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Protein Structure and Function


Protein Structure and Function – PowerPoint PPT presentation

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Title: Protein Structure and Function

Chapter 4
  • Protein Structureand Function

  • Make up about 15 of the cell
  • Have many functions in the cell
  • Enzymes
  • Structural
  • Transport
  • Motor
  • Storage
  • Signaling
  • Receptors
  • Gene regulation
  • Special functions

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Shape Amino Acid Sequence
  • Proteins are made of 20 amino acids linked by
    peptide bonds making a polypeptide
  • Polypeptide backbone is the repeating sequence of
    the N-C-C-N-C-C following the peptide bond
  • The side chain or R group is not part of the
    backbone or the peptide bond

Polypeptide Backbone
Amino AcidsNOTE You need to know this table
Protein Folding
  • The peptide bond allows for rotation around it
    and therefore the protein can fold and orient the
    R groups in favorable positions
  • Weak non-covalent interactions will hold the
    protein in its functional shape these are weak
    and will take many to hold the shape

Non-covalent Bonds in Proteins
Globular Proteins
  • The side chains will help determine the
    conformation in an aqueous solution

Hydrogen Bonds in Proteins
  • H-bonds form between 1) atoms involved in the
    peptide bond 2) peptide bond atoms and R groups
    3) R groups

Protein Folding
  • Proteins shape is determined by the sequence of
    the amino acids
  • The final shape is called the conformation and
    has the lowest free energy possible
  • Denaturation is the process of unfolding the
  • Can be down with heat, pH or chemical compounds
  • In the chemical compound, can remove and have the
    protein renature or refold

  • Molecular chaperones are small proteins that help
    guide the folding and can help keep the new
    protein from associating with the wrong partner

Prion Proteins
Shape Dictates Function
Protein Folding
  • 2 regular folding patterns have been identified
    formed between the bonds of the peptide backbone
    (N-H and CO)
  • ?-helix protein turns like a spiral fibrous
    proteins (hair, nails, horns)
  • ?-sheet protein folds back on itself as in a
    ribbon globular protein

? Sheets
  • Core of many proteins is the ? sheet
  • Form rigid structures with the H-bond
  • Can be of 2 types
  • Anti-parallel run in an opposite direction of
    its neighbor (A)
  • Parallel run in the same direction with longer
    looping sections between them (B)

? Helix
  • Formed by a H-bond between every 4th peptide bond
    CO to N-H
  • Usually in proteins that span a membrane
  • The ? helix can either coil to the right or the
  • Can also coil around each other coiled-coil
    shape a framework for structural proteins such
    as nails and skin

CD from Text
  • The CD that is included on your textbook back
    cover has some video clips that will show the ?
    helix and ? sheets as well as other things in
    this chapter. You will want to look at them. If
    you have problems, we will look at them during

Levels of Organization
  • Primary structure
  • Amino acid sequence of the protein
  • Secondary structure
  • H bonds in the peptide chain backbone
  • ?-helix and ?-sheets
  • Tertiary structure
  • Non-covalent interactions between the R groups
    within the protein
  • Quanternary structure
  • Interaction between 2 polypeptide chains

  • A domain is a basic structural unit of a protein
    structure distinct from those that make up the
    conformations (100-250 amino acids)
  • Part of protein that can fold into a stable
    structure independently
  • Different domains can impart different functions
    to proteins
  • Proteins can have one to many domains depending
    on protein size

Protein Structure
Useful Proteins
  • There are thousands and thousands of different
    combinations of amino acids that can make up
    proteins and that would increase if each one had
    multiple shapes
  • Proteins usually have only one useful
    conformation because otherwise it would not be
    efficient use of the energy available to the
  • Natural selection has eliminated proteins that do
    not perform a specific function in the cell

Protein Families
  • Have similarities in amino acid sequence and 3-D
  • Have similar functions such as breakdown proteins
    but do it differently

Proteins Multiple Peptides
  • Non-covalent bonds can form interactions between
    individual polypeptide chains
  • Binding site where proteins interact with one
    another non-covalent bonds
  • Subunit each polypeptide chain of large protein
  • Dimer protein made of 2 subunits
  • Can be same subunit or different subunits

Single Subunit Proteins
Different Subunit Proteins
  • Hemoglobin
  • 2 ? globin subunits
  • 2 ? globin subunits

Protein Assemblies
  • Proteins can form very large assemblies
  • Can form long chains if the protein has 2 binding
    sites link together as a helix or a ring
  • Actin fibers in muscles and cytoskeleton is
    made from thousands of actin molecules as a
    helical fiber

Types of Proteins
  • Globular Proteins most of what we have dealt
    with so far
  • Compact shape like a ball with irregular surfaces
  • Enzymes are globular
  • Fibrous Proteins usually span a long distance
    in the cell
  • 3-D structure is usually long and rod shaped

Important Fibrous Proteins
  • Intermediate filaments of the cytoskeleton
  • Structural scaffold inside the cell
  • Keratin in hair, horns and nails
  • Extracellular matrix
  • Bind cells together to make tissues
  • Secreted from cells and assemble in long fibers
  • Collagen fiber with a glycine every third amino
    acid in the protein
  • Elastin unstructured fibers that gives tissue
    an elastic characteristic

