Biochemistry Flashcards
(39 cards)
At physiological pH, what is the charge of the amino and carboxyl group of an amino acid?
Amino group is protonated (+) and carboxyl group is deprotonated (-)
At physiological pH amino acids are zwitterions (contain positive and negative charge on the same molecule)
Which amino acids have non polar side chains??
Glycine, alanine, valine, leucine, isoleucine, methionine, phenylalanine, tryptophan, proline, and tyrosine
Which amino acids have polar side chains
Serine, threonine, cysteine, asparagine, glutamine
What type of reaction is the formation of a peptide bond?
Peptide bond forms between two amino acids – type of a nucleophilic substitution reaction (carbonyl group of carboxylic acid acts as the electrophile and nitrogen of the amino group is the nucleophile)
Note that the carbonyl group of the carboxylic acid is an electrophile. The nucleophile is the nitrogen of the amino group. The nitrogen of the second amino acid has a free lone pair that can attack the carbonyl group, forming an N-C bond.
In the process, electrons from the second bond of the C=O are sent to the carbonyl oxygen. These electrons then reform a second bond, and the leaving group (-OH) leaves with a lone pair of electrons to form a molecule of water.
What kind of reaction is this?
Dehydration reaction
Why are peptide/amide bonds said to have partial double bond character?
Carbon of the amide bond is also double-bonded to oxygen atom. Nitrogen has a lone pair (partial double bond cannot freely rotate like a single bond)
How are peptide bonds broken?
Peptide bond hydrolysis - broken by water molecules
What level of protein structure is defined solely by the identity of the amino acids within it?
Primary structure
What kind of bonding is characteristic of secondary protein structure, and between what components does it occur?
Hydrogen bonding – between atoms forming the backbone of the protein chain NOT between side chains of each amino acid (H of N-H of one amino acid and carbonyl O of another amino acid)
How do R groups contribute to the hydrogen bonding forming the alpha helix?
They do not
What are interactions that arise between side chains of amino acids?
Concerns tertiary structure – ionic interactions, hydrophobic interactions
When do post-translational modifications occur and what are some examples?
Occur after the protein has completely been translated from RNA. Phosphorylation, formation of disulfide bonds, ubiquitination, glycosylation
Where in a protein would glycine be found and why?
Least sterically hindered amino acid - found in areas that require a high amount of flexibility and rotation
What amino acid is involved in disulfide bond?
Cysteine
How does proline contribute to protein structure and why?
Most sterically hindered – creates a kink – found in areas that need a bend or should be immobile
What is the hydrophobic effect and how does it relate to entropy?
Consequence of polar and non polar interactions – hydrophobic amino acids typically found within interior of a protein – surrounding water molecules therefore have more area to bind to surface of protein
What are some factors that can disrupt protein folding?
High/low pH, high salt concentration, high temperature
What is the process by which proteins unfold/lose their correct 3D structure and how can this be mediated?
Called denaturation – chaperones can fold them back into their native state
What structures serve as a scaffold for a) cell and b) tissue and what proteins are they composed of?
a) Cytoskeleton (actin, tubulin)
b) ECM (collagen, keratin, elastin)
Composed of five primary proteins: actin, keratin, elastin, collagen, and tubulin
Where do actin monomers attach/detach to microfilments?
Attach at (+) end and detach at (-) end – Association and dissociation of actin molecules is regulated by ATP (cycle is known as tread milling)
What enables myosin to generate its power stroke and generate force.
Dissociation of phosphate
What structure is vital in mitosis and meiosis to ensure that chromosomes are separated?
Microtubules (recall that they have polarity which allows kinesins and dyenins to walk along microtubules).
How to kinesins and dyenins move in the cell?
They are motor proteins - move by hydrolyzing ATP. Polarity allows them to travel in opposite directions. Kinesin - positive end. Dyenin - negative end.
In addition to nonenzymatic proteins providing structure within the cell and transmembrane proteins embedded in the cell membrane, there are also nonenzymatic proteins circulating in our blood. What are these called?
Hormones
