Proteins

• Shape dictates everything, and it is directed by amino acid sequence

Learning Outcomes

• Define the classes of proteins based on their shape, whether they are fibrous or globular.
• Compare and contrast simple vs conjugated proteins.
• Define and describe the four levels of protein structure, including the bonds that are present in each.
• Describe the post-translational protein modifications; irreversible (including peptide bond cleavage, glycosylation), and reversible covalent modifications (including phosphorylation/dephosphorylation, allosteric modification).
• Briefly describe how proteins are folded.
• Briefly describe how proteins are localized to specific cellular locations/secreted from the cell and how compartmentalization helps with enzyme regulation.
• Define protein denaturation and describe how strong acids/bases, organic solvents, salts, and heavy metal ions denature proteins.
• Describe the ubiquitin pathway process that involves the degradation of proteins.

Outline

• Classify proteins by their shape and/or composition.
• Describe the four levels of protein structure, including primary, secondary, tertiary, and quaternary structures.
• Give an overview of post-translational protein modifications.
• Describe protein denaturation.
• Talk about protein degradation.

Protein Classification: Shape

• Proteins can be either fibrous and globular.

• Fibrous proteins

• Have long and rod-like shapes.

• Have structural functions, and provide strength.

• Are insoluble in water.

• Examples are keratin or collagen.

• Globular proteins

• Have compact and spherical shapes.

• Generally have dynamic functions.

• Catalyze reactions with enzymes.

• Can also act as carrier proteins.

• Are generally soluble in water.

• Examples are enzymes, hemoglobin, and albumin.

Protein Classification: Composition

• Proteins are also classified as simple proteins.
• Simple proteins are made up of only amino acids.
• Proteins are also classified as conjugated proteins.
• Conjugated proteins are composed of a protein portion and a non-protein portion.
  • The protein portion contains only amino acids.
  • The non-protein portion is called a prosthetic group.
• A conjugated protein without its prosthetic group is called an apoprotein.
• Examples of conjugated proteins are hemoglobin and myoglobin.

Protein Structures

• There are four important levels of protein structure; primary, secondary, tertiary and quaternary.
• Primary structure is from the amino terminal end to the C-terminal end.
• Secondary structure depends on how the protein's backbone is (in a beta sheet or an alpha helix).
• Tertiary structure is the overall structure of the protein
• Quaternary structure depends on how various subunits interact.

Protein Structure - Primary

• Primary protein structure is simply a polypeptide chain, composed of a linear sequence of amino acids.
• They are synthesized from mRNA transcript via translation, which is derived from a gene (DNA).
• Linked via a peptide bond which is very strong.

Protein structure - Secondary

• The regularly repeating backbone conformations formed by H-bonds between carboxyl and amino groups.

• There are two main types of secondary structures.

• Alpha helix.

• Rigid rod like structure.

• Often depicted schematically like a piece of curled ribbon.

• Beta-pleated sheet

  • Involves two or more polypeptide segments of a protein line up side-by side.
  • Held together by Hydrogen bonds between distal carboxyl and amino groups.
  • Depicted as "SCB" schematically using arrows.

• Super secondary structure

  • Results from the combination of alpha helices and/or beta-pleated sheets.

Protein Structure - Tertiary

• A three-dimensional folded structure that utilizes side chain interactions like H-bonds, salt bridges, disulfide bridges, and/or hydrophobic interactions.
• Disulfide bonds in particular are very important in the structure of extracellular proteins.
• Disulfide bonds help protect the protein from denaturation due to changes in blood pH or salt concentrations.
• An example would be the A and B chains in insulin.

Protein Structure - Quaternary

• Many proteins use multiple polypeptide subunits.
• The association of all of the subunits form the quaternary structures of a protein.
• At this point the protein is functional.
• Consider hemoglobin, which has four subunits (2 beta and 2 alpha). Fe2+ (iron) must be in a ferrous state. Binding of oxygen changes the shape of the subunits, which changes the shape of hemoglobin.
• Oligomers are proteins composed of several subunits. Hemoglobin is considered to be an oligomer.
• Multimers are proteins composed of many subunits. Pyruvate dehydrogenase is a multimer.
• Protomer are any repeating structural unit within a multimeric protein.
• Hemoglobin is made of a pair of alpha-beta protomers.

Post-Translation Reminder

• Important events happen to the protein after full translation:
• May be modified; can folded into a specific 3-D shape.
• Proper folding is important as this determines its function, and determines the proteins cellular location.

