4.3 - 4.4 Flashcards
Tertiary proteins
The overall 3D arrangement of all atoms
Quaternary structure
Arrangement of protein subunits in 3D
What are the two major groups of proteins?
- Fibrous
- Globular
Fibrous proteins
Have polypeptide chains arranged in long strands
Globular proteins
Have polypeptides chains folded into a spherical or globular shape
______________ usually consist of a single type of secondary structure & their 3 structure is simple
Fibrous proteins
_________ are the most enzymes & regulaotry proteins (soluble in the cytoplasm)
Globular proteins
Fibrous proteins are adapted for ________ function
structural
Alpha keratin are made for __________ & favored only in mammals & found in hair, nails, wools, etc
Strength
Alpha keratin are part of the ________________
Intermediate filament (IF) proteins (All IFproteins have a structural function & share the structural features by the alpha keratin)
The alpha keratin helix a ________ helix
Right hand
The alpha helices of alpha keratins are arranged as a _____________ where two strads of alpha keratin are overlapped parallel & are wrapped together to form a supertwisted coiled coil (which makes it stronger)
Coiled coil
The supertwist of keratin forms a ________ helix & its surfaces is made up of hydrophobic amino acid residues (keratin is rich in hydrophobic residues such as Ala, Leu, Ile, Met,, & Phe)
Left hand
Protein function depends on its ____ structure
3D
Protein strucuture is determined by its ________ sequence
Primary
ALpha keratin has a ____ residue pseudo repeat of : abcdefg where a & d position are nonpolar & mostly on one side
7
Hair keratin has pairs of alpha helices to form a two - chain coiled coil where they then combine with other two chain coiled coil to make ____________ then protofibrils
Protofilamanets
Collagen is also made to provide _______ where its found in connective tissue like tendons, cartilage, bone, the eye, etc
Strength
Collagen helix is ______ & has 3 aa residues per turn
Left handed
The 4 structure of alpha keratin is made up of the________ wrapping around each other
supertwist
Collagen is also coiled coil but has 3 separate polypeptides called ____ chains that supertwist together to make its 3 & 4 structure
Alpha chains
The helical twisiting is ______ handed in collagen
right handed
The amino acid sequence in collagen is ________ where X is pro , Y is 4-hdp mostly made up of gly & the pro & 4-hyp provide thee sharp twisting of the collagen helix ).
Gly-X-Y
Collagen has a left hand helical twist but its supertwist forms a _____
right hand
Basic structure of collagen is a triple helix & is 3 left hand helices twist together to form a _________ supertwist
Right hand
________ provide strength, support, resiliency, & resistance (in tendons it has a rope like fiber & the skin has loosly woven fibers)
Fibers
________ create a rigid structure unable to adapt to alpha helix angles
Pro & 4-hyp
____ is located along central axis of a triple helix where other residues can’t fit
Gly
The __________ form between Gly N-H & Pro C-O in an adjacent chain in the triple helix twist
interchain H-bonds
_____________ (collagen fibrils) are made up of multiple triple helical collagen molecules
Tropocollagen
A single ____________ has a large effect on collagen function bc they disrupt the Gly - X-Y repeat that gives collagen its helical structure (Gly-X-Y can’t be replaced by another amino acid residue without having harmful effects on the collagen structure)
residue subsitituon
Silk fibrioin is produced by moths & spiders & its polypeptide chains are predominatly in the ____ conformation
beta conformation
Silk fibroin are also rich in ____ & ______ residues & its structure is stabilized by hydrogen bonding & London dispersion forces between sheets
Ala & Gly
_________ is an oxygen-binding protein of muscle cells & functions to store oxygen & to facilitate oxygen diffusion in contracting muscle tissue
Myoglobin
__________ is abundant in muscle of diving animals like whales, seals, etc bc storage & distribution of oxygen by muscle myoglobin permits the dinning mammals to remain submerge for a long time
Myoglobin
______ & globular protein structure is stabilized by hydrophobic effect
Myoglobin
The ______ group in myoglobin & hemoglobin is in a tight pocket were the accessibilty of the heme group is restricited since free heme group in an oxygenated solution oxidizes from Fe 2+(binds to O2) to Fe3+ (doesn’t bind to O2)
Heme group
Motif (fold)
Is a recognizable folding pattern involving two or more elements of 2 structure & the connections between them (like two 2 structure folded against each other) (can be alpha helix or beta sheets or both, ex. coilied coil of alpha keratin)
What are the two terms for describing structure pattern?
