Chapter 3. Proteins

Secondary structure of protein

Stretches of polypeptide chain that form α helices and β sheets. Refers to the way in which the chain of amino acids is folded within a polypeptide due to interactions between atoms of the backbone. - The backbone just refers to the polypeptide chain an not the the R groups - This means that secondary structure does not involve R group atoms. Two main types of secondary structures are the: α-helix and the β-sheets Both structures are held in shape by hydrogen bonds, which form between the carbonyl O of one amino acid and the amino H of another.

Ras protein

The Ras protein has an important role in cell signaling In its GTP-bound form, it is active and stimulates a cascade of protein phosphorylations in the cell. Most of the time, however, the protein is in its inactive, GDP-bound form. It becomes active when it exchanges its GDP for a GTP molecule in response to extracellular signals, such as growth factors, that bind to receptors in the plasma membrane

Src protein Contd.

The Src protein (pronounced "sarc" and named for the type of tumor, a sarcoma, that its deregulation can cause) was the first tyrosine kinase to be discovered. These kinases normally exist in an inactive conformation, in which a phosphorylated tyrosine near the C-terminus is bound to the SH2 domain, and the SH3 domain is bound to an internal peptide in a way that distorts the active site of the enzyme and helps to render it inactive. Turning the kinase on involves at least two specific inputs: removal of the C-terminal phosphate and the binding of the SH3 domain by a specific activating protein.

Polypeptide Backbone

Repeating sequence of atoms (-N-C-C-) that forms the core of a protein molecule (aka polypeptide chain) and to which the amino acid side chains are attached.

Protein Assemblies Diagram

(A) Protein subunit: Non-covalent bonds allow proteins to interact with other proteins at a specific binding site. (B) Protein dimer: Identical polypeptide chains bind "head to head" (C) Identical proteins (dimers) with two different binding sites often form long helical filaments or closed rings Ex: Actin fibers in muscle is made from thousands of actin protein molecules assembled together as a long helix

The Shape and Structure of Proteins Highlights

*The Shape of a Protein Is Specified by Its Amino Acid Sequence *Proteins Fold into a Conformation of Lowest Energy *The α Helix and the β Sheet Are Common Folding Patterns *Protein Domains Are Modular Units from Which Larger Proteins Are Built *Larger Protein Molecules Often Contain More Than One Polypeptide Chain *Some Globular Proteins Form Long Helical Filaments *Many Protein Molecules Have Elongated, Fibrous Shapes *Proteins Contain a Surprisingly Large Amount of Intrinsically Disordered Polypeptide Chain *Covalent Cross-Linkages Stabilize Extracellular Proteins *Protein Molecules Often Serve as Subunits for the Assembly of Large Structures *Many Structures in Cells Are Capable of Self-Assembly *Assembly Factors Often Aid the Formation of Complex Biological Structures

Protein Function Highlights

*All Proteins Bind to Other Molecules *The Surface Conformation of a Protein Determines Its Chemistry *Sequence Comparisons Between Protein Family Members Highlight Crucial Ligand-Binding Sites *Proteins Bind to Other Proteins Through Several Types of Interfaces *Antibody Binding Sites Are Especially Versatile *The Equilibrium Constant Measures Binding Strength *Enzymes Are Powerful and Highly Specific Catalysts *Substrate Binding Is the First Step in Enzyme Catalysis *Enzymes Speed Reactions by Selectively Stabilizing Transition States *Enzymes Can Use Simultaneous Acid and Base Catalysis *Lysozyme Illustrates How an Enzyme Works *Tightly Bound Small Molecules Add Extra Functions to Proteins *Multienzyme Complexes Help to Increase the Rate of Cell Metabolism *The Cell Regulates the Catalytic Activities of Its Enzymes *Allosteric Enzymes Have Two or More Binding Sites That Interact *Two Ligands Whose Binding Sites Are Coupled Must Reciprocally Affect Each Other's Binding *Symmetric Protein Assemblies Produce Cooperative Allosteric Transitions *Many Changes in Proteins Are Driven by Protein Phosphorylation *A Eukaryotic Cell Contains a Large Collection of Protein Kinases and Protein Phosphatases *The Regulation of the Src Protein Kinase Reveals How a Protein Can Function as a Microprocessor *Proteins That Bind and Hydrolyze GTP Are Ubiquitous Cell Regulators *Regulatory Proteins GAP and GEF Control the Activity of GTP-Binding Proteins by Determining Whether GTP or GDP Is Bound *Proteins Can Be Regulated by the Covalent Addition of Other Proteins *An Elaborate Ubiquitin-Conjugating System Is Used to Mark Proteins *Protein Complexes with Interchangeable Parts Make Efficient Use of Genetic Information *A GTP-Binding Protein Shows How Large Protein Movements Can Be Generated *Motor Proteins Produce Large Movements in Cells *Membrane-Bound Transporters Harness Energy to Pump Molecules Through Membranes *Proteins Often Form Large Complexes That Function as Protein Machines *Scaffolds Concentrate Sets of Interacting Proteins *Many Proteins Are Controlled by Covalent Modifications That Direct Them to Specific Sites Inside the Cell *A Complex Network of Protein Interactions Underlies Cell Function

