Chapter 1

Proteins

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

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

Polypeptide Backbone

Amino Acids NOTE: You need to know this table

Hydrophilic

Hydrophobic

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 protein

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

Folding@home

The Stanford Folding@home research goal is to understand protein folding, misfolding, and related diseases. Calculations to create models requires a supercomputer OR many smaller computers (distributed computing). You can participate by visiting:

Fold@home web site: http://folding.stanford.edu/ Article on Folding@home: http://www.sciencedaily.com/releases/2002/10/02102 2070813.htm

Refolding

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

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

 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 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

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.

Levels of Organization

Primary structure

Amino acid sequence of the protein H bonds in the peptide chain backbone
-helix

Secondary structure

and -sheets

Tertiary structure

Non-covalent interactions between the R groups within the protein Interaction between 2 polypeptide chains

Quanternary structure

Protein Structure

Domains
A domain 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

Domains

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

Protein Families

Have similarities in amino acid sequence and 3-D structure 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 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

globin subunits 2 globin subunits

2

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

fiber with a glycine every third amino acid in the protein Elastin unstructured fibers that gives tissue an elastic characteristic
Collagen

Collagen and Elastin

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

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

Ligand Binding

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 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

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

Antibodies

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 is reached number sticking is constant and number leaving is constant This can be determined for any protein and its ligand

Equilibrium Constant

Concentration of antigen, antibody and antigen/antibody complex at equilibrium can be measured equilibrium constant (K) Larger the K the tighter the binding or the more non-covalent bonds that hold the 2 together

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 5-2, p 168

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

Lysozyme

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

Features of Enzyme Catalysis

Enzyme Performance

E + S ES EP E + P Step 1 binding of the substrate

Limiting step depending on [S] and/or [E] Vmax maximum rate of the reaction Turnover number determines how fast the substrate can be processed = rate of rxn [E] State of substrate prior to becoming product Enzymes lowers the energy of transition state and therefore accelerates the reaction

Step 2 stabilize the transition state

Reaction Rates

KM [S] that allows rxn to proceed at it maximum rate

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 noncovalently linked to the protein

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 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

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

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

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

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

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, transmembrane signaling etc. Usually driven by ATP or GTP hydrolysis See video clip on CD in book