Chp 4: Protein Structure Flashcards
What are polymers made of proteins called?
Amino Acids
Draw the general structure of an amino acid at physiological pH
Under what conditions can cysteine form a disulfide bond?
Oxidative conditions
What is the approximate pKa of ionizable Asp?
4.0
What is the approximate pKa of ionizable His?
6.0
What is the approximate pKa of ionizable Glu?
4.0
What is the approximate pKa of ionizable NH3+ N-terminus?
9.0
What is the approximate pKa of ionizable Cys?
8.0
What is the approximate pKa of ionizable Tyr?
10.5
What is the approximate pKa of ionizable Lys?
10.5
What is the approximate pKa of ionizable Arg?
12.5
Relative abundance of amino acids in proteins
In nature, Leucine is the most abundant and Tryptophan is the least abundant
Average MW of an amino acid
110 Da when found in a protein
1 Da (Dalton) = 1 atomic mass unit (amu)
How the peptide bond is formed
Peptide bonds are made by condensation reactions. Amino acids in the peptide are called “amino acid residues” because only the residue atoms remain
Meaning of polypeptide chain-related terms: amino acid residue, amino- and carboxyl-terminal residues, and chain directionality
Properties of the peptide bond
The peptide bond has two resonance forms
Why rotation around N-Ca-C is restricted
Rotation around N-Ca-C is restricted due to steric constraints
The four levels of protein structure
Primary Structure
Secondary Structure
Tertiary Structure
Quaternary Structure
Definition of the secondary structure of proteins
The spatial arrangement of the polypeptides backbone
How the a-helix is specifically formed, stabilized, and ways to represent it
There are 3.6 amino acid residues in the helix.
H-bonds along the helical axis stabilize this structure
How the b-pleated sheet is specifically formed, stabilized, and ways to represent it
beta-pleated sheets are antiparallel and are extended compared to the double helix. Beta strands can be connected by turns or loops.
How the beta strands can be connected to form sheets
Colinear H-bonds create stability
How are B strands connected through H-bonds on the B sheet?
Beta strands can be connected by turns or loops of stabilizing H-bonds with irregular secondary structures. Antiparallel beta sheets are easily connected
Distinguish parallel and anti-parallel b-sheets
Parallel beta-sheet strands run up the same way starting with carbon and ending with nitrogen. Antiparallel beta-sheet strands run opposite to each other
Which beta sheet type is more stable and why
Antiparallel because the colinear H bonds create stability and are easily connected
How proteins differ in their composition
Proteins differ in their composition by the number of amino acid residues. The normal range of the number of amino acid residues is 153 (myoglobin) - 416 (phosphorylase kinase (yeast)).
(#AA residues)(110)=Molar mass
Definition of 3o structure of proteins, ways to represent it, and their advantages
The tertiary structure is the overall three-dimensional structure of a polypeptide made of interactions between the R-groups of the amino acids that make up the protein.
Tertiary structures have hydrophobic interactions, in which amino acids with nonpolar, hydrophobic R groups cluster together on the inside of the protein, leaving hydrophilic amino acids on the outside to interact with surrounding water molecules.
There’s one special type of covalent bond that can contribute to tertiary structure: the disulfide bond. Disulfide bonds, covalent linkages between the sulfur-containing side chains of cysteines, are much stronger than the other types of bonds that contribute to tertiary structure. They act like molecular “safety pins,” keeping parts of the polypeptide firmly attached to one another.
Recognize protein types: all-alpha, all-beta, alpha/beta
How to identify layers in proteins and the location of non-polar residues
polar molecules are exterior and nonpolar molecules are on the interior or the proteins
Major stabilizing force of the tertiary structure
The largest force governing protein structure is the hydrophobic effect which causes nonpolar groups to aggregate in order to minimize their contact with water.
