Biochemistry Notes on Proteins, Denaturation, and Structure

Below are some notes on proteins and structure that can be used for an understanding or refresher that is helpful and useful for the sciences; specifically biology, chemistry, and biochemistry.

Native conformations= conformations of proteins that have biological activity

Random coil= protein segments that have no regular repeating pattern

(The non-repeating structure is found in native conformation of all molecules of a given protein.)

Proteins= biologically active polymers consisting of amino acids linked by covalent peptide bonds.

Proteins:

• Can have many different conformations/3-D structures
• Are large molecules
• One-a few have biological activity
• Often have repeating structure
• Are defined in terms of four levels of structure
• Come in different types

Proteins can be denatured by:

• heat
• extremes of pH
• detergents

Denaturation=the unfolding of a protein

Under specific experimental conditions, denatured proteins can often be recovered or returned to their original formation/structure.

Protein denaturation:

Heat: Heat causes vibrations in molecule. Vibrations can break 3^o structure.

Extremes of pH: Some of the charges on the protein are missing and the stabilizing electrostatic attractions are reduced causing denaturation.

Detergents: Binding to detergents disrupts hydrophobic interactions, and if it is charged, it can also disrupt electrostatic interactions.

Protein re-folding:

Many different factors affect how and if a protein is able to re-fold, but given specific conditions and to a certain point, many proteins are able to be re-folded.

In the genetic disease sickle-cell anemia, the red blood cells cannot bind oxygen efficiently and have a sickle shape. These cells get stuck in blood vessels, cut off circulation, and cause organ damage. Sickle-cell anemia comes from a change in only one amino acid resident in the primary structure sequence.

Primary structure involves the sequence of amino acids or the order in which the amino acids are covalently linked together.

The primary structure specifies the 3D (tertiary) structure of a protein through its sequence.

Conformations of the side chains of the amino acids are not part of 2^o structure.

Major Determinant:backbone hydrogen bonding

Protein-folding can occur in parts of the chain independently from other parts of the chain/chain folding.

Protein parts that fold independently are called domains or super-secondary structure.

Only the peptide backbone is considered in 2^o structure.

Two commonly occurring 2^o structures are:

• alpha-helix
• beta-pleated sheet

There are other possible 2^o structures but these two are the most important.

Secondary structure is the way the atoms are arranged in space in the peptide backbone, and includes the hydrogen-bonded arrangement of the backbone of the protein (the polypeptide chain).

Alpha-helix and beta-pleated sheet arrangements are part of secondary structure.

Secondary structures have repeating interactions from the hydrogen bonding between N--H and the carbonyl groups in the peptide backbone.

The structures of alpha-helices and beta-pleated sheets repeat at regular intervals and they are both found in protein backbones.

In structure, the alpha-helix is rod-like, and has only one polypeptide chain.

The beta-pleated sheet has a two-dimensional array in structure and can involve one or more polypeptide chain.

Proline does not fit into the alpha-helix because: 1.) rotation around the bond between the nitrogen and the alpha-carbon is restricted, and 2.) proline's alpha-amino group cannot participate in intrachain hydrogen bonding.

Because proline does not fit into the alpha-helix it can cause the polypeptide helix to turn.

Turn=ending a alpha-helical segment.

Angstrom: 1A = 10^-8cm = 10^-10m

Nanometer: 1nm = 10^-9m

Picometer: 1pm = 10^-12m

Crowding of the alpha-carbon outside the helix occurs with valine, isoleucine, and threonine.

• Is stabilized by hydrogen bonds
• Helix has a linear arrangement of atoms involved in the H-bonds=bond maximum strength and high stability
• 3.6 residues for each turn of the helix
• pitch of the helix= 5.4A =.54nm = 540pm
• (Pitch=linear distance between corresponding points on successive turns; A=Angstrom)
• Side chains lie outside the helix because they do not fit in the interior
• Alpha carbon is outside the helix, and if it is bonded to two atoms other than hydrogen, crowding can occur.

Disruptions to the alpha-helix:

• Steric interferences
• Electrostatic interferences
• Disruptors

Steric interferences:

• Crowding; steric repulsion caused by the proximity of several bulky side chains

Electrostatic interferences:

• Localized factors involving the side chains; electrostatic repulsion due to the proximity of several charged groups of the same sign.

Disruptors:

• Amino acid proline creates a bend in the backbone because of its cyclic structure.

Intrachain bonds= hydrogen bonds formed from a beta-pleated sheet with different parts of a single chain that is doubled back on itself.

Interchain bonds= hydrogen bonds formed from a beta-pleated sheet between different chains.

Parallel=beta-pleated peptide chains that run in the same direction/are aligned in terms of their N-terminal and C-terminal ends.

Antiparallel= beta-pleated sheets that that run in opposite directions/have alternating chains with respect to N-terminal and C-terminal ends.

• Peptide backbone is almost completely extended.
• Hydrogen bonds can be formed as both intrachain bonds and interchain bonds
• Peptide chains can run in parallel or antiparallel directions
• The hydrogen bonding in the peptide chains gives a repeated zigzag structure.
• The hydrogen bonds are perpendicular to the direction of the protein chain, not parallel as seen in the alpha-helix structure.

Beta-sheets:

• No long amino acid R-groups
• Turns often Pro and Gly

R_A

R=the # of residues per turn

A=the # of atoms in the ring

Sometimes there are other structures found that end up changing or modifying the alpha-helix.

