Chapter 4 - Proteins

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the first item in each key is the ________—the Protein Database ID symbol for that particular motif.

"PDB identifier"

organization of proteins based on motifs they contain at the ________ database

"Structural Classification of Proteins"

"beta conformation" =

"beta sheet"

The protein folds when constrained in this

"capped can"!! chaperonins are elaborate protein complexes required for protein folding (of some proteins that don't fold spontaneously on their own)

The overall process is directed by information in the chain and driven by the _______ energetics of weak interaction formation

"dynamic" weak interaction like (like ionic interactions and hydrophobic interactions)

When there is no regular pattern for the psi and phi angles, it is called

"random coil"

NOT all proteins have more than 1 domain

(some just have a single domain)

many proteins can be denatured by (6)

- heat - pH changes (change protein charge—causes electrostatic repulsion) - organic solvents (such as alcohol) - certain solutes (urea) - detergents

Proteostasis is accomplished by the coordination of many different pathways, for (4)

- protein synthesis - folding - re-folding - degradation.

A = _____ nm A= _____ m

0.1 nm 10^-10 m

Repeating unit is a single turn of the helix, extending ____nm , or ____ angstroms

0.54 nm = 5.4 A

Two major groups of proteins based on tertiary structure

1) fibrous proteins 2) globular proteins

what are the three driving forces for protein folding

1. increase in the entropy of the surrounding water (due to release of water molecules when the protein folds) 2. the hydrophobic effect (clustering hydrophobic AA inside the protein) 3. Disulfide bond formation

A score of ______ indicates a probability of 100% that a protein will be disordered.

1.0

Up to ____ of all human proteins may be unstructured, at least in significant part

1/3

from the 80,000 proteins currently with known structures (x-ray), there are only about ______ different folds or motifs (which show up repetitively)

1200

phi and psi are defined as _____ when the polypeptide is fully extended

180

the degree of a β turn

180

"alpha" and "beta" here, in hemoglobin, do not refer to alpha-helices and beta-sheets (secondary structure) --instead, "alpha" and "beta" here are just used to distinguish_____ within a multisubunit protein, regardless of the predominate types of secondary structure within each subunit

2 different kinds of subunits

the coiled-coil is made from

2 strands of alpha-keratin

Proline in position _____ or glycine in position ____ are common in β turns

2, 3

Under physiological conditions, for typical proteins, the difference between the folded and unfolded states can be on the order of ΔG = ____ kJ/mole.

20-65

Tobacco mosaic virus is made up of

2000 identical subunits

A protein family may be widespread in all

3 domains of cell life: Bacteria, Arachaea, and Eurkarya

Each helical turn = ____ amino acid residues.

3.6

hemoglobin (here) = 1st oligomeric (= multisubunit) protein to have its _____ determined

3D structure

the computer program used for this model has been highly successful in predicting the

3D structure of small proteins from their AA sequence

Hsp______interacts with the unfolded protein Hsp____ is complex and triggers ATP hydrolysis --> produces the closed form of the complex

40 70

all ____ atoms of the peptide bond are in plane

6

quaternary structure of a protein

A number of polypeptide chains linked together into assembled subunits

in a folded protein in native conformation, new bonds form between the

AA

in a folded protein in native conformation, new ionic interactions form among the

AA - some attractive, some repulsive

The 3-D structure of a protein is determined by its

AA sequence

constraining the protein within this chamber prevents inappropriate protein aggregation and restricts the possible conformations that a polypeptide chain can explore as it folds this process is _____ dependent

ATP

chaperones bind and release polypeptide by using energy from ____ and _____

ATP hydrolysis and some other proteins

Alpha keratin is rich in _____ residues

Ala, Val, Lue, Ile, Phe (hydrophobic) and Cys

______ is the most likely amino acid to show up in alpha helices.

Alanine - because it is small

It can then assemble slowly into amyloid fibrils, rich in β sheets, which contribute to the characteristic plaques on the exterior of nervous tissue in people with ______ disease

