Lecture 1: Levels of Protein Structure Flashcards
Key Types of Proteins
- Enzymatic
- Defensive
- Storage
- Transport
- Hormonal
- Receptor
- Contractile/motor
- Structural
Primary Structure is based on…
Amino acid sequence
Structure of amino acids
- central tentrahedral carbon (alpha carbon)
- linked to:
1. amino group
2. side chain, r group
3. hydrogen atom
4. carboxylic acid
Most common form of amino acids
L form
*this means that the amino group is on the left, H on the right in fischer projection
*doesnt say anything about rotation of light!
(except glycine)
Enantiomers vs Diastereomers
(as it relates to amino acids)
enantiomers = mirror images
diastereomers = not mirror images but same connective order
This matters because there are L and D forms of amino acids
- L is more common, D is less common
- enantiomers are not interchangeable, usually one version is used/important and another version is not
Classifications of amino acids
(categories)
what are their characteristics at pH7?
- non-polar, aliphatic (alkyl groups)
- aromatic (ring)
- polar, uncharged
- positively charged (Basic)
- negatively charged (Acidic)
Nonpolar Aliphatic Amino Acid R Groups (acronym?)
- Glycine
- Alanine
- Proline
- Valine
- Leucine
- Isoleucine
- Methionine

Aromatic Amino acids
- Phenylalanine
- Tyrosine
- Tryptophan

Spectroscopic Properties of aromatic amino acids
Absorb in the 280-300 range
Can Id/measure proteins in samples
*Different ones absorb more, but that general range is wehre absorption is seen

Polar, uncharged amino acids
STCAG
- serine
- Threonine
- cysteine
- asparagine
- glutamine

cysteine and reversible disulfide bond formation
Cysteine forms disulfide bonds because has a -Ch2-SH R group
- C - CH2 - S - H

Positively charged amino acids
LAH
- lysine
- arginine
- histidine

Unique Property of Histidine
- Good to have at an active site to both stabilize and destabilize a substrate
- side chain has a pKa of 6.5 –> near a physiological pH
- exists in the protonated and deprotonated form at the same time
- R groups are what make the protein reactive, but it is still only reactive if it is reactive at a physiological pH

Negatively charged amino acids
- aspartate (-CH2 - COO)
- glutamate (- CH2 - CH2 - COO)

Zwitterion form of amino acid
- protonated amino group (NH3+)
- deprotonated carboxyl group (COO-)
*both are protonated at low pH
*both are deprotonated at high pH
Zwitterion formation based on ph
- 0-2: both protonated, NH3+ and COOH
- 2-9: zwitterion, NH3+ and COO-
- 9-14: both deprotonated, NH2 and COO-
Henderson Hasselbeck Equation
Describes the shape of the titration curve of any weak acif or amino acid
Ka = [H+] [A-] / [HA]
–> in terms of H+
–> negative of both sides
–> -log = ph or pKa
pH = pKa - log ([HA]/[A-])
Titration Curve of amino acid
Buffer regions
Equivalence point/PI
pKa

Key Pieces of info from Titration curve
- quant measure of the pKa of each of the two ionizing groups
- buffering regions
- relationship between net charge and pH of solution
PI (Isoelectronic point)
- characteristic pH at which net charge is zero
- equal amounts of + and - charged acid and zwitterions
- can be arithmetic mean of the two pKa values
Peptide Bond Formation Structure? Reaction?
two amino acids can be covalently joined through a substituted amide linkage (peptide bond) to yield dipeptide
loss of a water molecule, dehydration an form multiple –> oligopeptides, polypeptides

Properties of peptide bonds:
- resistant to hydrolysis and kinetically stable (high Ea and reverse Ea makes it unfavorable/difficult to go in reverse)
- planar due to partial double bond character of C-N bond
- contain a hydrogen bond donor (NH) and hydrogen bond acceptor (CO)
- uncharged, allowing proteins to form tightly packed globular structures
Resonance of Peptide bonds
- carbonyl is partially negative
- amide is aprtially positive
trans and cis

In what form are peptide bonds in proteins?
- trans
- steric clashes arise from cis
(proline is exception)

























