Structure of Proteins

Question 1

What are the functions of proteins and provide examples?

Answer 1

• protein structure - collagen (main component of connective tissue) - transport molecules - heamoglobin (oxygen) , LDL and LDL receptor (cholesterol) - defense - antibodies - regulation of genes - Lac repressor (controls expression of proteins metabolising lactose in bacteria - repressor binds to DNA and prevents expression of gene in absence of lactose)

Question 2

What causes the function of proteins?

Answer 2

due to the property of specific binding - binding depends on conformation

Question 3

What is the result of change of conformation?

Answer 3

change in activity

Question 4

What is the general structure of an AA?

Question 5

What defines the structure and function of a protein?

Answer 5

the chemical properties of the R group

Question 6

What are the hydrophylic AA?

Answer 6

• basic
  acidic
• polar

Question 7

What AA are basic?

Answer 7

argenine, lysine, histidine

Question 8

What makes an AA basic?

Answer 8

heir side chains contain nitrogen and resemble ammonia, which is a base. Their pKa’s are high enough that they tend to bind protons, gaining a positive charge in the process.

• form salt bridges (stabilize protein structure)

Question 9

What AA are acidic?

Answer 9

aspartic acid/aspartate and glutamic acid/glutamate,

Question 10

What makes an AA acidic?

Answer 10

acidic side chains at neutral pH, carboxylic acid groups, pKas are low enough to loose protons becoming negatively charged in the process

• forms salt bridges (stabilize protein structure)

Question 11

What AA are polar? (8)

Answer 11

• glutamine
• asparagine
• histidine
• serine
• threonine
• tyrosine
• cysteine
• tryptophan

Question 12

What makes an AA polar?

Answer 12

with uncharged R groups

• Polar amino acids are those with side-chains that prefer to reside in an aqueous environments - exposed on the surface of a protein
• usually participate in hydrogen bonds as proton donors or acceptors

Question 13

What AA are hydrophobic? (8)

Answer 13

• Alanine
• Isoleucine
• Leucine
• Methionine
• Phenylalanine
• Valine
• Proline
• Glycine

Question 14

What makes an AA hydrophobic?

Answer 14

• composed mostly of carbon and hydrogen
• have small dipole movements
• repelled from water - found in protein core

Question 15

Structure of glycine?

Answer 15

Question 16

Structure of proline?

Answer 16

Question 17

Structure of cysteine?

Answer 17

Question 18

Structure of histidine?

Answer 18

Question 19

Structure of aspartate?

Answer 19

Question 20

Define polypeptide?

Answer 20

a polymer of AA joined by peptide bonds

Question 21

Define AA residue?

Answer 21

when two or more AA join to form a peptide, the elements of water are removed, and what remains of the AA is the AA residue

Question 22

Define prosthetic?

Answer 22

a non protein group forming part of the protein or combined with the protein

Question 23

What does pKa mean?

Answer 23

pKa of an acid is equal to the pH at which half the molecules are dissociated

Question 24

How is pKa important in the function of proteins?

Answer 24

local environmnet can influence pKA - Dissociation largely occurs over 2 pH units centered on the pKa - The overall charge of an AA varies with pH - Close to the pKa, small changes in pH can cause significant change in the charge carried

Question 25

How is a peptide bond formed?