Coenzyme

A small molecule or metal atom tightly associated with an enzyme's active site that assists with their catalytic function. Many coenzymes are either vitamins or derivatives of vitamins, because they cannot be synthesized by humans, and must therefore be supplied in small quantities in our diet

Disulfide Bonds

Extracellular Proteins are often stabilized by Covalent Cross-Linkages Covalent disulfide bonds form between adjacent cysteine side chains. These cross-linkages can join either two parts of the same polypeptide chain or two different polypeptide chains. Since the energy required to break one covalent bond is much larger than the energy required to break even a whole set of noncovalent bonds, a disulfide bond can have a major stabilizing effect on a protein

Fibrous Proteins

Fibrous proteins exist because there are functions that require each individual protein molecule to span a large distance. These proteins generally have a relatively simple, elongated three-dimensional structure Ex: - Alpha-keratin: dimer of two identical subunits with long alpha helices that form a coiled-coil - Actin filaments of cytoskeleton cell are made up of fibrous proteins molecules

An Ex. of Assembly Factors Proteolytic cleavage in insulin assembly

Not all cellular structures held together by noncovalent bonds self-assemble In these cases, part of the assembly information is provided by special enzymes and other proteins that perform the function of templates, serving as assembly factors that guide construction but take no part in the final assembled structure. Ex: The polypeptide hormone insulin cannot spontaneously re-form efficiently if its disulfide bonds are disrupted. It is synthesized as a larger protein (proinsulin) that is cleaved by a proteolytic enzyme after the protein chain has folded into a specific shape. Extraction of part of the proinsulin polypeptide chain removes some of the information needed for the protein to fold spontaneously into its normal conformation. Once insulin has been denatured and its two polypeptide chains have separated, its ability to reassemble is lost.

Types of Regulatory Feedback

Positive Feedback: stimulates enzyme activity. It occurs when a product in one branch of the metabolic network stimulates the activity of an enzyme in another pathway. Ex: The accumulation of ADP activates several enzymes involved in the oxidation of sugar molecules, thereby stimulating the cell to convert more ADP to ATP. Negative Feedback: prevents enzyme activity and thereby controls its own level in the cell; typically occurs within the same pathway

Many Changes in Proteins Are Driven by Protein Phosphorylation

Proteins are regulated by more than the reversible binding of other molecules which affects protein conformation (Allostery). A second method that eukaryotic cells use extensively to regulate a protein's function is the covalent addition of a phosphate group to one or more of its amino acid side chains.

Protein structure

To understand how a protein gets its final shape or conformation, we need to understand the four levels of protein structure: 1. primary - The amino acid sequence 2. secondary - Stretches of polypeptide chain that form α helices and β sheets 3. tertiary - The full three-dimensional organization of a polypeptide chain 4. quaternary - The complete protein structure Protein structure is the 3-D arrangement of atoms in an amino acid-chain molecule.

Mechanisms of Protein Regulation by Enzymes

• A living cell contains thousands of enzymes, many of which operate at the same time and in the same small volume of the cytosol. • By their catalytic action, these enzymes generate a complex web of metabolic pathways, each composed of chains of chemical reactions in which the product of one enzyme becomes the substrate of the next. • The system is complex and elaborate controls are required to regulate when and how rapidly each reaction occurs Enzyme activity is regulated by 4 mechanisms: 1. Controlling the level of gene expression of the enzyme 2. Confining enzymes to specific subcellular compartments 3. Covalent modification of the protein 4. Regulation by a molecule other than the substrate • 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

Protein Kinases and Protein Phosphatases

(A) The general protein phosphorylation reaction transfers a phosphate group from ATP to an amino acid side chain of the target protein which is catalyzed by a protein kinase. - Removal of the phosphate group is catalyzed by a second enzyme, a protein phosphatase. - In this ex. the phosphate is added to a serine side chain; in other cases, the phosphate is instead linked to the -OH group of a threonine or a tyrosine in the protein.

