Module 2 Flashcards
Name the 4 levels of protein structure and their (very) basic definition.
Primary - sequence of amino acids
Secondary - repeating interactions of amino acids
Tertiary - arrangement of atoms in a subunit
Quaternary - arrangement of subunits
T or F: Fibrous proteins are more soluble than globular proteins.
False
What are the two common secondary protein structures?
alpha-helix and beta-pleated sheets
What bonds do the Φ and Ψ describe?
Φ - alpha-carbon and nitrogen bond
Ψ - alpha-carbon and carbon bond
T or F: Trans configuration for chain of amino acids have more steric hindrance; therefore, it is less stable.
False. Less; more stable
What are the two exceptions for the Ramachandran Plot?
Proline and Glycine
Its permissible range of Φ and Ψ covers a large area of the Ramachandran diagram. Which amino acid is described?
Glycine
It is the most conformationally restricted amino acid.
Proline
Pitch of alpha-helix.
5.4 Å
How many amino acids per turn in an alpha-helix structure.
3.6
This amino acid creates a bend, disrupting alpha-helix structures.
Proline
What are the three alpha-helix disruptions?
- Presence of proline
- Strong electrostatic repulsion - K and R
- Crowding or steric repulsion
In alpha-keratin, how much residue-units are repeated to form the structure?
Seven
Collagen
- consists of three extended helical chains wrapped into a triple helix (superhelix)
Amino acid derivatives found in collagen.
Hydroxyproline and hydroxylysine
The smallest component of hair cortex, composed of four alpha-keratins twisted into a left-handed superhelix
Protofibril
Component of hair cortex
Cortex -> Macrofibril -> Microfibril -> Protofibril
Type of beta-sheet in which the hydrogen-bonded chains extend in the same direction
Parallel sheet
Describe antiparallel sheet.
Neighboring hydrogen-bonded chains run in opposite directions
T or F: Parallel beta-sheets are less stable than antiparallel beta-sheets
True
Describe the parallelism of fibroin.
Anti-parallel
Which interactions hold the tertiary structure of proteins?
- Hydrogen bonding:
+ between peptide groups
+ between side chains - Metal ion coordination
- Disulfide bonds
- Hydrophobic interactions
- Ionic linkages
Protein that is responsible for storing oxygen in muscles.
Myoglobin
T or F: Hemoglobin is a quaternary tetrameric protein.
True
What is the function of hemoglobin?
Transportation of oxygen
Refers to the property of hemoglobin where if one heme group is bound with oxygen, it becomes easier for the next oxygen to bond.
Cooperative binding
What are the compounds that lower the affinity of oxygen to hemoglobin?
H+
CO2
BPG (D-2,3-bisphosphoglycerate)
What is the reagent used in Edman degradation?
PITC (phenyl isothiocynate)
What is the Sanger’s reagent’s full name?
2,4-Dinitrofluorobenzene
This analysis is done to identify amino acids.
Sanger Analysis
It is an efficient way to identify the N-terminal amino acid
Edman degradation
It cleaves internal peptide bonds
Endopeptidases
It cleaves the scissile peptide bond flanked by the residues with specific side chain requirements
Protease
It cleaves either N or C terminal
Exopeptidase
Which amino acids do trypsin cleave?
R Arginine
K Lysine
This enzyme cleaves L F W and Y
Pepsin
Which amino acids do chymotrypsin cleave?
F W Y
T or F: Endopeptidase V8 cleaves Glutamate.
False. Glutamine.
The amino acids valine, glycine, alanine, and serine are cleaved by _______________.
Elastase
T or F: Cyanogen bromide cleaves the carboxyl side of every methionine residue
True