Protein Modification - Covalent Modifications

• Covalent modifications
  • Alters proteins structure by forming or breaking covalent bonds.
• There are two types of covalent modification; irreversible and reversible.
• Irreversible reactions include
  • Peptide bond cleavage via methyanine (an example).
  • Addition of a carbohydrate to the protein; known as glycosylation can impact its characteristics.
• Reversible reactions alter protein structure by covalent modifications.
  • A few examples phosphorylation/de-phosphorylation, adding or removing phosphorus.
  • Changes what allosteric state of enzymes is in.
  • Allosteric binding

Irreversible Covalent Modification - Cleavage

• Makes sure a protein or enzyme is only used when needed and in the correct location.
• Prior to cleavage, an enzyme might be called a proenzyme (or zymogen).
• Insulin's activation induces the cleaving and removal of part of the original portion of the protein.

Irreversible Covalent Modification - Glycosylation

• Proteins that are secreted or bound to the cell membrane will be glycosylated. N-linked glycosylation
• Attaches carbohydrates to the N on asparagine in the rough endoplasmic reticulum. -A carbohydrate component is pre-assembled on a lipid molecule (dolichol) and then transferred onto the protein in one step with the help a glycosyltransferase enzyme.
• From there it is transferred up to the Golgi for further modifications. O-linked glycosylation
• Attaches a carbohydrate to the OH on serine or threonine.
• At that point Protiens are sent to the Golgi after translation, where the carbohydrate is added in a step-wise fashion with the help of glycosyltransferases enzymes.

Reversible Covalent Modifications

• A group as specific as a phosphate group is added/removed.
• Whether adding phosphates turns an enzyme on or off

Reversible Covalent Modification - Allosteric

• Controls regulatory enzymes by having allosteric modification of proteins that are allosteric enzymes
• Binding to an enzyme's allosteric site changes the conformation and activity of the enzyme

Reversible Covalent Modification - Allosteric Enzymes

• Has more than one subunit.
• The Active site is on one subunit, allosteric side on the other.
• Allosteric enzymes can increase or prevent the substrate binding to the enzyme.

Protein Folding

• Post-protein translation, proteins will begin folding into tertiary and quaternary shapes. Chaperones are protiens that helo other protiens fold into their corect shape.
• Stabilize proteins in the correct cellular location.
• Common chaperones include hsp (heat shock proteins) and stabilize the location of the protein not yet folded.
• Eventually these proteins bind and stabilize portions of the protein that have not yet been folded, being released through ATP hydrolysis.

Protein Compartmentalization

• Proteins are sent to specific cellular locations to carry our their functions.

• All translation occurs in the cytosol.

• Translation begins at the cytosol but finishes in the Rough ER

• From the ER, protiens can travel to the specific cellular locations, or secreted with the help of vesicles.

• Enzymes are a method of compartmentatization, which allows for enzymes to regulate

• Compartmentalization

• Enzymes separated will only contain the substrates, and will perform beta oxidations and fatty synthesis in the ctolasm.

• Other compartments will have different environments, such as specific pH's.

Loss of Protein Structure

• This disruption to folding or shape is more specifically called protien denaturing. This happens when the bonds holding the protien together are disrupted.

Protein Denaturation: General

• Proteins are denatured when bonds with in protiens are impacted via
• Strong acids or bases (adding or removing hydrogens).
• Affecting organic solvents
• Disrupting detergents, which affects charged interactions.
• High salt concentrations.

Protein Denaturation - Heavy Metals

• Lets consider what heavy metals do to denature protiens in mercury amount is crucial for
• Based on the amount of charge, the amino acid side chain will bind to the corresponding heavy metal

Protein Denaturation - Heavy Metals Cont

• Charged groups of heavy metals can bind to sulfhydryl groups, altering the shape of the protein.
• The binding of Pb+2 is an example as it alters the shape needed to synthesize Hemoglobin.

Protien Degradation

• One of the key pathways for protien degradation is utilizing a ubiquitin pathway.
• This accumulation can degrade folding and accumulate folding, so instead it targets "tagged" protiens that have 1 or more ubiquitin.
• The Ubiquitin pathway is responsible for degrading half lives with enzymes.

Enzymes Preview

• Enzymes can be regulated through reversible and irreversible covalent modifications, and gene transcripts.

This lesson explores protein structure, discussing hemoglobin subunit interactions, proline's effect on alpha helices, disulfide bonds, glycosylation, and heavy metals. It further examines myoglobin vs. hemoglobin function, ketone body metabolism in the liver, insulin's role in fed state, and hemoglobin breakdown after red blood cell death.