Some examples of these are the 3₁₀helix, the 2₇helix, and the 4.4₁₆helix. The 3₁₀helix has three residues for each turn and 10 atoms in the ring.

motif:

• A repetitive secondary structure
• Can be small or large
• Smaller motifs can be organized into larger ones
• Tell us about the folding of proteins
• Are found in proteins and enzymes with dissimilar functions
• Cannot be used to predict the biological function of the protein

Structure is related to function:

Many proteins will have similar protein sequences when they are similar in function.

The alpha-helix, beta-pleated sheets, and any other variation in secondary structure can come together in different ways allowing for different types of polypeptide chain folding. This results in the formation of different protein structures.

These different structures are called supersecondary structures.

Some of these protein structures include:

• Beta-alpha-beta unit
• Alpha-alpha unit
• B-meander unit
• Greek Key

Beta-alpha-beta unit:Two parallel strands of beta-sheet are connected by an alpha-helix.

Alpha-alpha unit: Two anti-parallel alpha-helices.

B-meander unit: anti-parallel sheet is formed by a series of tight reverse turns that connect the polypeptide chain.

Greek Key:anti-parallel sheet that has the polypeptide chain doubling back on itself in a pattern.

• Backbone folds back on itself (spherical shape)
• Have helical and beta-pleated sheet parts
• Are water-soluble
• Have compact structures
• Can have complex 3^o and 4^o structures

• Are not water-soluble
• Consists of alpha-helices

Prosthetic groups=groups of atoms other than amino acids

Myoglobin has 3^o structure.

Complete Covalent Structure= [1^o structure] + [Positions of the Disfulfide Bonds]

(The order of the amino acids that includes the positions of the disulfide bonds)

Tertiary structure includes the arrangement of all of the atoms in the protein, including the side chains and in any prosthetic groups.

Non-polar residues come together in the interior of protein molecules because of hydrophobic interactions.

Electrostatic attraction causes oppositely charged groups to cbondsome close to one another on the molecule's surface.

Disulfide bonds bond covalently to cysteine side-chains which limits the way in which polypeptides can fold.

Hydrogen bonds, electrostatic interactions, and hydrophobic interactions occur in most proteins.

The 3^o structure of a protein is the product of all the stabilizing forces.

Nuclear Magnetic Resonance (NMR) Spectroscopy= large collections of data points are analyzed with a computer.

• Uses protein samples in aqueous solution
• Environment is close to protein environment of cells
• Widely-used in determination of protein structure
• Depends on the distance between hydrogen atoms

X-Ray Crystallography= an experimental technique used to determine the 3^o structure of a protein; this method exposes a beam of X-rays into pure crystals and a diffraction pattern results.

• # of e^- in the atom determines the intensity of the scattering of the crystal's X-rays
• Heavier atoms scatter more effectively than lighter atoms
• Scattered X-rays can reinforce each other or cancel each other out
• Diffraction patterns taken from several angles can be used to determine 3^o structure

Quaternary protein=protein that consists of more than one polypeptide chain.

Subunits=a chain in a quarternary protein.

Oligomer=generic term for a molecule made up of a small number of subunits.

Hemoglobin has 4^o structure.

Quarternary structure includes the arrangement of subunits with respect to one another in the amino acid. It is found in proteins with more than one polypeptide subunit.

Quarternary structures can be allosteric, meaning that changes in structure in one part of the protein molecule can cause notable changes in other parts of the protein.

• Polar head groups facing the aqueous environment and non-polar tails in contact with each other being kept away from each other
• Interactions between the bilayer of embedded proteins

• Proteins tend to fold so that the non-polar hydrophobic side chains are put aside away from water in the interior of the protein and the polar hydrophilic side chains are on the exterior of the protein interacting with the aqueous environment.

Chaperone proteins:

• Exist in prokaryotes, eukaryotes, humans
• Prevent undesirable interactions with other proteins
• Prevent undesirable interactions with the protein itself
• Help to ensure proper protein folding

Hydrophobic interactions=spontaneous processes; Change S_univ>0

Entropy increases when there are hydrophobic interactions.

Hydrophobic interactions depend on the unfavorable entropy of the water of hydration that surrounds non-polar solutes and are very important for protein folding.

Non-polar substances do not dissolve in water but instead interact with each other through hydrophobic interactions and not involved with water. Non-polar amino acid groups are forced together to avoid interacting with water.

Protein Folding:

• Correctly-folded proteins are usually soluble in aqueous cell environments or can attach to membranes
• Incorrectly-folded proteins may interact with other proteins, forming aggregates.
• Incorrect folding is a result of hydrophobic regions interacting with other hydrophobic regions on other molecules when they are supposed to be buried inside the protein.
• Chaperone proteins help proteins to fold correctly by preventing proteins from interacting with a protein that it should not be interacting with or by keeping it from interacting with itself in ways that it should not.

• Notes on Water and Polarity
• Notes on Acids, Bases, and pH
• Notes on Titration
• Notes on Buffers
• Notes on Peptides

The information used for this hub was taken from the following sources:

"Biochemistry" by Mary K. Campbell and Shawn O. Farrel; 7th edition.

My biochemistry lectures at school.

Knowledge and notes taken from previous courses in chemistry and biology.

http://www.uic.edu/classes/bios/bios100/lectures/chemistry.htm