Amino Acids, Peptides, and Proteins I and II Flashcards
Identify alpha carbon, amino group, carboxylic acid group, and side chains of an amino acid.
Amino group - NH3+
Side chain - R
Alpha carbon - (NH3)-C-(COOH)
Carboxylic Acid Group- COOH
What are the hydrophobic, nonpolar amino acids? (Aliphatic)
What are the aromatic amino acids?
Glycine (G), Valine V), Alanine (A), Leucine (L), Isoleucine (I), Methionine (M)
Phenylalanine (F), Tyrosine (Y), Tryptophan (W)
What are the polar, uncharged and charged amino acids?
Uncharged: Serine (S), Threonine (T), Cysteine (C), Proline (P), Asparagine (N), Glutamine (Q)
+ Charged: Histidine (H), Lysine (K), Arginine (R)
- Charged: Aspartate(D), Glutamate(E)
Disulfide Bond and Function
Covalent linkage between two sulfur atoms.
In amino acids, between thiol groups of two cysteines. Functions to connect chains and stabilize secondary and tertiary structure (has ability to make inter and intra chain linkages).
List Major Post-Translational Covalent Modifications of Amino Side Chains.
- Hydroxylation of Proline
- Carboxylation of Glutamate
- Glycosylation
- Modification of Side Chains by Acetylation and Methylation
- Reversible Phosphorylation/Dephosphorylation of Ser, Thr, and Tyr.
- Ubiquitination
What enzyme is responsible for hydroxylation of proline?
Prolyl hydroxylase.
What creates a proline helix?
Multiple prolines and hydroxyprolines in a row. This is a predominant secondary structure in collagen.
Does addition of hydroxyl groups to proline increase or decrease the stability of collagen?
Increase
Prolyl hydroxylase relies on what co factor to be active?
Vitamin C
What is the condition Scurvy caused by?
Lack in Vitamin C. Prolyl hydroxylase cannot function without this cofactor, thus cannot hydroxylate proline resulting in loss of integrity of collagen in the body.
The addition of a carboxyl group to the side chain of glutamate is carried out by what enzyme?
Gamma-glutamyl carboxylase.
What cofactor does gamma-glutamyl carboxylase acquire to function?
Vitamin K
Where is carboxylation of glutamate found?
In clotting factors.
Why would a Vitamin K deficiency result in hemorrhage?
Gamma-glutamyl carboxylase cannot carboxylate glutamate without its cofactor, thus results in clot formation.
How does Waarfain prevent clotting?
Waarfin inhibits the activity of gamma-glutamyl carboxylase.
Where does acetylation by HATs (Histone Acetyl Transferases) usually occur at?
Lysine residues on free tails of histones.
Where does methylation by methyltransferases usually occur at?
At lysine and arginine residues. Dimethyl lysine, dimethyl arginine.
How does acetylation and methylation modify the protein when it does?
They alter the charge on the amino acid, resulting in activation of transcription.
What is Vorinostat?
An HDAC inhibitor used in cancer therapies. It prevents the removal of acetyl groups from histones by histone deacetylase, which is responsible for silencing tumor supressor genes.
What is glycosylation?
Site specific enzymatic process that attaches glycans to proteins. Makes protein more polar.
Why are glycans important?
They serve a variety of structural and functional role in membrane and secreted proteins.
What are the five glycans that are produced?
N-linked: glycans to N of Asp and Arg
O-linked: glycans attached to hydroxy O
Phospho-glycans
C-linked glycans
Functions of Glycosylation
Proper protein folding, increased stability of secreted glycoproteins, cell-cell adhesion, role in recognition
What is the Congenital Disorder of Glycosylation (CDG)?
N-linked glycosylation is interrupted. Results in developmental delay and hypertonia.
What is Gleevac?
A tyrosine kinase inhibitor used to treat chronic myelogenous leukemia (CML).
What is Ubiquitination?
Targets protein for destruction by proteosome by adding ubiquitin to lysine residues.
What is Bortezomib?
Proteosome inhibitor used to treat multiple myeloma.
Where is the peptide bond in a chain of amino acids?
Btwn the carbonyl carbon and amide carbon.
Why can mutation in an amino acid sequence cause disease?
Alter the function of the protein because protein is misfolded, unstable, truncated or extended, or no longer responding to regulation.
Phi angle
angle around alpha carbon and amide nitrogen bond
Psi angle
angle around alpha carbon and carbonyl carbon
What is the general important function of proteases?
Break peptide bonds to ensure proteins are not active in locations where they could be destructive. (general and specific proteases)
What is a hydrogen bond?
Interaction of hydrogen atom with electronegative atom, F O N.
What is the role of hydrogen bond in alpha helices?
H bonds form between the carbonyl oxygen of the nth amino acid and amide nitrogen of the nth + 4 amino acid. Results in right handed helical structure and side chains pointing outward.
What is the role of hydrogen bonds in beta sheets?
To link two polypetide chains, can be parallel or antiparallel.
