1. Amino acids Flashcards
Which functional groups do aa contain? What is a zwitterion?
amino and carboxyl group, R side chain and H
zwitterion - molec w/ functional groups of both 1 pos charge and 1 neg charge
Know D vs L aa
If H is pointing AWAY from you, amino = right side –> L; amino = left side –> D (it’s basically the opposite of H is pointing towards you)
L aa have S config except cysteine has R config because -CH2SH > -COOH
Name and describe proteins’ 4 levels of structure
Primary: aa seq stabilized by covalent peptide bonds, secondary: a helix or beta sheets stabilized by H bonds B/W THE BACKBONE (ie. R GROUPS HAVE NOTHING TO DO WITH SECONDARY STRUCTURE), tertiary: 3D structure to show hydrophobicity/phillicity, quaternary: multiple subunits
At which structure does denaturation occur?
Tert —> protein loses its function. High conc of salts and detergents can denature, heat can denature. Sometimes it can affect sec and quat structures but NEVER primary —> can’t break peptide bonds
What are conjugated proteins?
Proteins that COVALENTLY attach to prosthetic group to do a function (ex: heme, lipoproteins, glycoproteins, nucleoproteins)
Prosthetic groups = tightly bound cofactors/coenzymes necessary for enzyme function
What is and how to find pI?
pH at which aa = electrically neutral; (pKa of amino + pKa of carboxyl)/2
THIS DOESNT MEAN PHYSIOLOGICAL PH. YOU ALWAYS HAVE TO FIND AVG OF SOME PKAS TO GET A PI VALUE
Type of rxn when making vs breaking peptide bond. Know which one is ender/exergonic
Lose a water molec => dehydration/condensation; endergonic vs using a water molec => hydrolysis (when breaking peptide bond, you add H to amide nitrogen and OH to carbonyl carbon); exergonic
Bases can catalyze peptide bond hydrolysis
Which type of bonds help determine tertiary structure?
H bonds and disulfide bonds; disulfide bonds create loops (ex: curly hair)
How are alpha helices and beta sheets stabilized?
H bonds B/W BACKBONE, NOT R GROUPS
Parallel vs antiparallel beta sheets w/ hydrophobicity
Hydrophobic residues on both sides of sheet vs on one side
Type I vs II beta turn. Know alpha helix breakers
Proline –> tight turn vs glycine –> flexible turn. Both = alpha helix breakers since they form kinks
Strecker and Gabriel syntheses of aa make what type of mixture?
Racemic mixture of aa
Do bulky aa tend to favor alpha helices or beta sheets?
Beta sheets
Histidine has pKa of 6.5, close to physiological pH. What does this mean?
exists both in de/protonated forms
Proline has what type of amino group? How are they involved in secondary structure?
secondary alpha amino group
Proline = found in start of alpha helix or turns in beta sheets, rarely in the middle of structures b/c it’s too rigid
Cysteine vs cystine. What’s a thiol group?
reduced form vs oxidized form; 2 cysteines makes 1 cystine; intracellular environ favors [H] form and extracellular environ favors [O] form
Thiol = -SH
Average pKas for carboxyl vs amino groups
2 vs 9-10
What happens with pH > vs < pKa?
Deprotonated vs protonated
Strecker synthesis
1) ald/ket + ammonia in presence of H+ –> imine + H2O
2) imine + KCN in presence of H+ –> alpha amino nitrile
3) alpha amino nitrile + H3O+ –> alpha amino acid
List essential aa
Very Heavy MILK is essential? - WTF
V, H, M, I, L, K, W, T, F
Avg molec weight of aa
110 Daltons
Do peptide bonds have free rotation? Need enzyme to break em?
Peptide bonds have partial bond character —> no free rotation. Even though breaking them is exergonic, they still have high Ea —> need enzymes to break em
Most polar vs least polar of nonpolar aa
proline vs isoleucine b/c long alkyl chain
Which aa can be phosphorylated?
ser and thr; and his (in proks)
