Chapter 3 & 4 Flashcards
Nonpolar amino acids
Glycine, Alanine, Proline, Valine, Leucine, Isoleucine, Methionine
Aromatic amino acids
Phenylalanine, Tyrosine, Tryptophan
Polar amino acids
Serine, Threonine, Cysteine, Asparagine, Glutamine
Basic amino acids
Lysine, Arginine, Histidine
Acidic amino acids
Aspartate, Glutamate
What is the equation for isoelectric point?
pI = (pka1 + pka2)/2
What does the isoelectric point tell us?
What pH the molecule has no charge
How to find the pI of acidic amino acids
Take the pI of the two smaller pKas
How to find the pI of basic amino acids
Take the pI of the two larger pKas
Label the phi, psi, and omega bonds of
R O
I II
N --- C ---- C -_- N
I
HPhi: between first carbon and nitrogen
Psi: between two carbons
Omega: between second carbon and nitrogen (with O)
Properties of alpha helix
- Lots of alanine (not glycine because it’s too small and flexible)
- Right handed helix most common (can be left handed)
- Like a battery with the positive charge on top, and negative charge on bottom
- No proline
- Stabilized by hydrogen bonds
Properties of beta sheets
- Parallel or anti-parallel
- Rigid
- Beta turns
- Zig Zag like pattern
- Ring structure
- Stabilized by H bonds
What are beta turns?
Connect antiparallel and parallel beta sheets when the carbonyl of the first amino acid forms an H-bond with the amino of the fourth amino acid
How many types of beta turns exist?
2
What is a type I beta turn?
The most common beta turn where proline is in the cis formation, in the second position
What is a type II beta turn
The lesser common beta turn where glycine is in the third position
What characteristics of glycine makes it a destabilizer or stabilizer of protein structure?
Small R group present that allows it to fold in on itself. Too many glycine present leads to increased flexibility of beta sheet and increased instability
What characteristics of proline make it a stabilizer of protein structure?
R group is in cyclic formation which causes a rigid, stable structure
Primary structure example and which bonds?
Single amino acids connected by covalent bonds
Secondary structure example and which bonds?
Alpha helices and beta sheets with hydrogen bonding
Tertiary structure example and which bonds?
Multiple alpha helices and beta sheets connected together with disulfide bonds, hydrogen bonds, and motifs.
Quaternary structure example and which bonds?
Complexes of several proteins with hydrophobic and van der waals interactions
Alpha-keratin characteristics
- Two parallel right handed helix
- forms left handed super twist* that are connected with disulfide bonds and called pseudorepeats
- Pseudorepeats come together to make protofilaments, protofilaments come together to make protofibrils where the strands are kept together by H bonds
- Lots of alanine and glycine
- Tough
- Stabilized by cysteine disulfide bonds (15%)
- Present in hair and nails
Beta-keratin characteristics
- Parallel beta sheets
- Lots of alanine and glycine repeats
- Soft, flexible
- Present in silk fibroin (spider’s web)
Collagen characteristics
- Left handed alpha helix with three amino acids per turn
- forms 3 alpha-chains
- The three alpha chains super twist into a right handed helix
- Tri repeat of Glycine - Proline - 4 hydroxyproline
- Covalently linked
- Insoluble
- Present in tendons and carilage
Fibrous protein characteristics
- Less common
- Strands/sheets
- One type of secondary structure
- Simple tertiary structure
- Strong, flexible support
- Insoluble and phobic amino acid
Globular protein characteristics
- More common
- Folded, spherical shape
- Many alpha helices and beta sheets
- Large
Describe a heat shock protein
Binds to regions of unfolded polypeptides that are rich in hydrophobic residues, thus protecting proteins subject to denaturation. Also protect other proteins from being folded if they need to be straight
Describe a chaperone protein
Assist unfolded, partially folded, or improperly folded proteins in finding their shape
-Require ATP
Prosthetic group
Organometallic structure that is tightly bound to proteins
Cofactor
Non-protein chemical compound that is required for protein’s biological activity
Coenzyme
Organic or organometallic structure that is loosely bound to proteins
Motifs
A recognizable folding pattern involving two or more elements of secondary structure and the connections between them
Parallel Beta Sheets
N –> C
N –> C
Consistent ring size (12)
Bent H bonds
Antiparallel beta sheets
N –> C
C –> N
Alternate ring size (10/14)
Linear H bonds (stronger)
Peptide bond common conformation
Cis
Renaturation
Reformation of disulfide bonds that were broken during denaturation
