Protein Structure

Question 1

primary structure

Answer 1

sequence of amino acids

Question 2

secondary structure

Answer 2

simple, repetitive motifs that are found in almost all proteins

Question 3

tertiary structure

Answer 3

overall fold of a protein

Question 4

quaternary structure

Answer 4

when several proteins fold together

Question 5

Polypeptide chains

Answer 5

Peptide bond in the chain has a partial double bond character

C-N 1.49 angstroms
C=N 1.27 angstroms
Peptide bond 1.32 angstroms

Question 6

rotation about bonds

Answer 6

structure adjusted by rotation about 2 pure single bonds
phi and psi

determine the path of polypeptide chain

Question 7

Phi rotation

Answer 7

angle of rotation about bond
between N and alpha C

Question 8

Psi rotation

Answer 8

angle of rotation about bond
between alpha C and carbonyl C

Question 9

combinations of phi and psi

Answer 9

many combinations of the two rotations forbidden
due to steric collusions between atoms

values visualised on 2D plot called Ramachandran plot

Question 10

folded structures

Answer 10

highly flexible polymers
large number of possible conformities
do not fold into unique structures

Question 11

rigidity of phi and psi and peptide

Answer 11

limits the number of structures accessible to unfolded protein form

Question 12

define the secondary structures

Answer 12

alpha helix
beta pleated sheet
turns and loops

Question 13

Ramachandran Plot

LOOK AT GRAPH

Answer 13

Plot of angles phi and psi
red areas conly show where the combinations of the bonds can form the secondary structures

Question 14

define: alpha helix

Answer 14

secondary structure
arises dur to H bonding capacity of N-H backbone and C-O groups

Question 15

Properties of alpha helix

Answer 15

right handed
no residues (turns) = 3.6
pitch (distance helix rises) = 5.4 angstroms
H bonding
C=O bond points towards peptide N-H group
H bond at nearly optimal length
R groups point outwards
11 residues in globular proteins

Question 16

Hydrogen bonding in alpha helices

LOOK AT DIAGRAM

Answer 16

CO group of residue n forms H bonds with amine group n+4
fold on top of each other every 4 residues

Question 17

Helical wheel

Answer 17

amino acid residues facing out are in contact with water
hydrophilic are on outside
hydrophobic are on inside

Question 18

what proteins are rich in alpha helices?

Answer 18

ranges widely

75% residues in ferritin are alpha helices

roughly 25% all soluble proteins are alpha helices connected by loops and turns

Question 19

define: beta sheet

Answer 19

secondary structure composed of B strands

Question 20

properties of data sheets:

Answer 20

at least two polypeptide chains
parallel or antiparallel
rippled or pleated
successive r groups
2 residue repeat of 7 angstroms
H bonding between C=O of one chain and N-H of another
15 residues long in globular proteins
4-5 (max 10) strands can come together in B pleated sheets
can be purely parallel or antiparallel or a mix

Question 21

proteins rich in B sheet

Answer 21

usually depicted by arrows pointing in direction of carboxyl terminal end

Question 22

B sheet: reverse turn

LOOK AT DIAGRAM

Answer 22

CO group of residue (i) is H bonded to NH of reside (i+3)
Stabilises abrupt changes of direction of polypeptide chain

It kind of turns back on itself to form a bond between i and i+3
forms

Question 23

Define: loops

Answer 23

do not have regular periodic structure
often rigid and well defined

lie on the surfaces of proteins interact with other proteins/ molecules

Question 24

define: super-secondary structure

Answer 24

elements on secondary structures that link together in different combinations

form mini domains that have own stability
formed in early process of making whole protein structure

many are symmetrical

Question 25

define: tertiary structure

Answer 25

overall fold of the whole protein can be made from any combination of alpha helices, beta sheets and loops

Question 26

What is myoglobin?

Answer 26

an all alpha helix protein single polypeptide chain of 153 amino acids binds heme as a prosthetic group 70% of main chain folded into 8 alpha helices & rest is turns and loops

Question 27

What is concanavalin A?

Answer 27

an all beta-sheet protein a lectin (carbohydrate binding protein) 14 B strands in the molecules

Question 28

define: structural motifs

Answer 28

most proteins has mix of alpha helices and beta sheets common motif known as a beta barrel

Question 29

define: domains

Answer 29

protein sections that could fold independently each protein has at least one domain some can have as many as 10

Question 30

define: Quaternary structure

Answer 30

Many proteins form in groups of 2+ chains

Question 31

define; homomultimers

Answer 31

quaternary structure with the same protein with 2+ copies

Question 32

define; heteromultimers

Answer 32

quaternary structure with different proteins

Question 33

What are fibrous proteins?

Answer 33

important components of elk cells alpha helix e.g. hair beta sheet e.g. insect silk

Question 34

Alpha helix fibrous protein

Answer 34

all alpha helix hair very stable structure have length of 1000 angstroms cross linked by weak interactions - van Der walls and ionic interactions

Question 35

all beta sheet silk

Answer 35

structure made from repeating hexapeptide

Question 36

collagen

Answer 36

main fibrous component of skin, bone, tendon, cartilage and teeth three helical polypeptides, each roughly 1000 residues long 3 helices wound together making it rigid and string crosslinks between all three chains