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Molecular Enzymes > Protein Structure > Flashcards

Protein Structure Flashcards

1
Q

Covalent bonds bind which degree of protein structure

A

Primary

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2
Q

Noncovalent interactions bind which degree(s) of protein structure

A

Secondary
Tertiary
Quaternity

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3
Q

Primary structure

A

The sequence of amino acid residues

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4
Q

Secondary structure

A

The localized conformation of the polypeptide backbone

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5
Q

Tertiary structure

A

The three-dimensional structure of an entire polypeptide, including all of its side chains

the packing of structural elements like the alpha helices and the beta sheets into a complicated and roughly spherical globular protein

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6
Q

Quaternary structure

A

The spatial arrangement of polypeptide chains in a protein with multiple subunits

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7
Q

Which factors are most important in determining the higher levels of protein structure

A

Protein folding and protein stabalization depends of non-covalent interactions

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8
Q

Intermolecular interactions

A

involved in interactions between molecules

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9
Q

intramolecular interactions

A

involved in interactions between different parts of the same molecule

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10
Q

Types of non-covalent interactions

A

ionic

vander waals forces (includes H bonds, diplole-dipole interactions and London dispersion forces)

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11
Q

Ionic interactions

A

involve permanently charges species
ion-ion
ion-dipole

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12
Q

Salt bridges

A

favourable ionic interactions

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13
Q

Van der waals interactions

A

noncovalent associations between neutral molecules

can involve permanent, induced, or spontaneous dipoles

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14
Q

London dispersion forces

A

type of van der waals

non-permanent dipole interactions

weak, but cumulatively are super strong

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15
Q

Hydrogen bonds

A

a special kinf of dipole-dipole interaction

an attractive interaction between the H atom of a donor group and a pair of nonbonding electrons on the acceptor group

The hydrogen donor must be strongly electronegative (N, O, F)

The hydrogen acceptor must have a free lone pair of elections and be relatively small (F, O and N)

H bonds are weak compared to covalent bonds but are stronger than normal dipole-dipole interactions

H-bond is directional and only capable of forming one H-bond

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16
Q

Is a linear of bent hydrogen bond stronger

A

linear

R-OH - - - OR

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17
Q

Formation of favourable noncovalent interactions

A

result in a negative deltaH and a favourable contribution to deltaG

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18
Q

Formation of unfavourable noncovalent interactions

A

result in a positive deltaH and and unfavourable contribution to deltaG

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19
Q

What are the most electronegative elements we will be dealing with

A

O and N

20
Q

Non-covalent interactions in biomolecules

A

Play an important role in structure and fuction

examples include:

multi-subunit enzymes that catalyze biochemical reactions: assembly and dissaembly of protein monomers

Interactions between enzymes and substrate

21
Q

What is an importanty similarity between a hydrogen bond and a dipole-dipole interactins

A

Both are intermolecular interactions

Transient and polar in nature and help to stabilize transition states

non-charges

22
Q

What is the difference between a hydrogen bond and a dipole-dipole interaction

A

H-bond is btwn H-FON

Dipole-dipole not directional in nature, but h-bonding is

23
Q

Is sulfur electronagative

A

nope, for us it will be treated similarly to carbon

24
Q

How do water molecules dissolve proteins

A

they create a hydration shell around each ion

25
Q

Water as a solvent

A

chemicall inert, yet can dissolve a vast number of substances

Poor solvent for non-polar substances

is responsible for the 3D structure of proteins and other biomolecules

26
Q

Hydrophillic substances

A

soluble in water

tend to be ionic, strongly polar, and or are capable of H-bondig

27
Q

“Entropy Driven”

A

If something is entropy driven, it is the entropy term that makes the delta G negative

So, the -T delta S is negative and delta S is positive

process is spontaneous despite positive delta H

28
Q

Hydrophobic effect

A

The tendency of water to minimize its contact with hydrophobic molecules

Note: Hydrophobic interactions are not a separate “force” as such. Basically occurs in order to maximize the entropy of the system (ie hydrophobic compounds are excluded from water in order to prevent the unfavourable formation of the highly ordered “cage”

29
Q

What is the purpose of the cager water forms around dissolved solids

A

to maximize the entrophy of the system????

30
Q

Primary structure and the amide plane

A

Linking of amino acids by peptide bonds
resonace stabilization provided rigidity and means that the nitrogen cannot pick up an extra proton

also means that all amino acids are trans….. except for proline. This cis isomer is super useful for beta bends

31
Q

Alpha helixes beta strands

A

H-bonded to stabalize the backbone

R groups influence the shape of the backbone

Lysine and proline influence the B-bends

32
Q

Fibrous protiens

A

usually static and insoluable

ropelike

typically built upon a single type of secondary structure, this repetitive structure is usually assembled into cables or threads

ex// collagen, alpha keratin and silk fibroin

33
Q

Globular protiens

A

complex and dynamic

contain several types of secondary structure

compact and roughly spherical

can be water soluble, and, if so characteristically have hydrophobic interior and an hydrophilic surface = unimolecular micelle

can also be water insoluble (such as when bound to a biological membrane) if so, have a hydrophilic interior

34
Q

Protien misfolding in alzhiemers

A

missfolded protiens ex// Prp shows an increase in B-sheet formation

The overall flatness of these sheets allows the to stack and lead to protein aggregates

F198S (phe -> ser) causes this mutation

35
Q

Protein folds

A

collections of secondary structures

are observed in protein structure and are common in multiple protein families

36
Q

Alpha helix

A

uses the full H-bonding capacity of the polypeptide backbone

Carbonyl O of each reside forms an H-bonds with the backbone NH group four residues ahead

backbone H-bonds are parallel to the axis of the helix

R-groups protrude outward from helical backbone

37
Q

Can alpha helixes be amphipathic

A

YESSIR

38
Q

beta sheet// beta pleated sheet

A

uses sthe full H-bonding capacity of the polypeptide backbone

H-bonding occurs BETWEEN neighbouring peptide chains

R-groups extend above and below the plane of the sheet

peptide chain is fully extended

39
Q

Turns and loops

A

in a globular protein, nearly 1/3 of amino acids are in turns or loops where chain reverses direction

most commonly the Beta turn

40
Q

Beta turn

A

so named because often connects the ends of two adjacent segments of an antiparalle Beta sheet

Is a hair pin turn involving 4 amino acids

often includes gly and pro

41
Q

How are proteins flexible

A

dymanic alterations is non-covalent interactions

allows small and large conformational changes

42
Q

How are subunits associated in quaternary structures

A

noncovalent interactions and in some cases di-sulfide bonds

43
Q

What is the most important interaction for the maintenance of the tertiary structure of a protein

A

hydrophobic interactions!!!

44
Q

Which factor fo the gibbs free energy equation drives the nonpolar residues to reside mostly in the interior of a globular protein

A

Delta S

45
Q

Which factor fo the gibbs free energy equation drives the charged polar residues to be located on the surface of a globular protein

A

favourable delta H and delta S

46
Q

Which factor fo the gibbs free energy equation drives the formation of the alpha helix and beta sheets through hydrogen bonding

A

maximize favourable delta H

Molecular Enzymes (7 decks)

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