Collagen and Elastin
Stabilizing Cross-Links
  • Disulfide bonds (S-S) form between adjacent -SH
    groups on the amino acid cysteine
  • Cross linkages can be between 2 Cys of a single
    protein or between 2 subunits making up the
  • S-S bond is made in the ER as it is necessary for
    extracellular proteins and not for cytosolic

Proteins at Work
  • The conformation of a protein gives it a unique
  • To work proteins must interact with other
    molecules, usually 1 protein with 1 or a few
    molecules from the thousands in cell
  • Ligand the molecule that a protein can bind
  • Binding site part of the protein that interacts
    with the ligand
  • Consists of a cavity formed by a specific
    arrangement of amino acids

Ligand Binding
Formation of Binding Site
  • The binding site forms when amino acids from
    within the protein come together in the folding
  • Amino acids in binding site come from throughout
    the primary structure
  • The remaining sequences may play a role in
    regulating the proteins activity

Antibody Family
  • A family of proteins that can be created to bind
    to almost any molecule
  • Antibodies (immunoglobulins) are made in response
    to a foreign molecule ie. bacteria, virus,
    pollen called the antigen
  • Bind together tightly and therefore inactivates
    the antigen or marks it for destruction

  • Y-shaped molecules with 2 binding sites at the
    upper ends of the Y
  • The loops of polypeptides on the end of the
    binding site are what imparts the recognition of
    the antigen
  • Changes in the sequence of the loops make the
    antibody recognize different antigens -

Enzymes as Catalysts
  • Enzymes are proteins that bind to their ligand as
    the 1st step in a process
  • An enzymes ligand is called a substrate
  • May be 1 or more molecules
  • Output of the reaction is called the product
  • Enzymes can repeat these steps many times and
    rapidly, called catalysts
  • Many different kinds see table 4-1, p 147

Enzymes at Work
  • Lysozyme is an important enzyme that protects us
    from bacteria by making holes in the bacterial
    cell wall and causing it to break
  • Lysozyme adds H2O to the glycosidic bond in the
    cell wall
  • Lysozyme holds the polysaccharide in a position
    that allows the H2O to break the bond this is
    the transition state state between substrate
    and product
  • Active site is a special binding site in enzymes
    where the chemical reaction takes place

  • Non-covalent bonds hold the polysaccharide in the
    active site until the reaction occurs

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Features of Enzyme Catalysis
Proper orientation
Alter e- distribution
Change shape
Prosthetic Groups
  • Occasionally the sequence of the protein is not
    enough for the function of the protein
  • Some proteins require a non-protein molecule to
    enhance the performance of the protein
  • Hemoglobin requires heme (iron containing
    compound) to carry the O2
  • When a prosthetic group is required by an enzyme
    it is called a co-enzyme
  • Usually a metal or vitamin
  • These groups may be covalently or non-covalently
    linked to the protein

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Regulation of Enzymes
  • Regulation of enzymatic pathways prevent the
    deletion of substrate
  • Regulation happens at the level of the enzyme in
    a pathway
  • Feedback inhibition is when the end product
    regulates the enzyme early in the pathway

Feedback Regulation
  • Negative feedback pathway is inhibited by
    accumulation of final product prevents enzyme
    from working
  • Positive feedback a regulatory molecule
    stimulates the activity of the enzyme, usually
    between 2 pathways
  • ? ADP levels cause the activation of the
    glycolysis pathway to make more ATP

  • Conformational coupling of 2 widely separated
    binding sites must be responsible for regulation
    active site recognizes substrate and 2nd site
    recognizes the regulatory molecule
  • Protein regulated this way undergoes allosteric
    transition or a conformational change
  • Protein regulated in this manner is an allosteric

Allosteric Regulation
  • Method of regulation is also used in other
    proteins besides enzymes
  • Receptors, structural and motor proteins

Allosteric Regulation
  • Enzyme is only partially active with sugar only
    but much more active with sugar and ADP present

  • Some proteins are regulated by the addition of a
    PO4 group that allows for the attraction of
    charged side chains causing a conformation change
  • Reversible protein phosphorylations regulate many
    eukaryotic cell functions turning things on and
  • Protein kinases add the PO4 and protein
    phosphatase remove them

  • Kinases capable of putting the PO4 on 3 different
    amino acid residues
  • Have a OH group on R group
  • Serine
  • Threonine
  • Tyrosine
  • Phosphatases that remove the PO4 may be specific
    for 1 or 2 reactions or many be non-specific

GTP-Binding Proteins (GTPases)
  • GTP does not release its PO4 group but rather the
    guanine part binds tightly to the protein and the
    protein is active
  • Hydrolysis of the GTP to GDP (by the protein
    itself) and now the protein is inactive
  • Also a family of proteins usually involved in
    cell signaling switching proteins on and off

Molecular Switches
Motor Proteins
  • Proteins can move in the cell, say up and down a
    DNA strand but with very little uniformity
  • Adding ligands to change the conformation is not
    enough to regulate this process
  • The hydrolysis of ATP can direct the the
    movement as well as make it unidirectional
  • The motor proteins that move things along the
    actin filaments or myosin

Protein Machines
  • Complexes of 10 or more proteins that work
    together such as DNA replication, RNA or protein
    synthesis, trans-membrane signaling etc.
  • Usually driven by ATP or GTP hydrolysis
  • See video clip on CD in book
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