Protein Domain

A unit of organization distinct from the four level of protein structure mentioned above. Protein domain is a segment/substructure produced by any contiguous part of a polypeptide chain that can fold independently of the rest of the protein into a compact, stable structure. The different domains of a protein are often associated with different functions. A domain usually contains between 40 and 350 amino acids, and it is the module unit from which many larger proteins are constructed. The smallest protein molecules contain only a single domain, whereas larger proteins can contain several dozen domains. As this image illustrates, the central core of a domain can be constructed from α helices, from β sheets, or from various combinations of these two fundamental folding elements.

Protein Function Summary

- Proteins can form enormously sophisticated chemical devices, whose functions largely depend on the detailed chemical properties of their surfaces. - Binding sites for ligands are formed as surface cavities in which precisely positioned amino acid side chains are brought together by protein folding. In this way, normally unreactive amino acid side chains can be activated to make and break covalent bonds. - Enzymes are catalytic proteins that greatly speed up reaction rates by binding the high-energy transition states for a specific reaction path; they also can perform acid catalysis and base catalysis simultaneously. - The rates of enzyme reactions are often so fast that they are limited only by diffusion. Rates can be further increased only if enzymes that act sequentially on a substrate are joined into a single multienzyme complex, or if the enzymes and their substrates are attached to protein scaffolds, or otherwise confined to the same part of the cell. - Proteins reversibly change their shape when ligands bind to their surface. - The allosteric changes in protein conformation produced by one ligand affect the binding of a second ligand, and this linkage between two ligand-binding sites provides a crucial mechanism for regulating cell processes. - Metabolic pathways, for example, are controlled by feedback regulation: some small molecules inhibit and other small molecules activate enzymes early in a pathway. - Enzymes controlled in this way generally form symmetric assemblies, allowing cooperative conformational changes to create a steep response to changes in the concentrations of the ligandsthat regulate them. - The expenditure of chemical energy can drive unidirectional changes in protein shape. - By coupling allosteric shape changes to ATP hydrolysis, for example, proteins can do useful work, such as generating a mechanical force or moving for long distances in a single direction. - The three-dimensional structures of proteins have revealed how a small local change caused by nucleoside triphosphate hydrolysis is amplified to create major changes elsewhere in the protein. - By such means, these proteins can serve as input-output devices that transmit information, as assembly factors, as motors, or as membrane-bound pumps. - Highly efficient protein machines are formed by incorporating many different protein molecules into larger assemblies that coordinate the allosteric movements of the individual components. Such machines perform most of the important reactions in cells. - Proteins are subjected to many reversible, post-translational modifications, such as the covalent addition of a phosphate or an acetyl group to a specific amino acid side chain. - The addition of these modifying groups is used to regulate the activity of a protein, changing its conformation, its binding to other proteins, and its location inside the cell. - A typical protein in a cell will interact with more than five different partners. - Through proteomics, biologists can analyze thousands of proteins in one set of experiments. One important result is the production of detailed protein interaction maps, which aim at describing all of the binding interactions between the thousands of distinct proteins in a cell. - However, understanding these networks will require new biochemistry, through which small sets of interacting proteins can be purified and their chemistry dissected in detail. - In addition, new computational techniques will be required to deal with the enormous complexity.

Ligand

A molecule that binds specifically to a binding site of another molecule. It is the he substance that is bound by the protein. whether it is an ion, a small molecule, or a macromolecule of another protein—is referred to as a ligand for that protein

The components of a protein

A protein consists of a polypeptide backbone with attached side chains. Each type of protein differs in its sequence and number of amino acids; therefore, it is the sequence of the chemically different side chains that makes each protein distinct. The two ends of a polypeptide chain are chemically different: - The end carrying the free amino group (NH3 +, also written NH2) is the amino terminus, or N-terminus. - The end carrying the free carboxyl group (COO-, also written COOH) is the carboxyl terminus or C-terminus. The amino acid sequence of a protein is always presented in the N-to-C direction, reading from left to right.

