protein structure and function. proteins have many functions in the cell – enzymes – structural...
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Protein Structure and Function
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Proteins
• 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
• Polypeptide backbone is the repeating sequence of the N-C-C-N-C-C… in the peptide bond
• The side chain or R group is not part of the backbone or the peptide bond
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Polypeptide Backbone
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Figure 3-2 Molecular Biology of the Cell (© Garland Science 2008)
Amino Acids
Hydrophilic Hydrophobic
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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
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Figure 3-4 Molecular Biology of the Cell (© Garland Science 2008)
Non-covalent Bonds in Proteins
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Figure 3-5 Molecular Biology of the Cell (© Garland Science 2008)
Globular Proteins
• The side chains will help determine the conformation in an aqueous solution
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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
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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
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Figure 3-6a Molecular Biology of the Cell (© Garland Science 2008)
Refolding
• Molecular chaperones are small proteins that help guide the folding and can help keep the new protein from associating with the wrong partner
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Protein Folding
• 2 regular folding patterns have been identified – formed between the bonds of the peptide backbone
• -helix – protein turns like a spiral – fibrous proteins (hair, nails, horns)
• -sheet – protein folds back on itself as in a ribbon –globular protein
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Figure 3-7a,b,c Molecular Biology of the Cell (© Garland Science 2008)
-helix
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Figure 3-7d,e,f Molecular Biology of the Cell (© Garland Science 2008)
-sheet
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Figure 3-8 Molecular Biology of the Cell (© Garland Science 2008)
• 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)
Sheets
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Figure 3-9 Molecular Biology of the Cell (© Garland Science 2008)
• Formed by a H-bond between every 4th peptide bond – C=O 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
Helix
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Levels of Organization
• PrimaryPrimary structure– Amino acid sequence of the protein
• SecondarySecondary structure– H bonds in the peptide chain backbone
• -helix and -sheets
• TertiaryTertiary structure– Non-covalent interactions between the R groups
within the protein• QuanternaryQuanternary structure
– Interaction between 2 polypeptide chains
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Protein Structure
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Domains
• A domaindomain is a basic structural unit of a protein structure – distinct from those that make up the conformations
• 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
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Domains
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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
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Figure 3-12 Molecular Biology of the Cell (© Garland Science 2008)
Protein Families
• Have similarities in amino acid sequence and 3-D structure• Have similar functions such as breakdown proteins but do it
differently
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Proteins – Multiple Peptides
• Non-covalent bonds can form interactions between individual polypeptide chains– Binding site – where proteins interact with one
another– Subunit – each polypeptide chain of large protein– Dimer – protein made of 2 subunits
• Can be same subunit or different subunits
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Single Subunit Proteins
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Different Subunit Proteins
• Hemoglobin–2 globin
subunits–2 globin
subunits
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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
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Types of Proteins
• Globular ProteinsGlobular Proteins – most of what we have dealt with so far– Compact shape like a ball with irregular
surfaces– Enzymes are globular
• Fibrous ProteinsFibrous Proteins – usually span a long distance in the cell– 3-D structure is usually long and rod shaped
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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
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Collagen and Elastin
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Stabilizing Cross-Links
• Cross linkages can be between 2 parts of a protein or between 2 subunits
• Disulfide bonds (S-S) form between adjacent -SH groups on the amino acid cysteine
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Proteins at Work
• The conformation of a protein gives it a unique function
• To work proteins must interact with other molecules, usually 1 or a few molecules from the thousands to 1 protein
• 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
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Figure 3-36 Molecular Biology of the Cell (© Garland Science 2008)
Ligand Binding
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Formation of Binding Site
• The binding site forms when amino acids from within the protein come together in the folding
• The remaining sequences may play a role in regulating the protein’s activity
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Antibody Family
• A family of proteins that can be created to bind to almost any molecule
• AntibodiesAntibodies (immunoglobulins) are made in response to a foreign molecule ie. bacteria, virus, pollen… called the antigenantigen
• Bind together tightly and therefore inactivates the antigen or marks it for destruction
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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
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Figure 3-41 Molecular Biology of the Cell (© Garland Science 2008)
Antibodies
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Binding Strength• Can be measured directly• Antibodies and antigens are mixing around in a
solution, eventually they will bump into each other in a way that the antigen sticks to the antibody, eventually they will separate due to the motion in the molecules
• This process continues until the equilibrium equilibrium is reached – number sticking is constant and number leaving is constant
• This can be determined for any protein and its ligandligand
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Enzymes as Catalysts
• Enzymes are proteins that bind to their ligand as the 1st step in a process
• An enzyme’s ligand is called a substratesubstrate– 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 5-2, p 168
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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 statetransition state – state between substrate and product
• Active siteActive site is a special binding site in enzymes where the chemical reaction takes place
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Figure 3-50a Molecular Biology of the Cell (© Garland Science 2008)
Lysozyme
• Non-covalent bonds hold the polysaccharide in the active site until the reaction occurs
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Figure 3-52 Molecular Biology of the Cell (© Garland Science 2008)
Features of Enzyme Catalysis
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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 groupprosthetic group is required by an enzyme it is called a co-enzymeco-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
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Feedback Regulation
• Negative feedbackNegative feedback – pathway is inhibited by accumulation of final product
• Positive feedbackPositive 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
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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
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Allosteric Regulation
• Method of regulation is also used in other proteins besides enzymes– Receptors, structural and motor proteins
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Allosteric Regulation
• Enzyme is only partially active with sugar only but much more active with sugar and ADP present
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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 kinaseskinases add the PO4 and protein phosphatasephosphatase remove them
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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
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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
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Figure 3-71 Molecular Biology of the Cell (© Garland Science 2008)
Molecular Switches
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Figure 3-75 Molecular Biology of the Cell (© Garland Science 2008)
Molecular Switches
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Figure 3-76 Molecular Biology of the Cell (© Garland Science 2008)
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
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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
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