- Motif
- Domain
Domain
Is a part of a polypeptide chain that is independently stable or could undergo movement as a single entity to the entire protein
Usually large proteins with a few hundred aa residues fold into two or more _______ & a domain can still remain its native 3D structure even when separated from the polypeptide chain of the protein ( each domain may have its own function)
Domain
Small proteins usually have _____ domain where the domain itself is the whole protein
one
What are the constraints of folding for polypeptides?
- The hydrophobic effect makes a large contribution to the stability of protein structure
- When alpha helix & beta sheets are both in a protein they found at different structural layers bc the backbone of a polypeptide segment in the beta conformation can’t easily H Bond to an alpha helix that is adjacent to it
- Segments adjacent to each other in the amino acid sequence are usually stacked adjacent to each other in the folded structure
- The beta conformation is most stable in the right hand orientation
Intrinsically disordered proteins
Have properties different from classical structures where they lack a hydrophobic core & have charged amino acids such as Lys, Arg, & Glu (Also contain Pro residue which disrupt ordered structure )
Since __________ proteins lack an ordered structure they can facilitate a kind of protein interaction
intrinsically disordered
Protein family
Proteins with similar primary strucuture and/or similar 3 structure & function (ex. globin family & myoglobin)
Superfamilies
Two or more families that have little similarities in amino acid sequence but mostly the same structure
Most proteins are multisubunit (have mulitple subunits) where a multisubunit protein is called _________
A multimer
Oligomer
A multimer with just a few subunits
Protomer
The repeating structural unit in multieric proteins
_________ is the organization of proteins with multiple subunits (oligomer, dimer, tetramer, etc)
4 structure
______ subunits can be identical (like in protomers) or different & its structure is stabilized by weak noncovalent interaction
4 structure
___________ is a tetramer or a dimer of alpha beta protomer
Hemoglobin
Loss of protein structure results in loss of _______
Function
Denaturation
A loss of 3D structure which results in a loss of function (proteins denature when the environment they are in changes such as small increase in heat energy (or cold), pH changes (which alters ionization state of side chains & other groups & addition of chaotropic agents or detergents that disrupt the hydrophobic effect such asguanidiinium ions or Urea)
A protein denaturing curve is _______ shape which indicates cooperactivity
Sigmoid
Protein denaturation is ___________ due to the weak stabilizing forces which lead to the denaturation curve which lead to the sigmoid shape
Cooperative
Melting temp at _____ denaturated is the Tm (which depends on pH & ionic strength)
50%
Protein renature (reform) after denaturant is removed since only the _________ is needed to do so
Primary sequence
Globular single subunit is ______ in the cytoplasm (ex.myoglobin)
soluble
Globular subunits can have the same or _______ subunit (ex. hemopglobin)
Different
Unfolding of protein is a _________ process where loss of structure in one part of the protein destabilizes other parts
Cooperative
_________ sequence determines 4 structure ( the 3 structure of a globular protein is denatured by its amino acid sequence) (determines the native conformation)
Amino acid
Renaturations
When denatured protein returns to their native conformation
Describe the Anfinsen experiment
- Ribonuclease A in its native state is catalytically active but when urea & mercaptoethanol is added it unfolds
- In its unfolded state its inactive & disulfide cross-link are reduced to yield cys residues
- When urea & mercapoethamol is removed the protein (nonuclease) spontaneously returns to its native state where its catalytically active & disulfide cross- linked reforms
Polypeptides fold _______ by stepwise process
Rapidly
What are the other stabilizing forces?
- H-bonds (minor contribution, contributes to cooperative folding & 2 structure, 2-8kj/mol)
- Electrostatic interaction & ion pairs or salt bridge (small contribution)
- Vna der waals forces in the packed protein interior
- Disulfide bonds (form within or between polypeptide) chains between cysteines)
- Metal coordination (Metal coordination bu side chains)
________ interactions are the main stabilizers
Hydrophobic
Folding for many proteins requires ________ which are proteins that interact with partially folded or improperly folded polypeptides to make the correct folding occur
Chaperones
What are the two major types of chaperones?
- Hsp 70 family
- Chaperones
The _______ family is usually found in cells that are stressed by elevated temps & bind to regions of unfolded polypeptides that are rich in hydrophobic residues (bind & release peptide hydrophobic regions)
Hsp 70
The _______ protect proteins that are denatured by heat
Hsp 70
_________ are required for the folding of proteins that don’t spontaneously fold (its system is called Hsp 60)
Chaperones
Defects in protein folding provide the molecular basis for a wide range of human _________ disorders
Genetic
Many conditions such as ________ diabetes, Alzheimer disease & Parkinson disease are caused/ associated with a misfolding mechanism
Type 2