Alzheimer disease.

example of bulky adjacent R groups that destabilize the alpha helix if close together in the chain

Asn, Thr, Ser, Cys

how is a protein able to assume many conformation

Because free rotation is possible around many of the hundreds of bonds within a protein

Constraints affecting the stability of the α Helix 2) _______ of adjacent R groups

Bulkiness

which bonds of an AA can rotate

C-Calpha N-Calpha

ψ for the ____ bond

C-Cα

superhelical twisting: Three Stranded _____Superhelix (right-handed)

Collagen

______: part of a polypeptide chain that is independently stable or could undergo movements as a single entity with respect to the entire protein

Domains

The native conformation is a very LOW _______ state.

ENTROPY - low state of disorder

in a folded protein in native conformation, there are ____ H bonds between water and the protein

FEWER

4-Hydroxyproline function in Collagen

Forces Pro ring into favorable pucker and offers more H-bonds.

The native conformation usually has the lowest

Gibbs Free Energy (G)

When 2 or more β sheets are layered close together within a protein, the R groups of ___ and ____ touch surfaces

Gly and Ala have the smallest R groups

the alpha chain of collagen repeats what three AA

Gly-Pro-HyPro HyPro = 4-hydroxyproline, and uncommon aa

unfolded proteins are bound within pockets in the ______ complex

GroEL

The _______ Chaperonin system of E. coli assists protein folding in an ATP-dependent process

GroEL/GroES

_____ is a "lid" which transiently caps the GroEL pockets

GroES

the hydrogen bonds in an alpha helix occur between

H atom covalently bonded to electronegative N of the peptide bond. and the electronegative carbonyl O atom of the 4th amino acid away from that peptide bond. N—H | | | O

Every peptide bond in the helix participates in

H-bonding

the entropy of the water molecules surrounding the folded protein is

HIGHER - more randomness

conformational entropy of the unfolded polypeptide is noe

HIGHER - lots of disorder

parallel beta sheet

Having the same amino-to-carboxyl (N-C) orientations among the adjacent polypeptide chains in the beta-sheet

A General Theory of Protein Folding: the ______ Model

Hierarchical = orderly sequence of events

the analogous chaperonin system in eukaryotes is called

Hsp60

The cyclic pathway by which chaperones bind and release polypeptides is illustrated for the chaperone proteins

Hsp70 and Hsp40.

_______ is normally maximized in protein structure.

Hydrogen bonding

Proteins fold to the lowest-energy fold in the microsecond to second time scales.How can proteins fold so fast ?

It is mathematically impossible for protein folding to occur by randomly trying every conformation until the lowest-energy one is found (Levinthal's paradox) Search for the minimum is not random because the direction toward the native structure is thermodynamically most favorable

all amino acids in the alpha helix are ____-stereoisomers

L

the entropy of the water molecules surrounding the unfolded polypeptide is

LOW - lots of order

_______ form first ____ form sequently

Local units of 2o structure (ex. α-helices) form first Longer range interactions (helix-helix, etc) form later

______ are cellular systems that assist proteins in the folding process,

Molecular chaperones and chaperonins

φ for the _____ bond

N-Cα

_______ is one of the best available algorithms for predicting the likelihood that a given amino acid residue is in a region of intrinsic disorder, based on the surrounding amino acid sequence and amino acid composition.

PONDR

Constraints affecting the stability of the α Helix 4) ____ and ____ residues destabilize the helix

Pro and Gly pro: N in pro is part of a rigid ring, so N-Calpha bond rotation is not possible, and there is no H bonding to the N gly: too conformationally flexible

the ____ or ____ permit the sharp twisting of the collagen helix

Pro or HyPro

The different AAs have different propensities to participate in alpha-helices due to the properties of their

