Nap Attack 4

Question 1

peptide bond formation involves

Answer 1

a condensation reaction between the carboxyl group of one amino acid and the amino group of another

Question 2

protein synthesis is ___________

Answer 2

a complex process in which amino acids are first activated by ATP and then linked with tRNA

Question 3

oxygen of carboxyl and hydrogen of amide usually in trans config because

Answer 3

to avoid steric vdw interaction of side chain groups

Question 4

side chain groups being on opposite sides represents a difference of

Answer 4

conformation, not configuration

Question 5

____ % of non-proline cis peptide bonds, ____ % of proline cis peptide bonds

• a reason for this is _______
• a large majority of them occur where

Answer 5

0.5, 6
There is a relatively small difference in free energy between cis and trans proline
in surface accessible bent coils

Question 6

what seperates isomerization of the cis and trans configurations of proline peptide bonds

Answer 6

A high energy barrier

Question 7

Possible rate limiting step folding of a protein with X-prolyl peptide bonds

Answer 7

cis-trans isomermization because X-prolyl peptide bonds will not spontaneously adopt the intended confomation

Question 8

Prolyl isomerases can act as

Answer 8

chaperones

Question 9

interconversion of cis and trans can possibly

Answer 9

act as a switch to regulate protein function

Question 10

sterically forbidden conformations are

Answer 10

those in which any non-bonding interatomic distance, is less that its corresponding van der waals distance

Question 11

why theres not really glycine ramachandran plots

Answer 11

it has a hydrogen side cahin so it is less restricted in the amino acid conformations that it can adopt

Question 12

why theres not really proline ramachandran plots

Answer 12

it’s ring restricts freedom so it has the least number of allowable conformations

Question 13

Histidine-containing protein

Answer 13

serves as a phospho transfer protein in a bacterial sugar uptake system

Question 14

three dimensional structure of protein determined by

Answer 14

amino acid sequence

Question 15

function of a protein depends on

Answer 15

its structure

Question 16

isolated proteins usually exist in

Answer 16

one or a small number of stable structural forms

Question 17

most important forces stabilizing the specific structures of a given protein are

Answer 17

non-covalent

Question 18

within the huge number of protein structures there are

Answer 18

a limited number of common structural patterns

Question 19

Gene sequencing

Answer 19

easier than directly determining the sequence of a peptide or protein but will not determine post translational modifications

Question 20

secondary structure fun facts

Answer 20

they are regularities in local conformation that are maintained by main chain hydrogen bonds
- regions of it are characterized by a specific pattern of hydrogen bonding
- folding of a polypeptide is restricted by the limited flexibility of a peptide bond
(alpha helices) 310 helices, ß sheets, ß turns)

Question 21

To represent a viable form of secondary structure the folding pattern must

Answer 21

1) optimize the hydrogen bonding potential of the main chain carbonyl and amide groups
2) represent a favoured conformation of the polypeptide chain

Question 22

alpha helix fun facts

Answer 22

• all c=o groups point towards the c- terminus
• phi and psi angles of each residue are similar
• helix is stabilized by many hydrogen bonds which are nearly parallel to long axis of the helix
• each c=o (residue n) forms a hydrogen bond with the amide hydrogen of residue n+4

Question 23

Helix dipole

Answer 23

small electrical dipole exists in each peptide bond

• dipole communicated through the helix through hydrogen bonding
• sequence helps stabilize the dipole with positioning of charged residues at termini

Question 24

favored amino acids in forming alpha helix

Answer 24

• alanine (it has the lowest change in ∆∆G; 0)
• those with unbranched side chains (Leucine, lysine and methionine) (slender and don’t cause vdw crash as much)
• not glycine and proline

Question 25

Why almost no glycine and proline in alpha helices

Answer 25

• glycine imparts considerable freedom of rotation ( a
• residue in secondary structure should have decrease freedom and entropy)
• ## proline can only form hydrogen bonds with its carbonyl oxygen (only found at N terminus and in other places causes helix to break into two sections of smaller helices)

Question 26

constraints on alpha helix stability

Answer 26

1) electrostatic repulsion or attraction between successive residues with charged R groups
2) the bulkiness of adjacent R groups
3) the interactions between residues space 3 or 4 residues
4) the occurrence of proline or glycine
5) the interaction between amino acids at each end of the alpha helix and the helix dipole

Question 27

310 helix

Answer 27

• right handed helix with three residues a turn and 10 atoms within the ring formed by a hydrogen bond
• may serve as dynamic intermediary conformations
• follows n+3 hydrogen bonding patterns
  observed at n- or c- termini of alpha-helices

Question 28

conformation of ß strands

Answer 28

polypeptide chains that are almost fully extended

• ß sheet side chains project alternately above and below the plane of the ß strands
• one surface of a ß sheet may consist of hydrophobic side chains

Question 29

hydrogen bonding pattern of ß strands

Answer 29

stabilized by hydrogen bonds between C=O and -NH on adjacent strands

Question 30

anti-parrallel ß sheets

Answer 30

strands run in opposite N-C direction (more stable due to better geometry of hydrogen bonding)

Question 31

ß sheet fun facts

Answer 31

• can have a mixture of parrallel and anti parrallel strands

- ß-sheets adopt a twisted shape (in protein context)

Question 32

ß-turn fun facts

Answer 32

consist of hydrogen bond between the carbonyl oxygen of residue n and the amide of residue n+3, reversing the direction of the chain

  - most c=o and n-h groups in these four residues don't make hydrogen bonds with other backbone atoms but water molecules can donate and accept hydrogen bonds to these groups if the turn is not buried
 - then are found of the surfaces of proteins in contact with water
 - glycine and proline are common at positions 2 and 3

Question 33

tertiary structure

Answer 33

refers to spatial arrangement of amino acids of a single polypeptide chain

• different proteins follow the same rules for obtaining their tertiary structures
• amino acid sequence determines this

Question 34

Motifs

Answer 34

recognizable folding patterns involving two or more elements of secondary structure and the connections between them

Question 35

domains

Answer 35

part of a polypeptide chain that are independently stable or can undergo movements as a single entity with respect to the entire protein

• 100-200 residues
• maintain 3 dimentional structures outside the context of a protein
• have distinct biological functions
• may appear as globular lobes or make such extensive contact with the protein that they are difficult to visually identify

Question 36

motif fun facts

Answer 36

single motif like ß barrel may comprimise the entirety of the protein
may not be independently stable
not hierarchical structure between secondary and tertiary, rather then are simply a folding pattern
alpha-ß barrel is a complex motif built up from simple motifs

Question 37

what drives protein folding

Answer 37

hydrophobic interactions

Question 38

protein domain evolution

Answer 38

similar protein domains with homologous sequences are found in a variety of proteins

• evolved from common ancestral protein
• evolve when protein coding regions are duplicated and placed at a different place in the genome
• new functions may arise when mutiple domain coding regions are placed next to eachother (create a fusion protein)(an efficient way of finding new proteins with new functions)

Question 39

experimental advantages of modular nature of proteins

Answer 39

multi-domain protein has additive advantage of its constituent domains
easier to study one domain at a time
homologous domains have similar structure and function

Question 40

Why there is nothing new to report

Answer 40

there are 1300 unique folds, and the protein universe is made of combinations of these domains