Biochem exam # 2 Unit 3 part 1

Serine introduces a

random coil

Protein folding is driven be the .... and by.....

hydrophobic effect (Peptide chain must fold so as to "bury" the hydrophobic side chains, minimizing their contact with water and the amino acid sequence

Type 1 beta turn is

twice as frequent as type 2

What type of alpha helix is found in nature and what is the type that isn't found in nature ?

α-Helix in Nature is Right-Handed -The right-handedness of the α-helix is a consequence of the chirality of the α-amino acids The left-handed helix is not found in nature.

Which of the following does not represent a protein secondary structure? α-helix β- pleated sheets γ- turns Loops All of the above are protein secondary structures

γ- turns

Supersecondary Structures

• Supersecondary Structures are the Building Blocks of Protein Structures: are level of protein organization that are more complex than primary or secondary structures; • Are made up of multiple secondary elements: α-helices and β-sheet • They represent clusters of secondary structures; • Depend on the primary structure of a protein; • Are stabilized by hydrophobic interactions; • Motifs can act as modules that nature can just copy and paste into another protein

An Antiparallel β-Pleated Sheet

-Adjacent beta strands run in opposite directions (see the yellow arrows); Hydrogen bonds between N-H and C=O groups connect each amino acid to a single amino acid on an adjacent strand. Notice how the strand A aligns with strand B to form H-bond between the carbonyl oxygen of one strand and the amide hydrogen of the other strand, and vice versa..

Three Major Class of Proteins: 1. Globular proteins..... 2. Fibrous proteins ..... 3. Membrane proteins....

-Globular proteins: Somewhat spherical water soluble (myoglobin); -Fibrous proteins: rod-like, mostly insoluble, play structural role; (collagen); -Membrane proteins: poor solubility; ion channels (Na+/K+ pumps); needs detergent to dissolve.

What are the non covalent forces that drive the formation of higher order protein structures: *Although the 1˚ structure of a protein is determined by the covalently linked amino acid residues in the polypeptide backbone, 2˚ and higher orders of structures are determined principally by noncovalent forces!

-Hydrogen bond interactions: are fundamentally electrostatic Ionic interactions: -Van der Waals interactions: The basis for this interaction is that the distribution of electronic charge around an atom fluctuates with time leading to the formation of transiently complementary electrostatic interactions between two adjacent atoms -Disulfide bridges -Disulfide bridges are reversible covalent interactions that mainly defines protein 1˚ structures. -Hydrophobic interactions: In water, nonpolar molecules associates (9 kcal/mol.

Which of the following is least likely to be a conclusion from Anfinsen's classic experiment? -Once a protein denatures, the process is irreversible -All of these are valid conclusions from Anfinsen's classic experiment -Despite a protein losing its tertiary structure, it still has its primary sequence of amino acids -The primary sequence of amino acids determines the three dimensional structure of a protein pThe structure of a protein at the tertiary or quaternary level dictates the specific function of the protein

-Once a protein denatures, the process is irreversible This classical experiment demonstrates that the primary protein structure dictates the structure of a protein, which dictates the function. Denaturation does not affect the 1˚ peptide sequence. The experiment showed that denaturation can be reversible after removal of the denaturants.

Properties of the α-Helix

-Residues per turn: 3.6 -Rise per residue: 1.5 Angstroms -Rise per turn (pitch): 3.6 residues x 1.5Å = 5.4 Angstroms -φ = -47 degrees, ψ = -60 degrees (phi and psi) -Hydrogen bonds at almost optimal length and are intramolecular (within the same polypeptide) -Rigid structure;R groups stick out (purple spheres)

Properties of the beta sheet

-The β-Sheet is the second most common secondary structure found in proteins -composed of β-strands, which may be parallel or antiparallel; -N-H and C=O groups are hydrogen bonded interstrand (between different polypeptide strands); Successive side chains project to opposite sides of the sheet; Average length of a chain within β sheet: 6 residues; Number of strands Formed by extended polypeptides; Most forming a sheet: 2-15 Rise per residue: 3.47 Angstroms for antiparallel strands; 3.25 Angstroms for parallel strands. -strand is more extended compared to the alpha helix; Also notice the zigzag (up and down) conformation of the β-sheet.

