that affect enzymes specificity
  and enzyme activity..
• Recognize factors that control metabolism.