The Shape and Structure of Proteins Summary

A protein molecule's amino acid sequence determines its three-dimensional conformation. Noncovalent interactions between different parts of the polypeptide chain stabilize its folded structure. The amino acids with hydrophobic side chains tend to cluster in the interior of the molecule, and local hydrogen-bond interactions between neighboring peptide bonds give rise to α helices and β sheets. Regions of amino acid sequence known as domains are the modular units from which many proteins are constructed. - Such domains generally contain 40-350 amino acids, often folded into a globular shape. Small proteins typically consist of only a single domain, while large proteins are formed from multiple domains linked together by various lengths of polypeptide chain, some of which can be relatively disordered. As proteins have evolved, domains have been modified and combined with other domains to construct large numbers of new proteins. Proteins are brought together into larger structures by the same noncovalent forces that determine protein folding. Proteins with binding sites for their own surface can assemble into dimers, closed rings, spherical shells, or helical polymers. The amyloid fibril is a long unbranched structure assembled through a repeating aggregate of β sheets. Although some mixtures of proteins and nucleic acids can assemble spontaneously into complex structures in a test tube, not all structures in the cell are capable of spontaneous reassembly after they have been dissociated into their component parts, because many biological assembly processes involve assembly factors that are not present in the final structure.

Protein

An organic compound that is made of one or more chains of amino acids and that is a principal component of all cells - Protein molecule is made from a long unbranched chain of these amino acids, each linked to its neighbor through a covalent peptide bond. - Proteins are therefore also known as polypeptides. - Each type of protein has a unique sequence of amino acids, and there are many thousands of different proteins in a cell.

Three ways in which two proteins can bind to each other

A. Surface-string: Rigid surface of one protein makes contact with the extended loop on a second protein. Ex: phosphorylation of SH2 domains B. Helix-Helix: Two alpha helices pair together in a coiled-coil = Regulatory proteins C. Surface-Surface: specific matching of two rigid surfaces = large numbers of weak bonds

α helix

Alpha (α) is one of two forms, of the secondary structure of proteins, arising from a specific pattern of hydrogen bonding between atoms of the polypeptide backbone (not the side chains/R group). An Alpha (α) helix is generated when a single polypeptide chain twists around on itself to form a rigid cylinder In an α helix, the carbonyl (C=O) of one amino acid is hydrogen bonded to the amino H (N-H) of an amino acid that is four down the chain. (E.g., the carbonyl of amino acid 1 would form a hydrogen bond to the N-H of amino acid 5.) - This pattern of bonding pulls the polypeptide chain into a helical structure that resembles a curled ribbon - The R groups of the amino acids stick outward from the α helix, where they are free to interact • Helices with large number of non-polar side chains on a side • Keep hydrophobic side chains (R-groups) away from hydrophilic surfaces

Peptide Bond

Amino acids are commonly joined together by an amide linkage, called a peptide bond.

The Role of Antibodies

Antibodies, or immunoglobulins, are proteins produced by the immune system in response to foreign molecules, such as those on the surface of an invading microorganism. Each antibody binds tightly to a particular target molecule, thereby either inactivating the target molecule directly or marking it for destruction. An antibody recognizes its target (called an antigen) with remarkable specificity. The antibody family is notable for its capacity for tight, highly selective binding

Binding Site

Any region of a protein's surface that can interact with another molecule through sets of noncovalent bonds A protein can contain binding sites for various large and small molecules. If a binding site recognizes the surface of a second protein, the tight binding of two folded polypeptide chains at this site creates a larger protein molecule with a precisely defined geometry. Each polypeptide chain in such a protein is called a protein subunit.

The binding site of a protein

Binding site forms when the folding of the polypeptide chain (protein molecule) creates a cavity on the protein surface. This cavity contains a set of amino acid side chains disposed in such a way that they can form noncovalent bonds only with certain ligands. • Exclude water to strengthen interaction = tighter hydrogen bonding in a hydrophobic environment • Charged amino acid side chains increase the attraction of ions

The 20 amino acids commonly found in proteins

Each amino acid has a three-letter and a one letter abbreviation. There are equal numbers of polar and nonpolar side chains

Cyclin-dependent Kinase Subfamily (cell-cycle control)

Cdk's include serine/threonine kinases • Required for normal cell-cycle control in eucaryotes; turn on or off in order as a cell proceeds through the cell cycle • Require 3 regulatory inputs