R groups

that there are hydrophobic interactions because the

R groups are close together

in the alpha helix, R groups

R groups protrude outside

Ribonuclease Refolding Experiment

Ribonuclease is a small protein that contains 8 cysteines linked via four disulfide bonds Urea in the presence of 2-mercaptoethanol fully denatures ribonuclease When urea and 2-mercaptoethanol are removed, the protein spontaneously refolds, and the correct disulfide bonds are reformed The sequence alone determines the native conformation **Quite "simple" experiment, but so important it earned Chris Anfinsen the 1972 Chemistry Nobel Prize

fibroin is rich in what AAs

Rich in Ala and Gly

the H bonds that crosslink adjacent segments of the polypeptide chain in an anti parallel beta sheet is

STRAIGHT

______causes tooth loss, poor wound healing, bone problems, heart failure

Scurvy

protein conformation refers to the

Spatial arrangement of atoms in a protein

this suggest

Suggests an ancient origin Alcohol dehydrogenase from 2 different organisms example

motifs = _____ structures

Supersecondary

______ is more reliably conserved than primary structure (AA sequence)

Tertiary structure conserve structure as well as function

Why is the alpha helix structure so stable and so common??

The alpha-helix makes great use of internal H bonds

peptide bond

The chemical bond that forms between the carboxyl group of one amino acid and the amino group of another amino acid

Proteostasis

The continual maintenance of the active set of cellular proteins required under a given set of conditions

A Protein's Conformation is Stabilized Largely by

Weak Interactions

t turns out that it would take more than 10^77 years to randomly try out all possible conformations --> so protein folding is NOT a

a completely random, trial-and-error process

Secondary structures of globular proteins

a helix B sheet B turn

The turn is stabilized by

a hydrogen bond from a carbonyl oxygen to amide proton three residues down the sequence (amine proton is the 4th AA residue)

oligomeric =

a multimer with just a few subunits

these peptide-bond electric dipoles are aligned/transmitted through the intrachain H bonds of the helix, resulting in

a net overall helix dipole extending along the helical axis

= a folding pattern that can describe

a part of a protein

these partial charges creates

a small electric dipole

globular proteins: polypeptide chains folded into

a spherical or globular shape

which of these amino acids listed below, would most likely be found in the interior of a globular protein?

alanine because it is non polar

Simplest arrangement the polypeptide chain can assume with its rigid peptide bonds is a helical structure.

alpha helix

The ______ can also have both hydrophilic and hydrophobic surfaces

alpha helix

the collagen helix is a unique secondary structure distinct from the

alpha helix

secondary structure of protein

alpha helix and beta pleated sheet

this motif exists in _______, a bacterial toxin that kills a cell by creating a hole in its membrane

alpha-hemolysin

a series of beta-alpha-beta loops, arranged so that the beta strands form a barrel, creates a particularly stable and common motif called the

alpha/beta barrel

on the beta sheet, the R groups

alternate sides of sheet

The numbers indicate the _________ in this 56 residue peptide that have acquired their final structure in each of the steps shown

amino acid residues

diseases involving formation of amyloid fibers due to protein misfolding are called

amyloidoses

Fatty Acid Binding Protein is formed in a large part of_______ beta sheet

anti parallel

fibroin has _____ beta sheets

antiparallel

β turns facilitate tight turns between 2 adjacent strands of _____ β sheets

antiparallel

The ________ side chains shown here play a significant role in stabilizing the amyloid structure, by HYDROPHOBIC effects.

aromatic

Some proteins need some ________ in order to fold:

assistance

the R groups point _____ from axis of helix

away

why is there not much nutritional value in jello?

because is extremely low in many amino acids that are essential to the human diet

Why are prolines common in beta turns?

because peptide bonds involving this cis configuration is amenable to a tight turn.

