4.3 - 4.4 Flashcards by nana Adusepoku

Tertiary proteins

The overall 3D arrangement of all atoms

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Quaternary structure

Arrangement of protein subunits in 3D

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What are the two major groups of proteins?

Fibrous
Globular

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Fibrous proteins

Have polypeptide chains arranged in long strands

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Globular proteins

Have polypeptides chains folded into a spherical or globular shape

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______________ usually consist of a single type of secondary structure & their 3 structure is simple

Fibrous proteins

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_________ are the most enzymes & regulaotry proteins (soluble in the cytoplasm)

Globular proteins

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Fibrous proteins are adapted for ________ function

structural

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Alpha keratin are made for __________ & favored only in mammals & found in hair, nails, wools, etc

Strength

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Alpha keratin are part of the ________________

Intermediate filament (IF) proteins (All IFproteins have a structural function & share the structural features by the alpha keratin)

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The alpha keratin helix a ________ helix

Right hand

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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

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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

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Protein function depends on its ____ structure

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Protein strucuture is determined by its ________ sequence

Primary

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ALpha keratin has a ____ residue pseudo repeat of : abcdefg where a & d position are nonpolar & mostly on one side

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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

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Collagen is also made to provide _______ where its found in connective tissue like tendons, cartilage, bone, the eye, etc

Strength

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Collagen helix is ______ & has 3 aa residues per turn

Left handed

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The 4 structure of alpha keratin is made up of the________ wrapping around each other

supertwist

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Collagen is also coiled coil but has 3 separate polypeptides called ____ chains that supertwist together to make its 3 & 4 structure

Alpha chains

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The helical twisiting is ______ handed in collagen

right handed

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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

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Collagen has a left hand helical twist but its supertwist forms a _____

right hand

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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?

1. Motif 2. 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?

1. The hydrophobic effect makes a large contribution to the stability of protein structure 2. 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 3. Segments adjacent to each other in the amino acid sequence are usually stacked adjacent to each other in the folded structure 4. 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

1. Ribonuclease A in its native state is catalytically active but when urea & mercaptoethanol is added it unfolds 2. In its unfolded state its inactive & disulfide cross-link are reduced to yield cys residues 3. 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?

1. H-bonds (minor contribution, contributes to cooperative folding & 2 structure, 2-8kj/mol) 2. Electrostatic interaction & ion pairs or salt bridge (small contribution) 3. Vna der waals forces in the packed protein interior 4. Disulfide bonds (form within or between polypeptide) chains between cysteines) 5. 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?

1. Hsp 70 family 2. 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

4.3 - 4.4 Flashcards

(75 cards)