Chapter 1: Amino Acids, Peptides, and Proteins Flashcards
What are the four groups attached to the central (Alpha) carbon of a proteinogenic amino acid.
- Amino Group (-NH2)
- A Carboxylic Acid Group (-COOH)
- Hydrogen atom
- An R group (Side Chain)
What is the stereochemistry of the chiral amino acid that appears in eukaryotic proteins?
- L or D?
- (R) or (S)? (Exception:)_____
- All chiral eukaryotic amino acids are L
- All chiral eukaryotic amino acids are (S), with the exception of cysteine (because cysteine is the only amino acid with an R group that has a higher priority than a carboxylic acid according to Cahn-Ingold-Prelog rules)
Amino Acids
Nonpolar, nonaromatic
There are seven of them
- Glycine
- Alanine
- Valine
- Leucine
- Isoleucine
- Methionine
- Proline
Amino Acids
Aromatic
There are three of them
- Tryptophan
- Phenylalanine
- Tyrosine
Amino Acids
Polar
There are five of them
- Serine
- Threonine
- Asparagine
- Glutamine
- Cysteine
Amino Acids
Negatively Charged/Acidic
There are two of them
- Asparagine
- Glutamate
Amino Acids
Positively Charged/Basic
There are three of them
- Lysine
- Arginine
- Histidine
Where do hydrophobic amino acids tend to reside with a protein? What about hydrophillic ones?
- Hydrophobic
- Tend to reside in the interior of a protein, away from water
- Hydrophilic
- Tend to remain on the surface if the protein, in cotact with water
Except for ___, all amino acids are chiral.
Except for ____, all amino acids have an (S) absolute configuration.
Glycine
Cysteine
Describe the mechanism for trypsin and chymotrypsin.
They break apart the amide bond by adding a hydrogenatom to the amide nitrogen and an OH group to the carbonyl carbon.
Describe the mechanism of a peptide bond formation
- The electrophilic carbonyl carbon on the first amino acid is attacked by the nucleophile amino group on the second amino acid.
- The hydrocy group of the carboxylic acid is kicked off.
- Amid Peptide Bond formation.
What is the difference between an amino a cid, a dipeptide, a tripeptide, an oligopeptide, and a polypeptide?
These species differ by the number of amino acids that make them up:
- Amino Acid = 1
- Dipeptide = 2
- Tripeptide = 3
- Oligopeptide = Few ( Less than 20)
- Poplypeptide = Many (more than 20)
What molecule is released during formation of a peptide bond?
Water
The primary structure of a protein is the order of its amino acids. The two main secindary structures are the ____ and _____, which both result from ______.
Alpha-Helix
Beta Pleated Sheet
Hydrogen Bonding
What role does proline serve in secondary structure?
Prolines rigid structure causes it to introduce kinks in alpha-helices or create turns in Beta pleated sheets
Which structure is this and describe its features.
- Alpha-Helix
- A rod like structure in which the peptide chain coils clockwise around a central axis.
Which structure is this and describe its features.
The peptide chains lie alongside one another, forming rows or strands held together by intramolecular hydrogen bons between carbonyl oxygen atoms on one chain and amide hydrogen atoms in an adjacent chain.
How is a tertiarty structure made?
By moving hydrophobic amino acid side chains into the interior of the protein.
What is the primary motivation for hydrophobic residues in polypeptide to move to the interior of the protein?
Increases the intropy by allowing water molecules on the surface of the protein to have more possible positions and configurations, The positive Delta S makes Delta G < 0, stabilizing the protein.
List the three different prosthetic groups that an be attached to a protein and name the conjugated protein.
- Lipids
- Carbohydrates
- Nucleic Acids
- They are known as lipoproteins, glycoproteins, and nucleoproteines.
What are the two main ways proteins are denatured?
- Heat
- Solutes
- Urea as such