the H bonds in a parallel beta sheet are

bent at an angle

green fluorescent protein, found in jellyfish has a ______ structure

beta barrel

Example of stable "α+β" motifs

beta barrel structure the alpha and beta regions are somewhat segregated

β-barrel

beta sheets twisted into a barrel shape

____ is another kind of protein secondary structure

beta turns/bends

an example of a simple motif

beta-alpha-beta loop

conformational changes do NOT involve

breaking covalent bonds ex. is rotation about single bonds

Molecular chaperones and chaperonins assist in the protein folding by (3)

by shielding them from unproductive interactions or by providing a protected folding environment or by preventing aggregation of the unfolded protein

intrinsically disordered proteins can act as

can act as scavengers, binding up small molecules and acting as reservoirs or garbage dumps

intrinsically disordered proteins can act as

can act as spacers, insulators, or linkers in larger structures

The intrinsically disordered ______ of p53 protein binds to at least ____ different binding partners and assumes a different structure in each of these complexes.

carboxyl terminus, 4

a denatured unfolded protein has no _____

catalytic activity

the post-translational processing is catalyzed by ________ and requires _____ and _____

catalyzed by prolyl hydroxylase requires oxygen and ascorbate (Vitamin C)

The p53 protein is made up of several different segments. Only the ______ is well ordered.

central domain the amino terminal and carboxyl terminal regions are disordered

the AAs in intrinsically disordered proteins

charged Lys, Arg, Glu, and destabilizing Pro

the beta sheets are NOT held together by

chemical crosslinks

usually, a domain from a large protein will retain its native 3D structure even when

cleaved away from the rest of the protein

the small R groups of Ala and Gly permit an interlocking arrangement of R groups --> results in

close packing of beta sheets

an example of a fibrous protein

collagen

gelatin Jello is derived from _______

collagen

because vitamin C doesn't work --> _______ isn't made --> connective tissue in the body ______

collagen, CT degenerates

β-barrel is a common

complex structural motif like a soda can

Proteins may change _____ as they bind to other molecules or catalyze reactions

conformation

do proteins have conformation or configuration

conformation

at top: the many unfolded states have a high degree of ____ and _____

conformational entropy and high free energy

The protein folding free energy funnel: as folding proceeds, the narrowing of the funnel reflects the decrease in the

conformational space that must be searched as the protein approaches its native state

see formation of α-helix and tertiary structure based solely on physical chemistry of

constituent functional groups. ex of hierarchical model, with orderly sequence of events

the atoms in the center of the alpha-helix are in very close

contact.

The monomers function together in a _____ manner when associated into this tetrameric form - really nice things result.

cooperative

Collagen superhelices are crosslinked side-by-side by _______ bonds between modified amino acids.

covalent

the amino acid sequence contains

covalent bonds

Connections between elements of secondary structure (Connections between β strands in layered β sheets) cannot

cross or form knots remember that these connections lines are still parts of the protein, so they are parts of the polypeptide chain, so they can't just be twisted up as if they were a piece of string

these new disulfide crosslinks exert twist on the bundles of alpha-helical coils in the hair's keratin get

curls!

in a denatured protein, the disulfide cross links are reduced to yield _____ residues

cys

as folding proceeds, ______ in the number of conformational species present =narrowing of the funnel =_______ in entropy and free energy

decrease, decrease

intrinsically disordered proteins: Contain protein segments that lack

definable structure

a loss of 3D structure sufficient to cause loss of function =

denaturation

The positive amino terminus (last 4 AAs) of the α-helix is destabilized by _____and is stabilized by ______

destabilized by positively charged AA residues stabilized by negatively charged AA residues

The very end of the carboxyl-terminal region has multiple binding partners and folds when it binds to each of them; however, the three-dimensional structure that is assumed when binding occurs is ________ for each of the interactions shown, and thus the color of this carboxyl-terminal segment (11 to 20 residues) is shown in a different color in each complex

different

resonance (partial sharing of electrons) in each peptide bond, between carbonyl O and amide N, creates a

dipole

the peptide bond has a strong

dipole moment - Carbonyl O is negative - Amide H is positive

the inactive aggregates accumulate in cells and cause

disease

Proteins folding follows a

distinct path

mercaptoethanol reduces/cleaves the ______ bonds

disulfide

an oxidizing agent to make NEW ______ bonds between Cys pairs will be added

disulfide bonds

keratin's _____ are manipulated in permanent waving

disulfide bonds

the 4 amino acids at each end of the helix

do NOT participate fully in the helix H bonds

if a person inherits a mutation such as substitution with an aromatic residue at a position that favors formation of amyloid fibrils, Alzheimer's disease symptoms can begin at an

