Biochemistry - Chapter 7

What kind of amino acids are necessary for the external surfaces of a cytoplasmic protein?

Polar amino acids to interact with the polar, water-like cytoplasm.

Polypeptide coils

Polypeptide features which appear during the second level of protein folding. While not entirely random, their organization is less-defined than the helices or sheets. They form flexible hinges.

Proline and secondary structure

Proline, due to an unusual shape, cannot fit into an alpha helix. Nicknamed the "helix breaker" even one can end a helical domain.

Globular proteins

Proteins (like myoglobin) which form a densely-packed hydrophobic core. Globular proteins place polar amino acid side chains on the outside as insulation.

What kind of saturation curve does hemoglobin achieve?

Sigmoidal. This shape suggests that when the pressure of oxygen is high (as in the lungs), the molecule is fully-saturated. At lower pressures, however, hemoglobin molecules cannot bind oxygen as well as myoglobin. This is a result of a lower oxygen affinity (than myoglobin) and the positive effects of subunit cooperation.

Are parallel or antiparallel β-sheets considered skewed?

Since parallel β-sheets are arrange such that one amino acid is hydrogen-bonded to two others in the opposite strand, they are considered skewed. Antiparallel sheets match more evenly.

Native conformation

The native state of a protein or nucleic acid is its properly folded and/or assembled form, which is operative and functional. This is in contrast to the denatured state, in which these weak interactions are disrupted, leading to the loss of these forms of structure and retaining only the biomolecule's primary structure. The native form is determined by the primary structure of the polypeptide.

Hemoglobin T state

The natural, tensed state of hemoglobin. In this stage, the molecule has low affinity for oxygen gas. Hemoglobin enters the relaxed state when prompted by conformational change accompanying the binding of other subunits to O₂.

What amino acids are used on the surface of globular proteins to maintain a "water seal?"

The polar charged amino acids [Arg, His, Lys, Asp, and Glu] Charged side chains often bind inorganic ions (e.g., K⁺, PO₄³⁺ , or Cl⁻) to decrease repulsion between like charges

Association constant K₂

The rate at which ligand and protein dissociate

Association constant K₁

The rate at which ligand and protein form a complex

tertiary protein structure

The tertiary structure involves folding of the secondary structural elements into an overall three-dimensional conformation.

Are proteins rigid or flexible?

The three dimensional structure must exhibit the degrees of flexibility and rigidity required to carry out its specific function. Some rigidity is essential for the creation of binding sites and for a stable structure. However, an appropriate degree of flexibility and mobility in structure enables the protein to fold as it is synthesized, and to adapt as it binds other proteins and small molecules.

Why cant we degrade prions like proteins

Their folding pattern often resists proteolytic degregation. Fortunately, there's a high energy barrier to spontaneous generation.

protein disulfide isomerases

This enzyme catalyzes the formation and breakage of disulfide bonds between cysteine residues within proteins as they fold. It's required for some basic protein folding.

cis-trans-prolyl isomererases

This enzyme interconverts the cis and trans isomers of peptide bonds with the amino acid proline. If you ever want to add or remove a turn, this is how.

Are peptide bonds usually tans or cis?

Trans

Antiparallel β-sheet [Are both sides equal? Are these sheets made from one polypeptide chain or multiple?]

When two polypeptide strands run in opposite directions (as defined by their amino and carboxy terminals). Antiparallel strands are often the same polypeptide chain folded back on itself, with simple hairpin turns or long runs of polypeptide chain connecting the strands. Antiparallel sheets usually have a hydrophobic side and a hydro- philic side

Parallel β-sheet [Are both sides equal? Are these sheets made from one polypeptide chain or multiple?]

When two polypeptide strands run in the same direction (as defined by their amino and carboxy terminals). Parallel sheets tend to have hydrophobic residues on both sides of the sheets.

In which protein structures are α-helixes commonplace?

lobular proteins, membrane-spanning domains, and DNA-binding proteins.

secondary protein structure

local regions of polypeptide chains formed into structures that are stabilized by a repeating pattern of hydrogen bonds, such as the regular structures called α-helices and β-sheets. The rigidity of the peptide backbone determines the types of secondary structure that can occur.

Denaturation of proteins

loss or randomization of native conformation due to disruption of hydrophobic interactions or modification of charges on proteins. Denaturants include heat, extremes of pH, organic solvents or detergents/urea

primary protein structure

the linear sequence of amino acids in the polypeptide chain.

Apoprotein

A ligand binding protein which doesn't currently have a ligand bound

β-turns

A nonrepetitive secondary structure four amino acids in length. They are often used to connect antiparallel β-sheets.

Ω-loops

A nonrepetitive secondary structure with a neck appropriately shaped like an Ω. They are often used on the surface of large globular proteins.

mutlimer

A protein containing multiple subunits of more than one type

globin fold

A protein fold consisting of eight alpha helices connected by short coils. It is found in both myo- and hemoglobins.

Holoprotein

A protein with attached ligand

Nucleotide-binding fold

A single-domain fold which promotes binding of NAD⁺ or similar molecules.

