Introduction to Proteins

The structure of a protein can be analyzed at four levels:

1) Amino acid sequence 2) Substructures called alpha-helices and beta-pleated sheets 3) Interactions between amino acids that dictate a protein's overall shape 4) Combinations of individual proteins that make up larger, multiunit molecules

Primary Structure

A protein's primary structure is its unique sequence of amino acids. Because the amino acid R-groups affect a polypeptide's properties and function, just a single amino acid change can radically alter protein function.

Summary of Protein Structure

Note that protein structure is hierarchical. Quaternary structure is based on tertiary structure, which is based in part on secondary structure. All three of the higher-level structures are based on primary structure. The combined effects of primary, secondary, tertiary, and sometimes quaternary structure allow for amazing diversity in protein form and function.

Prions and Protein Folding

• Prions are improperly folded forms of normal proteins that are present in healthy individuals. - Amino acid sequence does not differ from a normal protein, but shape is radically different. - Prions can induce normal protein molecules to change their shape to the altered form. - Prions are thought to be the causative agent in spongiform encephalopathy - Scrapie Disease (Sheep) - "Mad Cow" (Bovine) - Chronic Wasting (Wild Ungulates) - Creutzfeld-Jacob (Human)

Folding and Function

• Protein folding is often spontaneous, because the hydrogen bonds and van der Waals interactions make the folded molecule more energetically stable than the unfolded molecule. • A denatured (unfolded) protein is unable to function normally. • Proteins called molecular chaperones help proteins fold correctly in cells.

Do Enzymes Act Alone?

• Some enzymes require cofactors to function normally. These are either metal ions or small organic molecules called coenzymes. • Most enzymes are regulated by molecules that are not part of the enzyme itself.

Activation Energy and Rates of Chemical Reactions

• The activation energy (Ea) of a reaction is the amount of free energy required to reach the intermediate condition, or transition state. • Reactions occur when reactants have enough kinetic energy to reach the transition state. - The kinetic energy of molecules is a function of their temperature. • Thus, reaction rates depend on: - The kinetic energy of the reactants - The activation energy of the particular reaction (the free energy of the transition state)

Rate of Enzyme-Catalyzed Reactions

• To summarize, the rate of an enzyme-catalyzed reaction depends on: 1. Substrate concentration 2. The enzyme's intrinsic affinity for the substrate 3. Temperature 4. pH

The Nature of Side Chains

The 20 amino acids differ only in the unique R-group attached to the central carbon. The properties of amino acids vary because their R-groups vary.

Tertiary Structure

The tertiary structure of a polypeptide results from interactions between R-groups or between R-groups and the peptide backbone. These contacts cause the backbone to bend and fold, and contribute to the distinctive three-dimensional shape of the polypeptide. R-group interactions include hydrogen bonds, hydrophobic interactions, van der Waals interactions, covalent disulfide bonds, and ionic bonds.

Proteins are made of _____

amino acids!

The Structure of Amino Acids

All proteins are made from just 20 amino acid building blocks. All amino acids have a central carbon atom that bonds to NH2, COOH, H, and a variable side chain ("R-group"). In water (pH 7), the amino and carboxyl groups ionize to NH3+ and COO-, respectively—this helps amino acids stay in solution and makes them more reactive.

The Peptide Bond

Condensation reactions bond the carboxyl group of one amino acid to the amino group of another to form a peptide bond. A chain of amino acids linked by peptide bonds is called a polypeptide. Polypeptides containing fewer than 50 amino acids are called oligopeptides (peptides). Polypeptides containing more than 50 amino acids are called proteins.

Secondary Structure

Hydrogen bonds between the carbonyl group of one amino acid and the amino group of another form a protein's secondary structure. A polypeptide must bend to allow this hydrogen bonding, forming: alpha-helices beta-pleated sheets Secondary structure depends on the primary structure. Some amino acids are more likely to be involved in -helices; others, in -pleated sheets. The large number of hydrogen bonds in a protein's secondary structure increases its stability.