Beta Turns or Loops

-The β-turns is a class of local secondary structures (consists of four amino acid residues) -Allows peptide chains to reverse direction so that proteins can fold back on itself; They interrupt 2˚ structures. -Carbonyl oxygen of one residue is H-bonded to the amide proton of a residue three residues away; -Proline and glycine are prevalent in β-turns- becuase it needs flexibility and kinks to reverse on itself Four residues are required to form a β-turn, first and last form H-bond; -There are two types of beta-turns: Type I and Type II.

Hydrogen-bonding Scheme for an α-Helix: Q: In the alpha helix, the C=O group of residue i forms hydrogen bond with the N-H group of residue....

-i + 4 (this is four residues along the chain); -Note how the C=O group of residue i is aligned in the same direction with the -NH group of residue i + 4. -Notice that the hydrogen bonds are formed within the same strand-intrastrand

Circular dichroism (CD)

-refers to the differential absorption of left and right circularly polarized light -Biochemists use this technique to determine if proteins are folded, or estimate the fraction of the proteins that is folded into alpha or beta structures

Which of the following is not a step in x-ray crystallography? Calculating an electron density map Proposing a structural model Growing crystals Correct 1H-NMR analysis Producing a diffraction pattern

1H-NMR analysis All of these are necessary steps for solving the crystal structure of a macromolecule, except 1H-NMR analysis. 1H-NMR analysis is a completely different technique for solving the structure of a protein.

What is the increasing level of complexity of proteins?

1˚ Structure - 2˚ Structure - Supersecondary structures -Domains (are part of a 3˚ structure) - 3˚ structure (a single polypeptide with 1 or more domains) - 4˚ structure (2 or more polypeptides assembled together.

Which of the following is not one of the structural and functional advantages driving quaternary association in nuture? Bringing catalytic sites together Genetic economy Cooperativity Stability All of the above drive quaternary association

All of the above drive quaternary association

A Parallel β-Pleated Sheet

Adjacent beta strands run in the same directions (yellow arrows); Hydrogen bonds between N-H and C=O groups connect each amino acid with two different amino acids on an adjacent strand.

Which of the following is true about the effect of salts on protein structures? They can stabilize protein structure They can destabilize protein structure They can disrupt hydrophobic interactions They can be indifferent to protein structure All of these are true about salt effects in proteins

All of these are true about salt effects in proteins Salts can cause three different effects: 1) stabilize protein structure; 2) destabilized protein structure; or 3) they can be indifferent, meaning that they neither stabilize nor destabilize protein structure. Some salts do disrupt the hydrophobic interactions, therefore, destabilizing protein structures.

Which of the following examples or features is typical of a fibrous protein? Water-insoluble Collagen All of these choices are examples or features of fibrous proteins Tendons Structural support

All of these choices are examples or features of fibrous proteins Fibrous proteins provide structural support, are water-insoluble, and collagen and tendons are examples of fibrous proteins.

Types of secondary structures

Alpha helices Beta sheets Beta turns Loops

Which of the following treatments will most like cleave the disulfide bridges of a folded protein? None of the these treatments can cleave the disulfide bridge in folded proteins Guanidinium chloride Urea pH Beta-mercaptoethanol

Beta-mercaptoethanol

Which of the following treatments is least likely to denature a protein that has catalytic activity? A change in pH Organic solvents A change in temperature Binding of the substrate to the active site Addition of detergents

Binding of the substrate to the active site

Which of the following is not a type of secondary structures in proteins? Alpha-helix Reverse turns Domains Beta-sheets All of these are types of secondary structures in proteins

Domains Domains are not a type of secondary structure in proteins. A domain is a 3˚ structure.

The difference between domains and quaternary structure is that?

Domains are part of a single protein or polypeptide. They should not be confused with the quaternary structure of a protein, which is an assembly of different proteins or polypeptides. To distinguish a protein with multiple domains from a 4˚ protein structure, just take a close look and you will see that domains are continuous as they are joined by a polypeptide segment. You can notice that the different subunits of a 4˚ protein are discontinuous.

Which of the following amino acids is most likely to be found in collagen? His Ala Gly Leu Cys

Gly

Properties of The Quaternary Level of Protein Structure:

In the quaternary structure, proteins polypeptide chains can assemble into multisubunit structures; -Each individual polypeptide chain is called a subunit;

Which of the following is NOT a property of an alpha helix It is a secondary protein structure It is a left handed helix 3.6 residues per turn Hydrogen bonds are intramolecular All of the above are properties of an alpha helix

It is a left handed helix

Which of the following is true about the following amino acids? Glycine and Alanine are helix formers Glycine and Proline are helix formers Leucine and Methionine are helix breakers Proline and Serine are helix breakers None of the above are correct

Proline and Serine are helix breakers

What are the structural and functional advantages driving quaternary association?

