1. Key Concepts Most cell functions depend on proteins.
Proteins are made of amino acids. Amino acids vary in structure and function.
The structure of a protein can be analyzed at four levels:
Amino acid sequence
Substructures called -helices and -pleated sheets
Interactions between amino acids that dictate a protein’s overall shape
Combinations of individual proteins that make up larger, multiunit molecules
In cells, most proteins are enzymes that function as catalysts.

2. 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.

4. 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.

5. Functional Groups Affect Reactivity
R-groups differ in their size, shape, reactivity, and interactions with water.
Nonpolar R-groups: hydrophobic; do not form hydrogen bonds; coalesce in water
Polar R-groups: hydrophilic; form hydrogen bonds; readily dissolve in water
Amino acids with hydroxyl, amino, carboxyl, or sulfhydryl functional groups in their side chains are more chemically reactive than those with side chains composed of only carbon and hydrogen atoms.

8. Monomers and Polymers
Many mid-size molecules, such as amino acids and nucleotides, are individual units called monomers. They link together (polymerize) to form polymers, such as proteins and nucleic acids.
Macromolecules are very large polymers made up of many monomers linked together.
Thus, proteins are macromolecules consisting of linked amino acid monomers.

10. Assembling and Breaking Apart Polymers
Polymerization requires energy and is nonspontaneous.
Monomers polymerize through condensation (dehydration) reactions, which release a water molecule.
Hydrolysis is the reverse reaction, which breaks polymers apart by adding a water molecule.
In the prebiotic soup, hydrolysis is energetically favorable and thus would predominate over condensation. However, polymers clinging to a mineral surface are protected from hydrolysis, and thus polymerization of the amino acids into proteins may have occurred spontaneously.

12. 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.

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

17. 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.

18. What Do Proteins Look Like?
Proteins can serve diverse functions in cells because they are diverse in size and shape as well as in the chemical properties of their amino acids.
All proteins have just four basic levels of structure: primary, secondary, tertiary, and quaternary.

19. 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.

21. 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:
-helices
-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.

23. 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.

24. 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.

26. 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.

28. 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.

30. 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.

32. 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.

34. 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

35. 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)

38. 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.

40. Enzymes
Enzymes are protein catalysts and typically catalyze only one reaction.
Most biological chemical reactions occur at meaningful rates only in the presence of an enzyme.
Enzymes:
Bring reactants together in precise orientations
Stabilize transition states
Protein catalysts are important because they speed up the chemical reactions that are required for life.

41. 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.

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

45. 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.

46. 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.

48. 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.

50. 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.

52. Rate of Enzyme-Catalyzed Reactions
To summarize, the rate of an enzyme-catalyzed reaction depends on:
Substrate concentration
The enzyme’s intrinsic affinity for the substrate
Temperature pH