Regulation by the Covalent Addition of Other Proteins

Cells contain a special family of small proteins whose members are covalently attached to many other proteins to determine the activity or fate of the second protein. The first such protein discovered, and the most abundantly used, is ubiquitin. Ubiquity can be covalently attached to target proteins in a variety of ways, each of which has a different meaning for cells. Ex of ubiquitin Ligases: - The SCF ubiquitin ligase

Regulation by Phosphorylation of GTP-binding proteins

GTP-binding proteins are another way how eukaryotic cells can control protein activity by phosphate addition and removal (phosphorylation/dephosphorylation). In general, proteins regulated in this way are in their active conformations with GTP bound. The loss of a phosphate group occurs when the bound GTP is hydrolyzed to GDP in a reaction catalyzed by the protein itself, and in its GDP-bound state the protein is inactive. In this way, GTP-binding proteins act as on-off switches whose activity is determined by the presence or absence of an additional phosphate on a bound GDP molecule GTP-binding proteins (also called GTPases because of the GTP hydrolysis they catalyze). When a tightly bound GTP is hydrolyzed by the GTP-binding protein to GDP, this domain undergoes a conformational change that inactivates the protein.

The selective binding of a protein to another molecule

Many weak bonds are needed to enable a protein to bind tightly to a second molecule, or ligand. A ligand must therefore fit precisely into a protein's binding site, like a hand into a glove, so that a large number of noncovalent bonds form between the protein and the ligand.

PROTEIN FUNCTION

In this section, we explain how proteins bind to other selected molecules and how a protein's activity depends on such binding. We show that the ability to bind to other molecules enables proteins to act as catalysts, signal receptors, switches, motors, or tiny pumps. We have seen that each type of protein consists of a precise sequence of amino acids that allows it to fold up into a particular three-dimensional shape, or conformation. But proteins are not rigid lumps of material. They often have precisely engineered moving parts whose mechanical actions are coupled to chemical events. - It is this coupling of chemistry and movement that gives proteins the extraordinary capabilities that underlie the dynamic processes in living cells.

Protein Subunit

Is a single protein molecule that assembles with other protein molecules to form a protein complex. Most functional proteins are composed of two or more polypeptides chains (2 protein subunits bonded together)

Allostery

Is change in protein conformation from the binding of a regulatory ligand or by covalent modification which alters protein activity • Allosteric proteins have two sites: - Active Site: Recognizes the substrate - Regulatory Site: Recognizes the regulatory molecule ------------------ • The interaction between separated sites on a protein molecule is now known to depend on a conformational change in the protein: - binding at one of the sites causes a shift from one folded shape to a slightly different folded shape. • It is thought that most protein molecules are allosteric. • This is true not only for enzymes but also for many other proteins, including receptors, structural proteins, and motor proteins. • In all instances of allosteric regulation, each conformation of the protein has somewhat different surface contours, and the protein's binding sites for ligands are altered when the protein changes shape. • Allosteric proteins serve as general switches that, in principle, can allow one molecule in a cell to affect the fate of any other.

Ubiquitylation

Is the process of attaching ubiquitin, a small protein found in almost all tissues of eukaryotic organisms, to another targeted protein.

Side Chains ( aka R groups)

Portion of an amino acid not involved in forming peptide bonds - Its chemical identity gives each amino acid its unique properties. - There are 20 different amino acid side chains

Enzymes

Proteins that catalyze chemical reactions They are remarkable molecules that cause the chemical transformations that make and break covalent bonds in cells. They bind to one or more ligands, called substrates, and convert them into one or more chemically modified products, doing this over and over again with amazing rapidity. Enzymes speed up reactions, often by a factor of a million or more, without themselves being changed—that is, they act as catalysts that permit cells to make or break covalent bonds in a controlled way. It is the catalysis of organized sets of chemical reactions by enzymes that creates and maintains the cell, making life possible. Enzyme names typically end in "-ase," with the exception of some enzymes, such as pepsin, trypsin, thrombin, & lysozyme. The common name of an enzyme usually indicates the substrate or product and the nature of the reaction catalyzed. Ex: citrate synthase catalyzes the synthesis of citrate by a reaction between acetyl CoA & oxaloacetate.

The general formula of an amino acid

R is commonly one of 20 different side chains. At pH 7 both the amino and carboxyl groups are ionized.

