Protein Structure

Question 1

Covalent bonds bind which degree of protein structure

Answer 1

Primary

Question 2

Noncovalent interactions bind which degree(s) of protein structure

Answer 2

Secondary
Tertiary
Quaternity

Question 3

Primary structure

Answer 3

The sequence of amino acid residues

Question 4

Secondary structure

Answer 4

The localized conformation of the polypeptide backbone

Question 5

Tertiary structure

Answer 5

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

Question 6

Quaternary structure

Answer 6

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

Question 7

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

Answer 7

Protein folding and protein stabalization depends of non-covalent interactions

Question 8

Intermolecular interactions

Answer 8

involved in interactions between molecules

Question 9

intramolecular interactions

Answer 9

involved in interactions between different parts of the same molecule

Question 10

Types of non-covalent interactions

Answer 10

ionic

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

Question 11

Ionic interactions

Answer 11

involve permanently charges species
ion-ion
ion-dipole

Question 12

Salt bridges

Answer 12

favourable ionic interactions

Question 13

Van der waals interactions

Answer 13

noncovalent associations between neutral molecules

can involve permanent, induced, or spontaneous dipoles

Question 14

London dispersion forces

Answer 14

type of van der waals

non-permanent dipole interactions

weak, but cumulatively are super strong

Question 15

Hydrogen bonds

Answer 15

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

Question 16

Is a linear of bent hydrogen bond stronger

Answer 16

linear

R-OH - - - OR

Question 17

Formation of favourable noncovalent interactions

Answer 17

result in a negative deltaH and a favourable contribution to deltaG

Question 18

Formation of unfavourable noncovalent interactions

Answer 18

result in a positive deltaH and and unfavourable contribution to deltaG

Question 19

What are the most electronegative elements we will be dealing with

Answer 19

O and N

Question 20

Non-covalent interactions in biomolecules

Answer 20

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

Question 21

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

Answer 21

Both are intermolecular interactions

Transient and polar in nature and help to stabilize transition states

non-charges

Question 22

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

Answer 22

H-bond is btwn H-FON

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

Question 23

Is sulfur electronagative

Answer 23

nope, for us it will be treated similarly to carbon

Question 24

How do water molecules dissolve proteins

Answer 24

they create a hydration shell around each ion

Question 25

Water as a solvent

Answer 25

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

Question 26

Hydrophillic substances

Answer 26

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

Question 27

"Entropy Driven"

Answer 27

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

Question 28

Hydrophobic effect

Answer 28

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"

Question 29

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

Answer 29

to maximize the entrophy of the system????

Question 30

Primary structure and the amide plane

Answer 30

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

Question 31

Alpha helixes beta strands

Answer 31

H-bonded to stabalize the backbone R groups influence the shape of the backbone Lysine and proline influence the B-bends

Question 32

Fibrous protiens

Answer 32

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

Question 33

Globular protiens

Answer 33

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

Question 34

Protien misfolding in alzhiemers

Answer 34

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

Question 35

Protein folds

Answer 35

collections of secondary structures are observed in protein structure and are common in multiple protein families

Question 36

Alpha helix

Answer 36

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

Question 37

Can alpha helixes be amphipathic

Answer 37

YESSIR

Question 38

beta sheet// beta pleated sheet

Answer 38

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

Question 39

Turns and loops

Answer 39

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

Question 40

Beta turn

Answer 40

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

Question 41

How are proteins flexible

Answer 41

dymanic alterations is non-covalent interactions allows small and large conformational changes

Question 42

How are subunits associated in quaternary structures

Answer 42

noncovalent interactions and in some cases di-sulfide bonds

Question 43

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

Answer 43

hydrophobic interactions!!!

Question 44

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

Answer 44

Delta S

Question 45

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

Answer 45

favourable delta H and delta S

Question 46

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

Answer 46

maximize favourable delta H