Stability: reduction of surface to volume ratio; - Genetic economy and efficiency; - Bringing catalytic sites together; - Cooperativity.

Water on the protein surface of globular proteins will.....

Stabilize the Structure. The polar backbone and side chain groups on the protein surface make H-bonds with solvent water; α-Helices on a protein surface are usually amphiphilic, with polar and charged residues facing the solvent and nonpolar residues facing the interior; A helical wheel presentation can reveal the amphiphilic nature of an α-helix; Some α-helices are hydrophobic and buried in the protein interior; Some helices are polar and entirely solvent-exposed (see next slide

The 3D structures of proteins and their biological functions are linked by several overarching principles BIG IDEA?

The amino acid sequence dictates the 3D structure; Protein structure dictates its function; Proteins are not rigid entities. Motion and flexibility enable protein function; The number of protein folding patterns is large but finite; Protein folding is not random; Structures of globular proteins are marginally stable; Marginal stability facilitates motion. General Theme: There is a structure-and-function relationship in life dictated by the amino acid sequence!

The α-Helix Has a Substantial Net Dipole Moment because...

The arrangement of N-H and C=O groups (each with an individual dipole moment) along the helix axis . -Because of this dipole moment, negatively charge ligands (e.g., phosphates in DNA and RNA) frequently bind to proteins near the N-terminus of an alpha helix

Which of the following is not true about globular protein tertiary structures? The protein surface can be a landscape of binding sties for specific molecules Contacts are defined by amino acid side chains rather than backbone interactions The protein structures are mainly held together by long-range covalent bonds Nonpolar amino acids form the core of the protein Largely, polar amino acids interacting with water

The protein structures are mainly held together by long-range covalent bonds -Explanation why not true: The tertiary structure of a globular protein is mainly held together by non-covalent, long distance interactions involving the amino acid's side chains. They are not mainly held by long-range covalent bonds.

Which of the following is not true about β-sheets? It is the second most common secondary structure found in proteins The β-sheets are only parallel A sheet is made up of 2-15 strands The average length of a chain within a β-sheet is 6 residues It has a zig-zag confirmation

The β-sheets are only parallel

Secondary structures are

are local structural motifs that are stabilized exclusively by backbone hydrogen bond interactions involving the C=O and -NH; (It describes conformations of the oligopeptide backbone.) the 2˚ structure of proteins is formed by local structures involving hydrogen bond interactions between amino acids less than 10 amino acids apart from each other

α-helix and the β-pleated strand

are the two principal secondary structures found in proteins

Sububnits in the Quaternary structure are held together by ...

by noncovalent bonds; ,(essentially the same types of interactions seen in 3˚ structures)

Hydrogen bonding interactions within the 1˚ amino acid sequence forms local structures that

constitute the 2˚structures.

. The 1˚ structure of proteins is described by disulfide....

crosslinking.

Domains are...

distinct compact, globular, and folded tertiary functional units in protein structures that are usually stable by themselves in aqueous solution; Larger globular proteins are typically made up of two or more recognizable and distinct structures, termed domains; Most domains consist of a single continuous portion of the protein sequence (top image) connected by a flexible polypeptide segment;

Glutamate and leucine are alpha helix ....

formers!

Globular proteins fold into ....

into compact, asymmetrical, 3D-structures with nonpolar amino acids forming the core, as dictated by the hydrophobic effect; the surface is formed largely by polar amino acids interacting with water; Enzymes are globular proteins.

Proline introduces

kinks; mostly absent from α helices; Proline is an alpha helix breaker;

Protein folding can be assisted by....

molecular chaperones`

Random coil is a structure conformation ....

normally seen in proteins; -These are loop segments of the proteins that are neither helix, sheet, nor turn; -They are not random structures as the name implies. They are organized and stable

helical wheel presentation can reveal....

reveal the polar or nonpolar character of α-helices. In some globular proteins, it is common for one face of the alpha helix to be exposed to the water solvent, with the other face toward the hydrophobic interior of the protein. These are amphiphilic helices.

Multimeric proteins are

symmetric arrangements of asymmetric objects;

an increase in entropy drives what process forward

the hydrophobic effect