earlier age

likely are linked _____

evolutionarily

Association can ______ existing functionality of subunits

expand

even mild vit. C deficiency causes

fatigue, increased respiratory infection, etc

Structures that maximize hydrogen bonding potential are generally ______ in protein architecture

favored

Additional protein molecules slowly associate with the amyloid and extend it to form a

fibril.

alpha keratin is a _____ protein

fibrous

Fibroin is another

fibrous protein

This core is extremely important both in the _____ and ____ of these very compact proteins.

folding and structural stability

humans cannot make vit. C and must obtain it from

food, like citrus scurvy was lethal to humans making long voyages hundreds of years ago

The 180° turn is accomplished over _____ amino acids

four

phi and psi can have any value between -180 and +180, except when

free rotation is prohibited by steric interference between atoms in the polypeptide backbone and the amino acid side chains

protein needs to be folded properly in order to______

function properly

most enzymes, regulatory proteins, transport proteins, immunoglobulins, motor proteins... are

globular

most enzymes are

globular proteins

example of 3 groups that repel each other and would prevent an alpha helix from forming

glu, lys and arg

this motif also exists in ______ proteins...

green fluorescent

all fibrous proteins are insoluble in water because

have a high concentration of hydrophobic amino acid residues

anti-parallel beta sheet

having opposite amino-to-carboxyl (N-C) orientations among the adjacent polypeptide chains in the beta-sheet

Some are called ____ proteins since they are synthesized during periods of _____

heat shock proteins or stress proteins synthesizes during period of stress

these peptide-bond electric dipoles increases as

helical length increases

Protein MISfolding is the basis of numerous

human diseases Type II Diabetes Alzheimer's Disease Huntington's Disease Parkinson's Disease Prion diseases like Mad Cow and CJD

When they are interior there is maximal ______ of polar groups.

hydrogen bonding

Sheet-like arrangement of backbone is held together by _____ bonds between the backbone amides in different strands

hydrogen bonds

Hb subunit is the tetramer with four subunits (2 α chains and 2 β) held together mainly by _______

hydrogen bonds and ionic interactions.

2 aromatics 3-4 residues away from each other is a _______ interaction

hydrophobic

proteins that are not properly folded often have exposed ______ surfaces that render them "sticky," leading to the formation of inactive aggregates

hydrophobic

urea (or organic solvents or detergent) disrupts _____ interactions in the core, and urea also disrupts _____

hydrophobic and H bonds

since R groups alternate sides of sheet, it is possible to make β-sheets with ____ and /or_____ surfaces

hydrophobic and/or hydrophilic (bc R groups could be hydrophobic or hydrophilic)

intrinsically disordered proteins lack a

hydrophobic core

The interior of most globular proteins consists of a _____

hydrophobic core with little or no water present. (Hydrophobic and van der Waal's interactions)

the photo fibril is stabilized mainly by

hydrophobic interactions and disulfide crosslinks

hsps bind to regions of unfolded polypeptides that are rich in ______, preventing inappropriate aggregation

hydrophobic residues

The core of the helix is somewhat

hydrophobic.

The tendency of a given segment of a polypeptide chain to form an alpha-helix depends on the

identity and sequence of amino acid residues within the segment.