Prosthetic group

A tightly-bound organic ligand

advanced glycosylation end products

AGEs are a form of protein damage which is irreversible. The process is considered nonenzymatic glycosylation since it occurs without prompting from enzymes, and involves the addition of sugar. It is far more common in individuals with elevated blood sugar, such as diabetics. They slowly accumulate with time and can cause problems in the elderly.

Can you have a protein constructed from multiple domains?

Absolutely, it's common

Two types of folds in globular proteins

Actin fold, nucleotide-binding fold

How do add a kink to a protein's native conformation?

Addition or removal of proline with a cis-trans-prolyl isomererase

What requirement must all proteins meet in case of dysfunction or damage?

All proteins must be degradable when needed.

Porphyrin Ring

An organic structure consisting of four pyrrole rings. Heme is a porphyrin ring; it carries the Fe²⁺ which allows hemoglobin to function. As the ring of the heme group binds oxygen, a conformational change pulls the group into the plane of the ring.

Ligands

Any small molecular which may be bound in the active site of a protein.

Can you have a domain constructed from multiple polypeptides?

Each domains is a singly polypeptide

α-helix hydrogen bonding

Each peptide bond is connected by hydrogen bonds to the peptide bond four amino acid residues ahead of it and four amino acid residues behind it in the amino acid sequence. Unlike the β-sheet, all H-bonds occur within a single strand

HSP 70

Hsp 60 proteins (chaperonins) are large cylindrical proteins which assist hsp 70 when needed. They have ATPase activity which allows them to play an active part in avoiding misfolding.

HSP 60

Hsp 70 proteins bind to the polypeptides as they are synthesized on the ribosomes, shielding the hydrophobic surfaces to prevent aggregation until the full chain is synthesized and folding can occur.

What kind of saturation curve does myoglobin achieve?

Hyperbolic. This shape suggests that even at low pressure, myoglobin has a high affinity oxygen.

Chaperone proteins

Molecular chaperones are proteins that assist the non-covalent folding or unfolding and the assembly or disassembly of proteins. Many are also heat shock proteins (which prevent protein clumping/aggregation prior to completion of folding) Two most-prevalent chaperones are HSP 60 and HSP 70.

What does "Mb" stand for?

Myoglobin

Actin fold

Named for the first protein in which it was described, this fold is associated with ATP binding and hydrolysis. Although all have the same structure and function, the family shares little sequence similarity. Each variation contains multiple domains (usually four) The protein has a large cleft where ATP may enter and bind. ATP binding promotes a conformational change which closes the cleft.

heme

The iron-containing cofactor of hemoglobin.

Roles of the tertiary structure

1) formation of binding sites 2) maintains a proper surface or shell for the environment 3) retain flexibility (wiggling/shaking, not unfolding)

protomer

For proteins with multiple subunits, protomers may be used to describe their divisions. If hemoglobin has two α and two β subunits, it can be said to be a dimer of αβ-protomer

ionic bonds and salt bridges

Form around the polar shells of many cytosolic proteins. These attachments manage ionic charge and keep the proteins balanced.

β-sheet hydrogen bonding

Form between the carbonyl oxygen of one strand and the -NH amide bond of the other. Optimal binding occurs when the sheets are bent. Unlike the α-helices, β-sheet H-bonding occurs between separate strands.

Myoglobin [what does it look like?]

Globular protein composed of a single polypeptide. Has only one O₂ binding site. It is very similar in composition to the β-subunit of hemoglobin. Found in the skeletal and heart muscles.

Three major structural classifications of proteins

Globular, fibrous, transmembrane

What does "Hb" stand for?

Hemoglobin

Hemoglobin R state

Hemoglobin enters the relaxed (R) state when prompted by conformational change accompanying the binding of other subunits to O₂. This R state has a higher affinity for O₂ gas.

Hemoglobin

Hemoglobin is an RBC protein tetramer composed of two different types of subunits (2α- and 2β-polypeptide chains, referred to as two αβ-protomers). All four subunits have O₂ binding sites. The subunits are held together by noncovalent forces.

Fibrous protein

Proteins that are geometrically linear, arranged around a single axis, and have a repeating unit structure.

Transmembrane protein

Proteins that have one or more regions aligned to cross the lipid membrane

What happens if denaturating conditions are removed?

Proteins will renature, indicating that all, or practically all, information needed to specify the 3-D structure is contained in covalent sequence.

Structural domains

Regions of protein structure that fold independently. Multiple domains can be linked together to form a functional protein.

What is a protein fold?

Relatively large patterns of three-dimensional structure that have been recognized in many proteins. They serve a variety of distinct purposes, generally classified by the type of fold.

Motifs

Relatively small arrangements of secondary structure that are recognized in many different proteins

Benefits of α-helix?

Rigid structure. Allows controlled rotation at certain angles. Maximum hydrogen bonding Minimized steric hinderance (outward amino acid angle)

quaternary protein structure

Some proteins exhibit quaternary structure, the combination of two or more subunits, each composed of a polypeptide chain.

Association constant Ka

The association constant for a binding site on a protein. The higher the Ka, the tighter the bonding of ligand to protein.

Forces which maintain tertiary structure

The forces that maintain tertiary structure are hydrogen bonds, ionic bonds, van der Waals interactions, hydrophobic interactions and disulfide bond formation.

Dissociation constant Kd

The higher the Kd, the worse the bond between ligand and protein