Quaternary structure of proteins

Refer to the three-dimensional structure consisting of the linkage of two or more individual polypeptide chains (subunits) that operate as a single functional unit (multimer). - The resulting multimer is stabilized by the same non-covalent interactions and disulfide bonds as in tertiary structure. Many proteins are made up of a single polypeptide chain and have only three levels of structure (the ones above). However, some proteins are made up of multiple polypeptide chains, and when these come together (subunits+subunits=multimer), they give the protein its quaternary structure.

Primary structure of protein

Refers to the sequence of amino acids in the polypeptide chain. The primary structure is held together by peptide bonds The two ends of the polypeptide chain are referred to as the: - carboxyl terminus (C-terminus) and the - amino terminus (N-terminus) The primary structure of a protein is determined by the gene corresponding to the protein. A specific sequence of nucleotides in DNA is transcribed into mRNA, which is read by the ribosome in a process called translation.

SCF ubiquitin ligase

SCF ubiquitin ligase is a protein complex that binds different "target proteins" at different times in the cell cycle, covalently adding polyubiquitin polypeptide chains to these targets. - Its C-shaped structure is formed from five protein subunits, the largest of which serves as a scaffold on which the rest of the complex is built.

A protein formed from multiple domains

The Src protein kinase, which functions in signaling pathways inside vertebrate cells (Src is pronounced "sarc"). This proteinis considered to have three domains: the SH2 and SH3 domains have regulatory roles, while the C-terminal domain is responsible for the kinase catalytic activity.

Protein Specificity

The conformation of a protein gives it a unique function A protein molecule's physical interaction with other molecules determines its biological properties. All proteins stick, or bind, to other molecules. In some cases, this binding is very tight; in others it is weak and short-lived. But the binding always shows great specificity: each protein molecule can usually bind just one or a few molecules out of the many thousands of different types it encounters. Protein specificity depends on binding site affinity to the ligand.

Three types of noncovalent bonds help proteins fold

The folding of a protein chain is also determined by many different sets of weak noncovalent bonds that form between one part of the chain and another. These involve atoms in the polypeptide backbone, as well as atoms in the amino acid side chains. There are three types of these weak bonds: 1. Hydrogen bonds 2. Ionic (electrostatic) attractions 3. Van der Waals attractions

The Regulation of the Src Protein Kinase Reveals How a Protein Can Function as a Microprocessor

The hundreds of different protein kinases in a eukaryotic cell are organized into complex networks of signaling pathways that help to coordinate the cell's activities, drive the cell cycle, and relay signals into the cell from the cell's environment. Many of the extracellular signals involved need to be both integrated and amplified by the cell. Individual protein kinases (and other signaling proteins) serve as input-output devices, or "microprocessors," in the integration process of such extracellular signals. An important part of the input to these signal-processing proteins comes from the control that is exerted by phosphates added and removed from them by protein kinases and protein phosphatases, respectively. The Src family of protein kinases exhibits such behavior.

Tertiary structure of protein

The overall 3-D structure of a polypeptide. This protein structure is formed when the twists and folds of the secondary structure fold again to from a larger 3-D structure The tertiary structure is primarily due to interactions between the R groups of the amino acids that make up the protein. R group interactions that contribute to tertiary structure include hydrogen bonding, ionic bonding, dipole-dipole interactions, and London dispersion forces (basically, the whole gamut of non-covalent bonds) * Hydrophobic interactions are also important to tertiary structure. - In hydrophobic interactions, the amino acids with nonpolar, hydrophobic R groups cluster together on the inside of the protein, leaving hydrophilic amino acids on the outside to interact with surrounding water molecules. *There's one special type of covalent bond that can contribute to tertiary structure: the disulfide bond. - Disulfide bonds are covalent linkages between the sulfur-containing side chains of cysteines, which are much stronger than the other types of bonds that contribute to tertiary structure.

Some Known Modifications of Protein p53

The pattern of some covalent modifications to the protein p53.

Turning Off or On Different Enzymes

The phosphorylation of a protein by a protein kinase can either increase or decrease the protein's activity, depending on the site of phosphorylation and thestructure of the protein. The energy required to drive this phosphorylation cycle is derived from the free energy of ATP hydrolysis, one molecule of which is consumed for each phosphorylation event

How a protein folds into a compact conformation

The polar amino acid side chains tend to lie on the outside of the protein, where they can interact with water. The nonpolar (hydrophobic) amino acid side chains are buried on the inside forming a tightly packed hydrophobic core of atoms that are hidden from water. In this schematic drawing, the protein contains only about 35 amino acids.

