Lecture 5 (Protein Structure) Flashcards
Macromolecules account for what percent of the dry weight of bacterial cells?
87% This includes proteins, fatty acids, nucleic acids
Condensation reaction between two amino acids takes place between what groups?
The carbonyl group of one amino acid and the amino group of the other amino acid. The condensation reaction causes water to be lost.
Zwitterion
At physiological pH of 7. amino acids are zwitterions. Molecules that contain both a positive and a negative charge.
Methionine and Cysteine
Sulfur bearing amino acids. These two amino acids are considered to be non-polar
What are some of the modifications that can be done to Lysine?
Methylation, acetylation, ubiquination, sumosylation
What are some of the modifications that can be done to Asp, blu, his, arg?
Ligand binding & catalysis
What are some of the modifications that can be performed on Tyrosine, threonine, serene
Phosphorylation and glycosylation
The non-polar amino acids serve what function in the cell?
Conformational support/stability
True or False.
A protein can fold into more than one single conformation.
False. Although allosteric binding causes some sort of conformational alteration, the protein cannot just adopt a different conformation
Protein conformation is stabilized by _______ bonds.
Non-covalent. These includes van der waals interactions, hydrophobic interactions, hydrogen bonding, as well as electrostatic interactions
The strength of Van der Waasl attraction in water and in vacuum
Are the same. This is because Van der Waals interactions deal with atomic attraction caused by close proximity between atoms and electrostatic fluctuations when two atoms are positioned near one another
The hydrophobic Effect
Entropically driven exclusion of non-polar compounds in polar media. When they aggregate together is more thermodynamically favored due to less disruption of the hydrogen bonds and less surface area that is exposed to the polar solvent
Hydrophobic Effect on proteins
Most proteins have a hydrophobic core. This are typically situated in the core of the protein to diminish their exposure to the aqueous media.
Studies into protein folding and denaturation reveal what?
That the protein is able to adopt its native conformation after being denatured. This means that all the information required to direct proper protein folding is recorded in the primary protein sequence
non-Adjacent Amino acids
Proper protein folding allows an active site where substrate binding occurs. The active site brings non-adjacent amino acids to participate in reaction.
Chaperone Proteins
These proteins bind to nonpolar chains of partially folded proteins and prevent misfolding of proteins to occur
Protein Primary Structure
The amino acid sequence
Protein Secondary Structure
Structural elements like beta sheets and alpha helices
Protein Tertiary Structure
Domains (functional/structural)
Protein Quaternary structure
Multimeric complexes
What are some elements of secondary structure?
Alpha helices Beta Sheets Loops Turns Disulfide Bridges
The Alpha Helix and beta sheet account for what percent of protein secondary structure`
60%
The alpha Helix
3.6 residues per turn
Amino acids chains directed outward
Stabilized by hydrogen bonds (between amide HN and carbonyl CO)
Can have amphipathic character
How many amino acids are sufficient to traverse the plasma membrane?
18-22 amino acids
The Beta Sheet
Composed of Beta strands arranged in either parallel of anti-parallel orientation. Strands are stabilized by hydrogen bonds. Amino acids project towards alternate faces of the sheet
Which of the two major secondary structures can have amphipathic character?
Both the alpha helix and the beta sheet can have non-polar and polar regions
Beta Sheet Stacking
Beta Sheets composed largely of hydrophobic amino acid side chains can form large aggregates that are difficult to degrade, tend to accumulate in tissue, and are toxic to the tissue in which the are located
Coiled Coil
Associations of TWO alpha helices bound together by hydrophobic interactions between non-polar amino acids present along one side of each helix
What does a coiled coil do?
Stabilizes protein-protein interactions
Leucine Zipper
Also the name for a coiled coil. A non polar amino acid must repeat every three and every two.
L A**LV**L
Domains
Stable regions of a protein consisting of groups of secondary structural elements
What occurs as a nascent polypeptide emerges from the ribosome?
1) Secondary elements form
2) Domains fold
Protein begins folding while it is still being translated in the ribosome. It finishes flooding entirely once it is out of the ribosome
What are protein Modules
Domains that appear in many different proteins. A result of protein evolution that involves recombination of modules and yields proteins with new functionality
Modular Mix and Match
Gives rise to proteins with new combinations of properties
Is tertiary structure preserved?
Tertiary structure is preserved within protein families
Immunoglobulin is comprised of
both heavy and light chains
The inside of the cell is a _______ environment
Reducing. Since most cellular compartments are reducing environment, in general, disulfide bonds are unstable in the cytosol.
Immunoglubulin
Antibody. The Ig Y shaped domain that consists of four polypeptide chains: two identical heavy chains and two identical light chains that are connected by disulfide bonds
Hemoglobin
Heterotetrameric complex (2 alpha and 2 beta). An assembly of four globular protein complexes.
Neuraminidase
Used in viral antigen against influenza virus. Cleaves glycosidic linkages of neruraminic acids. Used in the prevention of spread of influenza virus. Composed of a homotetrameric protein complex. The tetramers are held together always by the same two domains. Like a snake circle. “Blue and orange domains bind.”
