Chapter 4 - Tertiary structure Flashcards by Taylor Nunes

The majority of 3D structures are stabilized by ______, but some are stabilized by ______ or coordinated ____ atoms.

numerous weak interactions

covalent disulfide bonds

metal

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weak interactions

Hydrogen bonding

electrostatic interaction

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Disulfide bonds are formed when:

two nearby cysteine residues are oxidized

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____ and ____ are the most
common metal ions in
proteins

Zinc

Iron

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First protein structure determined

Myoglobin

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Myoglobin

largely α-helical in structure

153 amino acids

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4 major classes of structure

all alpha helices
all beta sheets
alpha/beta (intermixed)
mixed alpha + beta (separate regions)

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Fold types:

Four helix bundle fold

Greek key fold

Rossmann fold

TIM barrel fold

FERM domain fold

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fold in Heme domain of cytochrome b:

Four helix bundle

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Four helix bundle provides ______ for the heme group

hydrophobic pocket

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fold in Bacterial CusF copper binding protein

Greek key fold

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Fold in bacterial lactate dehydrogenase, with bound

nicotinamide adenine dinucleotide

Rossman fold

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Rossman fold is found in:

Proteins that bind nucleotides

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TIM Barrel aka:

a/b barrel

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TIM barrel found in:

A large number of metabolic

enzymes

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Fold found in triose phosphate isomerase

TIM Barrel

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FERM domain fold components:

FA: Mostly beta sheets

FB: Only alpha helices

FC: Mostly beta sheets

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Quaternary Structure

Polypeptide chains organized in

multiple subunit protein complexes

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Homodimer

Simplest quaternary structure

Contains two identical protein subunits

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Heterodimer

Contains subunits from different gene products

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Quaternary Structures Increase _______

Functionality

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Quaternary structure provide:

structural properties not present in individual properties

a mechanism for regulation of protein function through conformational change

Bring linked functional components into close
proximity

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Fibrous Proteins

Keratin

Silk

Collagen

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Collagen

Primarily found in soft tissues that holds bones together and is the major
constituent of tendons and cartilage.

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Multi-subunit complexes that are abundant in | nature

Fibrous proteins

Spherical proteins that consist of multi-subunit protein complexes

Globular proteins

An Example of Globular Proteins

Immunoglobulins

Structure and function are dependent on:

Folding

The free energy difference between the native (folded) and denatured (unfolded) must be:

favorable (G < 0)

_____ changes can contribute to the folding | process.

Entropy

Chaperone proteins

Proteins that facilitate the formation of stable 3D | structures

Chaperone fxn:

Help newly synthesized proteins fold properly Rescue mis-folded proteins Disrupt protein aggregates

2 types of chaperone protein:

Clamp type (Hsp 70) Chamber type (GroEL-GroES complex)

Chaperones selectively bind to short stretches of_______ that tend to be exposed in ____ but buried in proteins having a ______ conformation

hydrophobic amino acids non-native proteins native

GroEL-GroES has:

seven subunits, 97 residues each.

Tm = 0.5 (50%)

Half of molecules are unfolded

Alzheimers caused by aggregation of:

small Aβ peptides (β-amyloid) causing neuronal death

β-amyloid peptide is released by: followed by:

the cleavage of amyloid precursor protein by β-secretase cleavage involving γ-secretase

_____ is then thought to self associate under certain | circumstances to form _____ called _____ in the brain

β-amyloid protein aggregates β-amyloid

3 protein folding models:

Hydrophobic collapse Framework model Nucleation model

loosely folded tertiary structure

molten globule

______ is necessary since no amino acid side chains can reversibly bind to oxygen.

The Fe2+ -porphyrin | complex

Oxygen only binds to the

prosthetic group with iron in its reduced state (ferrous state)

The Fe2+ -porphyrin complex is called _____ and fxns as a _____

heme prosthetic group

Myoglobin and hemoglobin are both ______

heme-using oxygen binding proteins

Hemoglobin fxn as

transport of heme bound O2 from lungs and through out circulatory system

Myoglobin fxns as

O2 depot stored in muscle tissue

Two histidine residues are crucial in for O2 binding in globin proteins:

His F7 | His F8

His F7

Distal histidine Hydrogen bound to O2 which is bound to Fe2 Attached to E helix

His F8

Proximal histidine coordinates to Fe2 directly Attached to F helix

Oxygenation alters the _____ of the Fe(II)-heme complex

electronic state

the color of hemoglobin in venous blood

dark purple (de oxygenated)

the color of hemoglobin in arterial blood

brilliant scarlet (oxygenated)

These proteins are responsible for the brown color of old meat and dried blood

the Fe(II) becomes oxidized to Fe (III) to form metmyoglobin or methemoglobin

Why is an oxygen carrier such as heme important:

O2 has poor solubility | O2 has poor diffusion through our skin

α1-β1 and α2-β2

Have 35 residues that interact

α1-β2 and α2-β1

Have 19 residues that interact

α-β interactions are mostly:

Hydrophobic, H bonding and ion pairing

In hemoglobin, solvent F channel _____ when O2 is bound

Narrows

How does channel narrow?

α-β complexes shift by 15 degrees in clockwise direction, bring β1-β2 closer together

α -β arrangement in hemoglobin

α2 β1 | β2 α1

T state

Tense state | O2 unbound

R state

Relaxed state | O2 is bound

In the T state _____ is ~____ out of the _____ | Which is called ______ heme

Fe 0..6 Angstroms heme plane Puckered

In R state ___ drags ___ and attached _____ | Binding to _____ making heme ____

Fe II His F8 F helix O2 planar

Helix F tilta and translates by:

~1 Angstrom

____ are released in T-R transition

Protons

T-R transition requires breakage and reformation of:

many non-covalent interactions between adjacent α -β sub-units

As O2 binds, the other subunits ______, increasing the likelihood of additional O2 binding.

change conformation

Information about the O2-binding status of a heme group is _____ transmitted to the other heme groups by: .

mechanically motions of the protein

binding of a ligand at one site affects the binding of | another ligand at another site

Allosteric effects

Two models proposed for allosteric effects:

Concerted Model of Allosterism Sequential Model of Allosterism

Concerted Model of Allosterism

All the subunits must be in either T or R form, model does not allow combinations of T and R state Binding of ligand increases the population of the R state.

Sequential Model of Allosterism

Ligand binding progressively induces conformational changes in the subunits greatest changes occurring in those subunits that have bound ligand.

Protein folding:

G = H - TS G should be favored (-) H = (-) S = (-)

Entropy of water molecules

H2O forms cages around hydrophobic AA, when they get folded, they are free to move around increasing surrounding entropy