Protein Structure and Function

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Protein Structure and Function

• Chapter 3

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Protein Structure
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Proteins

• Polymers constructed from amino acid monomers
• Thousands of proteins in the human body
• Unique 3D structure the corresponds to a specific
  function
• Seven major classes of proteins

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Protein Classes

• Structural- hair, fiber in ligaments or tendons
• Contractile- provide muscular movement
• Storage- Ovalbumin, in egg whites
• Defensive- antibodies that fight infection
• Transport- hemoglobin, conveys oxygen
• Signal- coordinate bodily activities
• Enzymes- chemical catalyst

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Amino Acids

• Proteins are made up of multiple variations of 20
  different amino acids
• AAs have an amino group and a carboxyl group
  attached to the central (?) carbon
• ? carbon also is bonded to an H and an R group
• The R group is a chemical group which
  characterizes the amino acid

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R- Groups

• The 20 amino acids differ only in their R-groups
• R-groups differ in their
• Size- can be a few atoms or several atoms
• Shape- can have rings or be straight chain
• Reactivity- can be very reactive or not at all
• interactions with water- hydrophobic or
  hydrophilic

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R-Groups

• Non-polar groups do not interact with water
• Polar groups readily interact with water

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Formation of Proteins

• Proteins are polymers made of monomers
• Polymerization requires energy
• Not spontaneous

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Formation of Proteins

• Polymerize through condensation reactions
• Release a water molecule
• Breakdown of polymers involves hydrolysis
• Uses a water molecule

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Polypeptides

• The bond between the carboxyl group of one amino
  acid to the amino group is called a peptide bond

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Polypeptides

• Polypeptides are flexible and directional
• One end has the N-terminus has a free amino
  group, the C-terminus a free carboxyl group
• Side chains extend out from the backbone

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Protein Shape

• Proteins have four levels of structure primary,
  secondary, tertiary, and quaternary.
• A proteins primary structure is its unique
  sequence of amino acids.
• Even a single amino acid change can radically
  alter protein function
• Changes its reactivity, shape, and interactions
  with water

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Primary Structure
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Secondary Structure

• Hydrogen bonding between the carboxyl oxygen of
  one amino acid and the amino hydrogen of another.
• Causes polypeptide to bend, forms an a-helix or
  b-pleated sheet
• Makes protein more stable

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Tertiary Structure

• A polypeptides three-dimensional shape
• R-groups can interact with other side chains
  causing the polypeptide to bend and fold into a
  precise shape

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Tertiary Structure
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Quaternary Structure

• Some proteins contain several polypeptide
  subunits the bonding of two or more subunits
  produces quaternary structure

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Protein Folding and Function

• Fold as soon as they are made
• Based on hydrogen bonds or van der Waals
  interactions
• Make molecule more stable
• Special proteins called chaperones help protein
  fold correctly

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Protein Function
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Enzymes

• Reaction rates depend on the amount of energy
  required to achieve the transition state
• Activation energy (Ea)
• A catalyst lowers the activation energy of a
  reaction
• Increases the rate of reaction
• Does not get used up in the reaction

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Enzymes

• Enzymes are protein catalysts
• Bring substrates together in specific positions
  that facilitate reactions
• Most biological processes require enzymes
• Most enzymes are specific to which reactions they
  catalyze
• Dependent on their 3D shape

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Enzymes

• Substrates bind at active sites
• Stabilize the transition state and decrease the
  activation energy.
• Induced fit

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Enzyme Action

• 3 Steps
• initiation, reactants are correctly oriented as
  they bind to the active site
• transition state facilitation, interactions
  between the substrate and active site R-groups
  lower the activation energy
• termination, reaction products are released from
  the enzyme

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Enzyme Action
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Regulating Enzymes

• Some enzymes require cofactors to function
  normally (coenzymes)
• Metal ions
• Small organic molecules
• Competitive inhibition- molecule competes with
  the substrate for active site binding
• Allosteric regulation a molecule causes a change
  in enzyme shape by binding to the enzyme at a
  location other than the active site

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Physical Constraints on Enzymes

• Enzymes function best at some particular
  temperature and pH
• Optimal Conditions
• Reflect the environment in which an enzyme
  functions.