An evolutionary tree of protein kinases

The protein kinases that phosphorylate proteins in eukaryotic cells belong to a very large family of enzymes that share a catalytic (kinase) sequence of about 290 amino acids. By comparing the number of amino acid sequence differences between the various members of a protein family, we can construct an "evolutionary tree" which reflects the pattern of gene duplication and divergence that gave rise to the family. In the tree of protein kinases, kinases with related functions are often located on nearby branches of the tree A higher eukaryotic cell contains hundreds of such enzymes, and the human genome codes for more than 500.

Catalysis by the Lysosomes Enzyme

The reaction that lysozyme catalyzes is a hydrolysis: it adds a molecule of water to a single bond between two adjacent sugar groups in the polysaccharide chain, thereby causing the bond to break Lysosomes catalyzes the cutting of polysaccharide chains in the cell walls of bacteria. The bacterial cell is under pressure from osmotic forces, and cutting even a small number of these chains causes the cell wall to rupture and the cell to burst.

Feedback inhibition of a single biosynthetic pathway.

This is an example of negative regulation. The end product Z inhibits the first enzyme that is unique to its synthesis and thereby controls its own level in the cell. A product produced late in a reaction pathway inhibits an enzyme that acts earlier in the pathway. Thus, whenever large quantities of the final product begin to accumulate, this product binds to the enzyme and slows down its catalytic action, thereby limiting the further entry of substrates into that reaction pathway

Protein Dimer

Two Identical protein molecules (polypeptides) that bind "head to head" make a protein dimer

Common Types of Enzymes

We can group enzymes into functional classes that perform similar chemical reactions Each type of enzyme within such a class is highly specific, catalyzing only a single type of reaction. Enzymes work in teams, with the product of one enzyme becoming the substrate for the next. The result is an elaborate network of metabolic pathways that provides the cell with energy and generates the many large and small molecules that the cell needs.

Many Proteins Are Controlled by Covalent Modifications That Direct Them to Specific Sites Inside the Cell

We have thus far described only a few ways in which proteins are post-translationally modified. A large number of other such modifications also occur, more than 200 distinct types being known. This table represents a few of the modifying groups with known regulatory roles.

THE SHAPE AND STRUCTURE OF PROTEINS

When we look at a cell through a microscope or analyze its electrical or biochemical activity, we are, in essence, observing proteins. Proteins constitute most of a cell's dry mass. They are not only the cell's building blocks; they also execute the majority of the cell's functions. Thus, proteins that are enzymes provide the complex molecular surfaces inside a cell that catalyze its many chemical reactions. In this section, we consider how the location of each amino acid in the long string of amino acids that forms a protein determines its three-dimensional shape. Later in the chapter, we use this understanding of protein structure at the atomic level to describe how the precise shape of each protein molecule determines its function in a cell.

Regulation by 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 phosphorylationregulate many eukaryotic cell functions turning things on and off • Protein kinases add the PO4 and protein phosphatase remove them

2 types of proteins

fibrous and globular Globular: Most of the proteins that we have discussed so far are globular proteins, in which the polypeptide chain folds up into a compact shape like a ball with an irregular surface. Ex: - Enzymes tend to be globular proteins

Enzymes as Catalysts

• Enzymes are proteins that bind to their ligand as the necessary 1st step in a protein so they can perform their function • An enzyme's 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 • There Many different kinds

Src Protein Kinases

• First of the tyrosine kinases to be discovered • Through tyrosine phosphorylation they transmit intracellular signals from receptors • Attaches to plasma membrane by hydrophobic fatty acid in N terminal (myristate) Enzyme has 3 main domains: - Src homology 3 (SH3) - Src homology 2 (SH2) - Catalytic kinase (SH1)

β pleated sheet

β sheets are the other form of the secondary structure of proteins in which the polypeptide backbone chain folds back and forth. (does not involve R groups) Both types of β sheet produce a very rigid structure, in which two or more segments of the polypeptide chain line up next to each other, forming a sheet-like structure held together by hydrogen bonds. The hydrogen bonds form between carbonyl and amino groups of backbone, while the R groups extend above and below the plane of the sheet The strands of a β pleated sheet may be parallel or antiparallel Parallel = pointing in the same direction (meaning that their N- and C-termini match up) Antiparallel, pointing in opposite directions (meaning that the N-terminus of one strand is positioned next to the C-terminus of the other)

Antibodies Structure

• 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