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Protein Structure and Function

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Title: Protein Structure and Function


1
Chapter 4
  • Protein Structure and Function

2
Proteins
  • Make up about 15 of the cell
  • Have many functions in the cell
  • Enzymes
  • Structural
  • Transport
  • Motor
  • Storage
  • Signaling
  • Receptors
  • Gene regulation
  • Special functions

3
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4
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

5
Polypeptide Backbone
6
Amino Acids NOTE You need to know this table
Hydrophilic
Hydrophobic
7
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

8
Non-covalent Bonds in Proteins
9
Globular Proteins
  • The side chains will help determine the
    conformation in an aqueous solution

10
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

11
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
    protein
  • Can be down with heat, pH or chemical compounds
  • In the chemical compound, can remove and have the
    protein renature or refold

12
Refolding
  • Molecular chaperones are small proteins that help
    guide the folding and can help keep the new
    protein from associating with the wrong partner

13
Prion Proteins
14
Shape Dictates Function
15
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

16
? 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)

17
? 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
    left
  • Can also coil around each other coiled-coil
    shape a framework for structural proteins such
    as nails and skin

18
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
    lab.

19
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

20
Domains
  • 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

21
Protein Structure
22
Domains
23
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
    system
  • Natural selection has eliminated proteins that do
    not perform a specific function in the cell

24
Protein Families
  • Have similarities in amino acid sequence and 3-D
    structure
  • Have similar functions such as breakdown proteins
    but do it differently

25
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

26
Single Subunit Proteins
27
Different Subunit Proteins
  • Hemoglobin
  • 2 ? globin subunits
  • 2 ? globin subunits

28
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

29
Shapes
30
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

31
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

32
Collagen and Elastin
33
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
    protein
  • S-S bond is made in the ER as it is necessary for
    extracellular proteins and not for cytosolic
    proteins

34
Proteins at Work
  • The conformation of a protein gives it a unique
    function
  • 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

35
Ligand Binding
36
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

37
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

38
Antibodies
  • 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 -
    specificity

39
Antibodies
40
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

41
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

42
Lysozyme
  • Non-covalent bonds hold the polysaccharide in the
    active site until the reaction occurs

43
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44
Features of Enzyme Catalysis
Proper orientation
Alter e- distribution
Change shape
45
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

46
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47
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

48
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

49
Allostery
  • 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
    protein

50
Allosteric Regulation
  • Method of regulation is also used in other
    proteins besides enzymes
  • Receptors, structural and motor proteins

51
Allosteric Regulation
  • Enzyme is only partially active with sugar only
    but much more active with sugar and ADP present

52
Phosphorylation
  • 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
    off
  • Protein kinases add the PO4 and protein
    phosphatase remove them

53
Phosphorylation/Dephosphorylation
  • 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

54
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

55
Molecular Switches
56
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

57
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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