FINAL - CH 4 Flashcards
oligopeptides
Short polypeptides less than 40 amino acids in length
Enantiomers
Molecules that are non-superimposable mirror images of one another
Able to rotate light (optically active)
Most AA’s are _____ besides ____
Chiral
Glycine
Each AA has a ____ and ____ form
D and L
L are used to build proteins/only found in humans
the only amino acid that can form disulfide bonds
Cysteine - stabilizes 3D structure
Isoelectric Point
pH at which the amino acid is neutral
Electrically neutral molecule with positive (amino) and negative (carboxyl groups)
Zwitterion
Average molecular weight if an AA
110 g/mol OR dalton
How to find PI if there are two Pka’s
Take average
How to find PI if there are 3 Pka’s
Draw the structure starting form fully protonated to fully deprotonated.. take the average of the two Pka’s where the molecule is neutral
Pka is the pH where:
half the molecules of an amino acid in solution have side chains that are charged. Half are uncharged
stimulates water resorption by kidneys and
increases blood pressure
Vasopressin
stimulates uterine contractions during childbirth – induces labor
Oxytocin
the angle of rotation around the N-Cα
phi (φ)
the angle of rotation around the Cα–C
psi (Ψ)
Secondary structures
β strands
α helices
β turns
α helices
Right handed
Stabilized by hydrogen bonding
Has 3.6 residues per turn
H bonding and alpha helices
N + 4 rule
α helices have ______ H bonding
Intrastranded
The most common location for an α-helix
along the outside of the protein, with one side of helix facing the solution and the other side facing the hydrophobic interior
β turns
Connect two β strands in antiparallel β sheet
β sheets have ______ H bonding
Interstranded
β strands can interact in two ways to form a pleated sheet: _____________
parallel and antiparallel
Antiparallel β sheets H bonds
More narrow and more stable
Parallel β sheets H bonds
Equally spaced, H bonds are at an angle
_____ is made from β sheets
Silk
Beta Turns
Type I: Turn with the carbonyl oxygen inward
Type II: Turn with the carbonyl oxygen facing outward
_______ Observed in tertiary
structure
Disulfide bonds
First protein structure determined
Myoglobin
Largely α helical in structure
Tertiary structures protein folds
Four helix bundle fold Greek key fold Rossmann fold TIM barrel fold (also called an α/β barrel) FERM domain fold
Homodimer
Simplest quaternary structure
Contains two identical protein subunits
Heterodimer
Contains subunits from different gene products
Hemoglobin
Has four polypeptide chains, non-covalently bound
Mostly α-helical
NO beta strands
Fibrous Proteins
Keratin
Silk
Collagen
Collagen Consists of ____________________
three intertwined left-handed helices
Globular Proteins
Spherical proteins that consist of multi subunit protein complexes
EX: immunoglobulins
Most abundant protein in the human body
Collagen
Four major classes of structures
Predominately α helices
Predominately β heet
α /β combined
Mixed α & β
3 models for protien folding
Hydrophobic collapse
Nucleation model
Framework model
Chaperone Proteins
Proteins that facilitate the formation of stable 3D
structures
Chaperone Proteins Functions:
Help newly synthesized proteins fold properly
Rescue misfolded proteins
Disrupt protein aggregates
Two types of chaperone proteins
Clamp type (HSP 70)
Chamber type (GroEL-GroES protein complex)
Both types of chaperones bind to misfolded proteins and use _______ to facilitate correct folding
ATP hydrolysis
GroEL has _____ subunits
14
pH < Pka
Protonation
pH > Pka
Deprotonation
Tm
Transition curve mid point - half of proteins are unfolded
Tm is on X axis
Alzheimers disease
caused by the aggregation of Aβ peptides
Aggregates are referred to as β-amyloid plaques
bps per turn in B DNA
10.5 bp/turn
bps per turn in A DNA
11 bp/turn
bps per turn in Z DNA
12 bp/turn
The isoelectric point is where:
AA has no charge
_____ is not found in Alpha helices
Proline
Angles in beta sheet
+psi
-phi
Angles in alpha helix
- psi
- phi