Higher order structures formed by specific subunit associations often have new binding, catalytic or regulatory functionality not found in the

individual subunit monomers.

silk is made by

insects and spiders

Typical Globular Protein Tertiary Structure: Most hydrophobic amino acids are on the _____ of the folded protein and may contribute to the hydrophobic core.

inside

Common mechanism: a normally-secreted soluble protein is misfolded and converted into

insoluble extracellular amyloid fibers

amino acids that are far apart in the polypeptide sequence and are in different types of secondary structure may actually

interact with each other within the completely-folded structure of a protein

Polar-noncharged amino acids also tend to appear on the protein surface but may be in the

interior

the hydrophobic AA now buried/ cluster in the

interior of the protein

positive R's often found 3-4 away from negative R's =

ion pair formation positively charged AAs found 3-4 away from negatively-charged amino acids

Human hair is made out of what protein

keratin

the binding of small molecules may affect the interaction between subunits --> causing

large changes in the protein's activity in response to small changes in the concentration of substrate or regulatory molecules

In some cases, the only feasible way to get the required functionality is to form

large multimeric quaternary structures

close packing of the polypeptide chains within the

left-handed supertwist

intrinsically disordered proteins are composed of amino acids whose higher concentration forces...

less-defined structure

secondary structure refers to a

local spatial arrangement (conformation) of the polypeptide backbone

fibrous proteins: polypeptide chains arranged in

long strands or sheets

the conformational entropy of folded protein is

low - lots of order

The α helix has a large

macroscopic dipole moment

stability of a protein refers to its tendency to

maintain a native conformation

the molecular motions of the peptide and the effects of the water molecules were taken into account in

mapping the most-likely paths to the final structure among countless alternatives

The native conformation of most proteins is ______ stable

marginally stable (its tendency to remain folded is marginal)

Chaperones prevent

misfolding

_____ are particularly stable arrangements of 2 or more elements of secondary structure and the connections between them

motifs

Common, regular folding patterns of the polypeptide backbone are stabilized by

multiple non-covalent interactions.

This is because left-handed connections

must traverse sharper angles, are longer, and are harder to form

Some fraction of the molecules released at the end of the cycle are in the

native conformation

An isolated protein has a unique, or nearly unique, stable structural form called the

native fold

there are no _____ bonds or ____ interaction between AA

no H bonds no ionic interactions

the 3 D shape of the formed as the tertiary structure contains _____ bonds

non covalent bonds, weak interactions

these assembled subunits of folded polypeptide chains contain _______ bonds

non covalent bonds, weak interactions

the alpha helix and beta pleated sheet contain ____ interactions

non-covalent bonds, weak interactions

The most important forces in stabilizing the specific functional structure of a given protein are

non-covalent interactions (H bonds, hydrophobic effect, ionic interactions, van der Waals forces).

Very heat-stable proteins of thermophilic bacteria (living in near-boiling water of hot springs) are stabilized by

numerous ion pairs, therefore have very tightly-packed hydrophobic cores

fibrous proteins usually consist of mostly

one type of secondary structure

this 20-65 kJ/mole corresponds to

only a "few" weak interactions holding the whole protein together!.

the R groups of adjacent amino acids protrude from the zigzag structure in

opposite directions create the alternating pattern seen in the side view above

All peptide bonds in the α helix have a similar

orientation

Charged amino acids usually are found on the ______ of the protein. Favorable charge-charge interactions (+/-) may contribute to protein stability.

outer surface

_______ protein is critical in the control of cell division

p53

The planes of the rigid peptide bonds are _____ to the long axis of the helix

parallel

Amyloid-β peptide may take the form of two layers of extended _______

parallel β sheet.

a peptide C-N bond cannot rotate freely because of

partial double bond character - o partial negative charge - H bonded to N has partial positive charge

this influences the _____ of the polypeptide connection between the segments

path

so the partial pos and neg charges of the helix dipole actually reside on the

peptide amino and carbonyl grps near the N-terminal and C-terminal ends of the helix

Peptide conformation is defined by angles

phi & psi: φ and ψ -these are the angles at the intersection of the 2 planes

The planarity of the peptide bond and tetrahedral geometry of the α-carbon create a

pleated sheet-like structure β Sheets

Side chains can be and often are ordered in such a way as to make the helix structure _____ on one side and _____ on the other side

polar , hydrophobic

Negatively charged residues often occur near the ______ end of the helix dipole

positive

OVERALL, the N-terminus is ______and the C-terminus is _______

positive, negative

The negative carboxyl terminus (last 4 AAs) of the α-helix is stabilized by ______ and is destabilized by ______

positively charged AA residues negatively charged AA residues

When 2 or more β sheets are layered close together within a protein, the R groups of the AA residues on the touching surfaces must be

pretty small

The chaperones do not actively promote the folding of the substrate protein, but instead

prevent aggregation of unfolded peptides.

