proteins

Question 1

what is the importance of proteins

Answer 1

• Vital for cellular functions
• Shape is crucial to function
• Polymer macromolecules
• Tens of thousands exist
• Specific three dimensional structure
• Specific function

Question 2

polypepetides

Answer 2

sequence of amino acids joined by peptide bonds

Question 3

amino acids

Answer 3

• 20 amino acids used
• Possess carboxyl and amino groups
• Chiral (L form)
amino acids can be chiral

Question 4

amino acid ionisation

Answer 4

amino acid has low pH when H+ added.
amino acid is a zwitterionic form when H+ is lost coo-.
pH increases when H+ is lost from nh3

Question 5

• Physical and chemical properties of the amino acid is determined by the R group
• R group can be:

Answer 5

hydrophobic amino acids;
Nonpolar (9) 
hydrophilic amino acids:
•	Polar (6)
•	Acidic (2)	 
•	Basic (3)

Question 6

what amino acids have nonpolar R groups

Answer 6

glycine, alanine, valine, leucine, isoleucine(lle), methionine, phenylalanine, tryptophan, proline

Question 7

what amino acids have polar R groups

Answer 7

serine,threonine,cysteine

Question 8

which amino acid makes disulphide bridge

Answer 8

cyteine (S-H) to oxidised make S-S + 2H+ , 2e-. this makes cystine

Question 9

what amino acids have polar R groups?

Answer 9

Tyrosine, Asparagine(Asn), Glutamine(Gln)

Question 10

name the two amino acid which have an acidic R gruop

Answer 10

Aspartic acid

Glutamic acid

Question 11

name the 3 amino acid which have an basic R gruop

Answer 11

Lysine
Arginine
Histidine

Question 12

how is a peptide bond formed?

Answer 12

OH group is removed along with a H from NH2 group from another amino acid. this creates a covalent bond between C-NH . water is produced as byproduct.

Question 13

what is the backbone of the amino acid?

Answer 13

the backbone is the amno acid chain which are linked by peptide bonds.
the R groups are considered as side chain.

Question 14

what is the directionality of protein?

Answer 14

from left to right . amino terminal at the left hand side and carboxyl terminal on the right hand side.

Question 15

why is peptide bonds rigid and planer ?

Answer 15

the lewis structure shows double bond on either the oxygen and carbon or between carbon and nitrogen. thus the true structure has bond resonance which causes peptide bond to be rigid and planer

Question 16

which form of isomer is present the most in peptides?

Answer 16

Rotation at C usually limited by steric clashes between R groups, so the trans form is the most common

Question 17

When does the cis form occur?

Answer 17

cis occurs in peptide bonds when they come after a proline residue

Question 18

state the levels of protein structure

Answer 18

• Primary Structure
• Sequence
• Secondary Structure
• α helices
• Beta sheets
• Loops/random coils
• Tertiary Structure
• Attractions/folding
• Quaternary Structure
• Assembly

Question 19

what is the primary structure

Answer 19

• Sequence of amino acids: N to C terminus

* Genetically determined for each protein

Question 20

what is the importance of primary structure?

Answer 20

• Dictates final protein structure because sequential arrangement of R groups will influence subsequent 2°, 3° and 4° structures
• Protein structure dictates function

Question 21

name an example of a disease that arises due to mutation of primary structure ?

Answer 21

• Genetic mutation can lead to 1° structure changes that can alter structure and function
• Sickle cell anaemia caused by a single mutation

Question 22

can two 3D structures of protein have different sequence of amino acid ?

Answer 22

3D structure is more strongly preserved by evolution than sequence

• Human and and sea hare myoglobin have the same 3D structure but sequence is only 19% identical

Question 23

what amino acid is replaced in sickle cell anaemia?

Answer 23

Glu to Val

Question 24

what are the two types of secondary structure

Answer 24

• Parts of polypeptide chains take on regular patterns of hydrogen bonding resulting in:

• α-helices
• Beta-pleated sheets

The above patterns are connected by short turns and longer loops/random coils

Question 25

describe the alpha helix structure

Answer 25

• Coiled like a spring
• Efficient hydrogen bonding
• Often amphipathic
• Numerous in membrane-spanning pore-forming proteins
• 3.6 amino acids per turn
• Usually right-handed
• Flexible and elastic

Question 26

describe the The Beta-sheet structure .

Answer 26

• Flat sheets
• Pleated
• Short runs of 5-10 AAs
• Parallel, anti-parallel or mixed
• Sheets held together by hydrogen bonding
• Strong and resilient
• Multiple sheets often connected by short loops known as hairpin loops or turns

Question 27

describe parallel and anti-parallel.

Answer 27

parallel has two or more peptides parallel to each other bond via hydrogen bonding

in anti-parallel: the peptide is alternating and bonds are formed (hydrogen bonding )

Question 28

describe Loops (random coils)

Answer 28

• Connect 2° structure elements
• Usually located on the surface
• Not connected by hydrogen bonds
• Rich in polar and charged residues
• Length varies from 2 to more than 20 AAs
• Far less well conserved than other 2° structure elements
• Differences between structurally similar proteins occur almost exclusively in loops

Question 29

where is random coils found ?

Answer 29

Frequently form part of enzyme active sites