Lecture 1/2: Amino Acid Structure and Properties Flashcards
(25 cards)
Explain three types of protein cofactors
prosthetic groups: larger chemicals tightly bound by covalent or non-covalent forces
coenzyme: type of cofactor that shuttles commonly-used functional groups in chemical reactions
Metal ion cofactors: interact with the protein to help with its structure or be involved in enzyme catalysis
Describe covalent bonds
electron sharing between two adjacent atoms
Describe ionic/electrostatic interactions
strength depends on the polarity of the charged species . Sometimes known as salt bridges for full negative to positive interactions
Describe hydrogen bonds
strength is proportional to the polarity of the H bond donor and acceptor
Describe hydrophobic interactions
Dependant upon the entropy of water being released, causing hydrophobic regions to ocme together
Describe van der waals forces
relatively weak forces that depend on the size of the atoms and the distance between them
Describe hydrogen bond formation in water
Can form up to 4 transient hydrogen bonds due to the unequal sharing of electrons
Important for molecule solubilization and the formulation of complex structures
Amphiphiles/amphipathic molecules
molecules that can be both hydrophobic and hydrophyllic
What is primarily responsible for driving protein folding
The hydrophobic effect and Hydrogen-bonding
Why do we only see L amino acids in cells?
Physiologically relevent because steric strain is minimized allowing for best possible binding (clockwise/ R stereochemistry)
What are five non-covalent interactions in cells?
1) H-bonds between hydroxyl, carboxyl, thiol, and amino groups to help with solubility
2) H-bonds between side chains
3) Hydrophobic interactions between aliphatic and hydrophobic side chains
4) Ionic interactions important for ligand, cofactor, and substrate binding
5) salt bridges btwn positively and negatively charged amino acids
What are disulfide bridges
occur within a chain or between different polypeptide chains due to the formation of disulfide bonds, the cross linkage of two cystines
PDI
Protien Disulfide Isomerase; enzymes that help catayze the oxidation rxn to for disulfide bonds
Where does disulfide bond formation occur
post-translational modification that occurs in some secreted proteins as they pass through the endoplasmic reticulum, rxn catalyzed by PDI
Why do cytosolic protiens contain ‘free’ cytesines?
Due to the reducing nature of cytosol
How can disulfide bonds be broken
By reducing agents in the cytosol or in the lab
- in lab: beta-mercaptoethanol, BME can break disulfide bonds via reduction
How do disulfide bonds contribute to curly hair? perms?
Alpha keratin has a high content of cytesines and cystines, the H-bonding between karatin fibres contribute to curly hair
perms reduce the crosslinks with heat and chemicals to break the non-covalent interactions, then make the new desired crosslinks by adding an oxidizing agent
Where can hydrophobic amino acids be found in a protein
- found on the interior of proteins to maximize the number of hydrophillic interactions with water
- some may be found on the surface to allow for non covalent interactions
What are four molecules amino acids can be metabolized to
- hormones
- neurotransmitters
- nitrogenous bases
- energy-producing intermediates
What are two nonessential amino acids and why
Asparganine (N) and Glutamine (Q) are non-essential because they can be derived from Aspartate (D) and Glutamate (E)
Name seven important covalent post-translational modifcations
- Phosphorylation
- Ubiquitination
- Glycosylation
- Acetylation
- Methylation
- Hydroxylation
- Carboxylation
What is a silent mutation
A single nucleotide mutation in the code that does not result in a change of the amino acid produced
What is a conservative mutation
A mutation that results in a change in amino acid that retains similar physical properties as the original amino acid, eg one hydrophobic amino acid to another (Leu to Ile)
What is a non-conservative mutation
A change in nucleotide that results in a change in code such that a different amino acid with different physical properties is produced