The Ribosome: Ensures correct translation of the genetic code into the protein ______ structure

primary

what is only AA that contains a trans C-N bond

proline

example of "all beta" motifs

propeller

proteins with significant similarity in either primary sequence AND/OR in tertiary structure/function are said to be in the same

protein family

Fibroin

protein in silk

tertiary structure of protein

protein structure is formed when the twists and folds of the secondary structure fold again to from a larger 3D structure

Disordered regions of these proteins can bind to many different

proteins, facilitating interaction with numerous different partner proteins

in the alpha helix conformation, the polypeptide backbone is tightly wound around an imaginary axis drawn longitudinally through the middle of the helix, with the R groups

protruding outward

fibrous proteins function to

provide support, shape, external protection to vertebrates

the Tobacco mosaic virus is an example of a _____ structure

quaternary

this is an example of _____ structure (multiple subunits assembled together) Hb has 4 subunits together

quaternary

Rigid peptide bonds limit the

range of conformations possible for a polypeptide chain.

the three steps to form wavy hair

reduce, curl, oxidized

Association of______protein subunits can form structural, protective, or dynamic quaternary aggregates

repetitive

all 6 atoms of the peptide bond are in plane due to

resonance between the carbonyl oxygen and the amide nitrogen

There are lots of turns or loops in compactly-folded, globular proteins where the polypeptide chain needs to _____ in order to do the folding.

reverse direction

the expt showed that the denaturation of some proteins is

reversible

The ________ is made up of dozens of protein subunits, plus several RNA molecules, all associated together!

ribosome

all proteins begin their existence on a ________, as linear sequence of amino acid residues

ribosome

Collagen superhelix is _____ handed

right

Connections between strands of a parallel β-sheets are almost always

right-handed

Helical twist is _______in most proteins

right-handed -clockwise

the peptide bond is ___ and ____

rigid and planar

a peptide C-N bond cannot

rotate freely

the primary structure is NOT totally static

rotational conformational changes around single bonds

even quite different AA sequences might fold up into the

same type of motif

without vitamin C, you get the disease _____

scurvy

A motif is a structural element falling between ____ and _____ structure

secondary and tertiary

Small regions of _______ are assembled first and then gradually incorporated into larger structures.

secondary structure

in eukaryotes, disulfide bonds are found primarily in

secreted, extracellular proteins

the small depressions along the funnel's sides =

semistable intermediates

primary structure of protein

sequence of amino acids (amino acid residues)

globular proteins: often contain ______ types of secondary structure and a typically water or lipid-soluble

several

The beta (β) conformation organizes polypeptide chains into

sheets zigzag polypeptide chains can be arranged side-by-side to form this pleated structure:

in each fibrous protein, the fundamental structural unit is a

simple repeating element of secondary structure most enzymes are globular

Complex structural motifs are often built up from

simpler, often repetitive motif elements

sometimes a ______ may comprise the entire protein

single large motif

at bottom of funnel, an ensemble of folding intermediates has been reduced to a _____.

single native conformation (or a few)

The most stable configuration for the β-sheet is a

slight twist. this is why the beta-barrel can exist

(fibroin) silk is ____ and _____

soft and flexible

Constraints affecting the stability of the α Helix 3) interaction between AA side chains spaced

spaced 3 0r 4 residues apart

the 3 D shape of the protein at the tertiary structure contains

spatial arrangement of atoms

Often each domain has a

specific, related function

globular proteins have polypeptide chains folded very compactly into a ____ shape

spherical or globular

globular proteins

spherical, water-soluble proteins.

