Chapter 5: 3-D Structure of Proteins Flashcards
The rigidity of a peptide group can be attributed to..
the double bond character
Is a peptide’s carbonyl-nitrogen bond shorter or longer than a regular carbon-nitrogen single bond?
shorter
Peptide groups usually assume the….
trans conformation
In the trans conformation of a peptide group the alpha carbons are found on the ___________ side of the amide groups
opposite
Why is the trans conformation more stable?
b/c of the steric interference of the R groups or side chains
The ________ of a peptide are the atoms that participate in peptide bonds while ignoring the side chains.
backbone
The torsion angle about the alpha C-N bond is known as
Phi (Φ)
The torsion angle about the alpha C-C bond is known as
Psi (Ψ)
The angles that Phi and Psi can adopt in a peptide bond can be depicted in a diagram called a…
Ramachandran Diagram
The Ramachandran Diagram is about 75% blank, what does this indicate?
most conformation of Phi and Psi are conformationally inaccessible
In a Ramachandran Diagram, heavy clustering on the top right-hand side is indicative of…
left-handed α helix
In a Ramachandran Diagram, heavy clustering on the bottom left-hand side is indicative of…
right-handed α helix
In a Ramachandran Diagram, heavy clustering on the top left-hand side is indicative of…
β pleated sheets
On a Ramachandran Diagram antiparallel β pleated sheets are found…
on the top left-hand side slightly more to the left
On a Ramachandran Diagram parallel β pleated sheets are found…
on the top left-hand side slightly more to the right
Helical structures can be characterized by
the # of peptide units (n) and pitch (p)
define pitch
the distance the helix rises per turn
right-handed helices have a _______ “n” value
positive
left-handed helices have a _______ “n” value
negative
What is a helical polypeptide arrangement that has both allowed conformation angles and favorable hydrogen bonds
α helix
Linus Pauling discovered the
α helix
The α helix is a common secondary structure found in…
fibrous & globular proteins
How are right-handed α helices formed?
from polypeptides made from L-α-amino acid residues
How are left-handed α helices formed?
from polypeptides made from D-α-amino acid residues
In β pleated sheets hydrogen bonding occurs between
neighboring chains
What are common structural motifs of proteins
β sheets
What type of β sheet is less stable? Why?
- parallel
- b/c they are distorted when compared to antiparallel
What were the 2 repetitive structures discussed?
β bends
Ω loops
β bends normally connect successive strands of
antiparallel β sheets
What normally occur at protein surfaces
β bends & Ω sheets
In type II β bends, residue 2 is usually ____ while residue 3 is usually ____.
proline
glycine
What were the fibrous proteins discussed?
keratin & collagen
α keratins normally occur in
mammals
β keratins occur in
birds and reptiles
acidic polypeptides are composed of
type I keratin chains
basic polypeptides are composed of
type II keratin chains
What is a unique characteristic of keratin?
it has a heptad pseudorepeat
the heptad pseudorepeat has a and d positions that form the
hydrophobic strip
Keratin is rich in what type of residues?
cysteine (Cys)
Cysteine residues in keratin form disulfide bonds that cross link
adjacent polypeptide chains
makes it resistant to stretching
Keratins can be _____ like _____ and _____, or ____ like _____.
hard
hair
nails
soft
skin
Mutation of the keratin gene leads to
Epidermolysis Bullosa
Describe Epidermolysis Bullosa
rupturing of epithelial cells resulting in skin blistering
What protein occurs in multicellular animals, is extracellular, and occurs most abundantly in vertebrates.
collagen
collagen is organized into….
insoluble fibers w/ incredible tensile strength
what is a major stress-bearing component of connective tissue
collagen
Collagen has distinct amino acid composition with high levels of
Gly
Pro
Hyp
Hyp- hydroyproline
-OH group @ C3
Hydroxylated residues of hydroxyproline result from
synthesis by prolyhydroxylase
prolyhydroxylase requires ______ for its activity
ascorbic acid (vitamin c)
What disease results from vitamin c deficiency
Scurvy
Scurvy results in
skin lesions
blood vessel fragility
When do collagen residues denature @ 25°C?
when they are synthesized w/o Hyp
Collagen consists if repeating triplets of Gly-X-Y amino acids where X is ____ and Y is _____
proline
hydroxyproline
What heritable disorder results from the mutation of Type I collagen
Osteogenesis Imperfecta
All known amino acid changes within the…..results in abnormalities
triple helices region of Type I collagen
Examples of globular proteins include
- enzymes
- transport & receptor proteins
globular proteins contain both
α and β sheets
functions of carbonic anhydrase
- converts CO2 to bicarbonate (HCO3-)
- maintains acid-base balance
- helps transport CO2 out of tissues
- metalloenzyme
Metalloenzyme means
it requires a metal in its active site for activity
What is the metal needed for carbonic anhydrase?
zinc ion
The zinc ion is held in place by
imidazole rings of 3 His residues
What does NOSEY stand for
Nuclear Overhauser Effect Spectroscopy
NOE determines interproton distances through
space
