Chapter 6- Secondary Structures of Proteins

Question 1

What happens in sickle cell?

Answer 1

a glutamine is replaced with a valine= alters hemoglobin structures and function.

Question 2

What does protein function depend on?

Answer 2

on protein structure

Question 3

What is the relationship of protein sequence to function dependent on?

Answer 3

the 3D folding of proteins and inferring protein functions from these 3D structures (binding sites, catalytic activities, interactions w/ other molecules)

Question 4

What are the importance of proteins ?

Answer 4

motor proteins, structural components of cells, enzymes, antibodies, hormones, hemoglobin/ myblobin, transport proteins in blood.

Question 5

What are the 4 levels of protein structure and define them?

Answer 5

primary- amino acid linear sequence (from n term to c term) determines structure and function

secondary- regions of regularly repeating conformation of the peptide chain (a-helices ad beta sheet). joined by turns and loops

tertiary- describes shape of fully folded folded polypeptide chain

quaternary- arrangement of two or more polypeptide chains into a multi subunit molecule

Question 6

What are the first 5 amino acids residues in lysozyme?

Answer 6

Lys-Val-Phe-Gly-Arg (2,3,4- hydrophobic-faces in)

Question 7

What makes polypeptides fold in water into 3D structues? (tertiary )

Answer 7

bond rotation within the polypeptide backbone

Question 8

What causes secondary structure?

Answer 8

regularly spaced hydrogen bonds (a-helix, beta sheet, beta turn, loop)

Question 9

are alpha helices right or heft handed?

Answer 9

right handed

Question 10

describe the a-helix structure. shape? what bonds? between what?

Answer 10

cork screw, telephone cord held by H bonds rom -N-H groups and the O- of c+o of the fourth amino acid along chain

Question 11

what stabilizes the helix ?

Answer 11

the H bonds between back bone atoms Not R groups

Question 12

which way do the r groups of a helix face?

Answer 12

perpendicular to helix axis

Question 13

What is a triple helix?eg.

why are they so strong?

typical of what ?

Answer 13

3 polypeptide chain woven together ?
Glycine, Proline, Hydroxyproline, Hydroxylysine

because of the H bonding between -OH groups

collagen, connective tissue, skin, tendons, cartilage (cccts)

Question 14

Why are helices short and why do they overlap?

Answer 14

so they are strong

Question 15

a-helices are major components of many proteins, connected by turns. some interesting a helices are…

Answer 15

small DNA binding helices -
Membrane- spanning helices
amphipathic helices
coiled coils

Question 16

how are a-helices are major component of small DNA binding helices?

Answer 16

fit in the major groove of double stranded DNA

Question 17

how are a-helices are major component of membrane- spanning helices
?

Answer 17

they have hydrophobic amino amine in the central region that allow the helices to enter the bilayer

Question 18

how are a-helices are major component of amphipathic helices?

Answer 18

the helices have some hydrophilic amino acids on one side and hydrophobic ones on the other side - integral protein.

Question 19

Most amino acids like to in an a-helix except for?

Answer 19

Glycine and proline

Question 20

proline is not an amino acid but a?

Answer 20

imino acid (secondary amino acid, N-bonded to 2 carbons, not bonded to any H )

Question 21

what do proline residues do?

Answer 21

they act as a-helix breakers

Question 22

where are proline residues normally found?

Answer 22

at the boundaries of a-helices and in turns

Question 23

describe beta sheets? shape? what bonds?

Answer 23

the are like an accordion, they can join distant parts of the protein together due to H-bonds

Question 24

how are beta pleated sheets arranged ?where residues face? bonds? where do r groups extend? eg.

Answer 24

the polypeptide chains are side by side and H bonds forms between chains (residues are rotated 180 from neighbour-side chains protrude on opposite ends). R groups extend above and below sheet. Silk

Question 25

beta sheets can be parallel or anti parallel

Answer 25

anti= 2 bond close the gap etc.

Question 26

beta sheet unit, what is the super structure they can form?

Answer 26

beta strand
beta barrels- strands are twisted and at an incline, r groups stick out on either face. r groups inside the barres are often beta-branched or hydrophobics

Question 27

where do b-sheets fit?

Answer 27

In the minor groove of DNA double helix , can also used in DNA binding but are less common