Protein Structure Flashcards
What are polypeptides?
They are the polymers of sequentially bounded amino acids. They form proteins
Describe a proteins Primary Structure?
Linear chain of amino acids that forms the backbone of the protein. Formed by covalent peptide bonds.
How many amino acids does each have?
- Peptide chain
- Dipeptide
- Oligopeptide
- Polypeptide
- Less than 50
- 2
- Up tp 20
- More than 20
Can proteins contain more than one polypeptide chain?
Yes
What are the range of protein sizes?
Fifty amino acids to tens of thousands.
How much does the average amino acid weigh?
110 Daltons (Da)
How much does an average protein weigh and how many amino acids does this translate to?
50 kDa or 50,000 Da so about 500 amino acids
Is a peptide bond an intramolecular or intermolecular bond?
Intramolecular because it is a covalent bond.
What makes the primary structure of a protein very different from the other structures?
It is resistant to environmental variations like changes in pH or temperature extremes.
What is the only way to free individual amino acids in a peptide chain?
Hydrolysis
What enzymes do cells use to speed up hydrolysis?
Peptidases/Proteases that lower the energy barrier for hydrolysis.
What does it mean if primary structure has directionality?
Amino acids are always added to the carboxyl (C) terminus. The first amino acid in a chain has exposed amine group which is the amino (N) terminus.
How are amino acids listed when primary sequence is written out?
From N terminus to C terminus. This is also the order to how proteins are synthesized on the ribosome.
Describe a protein’s Secondary Structure.
First/most basic level of protein folding. It refers to local/small regions of protein folding. It involves BACKBONE interactions, not side chain interactions. Stabilized by hydrogen bonding between amino and carboxylic acid groups and nearby amino acids.
What are the common motifs of the secondary structure.
Alpha-Helices and Beta-Pleated Sheets.
What are alpha-helices?
Right handed spirals that are stabilized by hydrogen bonds between amino hydrogen of one amino acid and the carbonyl oxygen of another amino acid four residues down the chain. Common in DNA binding proteins because it fits neatly into the groove of a DNA double helix. Also common in membrane spanning proteins.
What are Beta-Pleated Sheets?
They are formed of beta-strands which are segments of a polypeptide chain that line up next to each other in a parallel of antiparallel orientation to form sheet like structure. They are held together by hydrogen bonds between carbonyl O2 of one strand and an amino H+ on an adjacent strand.
What type of secondary structure motif plays a big role in the disease amyloidosis? What are some example of amyloidosis diseases?
Beta-Pleated Sheets because this disease is characterized by the buildup of misfolded proteins called amyloid fibrils.
Alzheimer’s and Parkinson’s Disease
What are amyloid fibrils?
They are composed of improperly folded beta-sheets that group together in a cluster
What does the amino acid Proline do to a proteins secondary structure?
Because of its unique structure, its cyclic side tends to make a kink in polypeptide chains. Therefore, it is rarely found in alpha helices but can be found at the turn of beta- sheets.
Describe a protein’s Tertiary Structure.
It determines fully folded functional state. 3D folding pattern that results from amino acid SIDE CHAIN interactions. Non-covalent interactions driven by polarity/charge. This includes hydrophobic interactions, salt bridges (ionic), and hydrogen bonding. Also has covalent disulfide bonds that form between the sulfur atoms of two cysteine residues. (This makes it the strongest bond in the tertiary structure)
How are disulfide bonds formed?
Via oxidation
How are disulfide bonds broken?
Via reduction. Can use the reducing agent beta-mercaptoethanol to accomplish this.
What are Salt Bridges (Ionic Bond) in the tertiary structure?
When positive and negative side chains come together. Elements of both ionic and hydrogen bonding.
Describe a protein’s Quaternary Structure.
Assembly of multiple protein subunits into a larger complex. Each subunit is a polypeptide, but each is a piece of a larger structure and usually cannot function on its own. Held together by the same interactions that maintain tertiary structure (salt bridges, hydrophobic interactions, hydrogen bonds, and disulfide bonds)
What is a dimer? A trimer? A tetramer?
Protein with 2 subunits. 3 subunits. And 4 subunits.
Describe protein folding.
It is how secondary and tertiary structure of a protein generate a 3-dimensional shape. It is difficult to predict but most stable is preferred. It is also spontaneous and thermodynamically favorable.
What is entropy (𝚫S)?
It is the lack of order, degree of disorder or randomness of a system.
What is enthalpy (𝚫H)?
How much heat and work was added or removed from the substance.
How are proteins synthesized?
From the N to C terminus. mRNA is read from 5’ to 3’.
What structures do all proteins have?
Primary, Secondary, and Tertiary. (Only some have a Quaternary)
What is hemoglobin?
It has a quaternary structure. It is a tetramer (made up of 4 subunits). Can bind 4 oxygens and the binding of one oxygen alters the conformation of the other subunits in a way that facilitates oxygen binding.
What does the function of a protein depend on?
On the proteins 3D structure.
What is most likely to happen if a proteins 3D structure is disrupted?
The proteins function will also be disrupted.
What is denaturation?
The breaking up of the non-primary structures of a protein.
What do denaturing agents do?
Inactivate protein.
What are some denaturing agents?
Temperature High and Low pHs Solvents like alcohol or acetone. Detergents Urea and more solutes
What is Taq Polymerase?
It is a heat resistant protein that allows the polymerase chain reaction (PCR) to work.
Is denaturing permanent? Why?
No, since primary structure is not affected.
If something has high entropy it is energetically…?
Favorable
Where are hydrophobic amino acids found in a globular protein?
In its interior.
