2 AA Chem & Prot Organization Flashcards
Major structural and fxnal polymers in living systems
Proteins
Alphabet of protein structure lol
Amino acids
Essential AAs vs Non-Essential AAs vs. Semi-Essential
ESSENTIAL:
PVTTIMHALL
*Non-the rest
Semi-essential: some people need it; others don’t i.e. Arg, His
Chirality of amino acids
Property of bending light to the left or to the right
If bends to the left = L-config
*natural config in the body
If to the right = D-config
Different classifications of amino acids?
- Non-polar
FLAV & I Met & Trp at PGC
A. Aliphatic
GLAVI
- Polar
STYNQ - (+) Charge
Hug Kiss Run - (-) Charge
Ef
5. Aromatic FYT not H F -benzene Y - phenyl W - indole
*Histidine not considered aromatic because its absorption is very weak compared to other amino acids + not aromatic under high pH conditions
Primary sites of linkage of sugars to proteins? Classify.
Serine, Threonine, Asparagine (STN)
Polar.
Which of the polar amino acids have a weakly acidic hydroxyl group and may be found on the surface of proteins?
Tyrosine.
Which polar AA’s have an amine side chain?
N, Q
Why are there (-) charged amino acids?
D and E have carboxylic acids in their side chains. These are ionized at pH 7 and thus, carry negative charges on their beta and gamma carboxyl groups.
What is the general acid-base catalyst of many enzymes? What type of ring does it contain?
Histidine, imidazole
C
- Classification
- Importance
- Oxidized form
Cysteine
1. Non-polar sulfur AA
- Important for stabilization of protein structure and formation of a disulfide bond with other cysteine residues
- Cystine
Non-polar AA containing a nonpolar methyl thioether group in its side chain
Methionine
Cyclic imino acid?
Proline
-has a pyrrolidine ring
Glucogenic vs Ketogenic amino acids?
Glucogenic - amino acid can be converted to glucose
Ketogenic - amino acid can be converted to ketone bodies
Classification:
G: Rest (*including oxidized C)
K: L K
Both: WIFTY
Amino acids are acidic or basic?
Both!! They’re amphoteric.
What is a zwitterion?
Compounds with no overall electrical charge but contain separate parts which are + & - charged.
pH vs. pKa vs. pI
pH - indication if a system is acidic or alkaline
pKa - gives details of dissociation of an acid in aqueous solution
pI - pH at which aa is in its zwitterion form
Wild Card:
Draw the structures of the amino acids :)
Hehehehe
Four levels of protein structure.
1’ - aa sequence
2’ - interactions betweens adjacent aa
Tertiary - 3D folding of the polypeptide
Quarternary - arrangements of multiple polypeptides
Reaction occurring to form 1’ structure of protein
(Between 2 AA forming polypeptide chain): Condensation reaction
2’ structure: Alpha-Helix
- Bonds occurring to stabilize structure
- Which aa’s favor this structure?
- Usually right or left-handed?
- H bonds at adjacent regions of helical backbone
- DELMA
- Right-handed
2’ Structure: Beta sheet
- stabilized by which bond?
- Which aa’s more likely to have this form?
- H-bond laterally between peptide band
- IVY
Bonds found in a protein
1. Between side chain and carboxyl oxygen
- Between two side chains
- Between hydrophobic molecules
- Between charged particle
- Between cysteine amino acids
- H bond
- H bond
- Hydrophobic interaction or Van der Waals
- Ionic bond
- Disulfide bond/bridge
Quaternary structure: Peptide structural organization
Bonds:
1. Chemical bond involving sharing of e-
- Chemical bond not involving sharing of e-
- Involves electrostatic attraction between oppositely charged ions
- Between hydrophobic groups
- Between side chains or side chain + carboxyl oxygen
- Covalent Disulfide bonds
- Non-covalent Bond
- Salt Bridges Ionic Bonding
- Hydrophobic interaction
- Hydrogen bonds
A solution of pure protein is bombarded with radio waves as it is held in a strong magnetic field
NMR Spectroscopy
Determine 3D surface contours of protein & works well with proteins that form regular pattern in a small crystal or even a membrane
Electron microscopy
Factors affecting denaturation
- pH
- Temperature
- Acid/Base
- Pressure
- Detergents
Chaperones or HSP, disulfide isomerases assist in what process?
Protein Folding
What if you have abnormalities in:
- amyloid beta?
- Tau protein?
- Alpha-synuclein
- Prions
- transthyretin
Alzheimer’s Disease: 1, 2
Parkinson’s Disease: 1, 2, 3
Mad Cow Disease: 2, 4
Transthyretin Amyloidosis: 5
Which part of the amino acid pathway could cause these diseases:
- Albinism
- Alkaptonuria
- Maple Syrup Urine Disease (MSUD)
- Tyrosinase (Tyrosine -> Melanin conversion)
- Urine turns black when exposed to air (Between homogentisic acid —> acetoacetatefumarate)
- Branched chain alpha-keto dehydrogenase
