Essential Concepts of Metabolism

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Essential Concepts of Metabolism
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What is Metabolism?

• Metabolism
• -
• Why do we want to learn about it?
• By studying metabolism
• 1. scientists can identify and develop treatment
  for metabolic diseases (diabetes,
  mucopolysachharidosis)
• 2. find microbes with unique metabolic pathways
  or enzymes that can be used to detoxify wastes or
  produce useful products.
• 3. understand how different organisms interact in
  different ecosystems.

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Metabolism

• Metabolism in bacteria is similar to that in
  eukaryotes.
• -
• However, bacteria also have unique enzymes that
  allow them to adapt to many niches.
• How do horses and cows digest cellulose?
• How do bacteria live at the depths of the ocean?
• They have special enzymes which have been adapted
  for specific environments.

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Metabolism

• What components do we need to build a cell?
• We need components similar to those we would need
  if we were building a house
• 1
• 2
• 3

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Yin Yang of Metabolism

• Metabolism is a balanced process
• Consists of 2 opposite reactions.
• Catabolism
• -
• Anabolism
• -

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Catabolism vs. Anabolism

• Why do we need catabolism and anabolism?
• We need catabolism to produce energy
• We need catabolism to break down nutrients into
  simpler molecules
• We need anabolism to take the simpler molecules
  (result of catabolism) and build molecules and
  structures needed by cells.
• For instance, can you eat a ribosome or plasma
  membrane? No, you need to eat a Snickers bar ?,
  catabolize the peanuts and caramel into simple
  building blocks and energy and then anabolism
  takes the building blocks and energy and produces
  ribosomes.

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Catabolism vs. Anabolism

• Catabolic examples
• Proteins--gt
• Lipids--gt
• Carbohydrates--gt
• DNA--gt
• We need to break down what we eat into products
  that our individual cells can use.

• Anabolic examples
• _____? proteins
• _____? lipids
• _____? DNA
• Structures like cell membranes, ribosomes
• enzymes

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All Catabolic reactions involve electron transfer

• Electron transfer
• allows energy to be captured in high-energy
  bonds in ATP and similar molceules.
• Directly related to oxidation reduction
  (remember those redox reactions from chemistry?)
• Oxidation
• Reduction

• Imagine Aorganic molecule like glucose
• Imagine BNAD coenzyme, an electron carrier

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Microbes are classified according to their
carbon and energy sources.

• How are plants classified?
• Photoautotrophs because they use CO2(AUTO aka
  LITHO) to make their own food (lucky for us,
  their waste product is oxygen) and they use light
  for energy (PHOTO)
• How are humans classified?
• We are chemoheterotrophs because we cannot make
  our own food and rely on organic materials
  (HETERO) and we use organic compounds (nutrients)
  for our energy source (CHEMO).

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Chemoheterotrophs using respiration and
photoautotrophs using photosynthesis form a
cycle.

• How are plants classified?
• Photoautotrophs because they use CO2(AUTO aka
  LITHO) to make their own food (lucky for us,
  their waste product is oxygen) and they use light
  for energy (PHOTO)
• How are humans classified?
• We are chemoheterotrophs because we cannot make
  our own food and rely on organic materials
  (HETERO) and we use organic compounds (nutrients)
  for our energy source (CHEMO).

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How do chemical reactions take place?

• Chemical reactions occur when molecular bonds are
  BROKEN or FORMED
• All molecules possess kinetic energy that
  produces continual motion.
• When molecules collide they can either break or
  form bonds causing a chemical reaction

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How do chemical reactions take place?

• In order for bonds to be FORMED or BROKEN, there
  has to be a minimal amount of energy available.
  This minimal amount of energy is termed
  activation energy.

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How do chemical reactions take place?

• Activation energy can be in the form of
  temperature or pressure, etc. to increase the
  number of particle collisions.
• Paradoxically, the temperature and pressure that
  humans and bacteria would require for their
  chemical reactions would KILL them!
• How do we solve this problem?
• ENZYMES!!
• Enzymes reduce the amount of activation energy
  needed for chemical reactions.

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Enzymes are

• Biological catalysts that lower activation energy
• VERY EFFICIENT
• Enzymes can catalyze reactions up to 10 billion
  times faster
• There is a high turnover rate. One enzyme can
  catalyze many reactions.
• VERY SPECIFIC
• 1 enzyme for 1 substrate, similar to 1 key for 1
  lock, difficult to open any car in the parking
  lot with your key

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Enzymes

• Enzymes have specific active sites that bind to
  specific substrates.

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Naming enzymes

• Most enzymes end in the suffix, -ase.
• Lactase
• Transferase
• Oxidase
• However, there are exceptions.
• Hemolysin
• Prodgisin

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The Parts of an Enzyme

• The main enzyme portion is a globular protein
  called an APOENZYME
• Many times additional components are required
• COFACTOR
• -
• COENZYME
• -
• -
• For example, nicotinamide (NAD) from niacin and
  flavin adenine dinucleotide (FAD)

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The Parts of an Enzyme
Apoenzyme Cofactor Coenzyme __________
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Competitive Inhibition of Enzymes

• Competitive inhibitors ____________ for binding
  at the active site.

