Wolberger_proteins

Question 1

T/F: proteins constitute majority of cells dry mass

Answer 1

True

Question 2

components of a protein (4)

Answer 2

N-terminus (NH2, amino), side chains, polypeptide backbone, and C-terminus (COO-, carboxyl)

Question 3

polar amino acids with uncharged side chain (5)

Answer 3

Asparagine, glutamine, serine, threonine, tyrosine - “All good souls thank tyra” - STTAG

Question 4

polar amino acids with positive side chain (3)

Answer 4

Arginine, lysine, histidine - HAL

Question 5

polar amino acids with negative side chain (2)

Answer 5

Aspartic acid, glutamic acid

Question 6

hydrophobic amino acids (10)

Answer 6

FAMILY WV - phenylalanine (F), alanine (A), methionine (M), isoleucine (I), leucine (L), cysteine (Y), tryptophan (W), valine (V)

Question 7

four weak forces shaping protein structure

Answer 7

hydrophobic force, ionic bonds, hydrogen bonds and van der waals attractions

Question 8

At pH=7 the amino and carboxyl groups are -

Answer 8

ionized

Question 9

Proteins consist exclusively of L or D-amino acids?

Answer 9

L

Question 10

basic amino acids (3)

Answer 10

same as amino acids with positive side chain - arginine, lysine, and histidine

Question 11

size range of majority of proteins

Answer 11

50-2000AA

Question 12

why are alpha helices and beta sheets so prevalent?

Answer 12

because they result from hydrogen bonding between N-H and C=O groups in polypeptide backbone, meaning they are largely agnostic to amino acid side chain composition and can adopt a regular, repeated conformation despite AA seq (mosttly)

Question 13

coiled-coil

Answer 13

secondary structure formed of alpha helices wrapped around each other (largely 2, sometimes 3 or 4), such that the nonpolar side chains are protected from aqueous environment

Question 14

protein domain

Answer 14

substructure of a protein that can fold independently of the rest of the protein into a compact, stable structure

Question 15

two types of b sheet structures

Answer 15

antiparallel (polypeptide backbone folds back and forth upon itself, with each section of the chain running in the direction opposite to its immediate neighbors), parallel (sheets form from neighboring segments of the polypeptide backbone that run in the same orientation)

Question 16

how many domains can proteins have

Answer 16

1 to several dozen, connnected by short, relatively unstructured lengths of polypeptide chain

Question 17

some advantages to intrinsically unstructured regions (5)

Answer 17

1] allow for movement and flexibility, ie elastin - 2/3] binding/signaling - form binding sites for other proteins that are of high specificity, yet readily altered by posttranslational mods , ie RNA pol, 4] tethering - can hold two protein domains in close proximity to bolster their interactions, ie scaffold proteins 5] diffusion barrier - clumps of disordered protein chains can create micro-regions of gel-like consistency in the cell that restrict diffusion

Question 18

most common cross-linkage?

Answer 18

disulfide bonds

Question 19

advantages to smaller subunits for the assembly of larger structures (3)

Answer 19

1] start-up cost - less genetic information needed, 2] errors not as big of a deal, 3] regulation - assembly and disassembly can be readily controlled through reversible processes

Question 20

most conformationally flexible side chain

Answer 20

glycine, can adopt any phi/psi angle

Question 21

most rigid side chain

Answer 21

proline, covalently linked to peptide NH, favorable at N-terminus of alpha helix

Question 22

why does hydrophobic effect happen?

Answer 22

entropy of water increased when waters previously orientated at hydrophobic surfaces are released upon interactions of nonpolar molecules

Question 23

Five organizing principles of proteins

Answer 23

hydrophobic effect, sequence, h-bonding, backbone restriction, packing

Question 24

what is backbone restriction

Answer 24

a limitation of the phi/psi angles at which side chains can rotate due to steric clashes between atoms

Question 25

T/F. Native H-bonds are stabilizing.

Answer 25

False, they are not inherently stabilizing, it is NOT having them which is destabilizing

Question 26

why are alpha helices most common transmembrane domain?

Answer 26

this secondary structure allows for the burial of polar groups in a hydrophobic core, which minimizes unpaired H bonds in protein interior

Question 27

what is the percent sequence identity which implies two proteins have similar structure and function?

Answer 27

> 25%, but can be even lower in some cases

Question 28

T/F. Primary structure is more conserved than tertiary structure.

Answer 28

False, tertiary structure is often very similar with disparate AA sequence

Question 29

3 major groups of membrane lipids

Answer 29

phospholipids, glycolipids and neutral lipids

Question 30

what is a fatty acid?

Answer 30

hydrocarbon chain with carboxylic acid at one end. Can be saturated (fully extended, lowest energy conformation) or unsaturated (double bonds with cis configuration)

Question 31

what is amphipathy?

Answer 31

partly hydrophobic-partly hydrophilic molecule, describes membrane phospholipids

Question 32

three parts of a membrane phospholipids

Answer 32

hydrophilic head, glycerol, and two hydrophobic tails

Question 33

membrane fluidity is dictated by: (3 things)

Answer 33

Fatty acid chain length, number of double bonds, and presence of sterols

Question 34

T/F. Longer fatty acid chains are more fluid

Answer 34

False, they are less fluid with a higher Tm

Question 35

T/F. More double bonds in fatty acids chains make them more fluid.

Answer 35

True, more double bonds give you lower Tm

Question 36

T/F. Sterol effects on membrane fluidity depend on temperature.

Answer 36

True, if temp is above the melting temperature, then membrane fluidity decreases due to reduction of freedom of neighboring FA chains. But below the Tm, rigid planar sterol prevents packing and increases membrane fluidity

Question 37

Kyte-doolittle hydropathy plot

Answer 37

allows you to sum the hydropathy index for neighboring AA in a primary sequence to predict regions of hydrophobicity/likely membrane spanning domains