Chapter 3 - Protein Primary Structure Flashcards
Proteins are _______ composed of __ amino acids (AAs).
polymers; 20
Describe the structure of a protein.
All are alpha AAs, an -NH2 & a -COOH attached to the same alpha carbon, and an R group
At physiological pH (_____): The -NH2 is _______ (pKa ~_), The -COOH is ________ (pKa ___)
7.1-7.4; protonated; 9; deprotonated; < 3
At pH 6.8-7.4, most AAs are _______(dipolar ions) and the molecule has a net charge of ____.
zwitterions; 0
Why do chemists rarely use R/S nomenclature to describe AAs?
In nature __-AAs are used to construct proteins, __-AAs are rare in nature.
Because priorities change due to
differences in sidechain structure; L; D
What are the different types of AAs classified by R groups?
Aliphatic (hydrophobic), Aromatic (hydrophobic), Sulfur-containing, Alcohol-containing, Basic, Acidic
Glycine is the only AA without…
a chiral carbon.
Each of the aliphatic AAs, contains…
hydrophobic sidechains (glycine is not very hydrophobic)
L-Tyr and L-Trp absorb _______ at ___ nm, can be used to determine the ______ in solution.
UV-light; 280; protein
List the sulfur-containing AAs.
L-Methionine and L-Cysteine
Describe L-Methionine.
Has a nonpolar methyl thioether, fairly hydrophobic, often is the 1st
AA in a polypeptide chain.
Describe L-Cysteine.
Has a Beta thiol, ionizable at physiological pH
(pKa = 8.4), form weak H-bonds with N, O, 2 sulfhydryl can form a
disulfide bond (e.g., cystine)
List the alcohol-containing AAs and describe them.
L-Serine and L-threonine; β-OH groups on side chains, weakly ionizable sidechains (pKa ~16), nucleophilic, have 2 chiral centers, L-Threonine has a second chiral center
Why does salt have a high melting point?
Bc for non-covalent interactions, whole (+) charge to (-) charge interactions are strongest.
Is H-bonds stronger than whole charge/charge interactions? What about Van der Waals interactions?
Weaker than whole charge/charge, stronger than Van der Waals interactions
Describe basic AAs.
Sidechain has basic N atom, polar, at physiological pH: protonated
Describe acidic AAs & amide derivatives. Give ex.s
Acidic : L-Aspartate & L-glutamate have carboxylic acids in sidechains,
deprotonated at physiological pH, negatively charged
Amide: L-Asparagine & L-glutamine are primary amide derivatives
of L-Asp and L-Glu, highly polar, but uncharged
Define hydropathy.
Quantitative hydropathy scales rely on… and is based on…
It heavily influences what?
the relative hydrophobicity/hydrophilicity of an AA; hydrophobic/hydrophilic environments; based on ΔG for
transfer of an AA from a lipid bilayer to water; protein folding
Each AA has at least __pKa
values (α-_____ & α-____)…more if __ contains _____ functional
group.
2; carboxy; amino; R; ionizable
Ionization of AAs influences…
3D shape of proteins and enzyme catalysis
The isoelectric point (pI) is the
pH when…
the AA exists in dipolar
form, electronically neutral, net
charge is ‘0’ (‘zwitterion’).
How are peptide bonds formed?
α-Carboxyl of 1st AA reacts
with α-amino of 2nd AA
forms peptide bond
For peptide bonds, there is a partial __________. ______________ decreases steric hinderance of __ groups.
double bond; Trans configuration; R
How to name peptides?
Change -ine or -ate to -yl
How do you classify peptides?
Based on the # of amino acids: Oligopeptides have 2~20 AA, Polypeptides have > 20 AAs
Based on the shape of the molecule: chain, cyclic
Define proteins and how they are classified (6).
biopolymers of amino acids (>50)
Polypeptide, long, continuous and unbranched;
Monomeric: 1 peptide chain.
Multimeric: more than 1 subunits.
Simple: hydrolyze to amino acids only.
Conjugated: bonded to a prosthetic group (sugar, nucleic acid, lipid…) Fibrous: long/stringy filaments, water insoluble, function
Globular: folded into spherical shape, most are functional (enzymes, hormones, transport proteins…)
Describe the overview protein structure for primary, secondary, tertiary and quaternary structures.
1: Linear sequence of amino acids (N-terminus to C-terminus)
2: Polypeptides form regular arrangements w/regional motifs based on H-bonding –> α-helix / β-sheets/bends
3: Most proteins form complex 3D structure stabilized by cumulative
effects of large # weak chemical interactions and others
4: Interactions among complex proteins: multiple subunits
What forces normal protein folding? What happens when proteins are misfolded?
Hydrophobic effects; result in incorrect function, lead to disease
List the steps of protein purification.
- Extraction of protein from whole cells
- Use of salting/dialysis to remove some impurities
- Use chromatography methods to isolate proteins
Explain salting and dialysis.
Salting: Increasing [salt] to precipitate proteins based on solubility
Dialysis: Salted protein solution is placed in a bag with a semi-impermeable membrane, soaks in buffer
AAs that are more hydrophobic have larger or smaller free energy charge transfer numbers?
Higher numbers.
List the AAs of the aromatic group.
Phenylalanine, tryosine, tryptophan
List the AAs of the aliphatic group.
Glycine, alanine, valine, leucine, isoleucine, proline
