Protein Structure

Question 1

what are the two types of secondary protein structures

Answer 1

alpha helix and beta pleated sheet

Question 1

what are the features of the alpha helix

Answer 1

backbone interactions (polypeptide chains twists itself –> spiral; R-chains point outward)

Question 2

describe secondary protein structure

Answer 2

• folds into regular structures
• results from ‘local’ interactions between amino acids in polypeptide backbone
  
  • involve hydrogen bonds

Question 3

small changes in amino acid sequence are important because

Answer 3

they can be advantageous and disadvantageous

Question 4

what are the negatively charged amino acids

Answer 4

aspartic acid, glutamic acid

Question 5

what are the positively charged amino acids

Answer 5

lysine, arginine, histidine

Question 6

what are the uncharged polar amino acids

Answer 6

serine, threonine, tyrosine, asparagine, glutamine

Question 7

what are the non polar amino acids

Answer 7

glycine, alanine, valine, cysteine, proline, leucine, isoleucine, methionine, tryptophan, phenylalanine

Question 8

a protein consists of

Answer 8

amino group, carboxyl group, peptide bonds, side (R) chains, polypeptide backbone

Question 9

why are side chains important in polypeptides

Answer 9

provide different functional properties of protein

Question 10

what is the purpose of the peptide backbone in polypeptides

Answer 10

most important for protein folding by hydrogen bonding

Question 11

what are the key features of a polypeptide

Answer 11

• peptide backbone
• side chains

Question 12

how many different amino acids are there

Answer 12

20

Question 13

how are proteins formed

Answer 13

strings of amino acids called polypeptides

Question 14

what happens to phospholipids in membranes

Answer 14

heads align (outside) and tails align (inside)

Question 15

what are the features of the beta-pleated sheet

Answer 15

backbone interactions (proteins backbone folds into zig-zag shape; H bonds form between amino acids in separate areas of a protein)

Question 16

what is the primary protein structure

Answer 16

amino acid sequence

Question 17

what is the tertiary protein structure

Answer 17

full three-dimensional structure of protein
- alpha helices, beta sheets, random coils and other loops
- resulting in protein with different domains or regions that have different functions

Question 18

describe the catabolite activator protein (CAP)

Answer 18

• found in bacteria
• has two domains
• has alpha helices and beta sheets

Question 19

CAP has two domains. What do they bind to?

Answer 19

• small: DNA
• large: cAMP (changes conformation of CAP, enables it to bind DNA and promote the expression of genes

Question 20

explain how proteins and ligands bind

Answer 20

• ligand usually binds to amino acid side chains
• needs to fold correctly so that side chains are in proper position and order as unfolded
• ligand sits in binding site through non-covalent bonding to amino acid side chains

Question 21

what happens when ligands and proteins bind

Answer 21

protein conformation changes, which creates protein activation

Question 22

what are some advantages of the quaternary protein structure

Answer 22

• construction of large proteins
• proteins gain complex properties (like cooperativity)

Question 22

what is the quaternary protein structure

Answer 22

association between 2 or more polypeptides in a protein (with identical or different subunits)

Question 23

what are the types of quaternary structure

Answer 23

globular and fibrous proteins

Question 24

what is a globular protein and give an example

Answer 24

• has 4 globular subunits
• hemoglobin

Question 25

what is a fibrous protein and give an example

Answer 25

• has 3 helices supercoiled
• collagen

Question 26

what is denaturation; what structures relax due to it

Answer 26

loss of proteins activity from broken bonds or deformity (by heat or acidity)
- relaxation of secondary and tertiary structures

Question 27

why is protein folding critical to its function

Answer 27

can lead to diseases like cystic fibrosis, alzheimer’s, mad cow disease (CJD humans)

Question 28

what happens to the mutant protein in cystic fibrosis

Answer 28

mutant transport protein cannot fold properly

Question 29

what happens to the protein in alzheimer’s

Answer 29

amyloid protein forms large insoluble fibres that causes nerve cells to die

Question 30

what happens to the protein in mad cow disease (CJD)

Answer 30

prion proteins fold incorrectly which damages nerve cells and leads to death