pH and Protein Folding Flashcards
What forces / bonds hold a protein together at each of these levels of structure?
PRIMARY: Covalent peptide bonds
SECONDARY: Hydrogen bonds
TERTIARY: Ionic bond, Disulfide bridge, Hydrogen bond (Hydrophobic interactions)
QUATERNARY: Ionic bond, Disulfide bridge, Hydrogen bond (Hydrophobic interactions)
How does each level of structure contribute to the overall shape of a protein?
- Primary structure puts together the unique sequence of amino acids
- Secondary coils or folds the polypeptide (R groups not involved) with H bonds
- Tertiary gives the protein its 3D shape by R group interactions
- Quaternary bonds two or more polypeptide chains through disulfide bridges and H bonds
How are alpha helices and beta pleated sheets formed?
- In the secondary structure the polypeptide chain sometimes coils to form an alpha helix or folds to form a pleated sheet using H bonds
- Form between the carbonyl O of one amino acid and the amino H of another (NH to CO coming off of backbone) (never between R groups)
What does it mean for a protein to have fibrous shape? (ex)
Formed when polypeptides with helical subunits form long chains running parallel to each other linked by disulfide bridges, and have structural functions
- Construct connective tissues, tendons, bone and muscle fiber
- Keratins, collagens and elastins
What does it mean for a protein to have a globular shape? (ex)
Results from the compact combination of an alpha helix and several pleated sheet regions and have roles in metabolic reactions
-Haemoglobin, insulin and many enzymes in the body
What factors affect the shape of a protein?
Different types of bonds at different levels of structure, such as H-bonds, ionic bonds, hydrophobic interactions, and disulfide bridges
Given a polypeptide with certain properties and amino acid R groups, in a given environment (water, oil, vacuum) can you predict how this protein might behave / fold?
-
What kinds of forces may cause a protein to denature?
- Heat and changes in pH, changes in salt concentration
- pH affects the charge of the amino groups and carboxyl groups on an amino acid
What is the pH scale and what is it a measure of?
- It measures how acidic or basic a solution is, which is based on the amount of Hydrogen in a solution
- A pH of 0 has more Hydrogen atoms than 14, which has less
What does it mean for a solution to be at pH 7?
A pH of 7 is neutral, meaning it has an equal concentration of H+ and OH- ions
Acid (define, ex)
- A compound that donates Hydrogen atoms to solutions.
- Battery acid, lemon juice, vinegar
Base (define, ex)
- A compound that accept Hydrogen atoms and removes them from a solution.
- Oven cleaner, bleach, milk
Buffer (define, ex)
- A substance that minimizes the changes in pH by either accepting or donating hydrogens to keep the pH the same.
- Tricine, bicine, cacodylate
- Weak acid + corresponding base
- Carbonic acid in human blood (H2CO3)
How does a change in pH potentially affect protein structure?
-If a change in pH is too great, a protein may denature causing it to lose its shape and function. Secondary and up are affected.
Primary
-The unique sequence in which Amino Acids bond to each other through peptide bonds to create a polypeptide.
Secondary
-Parts of the polypeptide fold coil or fold into local patterns such as an alpha helix or pleated sheet.
Tertiary
-The 3D shape of a polypeptide due to the interactions of the R groups.
Quaternary
-Exists in some proteins where two or more polypeptide chains bond together through various types of bonding.
Covalent
-The sharing of electron pairs between two atoms.
Ionic
-Two ions with opposite charges attract to each other.
Hydrogen Bond
-Opposite ends of polar molecules stick together weakly.
Hydrophobic Interactions
-The tendency of nonpolar molecules in a polar solvent to interact with one another by avoiding the solvent.
Disulfide Bridge
-A covalent bond connected with two sulfur atoms connecting tertiary or quaternary structures.
Denature / Denaturation
-The process in which proteins unfold due to changes in temperature or pH. Secondary structure and up are affected.
pH
- The measure of how basic or acidic a solution is (Potential of Hydrogen)
- 0 is most acidic and 14 is least acidic.
Solution
-A liquid consisting of a uniform mixture of two or more substances.
Solvent
-The dissolving agent.
Solute
-The substance being dissolved.
Examples of proteins denaturing
- Irreversible - egg is fried, the albumin protein in the liquid egg white is denatured when placed in a hot pan
- Bacteria that survive in hot springs have proteins that function at temperatures close to boiling
- The stomach is also very acidic, has a low pH, and denatures proteins as part of the digestion process; however, the digestive enzymes of the stomach retain their activity under these conditions.
How do pH changes affect amino acid structure?
- Affects the charge of amino and carboxyl groups (and amino acid R groups)
- Ex: carboxyl (acid) group will be uncharged at a low pH (COOH), but charged at a high pH (COO - )
How do pH changes affect protein structure?
- In an aqueous solution, an equilibrium (balance) exists between the dipolar ion and the anionic and cationic forms of the amino acid
- These changes will affect bonding and weak attractions within the protein and between the protein and other molecules
Carboxyl group
Acts as an acid by contributing an H+ to a solution and becoming ionized
Amino group
Acts as a base by picking up an H+ from a solution