the beta conformation is most ______ when the individual segments are twisted slightly in a right-handed sense

stable

further assembled into collagen fibrils: tensile strength greater than that of

steel wire (of the same diameter)!

the fact that the beta sheets are held together by weak interactions imparts both

strength and flexibility

this super twisting of the filaments amplifies the

strength of the overall structure (like if you twisted 2 ropes together)

when alpha helices and beta sheets occur together in proteins, they are generally found in different

structural layers

proteins have common

structural patterns

The function of a protein depends on its

structure.

Constraints affecting the stability of the α Helix 1) electrostatic attraction or repulsion between

successive (close together) AA residues with charged R groups

Beta turns are often found near the ______ of a protein

surface

High tensile strength with no stretch - used in

tendons, bone matrix, cartilage

fibrous proteins have pretty simple

tertiary structure

part of the intermediate filament family of proteins, like

the IFs in the cytoskeleton

the Anfinsen experiment (using ribonuclease) provided the 1st evidence that

the aa sequence contains all the info required to fold the chain into its native, 3D (tertiary) structure

they are in different structural layers because

the backbone of protein segment in beta sheet cannot readily form H bonds to an alpha-helix aligned with it

silk cloth does not stretch because

the beta sheet is already a highly extended conformation

at the bottom, Stabilization of structure by _____, causes _____entropy and free energy

the hydrophobic core, H-bonds, ionic interactions, Van der Waals (VDW) interactions decreased

when urea and mercaptoethanol are removed,

the native tertiary structure, catalytically active state returns and the disulfide cross links are reformed

since the The sequence alone determines the native conformation....

the primary structure of the protein (amino acid sequence) contains the "molecular instructions" for 3D folding and tertiary structure.

protomer =

the repeating structural unit in a multimeric protein (would be 1 alpha plus 1 beta subunit in hemoglobin)

but structure is flexible because

the sheets are held together by numerous weak interactions rather than by covalent disulfide bonds (chemical crosslinks)

______, the folding process can be viewed as a free-energy funnel

thermodynamically

of all of the enormous number of possible ways to fold up even a simple protein, the "one" native conformation is the

thermodynamically most stable

the C-N bond all all but one AA is

trans

hsps also block the folding of certain proteins that must remain unfolded until they have been

translocated across a membrane

this chaperonin complex contains _______ in which proteins can fold in a relatively isolated environment.

two cavities

since these proteins are stabilized by these factors, they are less susceptible to

unfolding

Side chains protrude from the sheet alternating in

up and down direction

denaturing conditions

urea + mercaptoethanol

if gly gets substituted by a bulkier AA via a genetic disease,

very bad symptoms or lethality results due to the deleterious effects on collagen structure

the aa composition + supertwists of collagen =

very close packing = very strong!!

Association of repetitive coat protein subunits in the protects

viral RNA core.

un an unfolded polypeptide, hydrophobic AA are exposed to

water

in an unfolded polypeptide, hydrogen bonds occur between

water and the peptide

fibroin Forms bets sheets which are stacked and held together by

weak interactions (H bonding and van der Waals between sheets)

these factors of denaturation disturbs ______ interactions

weak non covalent, covalent bonds remain intact

the H bonds in a parallel beta sheet are ______ than the H bonds in anti-parallel sheets

weaker

intrinsically disordered proteins can inhibit the action of other proteins by

wrapping around their protein targets

intrinsically disordered proteins cannot be crystallized for structure determination by

x-ray crystallography

______ different protein families in the PDB

~4000

About ____of all AA residues found in proteins are found in alpha-helices

¼

Myoglobin is a small oxygen binding protein composed primarily of

α-helices

occur frequently whenever strands in β sheets change the direction

β turns

In a small number of the molecules, before folding is complete, the ______ regions of one polypeptide associate with the same region in another polypeptide, forming the nucleus of an amyloid.

β-sheet


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