LM1 proteins

Question 1

describe a peptide bond

Answer 1

condensation reaction of the alpha carboxyl group of one amino acid with the alpha amino group of another

Question 2

what is an amino acid residue

Answer 2

an amino acid that is part of a polypeptide chain

Question 2

how are peptide chains named

Answer 2

from the n-terminus to the c-terminus

Question 3

why are the n and c termini always charged

Answer 3

n-terminus is always positively charged as pH<pKa>pKa</pKa>

Question 4

why is rotation around the C-N bond in a peptide bond limited?

Answer 4

due to the double bond nature of the resonance hybrid form peptide group bonds are therefore planar

Question 5

describe the conformation of a peptide bond

Answer 5

they have some double properties so they are planar and their conformation is restricted to either cis or trans but the cis conformation is less favorable due to steric clashes

Question 6

what amino acid may have both cis and trans peptide bonds

Answer 6

proline

Question 7

what is the phi angle

Answer 7

the bond between nitrogen and the alpha carbon

Question 8

what is the psi angle

Answer 8

the bond between the alpha carbon and carboxyl carbon

Question 9

why is rotation around bonds restricted

Answer 9

steric clashes between main and side chain atoms

Question 10

what is the Ramachandran diagram

Answer 10

shows possible combinations of phi and psi angles when steric clashes between atoms are absent or minimized

Question 11

define protein conformation

Answer 11

3D shape

Question 12

define native conformation

Answer 12

each protein folds in to a single stable shape

Question 13

What does the biological function of a protein depend on

Answer 13

its native conformation

Question 14

describe the alpha helix

Answer 14

each C=O residue (n) forms a hydrogen bond with residue n+4 amide. The helix is stabilised by many hydrogen bonds which are nearly parallel to the axis

Question 15

what are some distinctive features of an alpha helix

Answer 15

all C=O groups point towards the c-terminus
3.6 amino acids per turn
right handed helices are most abundant

Question 16

define beta strands

Answer 16

polypeptide chains that are almost fully extended

Question 17

define a beta sheet

Answer 17

multiple beta strands arranged side by side and are stabilised by hydrogen bonds between C=O and N-H on adjacent strands

Question 18

describe hydrogen bonding in parallel beta sheets

Answer 18

the NH group is hydrogen bonded to the CO group of one amino acid on the adjacent strand
whereas the CO group is hydrogen bonded to the NH group on the amino acid two residues away

Question 19

Describe the hydrogen bonding in antiparallel beta sheets

Answer 19

the hydrogen bonds are nearly perpendicular to the chain

Question 20

describe the side chains on beta chains

Answer 20

side chains project alternately above and below the plane of the beta strands, one surface of a beta sheet may consist of hydrophobic side chains and then can interact with other hydrophobic residues

Question 21

what is the purpose of loops and turns

Answer 21

they connect alpha helices and bet strands and allow a peptide chain to fold back on itself to make a compact structure

Question 22

describe loops

Answer 22

often contain hydrophilic residues and are found on protein surfaces

Question 23

describe turns

Answer 23

loops containing 5 residues or less often containing glycine

Question 24

what is a super secondary structure (motif)

Answer 24

recurring protein structures

Question 25

give examples of super secondary structures

Answer 25

helix loop helix coiled coil helix bundle beta alpha beta unit hairpin beta meander greek key beta sandwich beta barrel

Question 26

describe globular proteins

Answer 26

usually water soluble compact and roughly spherical

Question 27

describe fibrous proteins

Answer 27

provide mechanical support and often assembled into large cables or threads for example alpha keratin and collagen

Question 28

describe a reverse turn

Answer 28

a CO group of residue i is hydrogen bonded to the NH group of i+3 residue to stabilise the turn

Question 29

define domain

Answer 29

independently folded compact units in proteins 25-300 residues in size and illustrates the evolutionary conservation of protein structure

Question 30

define primary structure

Answer 30

sequence of amino acids joined by an amide bond

Question 31

define secondary structure

Answer 31

alpha helices and beta strands stabilised by hydrogen bonds

Question 32

define tertiary structure

Answer 32

3 D structure

Question 33

define quaternary structure

Answer 33

made of more than one polypeptide subunit

Question 34

what is a heptad repeat

Answer 34

found in alpha keratin - where every 7th amino acid is repeated e.g. leucine

Question 35

define denaturation

Answer 35

loss of native 3D protein structure and results in a loss of biological function

Question 36

What can denaturation be caused by

Answer 36

increase in temperature extreme pH - leads to a lot of repulsion as side chains are either protonated or deprotonated denaturing substances such as urea or guanidium chloride

Question 37

what substance can reduce disulfide bridges

Answer 37

beta mercatoethanol

Question 38

define nucleation

Answer 38

preference for native structure drives folding