Biochem Lecture 4 Flashcards
Explain what tertiary structure is
Tertiary structure is the 3D structure of a polypeptide due to the condensation of secondary elements
Tertiary structures are stabilized by weak interactions
Very high density, but cavities exist
Covalent bonds, metal ion coordination and post-translational modifications can add stability to tertiary structure
What is a domain?
What is essential for a domain’s stability?
A domain is a compact unit of protein structure that is usually capable of folding stably on its own
Domains have hydrophobic cores. These hydrophobic cores are essential for the stability of domains.
Define structural motif
Define domain fold
Structural motif consists of small local arrangement of secondary structural elements which coalesce to form domains
Domain fold: combination of motifs
Explain what an helix turn helix is
Two helices lying antiparrallel connected by a turn/loop
Calmodulin is an example of this (it contains multiple alpha loop alpha)
Define the following terms: class, fold, family
Class: determined by predominant secondary structures
Fold: determined by arrangements of secondary structures within a domain
Family: sequence idenity
What is a superfold?
Superfolds are folds of similar structure that are in proteins of unrelated functions.
Explain the following about alpha helices (the secondary structure)
What is the pitch
How many residues per turn
What is bonded to what?
Describe confirmation/shape
Relationship btw dipole strength and length
So the pitch is 5.4 A, because the structure repeats itself every 5.4 angstroms
There are 3.6 AA residues per turn
(Rise per residue is pitch/residues per turn) = 1.5 A
Every main C=O and N-H are hydrogen bonded to a peptide bond 4 residues away
Peptide bonds are parallel to the helical axis
R groups point outwards and towards the N terminus
Strength of dipole increases with length
Two common motifs for alpha domains are the _________ & _________
Two common motifs for alpha domains are the 4 helix bundle and the globin fold.
Explain the all beta topology. What is there preferred arrangement? What does that mean for polar vs hydrophobic residues?
Most or entirely beta sheets means they will be antiparallel arrangement. Many of these anti-parallel domains consists of two beta sheets packed against each other, with hydrophobic side chains in the inside.
Sequence of alternating hydrophobic and polar residues
How can you identity an orthagonal beta sandwich?
Angle between sheets has a right handed twist of 90 degrees. The strands at one corner or two diagonally opposite corners bend at a 90 degree angle.
Antiparallel beta strand can form ____ and ____.
Sandwiches and barrels
Explain what a greek key is
A greek key has up-down beta strands connected by hairpins. The first structure is connected to the fourth.
“three up and down beta strands connected by hairpins”
Two major families in alpha/beta domains are?
Alpha/beta: twists and barrels
Give definitions of the following:
Beta-barrel
Beta sandwich
Jelly roll
Beta-barrel: single beta sheets forms cylindrical structure in which all strands are H bonded with one another
Beta sandwich: formed of two antiparallel beta sheets packed face to face
jelly roll is an extra swirl on a greek key
Explain the alpha/beta domain
All of the beta’s will be parrallel with each other
All of the alphas are parrallel with each other
Beta and alpha are antiparralel to each other
Form twists and folds
The rossman fold
beta strands are parrallel and H bonded to each other
Helices are parrallel and H bonded to each other
Helices are antiparrel to beta strands
Rossman fold is beta alpha beta alpha etc
Alpha + beta domains
do NOT exhibit wound alpha beta topology
Independent helical motifs packed against a beta sheet
Explain quaternary structure
Define “oligomer”
The NONCOVALENT arrangement of peptide chains in a multiunit protein
Oligomer: protein assembles composed of more than one polypeptide chain
What are the four types of fibrous proteins?
List the differences between globulin and fibrous proteins
Fibrous proteins: collagen, elastin, alpha keratin, tropomyosin
Fibrous proteins:
- contain larger amounts of regular secondary structure
- have extended clindrical/rod shape
- VERY LOW solubility
- play structural rather than dynamic role
Collagen is rich in which AA’s
What does the enzymatic conversion of proline to 4-hydroxyproline require?
Collagens are glycoproteins with the carbohydrate linked to the 5 hydroxylysine via______.
Collagen is rich in glycine, proline and 4-hydroxyproline and 5-hydroxylysine
Enzymatic concersion of proline to 4hproline requires Vitamin C, so in scurvy there is reduced collagen synthesis
via O-glycosidic linkages
Primary structure of Collagen
Basic unit of collagen is a polypeptide with the repeating sequence of :
(Gly-X-Y)n
where X is often proline and Y is often hydroxyproline
THREE residues repeated over and over starting with glycine
Three chains of a collagen molecule are wound about each other to form a ______.
This structure (superhelix) forms because_____.
The glycines in each chain are aligned along one side of the helix forming a _____.
The glycine edges associate _____ to form the superhelix structure.
Three chains of collagen are wound to create superhelix.
This superhelix forms because glycines have low steric bulk.
The glycines aligned along the side to form APOLAR edge.
The glycine edges associate noncovalently.
Covalent crosslinks in are formed in collagen via ______.
Formations of those _____ is catalyzed by?
Covalent crosslinkes are formed in collagen via allysine intermediates.
Formations of those allysines are catalyzed by lysyl amino oxidase.
NOTE: This covalent crosslinking within a strand via reaction of lysine residues to form aldol cross-links
THIS IS NOT QUATERNARY structure because it is now covalent.
Elastin is another fibrous protein with _____.
It lacks a ________.
Elastin is another fibrous protein with allysine generated crosslinking.
Lacks regular secondary structure but does form a coil
FORMS extensive crosslink structures via allysine
Alpha keratin and tropomyosin sequence show a tandem repitition of 7 residue segments:
a-b-c-d-e-f-g
Which are hydrophbic and which are polar?
a and d (1 and 4) have hydrophobic side chains
e and g (5 and 7) have polar side chains
Apolar residues form an edge
Apolipoproteins have a high ____ content when associated with lipid.
Why is that?
The helical regions have _________ properties.
Apolipoproteins have a high alpha helical content when associated with lipid. This is because every third or fourth residue is CHARGED and forms a POLAR edge that associate with water.
Helical regions have ampipathic properties.