Meaning of a protein domain
Domain: a polypeptide segment that has folded into a single structural unit with a hydrophobic core
General principles of globular proteins
- Typically at least 2 layers of secondary structure
- Hydrophobic core
- Typically rich in secondary structure
- H-bonds minimize hydrophilicity of the polar backbone groups
- Hydrophilic surface
- Typically with irregular structure
- Polar backbone groups of loops can form H-bonds with water
Correlation of residue’s hydrophobicity with location
The greater the residue’s hydrophobicity is, the more likely it is found in the interior of the protein
Role of ions pairs, disulfide bonds, and metals in the stabilization of proteins
Some proteins are stabilized by electrostatic or ionic interactions.
Characteristics of protein folding in vivo vs in vitro
In Vivo: a newly synthesized polypeptide begins to fold as it leaves the ribosome
- may require molecular chaperones
- post-translation process
In Vitro: full-length polypeptide is denatured and then allowed to renature.
- Not a random process
- Afinsen found that primary structure determines tertiary structure
Molecular chaperones: what they are and what they do
In the laboratory, certain small proteins can be repeatedly denatured and renatured, but in the cell, protein folding is more complicated and may require the assistance of other proteins. Some of these are known as molecular chaperones
Anfinsen’s postulate
The structure of a small globular protein is determined by the protein’s amino acid sequence
What is the driving force of protein folding
hydrophobic effect
The largest stabilizing force in proteins
Hydrophobic effect.
H-bonding is NOT a major determinant of protein stability
How to interpret the folding funnel
When the protein is in the unfolded state there are many forms and increased entropy. When the protein is in the folded state it has one conformation and decreased entropy.
Definition of quaternary structure
The spatial arrangement of polypeptides is known as the protein’s quaternary structure.
Most proteins, especially those with molecular masses greater than 100 kD, consist of more than one polypeptide chain. The individual chains, called subunits, may all be identical, in which case the protein is known as a homodimer, homotetramer, and so on. If the chains are not all identical, the prefix hetero- is used.
The forces that hold subunits together are similar to those that determine the tertiary structures of the individual polypeptides.
Meaning of a subunit
individual polypeptide chains and two or more are quarternary structures
Nomenclature used to distinguish the different types of quaternary structure
The individual polypeptide chains, called subunits, may all be identical, in which case the protein is known as a homodimer, homotetramer, and so on. If the chains are not all identical, the prefix hetero- is used.
Techniques used to separate proteins
Chromatography
Separation bases of size-exclusion chromatography
Separation based on size. Also called gel filtration
Other name of size-exclusion chromatography
gel filtration
Separation bases of ion-exchange chromatography
Protein separation based on differences in net charge.
(-) charged proteins bind to (+) charged solid supports and (+) charges proteins bind to (-) charges sold supports
Components of SDS-PAGE
Used to verify purification of a protein.
Separation is based on mass and size
Separation bases of SDS-PAGE
BetaME is added to reduce disulfide bonds. SDS is added to denature protein and add a (-) charge. 1 SDS bonds uniformly along the chain every 2 amino acid residues and the protein is separated on the basis of mass or size.
D. Asp
B
D. Asp
B. His
D. Polar Neutral
B. Acidic
C. Tyr
C. T N Y
B. +1
D. Cys
E. W, Y, F
E. W
C. Glu
E. His
E. L & W
B. b
C. A pentapeptide with 4 peptide bonds
E. 5
B. -1
E. +2
A. a
C. 5
18/3.6=5
C. It is not stabilized by the H-bonds
A. Alpha helix
D. An anitparallel Beta sheet
C. Parallel beta sheets are more stable than anti-parallel ones
C. The protein’s amino acid sequence (primary structure)
B. Disulfide bond
E. Hydrophobic interactions
B. The tendency of non-polar molecules to avoid interaction with water and thus aggregate
C. Leu; Ser
C. Glu (-) - Asn - Ser - Thr - Arg (+)
C. E (glutamate)
B. His; H-bond
Ser is polar nuetral
What is the abbreviated form of hemoglobin?
alpha2beta2
What are the 3 most commonly used types of chromatography?
- Ion-exchange chromatography
- Gel-filtration chromatography
- Affinity chromatography
D. Gel-filtration chromatography
E. All of the above
B. Largest
B. Size
E. Lysozyme, hemoglobin, TPI
D. Hemoglobin, TPI, myoglobin, lysozyme