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Noncompetitive Inhibition of Enzymes

• Some inhibitors ______________. Therefore, they
  are called noncompetitive inhibitors because they
  are not competing for the active site.

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What Factors Influence Enzyme Activity?

• 1.
• 2.
• 3.
• 4.

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Energy Production

• What is the cells fuel molecule?
• ATP _________
• When the ___________by breaking the bond, energy
  is released
• When molecules have _________, much energy can be
  ____________. This is one of the reasons that
  lipids have more energy than carbohydrates.
• _______ is unstable and volatile (like gasoline
  or kerosenelight a match and BOOM)
• Quick and convenient energy

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How is energy produced?

• Energy is produced using oxidation-reduction
  reactions
• Oxidation
• The _______
• Reduction
• The __________
• The movement of electrons produces energy in the
  form of _______
• The molecules that move electrons are the
  electron carriers, such as ________

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Energy transfer by carrier molecules

• _____, _______and ________ are all carrier
  molecules that carry electrons and help harness
  energy.

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Carbohydrate metabolism includes

• 1. Glycolysis
• -
• 2. Fermentation
• -
• 3. Anaerobic respiration
• -
• 4. Aerobic respiration
• -

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Glycolysis

• Most organisms contain DNA with instructions for
  the enzymes for glycolysis.
• Glycolysis
• 1
• 2
• Also known as Embden-Meyerhof pathway
• 10 chemical reactions, each with its specific
  enzyme and substrate (Glucose?Glucose 6-phosphate
  requires a specific enzyme)
• 4 important events
• 1
• 2
• 3
• 4

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Metabolic reactions in Glycolysis

• 10 steps make up glycolysis
• Dont worry about memorizing all the steps, you
  need to memorize the starting and end products
  and how much ATP is produced by this pathway (net
  of 2 ATP)

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Overview of Respiration Fermentation

• Notice that both _________ f_________ start out
  by using _________.
• Then, pathways are chosen based on the
  ______________possesses and the environmental
  conditions (oxygen or not)
• 3 Possible Pathways
• 1.
• 2
• 3

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Fermentation

• Many types of fermentation are possible
• Is any energy produced by fermentation?
  _____________________
• Again, the choice of pathways is based on the
  __________________and the ________________they
  are in.
• Shown are 2 different pathways
• A)
• B)

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Types of Fermentation

• Many types of fermentation exist.
• Each microbe has a specific set of ___________
  that __________ ____________ differently and
  therefore different end products are produced.

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Fermentation end-products

• This figure shows that different microbes produce
  different end-products even though they all
  started with pyruvic acid.
• In lab, we look at the end-products of
  fermentation to help us identify bacteria. Some
  produce acid when given lactose, etc.

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Lactic acid fermentation

• Notice that ___________one of its electrons to
  _________thereby reducing it and producing lactic
  acid.

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Aerobic Anaerobic Respiration

• Respiration uses _________, the _________and the
  _____________to produce energy.
• It can occur either _________ (with oxygen) or
  _________________ (without oxygen).
• Aerobic respiration is _____ times more efficient
  than fermentation and anaerobic respiration
• Aerobic respiration produces ______
• Fermentation and anaerobic fermentation produce
  ______

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Overview of Respiration

• Look at the blue circles numbered 1, 2 and 3.
• These are the 3 steps of respiration
• 1.
• 2
• 3

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The doorway into the Krebs cycle

• __________must first be converted to __________
  to enter the ________

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The Krebs cycle

• Aerobic respiration __________of the Krebs
  cycle. Anaerobic does not.
• You do not need to memorize the steps of the
  Krebs cycle, however be familiar with the
  start/end products.
• Also, notice __________is directly produced by
  the Krebs cycle.
• The Krebs cycle primarily produces
  ____________to be fed into the _________.

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Respiration

• Look at the blue circles numbered 1, 2 and 3.
• These are the 3 steps of respiration
• 1.
• 2.
• 3.

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Aerobic Respiration

• Memorize the molecules produced by each stage of
  respiration
• Which stage produces the most ATP?

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• During cellular respiration, most energy flows in
  this sequence
• -
• About ____of the energy in a glucose molecule is
  transferred to ATP during cellular respiration,
  making about _______.

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• During respiration, ________and _______are broken
  down in a series of steps.
• Electrons from organic compounds are usually
  first transferred to _______a coenzyme.
• As an electron acceptor, ______ functions as an
  oxidizing agent during __________.
• Each _______ is reduced to form ______, which
  represent stored energy that is tapped to
  synthesize ____.

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2 e 2 H
2 e H
H
NADH
NAD
Dehydrogenase
2H (from food)
H

Nicotinamide (reduced form)
Nicotinamide (oxidized form)
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The Electron Transport Chain

• Notice where the electron transport chain takes
  place.
• _________

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Bacterial Cell Membrane

• Structure
• Very similar to eukaryotic cells.
• -
• Functions
• -
• Location of the ___and _______ for the
  production of ____.

