protein structure

Question 1

how are peptode bonds formed?

Answer 1

by a condensation reaction which releases water

Question 2

what is the primary structure of a protein?

Answer 2

the amino acid sequnce

Question 3

what is the start and end of the polypeptide chain called?

Answer 3

start= terminal end
end= hydroxy terminal end

Question 4

what is the polypeptide chain made up of?

Answer 4

the backbone and the amino acid side chains

Question 5

how are disulphide bonds formed?

Answer 5

by 2 cystines being close enough together so they form the bonds

Question 6

give an example of a molecule that has disulphide bonds in it?

Answer 6

insulin
theyre used to hold the 2 chains together

Question 7

what are the 2 negatively charged amino acids?

Answer 7

aspartate (D) and glutamate (E)

Question 8

why is there conformational resitriction in peptide bonds?

Answer 8

because the peptide bond is planar with 6 atoms lying in a plane
the peptide bond stops the rotation as it has a partial double bond
the trans form is favoured because of the steric hindrance in the cis form, with both the R groups being on the same side of the double bond (this means that this version is only possible with small R groups)

Question 9

what are the 20 amino acids and their shortened names?

Answer 9

proline (P)
phenylalanine (F)
tryptophan (W)
tyrosine (Y)
histidine (H)
lysine (K)
arginine (R)
leucine (L)
methionine (M)
isoleucine (I)
glycine (G)
alanine (A)
valine (V)
serine (S)
threonine (T)
cysteine (C)
aspargenine (N)
glutamine (Q)
aspartate (D)
glutamate (E)

Question 10

what is the secodary structure of a protein?

Answer 10

its the 3D structure made by the H bonds between the NH and CO groups on the amino acids

Question 11

what are the things that make floding in a polypeptide chain possible?

Answer 11

restrictions by the rigidity of the peptide bond
a restricted set of allowed psi and omega angles

Question 12

what are alpha helices?

Answer 12

theyre tigtly coild structure with R groups sticking out from the axis
all of them are right hand turns

Question 13

what are beta strands and sheets?

Answer 13

beta-sheets- formed by adjacent beta strands and when the polypeptide chain is fully extended
the side chains alternate between above and below the strand
they can be parallel, antiparallel or mixed
they can also form a twist conformation

Question 14

what are beta turns?

Answer 14

theyre made when the chain makes a sharp turn
only possible with small R groups

Question 15

what are omega loops?

Answer 15

theyre bigger and more irregular than beta turns
they come in multiple conformations

Question 16

how can omega loops be determined?

Answer 16

by protein crystallography

Question 17

what is tertiary structure?

Answer 17

its the spatial arrangement of amino acids and the formation of disulphide bonds

Question 18

what does beta-mercaptoethanol do?

Answer 18

it helps to reduce disulphide bonds and is oxidized when it makes dimers
this makes a redox reaction then you can analyse the compounds on SDS-page

Question 19

what are globular proteins?

Answer 19

theyre compact protein with very little space/ no space in the protein
the inside is made up of mostly hydrophobic amino acids
the outside is charged and made up of hydrophilic amino acids

Question 20

what is an example of a globular protein?

Answer 20

myoglobin

Question 21

what is the structure of pores forming in the membrane?

Answer 21

outside the pore, theres mostly hydrophobic groupd and inside in hydrophilic
the center of the channel is lined with charged polar amino acids

Question 22

what are motifs? what is the typical example of them?

Answer 22

theyre combinations of secondary structure
theyre found in man proteins
the typical example is in transcription factors

Question 23

what are domains?

Answer 23

theyre 2 or more similar or identical compact structures
lots of helix domains are found together to help the domain bind to the DNA and repair it
[they’re really just the same as motifs but bigger]

Question 24

what is quaternary structure?

Answer 24

it’s only in proteins with multiple subunits
it can be as simple as 2 identical chains or as complicated as dozens of different chains

Question 25

what is an example of alternative conformations of polypeptide sequence?

Answer 25

VDKLLN
this has an alpha-helix conformation in one protein
it has a beta-strand in the other

Question 26

how can proetins be turned into their mature form?

Answer 26

proteolytic cleavage
N-terminal amino group
C-terminal carboxylic group
side-chains of amino acids throughout the length of the protein

Question 27

what pathological conditions can result from not having the appropriate psot-translational modifications?

Answer 27

• Chemical groups like hydroxy, carboxy, methyl, acetal or phosphate groups
• Small proteins like ubiquitin (ubiquitinylation)
• Fatty acids such as myristoyl or prenyl groups
• Branched glycosylations
• Glycosyl phosphatidyl inositol (GPI) receptors

Question 28

what are glycosyl phosphatidyl inositol (GPI) anchors?

Answer 28

theyre when a strech of amino acids are replaced by a spacer and the hydrophobic region with the GPI anchor at the carboxyl group of the terminal amino acid
fatty acids can be embedded into the membrane of the parasite and they can be changed to avoid the immune system

Question 29

what are the allowed attachment sites in GPI anchors? and why?

Answer 29

Ala, Asn, Asp, Cys, Gly or Ser this is because they’re amino acids with small side chains at the 2+ position going from the attachment site