R-group Interactions That Form Tertiary Structures

Hydrogen bonds form between hydrogen atoms and the carbonyl group in the peptide-bonded backbone, and between hydrogen and negatively charged atoms in side chains. - Hydrophobic interactions within a protein increase stability of surrounding water molecules by increasing hydrogen bonding. - van der Waals interactions are weak electrical interactions between hydrophobic side chains. - Covalent disulfide bonds form between sulfur-containing R-groups. - Ionic bonds form between groups that have full and opposing charges.

Quaternary Structure

Many proteins contain several distinct polypeptide subunits that interact to form a single structure; the bonding of two or more subunits produces quaternary structure.

What Do Proteins Do?

Proteins are crucial to most tasks required for cells to exist: - Catalysis - enzymes speed up chemical reactions. - Defense - antibodies and complement proteins attack pathogens. - Movement - motor and contractile proteins move the cell or molecules within the cell. - Signaling - proteins convey signals between cells. - Structure - structural proteins define cell shape and comprise body structures. - Transport - transport proteins carry materials; membrane proteins control molecular movement into and out of the cell.

Functional Groups Affect Reactivity

R-groups differ in their size, shape, reactivity, and interactions with water. 1) Nonpolar R-groups: hydrophobic; do not form hydrogen bonds; coalesce in water 2) Polar R-groups: hydrophilic; form hydrogen bonds; readily dissolve in water - Amino acids with hydroxyl (-OH), amino (-NH2), carboxyl(-COO-, or sulfhydryl (-SH) functional groups in their side chains are more chemically reactive than those with side chains composed of only carbon and hydrogen atoms.

Polypeptide Characteristics

Within the polypeptide, the peptide bonds form a "backbone" with three key characteristics: 1) R-group orientation - Side chains can interact with each other or water. 2) Directionality - Free amino group, on the left, is called the N-terminus. 3) Free carboxyl group, on the right, is called the C-terminus. 4)Flexibility - Single bonds on either side of the peptide bond can rotate, making the entire structure flexible.

Catalysts and Free Energy

• A catalyst is a substance that lowers the activation energy of a reaction and increases the rate of the reaction. • Catalysts lower the activation energy of a reaction by lowering the free energy of the transition state. • Catalysts do not change ΔG and are not consumed in the reaction.

An Introduction to Catalysis

• Catalysis may be the most fundamental of protein functions. • Reactions take place when: - Reactants collide in precise orientation - Reactants have enough kinetic energy to overcome repulsion between the electrons that come in contact during bond formation • Enzymes perform two functions: - Bring substrates together in precise orientation so that the electrons involved in the reaction can interact - Decrease the amount of kinetic energy reactants must have for the reaction to proceed

Enzyme Regulation

• Competitive inhibition occurs when a molecule similar in size and shape to the substrate competes with the substrate for access to the active site. • Allosteric regulation occurs when a molecule causes a change in enzyme shape by binding to the enzyme at a location other than the active site. - Allosteric regulation can activate or deactivate the enzyme.

The Steps of Enzyme Catalysis

• Enzyme catalysis has three steps: 1. Initiation - Substrates are precisely oriented as they bind to the active site. 2. Transition state facilitation - Interactions between the substrate and active site R-groups lower the activation energy. 3. Termination - Reaction products are released from the enzyme.

What Limits the Rate of Catalysis?

• Enzymes are saturable; in other words, the rate of a reaction is limited by the amounts of substrate present and available enzyme. - The speed of an enzyme-catalyzed reaction increases linearly at low substrate concentrations. - The increase slows as substrate concentration increases - The reaction rate reaches maximum speed at high substrate concentrations. • All enzymes show this type of saturation kinetics. - At some point, active sites cannot accept substrates any faster, no matter how large the concentration of substrates gets.

How Do Enzymes Work?

• Enzymes bring substrates together in specific positions that facilitate reactions, and are very specific in which reactions they catalyze. • Substrates bind to the enzyme's active site. • Many enzymes undergo a conformational change when the substrates are bound to the active site; this change is called an induced fit. • Interactions between the enzyme and the substrate stabilize the transition state and lower the activation energy required for the reaction to proceed.

Physical Conditions Affect Enzyme Function

• Enzymes function best at some particular temperature and pH. - Temperature affects the movement of the substrates and enzyme. - pH affects the enzyme's shape and reactivity.