Biological Molecules Flashcards
Are polar/ionic amino acids more likely to be found on the periphery of proteins? Or near the centre?
Polar and/or ionic amino acids are found at the periphery of amino acids to make them hydrophilic with a hydrophobic core.
(this isn’t always the case however!)
What is the only non optically active amino acid? Where is glycine usually found in proteins?
Glycine
Often found at the corners of proteins. It is small and although hydrophobic, is found on the surface of proteins.
What is molecule called when it has both acid and basic components?
What are they called in aqueous solutions because of this property?
Amphoteric
Amino acids are examples. Amino acids in aqueous solutions have their NH2 group become ammonium ion (NH3+) and their COOH group become a carboxylate ion (COO-). As a result, they are called zwitterions (dipolar ions) in aqueous solution
In aqueous solution there is an equilibrium present between the dipolar, the anionic and the cationic forms of the amino acid. Therefore the charge on the amino acid will vary with the pH of the solution , and with the isoelectric point.
What makes histidine a good biological buffer?
It can act as either an acid or a base, depending on the pH of the solution that its in.
Describe amino acid charge in aqueous solution. What is the isoelectric point?
In aqueous solution there is an equilibrium present between the dipolar, the anionic and the cationic forms of the amino acid. Therefore the charge on the amino acid will vary with the pH of the solution , and with the isoelectric point.
The isoelectric point is the average of the two pKa values of an amino acid (depending on the dissociated group)
What will the charge of an amino acid above and below its isoelectric point?
Above (basic conditions): net negative charge
Below (acidic conditions): net positive charge
What are peptide bonds and how can they be broken?
Amide bonds formed with condensation reactions (water removed)
They can be broken by adding water (hydrolysis)
If there is an excess of acidic amino acids in a protein, will the isoelectric point be below 7 or above 7?
What will their charge be at neutral pH (7)
Below 7
At pH = 7 these proteins will have net negative charge
Quickly define the four types of protein structure
Primary: sequence of amino acids determined by DNA and location of covalent bonds (eg. disulfide bonds)
Secondary: Hydrogen bonding introduced, α-helix or β-pleated sheets
Tertiary: Folding with noncovalent bonds to make globular protein with hydrophobic interior and hydrophilic interior. Covalent bonding of cysteine (cystine disulfide bridges) helps stabilize the 3’ structure.
Quaternary: Two or more protein chains (subunits) bond together by noncovalent bonds
Why is proline usually found at the beginning or end of a molecule?
It disrupts the alpha helix of a protein’s secondary structure
What are the two types of carbohydrates?
Polyhydroxy aldehydes (aldose) and ketones (ketose)
How can you classify carbohydrates?
- Aldose or ketose
- Carbons in ring (eg furanose, pyranose)
- α or β anomers
What are carbohydrate anomers and epimers? What is the most naturally occurring conformation?
Either alpha or beta
- Anomers occur when 2 cyclic forms of the molecule differ in conformation only at the hemiacetal carbon (carbon 1). Generally, pyranose take the chair conformation, as it is very stable, with all (usually) hydroxyl groups at the equatorial position. Epimers are 2 monosaccharides which differ in the conformation of one hydroxyl group
Describe the important reactions of carbohydrates
- Glycosidic bond formation between the hemiacetal carbon of one molecule and the hydroxyl group of another. (α-1,4 for α anomer, β-1,4 for β anomer). One molecule of water is released (condensation reaction).
Define the following:
Sucrose (common sugar):
Lactose:
Maltose:
Cellobiose:
Sucrose (common sugar): glucose + fructose
Lactose: Glucose + galactose
Maltose: glucose + glucose (α-1,4 bond)
Cellobiose: glucose and glucose (β-1,4 bond)