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• Electron transport begins when electron carriers
  such as __________________release electrons
  (typically in the form of hydrogen atoms) to
  membrane-bound electron carriers.
• _______ are translocated across the cell
  membrane, from the cytoplasm to the
  ___________just outside the membrane.
• As ___________and ___________ into the ETC, the
  ______________, with H building up _________ the
  cell membrane, and OH- __________ the membrane.

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Pathway of Electron Transport

• __________ passes the electrons to the electron
  transport chain.
• Most of the chains components are ________,
  which exist in multiprotein complexes. Theses
  proteins are, in order of electron flow,
  _________, ________, __________, and _________.
• The carriers alternate between ________ and
  ________ states as they accept and donate
  electrons.

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Pathway of Electron Transport

• Electrons drop in free energy as they go down the
  chain and are finally passed to ____, forming
  ________.
• The energy yielded is used to regenerate
  ________.
• Electron transport is ________. For example,
  electron transfer from _________during the
  aerobic respiration electron transport chain
  gives off ______ kcal/mole. Which is really hot
  to do all at once.

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Final Electron Acceptors

• Aerobic respiration, anaerobic respiration, and
  fermentation all use different final electron
  acceptors.
• Where do the electrons come from?
• -

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The Electron Transport Chain (ETC)

• The chains function is to break the
  ________________ into smaller steps that release
  energy in manageable amounts.
• As the electrons are ______________ around by the
  electron carriers, energy is harnessed in the
  form of ________.
• The ETC is similar to a _________ with a lot of
  ________at the top of the waterfall turning into
  ________as the water rushes downward.

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• One of the most important metabolic processes of
  life, _________, involves a ________.
• ___ is actively ________ to one side of a
  ________, building up ________, _______, and
  _________. As the accumulated H move back
  through a membrane transport protein
  (______________), their force is used to
  synthesize __________.

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• The concentration of H in the intermembrane
  space establishes a ________, _____, and
  _____that has an inherent potential energy value.
  There can be as much as a ___________concentration
  on the different sides of the membrane.
• The accumulated H ions, known as the
  ____________, diffuse through the channels of the
  ___________back into the ___________.
• The ___________uses the __________of H ions to
  ________, forming ________ in the _________,
  hence called _________.

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• Chemiosmosis diffuses __________. More
  specifically, the ____________ by the movement of
  H across a membrane.
• ___________is the enzyme that makes _______ by
  ___________. It allows protons to pass through
  the membrane using the kinetic energy to ________
  ____________.

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• Not all of the ATP produced is by Chemiosmosis
  during electron transport phosphorylation.
• ATP is also synthesized by the _________of
  ___________ from a ______________ molecule to
  ADP. This process is called ____________________.
  

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Key Points to Remember

• __________ are first translocated ________ the
  membrane, from the __________ to the __________.
• __________are transported ________ the membrane,
  through a series of _______.
• As ________delivers more ___________into the ETC,
  the __________. Building up ______ outside the
  cell membrane, and _________ inside the membrane.
• ________is ________electron acceptor, combining
  with electrons and H ions to produce ________.

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• H then ___________the membrane, passing through
  channels in __________.
• ___________uses ______________to drive
  phosphorylation of ADP.
• -
• This is __________, the use of energy in a H
  gradient to drive ______________.

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• Electron pass from ________ to ________.
  ____________
• ETC produces _________.
• O2 ________ electrons and becomes ________.
  _________, __________, and _________
• ________makes _____ from ________.

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The Catabolism of Fats

• Fats are catabolized into Fatty acids and
  glycerol.
• Fatty acids then go through beta oxidation and
  enter aerobic respiration at the doorway to
  Krebs cycle
• Glycerol enters aerobic respiration in glycolysis

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The Catabolism of Proteins

• Proteins are catabolized into amino acids,
  deaminated, and then enter the Krebs cycle

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Metabolism of the major classes of biomolecules
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How do we make products like amino acids, ribose
and nucleic acid bases?
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We use metabolism to catabolize nutrients into
simpler molecules energy and then use those to
build our required cell components.
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Favorite metabolism websites

• http//www.sp.uconn.edu/terry/229sp02/lectures/Le
  ct6.html
• These are fairly detailed lecture notes, but
  embedded in them you will find lots of links and
  animations relating to metabolism. Feel free to
  skip the Free energy section discussing G and G0
  section detailing the thermodynamic reactions of
  metabolism.
• http//biology.fullerton.edu/biol302/metab.html
• These are more generalized lecture notes about
  metabolism.
• http//www.cat.cc.md.us/courses/bio141/lecguide/un
  it4/index.htmlenergy
• This site is a set of lecture notes for
  Metabolism, Growth and Genetics. You have to
  link to each subject in the table of contents. A
  nice feature of this site is the short quiz with
  each subject section.