Biochem Protein Lecture 9 Flashcards
α helix + β sheet conformations joined by connecting segments are considered…
Globular Proteins
These folding patterns (motifs/folds) are particularly stable arrangement of several elements of secondary structure and the connections between them
Supersecondary Structures
These may be simple or complex Examples are an α-β loop and a β barrel
Motifs
These are defiend as two or more stable, globular units; present when there are > 100 aa residues
Domains
How many domains do small proteins have?
One domain (the protein itself)
The burial of hydrophobic R groups requires two layers of ___ structure (folding rule for polypeptides, hydrophobic interaction make large contribution to stability)
What creates the two layers?
Secondary Structure
Simple motifs (β-α-β)
Know the structures of beta barrel, etc.
!
A folding rule for polypeptides in simple motif: when occurring in the same protein, alpha helices and beta sheets are found in the same or different structural layers?
Different
A folding rule for polypeptides in simple motifs: the polypeptides that are adjacent to each other in the primary sequqnce are usually stacked ____ to each other in the secondary structure
Adjacent
In hemoglobin structure, deoxy means no Oxygen binded to heme, oxy is opposite
Double check this
Note: urea disrupts hydrophobic interactions)
! She said this specifically in class
Connections between elements of secondary structure CAN/CANNOT form knots or cross
CANNOT form knots or cross
The β conformation is most stable when individual segments are twisted slightly in a ______ hand sense
Right Hand Sense
Consider two parallel β strands, in proteins, the crossover is always _____ handed which is shorter, bends through smaller angles making it easier to form
Right handed
When many segments of β parallel strands are connected, the twisting of the β sheets leads to twisting of the structure. ______ and twisted _____ results
β barrel and twisted β sheet result
The α/β barell arises from repetitions of the βαβ loop motif. The α/β barrel is found in many ________
Enzymes
Domains which show similar folding patterns are described as having the same
“Motif”
Structural Classification of Proteins database (SCOP) divides protein structures into ___ classes
What are they?
4 Classes
1) All α
2) All β
3) α/β (interspersed)
4) α + β (α + β regions are somewhat spaced)
Fewer than _______ motifs (folds) may exist in all proteins
1000
Proteins with very similar primary sequence and/or similar structure and function are in the same protein ______
Family
Proteins with the same major structural motif and some functional similarities (but little primary sequence similarity) are part of the same ________
Superfamily
As mentioned in previous lecture, quaternary structure refers to the interaction between polypeptide chains in a protein where each chain has its own secondary and tertiary structure
!
This term means a multisubunit protein
Multimer
This means a multimer with just a few subunits
This means a multimer where the repeating structural unit is a multimer
Oligomer
Protomer
What interactions may contribute to the bonding between chains in quaternary structure
Hydrophobic, H-bonding, salt, metal-ligand and disulfide interactions`
The first oligomeric protein 3-D structural determination was conducted on
Hb
The protein in red blood cells that is responsible for oxygen transport
Hb
What is the Mr of hemoglobin?
64,500
How many polypeptide chains and how many heme prosthetic groups are in Hb?
4 polypeptide chains and 4 heme prosthetic groups
What state is iron in in Hb?
Ferrous (Fe2+)
Globin consists of two ____ chains and two ___ chains
α, β
In globin, do β and α refer to secondary structure?
Hemoglobin is a _____ or a _____ of αβ protomers
No.
Tetramer or a dimer
How many residues are in the β and α chains of globin?
141 in α
146 in β
Identical subunits of multimers are arranged this way
Symmetrical Patterns
Oligimers can have two types of symmetry, what are they?
Rotational Symmetry and Helical symmetry
This type of oligomeric symmetry occurs when individual subunits can be superimposed on others by rotation about one or more rotational axes
This type of oligomeric symmetry occurs when subunits can be superimposed by helical rotation
Rotational Symmetry
Helical Symmetry
For rotational symmetry, subunits pack to form
For helical symmetry, structures are more open ended with subunits added in a _____
Closed structures
Spiraling Array
X-ray crystal structure determinations have shown that there are several forms of rotational symmetry that occur in proteins.
!
This type of rotational symmetry involves rotation about a single axis. Symmetry is defined as _____
Cyclic Symmetry
Cn (C for cyclic and n for the number of subunits related by the axis)
The αβ protomers of Hb have ___ symmetry
C2
This type of rotational symmetry is a more complicated form of rotational symmetry, a two fold rotational axis intersects an n-fold axis at right angles.
The symmetry is
Dihedral Symmetry
Dn
Cyclic and dihedral symmetry are most common true or false
A more complicated symmetry than these is
An example of this is the
True
Icosahedral Symmetry
Human Polio Virus
This means the loss of 3-D structure sufficient to cause a loss of protein function
Denaturation
Under most conditions, denatured proteins exist in ______ states
Partially Folded
Most proteins can be denatured by
Heat
When proteins are denatured by heat, there tends to be a sudden or gradual loss of structure over a narrow range?
What does this suggest?
Sudden
Folding is cooperative
This term means that loss of structure in one part of a protein destabilizes other parts
Cooperativity
Are the effects of heat on proteins readily predictable?
No.
What are two other ways of denaturing protein than heat?
pH extremes
The use of chemical agents
What do pH extremes do to protein?
What do chemical agents do?
Alter the net charge and disrupt H bonding
Disrupt hydrophobic interactions
What are examples of chemical agents that can denature proteins?
Organic Solvents (alcohol, acetone),
solutes like urea or guanidine hydrochloride
detergents
Certain globular proteins which have been denatured regain their native structure and biological activity if returned to conditions where the native conformation is stable. What is this process called?
Renaturation
What molecule was used as an example of protein renaturation?
Ribonuclease A
Treating ribonuclease A with ura and mercaptoethanol resulted in complete loss off the enzyme’s catalytic activity. What happened when urea and mercaptoethanol were removed?
It regained its tertiary structure including the same disulfide bond positions. Catalytic activity was restored
What did the ribonuclease A experiment show?
The aa sequence of a polypeptide chain has al the information required to fold the chain into its native 3 D structure
Do some proteins require folding assistance?
Yes
Polypeptides rapidly fold by what type of process?
E coli cells can make a complete biologically active protein molecule containing 100 aa residues in about 5 seconds at 37 degrees
Stepwise
The rapid, stepwise folding of proteins indicates that principles must guide protein folding in their native states.
The thermodynamics of protein folding can be described by a
Free-energy tunnel
In the free energy tunnel, what is at the top?
As the folding proceeds, the narrowing of the funnel represents a INCREASE/DECREASE in the number of conformational species present
The number of folded states (and the conformational Entropy)
Decrease
At the bottom of the free energy funnel, what is there?
A single native conformation (or a small set of them)
Defects in protein folding account for wide range of genetic disorders.
In this one, there are defects in CFTR, a membrane bound protein which acts as a channel for chloride ions
Cystic Fibrosis (CFTR= cystic fibrosis transmembrane conductance regulator)
The most common mutation of cystic fibrosis is a deletion of the ___ residue in position 508 in CFTR, resulting in improper folding
Phe
Proteins that interact with partially folded or improperly folded polypeptides. They promote the correct folding pathways or provide microenvironments where folding can occur
Molecular Chaperones
Two well studied chaperones are
Hsp70 and Chaperonins
This chaperone is a heat shock protein that is more abundant in temperature stressed cells
They bind to regions rich in ____ residues and prevent inappropriate aggregation
Hsp70
Hydrophobic
These chaperones are elaborate protein complexes that are required to fold cullular proteins that don’t fold spontaneously
Chaperonins
